Dev

clickhouse_search/search.py

@@ -129,9 +129,11 @@ def _parse_locus_search(locus, genome_version, search):
     exclude_locations = bool(exclude.get('rawItems'))
     if locus and exclude_locations:
         raise InvalidSearchException('Cannot specify both Location and Excluded Genes/Intervals')
+    if not (locus or exclude_locations):
+        return
 
     genes, intervals, invalid_items = parse_locus_list_items(
-        locus or exclude, genome_version=genome_version, get_genes_func=_get_genes,
+        locus or exclude, genome_version=genome_version, get_genes_func=get_search_genes,
     )
     if invalid_items:
         raise InvalidSearchException('Invalid genes/intervals: {}'.format(', '.join(invalid_items)))
@@ -151,7 +153,7 @@ def _parse_locus_search(locus, genome_version, search):
     exclude.pop('rawItems', None)
 
 
-def _get_genes(gene_ids, genome_version):
+def get_search_genes(gene_ids, genome_version):
     genes = GeneInfo.objects.filter(**{'gene_id__in': gene_ids, f'start_grch{genome_version}__isnull': False}).values(
         'id', 'gene_id', **{field: F(f'{field}_grch{genome_version}') for field in ['chrom', 'start', 'end']},
     )

clickhouse_search/search_tests.py

@@ -1054,8 +1054,8 @@ def test_variant_lookup(self, mock_liftover):
             },
             'I2_F0_1-10439-AC-A': {
                 'affected': 'A', 'familyGuid': 'F0_1-10439-AC-A', 'individualGuid': 'I2_F0_1-10439-AC-A', 'sex': 'X0',
-                'features': [{'category': 'HP:0000707', 'label': '1 terms'},
-                             {'category': 'HP:0001626', 'label': '1 terms'}],
+                'features': [{'category': 'HP:0000707', 'label': 'Morphological abnormality of the central nervous system', 'id': 'HP:0002011'},
+                             {'category': 'HP:0001626', 'label': 'Arrhythmia', 'id': 'HP:0011675'}],
                 'vlmContactEmail': 'test@broadinstitute.org,vlm@broadinstitute.org',
             },
         }
@@ -1128,8 +1128,8 @@ def test_variant_lookup(self, mock_liftover):
             },
             'I2_F0_suffix_140608_DUP': {
                 'affected': 'A', 'familyGuid': 'F0_suffix_140608_DUP', 'individualGuid': 'I2_F0_suffix_140608_DUP',
-                'features': [{'category': 'HP:0000707', 'label': '1 terms'},
-                             {'category': 'HP:0001626', 'label': '1 terms'}],
+                'features': [{'category': 'HP:0000707', 'label': 'Morphological abnormality of the central nervous system', 'id': 'HP:0002011'},
+                             {'category': 'HP:0001626', 'label': 'Arrhythmia', 'id': 'HP:0011675'}],
                 'sex': 'X0', 'vlmContactEmail': 'test@broadinstitute.org,vlm@broadinstitute.org',
             },
         }

seqr/fixtures/1kg_project.json

@@ -63,6 +63,7 @@
     "workspace_namespace": "my-seqr-billing",
 	"is_mme_enabled": true,
     "is_demo": true,
+    "restrict_sharing": true,
 	"mme_primary_data_owner": "",
     "mme_contact_url": "mailto:seqr-test@gmail.com,test@broadinstitute.org",
     "vlm_contact_email": "seqr-test@gmail.com,test@broadinstitute.org",

seqr/management/commands/tag_seqr_prioritized_variants.py

@@ -6,12 +6,11 @@
 from django.db.models.functions import JSONObject
 import json
 
-from clickhouse_search.search import get_clickhouse_variants, ENTRY_CLASS_MAP
+from clickhouse_search.search import get_clickhouse_variants, get_search_genes, ENTRY_CLASS_MAP
 from panelapp.models import PaLocusListGene
 from reference_data.models import GENOME_VERSION_GRCh38
 from seqr.models import Project, Family, Individual, Sample, LocusList
 from seqr.utils.communication_utils import send_project_notification
-from seqr.utils.gene_utils import get_genes
 from clickhouse_search.constants import ANY_AFFECTED, HOMOZYGOUS_RECESSIVE, X_LINKED_RECESSIVE_MALE_AFFECTED, DE_NOVO, COMPOUND_HET
 from seqr.views.utils.json_utils import DjangoJSONEncoderWithSets
 from seqr.views.utils.orm_to_json_utils import SEQR_TAG_TYPE
@@ -475,7 +474,7 @@ def handle(self, *args, **options):
             family_guid_map[guid] = db_id
             family_name_map[db_id] = family_id
 
-        exclude_genes = get_genes(EXCLUDE_GENE_IDS, genome_version=GENOME_VERSION_GRCh38)
+        exclude_genes = get_search_genes(EXCLUDE_GENE_IDS, genome_version=GENOME_VERSION_GRCh38)
         gene_by_moi = defaultdict(dict)
         for gene_list in GENE_LISTS:
             self._get_gene_list_genes(gene_list['name'], gene_list['confidences'], gene_by_moi, exclude_genes.keys())
@@ -487,7 +486,7 @@ def handle(self, *args, **options):
         for dataset_type, searches in SEARCHES.items():
             self._run_dataset_type_searches(
                 dataset_type, searches, sample_qs, updates, search_counts, samples_by_dataset_type, family_guid_map,
-                project, exclude_genes, gene_by_moi,
+                project, list(exclude_genes.values()), gene_by_moi,
             )
 
         self._run_multi_data_type_comp_het_search(
@@ -517,7 +516,7 @@ def handle(self, *args, **options):
         )
 
     @classmethod
-    def _run_dataset_type_searches(cls, dataset_type, searches, sample_qs, updates, search_counts, samples_by_dataset_type, family_guid_map, project, exclude_genes, gene_by_moi):
+    def _run_dataset_type_searches(cls, dataset_type, searches, sample_qs, updates, search_counts, samples_by_dataset_type, family_guid_map, project, exclude_intervals, gene_by_moi):
         is_sv = dataset_type == Sample.DATASET_TYPE_SV_CALLS
         sample_qs = sample_qs.filter(dataset_type=dataset_type)
         if is_sv:
@@ -545,14 +544,15 @@ def _run_dataset_type_searches(cls, dataset_type, searches, sample_qs, updates,
         logger.info(f'Searching for prioritized {dataset_type} variants in {len(samples_by_family)} families in project {project.name}')
         for search_name, config_search in searches.items():
             logger.info(f'Searching for criteria: {search_name}')
-            exclude_locations = not config_search.get('gene_list_moi')
-            search_genes = exclude_genes if exclude_locations else gene_by_moi[config_search['gene_list_moi']]
+            search_genes = gene_by_moi[config_search['gene_list_moi']] if config_search.get('gene_list_moi') else None
+            if search_genes:
+                exclude_intervals = None
             sample_data = cls._get_valid_family_sample_data(
                 project, sample_type, samples_by_family, config_search.get('family_filter'),
             )
             num_results = cls._execute_search(
                 {dataset_type: sample_data}, search_name, family_variant_data, family_guid_map,
-                exclude_locations=exclude_locations, genes=search_genes, **config_search, **ALL_SEARCHES_CRITERIA,
+                exclude_intervals=exclude_intervals, genes=search_genes, **config_search, **ALL_SEARCHES_CRITERIA,
             ) if sample_data['num_families'] else 0
             search_counts[search_name] = num_results
 
@@ -699,7 +699,7 @@ def _get_gene_list_genes(name, confidences, gene_by_moi, exclude_gene_ids):
         ]).values('gene_id', 'is_dominant', 'is_recessive', 'is_mito')
 
         gene_id_mois = {g['gene_id']: g for g in moi_gene_ids}
-        genes_by_id = get_genes(gene_id_mois.keys(), genome_version=GENOME_VERSION_GRCh38, additional_model_fields=['id'])
+        genes_by_id = get_search_genes(gene_id_mois.keys(), genome_version=GENOME_VERSION_GRCh38)
         gene_by_moi[DOMINANT_MOI].update({gene_id: gene for gene_id, gene in genes_by_id.items() if not gene_id_mois[gene_id]['is_recessive']})
         gene_by_moi[RECESSIVE_MOI].update({gene_id: gene for gene_id, gene in genes_by_id.items() if not gene_id_mois[gene_id]['is_dominant']})
         gene_by_moi[MITO_MOI].update({gene_id: gene for gene_id, gene in genes_by_id.items() if gene_id_mois[gene_id]['is_mito']})

seqr/views/apis/variant_search_api.py

@@ -563,6 +563,7 @@ def _update_lookup_variant(variant, response, individual_guid_map, user):
         for i in Individual.objects.filter(family__guid__in=no_access_families).values(
             'family__guid', 'individual_id', 'affected', 'sex', 'features', 'guid',
             vlmContactEmail=F('family__project__vlm_contact_email'),
+            restrict_sharing=F('family__project__restrict_sharing'),
         )
     }
     add_individual_hpo_details([i for _, i in individual_summary_map.values()])
@@ -598,17 +599,20 @@ def _update_lookup_variant(variant, response, individual_guid_map, user):
                 continue
             individual_guid = f'I{j}_{family_guid}'
             individual_guid_map[unmapped_individual_guid] = individual_guid
-            feature_category_count = defaultdict(int)
-            for feature in individual['features'] or []:
-                feature_category_count[feature.get('category', 'Other')] += 1
+            features = individual['features'] or []
+            if individual.pop('restrict_sharing'):
+                feature_category_count = defaultdict(int)
+                for feature in features:
+                    feature_category_count[feature.get('category', 'Other')] += 1
+                features = [
+                    {'category': category, 'label': f'{count} terms'}
+                    for category, count in feature_category_count.items()
+                ]
             response['individualsByGuid'][individual_guid] = {
                 **individual,
                 'familyGuid': family_guid,
                 'individualGuid': individual_guid,
-                'features': [
-                    {'category': category, 'label': f'{count} terms'}
-                    for category, count in feature_category_count.items()
-                ],
+                'features': features,
             }
             variant['genotypes'][individual_guid] = genotype