Dev

clickhouse_search/all_search_tests.py

@@ -1318,13 +1318,43 @@ def test_variant_lookup(self, mock_liftover):
             project_guids=['R0001_1kg'], family_guids=['F000002_2'],
             individual_guids=['I000006_hg00733', 'I000005_hg00732', 'I000004_hg00731']
         )
-        self.assert_json_logs(self.manager_user, [
+        unmapped_sample_logs = [
             ('Looking up variant 7-143270172-A-G with data type SNV_INDEL', None),
             ('Unable to map sample HG00733 in family F000002_2 to an individual for variant 7-143270172-A-G', {
                 'severity': 'ERROR',
                 '@type': 'type.googleapis.com/google.devtools.clouderrorreporting.v1beta1.ReportedErrorEvent',
             }),
-        ])
+        ]
+        self.assert_json_logs(self.manager_user, unmapped_sample_logs)
+
+        self.login_base_user()
+        self.reset_logs()
+        expected_individuals = {'I1_F0_7-143270172-A-G': {
+            'affected': 'A',
+            'familyGuid': 'F0_7-143270172-A-G',
+            'features': [
+                {'category': 'HP:0000707', 'id': 'HP:0002011', 'label': 'Morphological abnormality of the central nervous system'},
+                {'category': 'HP:0001626', 'id': 'HP:0011675',  'label': 'Arrhythmia'},
+            ],
+            'individualGuid': 'I1_F0_7-143270172-A-G',
+            'sex': 'X0',
+            'vlmContactEmail': 'test@broadinstitute.org,vlm@broadinstitute.org',
+        }}
+        no_access_missing_gt_variant = {
+            **GRCH37_VARIANT,
+            'familyGuids': ['F0_7-143270172-A-G'],
+            'genotypes': {'I1_F0_7-143270172-A-G': {
+                k: v for k, v in GRCH37_VARIANT['genotypes']['I000004_hg00731'].items()
+                if k not in {'familyGuid', 'individualGuid', 'sampleId'}
+            }}
+        }
+        self._assert_expected_lookup(
+            '7-143270172-A-G', no_access_missing_gt_variant, cache_key, cached_variants=[GRCH37_VARIANT],
+            genome_version='37', expected_individuals=expected_individuals, locusListsByGuid={}, skip_fields={
+                'variantFunctionalDataByGuid', 'variantNotesByGuid', 'variantTagsByGuid',
+            },
+        )
+        self.assert_json_logs(self.no_access_user, unmapped_sample_logs)
 
     def _assert_expected_lookup(self, variant_id, variant, cache_key, genome_version='38', hom_only=False, affected_only=False, project_guids=None, family_guids=None, individual_guids=None, expected_individuals=None, skip_fields=None, cached_variants=None, additional_variant=None, sample_type=None, **kwargs):
         url = f'{reverse(variant_lookup_handler)}?variantId={variant_id}&genomeVersion={genome_version}'

seqr/admin.py

@@ -3,13 +3,14 @@
 from matchmaker.models import MatchmakerSubmission, MatchmakerIncomingQuery, MatchmakerResult, MatchmakerContactNotes
 from seqr.models import Project, Family, Individual, Dataset, LocusList, LocusListGene, LocusListInterval, VariantNote, \
     VariantTag, VariantTagType, VariantFunctionalData, SavedVariant, GeneNote, AnalysisGroup, ProjectCategory, \
-    FamilyAnalysedBy, VariantSearch, VariantSearchResults, IgvSample, UserPolicy, WarningMessage, FamilyNote, DynamicAnalysisGroup
+    FamilyAnalysedBy, VariantSearch, VariantSearchResults, IgvSample, UserPolicy, WarningMessage, FamilyNote, DynamicAnalysisGroup, \
+    RnaSample, PhenotypePrioritization
 
 for model_class in [
     Project, Family, Individual, Dataset, IgvSample, LocusList, LocusListGene, LocusListInterval, VariantNote, VariantTag,
     VariantTagType, VariantFunctionalData, SavedVariant, GeneNote, AnalysisGroup, ProjectCategory, FamilyAnalysedBy,
     VariantSearch, VariantSearchResults, MatchmakerSubmission, MatchmakerIncomingQuery, MatchmakerResult,
-    MatchmakerContactNotes, FamilyNote, DynamicAnalysisGroup,
+    MatchmakerContactNotes, FamilyNote, DynamicAnalysisGroup, RnaSample, PhenotypePrioritization,
 ]:
 
     @admin.register(model_class)

seqr/views/apis/variant_search_api.py

@@ -666,7 +666,14 @@ def _update_lookup_variant(variant, response, individual_guid_map, user):
             variant['liftedFamilyGuids'][variant['liftedFamilyGuids'].index(unmapped_family_guid)] = family_guid
         individual_guid_map = {}
         for j, genotype in enumerate(genotypes):
-            unmapped_individual_guid, individual = individual_summary_map[(genotype.pop('familyGuid'), genotype.pop('sampleId'))]
+            individual_key = (genotype.pop('familyGuid'), genotype.pop('sampleId'))
+            if individual_key not in individual_summary_map:
+                logger.error(
+                    f'Unable to map sample {individual_key[1]} in family {individual_key[0]} to an individual for variant {variant["variantId"]}',
+                    user,
+                )
+                continue
+            unmapped_individual_guid, individual = individual_summary_map[individual_key]
             if unmapped_individual_guid in individual_guid_map:
                 individual_guid = individual_guid_map[unmapped_individual_guid]
                 variant['genotypes'][individual_guid] = [variant['genotypes'][individual_guid], genotype]

ui/pages/Project/fixtures.js

@@ -66,7 +66,6 @@ export const STATE1 = {
           label: 'Skeletal dysplasia',
         },
       ],
-      sampleGuids: [],
       sex: 'F',
     },
     I021475_na19675: {
@@ -101,7 +100,6 @@ export const STATE1 = {
           gene: 'LGMD panel',
         },
       ],
-      sampleGuids: [],
       sex: 'M',
     },
     I021476_na19678: {
@@ -117,7 +115,6 @@ export const STATE1 = {
       maternalId: '',
       paternalId: '',
       death_year: 2008,
-      sampleGuids: [],
       sex: 'M',
     },
   },
@@ -211,7 +208,6 @@ export const STATE_WITH_2_FAMILIES = {
       caseReviewStatusLastModifiedBy: null,
       caseReviewStatusLastModifiedDate: '2016-12-05T10:28:00.000Z',
       createdDate: '2016-12-05T10:28:00.000Z',
-      sampleGuids: [],
       sex: 'F',
     },
     I021475_na19675_1: {
@@ -223,7 +219,6 @@ export const STATE_WITH_2_FAMILIES = {
       caseReviewStatusLastModifiedBy: null,
       caseReviewStatusLastModifiedDate: '2016-12-05T10:29:00.000Z',
       createdDate: '2016-12-05T10:29:00.000Z',
-      sampleGuids: [],
       sex: 'M',
       birthYear: 2010,
       deathYear: 0,
@@ -267,7 +262,6 @@ export const STATE_WITH_2_FAMILIES = {
       caseReviewStatusLastModifiedBy: null,
       caseReviewStatusLastModifiedDate: '2016-12-05T10:30:00.000Z',
       createdDate: '2016-12-05T10:30:00.000Z',
-      sampleGuids: [],
       sex: 'M',
     },
     I021476_na19678_2: {
@@ -281,7 +275,6 @@ export const STATE_WITH_2_FAMILIES = {
       caseReviewStatusLastModifiedBy: null,
       caseReviewStatusLastModifiedDate: '2016-12-06T10:28:00.000Z',
       createdDate: '2016-12-06T10:28:00.000Z',
-      sampleGuids: ['S2310656_wal_mc16200_mc16203'],
       igvSampleGuids: ['IS2310656_wal_mc16200_mc16203'],
       sex: 'F',
     },
@@ -294,7 +287,6 @@ export const STATE_WITH_2_FAMILIES = {
       caseReviewStatusLastModifiedBy: null,
       caseReviewStatusLastModifiedDate: '2016-12-06T10:29:00.000Z',
       createdDate: '2016-12-06T10:29:00.000Z',
-      sampleGuids: [],
       sex: 'M',
     },
     I021474_na19679_2: {
@@ -306,7 +298,6 @@ export const STATE_WITH_2_FAMILIES = {
       caseReviewStatusLastModifiedBy: null,
       caseReviewStatusLastModifiedDate: '2016-12-06T10:30:00.000Z',
       createdDate: '2016-12-06T10:30:00.000Z',
-      sampleGuids: [],
       sex: 'M',
     },
   },

ui/pages/Search/components/filters/CustomInheritanceFilter.jsx

@@ -5,7 +5,7 @@ import { FormSpy } from 'react-final-form'
 import { Table, Header, Popup, Loader, Divider } from 'semantic-ui-react'
 
 import { loadFamilyDetails } from 'redux/rootReducer'
-import { getFamiliesByGuid, getIndividualsByGuid, getFamilyDetailsLoading } from 'redux/selectors'
+import { getFamiliesByGuid, getIndividualsByGuid, getFamilyDetailsLoading, getActiveDatasetsByIndividual } from 'redux/selectors'
 import DataLoader from 'shared/components/DataLoader'
 import { helpLabel } from 'shared/components/form/FormHelpers'
 import { Select, InlineToggle } from 'shared/components/form/Inputs'
@@ -19,7 +19,9 @@ const CUSTOM_FILTERS = [
   { filterField: 'genotype', options: NUM_ALT_OPTIONS, placeholder: 'Allele count' },
 ]
 
-const CustomInheritanceFilterContent = React.memo(({ value, onChange, family, individualsByGuid }) => {
+const CustomInheritanceFilterContent = React.memo((
+  { value, onChange, family, individualsByGuid, activeDatasetsByIndividual },
+) => {
   const individuals = (family.individualGuids || []).map(individualGuid => individualsByGuid[individualGuid]).filter(
     individual => individual,
   )
@@ -70,7 +72,7 @@ const CustomInheritanceFilterContent = React.memo(({ value, onChange, family, in
                 <Table.Cell key={filterField}>
                   <Select
                     {...fieldProps}
-                    disabled={!individual.sampleGuids.length}
+                    disabled={!activeDatasetsByIndividual[individual.individualGuid]?.length}
                     value={individualFilters[individual.individualGuid][filterField]}
                     onChange={handleChange(individual, filterField)}
                   />
@@ -84,7 +86,7 @@ const CustomInheritanceFilterContent = React.memo(({ value, onChange, family, in
               ) : <Table.Cell collapsing />}
             </Table.Row>
           )
-          return individual.sampleGuids.length ? row : (
+          return activeDatasetsByIndividual[individual.individualGuid]?.length ? row : (
             <Popup
               key={individual.individualGuid}
               trigger={row}
@@ -102,6 +104,7 @@ CustomInheritanceFilterContent.propTypes = {
   onChange: PropTypes.func,
   family: PropTypes.object,
   individualsByGuid: PropTypes.object,
+  activeDatasetsByIndividual: PropTypes.object,
 }
 
 const NO_CALL_FIELD = 'allowNoCall'
@@ -146,6 +149,7 @@ const CustomInheritanceFilter = React.memo(({ load, loading, family, individuals
 const mapStateToProps = (state, ownProps) => ({
   family: getFamiliesByGuid(state)[ownProps.familyGuid],
   individualsByGuid: getIndividualsByGuid(state),
+  activeDatasetsByIndividual: getActiveDatasetsByIndividual(state),
   loading: !!getFamilyDetailsLoading(state)[ownProps.familyGuid],
 })
 

ui/pages/Search/fixtures.js

@@ -105,7 +105,6 @@ export const STATE = {
           label: 'Skeletal dysplasia',
         },
       ],
-      sampleGuids: [],
       sex: 'F',
       familyGuid: FAMILY_GUID,
     },
@@ -141,7 +140,6 @@ export const STATE = {
           gene: 'LGMD panel',
         },
       ],
-      sampleGuids: [],
       sex: 'M',
     },
     I021476_na19678: {

ui/shared/components/panel/fixtures.js

@@ -320,7 +320,6 @@ export const STATE1 = {
         },
       ],
       sex: 'F',
-      sampleGuids: [],
     },
     I021475_na19675: {
       affected: 'A',
@@ -355,7 +354,6 @@ export const STATE1 = {
         },
       ],
       sex: 'M',
-      sampleGuids: [],
     },
     I021476_na19678: {
       affected: 'N',
@@ -370,7 +368,6 @@ export const STATE1 = {
       maternalId: '',
       paternalId: '',
       sex: 'M',
-      sampleGuids: [],
     },
   },
   analysisGroupsByGuid: {},