Merge pull request #3955 from broadinstitute/probably-solved

Probably solved

CHANGELOG.md

@@ -1,6 +1,7 @@
 # _seqr_ Changes
 
 ## dev
+* Add "Probably Solved" analysis status (REQUIRES DB MIGRATION)
 
 ## 3/1/24
 * Add subscribable project notifications (REQUIRES DB MIGRATION)

seqr/migrations/0060_alter_family_analysis_status.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.23 on 2024-03-07 19:13
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('seqr', '0059_project_subscribers'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='family',
+            name='analysis_status',
+            field=models.CharField(choices=[('S', 'S'), ('S_kgfp', 'S'), ('S_kgdp', 'S'), ('S_ng', 'S'), ('ES', 'E'), ('Sc_kgfp', 'S'), ('Sc_kgdp', 'S'), ('Sc_ng', 'S'), ('Rcpc', 'R'), ('Rncc', 'R'), ('C', 'C'), ('PB', 'P'), ('P', 'P'), ('I', 'A'), ('Q', 'W'), ('N', 'N')], default='Q', max_length=10),
+        ),
+    ]

seqr/models.py

@@ -278,6 +278,7 @@ def _compute_guid(self):
 class Family(ModelWithGUID):
     ANALYSIS_STATUS_ANALYSIS_IN_PROGRESS='I'
     ANALYSIS_STATUS_PARTIAL_SOLVE = 'P'
+    ANALYSIS_STATUS_PROBABLE_SOLVE = 'PB'
     ANALYSIS_STATUS_WAITING_FOR_DATA='Q'
     SOLVED_ANALYSIS_STATUS_CHOICES = (
         ('S', 'Solved'),
@@ -297,6 +298,7 @@ class Family(ModelWithGUID):
         ('Rcpc', 'Reviewed, currently pursuing candidates'),
         ('Rncc', 'Reviewed, no clear candidate'),
         ('C', 'Closed, no longer under analysis'),
+        (ANALYSIS_STATUS_PROBABLE_SOLVE, 'Probably Solved'),
         (ANALYSIS_STATUS_PARTIAL_SOLVE, 'Partial Solve - Analysis in Progress'),
         (ANALYSIS_STATUS_ANALYSIS_IN_PROGRESS, 'Analysis in Progress'),
         (ANALYSIS_STATUS_WAITING_FOR_DATA, 'Waiting for data'),

seqr/views/apis/report_api_tests.py

@@ -250,7 +250,7 @@
                 {'column': 'affected_status', 'required': True, 'data_type': 'enumeration', 'enumerations': ['Affected', 'Unaffected', 'Unknown']},
                 {'column': 'phenotype_description'},
                 {'column': 'age_at_enrollment'},
-                {'column': 'solve_status', 'required': True, 'data_type': 'enumeration', 'enumerations': ['Yes', 'Likely', 'No', 'Partial']},
+                {'column': 'solve_status', 'required': True, 'data_type': 'enumeration', 'enumerations': ['Solved', 'Partially solved', 'Probably solved', 'Unsolved', 'Unaffected']},
                 {'column': 'missing_variant_case', 'required': True, 'data_type': 'enumeration', 'enumerations': ['Yes', 'No']},
             ],
         },
@@ -505,7 +505,7 @@
     'phenotype_description': None,
     'pmid_id': None,
     'seqr_chosen_consequence': None,
-    'solve_status': 'No',
+    'solve_status': 'Unsolved',
     'svName': None,
     'svType': None,
     'sv_name': None,
@@ -589,7 +589,7 @@ def test_anvil_export(self, mock_google_authenticated,  mock_zip):
             'dbgap_subject_id_1', 'No', '1', 'NA19678', 'NA19679', '-', 'Self', 'Male', 'Middle Eastern or North African', '-', '-',
             '-', 'OMIM:615120', 'Myasthenic syndrome, congenital, 8, with pre- and postsynaptic defects',
             'Affected', 'Adult onset', '-', 'HP:0001631|HP:0002011|HP:0001636', 'HP:0011675|HP:0001674|HP:0001508',
-            'myopathy', 'No'], subject_file)
+            'myopathy', 'Unsolved'], subject_file)
 
         self.assertEqual(sample_file[0], [
             'entity:sample_id', '01-subject_id', '02-sample_id', '03-dbgap_sample_id', '04-sequencing_center',
@@ -809,23 +809,23 @@ def _assert_expected_gregor_files(self, mock_open, has_second_project=False):
         self.assertListEqual([
             'Broad_NA19675_1', 'Broad_1kg project nme with unide', 'BROAD', 'HMB', 'Yes', 'IKBKAP|CCDC102B|CMA - normal',
             '34415322', 'Broad_1', 'Broad_NA19678', 'Broad_NA19679', '', 'Self', '', 'Male', '',
-            'Middle Eastern or North African', '', '', '21', 'Affected', 'myopathy', '18', 'No', 'No',
+            'Middle Eastern or North African', '', '', '21', 'Affected', 'myopathy', '18', 'Unsolved', 'No',
         ], row)
         hispanic_row = next(r for r in participant_file if r[0] == 'Broad_HG00731')
         self.assertListEqual([
             'Broad_HG00731', 'Broad_1kg project nme with unide', 'BROAD', 'HMB', '', '', '', 'Broad_2', 'Broad_HG00732',
-            'Broad_HG00733', '', 'Self', '', 'Female', '', '', 'Hispanic or Latino', 'Other', '', 'Affected', '', '', 'No', 'No',
+            'Broad_HG00733', '', 'Self', '', 'Female', '', '', 'Hispanic or Latino', 'Other', '', 'Affected', '', '', 'Unsolved', 'No',
         ], hispanic_row)
         solved_row = next(r for r in participant_file if r[0] == 'Broad_NA20876')
         self.assertListEqual([
             'Broad_NA20876', 'Broad_1kg project nme with unide', 'BROAD', 'HMB', '', '', '', 'Broad_7', '0',
-            '0', '', '', '', 'Male', '', '', '', '', '', 'Affected', '', '', 'Yes', 'No',
+            '0', '', '', '', 'Male', '', '', '', '', '', 'Affected', '', '', 'Solved', 'No',
         ], solved_row)
         multi_data_type_row = next(r for r in participant_file if r[0] == 'Broad_NA20888')
         self.assertListEqual([
             'Broad_NA20888', 'Broad_Test Reprocessed Project' if has_second_project else 'Broad_1kg project nme with unide',
             'BROAD', 'HMB', 'No', '', '', 'Broad_12' if has_second_project else 'Broad_8', '0', '0', '', '', '',
-            'Male' if has_second_project else 'Female', '', '', '', '', '', 'Affected', '', '', 'No', 'No',
+            'Male' if has_second_project else 'Female', '', '', '', '', '', 'Affected', '', '', 'Unsolved', 'No',
         ], multi_data_type_row)
 
         self.assertEqual(len(family_file), 11 if has_second_project else 10)
@@ -1076,7 +1076,7 @@ def test_family_metadata(self):
             'familyGuid': 'F000012_12',
             'family_id': '12',
             'displayName': '12',
-            'solve_status': 'No',
+            'solve_status': 'Unsolved',
             'actual_inheritance': 'unknown',
             'date_data_generation': '2017-02-05',
             'data_type': 'WES',
@@ -1111,7 +1111,7 @@ def test_family_metadata(self):
             'familyGuid': 'F000003_3',
             'family_id': '3',
             'displayName': '3',
-            'solve_status': 'No',
+            'solve_status': 'Unsolved',
             'actual_inheritance': '',
             'date_data_generation': '2017-02-05',
             'data_type': 'WES',

seqr/views/apis/summary_data_api_tests.py

@@ -35,7 +35,7 @@
 EXPECTED_NO_AIRTABLE_SAMPLE_METADATA_ROW = {
     "projectGuid": "R0003_test",
     "num_saved_variants": 2,
-    "solve_status": "No",
+    "solve_status": "Unsolved",
     "sample_id": "NA20889",
     "gene_known_for_phenotype-1": "Known",
     "gene_known_for_phenotype-2": "Known",
@@ -143,7 +143,7 @@
     'pmid_id': None,
     'proband_relationship': 'Self',
     'sex': 'Female',
-    'solve_status': 'No',
+    'solve_status': 'Unsolved',
     'alt-1': 'T',
     'chrom-1': '1',
     'gene_known_for_phenotype-1': 'Candidate',

seqr/views/utils/anvil_metadata_utils.py

@@ -51,9 +51,9 @@
 }
 
 SOLVE_STATUS_LOOKUP = {
-    **{s: 'Yes' for s in Family.SOLVED_ANALYSIS_STATUSES},
-    **{s: 'Likely' for s in Family.STRONG_CANDIDATE_ANALYSIS_STATUSES},
-    Family.ANALYSIS_STATUS_PARTIAL_SOLVE: 'Partial',
+    **{s: 'Solved' for s in Family.SOLVED_ANALYSIS_STATUSES},
+    Family.ANALYSIS_STATUS_PARTIAL_SOLVE: 'Partially solved',
+    Family.ANALYSIS_STATUS_PROBABLE_SOLVE: 'Probably solved',
 }
 
 MIM_INHERITANCE_MAP = {
@@ -103,7 +103,7 @@ def _get_family_metadata(family_filter, family_fields, include_metadata, include
     for f in family_data:
         family_id = f.pop('id')
         f.update({
-            'solve_status': SOLVE_STATUS_LOOKUP.get(f['analysisStatus'], 'No'),
+            'solve_status': SOLVE_STATUS_LOOKUP.get(f['analysisStatus'], 'Unsolved'),
             **{k: v['format'](f) for k, v in (family_fields or {}).items()},
         })
         if format_id:
@@ -201,6 +201,8 @@ def parse_anvil_metadata(
             if individual.id in matchmaker_individuals:
                 subject_row['MME'] = matchmaker_individuals[individual.id] if mme_values else 'Yes'
             subject_row.update(family_subject_row)
+            if individual.affected != Individual.AFFECTED_STATUS_AFFECTED:
+                subject_row['solve_status'] = 'Unaffected'
             add_row(subject_row, family_id, SUBJECT_ROW_TYPE)
 
             participant_id = subject_row['participant_id']

ui/shared/utils/constants.js

@@ -145,6 +145,7 @@ const FAMILY_STATUS_SOLVED_KNOWN_GENE_KNOWN_PHENOTYPE = 'S_kgfp'
 const FAMILY_STATUS_SOLVED_KNOWN_GENE_DIFFERENT_PHENOTYPE = 'S_kgdp'
 const FAMILY_STATUS_SOLVED_NOVEL_GENE = 'S_ng'
 const FAMILY_STATUS_EXTERNAL_SOLVE = 'ES'
+const FAMILY_STATUS_PROBABLE_SOLVE = 'PB'
 const FAMILY_STATUS_STRONG_CANDIDATE_KNOWN_GENE_KNOWN_PHENOTYPE = 'Sc_kgfp'
 const FAMILY_STATUS_STRONG_CANDIDATE_KNOWN_GENE_DIFFERENT_PHENOTYPE = 'Sc_kgdp'
 const FAMILY_STATUS_STRONG_CANDIDATE_NOVEL_GENE = 'Sc_ng'
@@ -164,6 +165,7 @@ export const SELECTABLE_FAMILY_ANALYSIS_STATUS_OPTIONS = [
   { value: FAMILY_STATUS_SOLVED_KNOWN_GENE_DIFFERENT_PHENOTYPE, color: '#4CAF50', name: 'Solved - gene linked to different phenotype' },
   { value: FAMILY_STATUS_SOLVED_NOVEL_GENE, color: '#4CAF50', name: 'Solved - novel gene' },
   { value: FAMILY_STATUS_EXTERNAL_SOLVE, color: '#146917', name: 'External Solve' },
+  { value: FAMILY_STATUS_PROBABLE_SOLVE, color: '#ACD657', name: 'Probably Solved' },
   { value: FAMILY_STATUS_STRONG_CANDIDATE_KNOWN_GENE_KNOWN_PHENOTYPE, color: '#CDDC39', name: 'Strong candidate - known gene for phenotype' },
   { value: FAMILY_STATUS_STRONG_CANDIDATE_KNOWN_GENE_DIFFERENT_PHENOTYPE, color: '#CDDC39', name: 'Strong candidate - gene linked to different phenotype' },
   { value: FAMILY_STATUS_STRONG_CANDIDATE_NOVEL_GENE, color: '#CDDC39', name: 'Strong candidate - novel gene' },