From 6da07318481c6742cf39ab0393d532828aeec7eb Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Tue, 12 May 2026 16:47:34 -0400
Subject: [PATCH 01/12] add models missign from django admin

---
 seqr/admin.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/seqr/admin.py b/seqr/admin.py
index 09d595c0be..cb86f6b040 100644
--- a/seqr/admin.py
+++ b/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)

From 50e390cbf5d3c1f94ade6e3f67cf6f26492165b8 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 11:49:18 -0400
Subject: [PATCH 02/12] fix active samples check to not use deprecated sample
 ids

---
 ui/pages/Project/fixtures.js                           |  9 ---------
 .../components/filters/CustomInheritanceFilter.jsx     | 10 ++++++----
 ui/pages/Search/fixtures.js                            |  2 --
 ui/shared/components/panel/fixtures.js                 |  3 ---
 4 files changed, 6 insertions(+), 18 deletions(-)

diff --git a/ui/pages/Project/fixtures.js b/ui/pages/Project/fixtures.js
index 6689bcb1e0..8829d75078 100644
--- a/ui/pages/Project/fixtures.js
+++ b/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',
     },
   },
diff --git a/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx b/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
index ca61361fbe..580e8c78ef 100644
--- a/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
+++ b/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 +19,7 @@ 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 +70,7 @@ 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 +84,7 @@ 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 +102,7 @@ CustomInheritanceFilterContent.propTypes = {
   onChange: PropTypes.func,
   family: PropTypes.object,
   individualsByGuid: PropTypes.object,
+  activeDatasetsByIndividual: PropTypes.object,
 }
 
 const NO_CALL_FIELD = 'allowNoCall'
@@ -146,6 +147,7 @@ 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],
 })
 
diff --git a/ui/pages/Search/fixtures.js b/ui/pages/Search/fixtures.js
index 013130e72e..37b265b0ac 100644
--- a/ui/pages/Search/fixtures.js
+++ b/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: {
diff --git a/ui/shared/components/panel/fixtures.js b/ui/shared/components/panel/fixtures.js
index f05658a765..926ff160c4 100644
--- a/ui/shared/components/panel/fixtures.js
+++ b/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: {},

From 54d096d180ed3ba3f8da0fae7333a4e8c52eaa8d Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 11:51:25 -0400
Subject: [PATCH 03/12] linting fix

---
 .../Search/components/filters/CustomInheritanceFilter.jsx     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx b/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
index ca61361fbe..031991131f 100644
--- a/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
+++ b/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
@@ -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 },
+) => {
   const individuals = (family.individualGuids || []).map(individualGuid => individualsByGuid[individualGuid]).filter(
     individual => individual,
   )

From b774a380d58851a26293becea32a53cad42df3d7 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 11:53:21 -0400
Subject: [PATCH 04/12] Revert "linting fix"

This reverts commit 54d096d180ed3ba3f8da0fae7333a4e8c52eaa8d.
---
 .../Search/components/filters/CustomInheritanceFilter.jsx     | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx b/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
index 031991131f..ca61361fbe 100644
--- a/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
+++ b/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
@@ -19,9 +19,7 @@ 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 }) => {
   const individuals = (family.individualGuids || []).map(individualGuid => individualsByGuid[individualGuid]).filter(
     individual => individual,
   )

From 9054b32a3bc9e60267cbc69df98789734fb4d584 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 11:53:44 -0400
Subject: [PATCH 05/12] linting fix

---
 .../Search/components/filters/CustomInheritanceFilter.jsx     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx b/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
index 580e8c78ef..d224b40bf1 100644
--- a/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
+++ b/ui/pages/Search/components/filters/CustomInheritanceFilter.jsx
@@ -19,7 +19,9 @@ const CUSTOM_FILTERS = [
   { filterField: 'genotype', options: NUM_ALT_OPTIONS, placeholder: 'Allele count' },
 ]
 
-const CustomInheritanceFilterContent = React.memo(({ value, onChange, family, individualsByGuid, activeDatasetsByIndividual }) => {
+const CustomInheritanceFilterContent = React.memo((
+  { value, onChange, family, individualsByGuid, activeDatasetsByIndividual },
+) => {
   const individuals = (family.individualGuids || []).map(individualGuid => individualsByGuid[individualGuid]).filter(
     individual => individual,
   )

From ab6b6e530533571c8dc3df6f636d6708d1eb4f6a Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 11:59:52 -0400
Subject: [PATCH 06/12] error handling when lifted over variant has unmapped
 sample id

---
 clickhouse_search/all_search_tests.py | 13 +++++++++++++
 seqr/views/apis/variant_search_api.py |  9 ++++++++-
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/clickhouse_search/all_search_tests.py b/clickhouse_search/all_search_tests.py
index 88f80e2dc6..7f58df4279 100644
--- a/clickhouse_search/all_search_tests.py
+++ b/clickhouse_search/all_search_tests.py
@@ -1326,6 +1326,19 @@ def test_variant_lookup(self, mock_liftover):
             }),
         ])
 
+        self._assert_expected_lookup(
+            '7-143260172-A-G', missing_gt_variant, 'variant_lookup_results__7-143260172-A-G__38',
+            cached_variants=[GRCH37_VARIANT], project_guids=['R0001_1kg'], family_guids=['F000002_2'],
+            individual_guids=['I000006_hg00733', 'I000005_hg00732', 'I000004_hg00731']
+        )
+        self.assert_json_logs(self.manager_user, [
+            ('Looking up variant 7-143260172-A-G with data type SNV_INDEL', None),
+            ('Unable to map sample HG00733 in family F000002_2 to an individual for variant 7-143260172-A-G', {
+                'severity': 'ERROR',
+                '@type': 'type.googleapis.com/google.devtools.clouderrorreporting.v1beta1.ReportedErrorEvent',
+            }),
+        ])
+
     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}'
         if hom_only:
diff --git a/seqr/views/apis/variant_search_api.py b/seqr/views/apis/variant_search_api.py
index 61f1748532..c2c4f68870 100644
--- a/seqr/views/apis/variant_search_api.py
+++ b/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 {genotype["sampleId"]} in family {family_guid} 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]

From 4df02d994977ed5ce0237398bc4b42aa865d7a68 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 12:05:01 -0400
Subject: [PATCH 07/12] fix test

---
 clickhouse_search/all_search_tests.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/clickhouse_search/all_search_tests.py b/clickhouse_search/all_search_tests.py
index 7f58df4279..ccf1e9f0cb 100644
--- a/clickhouse_search/all_search_tests.py
+++ b/clickhouse_search/all_search_tests.py
@@ -1326,14 +1326,16 @@ def test_variant_lookup(self, mock_liftover):
             }),
         ])
 
+        self.login_base_user()
+        self.maxDiff = None
         self._assert_expected_lookup(
-            '7-143260172-A-G', missing_gt_variant, 'variant_lookup_results__7-143260172-A-G__38',
-            cached_variants=[GRCH37_VARIANT], project_guids=['R0001_1kg'], family_guids=['F000002_2'],
+            '7-143270172-A-G', missing_gt_variant, cache_key, cached_variants=[GRCH37_VARIANT], genome_version='37',
+            project_guids=['R0001_1kg'], family_guids=['F000002_2'],
             individual_guids=['I000006_hg00733', 'I000005_hg00732', 'I000004_hg00731']
         )
         self.assert_json_logs(self.manager_user, [
-            ('Looking up variant 7-143260172-A-G with data type SNV_INDEL', None),
-            ('Unable to map sample HG00733 in family F000002_2 to an individual for variant 7-143260172-A-G', {
+            ('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',
             }),

From 3c2142cc297341497e624375d4042de17a9ac472 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 12:06:04 -0400
Subject: [PATCH 08/12] fix log

---
 seqr/views/apis/variant_search_api.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seqr/views/apis/variant_search_api.py b/seqr/views/apis/variant_search_api.py
index c2c4f68870..85875748b6 100644
--- a/seqr/views/apis/variant_search_api.py
+++ b/seqr/views/apis/variant_search_api.py
@@ -669,7 +669,7 @@ def _update_lookup_variant(variant, response, individual_guid_map, user):
             individual_key = (genotype.pop('familyGuid'), genotype.pop('sampleId'))
             if individual_key not in individual_summary_map:
                 logger.error(
-                    f'Unable to map sample {genotype["sampleId"]} in family {family_guid} to an individual for variant {variant["variantId"]}',
+                    f'Unable to map sample {individual_key[1]} in family {individual_key[0]} to an individual for variant {variant["variantId"]}',
                     user,
                 )
                 continue

From 9a25031b75e49e327ffcc29f08effeb795feef7e Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 12:26:49 -0400
Subject: [PATCH 09/12] fix test

---
 clickhouse_search/all_search_tests.py | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/clickhouse_search/all_search_tests.py b/clickhouse_search/all_search_tests.py
index ccf1e9f0cb..c54982d4bd 100644
--- a/clickhouse_search/all_search_tests.py
+++ b/clickhouse_search/all_search_tests.py
@@ -1327,11 +1327,26 @@ def test_variant_lookup(self, mock_liftover):
         ])
 
         self.login_base_user()
+        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': GRCH37_VARIANT['genotypes']['I000004_hg00731']},
+        }
         self.maxDiff = None
         self._assert_expected_lookup(
-            '7-143270172-A-G', missing_gt_variant, cache_key, cached_variants=[GRCH37_VARIANT], genome_version='37',
-            project_guids=['R0001_1kg'], family_guids=['F000002_2'],
-            individual_guids=['I000006_hg00733', 'I000005_hg00732', 'I000004_hg00731']
+            '7-143270172-A-G', no_access_missing_gt_variant, cache_key, cached_variants=[GRCH37_VARIANT],
+            genome_version='37', expected_individuals=expected_individuals, locusListsByGuid={},
         )
         self.assert_json_logs(self.manager_user, [
             ('Looking up variant 7-143270172-A-G with data type SNV_INDEL', None),

From b0975533e7c19fab88e461a563a14bc5b2c67d36 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 12:31:44 -0400
Subject: [PATCH 10/12] actually fix test

---
 clickhouse_search/all_search_tests.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/clickhouse_search/all_search_tests.py b/clickhouse_search/all_search_tests.py
index c54982d4bd..f8394f41b5 100644
--- a/clickhouse_search/all_search_tests.py
+++ b/clickhouse_search/all_search_tests.py
@@ -1341,12 +1341,16 @@ def test_variant_lookup(self, mock_liftover):
         no_access_missing_gt_variant = {
             **GRCH37_VARIANT,
             'familyGuids': ['F0_7-143270172-A-G'],
-            'genotypes': {'I1_F0_7-143270172-A-G': GRCH37_VARIANT['genotypes']['I000004_hg00731']},
+            '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.maxDiff = None
         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={},
+            genome_version='37', expected_individuals=expected_individuals, locusListsByGuid={}, skip_fields={
+                'variantFunctionalDataByGuid', 'variantNotesByGuid', 'variantTagsByGuid',
+            },
         )
         self.assert_json_logs(self.manager_user, [
             ('Looking up variant 7-143270172-A-G with data type SNV_INDEL', None),

From a8781188ce8ca7472410ef71231849a84b22cfaa Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 12:34:22 -0400
Subject: [PATCH 11/12] better shared cosntant

---
 clickhouse_search/all_search_tests.py | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/clickhouse_search/all_search_tests.py b/clickhouse_search/all_search_tests.py
index f8394f41b5..f15a2c865f 100644
--- a/clickhouse_search/all_search_tests.py
+++ b/clickhouse_search/all_search_tests.py
@@ -1318,13 +1318,14 @@ 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()
         expected_individuals = {'I1_F0_7-143270172-A-G': {
@@ -1352,13 +1353,7 @@ def test_variant_lookup(self, mock_liftover):
                 'variantFunctionalDataByGuid', 'variantNotesByGuid', 'variantTagsByGuid',
             },
         )
-        self.assert_json_logs(self.manager_user, [
-            ('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)
 
     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}'

From f72ca5b3472afd85387533eaa257d298718f51b9 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Wed, 13 May 2026 12:35:26 -0400
Subject: [PATCH 12/12] actually test logs

---
 clickhouse_search/all_search_tests.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/clickhouse_search/all_search_tests.py b/clickhouse_search/all_search_tests.py
index f15a2c865f..fc11948cdc 100644
--- a/clickhouse_search/all_search_tests.py
+++ b/clickhouse_search/all_search_tests.py
@@ -1328,6 +1328,7 @@ def test_variant_lookup(self, mock_liftover):
         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',
@@ -1353,7 +1354,7 @@ def test_variant_lookup(self, mock_liftover):
                 'variantFunctionalDataByGuid', 'variantNotesByGuid', 'variantTagsByGuid',
             },
         )
-        self.assert_json_logs(self.manager_user, unmapped_sample_logs)
+        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}'