Merge pull request #4488 from broadinstitute/report-variant-note

Report variant note

CHANGELOG.md

@@ -1,6 +1,7 @@
 # _seqr_ Changes
 
 ## dev
+* Migrate "Submit to Clinvar" to generic report flag for Variant Notes (REQUIRES DB MIGRATION)
 
 ## 10/28/24
 * Update RNA Tissue Type choices (REQUIRES DB MIGRATION)

seqr/fixtures/1kg_project.json

@@ -2177,7 +2177,7 @@
         "last_modified_date": "2018-02-23T17:32:23.054Z",
         "saved_variants": [2],
         "note": "test n\u00f8te",
-        "submit_to_clinvar": false,
+        "report": false,
         "search_hash": null
     }
 },
@@ -2191,7 +2191,7 @@
         "last_modified_date": "2019-02-23T17:32:23.054Z",
         "saved_variants": [2],
         "note": "a later note",
-        "submit_to_clinvar": false,
+        "report": false,
         "search_hash": null
     }
 },

seqr/fixtures/report_variants.json

@@ -143,6 +143,19 @@
         "search_hash": null
     }
 },
+{
+    "model": "seqr.variantnote",
+    "pk": 123,
+    "fields": {
+        "guid": "VN0000123_prefix_19107_DEL_r0",
+        "created_date": "2019-05-15T14:51:58.410Z",
+        "created_by": null,
+        "last_modified_date": "2019-02-23T17:32:23.054Z",
+        "saved_variants": [7],
+        "note": "Phasing incorrect in input VCF",
+        "report": true
+    }
+},
 {
     "model": "seqr.variantfunctionaldata",
     "pk": 29,

seqr/migrations/0078_rename_submit_to_clinvar_variantnote_report.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.16 on 2024-11-19 15:19
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('seqr', '0077_alter_rnasample_tissue_type'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='variantnote',
+            old_name='submit_to_clinvar',
+            new_name='report',
+        ),
+    ]

seqr/models.py

@@ -903,7 +903,7 @@ class Meta:
 class VariantNote(ModelWithGUID):
     saved_variants = models.ManyToManyField('SavedVariant')
     note = models.TextField()
-    submit_to_clinvar = models.BooleanField(default=False)
+    report = models.BooleanField(default=False)
 
     # these are for context
     search_hash = models.CharField(max_length=50, null=True)
@@ -915,7 +915,7 @@ def __unicode__(self):
     GUID_PREFIX = 'VN'
 
     class Meta:
-        json_fields = ['guid', 'note', 'submit_to_clinvar', 'last_modified_date', 'created_by']
+        json_fields = ['guid', 'note', 'report', 'last_modified_date', 'created_by']
 
 
 class VariantFunctionalData(ModelWithGUID):

seqr/views/apis/report_api_tests.py

@@ -636,8 +636,8 @@
     ], [
         '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', '', 'DEL', '',
-        '249045898', '1', 'DEL:chr1:249045123-249045456', '',
+        'Immunodeficiency 38', 'OMIM:616126', 'Autosomal recessive', 'Full', '', '', 'SR-ES',
+        'Phasing incorrect in input VCF', 'DEL', '', '249045898', '1', 'DEL:chr1:249045123-249045456', '',
     ],
 ]
 
@@ -1428,6 +1428,7 @@ def test_variant_metadata(self):
             'gene_id': None,
             'gene_known_for_phenotype': 'Candidate',
             'genetic_findings_id': 'NA20889_1_249045487_DEL',
+            'notes': 'Phasing incorrect in input VCF',
             'participant_id': 'NA20889',
             'pos': 249045487,
             'projectGuid': 'R0003_test',

seqr/views/apis/saved_variant_api.py

@@ -116,7 +116,7 @@ def create_variant_note_handler(request, variant_guids):
 def _create_variant_note(saved_variants, note_json, user):
     note = create_model_from_json(VariantNote, {
         'note': note_json.get('note'),
-        'submit_to_clinvar': note_json.get('submitToClinvar') or False,
+        'report': note_json.get('report') or False,
         'search_hash': note_json.get('searchHash'),
     }, user)
     note.saved_variants.set(saved_variants)

seqr/views/apis/saved_variant_api_tests.py

@@ -518,19 +518,19 @@ def test_create_update_and_delete_variant_note(self):
 
         # send valid request to create variant_note
         response = self.client.post(create_variant_note_url, content_type='application/json', data=json.dumps(
-            {'note': 'new_variant_note', 'submitToClinvar': True, 'familyGuid': 'F000001_1'}
+            {'note': 'new_variant_note', 'report': True, 'familyGuid': 'F000001_1'}
         ))
 
         self.assertEqual(response.status_code, 200)
         new_note_guid = response.json()['savedVariantsByGuid'][VARIANT_GUID]['noteGuids'][0]
         new_note_response = response.json()['variantNotesByGuid'][new_note_guid]
         self.assertEqual(new_note_response['note'], 'new_variant_note')
-        self.assertEqual(new_note_response['submitToClinvar'], True)
+        self.assertEqual(new_note_response['report'], True)
 
         new_variant_note = VariantNote.objects.filter(guid=new_note_guid).first()
         self.assertIsNotNone(new_variant_note)
         self.assertEqual(new_variant_note.note, new_note_response['note'])
-        self.assertEqual(new_variant_note.submit_to_clinvar, new_note_response['submitToClinvar'])
+        self.assertEqual(new_variant_note.report, new_note_response['report'])
 
         # save variant_note as gene_note
         response = self.client.post(create_variant_note_url, content_type='application/json', data=json.dumps(
@@ -568,18 +568,18 @@ def test_create_update_and_delete_variant_note(self):
         # update the variant_note
         update_variant_note_url = reverse(update_variant_note_handler, args=[VARIANT_GUID, new_note_guid])
         response = self.client.post(update_variant_note_url, content_type='application/json',  data=json.dumps(
-            {'note': 'updated_variant_note', 'submitToClinvar': False}))
+            {'note': 'updated_variant_note', 'report': False}))
 
         self.assertEqual(response.status_code, 200)
 
         updated_note_response = response.json()['variantNotesByGuid'][new_note_guid]
         self.assertEqual(updated_note_response['note'], 'updated_variant_note')
-        self.assertEqual(updated_note_response['submitToClinvar'], False)
+        self.assertEqual(updated_note_response['report'], False)
 
         updated_variant_note = VariantNote.objects.filter(guid=updated_note_response['noteGuid']).first()
         self.assertIsNotNone(updated_variant_note)
         self.assertEqual(updated_variant_note.note, updated_note_response['note'])
-        self.assertEqual(updated_variant_note.submit_to_clinvar, updated_note_response['submitToClinvar'])
+        self.assertEqual(updated_variant_note.report, updated_note_response['report'])
 
         # delete the variant_note
         delete_variant_note_url = reverse(delete_variant_note_handler, args=[VARIANT_GUID, updated_variant_note.guid])
@@ -603,7 +603,7 @@ def test_create_partially_saved_compound_het_variant_note(self):
                 'tagGuids': ['VT1708633_2103343353_r0390_100', 'VT1726961_2103343353_r0390_100'], 'noteGuids': []},
             ],
             'note': 'one_saved_one_not_saved_compount_hets_note',
-            'submitToClinvar': True,
+            'report': True,
             'familyGuid': 'F000001_1',
         }
         response = self.client.post(create_saved_variant_url, content_type='application/json', data=json.dumps(request_body))
@@ -643,20 +643,20 @@ def test_create_update_and_delete_compound_hets_variant_note(self):
         invalid_comp_hets_variant_note_url = reverse(
             create_variant_note_handler, args=['not_variant,{}'.format(COMPOUND_HET_1_GUID)])
         response = self.client.post(invalid_comp_hets_variant_note_url, content_type='application/json', data=json.dumps(
-            {'note': 'new_compound_hets_variant_note', 'submitToClinvar': True, 'familyGuid': 'F000001_1'}
+            {'note': 'new_compound_hets_variant_note', 'report': True, 'familyGuid': 'F000001_1'}
         ))
         self.assertEqual(response.status_code, 400)
         self.assertDictEqual(response.json(), {'error': 'Unable to find the following variant(s): not_variant'})
 
         response = self.client.post(create_comp_hets_variant_note_url, content_type='application/json', data=json.dumps(
-            {'note': 'new_compound_hets_variant_note', 'submitToClinvar': True, 'familyGuid': 'F000001_1'}
+            {'note': 'new_compound_hets_variant_note', 'report': True, 'familyGuid': 'F000001_1'}
         ))
 
         self.assertEqual(response.status_code, 200)
         response_json = response.json()
         for note in response.json()['variantNotesByGuid'].values():
             self.assertEqual(note['note'], 'new_compound_hets_variant_note')
-            self.assertEqual(note['submitToClinvar'], True)
+            self.assertEqual(note['report'], True)
 
         self.assertEqual(
             response_json['savedVariantsByGuid'][COMPOUND_HET_1_GUID]['noteGuids'][0],
@@ -666,24 +666,24 @@ def test_create_update_and_delete_compound_hets_variant_note(self):
         new_variant_note = VariantNote.objects.get(guid=new_note_guid)
         self.assertEqual(new_variant_note.note, response_json['variantNotesByGuid'][new_note_guid]['note'])
         self.assertEqual(
-            new_variant_note.submit_to_clinvar, response_json['variantNotesByGuid'][new_note_guid]['submitToClinvar']
+            new_variant_note.report, response_json['variantNotesByGuid'][new_note_guid]['report']
         )
 
         # update the variants_note for both compound hets
         update_variant_note_url = reverse(update_variant_note_handler,
                                           args=[','.join([COMPOUND_HET_1_GUID, COMPOUND_HET_2_GUID]), new_note_guid])
         response = self.client.post(update_variant_note_url, content_type='application/json', data=json.dumps(
-            {'note': 'updated_variant_note', 'submitToClinvar': False}))
+            {'note': 'updated_variant_note', 'report': False}))
 
         self.assertEqual(response.status_code, 200)
 
         updated_note_response = response.json()['variantNotesByGuid'][new_note_guid]
         self.assertEqual(updated_note_response['note'], 'updated_variant_note')
-        self.assertEqual(updated_note_response['submitToClinvar'], False)
+        self.assertEqual(updated_note_response['report'], False)
 
         updated_variant_note = VariantNote.objects.get(guid=new_note_guid)
         self.assertEqual(updated_variant_note.note, updated_note_response['note'])
-        self.assertEqual(updated_variant_note.submit_to_clinvar, updated_note_response['submitToClinvar'])
+        self.assertEqual(updated_variant_note.report, updated_note_response['report'])
 
         # save variant_note as gene_note for both compound hets
         response = self.client.post(

seqr/views/apis/summary_data_api_tests.py

@@ -108,7 +108,7 @@
     'chrom_end-1': None,
     'pos_end-1': None,
     'notes-1': '',
-    'notes-2': '',
+    'notes-2': 'Phasing incorrect in input VCF',
     'phenotype_contribution-1': 'Partial',
     'phenotype_contribution-2': 'Full',
     'partial_contribution_explained-1': 'HP:0000501|HP:0000365',

seqr/views/utils/anvil_metadata_utils.py

@@ -327,6 +327,7 @@ def _get_parsed_saved_discovery_variants_by_family(
 
     annotations = dict(
         tags=ArrayAgg('varianttag__variant_tag_type__name', distinct=True),
+        notes=ArrayAgg('variantnote__note', distinct=True, filter=Q(variantnote__report=True)),
         partial_hpo_terms=ArrayAgg('variantfunctionaldata__metadata', distinct=True, filter=Q(variantfunctionaldata__functional_data_tag='Partial Phenotype Contribution')),
         validated_name=ArrayAgg('variantfunctionaldata__metadata', distinct=True, filter=Q(variantfunctionaldata__functional_data_tag='Validated Name')),
     )
@@ -364,6 +365,7 @@ def _get_parsed_saved_discovery_variants_by_family(
             'gene_known_for_phenotype': 'Known' if 'Known gene for phenotype' in variant.tags else 'Candidate',
             'phenotype_contribution': phenotype_contribution,
             'partial_contribution_explained': partial_hpo_terms.replace(', ', '|'),
+            'notes': variant.notes,
             'sv_type': sv_type,
             'sv_name': (variant_json.get('svName') or '{svType}:chr{chrom}:{pos}-{end}'.format(**variant_json)) if sv_type else None,
             'variant_type': variant_type,
@@ -527,7 +529,7 @@ def _get_genetic_findings_rows(rows: list[dict], individual: Individual, family_
         del row['genotypes']
 
         gene_variants = variants_by_gene[row[GENE_COLUMN]]
-        notes = []
+        notes = row['notes'] or []
         if len(gene_variants) > 2:
             discovery_notes = _get_discovery_notes(row, gene_variants, omit_parent_mnvs)
             if discovery_notes is None:

seqr/views/utils/test_utils.py

@@ -815,7 +815,7 @@ def _get_list_param(call, param):
     'tagGuid', 'name', 'category', 'color', 'searchHash', 'metadata', 'lastModifiedDate', 'createdBy', 'variantGuids',
 }
 
-VARIANT_NOTE_FIELDS = {'noteGuid', 'note', 'submitToClinvar', 'lastModifiedDate', 'createdBy', 'variantGuids'}
+VARIANT_NOTE_FIELDS = {'noteGuid', 'note', 'report', 'lastModifiedDate', 'createdBy', 'variantGuids'}
 
 FUNCTIONAL_FIELDS = {
     'tagGuid', 'name', 'color', 'metadata', 'metadataTitle', 'lastModifiedDate', 'createdBy', 'variantGuids',

ui/shared/components/panel/variants/FamilyVariantTags.jsx

@@ -14,6 +14,7 @@ import {
   getVariantId,
   getMmeSubmissionsByGuid,
   getGenesById,
+  getUser,
 } from 'redux/selectors'
 import { DISCOVERY_CATEGORY_NAME, MME_TAG_NAME, GREGOR_FINDING_TAG_NAME } from 'shared/utils/constants'
 import { snakecaseToTitlecase } from 'shared/utils/stringUtils'
@@ -32,32 +33,23 @@ const TagTitle = styled.span`
   color: #999;
 `
 
-const RedItal = styled.i`
-  color: red;
-`
-
 const NO_DISPLAY = { display: 'none' }
 
 const SHORTCUT_TAGS = ['Review', 'Excluded']
 
 const VARIANT_NOTE_FIELDS = [{
-  name: 'submitToClinvar',
-  label: (
-    <label>
-      Add to
-      <RedItal>&nbsp; ClinVar &nbsp;</RedItal>
-      submission
-    </label>
-  ),
-  component: BooleanCheckbox,
-  style: { paddingTop: '2em' },
-},
-{
   name: 'saveAsGeneNote',
   label: 'Add to public gene notes',
   component: BooleanCheckbox,
 }]
 
+const ANALYST_VARIANT_NOTE_FIELDS = [{
+  name: 'report',
+  label: 'Include in report notes',
+  component: BooleanCheckbox,
+}, ...VARIANT_NOTE_FIELDS,
+]
+
 const DEPRECATED_MME_TAG = 'seqr MME (old)'
 const AIP_TAG_TYPE = 'AIP'
 const NO_EDIT_TAG_TYPES = [AIP_TAG_TYPE, GREGOR_FINDING_TAG_NAME]
@@ -258,7 +250,7 @@ MatchmakerLabel.propTypes = {
 const FamilyVariantTags = React.memo(({
   variant, variantTagNotes, family, projectTagTypes, projectFunctionalTagTypes, dispatchUpdateVariantNote,
   dispatchUpdateFamilyVariantTags, dispatchUpdateFamilyVariantFunctionalTags, isCompoundHet, variantId,
-  linkToSavedVariants, mmeSubmissionsByGuid, genesById,
+  linkToSavedVariants, mmeSubmissionsByGuid, genesById, user,
 }) => (
   family ? (
     <NoBorderTable basic="very" compact="very" celled>
@@ -337,7 +329,7 @@ const FamilyVariantTags = React.memo(({
               initialValues={variantTagNotes}
               modalId={family.familyGuid}
               modalTitle={`Variant Note for Family ${family.displayName}`}
-              additionalEditFields={VARIANT_NOTE_FIELDS}
+              additionalEditFields={user.isAnalyst ? ANALYST_VARIANT_NOTE_FIELDS : VARIANT_NOTE_FIELDS}
               defaultId={variantId}
               idField="variantGuids"
               isEditable
@@ -367,6 +359,7 @@ FamilyVariantTags.propTypes = {
   dispatchUpdateFamilyVariantFunctionalTags: PropTypes.func.isRequired,
   mmeSubmissionsByGuid: PropTypes.object,
   genesById: PropTypes.object,
+  user: PropTypes.object,
 }
 
 FamilyVariantTags.defaultProps = {
@@ -386,6 +379,7 @@ const mapStateToProps = (state, ownProps) => {
     variantTagNotes: ((getVariantTagNotesByFamilyVariants(state) || {})[ownProps.familyGuid] || {})[variantId],
     mmeSubmissionsByGuid: getMmeSubmissionsByGuid(state),
     genesById: getGenesById(state),
+    user: getUser(state),
   }
 }