Reload saved variants for families with new sample only

hail_search/queries/base.py

@@ -738,7 +738,12 @@ def _parse_intervals(self, intervals, gene_ids=None, variant_keys=None, variant_
             return intervals
 
         if variant_ids:
-            intervals = [(chrom, pos, pos+1) for chrom, pos, _, _ in variant_ids]
+            first_chrom = variant_ids[0][0]
+            if all(first_chrom == v[0] for v in variant_ids):
+                positions = [pos for _, pos, _, _ in variant_ids]
+                intervals = [(first_chrom, min(positions), max(positions) + 1)]
+            else:
+                intervals = [(chrom, pos, pos+1) for chrom, pos, _, _ in variant_ids]
 
         is_x_linked = self._inheritance_mode == X_LINKED_RECESSIVE
         if not (intervals or is_x_linked):

seqr/management/commands/check_for_new_samples_from_pipeline.py

@@ -3,8 +3,6 @@
 
 from django.contrib.postgres.aggregates import ArrayAgg
 from django.core.management.base import BaseCommand, CommandError
-from django.db.models import Q
-from django.db.models.functions import JSONObject
 import json
 import logging
 import re
@@ -186,7 +184,7 @@ def _load_new_samples(cls, metadata_path, genome_version, dataset_type, run_vers
 
         sample_type = metadata['sample_type']
         logger.info(f'Loading {len(sample_project_tuples)} {sample_type} {dataset_type} samples in {len(samples_by_project)} projects')
-        updated_samples, inactivated_sample_guids, *args = match_and_update_search_samples(
+        updated_samples, new_samples, *args = match_and_update_search_samples(
             projects=samples_by_project.keys(),
             sample_project_tuples=sample_project_tuples,
             sample_data={'data_source': run_version, 'elasticsearch_index': ';'.join(metadata['callsets'])},
@@ -196,9 +194,9 @@ def _load_new_samples(cls, metadata_path, genome_version, dataset_type, run_vers
         )
 
         # Send loading notifications and update Airtable PDOs
-        update_sample_data_by_project = {
-            s['individual__family__project']: s for s in updated_samples.values('individual__family__project').annotate(
-                samples=ArrayAgg(JSONObject(sample_id='sample_id', individual_id='individual_id')),
+        new_sample_data_by_project = {
+            s['individual__family__project']: s for s in updated_samples.filter(id__in=new_samples).values('individual__family__project').annotate(
+                samples=ArrayAgg('sample_id', distinct=True),
                 family_guids=ArrayAgg('individual__family__guid', distinct=True),
             )
         }
@@ -207,15 +205,16 @@ def _load_new_samples(cls, metadata_path, genome_version, dataset_type, run_vers
         split_project_pdos = {}
         session = AirtableSession(user=None, no_auth=True)
         for project, sample_ids in samples_by_project.items():
-            project_sample_data = update_sample_data_by_project[project.id]
+            project_sample_data = new_sample_data_by_project[project.id]
             is_internal = not project_has_anvil(project) or is_internal_anvil_project(project)
             notify_search_data_loaded(
-                project, is_internal, dataset_type, sample_type, inactivated_sample_guids,
-                updated_samples=project_sample_data['samples'], num_samples=len(sample_ids),
+                project, is_internal, dataset_type, sample_type, project_sample_data['samples'],
+                num_samples=len(sample_ids),
             )
             project_families = project_sample_data['family_guids']
-            updated_families.update(project_families)
-            updated_project_families.append((project.id, project.name, project.genome_version, project_families))
+            if project_families:
+                updated_families.update(project_families)
+                updated_project_families.append((project.id, project.name, project.genome_version, project_families))
             if is_internal and dataset_type == Sample.DATASET_TYPE_VARIANT_CALLS:
                 split_project_pdos[project.name] = cls._update_pdos(session, project.guid, sample_ids)
 
@@ -337,14 +336,21 @@ def _reload_shared_variant_annotations(data_type, genome_version, updated_varian
             variant_id: {k: v for k, v in variant.items() if k not in {'familyGuids', 'genotypes'}}
             for variant_id, variant in (updated_variants_by_id or {}).items()
         }
-        fetch_variant_ids = sorted(set(variants_by_id.keys()) - set(updated_variants_by_id.keys()))
+        fetch_variant_ids = set(variants_by_id.keys()) - set(updated_variants_by_id.keys())
         if fetch_variant_ids:
-            if not is_sv:
-                fetch_variant_ids = [parse_valid_variant_id(variant_id) for variant_id in fetch_variant_ids]
-            for i in range(0, len(fetch_variant_ids), MAX_LOOKUP_VARIANTS):
-                updated_variants = hail_variant_multi_lookup(USER_EMAIL, fetch_variant_ids[i:i+MAX_LOOKUP_VARIANTS], data_type, genome_version)
-                logger.info(f'Fetched {len(updated_variants)} additional variants')
-                updated_variants_by_id.update({variant['variantId']: variant for variant in updated_variants})
+            if is_sv:
+                variant_ids_by_chrom = {'all': fetch_variant_ids}
+            else:
+                variant_ids_by_chrom = defaultdict(list)
+                for variant_id in fetch_variant_ids:
+                    parsed_id = parse_valid_variant_id(variant_id)
+                    variant_ids_by_chrom[parsed_id[0]].append(parsed_id)
+            for chrom, variant_ids in sorted(variant_ids_by_chrom.items()):
+                variant_ids = sorted(variant_ids)
+                for i in range(0, len(variant_ids), MAX_LOOKUP_VARIANTS):
+                    updated_variants = hail_variant_multi_lookup(USER_EMAIL, variant_ids[i:i+MAX_LOOKUP_VARIANTS], data_type, genome_version)
+                    logger.info(f'Fetched {len(updated_variants)} additional variants in chromosome {chrom}')
+                    updated_variants_by_id.update({variant['variantId']: variant for variant in updated_variants})
 
         updated_variant_models = []
         for variant_id, variant in updated_variants_by_id.items():

seqr/management/tests/check_for_new_samples_from_pipeline_tests.py

@@ -423,7 +423,7 @@ def test_command(self, mock_email, mock_airtable_utils, mock_open_write_file, mo
                 {'individual_guid': 'I000017_na20889', 'family_guid': 'F000012_12', 'project_guid': 'R0003_test', 'affected': 'A', 'sample_id': 'NA20889', 'sample_type': 'WES'},
             ]}},
         ], reload_annotations_logs=[
-            'Reloading shared annotations for 3 SNV_INDEL GRCh38 saved variants (3 unique)', 'Fetched 1 additional variants', 'Fetched 1 additional variants', 'Updated 2 SNV_INDEL GRCh38 saved variants',
+            'Reloading shared annotations for 3 SNV_INDEL GRCh38 saved variants (3 unique)', 'Fetched 1 additional variants in chromosome 1', 'Fetched 1 additional variants in chromosome 1', 'Updated 2 SNV_INDEL GRCh38 saved variants',
             'No additional SV_WES GRCh38 saved variants to update',
         ], run_loading_logs={
             'GRCh38/SNV_INDEL': 'Loading 4 WES SNV_INDEL samples in 2 projects',
@@ -559,10 +559,10 @@ def test_command(self, mock_email, mock_airtable_utils, mock_open_write_file, mo
         self.assertEqual(annotation_updated_json['mainTranscriptId'], 'ENST00000505820')
         self.assertEqual(len(annotation_updated_json['genotypes']), 3)
 
-        self.mock_utils_logger.error.assert_called_with('Error in project Test Reprocessed Project: Bad Request')
+        self.mock_utils_logger.error.assert_called_with('Error reloading variants in Test Reprocessed Project: Bad Request')
         self.mock_utils_logger.info.assert_has_calls([
-            mock.call('Updated 0 variants for project Test Reprocessed Project'),
-            mock.call('Updated 1 variants for project Non-Analyst Project'),
+            mock.call('Updated 0 variants in 1 families for project Test Reprocessed Project'),
+            mock.call('Updated 1 variants in 1 families for project Non-Analyst Project'),
             mock.call('Reload Summary: '),
             mock.call('  Non-Analyst Project: Updated 1 variants'),
             mock.call('Reloading saved variants in 2 projects'),

seqr/management/tests/reload_saved_variant_annotations_tests.py

@@ -39,18 +39,24 @@ def test_command(self, mock_logger):
 
         mock_logger.info.assert_has_calls([mock.call(log) for log in [
             'Reloading shared annotations for 3 SNV_INDEL GRCh37 saved variants (3 unique)',
-            'Fetched 2 additional variants',
+            'Fetched 2 additional variants in chromosome 1',
+            'Fetched 2 additional variants in chromosome 21',
             'Updated 2 SNV_INDEL GRCh37 saved variants',
         ]])
 
-        self.assertEqual(len(responses.calls), 1)
-        multi_lookup_request = responses.calls[0].request
-        self.assertEqual(multi_lookup_request.url, f'{MOCK_HAIL_ORIGIN}:5000/multi_lookup')
-        self.assertEqual(multi_lookup_request.headers.get('From'), 'manage_command')
-        self.assertDictEqual(json.loads(multi_lookup_request.body), {
+        self.assertEqual(len(responses.calls), 2)
+        for call in responses.calls:
+            self.assertEqual(call.request.url, f'{MOCK_HAIL_ORIGIN}:5000/multi_lookup')
+            self.assertEqual(call.request.headers.get('From'), 'manage_command')
+        self.assertDictEqual(json.loads(responses.calls[0].request.body), {
             'genome_version': 'GRCh37',
             'data_type': 'SNV_INDEL',
-            'variant_ids': [['1', 248367227, 'TC', 'T'], ['1', 46859832, 'G', 'A'], ['21', 3343353, 'GAGA', 'G']],
+            'variant_ids': [['1', 46859832, 'G', 'A'], ['1', 248367227, 'TC', 'T']],
+        })
+        self.assertDictEqual(json.loads(responses.calls[1].request.body), {
+            'genome_version': 'GRCh37',
+            'data_type': 'SNV_INDEL',
+            'variant_ids': [['21', 3343353, 'GAGA', 'G']],
         })
 
         annotation_updated_json_1 = SavedVariant.objects.get(guid='SV0000002_1248367227_r0390_100').saved_variant_json
@@ -66,11 +72,12 @@ def test_command(self, mock_logger):
         self.assertEqual(len(annotation_updated_json_2['genotypes']), 3)
 
         # Test SVs
+        responses.calls.reset()
         Sample.objects.filter(guid='S000147_na21234').update(individual_id=20)
         call_command('reload_saved_variant_annotations', 'SV_WGS', 'GRCh37')
 
-        self.assertEqual(len(responses.calls), 2)
-        self.assertDictEqual(json.loads(responses.calls[1].request.body), {
+        self.assertEqual(len(responses.calls), 1)
+        self.assertDictEqual(json.loads(responses.calls[0].request.body), {
             'genome_version': 'GRCh37',
             'data_type': 'SV_WGS',
             'variant_ids': ['prefix_19107_DEL'],

seqr/management/tests/reload_saved_variant_json_tests.py

@@ -30,7 +30,7 @@ def test_with_param_command(self, mock_get_variants, mock_logger):
             [family_1], ['1-46859832-G-A','21-3343353-GAGA-G'], user=None, user_email='manage_command')
 
         logger_info_calls = [
-            mock.call('Updated 2 variants for project 1kg project n\xe5me with uni\xe7\xf8de'),
+            mock.call('Updated 2 variants in 1 families for project 1kg project n\xe5me with uni\xe7\xf8de'),
             mock.call('Reload Summary: '),
             mock.call('  1kg project n\xe5me with uni\xe7\xf8de: Updated 2 variants')
         ]
@@ -81,4 +81,4 @@ def test_with_param_command(self, mock_get_variants, mock_logger):
         ]
         mock_logger.info.assert_has_calls(logger_info_calls)
 
-        mock_logger.error.assert_called_with('Error in project 1kg project n\xe5me with uni\xe7\xf8de: Database error.')
+        mock_logger.error.assert_called_with('Error reloading variants in 1kg project n\xe5me with uni\xe7\xf8de: Database error.')

seqr/utils/search/add_data_utils.py

@@ -39,7 +39,7 @@ def add_new_es_search_samples(request_json, project, user, notify=False, expecte
         request_json['mappingFilePath'], user) if request_json.get('mappingFilePath') else {}
     ignore_extra_samples = request_json.get('ignoreExtraSamplesInCallset')
     sample_project_tuples = [(sample_id, project.name) for sample_id in sample_ids]
-    updated_samples, inactivated_sample_guids, num_skipped, updated_family_guids = match_and_update_search_samples(
+    updated_samples, new_samples, inactivated_sample_guids, num_skipped, updated_family_guids = match_and_update_search_samples(
         projects=[project],
         user=user,
         sample_project_tuples=sample_project_tuples,
@@ -52,45 +52,41 @@ def add_new_es_search_samples(request_json, project, user, notify=False, expecte
     )
 
     if notify:
-        updated_sample_data = updated_samples.values('sample_id', 'individual_id')
-        _basic_notify_search_data_loaded(project, dataset_type, sample_type, inactivated_sample_guids, updated_sample_data)
+        _basic_notify_search_data_loaded(project, dataset_type, sample_type, new_samples.values())
 
     return inactivated_sample_guids, updated_family_guids, updated_samples
 
 
-def _basic_notify_search_data_loaded(project, dataset_type, sample_type, inactivated_sample_guids, updated_samples, format_email=None, slack_channel=None, include_slack_detail=False):
-    previous_loaded_individuals = set(Sample.objects.filter(guid__in=inactivated_sample_guids).values_list('individual_id', flat=True))
-    new_sample_ids = [sample['sample_id'] for sample in updated_samples if sample['individual_id'] not in previous_loaded_individuals]
-
+def _basic_notify_search_data_loaded(project, dataset_type, sample_type, new_samples, email_template=None, slack_channel=None, include_slack_detail=False):
     msg_dataset_type = '' if dataset_type == Sample.DATASET_TYPE_VARIANT_CALLS else f' {dataset_type}'
-    num_new_samples = len(new_sample_ids)
+    num_new_samples = len(new_samples)
     sample_summary = f'{num_new_samples} new {sample_type}{msg_dataset_type} samples'
 
     return send_project_notification(
         project,
         notification=sample_summary,
-        email_template=format_email(num_new_samples) if format_email else None,
+        email_template=email_template,
         subject='New data available in seqr',
         slack_channel=slack_channel,
-        slack_detail=', '.join(sorted(new_sample_ids)) if include_slack_detail else None,
+        slack_detail=', '.join(sorted(new_samples)) if include_slack_detail else None,
     )
 
 
-def notify_search_data_loaded(project, is_internal, dataset_type, sample_type, inactivated_sample_guids, updated_samples, num_samples):
+def notify_search_data_loaded(project, is_internal, dataset_type, sample_type, new_samples, num_samples):
     if is_internal:
-        format_email = None
+        email_template = None
     else:
         workspace_name = f'{project.workspace_namespace}/{project.workspace_name}'
-        def format_email(num_new_samples):
-            reload_summary = f' and {num_samples - num_new_samples} re-loaded samples' if num_samples > num_new_samples else ''
-            return '\n'.join([
-                f'We are following up on the request to load data from AnVIL on {project.created_date.date().strftime("%B %d, %Y")}.',
-                f'We have loaded {{notification}}{reload_summary} from the AnVIL workspace <a href={ANVIL_UI_URL}#workspaces/{workspace_name}>{workspace_name}</a> to the corresponding seqr project {{project_link}}.',
-                'Let us know if you have any questions.',
-            ])
+        num_new_samples = len(new_samples)
+        reload_summary = f' and {num_samples - num_new_samples} re-loaded samples' if num_samples > num_new_samples else ''
+        email_template = '\n'.join([
+            f'We are following up on the request to load data from AnVIL on {project.created_date.date().strftime("%B %d, %Y")}.',
+            f'We have loaded {{notification}}{reload_summary} from the AnVIL workspace <a href={ANVIL_UI_URL}#workspaces/{workspace_name}>{workspace_name}</a> to the corresponding seqr project {{project_link}}.',
+            'Let us know if you have any questions.',
+        ])
 
     url = _basic_notify_search_data_loaded(
-        project, dataset_type, sample_type, inactivated_sample_guids, updated_samples, format_email=format_email,
+        project, dataset_type, sample_type, new_samples, email_template=email_template,
         slack_channel=SEQR_SLACK_DATA_ALERTS_NOTIFICATION_CHANNEL if is_internal else SEQR_SLACK_ANVIL_DATA_LOADING_CHANNEL,
         include_slack_detail=is_internal,
     )

seqr/views/utils/dataset_utils.py

@@ -222,7 +222,10 @@ def match_and_update_search_samples(
     Family.bulk_update(
         user, {'analysis_status': Family.ANALYSIS_STATUS_ANALYSIS_IN_PROGRESS}, guid__in=family_guids_to_update)
 
-    return updated_samples, inactivated_sample_guids, len(remaining_sample_keys), family_guids_to_update
+    previous_loaded_individuals = set(Sample.objects.filter(guid__in=inactivated_sample_guids).values_list('individual_id', flat=True))
+    new_samples = dict(updated_samples.exclude(individual_id__in=previous_loaded_individuals).values_list('id', 'sample_id'))
+
+    return updated_samples, new_samples, inactivated_sample_guids, len(remaining_sample_keys), family_guids_to_update
 
 
 def _parse_tsv_row(row):

seqr/views/utils/variant_utils.py

@@ -45,12 +45,13 @@ def update_projects_saved_variant_json(projects, user_email, **kwargs):
                 skipped[project_name] = True
             else:
                 success[project_name] = len(updated_saved_variants)
-                logger.info(f'Updated {len(updated_saved_variants)} variants for project {project_name}')
+                family_summary = f' in {len(family_guids)} families' if family_guids else ''
+                logger.info(f'Updated {len(updated_saved_variants)} variants{family_summary} for project {project_name}')
                 updated_variants_by_id.update({v.variant_id: v.saved_variant_json for v in updated_saved_variants.values()})
         except Exception as e:
             traceback_message = traceback.format_exc()
             logger.error(traceback_message)
-            logger.error(f'Error in project {project_name}: {e}')
+            logger.error(f'Error reloading variants in {project_name}: {e}')
             error[project_name] = e
 
     logger.info('Reload Summary: ')