From d1dfe496b22d2be93dac2ca59a284be28ce19fb0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 28 Aug 2025 11:39:00 -0400 Subject: [PATCH 1/8] squash clickhouse migrations --- ...move_gnomadgenomessnvindel_key_and_more.py | 1076 +++++++++++++++++ 1 file changed, 1076 insertions(+) create mode 100644 clickhouse_search/migrations/0001_squashed_0015_remove_gnomadgenomessnvindel_key_and_more.py diff --git a/clickhouse_search/migrations/0001_squashed_0015_remove_gnomadgenomessnvindel_key_and_more.py b/clickhouse_search/migrations/0001_squashed_0015_remove_gnomadgenomessnvindel_key_and_more.py new file mode 100644 index 0000000000..62f5bcffb0 --- /dev/null +++ b/clickhouse_search/migrations/0001_squashed_0015_remove_gnomadgenomessnvindel_key_and_more.py @@ -0,0 +1,1076 @@ +# Generated by Django 4.2.22 on 2025-08-28 15:22 + +import clickhouse_backend.models +import clickhouse_search.backend.engines +import clickhouse_search.backend.fields +import clickhouse_search.models + +from django.db import migrations, models +import django.db.models.deletion +import django.db.models.manager +import os +from string import Template + +from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR + +CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS = os.environ.get( + 'CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS', + '' +).split(',') +CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'clickhouse_test') +CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'clickhouse') + + +ENTRIES_TO_PROJECT_GT_STATS = Template(""" +CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/entries_to_project_gt_stats_mv` +TO `$reference_genome/$dataset_type/project_gt_stats` +AS SELECT + project_guid, + key, + $columns +FROM `$reference_genome/$dataset_type/entries` +GROUP BY $groupby_columns +""") + +PROJECT_GT_STATS_TO_GT_STATS = Template(Template(""" +CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/project_gt_stats_to_gt_stats_mv` +REFRESH EVERY 10 YEAR +TO `$reference_genome/$dataset_type/gt_stats` +AS SELECT + key, + $columns +FROM `$reference_genome/$dataset_type/project_gt_stats` +WHERE project_guid NOT IN $clickhouse_ac_excluded_project_guids +GROUP BY key +""").safe_substitute( + clickhouse_ac_excluded_project_guids=CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS +)) + +GT_STATS_DICT = Template(Template(""" +CREATE DICTIONARY `$reference_genome/$dataset_type/gt_stats_dict` +( + key UInt32, + $columns +) +PRIMARY KEY key +SOURCE(CLICKHOUSE(USER $clickhouse_writer_user PASSWORD $clickhouse_writer_password TABLE `$reference_genome/$dataset_type/gt_stats`)) +LIFETIME(MIN 0 MAX 0) +LAYOUT(FLAT(MAX_ARRAY_SIZE $size)) +""").safe_substitute( + # Note the nested Template-ing that allows + # double substitution these shared values + clickhouse_writer_user=CLICKHOUSE_WRITER_USER, + clickhouse_writer_password=CLICKHOUSE_WRITER_PASSWORD, +)) + +CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV = Template(""" +CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/clinvar_all_variants_to_clinvar_mv` +REFRESH EVERY 10 YEAR +TO `$reference_genome/$dataset_type/clinvar` +AS +SELECT + DISTINCT ON (key) + kl.key as key, + alleleId, + conflictingPathogenicities, + goldStars, + submitters, + conditions, + assertions, + pathogenicity +FROM `$reference_genome/$dataset_type/clinvar_all_variants` c +INNER JOIN `$reference_genome/$dataset_type/key_lookup` kl +ON c.variantId = kl.variantId +""") + + +class Migration(migrations.Migration): + + replaces = [('clickhouse_search', '0001_initial'), ('clickhouse_search', '0002_annotationsdiskgrch37snvindel_and_more'), ('clickhouse_search', '0003_annotationsdiskmito_annotationsmito_entriesmito_and_more'), ('clickhouse_search', '0004_annotationsdisksv_annotationssv_entriessv'), ('clickhouse_search', '0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more'), ('clickhouse_search', '0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more'), ('clickhouse_search', '0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more'), ('clickhouse_search', '0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more'), ('clickhouse_search', '0009_materializedviews_and_dictionaries'), ('clickhouse_search', '0010_clinvarallvariantsgrch37snvindel_and_more'), ('clickhouse_search', '0011_clinvar_materialized_view'), ('clickhouse_search', '0012_delete_annotationsdiskgcnv_and_more'), ('clickhouse_search', '0013_annotationsdiskgcnv_annotationsdiskmito_and_more'), ('clickhouse_search', '0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel'), ('clickhouse_search', '0015_remove_gnomadgenomessnvindel_key_and_more')] + + initial = True + + dependencies = [ + ] + + operations = [ + migrations.CreateModel( + name='AnnotationsDiskSnvIndel', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('pos', clickhouse_backend.models.UInt32Field()), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), + ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), + ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences')), + ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences')), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsSnvIndel', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('pos', clickhouse_backend.models.UInt32Field()), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), + ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), + ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences')), + ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences')), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesSnvIndel', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('is_gnomad_gt_5_percent', clickhouse_backend.models.BoolField()), + ('is_annotated_in_any_gene', clickhouse_backend.models.BoolField()), + ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('ab', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/entries', + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarSnvIndel', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriessnvindel')), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/clinvar', + 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='TranscriptsSnvIndel', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), + ('transcripts', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissense', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('pathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), ('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('exon', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('index', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('total', clickhouse_backend.models.Int32Field(blank=True, null=True))])), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('intron', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('index', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('total', clickhouse_backend.models.Int32Field(blank=True, null=True))])), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('manePlusClinical', clickhouse_backend.models.StringField(blank=True, null=True)), ('maneSelect', clickhouse_backend.models.StringField(blank=True, null=True)), ('refseqTranscriptId', clickhouse_backend.models.StringField(blank=True, null=True)), ('spliceregion', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('extended_intronic_splice_region_variant', clickhouse_backend.models.BoolField(blank=True, null=True))])), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field()), ('utrannotator', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('existingInframeOorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('existingOutofframeOorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('existingUorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('fiveutrAnnotation', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('AltStop', clickhouse_backend.models.StringField(blank=True, null=True)), ('AltStopDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('CapDistanceToStart', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('DistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('DistanceToStop', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('Evidence', clickhouse_backend.models.BoolField(blank=True, null=True)), ('FrameWithCDS', clickhouse_backend.models.StringField(blank=True, null=True)), ('KozakContext', clickhouse_backend.models.StringField(blank=True, null=True)), ('KozakStrength', clickhouse_backend.models.StringField(blank=True, null=True)), ('StartDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('alt_type', clickhouse_backend.models.StringField(blank=True, null=True)), ('alt_type_length', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('newSTOPDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('ref_StartDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('ref_type', clickhouse_backend.models.StringField(blank=True, null=True)), ('ref_type_length', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('type', clickhouse_backend.models.StringField(blank=True, null=True))])), ('fiveutrConsequence', clickhouse_backend.models.StringField(blank=True, null=True))]))])), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/transcripts', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/transcripts', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsDiskGRCh37SnvIndel', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('pos', clickhouse_backend.models.UInt32Field()), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsGRCh37SnvIndel', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('pos', clickhouse_backend.models.UInt32Field()), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh37/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsGcnv', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('end', clickhouse_backend.models.UInt32Field()), + ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), + ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ], + options={ + 'db_table': 'GRCh38/GCNV/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsMito', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), + ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), + ], + options={ + 'db_table': 'GRCh38/MITO/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsSv', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('end', clickhouse_backend.models.UInt32Field()), + ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), + ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), + ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), + ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), + ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), + ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), + ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), + ], + options={ + 'db_table': 'GRCh38/SV/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsDiskGcnv', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('end', clickhouse_backend.models.UInt32Field()), + ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), + ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ], + options={ + 'db_table': 'GRCh38/GCNV/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsDiskMito', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), + ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), + ], + options={ + 'db_table': 'GRCh38/MITO/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsDiskSv', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('end', clickhouse_backend.models.UInt32Field()), + ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), + ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), + ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), + ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), + ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), + ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), + ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), + ], + options={ + 'db_table': 'GRCh38/SV/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesGRCh37SnvIndel', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('is_gnomad_gt_5_percent', clickhouse_backend.models.BoolField()), + ('is_annotated_in_any_gene', clickhouse_backend.models.BoolField()), + ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('ab', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/entries', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='TranscriptsGRCh37SnvIndel', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), + ('transcripts', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())])), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/transcripts', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/transcripts', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarGRCh37SnvIndel', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriesgrch37snvindel')), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/clinvar', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesMito', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('hl', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitoCn', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('contamination', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh38/MITO/entries', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarMito', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriesmito')), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh38/MITO/clinvar', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesSv', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('cn', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('newCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevNumAlt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh38/SV/entries', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesGcnv', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgcnv')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('cn', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('qs', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('defragged', clickhouse_backend.models.BoolField(blank=True, null=True)), ('start', clickhouse_backend.models.UInt32Field(blank=True, null=True)), ('end', clickhouse_backend.models.UInt32Field(blank=True, null=True)), ('numExon', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('geneIds', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True))), ('newCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevOverlap', clickhouse_backend.models.BoolField(blank=True, null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh38/GCNV/entries', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupGcnv', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsgcnv')), + ], + options={ + 'db_table': 'GRCh38/GCNV/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/GCNV/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupGRCh37SnvIndel', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsgrch37snvindel')), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupMito', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsmito')), + ], + options={ + 'db_table': 'GRCh38/MITO/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/MITO/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupSnvIndel', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationssnvindel')), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupSv', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationssv')), + ], + options={ + 'db_table': 'GRCh38/SV/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SV/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ProjectGtStatsGRCh37SnvIndel', + fields=[ + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('ref_samples', clickhouse_backend.models.UInt32Field()), + ('het_samples', clickhouse_backend.models.UInt32Field()), + ('hom_samples', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/project_gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ProjectGtStatsMito', + fields=[ + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('ref_samples', clickhouse_backend.models.UInt32Field()), + ('het_samples', clickhouse_backend.models.UInt32Field()), + ('hom_samples', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/MITO/project_gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ProjectGtStatsSnvIndel', + fields=[ + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('ref_samples', clickhouse_backend.models.UInt32Field()), + ('het_samples', clickhouse_backend.models.UInt32Field()), + ('hom_samples', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/project_gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ProjectGtStatsSv', + fields=[ + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), + ('ref_samples', clickhouse_backend.models.UInt32Field()), + ('het_samples', clickhouse_backend.models.UInt32Field()), + ('hom_samples', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/SV/project_gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key'), partition_by='project_guid'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='GtStatsGRCh37SnvIndel', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), + ('ac_wes', clickhouse_backend.models.UInt32Field()), + ('ac_wgs', clickhouse_backend.models.UInt32Field()), + ('hom_wes', clickhouse_backend.models.UInt32Field()), + ('hom_wgs', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='GtStatsMito', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), + ('ac_het_wes', clickhouse_backend.models.UInt32Field()), + ('ac_het_wgs', clickhouse_backend.models.UInt32Field()), + ('ac_hom_wes', clickhouse_backend.models.UInt32Field()), + ('ac_hom_wgs', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/MITO/gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='GtStatsSnvIndel', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), + ('ac_wes', clickhouse_backend.models.UInt32Field()), + ('ac_wgs', clickhouse_backend.models.UInt32Field()), + ('hom_wes', clickhouse_backend.models.UInt32Field()), + ('hom_wgs', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='GtStatsSv', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), + ('ac_wgs', clickhouse_backend.models.UInt32Field()), + ('hom_wgs', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/SV/gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.RunSQL( + ENTRIES_TO_PROJECT_GT_STATS.substitute( + reference_genome='GRCh37', + dataset_type='SNV_INDEL', + columns=",\n ".join([ + 'sample_type', + "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", + ]), + groupby_columns='project_guid, key, sample_type', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + PROJECT_GT_STATS_TO_GT_STATS.substitute( + reference_genome='GRCh37', + dataset_type='SNV_INDEL', + columns=",\n ".join([ + "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes", + "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs", + "sumIf(hom_samples, sample_type = 'WES') AS hom_wes", + "sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs", + ]) + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + GT_STATS_DICT.substitute( + reference_genome='GRCh37', + dataset_type='SNV_INDEL', + columns= ",\n ".join([ + 'ac_wes UInt32', + 'ac_wgs UInt32', + 'hom_wes UInt32', + 'hom_wgs UInt32', + ]), + size=int(2e8), + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + ENTRIES_TO_PROJECT_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='SNV_INDEL', + columns=",\n ".join([ + 'sample_type', + "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", + ]), + groupby_columns='project_guid, key, sample_type', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + PROJECT_GT_STATS_TO_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='SNV_INDEL', + columns=",\n ".join([ + "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes", + "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs", + "sumIf(hom_samples, sample_type = 'WES') AS hom_wes", + "sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs", + ]) + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + GT_STATS_DICT.substitute( + reference_genome='GRCh38', + dataset_type='SNV_INDEL', + columns= ",\n ".join([ + 'ac_wes UInt32', + 'ac_wgs UInt32', + 'hom_wes UInt32', + 'hom_wgs UInt32', + ]), + size=int(1e9), + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + ENTRIES_TO_PROJECT_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='MITO', + columns=",\n ".join([ + 'sample_type', + "sum(toInt32(arrayCount(s -> (s.hl == '0'), calls) * sign)) AS ref_samples", + "sum(toInt32(arrayCount(s -> (s.hl > '0' AND s.hl < '0.95'), calls) * sign)) AS het_samples", + "sum(toInt32(arrayCount(s -> (s.hl >= '0.95'), calls) * sign)) AS hom_samples", + ]), + groupby_columns='project_guid, key, sample_type', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + PROJECT_GT_STATS_TO_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='MITO', + columns=",\n ".join([ + "sumIf(het_samples, sample_type = 'WES') AS ac_het_wes", + "sumIf(het_samples, sample_type = 'WGS') AS ac_het_wgs", + "sumIf(hom_samples, sample_type = 'WES') AS ac_hom_wes", + "sumIf(hom_samples, sample_type = 'WGS') AS ac_hom_wgs", + ]) + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + GT_STATS_DICT.substitute( + reference_genome='GRCh38', + dataset_type='MITO', + columns= ",\n ".join([ + 'ac_het_wes UInt32', + 'ac_het_wgs UInt32', + 'ac_hom_wes UInt32', + 'ac_hom_wgs UInt32', + ]), + size=int(1e6), + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + ENTRIES_TO_PROJECT_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='SV', + columns=",\n ".join([ + "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", + ]), + groupby_columns='project_guid, key', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + PROJECT_GT_STATS_TO_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='SV', + columns = ",\n ".join([ + 'sum((het_samples * 1) + (hom_samples * 2)) AS ac_wgs', + 'sum(hom_samples) AS hom_wgs', + ]), + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + GT_STATS_DICT.substitute( + reference_genome='GRCh38', + dataset_type='SV', + columns= ",\n ".join([ + 'ac_wgs UInt32', + 'hom_wgs UInt32' + ]), + size=int(5e6), + ), + hints={'clickhouse': True}, + ), + migrations.CreateModel( + name='ClinvarAllVariantsGRCh37SnvIndel', + fields=[ + ('version', clickhouse_backend.models.DateField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/clinvar_all_variants', + 'abstract': False, + 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarAllVariantsMito', + fields=[ + ('version', clickhouse_backend.models.DateField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh38/MITO/clinvar_all_variants', + 'abstract': False, + 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarAllVariantsSnvIndel', + fields=[ + ('version', clickhouse_backend.models.DateField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/clinvar_all_variants', + 'abstract': False, + 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.RunSQL( + CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( + reference_genome='GRCh37', + dataset_type='SNV_INDEL', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( + reference_genome='GRCh38', + dataset_type='SNV_INDEL', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( + reference_genome='GRCh38', + dataset_type='MITO', + ), + hints={'clickhouse': True}, + ), + ] From e4bdf8969bf0ff4e69566b785bf789db50b410e0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 28 Aug 2025 11:47:27 -0400 Subject: [PATCH 2/8] empty old migrations --- clickhouse_search/migrations/0001_initial.py | 123 ---------- ..._annotationsdiskgrch37snvindel_and_more.py | 121 ---------- ...to_annotationsmito_entriesmito_and_more.py | 99 --------- ...notationsdisksv_annotationssv_entriessv.py | 89 -------- ...nv_annotationsgcnv_entriesgcnv_and_more.py | 78 ------- ...upgrch37snvindel_keylookupmito_and_more.py | 77 ------- ...h37snvindel_projectgtstatsmito_and_more.py | 79 ------- ...el_gtstatsmito_gtstatssnvindel_and_more.py | 74 ------ ...0009_materializedviews_and_dictionaries.py | 210 ------------------ ...invarallvariantsgrch37snvindel_and_more.py | 69 ------ .../0011_clinvar_materialized_view.py | 42 ---- ...012_delete_annotationsdiskgcnv_and_more.py | 103 --------- ...nsdiskgcnv_annotationsdiskmito_and_more.py | 181 --------------- ...mesgrch37snvindel_gnomadgenomessnvindel.py | 69 ------ ...move_gnomadgenomessnvindel_key_and_more.py | 14 -- 15 files changed, 1428 deletions(-) diff --git a/clickhouse_search/migrations/0001_initial.py b/clickhouse_search/migrations/0001_initial.py index b733654f63..bd13bd3578 100644 --- a/clickhouse_search/migrations/0001_initial.py +++ b/clickhouse_search/migrations/0001_initial.py @@ -18,127 +18,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='AnnotationsDiskSnvIndel', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(return_int=False, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(return_int=False, db_column='liftedOverChrom', blank=True, null=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, return_int=False, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))], null_if_empty=True)), - ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, return_int=False, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, return_int=False, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, return_int=False, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), - ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences', null_when_empty=True)), - ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences', null_when_empty=True)), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/annotations', primary_key='key', flatten_nested=0), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsSnvIndel', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(return_int=False, db_column='liftedOverChrom', blank=True, null=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))], null_if_empty=True, rename_fields={'classification': 'class'})), - ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, return_int=False, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), - ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, return_int=False, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences', null_when_empty=True)), - ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, return_int=False, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, return_int=False, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences', null_when_empty=True)), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/SNV_INDEL/annotations', primary_key='key', flatten_nested=0), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesSnvIndel', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('is_gnomad_gt_5_percent', clickhouse_backend.models.BoolField()), - ('is_annotated_in_any_gene', clickhouse_backend.models.BoolField()), - ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('ab', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/entries', - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarSnvIndel', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriessnvindel')), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities', null_when_empty=True)), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')], return_int=False))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')], return_int=False)), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/clinvar', - 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', join_use_nulls=1, flatten_nested=0), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='TranscriptsSnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), - ('transcripts', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissense', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('pathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), ('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('exon', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('index', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('total', clickhouse_backend.models.Int32Field(blank=True, null=True))], null_if_empty=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('intron', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('index', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('total', clickhouse_backend.models.Int32Field(blank=True, null=True))], null_if_empty=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))], null_empty_arrays=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('manePlusClinical', clickhouse_backend.models.StringField(blank=True, null=True)), ('maneSelect', clickhouse_backend.models.StringField(blank=True, null=True)), ('refseqTranscriptId', clickhouse_backend.models.StringField(blank=True, null=True)), ('spliceregion', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('extended_intronic_splice_region_variant', clickhouse_backend.models.BoolField(blank=True, null=True))])), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field()), ('utrannotator', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('existingInframeOorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('existingOutofframeOorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('existingUorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('fiveutrAnnotation', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('AltStop', clickhouse_backend.models.StringField(blank=True, null=True)), ('AltStopDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('CapDistanceToStart', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('DistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('DistanceToStop', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('Evidence', clickhouse_backend.models.BoolField(blank=True, null=True)), ('FrameWithCDS', clickhouse_backend.models.StringField(blank=True, null=True)), ('KozakContext', clickhouse_backend.models.StringField(blank=True, null=True)), ('KozakStrength', clickhouse_backend.models.StringField(blank=True, null=True)), ('StartDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('alt_type', clickhouse_backend.models.StringField(blank=True, null=True)), ('alt_type_length', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('newSTOPDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('ref_StartDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('ref_type', clickhouse_backend.models.StringField(blank=True, null=True)), ('ref_type_length', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('type', clickhouse_backend.models.StringField(blank=True, null=True))], null_if_empty=True)), ('fiveutrConsequence', clickhouse_backend.models.StringField(blank=True, null=True))]))], group_by_key='geneId')), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/transcripts', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/transcripts', primary_key='key', flatten_nested=0), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0002_annotationsdiskgrch37snvindel_and_more.py b/clickhouse_search/migrations/0002_annotationsdiskgrch37snvindel_and_more.py index 27915f3895..55c2366060 100644 --- a/clickhouse_search/migrations/0002_annotationsdiskgrch37snvindel_and_more.py +++ b/clickhouse_search/migrations/0002_annotationsdiskgrch37snvindel_and_more.py @@ -8,8 +8,6 @@ import django.db.models.deletion import django.db.models.manager -from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR - class Migration(migrations.Migration): dependencies = [ @@ -17,123 +15,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='AnnotationsDiskGRCh37SnvIndel', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(return_int=False, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(return_int=False, db_column='liftedOverChrom', blank=True, null=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsGRCh37SnvIndel', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(return_int=False, db_column='liftedOverChrom', blank=True, null=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh37/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesGRCh37SnvIndel', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('is_gnomad_gt_5_percent', clickhouse_backend.models.BoolField()), - ('is_annotated_in_any_gene', clickhouse_backend.models.BoolField()), - ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('ab', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/entries', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='TranscriptsGRCh37SnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), - ('transcripts', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())])), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/transcripts', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/transcripts', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarGRCh37SnvIndel', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriesgrch37snvindel')), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities', null_when_empty=True)), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')], return_int=False))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/clinvar', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0003_annotationsdiskmito_annotationsmito_entriesmito_and_more.py b/clickhouse_search/migrations/0003_annotationsdiskmito_annotationsmito_entriesmito_and_more.py index 630bb5016b..222243fac1 100644 --- a/clickhouse_search/migrations/0003_annotationsdiskmito_annotationsmito_entriesmito_and_more.py +++ b/clickhouse_search/migrations/0003_annotationsdiskmito_annotationsmito_entriesmito_and_more.py @@ -7,8 +7,6 @@ import django.db.models.deletion import django.db.models.manager -from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR - class Migration(migrations.Migration): @@ -17,101 +15,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='AnnotationsDiskMito', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), - ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(null=True, blank=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences', group_by_key='geneId')), - ], - options={ - 'db_table': 'GRCh38/MITO/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/v0/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsMito', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), - ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(null=True, blank=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences', group_by_key='geneId')), - ], - options={ - 'db_table': 'GRCh38/MITO/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/v0/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesMito', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('hl', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitoCn', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('contamination', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh38/MITO/entries', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarMito', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriesmito')), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities', null_when_empty=True)), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')], return_int=False))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh38/MITO/clinvar', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0004_annotationsdisksv_annotationssv_entriessv.py b/clickhouse_search/migrations/0004_annotationsdisksv_annotationssv_entriessv.py index 0898f60849..def5ccdc14 100644 --- a/clickhouse_search/migrations/0004_annotationsdisksv_annotationssv_entriessv.py +++ b/clickhouse_search/migrations/0004_annotationsdisksv_annotationssv_entriessv.py @@ -7,8 +7,6 @@ import django.db.models.deletion import django.db.models.manager -from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR - class Migration(migrations.Migration): @@ -17,91 +15,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='AnnotationsDiskSv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('position', clickhouse_backend.models.UInt32Field(null=True, blank=True))], db_column='rg37LocusEnd')), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), - ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), - ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), - ('end_chrom', clickhouse_backend.models.Enum8Field(null=True, blank=True, db_column='endChrom', choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')]))], db_column='svSourceDetail')), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('sv_type_detail', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ], - options={ - 'db_table': 'GRCh38/SV/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/v0/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsSv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('position', clickhouse_backend.models.UInt32Field(null=True, blank=True))], db_column='rg37LocusEnd')), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), - ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), - ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), - ('end_chrom', clickhouse_backend.models.Enum8Field(null=True, blank=True, db_column='endChrom', choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')]))], db_column='svSourceDetail')), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('sv_type_detail', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ], - options={ - 'db_table': 'GRCh38/SV/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/v0/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesSv', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('cn', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('newCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevNumAlt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh38/SV/entries', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more.py b/clickhouse_search/migrations/0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more.py index cb3ca027d4..1f353491f7 100644 --- a/clickhouse_search/migrations/0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more.py +++ b/clickhouse_search/migrations/0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more.py @@ -7,8 +7,6 @@ import django.db.models.deletion import django.db.models.manager -from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR - class Migration(migrations.Migration): dependencies = [ @@ -16,80 +14,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='AnnotationsDiskGcnv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('position', clickhouse_backend.models.UInt32Field(null=True, blank=True))], db_column='rg37LocusEnd')), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ], - options={ - 'db_table': 'GRCh38/GCNV/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/v0/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsGcnv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('position', clickhouse_backend.models.UInt32Field(null=True, blank=True))], db_column='rg37LocusEnd')), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ], - options={ - 'db_table': 'GRCh38/GCNV/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/v0/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesGcnv', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgcnv')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('cn', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('qs', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('defragged', clickhouse_backend.models.BoolField(blank=True, null=True)), ('start', clickhouse_backend.models.UInt32Field(blank=True, null=True)), ('end', clickhouse_backend.models.UInt32Field(blank=True, null=True)), ('numExon', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('geneIds', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True))), ('newCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevOverlap', clickhouse_backend.models.BoolField(blank=True, null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh38/GCNV/entries', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more.py b/clickhouse_search/migrations/0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more.py index bade046ca9..3c039a54e7 100644 --- a/clickhouse_search/migrations/0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more.py +++ b/clickhouse_search/migrations/0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more.py @@ -6,8 +6,6 @@ import django.db.models.deletion import django.db.models.manager -from settings import CLICKHOUSE_DATA_DIR - class Migration(migrations.Migration): @@ -16,79 +14,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='KeyLookupGcnv', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsgcnv')), - ], - options={ - 'db_table': 'GRCh38/GCNV/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/GCNV/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='KeyLookupGRCh37SnvIndel', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsgrch37snvindel')), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='KeyLookupMito', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsmito')), - ], - options={ - 'db_table': 'GRCh38/MITO/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/MITO/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='KeyLookupSnvIndel', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationssnvindel')), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='KeyLookupSv', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationssv')), - ], - options={ - 'db_table': 'GRCh38/SV/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SV/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more.py b/clickhouse_search/migrations/0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more.py index 1aee55045c..2148ddbc76 100644 --- a/clickhouse_search/migrations/0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more.py +++ b/clickhouse_search/migrations/0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more.py @@ -13,83 +13,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='ProjectGtStatsGRCh37SnvIndel', - fields=[ - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('ref_samples', clickhouse_backend.models.UInt32Field()), - ('het_samples', clickhouse_backend.models.UInt32Field()), - ('hom_samples', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/project_gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ProjectGtStatsMito', - fields=[ - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('ref_samples', clickhouse_backend.models.UInt32Field()), - ('het_samples', clickhouse_backend.models.UInt32Field()), - ('hom_samples', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/MITO/project_gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ProjectGtStatsSnvIndel', - fields=[ - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('ref_samples', clickhouse_backend.models.UInt32Field()), - ('het_samples', clickhouse_backend.models.UInt32Field()), - ('hom_samples', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/project_gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ProjectGtStatsSv', - fields=[ - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), - ('ref_samples', clickhouse_backend.models.UInt32Field()), - ('het_samples', clickhouse_backend.models.UInt32Field()), - ('hom_samples', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/SV/project_gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key'), partition_by='project_guid'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more.py b/clickhouse_search/migrations/0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more.py index f0b675f6da..2ee138d740 100644 --- a/clickhouse_search/migrations/0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more.py +++ b/clickhouse_search/migrations/0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more.py @@ -13,78 +13,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='GtStatsGRCh37SnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), - ('ac_wes', clickhouse_backend.models.UInt32Field()), - ('ac_wgs', clickhouse_backend.models.UInt32Field()), - ('hom_wes', clickhouse_backend.models.UInt32Field()), - ('hom_wgs', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='GtStatsMito', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), - ('ac_het_wes', clickhouse_backend.models.UInt32Field()), - ('ac_het_wgs', clickhouse_backend.models.UInt32Field()), - ('ac_hom_wes', clickhouse_backend.models.UInt32Field()), - ('ac_hom_wgs', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/MITO/gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='GtStatsSnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), - ('ac_wes', clickhouse_backend.models.UInt32Field()), - ('ac_wgs', clickhouse_backend.models.UInt32Field()), - ('hom_wes', clickhouse_backend.models.UInt32Field()), - ('hom_wgs', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='GtStatsSv', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), - ('ac_wgs', clickhouse_backend.models.UInt32Field()), - ('hom_wgs', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/SV/gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0009_materializedviews_and_dictionaries.py b/clickhouse_search/migrations/0009_materializedviews_and_dictionaries.py index ece3274a22..5ab75c7902 100644 --- a/clickhouse_search/migrations/0009_materializedviews_and_dictionaries.py +++ b/clickhouse_search/migrations/0009_materializedviews_and_dictionaries.py @@ -1,58 +1,7 @@ # Generated manually by the seqr team. -import os -from string import Template from django.db import migrations -CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS = os.environ.get( - 'CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS', - '' -).split(',') -CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'clickhouse_test') -CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'clickhouse') - - -ENTRIES_TO_PROJECT_GT_STATS = Template(""" -CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/entries_to_project_gt_stats_mv` -TO `$reference_genome/$dataset_type/project_gt_stats` -AS SELECT - project_guid, - key, - $columns -FROM `$reference_genome/$dataset_type/entries` -GROUP BY $groupby_columns -""") - -PROJECT_GT_STATS_TO_GT_STATS = Template(Template(""" -CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/project_gt_stats_to_gt_stats_mv` -REFRESH EVERY 10 YEAR -TO `$reference_genome/$dataset_type/gt_stats` -AS SELECT - key, - $columns -FROM `$reference_genome/$dataset_type/project_gt_stats` -WHERE project_guid NOT IN $clickhouse_ac_excluded_project_guids -GROUP BY key -""").safe_substitute( - clickhouse_ac_excluded_project_guids=CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS -)) - -GT_STATS_DICT = Template(Template(""" -CREATE DICTIONARY `$reference_genome/$dataset_type/gt_stats_dict` -( - key UInt32, - $columns -) -PRIMARY KEY key -SOURCE(CLICKHOUSE(USER $clickhouse_writer_user PASSWORD $clickhouse_writer_password TABLE `$reference_genome/$dataset_type/gt_stats`)) -LIFETIME(MIN 0 MAX 0) -LAYOUT(FLAT(MAX_ARRAY_SIZE $size)) -""").safe_substitute( - # Note the nested Template-ing that allows - # double substitution these shared values - clickhouse_writer_user=CLICKHOUSE_WRITER_USER, - clickhouse_writer_password=CLICKHOUSE_WRITER_PASSWORD, -)) class Migration(migrations.Migration): @@ -61,164 +10,5 @@ class Migration(migrations.Migration): ] operations = [ - migrations.RunSQL( - ENTRIES_TO_PROJECT_GT_STATS.substitute( - reference_genome='GRCh37', - dataset_type='SNV_INDEL', - columns=",\n ".join([ - 'sample_type', - "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", - ]), - groupby_columns='project_guid, key, sample_type', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - PROJECT_GT_STATS_TO_GT_STATS.substitute( - reference_genome='GRCh37', - dataset_type='SNV_INDEL', - columns=",\n ".join([ - "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes", - "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs", - "sumIf(hom_samples, sample_type = 'WES') AS hom_wes", - "sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs", - ]) - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - GT_STATS_DICT.substitute( - reference_genome='GRCh37', - dataset_type='SNV_INDEL', - columns= ",\n ".join([ - 'ac_wes UInt32', - 'ac_wgs UInt32', - 'hom_wes UInt32', - 'hom_wgs UInt32', - ]), - size=int(2e8), - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - ENTRIES_TO_PROJECT_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='SNV_INDEL', - columns=",\n ".join([ - 'sample_type', - "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", - ]), - groupby_columns='project_guid, key, sample_type', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - PROJECT_GT_STATS_TO_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='SNV_INDEL', - columns=",\n ".join([ - "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes", - "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs", - "sumIf(hom_samples, sample_type = 'WES') AS hom_wes", - "sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs", - ]) - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - GT_STATS_DICT.substitute( - reference_genome='GRCh38', - dataset_type='SNV_INDEL', - columns= ",\n ".join([ - 'ac_wes UInt32', - 'ac_wgs UInt32', - 'hom_wes UInt32', - 'hom_wgs UInt32', - ]), - size=int(1e9), - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - ENTRIES_TO_PROJECT_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='MITO', - columns=",\n ".join([ - 'sample_type', - "sum(toInt32(arrayCount(s -> (s.hl == '0'), calls) * sign)) AS ref_samples", - "sum(toInt32(arrayCount(s -> (s.hl > '0' AND s.hl < '0.95'), calls) * sign)) AS het_samples", - "sum(toInt32(arrayCount(s -> (s.hl >= '0.95'), calls) * sign)) AS hom_samples", - ]), - groupby_columns='project_guid, key, sample_type', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - PROJECT_GT_STATS_TO_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='MITO', - columns=",\n ".join([ - "sumIf(het_samples, sample_type = 'WES') AS ac_het_wes", - "sumIf(het_samples, sample_type = 'WGS') AS ac_het_wgs", - "sumIf(hom_samples, sample_type = 'WES') AS ac_hom_wes", - "sumIf(hom_samples, sample_type = 'WGS') AS ac_hom_wgs", - ]) - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - GT_STATS_DICT.substitute( - reference_genome='GRCh38', - dataset_type='MITO', - columns= ",\n ".join([ - 'ac_het_wes UInt32', - 'ac_het_wgs UInt32', - 'ac_hom_wes UInt32', - 'ac_hom_wgs UInt32', - ]), - size=int(1e6), - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - ENTRIES_TO_PROJECT_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='SV', - columns=",\n ".join([ - "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", - ]), - groupby_columns='project_guid, key', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - PROJECT_GT_STATS_TO_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='SV', - columns = ",\n ".join([ - 'sum((het_samples * 1) + (hom_samples * 2)) AS ac_wgs', - 'sum(hom_samples) AS hom_wgs', - ]), - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - GT_STATS_DICT.substitute( - reference_genome='GRCh38', - dataset_type='SV', - columns= ",\n ".join([ - 'ac_wgs UInt32', - 'hom_wgs UInt32' - ]), - size=int(5e6), - ), - hints={'clickhouse': True}, - ), ] diff --git a/clickhouse_search/migrations/0010_clinvarallvariantsgrch37snvindel_and_more.py b/clickhouse_search/migrations/0010_clinvarallvariantsgrch37snvindel_and_more.py index de11a8ce50..c314b9708c 100644 --- a/clickhouse_search/migrations/0010_clinvarallvariantsgrch37snvindel_and_more.py +++ b/clickhouse_search/migrations/0010_clinvarallvariantsgrch37snvindel_and_more.py @@ -14,73 +14,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='ClinvarAllVariantsGRCh37SnvIndel', - fields=[ - ('version', clickhouse_backend.models.DateField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')], return_int=False))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/clinvar_all_variants', - 'abstract': False, - 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarAllVariantsMito', - fields=[ - ('version', clickhouse_backend.models.DateField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')], return_int=False))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh38/MITO/clinvar_all_variants', - 'abstract': False, - 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarAllVariantsSnvIndel', - fields=[ - ('version', clickhouse_backend.models.DateField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')], return_int=False))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/clinvar_all_variants', - 'abstract': False, - 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0011_clinvar_materialized_view.py b/clickhouse_search/migrations/0011_clinvar_materialized_view.py index ff6493c09f..53ceada47a 100644 --- a/clickhouse_search/migrations/0011_clinvar_materialized_view.py +++ b/clickhouse_search/migrations/0011_clinvar_materialized_view.py @@ -1,29 +1,8 @@ # Generated manually by the seqr team. -from string import Template from django.db import migrations -CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV = Template(""" -CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/clinvar_all_variants_to_clinvar_mv` -REFRESH EVERY 10 YEAR -TO `$reference_genome/$dataset_type/clinvar` -AS -SELECT - DISTINCT ON (key) - kl.key as key, - alleleId, - conflictingPathogenicities, - goldStars, - submitters, - conditions, - assertions, - pathogenicity -FROM `$reference_genome/$dataset_type/clinvar_all_variants` c -INNER JOIN `$reference_genome/$dataset_type/key_lookup` kl -ON c.variantId = kl.variantId -""") - class Migration(migrations.Migration): dependencies = [ @@ -31,26 +10,5 @@ class Migration(migrations.Migration): ] operations = [ - migrations.RunSQL( - CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( - reference_genome='GRCh37', - dataset_type='SNV_INDEL', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( - reference_genome='GRCh38', - dataset_type='SNV_INDEL', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( - reference_genome='GRCh38', - dataset_type='MITO', - ), - hints={'clickhouse': True}, - ), ] diff --git a/clickhouse_search/migrations/0012_delete_annotationsdiskgcnv_and_more.py b/clickhouse_search/migrations/0012_delete_annotationsdiskgcnv_and_more.py index d1fea85abc..e5105037b8 100644 --- a/clickhouse_search/migrations/0012_delete_annotationsdiskgcnv_and_more.py +++ b/clickhouse_search/migrations/0012_delete_annotationsdiskgcnv_and_more.py @@ -14,107 +14,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.DeleteModel( - name='AnnotationsDiskGcnv', - ), - migrations.DeleteModel( - name='AnnotationsDiskMito', - ), - migrations.DeleteModel( - name='AnnotationsDiskSv', - ), - migrations.DeleteModel( - name='AnnotationsGcnv', - ), - migrations.DeleteModel( - name='AnnotationsMito', - ), - migrations.DeleteModel( - name='AnnotationsSv', - ), - migrations.CreateModel( - name='AnnotationsMito', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), - ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(null=True, blank=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences', group_by_key='geneId')), - ], - options={ - 'db_table': 'GRCh38/MITO/annotations_memory', - 'engine': clickhouse_search.backend.engines.Join('ALL', 'INNER', 'key', join_use_nulls=1, flatten_nested=0), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsSv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('position', clickhouse_backend.models.UInt32Field(null=True, blank=True))], db_column='rg37LocusEnd')), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), - ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), - ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), - ('end_chrom', clickhouse_backend.models.Enum8Field(null=True, blank=True, db_column='endChrom', choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')]))], db_column='svSourceDetail')), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('sv_type_detail', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ], - options={ - 'db_table': 'GRCh38/SV/annotations_memory', - 'engine': clickhouse_search.backend.engines.Join('ALL', 'INNER', 'key', join_use_nulls=1, flatten_nested=0), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsGcnv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(null=True, blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('position', clickhouse_backend.models.UInt32Field(null=True, blank=True))], db_column='rg37LocusEnd')), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ], - options={ - 'db_table': 'GRCh38/GCNV/annotations_memory', - 'engine': clickhouse_search.backend.engines.Join('ALL', 'INNER', 'key', join_use_nulls=1, flatten_nested=0), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0013_annotationsdiskgcnv_annotationsdiskmito_and_more.py b/clickhouse_search/migrations/0013_annotationsdiskgcnv_annotationsdiskmito_and_more.py index 2f0926d315..02907c4bf7 100644 --- a/clickhouse_search/migrations/0013_annotationsdiskgcnv_annotationsdiskmito_and_more.py +++ b/clickhouse_search/migrations/0013_annotationsdiskgcnv_annotationsdiskmito_and_more.py @@ -4,8 +4,6 @@ from django.db import migrations import django.db.models.manager -from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR - class Migration(migrations.Migration): @@ -14,183 +12,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.DeleteModel( - name='AnnotationsGcnv', - ), - migrations.DeleteModel( - name='AnnotationsMito', - ), - migrations.DeleteModel( - name='AnnotationsSv', - ), - migrations.CreateModel( - name='AnnotationsGcnv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ], - options={ - 'db_table': 'GRCh38/GCNV/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsMito', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), - ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), - ], - options={ - 'db_table': 'GRCh38/MITO/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsSv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), - ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), - ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), - ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), - ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), - ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), - ], - options={ - 'db_table': 'GRCh38/SV/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsDiskGcnv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ], - options={ - 'db_table': 'GRCh38/GCNV/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsDiskMito', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), - ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), - ], - options={ - 'db_table': 'GRCh38/MITO/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsDiskSv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), - ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), - ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), - ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), - ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), - ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), - ], - options={ - 'db_table': 'GRCh38/SV/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), ] diff --git a/clickhouse_search/migrations/0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel.py b/clickhouse_search/migrations/0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel.py index 5b621c8477..9ee4312ad8 100644 --- a/clickhouse_search/migrations/0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel.py +++ b/clickhouse_search/migrations/0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel.py @@ -1,33 +1,10 @@ # Generated by Django 4.2.21 on 2025-08-13 19:35 and editted manually by the seqr team -import os -from string import Template - import clickhouse_backend.models from django.db import migrations, models import django.db.models.deletion import django.db.models.manager -CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'clickhouse_test') -CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'clickhouse') - -GNOMAD_GENOMES_DICT = Template(Template(""" -CREATE DICTIONARY `$reference_genome/$dataset_type/gnomad_genomes_dict` -( - key UInt32, - filter_af Decimal(9, 5) -) -PRIMARY KEY key -SOURCE(CLICKHOUSE(USER $clickhouse_writer_user PASSWORD $clickhouse_writer_password TABLE `$reference_genome/$dataset_type/gnomad_genomes`)) -LIFETIME(MIN 0 MAX 0) -LAYOUT(FLAT(MAX_ARRAY_SIZE $size)) -""").safe_substitute( - # Note the nested Template-ing that allows - # double substitution these shared values - clickhouse_writer_user=CLICKHOUSE_WRITER_USER, - clickhouse_writer_password=CLICKHOUSE_WRITER_PASSWORD, -)) - class Migration(migrations.Migration): @@ -36,50 +13,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.CreateModel( - name='GnomadGenomesGRCh37SnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), - ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/gnomad_genomes', - 'engine': clickhouse_backend.models.ReplacingMergeTree(order_by='key', primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='GnomadGenomesSnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), - ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/gnomad_genomes', - 'engine': clickhouse_backend.models.ReplacingMergeTree(order_by='key', primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.RunSQL( - GNOMAD_GENOMES_DICT.substitute( - reference_genome='GRCh37', - dataset_type='SNV_INDEL', - size=int(1e8), - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - GNOMAD_GENOMES_DICT.substitute( - reference_genome='GRCh38', - dataset_type='SNV_INDEL', - size=int(5e8), - ), - hints={'clickhouse': True}, - ), ] diff --git a/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py b/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py index 1c82f6d549..cc938fca7d 100644 --- a/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py +++ b/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py @@ -10,18 +10,4 @@ class Migration(migrations.Migration): ] operations = [ - migrations.RunSQL( - 'DROP DICTIONARY `GRCh37/SNV_INDEL/gnomad_genomes_dict`', - hints={'clickhouse': True}, - ), - migrations.RunSQL( - 'DROP DICTIONARY `GRCh38/SNV_INDEL/gnomad_genomes_dict`', - hints={'clickhouse': True}, - ), - migrations.DeleteModel( - name='GnomadGenomesGRCh37SnvIndel', - ), - migrations.DeleteModel( - name='GnomadGenomesSnvIndel', - ), ] From 4fd3c4cd18ba126dcc7bc26e20f8b7ed361284ee Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 28 Aug 2025 11:50:33 -0400 Subject: [PATCH 3/8] remove old migrations --- clickhouse_search/migrations/0001_initial.py | 21 - ...move_gnomadgenomessnvindel_key_and_more.py | 1076 ----------------- ..._annotationsdiskgrch37snvindel_and_more.py | 18 - ...to_annotationsmito_entriesmito_and_more.py | 18 - ...notationsdisksv_annotationssv_entriessv.py | 18 - ...nv_annotationsgcnv_entriesgcnv_and_more.py | 17 - ...upgrch37snvindel_keylookupmito_and_more.py | 17 - ...h37snvindel_projectgtstatsmito_and_more.py | 16 - ...el_gtstatsmito_gtstatssnvindel_and_more.py | 16 - ...0009_materializedviews_and_dictionaries.py | 14 - ...invarallvariantsgrch37snvindel_and_more.py | 17 - .../0011_clinvar_materialized_view.py | 14 - ...012_delete_annotationsdiskgcnv_and_more.py | 17 - ...nsdiskgcnv_annotationsdiskmito_and_more.py | 15 - ...mesgrch37snvindel_gnomadgenomessnvindel.py | 16 - ...move_gnomadgenomessnvindel_key_and_more.py | 1068 +++++++++++++++- 16 files changed, 1065 insertions(+), 1313 deletions(-) delete mode 100644 clickhouse_search/migrations/0001_initial.py delete mode 100644 clickhouse_search/migrations/0001_squashed_0015_remove_gnomadgenomessnvindel_key_and_more.py delete mode 100644 clickhouse_search/migrations/0002_annotationsdiskgrch37snvindel_and_more.py delete mode 100644 clickhouse_search/migrations/0003_annotationsdiskmito_annotationsmito_entriesmito_and_more.py delete mode 100644 clickhouse_search/migrations/0004_annotationsdisksv_annotationssv_entriessv.py delete mode 100644 clickhouse_search/migrations/0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more.py delete mode 100644 clickhouse_search/migrations/0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more.py delete mode 100644 clickhouse_search/migrations/0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more.py delete mode 100644 clickhouse_search/migrations/0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more.py delete mode 100644 clickhouse_search/migrations/0009_materializedviews_and_dictionaries.py delete mode 100644 clickhouse_search/migrations/0010_clinvarallvariantsgrch37snvindel_and_more.py delete mode 100644 clickhouse_search/migrations/0011_clinvar_materialized_view.py delete mode 100644 clickhouse_search/migrations/0012_delete_annotationsdiskgcnv_and_more.py delete mode 100644 clickhouse_search/migrations/0013_annotationsdiskgcnv_annotationsdiskmito_and_more.py delete mode 100644 clickhouse_search/migrations/0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel.py diff --git a/clickhouse_search/migrations/0001_initial.py b/clickhouse_search/migrations/0001_initial.py deleted file mode 100644 index bd13bd3578..0000000000 --- a/clickhouse_search/migrations/0001_initial.py +++ /dev/null @@ -1,21 +0,0 @@ -# Generated by Django 4.2.20 on 2025-04-25 20:26 - -import clickhouse_backend.models -import clickhouse_search.backend.fields -import clickhouse_search.backend.engines -import clickhouse_search.models -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager - -from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR - -class Migration(migrations.Migration): - - initial = True - - dependencies = [ - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0001_squashed_0015_remove_gnomadgenomessnvindel_key_and_more.py b/clickhouse_search/migrations/0001_squashed_0015_remove_gnomadgenomessnvindel_key_and_more.py deleted file mode 100644 index 62f5bcffb0..0000000000 --- a/clickhouse_search/migrations/0001_squashed_0015_remove_gnomadgenomessnvindel_key_and_more.py +++ /dev/null @@ -1,1076 +0,0 @@ -# Generated by Django 4.2.22 on 2025-08-28 15:22 - -import clickhouse_backend.models -import clickhouse_search.backend.engines -import clickhouse_search.backend.fields -import clickhouse_search.models - -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager -import os -from string import Template - -from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR - -CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS = os.environ.get( - 'CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS', - '' -).split(',') -CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'clickhouse_test') -CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'clickhouse') - - -ENTRIES_TO_PROJECT_GT_STATS = Template(""" -CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/entries_to_project_gt_stats_mv` -TO `$reference_genome/$dataset_type/project_gt_stats` -AS SELECT - project_guid, - key, - $columns -FROM `$reference_genome/$dataset_type/entries` -GROUP BY $groupby_columns -""") - -PROJECT_GT_STATS_TO_GT_STATS = Template(Template(""" -CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/project_gt_stats_to_gt_stats_mv` -REFRESH EVERY 10 YEAR -TO `$reference_genome/$dataset_type/gt_stats` -AS SELECT - key, - $columns -FROM `$reference_genome/$dataset_type/project_gt_stats` -WHERE project_guid NOT IN $clickhouse_ac_excluded_project_guids -GROUP BY key -""").safe_substitute( - clickhouse_ac_excluded_project_guids=CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS -)) - -GT_STATS_DICT = Template(Template(""" -CREATE DICTIONARY `$reference_genome/$dataset_type/gt_stats_dict` -( - key UInt32, - $columns -) -PRIMARY KEY key -SOURCE(CLICKHOUSE(USER $clickhouse_writer_user PASSWORD $clickhouse_writer_password TABLE `$reference_genome/$dataset_type/gt_stats`)) -LIFETIME(MIN 0 MAX 0) -LAYOUT(FLAT(MAX_ARRAY_SIZE $size)) -""").safe_substitute( - # Note the nested Template-ing that allows - # double substitution these shared values - clickhouse_writer_user=CLICKHOUSE_WRITER_USER, - clickhouse_writer_password=CLICKHOUSE_WRITER_PASSWORD, -)) - -CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV = Template(""" -CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/clinvar_all_variants_to_clinvar_mv` -REFRESH EVERY 10 YEAR -TO `$reference_genome/$dataset_type/clinvar` -AS -SELECT - DISTINCT ON (key) - kl.key as key, - alleleId, - conflictingPathogenicities, - goldStars, - submitters, - conditions, - assertions, - pathogenicity -FROM `$reference_genome/$dataset_type/clinvar_all_variants` c -INNER JOIN `$reference_genome/$dataset_type/key_lookup` kl -ON c.variantId = kl.variantId -""") - - -class Migration(migrations.Migration): - - replaces = [('clickhouse_search', '0001_initial'), ('clickhouse_search', '0002_annotationsdiskgrch37snvindel_and_more'), ('clickhouse_search', '0003_annotationsdiskmito_annotationsmito_entriesmito_and_more'), ('clickhouse_search', '0004_annotationsdisksv_annotationssv_entriessv'), ('clickhouse_search', '0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more'), ('clickhouse_search', '0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more'), ('clickhouse_search', '0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more'), ('clickhouse_search', '0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more'), ('clickhouse_search', '0009_materializedviews_and_dictionaries'), ('clickhouse_search', '0010_clinvarallvariantsgrch37snvindel_and_more'), ('clickhouse_search', '0011_clinvar_materialized_view'), ('clickhouse_search', '0012_delete_annotationsdiskgcnv_and_more'), ('clickhouse_search', '0013_annotationsdiskgcnv_annotationsdiskmito_and_more'), ('clickhouse_search', '0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel'), ('clickhouse_search', '0015_remove_gnomadgenomessnvindel_key_and_more')] - - initial = True - - dependencies = [ - ] - - operations = [ - migrations.CreateModel( - name='AnnotationsDiskSnvIndel', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), - ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), - ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences')), - ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences')), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsSnvIndel', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), - ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), - ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences')), - ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences')), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesSnvIndel', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('is_gnomad_gt_5_percent', clickhouse_backend.models.BoolField()), - ('is_annotated_in_any_gene', clickhouse_backend.models.BoolField()), - ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('ab', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/entries', - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarSnvIndel', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriessnvindel')), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/clinvar', - 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='TranscriptsSnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), - ('transcripts', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissense', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('pathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), ('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('exon', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('index', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('total', clickhouse_backend.models.Int32Field(blank=True, null=True))])), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('intron', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('index', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('total', clickhouse_backend.models.Int32Field(blank=True, null=True))])), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('manePlusClinical', clickhouse_backend.models.StringField(blank=True, null=True)), ('maneSelect', clickhouse_backend.models.StringField(blank=True, null=True)), ('refseqTranscriptId', clickhouse_backend.models.StringField(blank=True, null=True)), ('spliceregion', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('extended_intronic_splice_region_variant', clickhouse_backend.models.BoolField(blank=True, null=True))])), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field()), ('utrannotator', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('existingInframeOorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('existingOutofframeOorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('existingUorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('fiveutrAnnotation', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('AltStop', clickhouse_backend.models.StringField(blank=True, null=True)), ('AltStopDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('CapDistanceToStart', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('DistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('DistanceToStop', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('Evidence', clickhouse_backend.models.BoolField(blank=True, null=True)), ('FrameWithCDS', clickhouse_backend.models.StringField(blank=True, null=True)), ('KozakContext', clickhouse_backend.models.StringField(blank=True, null=True)), ('KozakStrength', clickhouse_backend.models.StringField(blank=True, null=True)), ('StartDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('alt_type', clickhouse_backend.models.StringField(blank=True, null=True)), ('alt_type_length', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('newSTOPDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('ref_StartDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('ref_type', clickhouse_backend.models.StringField(blank=True, null=True)), ('ref_type_length', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('type', clickhouse_backend.models.StringField(blank=True, null=True))])), ('fiveutrConsequence', clickhouse_backend.models.StringField(blank=True, null=True))]))])), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/transcripts', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/transcripts', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsDiskGRCh37SnvIndel', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsGRCh37SnvIndel', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('pos', clickhouse_backend.models.UInt32Field()), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh37/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsGcnv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ], - options={ - 'db_table': 'GRCh38/GCNV/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsMito', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), - ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), - ], - options={ - 'db_table': 'GRCh38/MITO/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsSv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), - ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), - ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), - ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), - ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), - ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), - ], - options={ - 'db_table': 'GRCh38/SV/annotations_memory', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsDiskGcnv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), - ], - options={ - 'db_table': 'GRCh38/GCNV/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsDiskMito', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('ref', clickhouse_backend.models.StringField()), - ('alt', clickhouse_backend.models.StringField()), - ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), - ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), - ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), - ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), - ], - options={ - 'db_table': 'GRCh38/MITO/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='AnnotationsDiskSv', - fields=[ - ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), - ('xpos', clickhouse_backend.models.UInt64Field()), - ('pos', clickhouse_backend.models.UInt32Field()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), - ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), - ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), - ('end', clickhouse_backend.models.UInt32Field()), - ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), - ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), - ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), - ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), - ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), - ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), - ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), - ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), - ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), - ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), - ], - options={ - 'db_table': 'GRCh38/SV/annotations_disk', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesGRCh37SnvIndel', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('is_gnomad_gt_5_percent', clickhouse_backend.models.BoolField()), - ('is_annotated_in_any_gene', clickhouse_backend.models.BoolField()), - ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('ab', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/entries', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='TranscriptsGRCh37SnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), - ('transcripts', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())])), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/transcripts', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/transcripts', flatten_nested=0, primary_key='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarGRCh37SnvIndel', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriesgrch37snvindel')), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/clinvar', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesMito', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('hl', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitoCn', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('contamination', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh38/MITO/entries', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarMito', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriesmito')), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh38/MITO/clinvar', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesSv', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('cn', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('newCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevNumAlt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh38/SV/entries', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='EntriesGcnv', - fields=[ - ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgcnv')), - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('family_guid', clickhouse_backend.models.StringField()), - ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), - ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), - ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('cn', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('qs', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('defragged', clickhouse_backend.models.BoolField(blank=True, null=True)), ('start', clickhouse_backend.models.UInt32Field(blank=True, null=True)), ('end', clickhouse_backend.models.UInt32Field(blank=True, null=True)), ('numExon', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('geneIds', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True))), ('newCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevOverlap', clickhouse_backend.models.BoolField(blank=True, null=True))]))), - ('sign', clickhouse_backend.models.Int8Field()), - ], - options={ - 'db_table': 'GRCh38/GCNV/entries', - 'abstract': False, - 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='KeyLookupGcnv', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsgcnv')), - ], - options={ - 'db_table': 'GRCh38/GCNV/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/GCNV/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='KeyLookupGRCh37SnvIndel', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsgrch37snvindel')), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='KeyLookupMito', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsmito')), - ], - options={ - 'db_table': 'GRCh38/MITO/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/MITO/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='KeyLookupSnvIndel', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationssnvindel')), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='KeyLookupSv', - fields=[ - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationssv')), - ], - options={ - 'db_table': 'GRCh38/SV/key_lookup', - 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SV/key_lookup', flatten_nested=0, primary_key='variant_id'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ProjectGtStatsGRCh37SnvIndel', - fields=[ - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('ref_samples', clickhouse_backend.models.UInt32Field()), - ('het_samples', clickhouse_backend.models.UInt32Field()), - ('hom_samples', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/project_gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ProjectGtStatsMito', - fields=[ - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('ref_samples', clickhouse_backend.models.UInt32Field()), - ('het_samples', clickhouse_backend.models.UInt32Field()), - ('hom_samples', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/MITO/project_gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ProjectGtStatsSnvIndel', - fields=[ - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), - ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), - ('ref_samples', clickhouse_backend.models.UInt32Field()), - ('het_samples', clickhouse_backend.models.UInt32Field()), - ('hom_samples', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/project_gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ProjectGtStatsSv', - fields=[ - ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), - ('ref_samples', clickhouse_backend.models.UInt32Field()), - ('het_samples', clickhouse_backend.models.UInt32Field()), - ('hom_samples', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/SV/project_gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key'), partition_by='project_guid'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='GtStatsGRCh37SnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), - ('ac_wes', clickhouse_backend.models.UInt32Field()), - ('ac_wgs', clickhouse_backend.models.UInt32Field()), - ('hom_wes', clickhouse_backend.models.UInt32Field()), - ('hom_wgs', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='GtStatsMito', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), - ('ac_het_wes', clickhouse_backend.models.UInt32Field()), - ('ac_het_wgs', clickhouse_backend.models.UInt32Field()), - ('ac_hom_wes', clickhouse_backend.models.UInt32Field()), - ('ac_hom_wgs', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/MITO/gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='GtStatsSnvIndel', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), - ('ac_wes', clickhouse_backend.models.UInt32Field()), - ('ac_wgs', clickhouse_backend.models.UInt32Field()), - ('hom_wes', clickhouse_backend.models.UInt32Field()), - ('hom_wgs', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='GtStatsSv', - fields=[ - ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), - ('ac_wgs', clickhouse_backend.models.UInt32Field()), - ('hom_wgs', clickhouse_backend.models.UInt32Field()), - ], - options={ - 'db_table': 'GRCh38/SV/gt_stats', - 'abstract': False, - 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.RunSQL( - ENTRIES_TO_PROJECT_GT_STATS.substitute( - reference_genome='GRCh37', - dataset_type='SNV_INDEL', - columns=",\n ".join([ - 'sample_type', - "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", - ]), - groupby_columns='project_guid, key, sample_type', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - PROJECT_GT_STATS_TO_GT_STATS.substitute( - reference_genome='GRCh37', - dataset_type='SNV_INDEL', - columns=",\n ".join([ - "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes", - "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs", - "sumIf(hom_samples, sample_type = 'WES') AS hom_wes", - "sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs", - ]) - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - GT_STATS_DICT.substitute( - reference_genome='GRCh37', - dataset_type='SNV_INDEL', - columns= ",\n ".join([ - 'ac_wes UInt32', - 'ac_wgs UInt32', - 'hom_wes UInt32', - 'hom_wgs UInt32', - ]), - size=int(2e8), - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - ENTRIES_TO_PROJECT_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='SNV_INDEL', - columns=",\n ".join([ - 'sample_type', - "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", - ]), - groupby_columns='project_guid, key, sample_type', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - PROJECT_GT_STATS_TO_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='SNV_INDEL', - columns=",\n ".join([ - "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes", - "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs", - "sumIf(hom_samples, sample_type = 'WES') AS hom_wes", - "sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs", - ]) - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - GT_STATS_DICT.substitute( - reference_genome='GRCh38', - dataset_type='SNV_INDEL', - columns= ",\n ".join([ - 'ac_wes UInt32', - 'ac_wgs UInt32', - 'hom_wes UInt32', - 'hom_wgs UInt32', - ]), - size=int(1e9), - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - ENTRIES_TO_PROJECT_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='MITO', - columns=",\n ".join([ - 'sample_type', - "sum(toInt32(arrayCount(s -> (s.hl == '0'), calls) * sign)) AS ref_samples", - "sum(toInt32(arrayCount(s -> (s.hl > '0' AND s.hl < '0.95'), calls) * sign)) AS het_samples", - "sum(toInt32(arrayCount(s -> (s.hl >= '0.95'), calls) * sign)) AS hom_samples", - ]), - groupby_columns='project_guid, key, sample_type', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - PROJECT_GT_STATS_TO_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='MITO', - columns=",\n ".join([ - "sumIf(het_samples, sample_type = 'WES') AS ac_het_wes", - "sumIf(het_samples, sample_type = 'WGS') AS ac_het_wgs", - "sumIf(hom_samples, sample_type = 'WES') AS ac_hom_wes", - "sumIf(hom_samples, sample_type = 'WGS') AS ac_hom_wgs", - ]) - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - GT_STATS_DICT.substitute( - reference_genome='GRCh38', - dataset_type='MITO', - columns= ",\n ".join([ - 'ac_het_wes UInt32', - 'ac_het_wgs UInt32', - 'ac_hom_wes UInt32', - 'ac_hom_wgs UInt32', - ]), - size=int(1e6), - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - ENTRIES_TO_PROJECT_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='SV', - columns=",\n ".join([ - "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", - "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", - ]), - groupby_columns='project_guid, key', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - PROJECT_GT_STATS_TO_GT_STATS.substitute( - reference_genome='GRCh38', - dataset_type='SV', - columns = ",\n ".join([ - 'sum((het_samples * 1) + (hom_samples * 2)) AS ac_wgs', - 'sum(hom_samples) AS hom_wgs', - ]), - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - GT_STATS_DICT.substitute( - reference_genome='GRCh38', - dataset_type='SV', - columns= ",\n ".join([ - 'ac_wgs UInt32', - 'hom_wgs UInt32' - ]), - size=int(5e6), - ), - hints={'clickhouse': True}, - ), - migrations.CreateModel( - name='ClinvarAllVariantsGRCh37SnvIndel', - fields=[ - ('version', clickhouse_backend.models.DateField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh37/SNV_INDEL/clinvar_all_variants', - 'abstract': False, - 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarAllVariantsMito', - fields=[ - ('version', clickhouse_backend.models.DateField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh38/MITO/clinvar_all_variants', - 'abstract': False, - 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.CreateModel( - name='ClinvarAllVariantsSnvIndel', - fields=[ - ('version', clickhouse_backend.models.DateField()), - ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), - ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), - ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), - ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), - ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), - ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), - ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), - ], - options={ - 'db_table': 'GRCh38/SNV_INDEL/clinvar_all_variants', - 'abstract': False, - 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), - }, - managers=[ - ('objects', django.db.models.manager.Manager()), - ('_overwrite_base_manager', django.db.models.manager.Manager()), - ], - ), - migrations.RunSQL( - CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( - reference_genome='GRCh37', - dataset_type='SNV_INDEL', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( - reference_genome='GRCh38', - dataset_type='SNV_INDEL', - ), - hints={'clickhouse': True}, - ), - migrations.RunSQL( - CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( - reference_genome='GRCh38', - dataset_type='MITO', - ), - hints={'clickhouse': True}, - ), - ] diff --git a/clickhouse_search/migrations/0002_annotationsdiskgrch37snvindel_and_more.py b/clickhouse_search/migrations/0002_annotationsdiskgrch37snvindel_and_more.py deleted file mode 100644 index 55c2366060..0000000000 --- a/clickhouse_search/migrations/0002_annotationsdiskgrch37snvindel_and_more.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.2.21 on 2025-06-12 21:14 - -import clickhouse_backend.models -import clickhouse_search.backend.engines -import clickhouse_search.backend.fields -import clickhouse_search.models -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0001_initial'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0003_annotationsdiskmito_annotationsmito_entriesmito_and_more.py b/clickhouse_search/migrations/0003_annotationsdiskmito_annotationsmito_entriesmito_and_more.py deleted file mode 100644 index 222243fac1..0000000000 --- a/clickhouse_search/migrations/0003_annotationsdiskmito_annotationsmito_entriesmito_and_more.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.2.21 on 2025-06-13 00:44 - -import clickhouse_backend.models -import clickhouse_search.backend.engines -import clickhouse_search.backend.fields -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0002_annotationsdiskgrch37snvindel_and_more'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0004_annotationsdisksv_annotationssv_entriessv.py b/clickhouse_search/migrations/0004_annotationsdisksv_annotationssv_entriessv.py deleted file mode 100644 index def5ccdc14..0000000000 --- a/clickhouse_search/migrations/0004_annotationsdisksv_annotationssv_entriessv.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.2.21 on 2025-06-12 20:56 - -import clickhouse_backend.models -import clickhouse_search.backend.engines -import clickhouse_search.backend.fields -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0003_annotationsdiskmito_annotationsmito_entriesmito_and_more'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more.py b/clickhouse_search/migrations/0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more.py deleted file mode 100644 index 1f353491f7..0000000000 --- a/clickhouse_search/migrations/0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more.py +++ /dev/null @@ -1,17 +0,0 @@ -# Generated by Django 4.2.21 on 2025-06-13 02:50 - -import clickhouse_backend.models -import clickhouse_search.backend.engines -import clickhouse_search.backend.fields -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0004_annotationsdisksv_annotationssv_entriessv'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more.py b/clickhouse_search/migrations/0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more.py deleted file mode 100644 index 3c039a54e7..0000000000 --- a/clickhouse_search/migrations/0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more.py +++ /dev/null @@ -1,17 +0,0 @@ -# Generated by Django 4.2.21 on 2025-06-23 14:57 - -import clickhouse_backend.models -import clickhouse_search.backend.engines -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0005_annotationsdiskgcnv_annotationsgcnv_entriesgcnv_and_more'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more.py b/clickhouse_search/migrations/0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more.py deleted file mode 100644 index 2148ddbc76..0000000000 --- a/clickhouse_search/migrations/0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more.py +++ /dev/null @@ -1,16 +0,0 @@ -# Generated by Django 4.2.21 on 2025-06-23 17:58 - -import clickhouse_backend.models -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0006_keylookupgcnv_keylookupgrch37snvindel_keylookupmito_and_more'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more.py b/clickhouse_search/migrations/0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more.py deleted file mode 100644 index 2ee138d740..0000000000 --- a/clickhouse_search/migrations/0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more.py +++ /dev/null @@ -1,16 +0,0 @@ -# Generated by Django 4.2.21 on 2025-06-23 20:06 - -import clickhouse_backend.models -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0007_projectgtstatsgrch37snvindel_projectgtstatsmito_and_more'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0009_materializedviews_and_dictionaries.py b/clickhouse_search/migrations/0009_materializedviews_and_dictionaries.py deleted file mode 100644 index 5ab75c7902..0000000000 --- a/clickhouse_search/migrations/0009_materializedviews_and_dictionaries.py +++ /dev/null @@ -1,14 +0,0 @@ -# Generated manually by the seqr team. - -from django.db import migrations - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0008_gtstatsgrch37snvindel_gtstatsmito_gtstatssnvindel_and_more'), - ] - - operations = [ - ] - diff --git a/clickhouse_search/migrations/0010_clinvarallvariantsgrch37snvindel_and_more.py b/clickhouse_search/migrations/0010_clinvarallvariantsgrch37snvindel_and_more.py deleted file mode 100644 index c314b9708c..0000000000 --- a/clickhouse_search/migrations/0010_clinvarallvariantsgrch37snvindel_and_more.py +++ /dev/null @@ -1,17 +0,0 @@ -# Generated by Django 4.2.21 on 2025-07-15 16:39 - -import clickhouse_backend.models -import clickhouse_search.backend.fields -import clickhouse_search.models -from django.db import migrations -import django.db.models.manager - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0009_materializedviews_and_dictionaries'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0011_clinvar_materialized_view.py b/clickhouse_search/migrations/0011_clinvar_materialized_view.py deleted file mode 100644 index 53ceada47a..0000000000 --- a/clickhouse_search/migrations/0011_clinvar_materialized_view.py +++ /dev/null @@ -1,14 +0,0 @@ -# Generated manually by the seqr team. - -from django.db import migrations - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0010_clinvarallvariantsgrch37snvindel_and_more'), - ] - - operations = [ - ] - diff --git a/clickhouse_search/migrations/0012_delete_annotationsdiskgcnv_and_more.py b/clickhouse_search/migrations/0012_delete_annotationsdiskgcnv_and_more.py deleted file mode 100644 index e5105037b8..0000000000 --- a/clickhouse_search/migrations/0012_delete_annotationsdiskgcnv_and_more.py +++ /dev/null @@ -1,17 +0,0 @@ -# Generated by Django 4.2.21 on 2025-08-06 00:31 - -import clickhouse_backend.models -import clickhouse_search.backend.fields -import clickhouse_search.backend.engines -from django.db import migrations -import django.db.models.manager - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0011_clinvar_materialized_view'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0013_annotationsdiskgcnv_annotationsdiskmito_and_more.py b/clickhouse_search/migrations/0013_annotationsdiskgcnv_annotationsdiskmito_and_more.py deleted file mode 100644 index 02907c4bf7..0000000000 --- a/clickhouse_search/migrations/0013_annotationsdiskgcnv_annotationsdiskmito_and_more.py +++ /dev/null @@ -1,15 +0,0 @@ -import clickhouse_backend.models -import clickhouse_search.backend.engines -import clickhouse_search.backend.fields -from django.db import migrations -import django.db.models.manager - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0012_delete_annotationsdiskgcnv_and_more'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel.py b/clickhouse_search/migrations/0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel.py deleted file mode 100644 index 9ee4312ad8..0000000000 --- a/clickhouse_search/migrations/0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel.py +++ /dev/null @@ -1,16 +0,0 @@ -# Generated by Django 4.2.21 on 2025-08-13 19:35 and editted manually by the seqr team - -import clickhouse_backend.models -from django.db import migrations, models -import django.db.models.deletion -import django.db.models.manager - - -class Migration(migrations.Migration): - - dependencies = [ - ('clickhouse_search', '0013_annotationsdiskgcnv_annotationsdiskmito_and_more'), - ] - - operations = [ - ] diff --git a/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py b/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py index cc938fca7d..cd237ffb99 100644 --- a/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py +++ b/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py @@ -1,13 +1,1075 @@ -# Generated by Django 4.2.22 on 2025-08-15 19:45 +# Generated by Django 4.2.22 on 2025-08-28 15:22 +# Squashed all previous migrations for clickhouse_search app -from django.db import migrations +import clickhouse_backend.models +import clickhouse_search.backend.engines +import clickhouse_search.backend.fields +import clickhouse_search.models + +from django.db import migrations, models +import django.db.models.deletion +import django.db.models.manager +import os +from string import Template + +from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR + +CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS = os.environ.get( + 'CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS', + '' +).split(',') +CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'clickhouse_test') +CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'clickhouse') + + +ENTRIES_TO_PROJECT_GT_STATS = Template(""" +CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/entries_to_project_gt_stats_mv` +TO `$reference_genome/$dataset_type/project_gt_stats` +AS SELECT + project_guid, + key, + $columns +FROM `$reference_genome/$dataset_type/entries` +GROUP BY $groupby_columns +""") + +PROJECT_GT_STATS_TO_GT_STATS = Template(Template(""" +CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/project_gt_stats_to_gt_stats_mv` +REFRESH EVERY 10 YEAR +TO `$reference_genome/$dataset_type/gt_stats` +AS SELECT + key, + $columns +FROM `$reference_genome/$dataset_type/project_gt_stats` +WHERE project_guid NOT IN $clickhouse_ac_excluded_project_guids +GROUP BY key +""").safe_substitute( + clickhouse_ac_excluded_project_guids=CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS +)) + +GT_STATS_DICT = Template(Template(""" +CREATE DICTIONARY `$reference_genome/$dataset_type/gt_stats_dict` +( + key UInt32, + $columns +) +PRIMARY KEY key +SOURCE(CLICKHOUSE(USER $clickhouse_writer_user PASSWORD $clickhouse_writer_password TABLE `$reference_genome/$dataset_type/gt_stats`)) +LIFETIME(MIN 0 MAX 0) +LAYOUT(FLAT(MAX_ARRAY_SIZE $size)) +""").safe_substitute( + # Note the nested Template-ing that allows + # double substitution these shared values + clickhouse_writer_user=CLICKHOUSE_WRITER_USER, + clickhouse_writer_password=CLICKHOUSE_WRITER_PASSWORD, +)) + +CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV = Template(""" +CREATE MATERIALIZED VIEW `$reference_genome/$dataset_type/clinvar_all_variants_to_clinvar_mv` +REFRESH EVERY 10 YEAR +TO `$reference_genome/$dataset_type/clinvar` +AS +SELECT + DISTINCT ON (key) + kl.key as key, + alleleId, + conflictingPathogenicities, + goldStars, + submitters, + conditions, + assertions, + pathogenicity +FROM `$reference_genome/$dataset_type/clinvar_all_variants` c +INNER JOIN `$reference_genome/$dataset_type/key_lookup` kl +ON c.variantId = kl.variantId +""") class Migration(migrations.Migration): + initial = True + dependencies = [ - ('clickhouse_search', '0014_gnomadgenomesgrch37snvindel_gnomadgenomessnvindel'), ] operations = [ + migrations.CreateModel( + name='AnnotationsDiskSnvIndel', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('pos', clickhouse_backend.models.UInt32Field()), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), + ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), + ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences')), + ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences')), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsSnvIndel', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('pos', clickhouse_backend.models.UInt32Field()), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), + ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), + ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences')), + ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences')), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesSnvIndel', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('is_gnomad_gt_5_percent', clickhouse_backend.models.BoolField()), + ('is_annotated_in_any_gene', clickhouse_backend.models.BoolField()), + ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('ab', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/entries', + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarSnvIndel', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriessnvindel')), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/clinvar', + 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='TranscriptsSnvIndel', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), + ('transcripts', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissense', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('pathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), ('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('exon', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('index', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('total', clickhouse_backend.models.Int32Field(blank=True, null=True))])), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('intron', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('index', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('total', clickhouse_backend.models.Int32Field(blank=True, null=True))])), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('manePlusClinical', clickhouse_backend.models.StringField(blank=True, null=True)), ('maneSelect', clickhouse_backend.models.StringField(blank=True, null=True)), ('refseqTranscriptId', clickhouse_backend.models.StringField(blank=True, null=True)), ('spliceregion', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('extended_intronic_splice_region_variant', clickhouse_backend.models.BoolField(blank=True, null=True))])), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field()), ('utrannotator', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('existingInframeOorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('existingOutofframeOorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('existingUorfs', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('fiveutrAnnotation', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('AltStop', clickhouse_backend.models.StringField(blank=True, null=True)), ('AltStopDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('CapDistanceToStart', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('DistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('DistanceToStop', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('Evidence', clickhouse_backend.models.BoolField(blank=True, null=True)), ('FrameWithCDS', clickhouse_backend.models.StringField(blank=True, null=True)), ('KozakContext', clickhouse_backend.models.StringField(blank=True, null=True)), ('KozakStrength', clickhouse_backend.models.StringField(blank=True, null=True)), ('StartDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('alt_type', clickhouse_backend.models.StringField(blank=True, null=True)), ('alt_type_length', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('newSTOPDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('ref_StartDistanceToCDS', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('ref_type', clickhouse_backend.models.StringField(blank=True, null=True)), ('ref_type_length', clickhouse_backend.models.Int32Field(blank=True, null=True)), ('type', clickhouse_backend.models.StringField(blank=True, null=True))])), ('fiveutrConsequence', clickhouse_backend.models.StringField(blank=True, null=True))]))])), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/transcripts', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/transcripts', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsDiskGRCh37SnvIndel', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('pos', clickhouse_backend.models.UInt32Field()), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsGRCh37SnvIndel', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('pos', clickhouse_backend.models.UInt32Field()), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('caid', clickhouse_backend.models.StringField(blank=True, db_column='CAID', null=True)), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh37/SNV_INDEL/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsGcnv', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('end', clickhouse_backend.models.UInt32Field()), + ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), + ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ], + options={ + 'db_table': 'GRCh38/GCNV/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsMito', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), + ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), + ], + options={ + 'db_table': 'GRCh38/MITO/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsSv', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('end', clickhouse_backend.models.UInt32Field()), + ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), + ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), + ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), + ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), + ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), + ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), + ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), + ], + options={ + 'db_table': 'GRCh38/SV/annotations_memory', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_IN_MEMORY_DIR}/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsDiskGcnv', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('end', clickhouse_backend.models.UInt32Field()), + ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), + ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ], + options={ + 'db_table': 'GRCh38/GCNV/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/GCNV/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsDiskMito', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('ref', clickhouse_backend.models.StringField()), + ('alt', clickhouse_backend.models.StringField()), + ('rsid', clickhouse_backend.models.StringField(blank=True, null=True)), + ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), + ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), + ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), + ], + options={ + 'db_table': 'GRCh38/MITO/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/MITO/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='AnnotationsDiskSv', + fields=[ + ('key', clickhouse_search.backend.fields.UInt32FieldDeltaCodecField(primary_key=True, serialize=False)), + ('xpos', clickhouse_backend.models.UInt64Field()), + ('pos', clickhouse_backend.models.UInt32Field()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId')), + ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), + ('chrom', clickhouse_search.backend.fields.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), + ('end', clickhouse_backend.models.UInt32Field()), + ('rg37_locus_end', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('contig', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True)), ('position', clickhouse_backend.models.UInt32Field(blank=True, null=True))], db_column='rg37LocusEnd')), + ('lifted_over_chrom', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='liftedOverChrom', null=True)), + ('sv_type', clickhouse_search.backend.fields.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')], db_column='svType')), + ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), + ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), + ('algorithms', clickhouse_backend.models.StringField(low_cardinality=True)), + ('bothsides_support', clickhouse_backend.models.BoolField(db_column='bothsidesSupport')), + ('cpx_intervals', clickhouse_search.backend.fields.NestedField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')])), ('start', clickhouse_backend.models.UInt32Field()), ('end', clickhouse_backend.models.UInt32Field()), ('type', clickhouse_backend.models.Enum8Field(choices=[(1, 'gCNV_DEL'), (2, 'gCNV_DUP'), (3, 'BND'), (4, 'CPX'), (5, 'CTX'), (6, 'DEL'), (7, 'DUP'), (8, 'INS'), (9, 'INV'), (10, 'CNV')]))], db_column='cpxIntervals')), + ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), + ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), + ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), + ], + options={ + 'db_table': 'GRCh38/SV/annotations_disk', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SV/annotations', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesGRCh37SnvIndel', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('is_gnomad_gt_5_percent', clickhouse_backend.models.BoolField()), + ('is_annotated_in_any_gene', clickhouse_backend.models.BoolField()), + ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('ab', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/entries', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='TranscriptsGRCh37SnvIndel', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), + ('transcripts', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())])), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/transcripts', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/transcripts', flatten_nested=0, primary_key='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarGRCh37SnvIndel', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriesgrch37snvindel')), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/clinvar', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesMito', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('dp', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('hl', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitoCn', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('contamination', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh38/MITO/entries', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarMito', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.PROTECT, primary_key=True, related_name='clinvar_join', serialize=False, to='clickhouse_search.entriesmito')), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh38/MITO/clinvar', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.Join('ALL', 'LEFT', 'key', flatten_nested=0, join_use_nulls=1), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesSv', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('geneId_ids', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.UInt32Field())), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('cn', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('gq', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('newCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevNumAlt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh38/SV/entries', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='EntriesGcnv', + fields=[ + ('key', models.ForeignKey(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgcnv')), + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('family_guid', clickhouse_backend.models.StringField()), + ('xpos', clickhouse_search.backend.fields.UInt64FieldDeltaCodecField()), + ('filters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(low_cardinality=True))), + ('calls', clickhouse_backend.models.ArrayField(base_field=clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sampleId', clickhouse_backend.models.StringField()), ('gt', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')], null=True)), ('cn', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('qs', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('defragged', clickhouse_backend.models.BoolField(blank=True, null=True)), ('start', clickhouse_backend.models.UInt32Field(blank=True, null=True)), ('end', clickhouse_backend.models.UInt32Field(blank=True, null=True)), ('numExon', clickhouse_backend.models.UInt16Field(blank=True, null=True)), ('geneIds', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True))), ('newCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevCall', clickhouse_backend.models.BoolField(blank=True, null=True)), ('prevOverlap', clickhouse_backend.models.BoolField(blank=True, null=True))]))), + ('sign', clickhouse_backend.models.Int8Field()), + ], + options={ + 'db_table': 'GRCh38/GCNV/entries', + 'abstract': False, + 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), + 'projection': clickhouse_search.models.Projection('xpos_projection', order_by='xpos'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupGcnv', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsgcnv')), + ], + options={ + 'db_table': 'GRCh38/GCNV/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/GCNV/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupGRCh37SnvIndel', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsgrch37snvindel')), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupMito', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationsmito')), + ], + options={ + 'db_table': 'GRCh38/MITO/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/MITO/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupSnvIndel', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationssnvindel')), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SNV_INDEL/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='KeyLookupSv', + fields=[ + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, to='clickhouse_search.annotationssv')), + ], + options={ + 'db_table': 'GRCh38/SV/key_lookup', + 'engine': clickhouse_search.backend.engines.EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh38/SV/key_lookup', flatten_nested=0, primary_key='variant_id'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ProjectGtStatsGRCh37SnvIndel', + fields=[ + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('ref_samples', clickhouse_backend.models.UInt32Field()), + ('het_samples', clickhouse_backend.models.UInt32Field()), + ('hom_samples', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/project_gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ProjectGtStatsMito', + fields=[ + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('ref_samples', clickhouse_backend.models.UInt32Field()), + ('het_samples', clickhouse_backend.models.UInt32Field()), + ('hom_samples', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/MITO/project_gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ProjectGtStatsSnvIndel', + fields=[ + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), + ('sample_type', clickhouse_backend.models.Enum8Field(choices=[(1, 'WES'), (2, 'WGS')])), + ('ref_samples', clickhouse_backend.models.UInt32Field()), + ('het_samples', clickhouse_backend.models.UInt32Field()), + ('hom_samples', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/project_gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key', 'sample_type'), partition_by='project_guid'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ProjectGtStatsSv', + fields=[ + ('project_guid', clickhouse_backend.models.StringField(low_cardinality=True)), + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), + ('ref_samples', clickhouse_backend.models.UInt32Field()), + ('het_samples', clickhouse_backend.models.UInt32Field()), + ('hom_samples', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/SV/project_gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by=('project_guid', 'key'), partition_by='project_guid'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='GtStatsGRCh37SnvIndel', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsgrch37snvindel')), + ('ac_wes', clickhouse_backend.models.UInt32Field()), + ('ac_wgs', clickhouse_backend.models.UInt32Field()), + ('hom_wes', clickhouse_backend.models.UInt32Field()), + ('hom_wgs', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='GtStatsMito', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationsmito')), + ('ac_het_wes', clickhouse_backend.models.UInt32Field()), + ('ac_het_wgs', clickhouse_backend.models.UInt32Field()), + ('ac_hom_wes', clickhouse_backend.models.UInt32Field()), + ('ac_hom_wgs', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/MITO/gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='GtStatsSnvIndel', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssnvindel')), + ('ac_wes', clickhouse_backend.models.UInt32Field()), + ('ac_wgs', clickhouse_backend.models.UInt32Field()), + ('hom_wes', clickhouse_backend.models.UInt32Field()), + ('hom_wgs', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='GtStatsSv', + fields=[ + ('key', models.OneToOneField(db_column='key', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='clickhouse_search.annotationssv')), + ('ac_wgs', clickhouse_backend.models.UInt32Field()), + ('hom_wgs', clickhouse_backend.models.UInt32Field()), + ], + options={ + 'db_table': 'GRCh38/SV/gt_stats', + 'abstract': False, + 'engine': clickhouse_backend.models.SummingMergeTree(index_granularity=8192, order_by='key'), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.RunSQL( + ENTRIES_TO_PROJECT_GT_STATS.substitute( + reference_genome='GRCh37', + dataset_type='SNV_INDEL', + columns=",\n ".join([ + 'sample_type', + "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", + ]), + groupby_columns='project_guid, key, sample_type', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + PROJECT_GT_STATS_TO_GT_STATS.substitute( + reference_genome='GRCh37', + dataset_type='SNV_INDEL', + columns=",\n ".join([ + "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes", + "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs", + "sumIf(hom_samples, sample_type = 'WES') AS hom_wes", + "sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs", + ]) + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + GT_STATS_DICT.substitute( + reference_genome='GRCh37', + dataset_type='SNV_INDEL', + columns= ",\n ".join([ + 'ac_wes UInt32', + 'ac_wgs UInt32', + 'hom_wes UInt32', + 'hom_wgs UInt32', + ]), + size=int(2e8), + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + ENTRIES_TO_PROJECT_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='SNV_INDEL', + columns=",\n ".join([ + 'sample_type', + "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", + ]), + groupby_columns='project_guid, key, sample_type', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + PROJECT_GT_STATS_TO_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='SNV_INDEL', + columns=",\n ".join([ + "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes", + "sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs", + "sumIf(hom_samples, sample_type = 'WES') AS hom_wes", + "sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs", + ]) + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + GT_STATS_DICT.substitute( + reference_genome='GRCh38', + dataset_type='SNV_INDEL', + columns= ",\n ".join([ + 'ac_wes UInt32', + 'ac_wgs UInt32', + 'hom_wes UInt32', + 'hom_wgs UInt32', + ]), + size=int(1e9), + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + ENTRIES_TO_PROJECT_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='MITO', + columns=",\n ".join([ + 'sample_type', + "sum(toInt32(arrayCount(s -> (s.hl == '0'), calls) * sign)) AS ref_samples", + "sum(toInt32(arrayCount(s -> (s.hl > '0' AND s.hl < '0.95'), calls) * sign)) AS het_samples", + "sum(toInt32(arrayCount(s -> (s.hl >= '0.95'), calls) * sign)) AS hom_samples", + ]), + groupby_columns='project_guid, key, sample_type', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + PROJECT_GT_STATS_TO_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='MITO', + columns=",\n ".join([ + "sumIf(het_samples, sample_type = 'WES') AS ac_het_wes", + "sumIf(het_samples, sample_type = 'WGS') AS ac_het_wgs", + "sumIf(hom_samples, sample_type = 'WES') AS ac_hom_wes", + "sumIf(hom_samples, sample_type = 'WGS') AS ac_hom_wgs", + ]) + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + GT_STATS_DICT.substitute( + reference_genome='GRCh38', + dataset_type='MITO', + columns= ",\n ".join([ + 'ac_het_wes UInt32', + 'ac_het_wgs UInt32', + 'ac_hom_wes UInt32', + 'ac_hom_wgs UInt32', + ]), + size=int(1e6), + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + ENTRIES_TO_PROJECT_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='SV', + columns=",\n ".join([ + "sum(toInt32(arrayCount(s -> (s.gt = 'REF'), calls) * sign)) AS ref_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples", + "sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples", + ]), + groupby_columns='project_guid, key', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + PROJECT_GT_STATS_TO_GT_STATS.substitute( + reference_genome='GRCh38', + dataset_type='SV', + columns = ",\n ".join([ + 'sum((het_samples * 1) + (hom_samples * 2)) AS ac_wgs', + 'sum(hom_samples) AS hom_wgs', + ]), + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + GT_STATS_DICT.substitute( + reference_genome='GRCh38', + dataset_type='SV', + columns= ",\n ".join([ + 'ac_wgs UInt32', + 'hom_wgs UInt32' + ]), + size=int(5e6), + ), + hints={'clickhouse': True}, + ), + migrations.CreateModel( + name='ClinvarAllVariantsGRCh37SnvIndel', + fields=[ + ('version', clickhouse_backend.models.DateField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh37/SNV_INDEL/clinvar_all_variants', + 'abstract': False, + 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarAllVariantsMito', + fields=[ + ('version', clickhouse_backend.models.DateField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh38/MITO/clinvar_all_variants', + 'abstract': False, + 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.CreateModel( + name='ClinvarAllVariantsSnvIndel', + fields=[ + ('version', clickhouse_backend.models.DateField()), + ('variant_id', clickhouse_backend.models.StringField(db_column='variantId', primary_key=True, serialize=False)), + ('allele_id', clickhouse_backend.models.UInt32Field(blank=True, db_column='alleleId', null=True)), + ('conflicting_pathogenicities', clickhouse_search.backend.fields.NestedField(base_fields=[('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), ('count', clickhouse_backend.models.UInt16Field())], db_column='conflictingPathogenicities')), + ('gold_stars', clickhouse_backend.models.UInt8Field(blank=True, db_column='goldStars', null=True)), + ('submitters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('conditions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField())), + ('assertions', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(choices=[(0, 'Affects'), (1, 'association'), (2, 'association_not_found'), (3, 'confers_sensitivity'), (4, 'drug_response'), (5, 'low_penetrance'), (6, 'not_provided'), (7, 'other'), (8, 'protective'), (9, 'risk_factor'), (10, 'no_classification_for_the_single_variant'), (11, 'no_classifications_from_unflagged_records')]))), + ('pathogenicity', clickhouse_backend.models.Enum8Field(choices=[(0, 'Pathogenic'), (1, 'Pathogenic/Likely_pathogenic'), (2, 'Pathogenic/Likely_pathogenic/Established_risk_allele'), (3, 'Pathogenic/Likely_pathogenic/Likely_risk_allele'), (4, 'Pathogenic/Likely_risk_allele'), (5, 'Likely_pathogenic'), (6, 'Likely_pathogenic/Likely_risk_allele'), (7, 'Established_risk_allele'), (8, 'Likely_risk_allele'), (9, 'Conflicting_classifications_of_pathogenicity'), (10, 'Uncertain_risk_allele'), (11, 'Uncertain_significance/Uncertain_risk_allele'), (12, 'Uncertain_significance'), (13, 'No_pathogenic_assertion'), (14, 'Likely_benign'), (15, 'Benign/Likely_benign'), (16, 'Benign')])), + ], + options={ + 'db_table': 'GRCh38/SNV_INDEL/clinvar_all_variants', + 'abstract': False, + 'engine': clickhouse_backend.models.MergeTree(order_by=('version', 'variant_id'), partition_by='version', primary_key=('version', 'variant_id')), + }, + managers=[ + ('objects', django.db.models.manager.Manager()), + ('_overwrite_base_manager', django.db.models.manager.Manager()), + ], + ), + migrations.RunSQL( + CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( + reference_genome='GRCh37', + dataset_type='SNV_INDEL', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( + reference_genome='GRCh38', + dataset_type='SNV_INDEL', + ), + hints={'clickhouse': True}, + ), + migrations.RunSQL( + CLINVAR_ALL_VARIANTS_TO_CLINVAR_MV.substitute( + reference_genome='GRCh38', + dataset_type='MITO', + ), + hints={'clickhouse': True}, + ), ] From 4294c002f9983a6332ddbf7b2000d65bccf02404 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 28 Aug 2025 12:20:40 -0400 Subject: [PATCH 4/8] move splice ai up in predicotr order --- ui/shared/utils/constants.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ui/shared/utils/constants.js b/ui/shared/utils/constants.js index bad3dbc88a..74991660a0 100644 --- a/ui/shared/utils/constants.js +++ b/ui/shared/utils/constants.js @@ -1507,7 +1507,6 @@ export const ORDERED_PREDICTOR_FIELDS = [ { field: 'revel', group: MISSENSE_IN_SILICO_GROUP, thresholds: [0.0161, 0.291, 0.644, 0.773, 0.932], fieldTitle: 'REVEL', requiresCitation: true }, { field: 'alphamissense', fieldTitle: 'AlphaMissense', displayOnly: true }, { field: 'vest', thresholds: [undefined, 0.45, 0.764, 0.861, 0.965], fieldTitle: 'VEST', requiresCitation: true }, - { field: 'mut_pred', thresholds: [0.0101, 0.392, 0.737, 0.829, 0.932], fieldTitle: 'MutPred', requiresCitation: true }, { field: 'mpc', group: MISSENSE_IN_SILICO_GROUP, thresholds: [undefined, undefined, 1.36, 1.828, undefined], max: 5, fieldTitle: 'MPC' }, { field: SPLICE_AI_FIELD, @@ -1521,6 +1520,7 @@ export const ORDERED_PREDICTOR_FIELDS = [ ), defaultValue: '?', }, + { field: 'mut_pred', thresholds: [0.0101, 0.392, 0.737, 0.829, 0.932], fieldTitle: 'MutPred', requiresCitation: true }, { field: 'primate_ai', group: MISSENSE_IN_SILICO_GROUP, thresholds: [undefined, 0.484, 0.79, 0.867, undefined], fieldTitle: 'PrimateAI', requiresCitation: true }, { field: 'eigen', group: CODING_IN_SILICO_GROUP, thresholds: [undefined, undefined, 1, 2, undefined], max: 99 }, { field: 'dann', displayOnly: true, thresholds: [undefined, undefined, 0.93, 0.96, undefined] }, From c919076be8ca77887585ef882e010b1d20404f52 Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Fri, 29 Aug 2025 10:59:27 -0400 Subject: [PATCH 5/8] af types (#4973) * af types * fix rounds * fix test * a few more * maxdiff * fix types * more * another * a few more * a few more * remove maxdiff --- .../fixtures/clickhouse_search.json | 40 +++++++++---------- ...move_gnomadgenomessnvindel_key_and_more.py | 20 +++++----- clickhouse_search/models.py | 26 ++++++------ clickhouse_search/test_utils.py | 4 +- seqr/views/apis/variant_search_api_tests.py | 16 ++++---- 5 files changed, 53 insertions(+), 53 deletions(-) diff --git a/clickhouse_search/fixtures/clickhouse_search.json b/clickhouse_search/fixtures/clickhouse_search.json index 11f38a06d1..3260b68c68 100644 --- a/clickhouse_search/fixtures/clickhouse_search.json +++ b/clickhouse_search/fixtures/clickhouse_search.json @@ -20,7 +20,7 @@ "populations": [ [0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], - [927, 0.03445, 26912, 0.04028, 0, 48], + [927, 0.03444932, 26912, 0.04027665, 0, 48], [20757, 0.07842, 264690, 20757, 0] ], "sorted_transcript_consequences": [], @@ -46,10 +46,10 @@ "screen_region_type": null, "predictions": [20.9, 2.001, 0, 5.86851, 0.28205, null, 3, 0.1, 0.46558, 0.197, 0.05, 0, 4, 0.211], "populations": [ - [35805, 0.295, 121372, 0.4153, 0, 24061, 5872], - [72672, 0.289, 251462, 0.41165, 0, 11567], + [35805, 0.29499999, 121372, 0.41530353, 0, 24061, 5872], + [72672, 0.28899795, 251462, 0.4116475, 0, 11567], [0, 0, 0, 0, 0, 0], - [65154, 0.24615, 264690, 47604, 8775] + [65154, 0.246152, 264690, 47604, 8775] ], "sorted_transcript_consequences": [ [0.99779, 1, ["missense_variant"], false, null, "ENSG00000177000"], @@ -84,7 +84,7 @@ "populations": [ [0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], - [57757, 0.38041, 151828, 0.47978, 0, 12204], + [57757, 0.38041073, 151828, 0.47977865, 0, 12204], [95998, 0.362681, 264690, 57260, 19369] ], "sorted_transcript_consequences": [ @@ -119,7 +119,7 @@ "populations": [ [0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], - [39, 0.00027, 147062, 0.0015, 0, 0], + [39, 0.00026519, 147062, 0.00150301, 0, 0], [0, 0, 0, 0, 0] ], "sorted_transcript_consequences": [ @@ -156,7 +156,7 @@ "populations": [ [0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], - [2, 0.00012, 16090, 0.00233, 0, 0], + [2, 0.0001243, 16090, 0.00233, 0, 0], [0, 0, 0, 0, 0] ], "sorted_transcript_consequences": [], @@ -654,10 +654,10 @@ "hgmd": [null, null], "predictions": [13.02, 3.951, null, null, null, null, null, 0.49064, null, null, 0, 4,null], "populations": [ - [66593, 0.63, 104352, 0.81988, 0, 22269, 22162], - [137532, 0.63542, 216442, 0.82261, 0, 45869], - [14649, 0.61365, 23872, 0.82844, 0, 4584], - [65461, 0.52132, 125568, 33149, 16156] + [66593, 0.63, 104352, 0.81987739, 0, 22269, 22162], + [137532, 0.63542193, 216442, 0.82261163, 0, 45869], + [14649, 0.61364776, 23872, 0.82843894, 0, 4584], + [65461, 0.52131897, 125568, 33149, 16156] ], "sorted_transcript_consequences": [ [1, ["missense_variant"], "ENSG00000271079"], @@ -729,7 +729,7 @@ [0, 0, 56419], [0, 0, 56419, 0], [0, 0, 195983], - [3, 0.00002, 195983, 0.20635] + [3, 0.00001531, 195983, 0.20635] ], "sorted_transcript_consequences": [ [ @@ -782,10 +782,10 @@ "mitomap_pathogenic": true, "predictions": [null, true, null, null, null, null, 0.7514], "populations": [ - [3118, 0.05535, 56336], - [3, 0.00005, 56336, 1], - [9573, 0.04885, 195983], - [18, 0.00009, 195983, 0.96269] + [3118, 0.05534649, 56336], + [3, 0.00005325, 56336, 1], + [9573, 0.04884607, 195983], + [18, 0.00009184, 195983, 0.96269] ], "sorted_transcript_consequences": [ [ @@ -1069,7 +1069,7 @@ "num_exon": 4, "predictions": [0.181], "populations": [ - [1763, 0.07649, 23048, 0, 0] + [1763, 0.07649254, 23048, 0, 0] ], "sorted_gene_consequences": [ ["ENSG00000129562", "COPY_GAIN"] @@ -1092,7 +1092,7 @@ "num_exon": 26, "predictions": [0.548], "populations": [ - [284, 0.01232, 23047, 0, 0] + [284, 0.01232211, 23047, 0, 0] ], "sorted_gene_consequences": [ ["ENSG00000013364", "LOF"], @@ -1121,7 +1121,7 @@ "num_exon": 3, "predictions": [0.786], "populations": [ - [35, 0.00152, 23048, 0, 0] + [35, 0.00151857, 23048, 0, 0] ], "sorted_gene_consequences": [ ["ENSG00000275023", "LOF"] @@ -1144,7 +1144,7 @@ "num_exon": 8, "predictions": [0.71], "populations": [ - [115, 0.00499, 23048, 0, 0] + [115, 0.00498959, 23048, 0, 0] ], "sorted_gene_consequences": [ ["ENSG00000275023", "LOF"], diff --git a/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py b/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py index cd237ffb99..1af5b2ef0f 100644 --- a/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py +++ b/clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py @@ -110,7 +110,7 @@ class Migration(migrations.Migration): ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences')), ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences')), @@ -141,7 +141,7 @@ class Migration(migrations.Migration): ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), ('screen_region_type', clickhouse_search.backend.fields.Enum8Field(blank=True, choices=[(0, 'CTCF-bound'), (1, 'CTCF-only'), (2, 'DNase-H3K4me3'), (3, 'PLS'), (4, 'dELS'), (5, 'pELS'), (6, 'DNase-only'), (7, 'low-DNase')], db_column='screenRegionType', null=True)), ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('gnomad_noncoding', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('alphamissensePathogenicity', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('extendedIntronicSpliceRegionVariant', clickhouse_backend.models.BoolField(blank=True, null=True)), ('fiveutrConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '5_prime_UTR_premature_start_codon_gain_variant'), (2, '5_prime_UTR_premature_start_codon_loss_variant'), (3, '5_prime_UTR_stop_codon_gain_variant'), (4, '5_prime_UTR_stop_codon_loss_variant'), (5, '5_prime_UTR_uORF_frameshift_variant')], null=True)), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), ('sorted_motif_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'TFBS_ablation'), (1, 'TFBS_amplification'), (2, 'TF_binding_site_variant'), (3, 'TFBS_fusion'), (4, 'TFBS_translocation')], null=True))), ('motifFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedMotifFeatureConsequences')), ('sorted_regulatory_feature_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('biotype', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'enhancer'), (1, 'promoter'), (2, 'CTCF_binding_site'), (3, 'TF_binding_site'), (4, 'open_chromatin_region')], null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'regulatory_region_ablation'), (1, 'regulatory_region_amplification'), (2, 'regulatory_region_variant'), (3, 'regulatory_region_fusion')], null=True))), ('regulatoryFeatureId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedRegulatoryFeatureConsequences')), @@ -232,7 +232,7 @@ class Migration(migrations.Migration): ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), ], options={ @@ -260,7 +260,7 @@ class Migration(migrations.Migration): ('lifted_over_pos', clickhouse_backend.models.UInt32Field(blank=True, db_column='liftedOverPos', null=True)), ('hgmd', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('accession', clickhouse_backend.models.StringField(blank=True, null=True)), ('classification', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'DM'), (1, 'DM?'), (2, 'DP'), (3, 'DFP'), (4, 'FP'), (5, 'R')], null=True))])), ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('cadd', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('eigen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('fathmm', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mpc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_pred', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('polyphen', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('primate_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('revel', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('splice_ai_consequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'Acceptor gain'), (1, 'Acceptor loss'), (2, 'Donor gain'), (3, 'Donor loss'), (4, 'No consequence')], null=True)), ('vest', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('exac', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_exomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('gnomad_genomes', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('filter_af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('hemi', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())])), ('topmed', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True))], db_column='sortedTranscriptConsequences')), ], options={ @@ -288,7 +288,7 @@ class Migration(migrations.Migration): ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), ], options={ 'db_table': 'GRCh38/GCNV/annotations_memory', @@ -313,7 +313,7 @@ class Migration(migrations.Migration): ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), ], options={ @@ -346,7 +346,7 @@ class Migration(migrations.Migration): ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), ], options={ 'db_table': 'GRCh38/SV/annotations_memory', @@ -373,7 +373,7 @@ class Migration(migrations.Migration): ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('strvctvre', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), ('sorted_gene_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'LOF'), (2, 'INTRAGENIC_EXON_DUP'), (3, 'PARTIAL_EXON_DUP'), (4, 'COPY_GAIN'), (5, 'DUP_PARTIAL'), (6, 'MSV_EXON_OVERLAP'), (7, 'INV_SPAN'), (8, 'UTR'), (9, 'PROMOTER'), (10, 'TSS_DUP'), (11, 'BREAKEND_EXONIC'), (12, 'INTRONIC'), (13, 'NEAREST_TSS')], null=True))], db_column='sortedGeneConsequences')), ('num_exon', clickhouse_backend.models.UInt16Field(db_column='numExon')), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('sv_callset', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field())]))])), ], options={ 'db_table': 'GRCh38/GCNV/annotations_disk', @@ -398,7 +398,7 @@ class Migration(migrations.Migration): ('common_low_heteroplasmy', clickhouse_backend.models.BoolField(blank=True, db_column='commonLowHeteroplasmy', null=True)), ('mitomap_pathogenic', clickhouse_backend.models.BoolField(blank=True, db_column='mitomapPathogenic', null=True)), ('predictions', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('apogee', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('haplogroup_defining', clickhouse_backend.models.BoolField(blank=True, null=True)), ('hmtvar', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mitotip', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'likely_pathogenic'), (1, 'possibly_pathogenic'), (2, 'possibly_benign'), (3, 'likely_benign')], null=True)), ('mut_taster', clickhouse_backend.models.Enum8Field(blank=True, choices=[(0, 'D'), (1, 'A'), (2, 'N'), (3, 'P')], null=True)), ('sift', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True)), ('mlc', clickhouse_backend.models.DecimalField(blank=True, decimal_places=5, max_digits=9, null=True))])), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_mito', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('gnomad_mito_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))])), ('helix', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field())])), ('helix_heteroplasmy', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('ac', clickhouse_backend.models.UInt32Field()), ('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('an', clickhouse_backend.models.UInt32Field()), ('max_hl', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9))]))])), ('sorted_transcript_consequences', clickhouse_search.backend.fields.NestedField(base_fields=[('aminoAcids', clickhouse_backend.models.StringField(blank=True, null=True)), ('biotype', clickhouse_backend.models.StringField(blank=True, null=True)), ('canonical', clickhouse_backend.models.UInt8Field(blank=True, null=True)), ('codons', clickhouse_backend.models.StringField(blank=True, null=True)), ('consequenceTerms', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True))), ('geneId', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsc', clickhouse_backend.models.StringField(blank=True, null=True)), ('hgvsp', clickhouse_backend.models.StringField(blank=True, null=True)), ('loftee', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('isLofNagnag', clickhouse_backend.models.BoolField(blank=True, null=True)), ('lofFilters', clickhouse_backend.models.ArrayField(base_field=clickhouse_backend.models.StringField(blank=True, null=True)))])), ('majorConsequence', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')], null=True)), ('transcriptId', clickhouse_backend.models.StringField()), ('transcriptRank', clickhouse_backend.models.UInt8Field())], db_column='sortedTranscriptConsequences')), ], options={ @@ -431,7 +431,7 @@ class Migration(migrations.Migration): ('end_chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], db_column='endChrom', null=True)), ('sv_source_detail', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('chrom', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, '1'), (2, '2'), (3, '3'), (4, '4'), (5, '5'), (6, '6'), (7, '7'), (8, '8'), (9, '9'), (10, '10'), (11, '11'), (12, '12'), (13, '13'), (14, '14'), (15, '15'), (16, '16'), (17, '17'), (18, '18'), (19, '19'), (20, '20'), (21, '21'), (22, '22'), (23, 'X'), (24, 'Y'), (25, 'M')], null=True))], db_column='svSourceDetail')), ('sv_type_detail', clickhouse_backend.models.Enum8Field(blank=True, choices=[(1, 'INS_iDEL'), (2, 'INVdel'), (3, 'INVdup'), (4, 'ME'), (5, 'ME:ALU'), (6, 'ME:LINE1'), (7, 'ME:SVA'), (8, 'dDUP'), (9, 'dDUP_iDEL'), (10, 'delINV'), (11, 'delINVdel'), (12, 'delINVdup'), (13, 'dupINV'), (14, 'dupINVdel'), (15, 'dupINVdup')], db_column='svTypeDetail', null=True)), - ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=5, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), + ('populations', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('gnomad_svs', clickhouse_search.backend.fields.NamedTupleField(base_fields=[('af', clickhouse_backend.models.DecimalField(decimal_places=8, max_digits=9)), ('het', clickhouse_backend.models.UInt32Field()), ('hom', clickhouse_backend.models.UInt32Field()), ('id', clickhouse_backend.models.StringField())]))])), ], options={ 'db_table': 'GRCh38/SV/annotations_disk', diff --git a/clickhouse_search/models.py b/clickhouse_search/models.py index 3e9d0688f9..e8717fc3d5 100644 --- a/clickhouse_search/models.py +++ b/clickhouse_search/models.py @@ -182,32 +182,32 @@ class BaseAnnotationsGRCh37SnvIndel(BaseAnnotationsMitoSnvIndel): POPULATION_FIELDS = [ ('exac', NamedTupleField([ ('ac', models.UInt32Field()), - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('an', models.UInt32Field()), - ('filter_af', models.DecimalField(max_digits=9, decimal_places=5)), + ('filter_af', models.DecimalField(max_digits=9, decimal_places=8)), ('hemi', models.UInt32Field()), ('het', models.UInt32Field()), ('hom', models.UInt32Field()), ])), ('gnomad_exomes', NamedTupleField([ ('ac', models.UInt32Field()), - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('an', models.UInt32Field()), - ('filter_af', models.DecimalField(max_digits=9, decimal_places=5)), + ('filter_af', models.DecimalField(max_digits=9, decimal_places=8)), ('hemi', models.UInt32Field()), ('hom', models.UInt32Field()), ])), ('gnomad_genomes', NamedTupleField([ ('ac', models.UInt32Field()), - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('an', models.UInt32Field()), - ('filter_af', models.DecimalField(max_digits=9, decimal_places=5)), + ('filter_af', models.DecimalField(max_digits=9, decimal_places=8)), ('hemi', models.UInt32Field()), ('hom', models.UInt32Field()), ])), ('topmed', NamedTupleField([ ('ac', models.UInt32Field()), - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('an', models.UInt32Field()), ('het', models.UInt32Field()), ('hom', models.UInt32Field()), @@ -317,23 +317,23 @@ class BaseAnnotationsMito(BaseAnnotationsMitoSnvIndel): POPULATION_FIELDS = [ ('gnomad_mito', NamedTupleField([ ('ac', models.UInt32Field()), - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('an', models.UInt32Field()), ])), ('gnomad_mito_heteroplasmy', NamedTupleField([ ('ac', models.UInt32Field()), - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('an', models.UInt32Field()), ('max_hl', models.DecimalField(max_digits=9, decimal_places=5)), ])), ('helix', NamedTupleField([ ('ac', models.UInt32Field()), - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('an', models.UInt32Field()), ])), ('helix_heteroplasmy', NamedTupleField([ ('ac', models.UInt32Field()), - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('an', models.UInt32Field()), ('max_hl', models.DecimalField(max_digits=9, decimal_places=5)), ])), @@ -377,7 +377,7 @@ class Meta: class BaseAnnotationsSv(BaseAnnotationsSvGcnv): POPULATION_FIELDS = [ ('gnomad_svs', NamedTupleField([ - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('het', models.UInt32Field()), ('hom', models.UInt32Field()), ('id', models.StringField()), @@ -421,7 +421,7 @@ class BaseAnnotationsGcnv(BaseAnnotationsSvGcnv): POPULATION_FIELDS = [ ('sv_callset', NamedTupleField([ ('ac', models.UInt32Field()), - ('af', models.DecimalField(max_digits=9, decimal_places=5)), + ('af', models.DecimalField(max_digits=9, decimal_places=8)), ('an', models.UInt32Field()), ('het', models.UInt32Field()), ('hom', models.UInt32Field()), diff --git a/clickhouse_search/test_utils.py b/clickhouse_search/test_utils.py index 0395005abf..091e253198 100644 --- a/clickhouse_search/test_utils.py +++ b/clickhouse_search/test_utils.py @@ -93,9 +93,9 @@ variant['predictions'][pred] = round(pred_val, 5) for pop in variant['populations'].values(): if 'af' in pop: - pop['af'] = round(pop['af'], 5) + pop['af'] = round(pop['af'], 8) if 'filter_af' in pop: - pop['filter_af'] = round(pop['filter_af'], 5) + pop['filter_af'] = round(pop['filter_af'], 8) if 'max_hl' in pop: pop['max_hl'] = round(pop['max_hl'], 5) for transcripts in variant['transcripts'].values(): diff --git a/seqr/views/apis/variant_search_api_tests.py b/seqr/views/apis/variant_search_api_tests.py index 89017e7d2d..2d3688a009 100644 --- a/seqr/views/apis/variant_search_api_tests.py +++ b/seqr/views/apis/variant_search_api_tests.py @@ -531,13 +531,13 @@ def test_query_variants(self, mock_get_variants, mock_get_gene_counts, mock_erro ['12', '48367227', 'TC', 'T', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '2', 'AIP (None)|Known gene for phenotype (None)|Excluded (None)', 'a later note (None)|test n\xf8te (None)', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', ''], - ['1', '38724419', 'T', 'G', 'ENSG00000177000', 'missense_variant', '10', '0.295', '0', - '0.289', '0.24615', '20.9', '0.197', + ['1', '38724419', 'T', 'G', 'ENSG00000177000', 'missense_variant', '10', '0.29499999', '0', + '0.28899795', '0.246152', '20.9', '0.197', '2.001', '0.0', '0.1', '0.05', '', '', 'rs1801131', 'ENST00000383791.8:c.156A>C', 'ENSP00000373301.3:p.Leu52Phe', 'Conflicting_classifications_of_pathogenicity', '1', '2', '', '', '', '', '', 'HG00731', '2', '', '99', '1.0', 'HG00732', '1', '', '99', '0.625', 'HG00733', '0', '', '40', '0.0'], - ['1', '91502721', 'G', 'A', 'ENSG00000097046', 'intron_variant', '7', '0.0', '0.38041', '0.0', - '0.36268', '2.754', '', '1.378', '0.01', '', '', '', + ['1', '91502721', 'G', 'A', 'ENSG00000097046', 'intron_variant', '7', '0.0', '0.38041073', '0.0', + '0.362681', '2.754', '', '1.378', '0.01', '', '', '', '', 'rs13447464', 'ENST00000234626.11:c.-63-251G>A', '', '', '', '2', '', '', '', '', '', 'HG00731', '1', '', '99', '1.0', 'HG00732', '0', '', '99', '0.45946', 'HG00733', '1', '', '99', '0.40741'], ] @@ -565,13 +565,13 @@ def test_query_variants(self, mock_get_variants, mock_get_gene_counts, mock_erro ['12', '48367227', 'TC', 'T', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '2', 'AIP (None)|Known gene for phenotype (None)|Excluded (None)', 'a later note (None)|test n\xf8te (None)', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',], - ['1', '38724419', 'T', 'G', 'ENSG00000177000', 'missense_variant', '10', '0.295', '0', - '0.289', '0.24615', '20.9', '0.197', + ['1', '38724419', 'T', 'G', 'ENSG00000177000', 'missense_variant', '10', '0.29499999', '0', + '0.28899795', '0.246152', '20.9', '0.197', '2.001', '0.0', '0.1', '0.05', '', '', 'rs1801131', 'ENST00000383791.8:c.156A>C', 'ENSP00000373301.3:p.Leu52Phe', 'Conflicting_classifications_of_pathogenicity', '1', '2', '', '', 'HG00731', '2', '', '99', '1.0', 'HG00732', '1', '', '99', '0.625', 'HG00733', '0', '', '40', '0.0'], - ['1', '91502721', 'G', 'A', 'ENSG00000097046', 'intron_variant', '7', '0.0', '0.38041', '0.0', - '0.36268', '2.754', '', '1.378', '0.01', '', '', + ['1', '91502721', 'G', 'A', 'ENSG00000097046', 'intron_variant', '7', '0.0', '0.38041073', '0.0', + '0.362681', '2.754', '', '1.378', '0.01', '', '', '', '', 'rs13447464', 'ENST00000234626.11:c.-63-251G>A', '', '', '', '2', '', '', 'HG00731', '1', '', '99', '1.0', 'HG00732', '0', '', '99', '0.45946', 'HG00733', '1', '', '99', '0.40741'], From 0da720b65522ed1ebf75b852d8fc663a6c9ac8b9 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 29 Aug 2025 12:10:15 -0400 Subject: [PATCH 6/8] change genotype map to only list samples once --- clickhouse_search/managers.py | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/clickhouse_search/managers.py b/clickhouse_search/managers.py index e9fbf20b55..1dc1dee55a 100644 --- a/clickhouse_search/managers.py +++ b/clickhouse_search/managers.py @@ -803,7 +803,7 @@ def _search_call_data(self, entries, sample_data, inheritance_mode=None, inherit return self._annotate_calls(entries, sample_data, annotate_hom_alts, skip_individual_guid, multi_sample_type_families) def _get_inheritance_quality_qs(self, sample_data, multi_sample_type_families, inheritance_mode, individual_genotype_filter, quality_filter, clinvar_override_q, annotate_carriers, custom_affected): - samples_by_gt = defaultdict(list) + samples_by_genotype = defaultdict(list) affected_samples = [] unaffected_samples = [] family_missing_type_samples = defaultdict(lambda: defaultdict(list)) @@ -815,8 +815,7 @@ def _get_inheritance_quality_qs(self, sample_data, multi_sample_type_families, i if affected == UNAFFECTED and annotate_carriers: unaffected_samples.append(sample['sample_id']) if (inheritance_mode and inheritance_mode != ANY_AFFECTED) or individual_genotype_filter: - for gt in self.genotype_lookup[genotype]: - samples_by_gt[gt].append(sample['sample_id']) + samples_by_genotype[genotype].append(sample['sample_id']) if sample['family_guid'] in multi_sample_type_families: sample_type = sample['sample_type'] missing_type = Sample.SAMPLE_TYPE_WES if sample_type == Sample.SAMPLE_TYPE_WGS else Sample.SAMPLE_TYPE_WGS @@ -830,9 +829,20 @@ def _get_inheritance_quality_qs(self, sample_data, multi_sample_type_families, i 'gt': (self.genotype_lookup[HAS_ALT], 'has({value}, {field})'), 'sampleId': (affected_samples, 'has({value}, {field})'), }) - elif samples_by_gt: - gt_filter_map = ', '.join([f"{gt}, {samples_by_gt[gt]}" for gt in [-1, 0, 1, 2]]) - gt_filter = (gt_filter_map, 'has(map({value})[ifNull({field}, -1)], x.sampleId)') + elif samples_by_genotype: + if all(len(self.genotype_lookup[genotype]) == 1 for genotype in samples_by_genotype.keys()): + samples_by_gt = {self.genotype_lookup[genotype][0]: samples for genotype, samples in samples_by_genotype.items()} + gt_filter_map = ', '.join([f"{gt}, {samples_by_gt.get(gt, [])}" for gt in [-1, 0, 1, 2]]) + gt_filter = (gt_filter_map, 'has(map({value})[ifNull({field}, -1)], x.sampleId)') + else: + genotype_sample_map = ', '.join([f"'{genotype or 'any'}', {samples}" for genotype, samples in samples_by_genotype.items()]) + gt_genotypes = defaultdict(list) + for genotype in samples_by_genotype.keys(): + for gt in self.genotype_lookup[genotype]: + gt_genotypes[gt].append(genotype or 'any') + gt_genotype_map = ', '.join([f"{gt}, {gt_genotypes[gt]}" for gt in [-1, 0, 1, 2]]) + genotype_maps = f'genotype -> map({genotype_sample_map})[genotype], map({gt_genotype_map})' + gt_filter = (genotype_maps, 'has(arrayFlatten(arrayMap({value}[ifNull({field}, -1)])), x.sampleId)') inheritance_q = Q(calls__array_all={'gt': gt_filter}) quality_q = self._quality_q(quality_filter, affected_samples, clinvar_override_q) From 781e23075fd5b203d91c277efbcf9d29ae8bcb31 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 2 Sep 2025 15:17:56 -0400 Subject: [PATCH 7/8] handle null sv "genes" --- ui/shared/components/panel/variants/VariantGene.jsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ui/shared/components/panel/variants/VariantGene.jsx b/ui/shared/components/panel/variants/VariantGene.jsx index 6b9aac3f9d..e4ca3a5866 100644 --- a/ui/shared/components/panel/variants/VariantGene.jsx +++ b/ui/shared/components/panel/variants/VariantGene.jsx @@ -725,7 +725,7 @@ class VariantGenes extends React.PureComponent { render() { const { variant, genesById, mainGeneId, showMainGene, individualGeneData, tpmGenes } = this.props const { showAll } = this.state - const geneIds = Object.keys(variant.transcripts || {}) + const geneIds = Object.keys(variant.transcripts || {}).filter(geneId => geneId !== 'null') const genes = geneIds.map(geneId => genesById[geneId]).filter(gene => gene) const geneSearchLink = !mainGeneId && geneIds.length > 0 && From 7e9ba3bb158cfd220b4bc99c20d545a79616c49f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 2 Sep 2025 15:32:34 -0400 Subject: [PATCH 8/8] add efault values for required metadata fields --- seqr/views/apis/individual_api_tests.py | 3 ++- seqr/views/apis/report_api.py | 2 ++ seqr/views/apis/report_api_tests.py | 23 ++++++++++++++--------- 3 files changed, 18 insertions(+), 10 deletions(-) diff --git a/seqr/views/apis/individual_api_tests.py b/seqr/views/apis/individual_api_tests.py index a43b2e9a3d..0d97ea3e43 100644 --- a/seqr/views/apis/individual_api_tests.py +++ b/seqr/views/apis/individual_api_tests.py @@ -1208,6 +1208,7 @@ def test_import_gregor_metadata(self, mock_subprocess): 'condition_id': 'OMIM:616126', 'known_condition_name': 'Immunodeficiency 38', 'condition_inheritance': 'Autosomal recessive', + 'GREGoR_variant_classification': 'Curation in progress', }) self.assertDictEqual(json.loads(next(t for t in new_variant_tags if t != comp_het_tag).metadata), { 'gene_known_for_phenotype': 'Candidate', @@ -1218,7 +1219,7 @@ def test_import_gregor_metadata(self, mock_subprocess): new_family_tag = variant_tags.get(saved_variants__guid=saved_variants[2]['guid']) self.assertDictEqual( - json.loads(new_family_tag.metadata), {'gene_known_for_phenotype': 'Known', 'condition_id': 'MONDO:0044970'}, + json.loads(new_family_tag.metadata), {'gene_known_for_phenotype': 'Known', 'condition_id': 'MONDO:0044970', 'GREGoR_variant_classification': 'Curation in progress'}, ) mock_subprocess.assert_has_calls([ diff --git a/seqr/views/apis/report_api.py b/seqr/views/apis/report_api.py index 4d748d14ab..600256d5be 100644 --- a/seqr/views/apis/report_api.py +++ b/seqr/views/apis/report_api.py @@ -636,6 +636,8 @@ def _post_process_gregor_variant(row, gene_variants): 'linked_variant': next( v['genetic_findings_id'] for v in gene_variants if v['genetic_findings_id'] != row['genetic_findings_id'] ) if len(gene_variants) > 1 else None, + 'gene_disease_validity': 'Curation in progress', + 'GREGoR_variant_classification': 'Curation in progress', } diff --git a/seqr/views/apis/report_api_tests.py b/seqr/views/apis/report_api_tests.py index e8c67004d1..57ab27742e 100644 --- a/seqr/views/apis/report_api_tests.py +++ b/seqr/views/apis/report_api_tests.py @@ -450,7 +450,8 @@ {'column': 'pos_end', 'data_type': 'integer'}, {'column': 'copy_number', 'data_type': 'integer'}, {'column': 'hgvs'}, - {'column': 'gene_disease_validity'}, + {'column': 'gene_disease_validity', 'required': True}, + {'column': 'GREGoR_variant_classification', 'required': True}, ] }, ] @@ -612,32 +613,35 @@ 'allele_balance_or_heteroplasmy_percentage', 'variant_inheritance', 'linked_variant', 'linked_variant_phase', 'gene_known_for_phenotype', 'known_condition_name', 'condition_id', 'condition_inheritance', 'phenotype_contribution', 'partial_contribution_explained', 'additional_family_members_with_variant', - 'method_of_discovery', 'notes', 'sv_type', 'chrom_end', 'pos_end', 'copy_number', 'hgvs', 'gene_disease_validity', + 'method_of_discovery', 'notes', 'sv_type', 'chrom_end', 'pos_end', 'copy_number', 'hgvs', 'gene_disease_validity', 'GREGoR_variant_classification', ], [ 'Broad_NA19675_1_21_3343353', 'Broad_NA19675_1', '', 'INDEL', 'GRCh37', '21', '3343353', 'GAGA', 'G', '', 'RP11', 'ENST00000258436.5', 'c.375_377delTCT', 'p.Leu126del', 'Heterozygous', '', 'de novo', '', '', 'Candidate', 'Myasthenic syndrome, congenital, 8, with pre- and postsynaptic defects', 'OMIM:615120', 'Autosomal recessive|X-linked', - 'Full', '', '', 'SR-ES', 'This individual is published in PMID34415322', '', '', '', '', '', '', + 'Full', '', '', 'SR-ES', 'This individual is published in PMID34415322', '', '', '', '', '', + 'Curation in progress', 'Curation in progress', ], [ 'Broad_HG00731_1_248367227', 'Broad_HG00731', 'Broad_exome_VCGS_FAM203_621_D2', 'INDEL', 'GRCh37', '1', '248367227', 'TC', 'T', 'CA1501729', 'RP11', 'ENST00000371839', '', '', 'Homozygous', '', 'paternal', '', '', 'Known', '', - 'MONDO:0044970', '', 'Uncertain', '', 'Broad_HG00732', 'SR-ES', '', '', '', '', '', '', '', + 'MONDO:0044970', '', 'Uncertain', '', 'Broad_HG00732', 'SR-ES', '', '', '', '', '', '', + 'Curation in progress', 'Curation in progress', ], [ 'Broad_HG00731_19_1912632', 'Broad_HG00731', 'Broad_exome_VCGS_FAM203_621_D2', 'SNV', 'GRCh37', '19', '1912632', 'G', 'C', '', 'OR4G11P', 'ENST00000371839', 'c.586_587delinsTT', 'p.Ala196Leu', 'Heterozygous', '', 'unknown', 'Broad_HG00731_19_1912634', '', 'Known', '', 'MONDO:0044970', '', 'Full', '', '', 'SR-ES', 'The following variants are part of the multinucleotide variant 19-1912632-G-C (c.586_587delinsTT, p.Ala196Leu): 19-1912633-G-T, 19-1912634-C-T', - '', '', '', '', '', '', + '', '', '', '', '', 'Curation in progress', 'Curation in progress', ], [ 'Broad_NA20889_1_248367227', 'Broad_NA20889', '', 'INDEL', 'GRCh37', '1', '248367227', 'TC', 'T', 'CA1501729', 'OR4G11P', 'ENST00000505820', 'c.3955G>A', 'c.1586-17C>G', 'Heterozygous', '', 'unknown', 'Broad_NA20889_1_249045487_DEL', '', 'Candidate', 'Immunodeficiency 38', 'OMIM:616126', 'Autosomal recessive', - 'Partial', 'HP:0000501|HP:0000365', '', 'SR-ES', '', '', '', '', '', '', '', + 'Partial', 'HP:0000501|HP:0000365', '', 'SR-ES', '', '', '', '', '', '', 'Curation in progress', 'Curation in progress', ], [ 'Broad_NA20889_1_249045487_DEL', 'Broad_NA20889', '', 'SV', 'GRCh37', '1', '249045487', '', '', '', 'OR4G11P', '', '', '', 'Heterozygous', '', 'unknown', 'Broad_NA20889_1_248367227', '', 'Candidate', 'Immunodeficiency 38', 'OMIM:616126', 'Autosomal recessive', 'Full', '', '', 'SR-ES', - 'Phasing incorrect in input VCF', 'DEL', '', '249045898', '1', 'DEL:chr1:249045123-249045456', '', + 'Phasing incorrect in input VCF', 'DEL', '', '249045898', '1', 'DEL:chr1:249045123-249045456', + 'Curation in progress', 'Curation in progress', ], ] @@ -933,11 +937,12 @@ def _test_gregor_export(self, url, mock_subprocess, mock_temp_dir, mock_open, mo 'RP11', 'ENST00000258436.5', 'c.375_377delTCT', 'p.Leu126del', 'Heterozygous', '', 'de novo', '', '', 'Candidate', 'Myasthenic syndrome, congenital, 8, with pre- and postsynaptic defects', 'OMIM:615120', 'Autosomal recessive|X-linked', 'Full', '', '', 'SR-ES', 'This individual is published in PMID34415322', - '', '', '', '', '', '', + '', '', '', '', '', 'Curation in progress', 'Curation in progress', ], [ 'Broad_HG00731_1_248367227', 'Broad_HG00731', 'Broad_exome_VCGS_FAM203_621_D2', 'INDEL', 'GRCh37', '1', '248367227', 'TC', 'T', 'CA1501729', 'RP11', 'ENST00000371839', '', '', 'Homozygous', '', 'paternal', '', '', 'Known', '', - 'MONDO:0044970', '', 'Uncertain', '', 'Broad_HG00732', 'SR-ES', '', '', '', '', '', '', '', + 'MONDO:0044970', '', 'Uncertain', '', 'Broad_HG00732', 'SR-ES', '', '', '', '', '', '', + 'Curation in progress', 'Curation in progress', ]], additional_calls=1) responses.calls.reset()