Merge pull request #5027 from broadinstitute/post-cleanup-coverage

Post-cleanup fix test coverage

Author: hanars

clickhouse_search/managers.py

@@ -1117,11 +1117,7 @@ def search_padded_interval(self, chrom, pos, padding):
         return self.filter(interval_q).result_values()
 
     @staticmethod
-    def _interval_query(chrom, start, end, offset=None, **kwargs):
-        if offset:
-            offset_pos = int((end - start) * offset)
-            start = max(start - offset_pos, MIN_POS)
-            end = min(end + offset_pos, MAX_POS)
+    def _interval_query(chrom, start, end, **kwargs):
         return Q(xpos__range=(get_xpos(chrom, start), get_xpos(chrom, end)))
 
     def _filter_seqr_frequency(self, entries, ac=None, hh=None, **kwargs):

clickhouse_search/search.py

@@ -189,15 +189,6 @@ def _get_comp_het_results_queryset(annotations_cls, primary_q, secondary_q, num_
                     {2: ('arrayIntersect(primary_familyGuids, secondary_familyGuids)', 'has({value}, {field})')},
                 ]),
             }
-        elif results.has_annotation('secondary_genotypes'):
-            genotype_expressions = {
-                'primary_familyGenotypes': ArrayFilter('primary_familyGenotypes', conditions=[
-                    {1: ('secondary_familyGuids', 'has({value}, {field})')},
-                ]),
-                'secondary_genotypes': ArrayFilter('secondary_genotypes', conditions=[
-                    {2: (None, 'arrayExists(g -> g.1 = {field}, primary_familyGenotypes)')},
-                ]),
-            }
         else:
             genotype_expressions = {
                 'primary_familyGenotypes': ArrayFilter('primary_familyGenotypes', conditions=[
@@ -699,10 +690,11 @@ def delete_clickhouse_family(project, family_guid, dataset_type, sample_type=Non
     return f'Clickhouse does not support deleting individual families from project. Manually delete {dataset_type} data for {family_guid} in project {project.guid}'
 
 
+SV_DATASET_TYPES = {
+    Sample.SAMPLE_TYPE_WGS: Sample.DATASET_TYPE_SV_CALLS,
+    Sample.SAMPLE_TYPE_WES: 'GCNV',
+}
 def _clickhouse_dataset_type(dataset_type, sample_type):
     if dataset_type == Sample.DATASET_TYPE_SV_CALLS:
-        if not sample_type:
-            raise ValueError('sample_type is required when dataset_type is SV')
-        if sample_type == Sample.SAMPLE_TYPE_WES:
-            return 'GCNV'
+        dataset_type = SV_DATASET_TYPES[sample_type]
     return dataset_type

clickhouse_search/search_tests.py

@@ -599,7 +599,7 @@ def test_location_search(self):
             [SV_VARIANT1, SV_VARIANT2], locus=sv_locus,
         )
         self._assert_expected_search(
-            [SV_VARIANT1], locus={'rawItems': 'chr1:9292894-9369532'}
+            [SV_VARIANT1], locus={'rawItems': 'chr1:9297894-9369732%10'}
         )
 
         self._reset_search_families()

reference_data/management/commands/utils/__init__.py

@@ -36,7 +36,6 @@
     'GCNV': f'{Sample.DATASET_TYPE_SV_CALLS}_WES',
     Sample.DATASET_TYPE_SV_CALLS: f'{Sample.DATASET_TYPE_SV_CALLS}_WGS',
 }
-USER_EMAIL = 'manage_command'
 RELATEDNESS_CHECK_NAME = 'relatedness_check'
 
 PDO_COPY_FIELDS = [
@@ -255,7 +254,7 @@ def _load_new_samples(cls, metadata_path, genome_version, dataset_type, run_vers
         # Reload saved variant JSON
         update_projects_saved_variant_json([
             (project.id, project.guid, project.name, project.genome_version, families) for project, families in families_by_project.items()
-        ], user_email=USER_EMAIL, dataset_type=dataset_type, update_function=cls._update_project_saved_variant_genotypes, samples=updated_samples, clickhouse_dataset_type=clickhouse_dataset_type)
+        ], dataset_type=dataset_type, update_function=cls._update_project_saved_variant_genotypes, samples=updated_samples, clickhouse_dataset_type=clickhouse_dataset_type)
 
     @classmethod
     def _is_internal_project(cls, project):
@@ -390,7 +389,7 @@ def _update_individuals_sample_qc(cls, sample_type, family_guids, sample_qc_map)
             )
 
     @classmethod
-    def _update_project_saved_variant_genotypes(cls, project_id, genome_version, user_email, family_guids, project_guid, samples=None, clickhouse_dataset_type=None, **kwargs):
+    def _update_project_saved_variant_genotypes(cls, project_id, genome_version, family_guids, project_guid, samples=None, clickhouse_dataset_type=None, **kwargs):
         updates = {}
         for family_guid in family_guids:
             variant_models_by_key = {

reference_data/management/commands/utils/update_utils.py

@@ -30,5 +30,5 @@ def handle(self, *args, **options):
 
         family_ids = [family_guid] if family_guid else None
         project_list = [(*project, family_ids) for project in projects.order_by('id').values_list('id', 'guid', 'name', 'genome_version')]
-        update_projects_saved_variant_json(project_list, user_email='manage_command', update_function=update_project_saved_variant_json)
+        update_projects_saved_variant_json(project_list, update_function=update_project_saved_variant_json)
         logger.info("Done")

seqr/management/commands/check_for_new_samples_from_pipeline.py

@@ -25,10 +25,9 @@ def _post_to_slack(channel, message):
         return None
 
     slack = Slacker(SLACK_TOKEN)
-    response = slack.chat.post_message(
+    slack.chat.post_message(
         channel, message, as_user=False, icon_emoji=":beaker:", username="Beaker (engineering-minion)",
     )
-    return response.raw
 
 
 def send_welcome_email(user, referrer):

seqr/management/commands/reload_saved_variant_json.py

@@ -560,14 +560,6 @@ def _filter_inheritance_family_samples(samples, inheritance_filter):
     ]
 
 
-def _format_interval(chrom=None, start=None, end=None, offset=None, **kwargs):
-    if offset:
-        offset_pos = int((end - start) * offset)
-        start = max(start - offset_pos, MIN_POS)
-        end = min(end + offset_pos, MAX_POS)
-    return [chrom, start, end]
-
-
 LIFTOVERS = {
     GENOME_VERSION_GRCh38: None,
     GENOME_VERSION_GRCh37: None,

seqr/utils/communication_utils.py

@@ -1274,9 +1274,6 @@ def _test_expected_vcf_responses(self, response, url):
         response = self.client.get(url, content_type='application/json')
         self.assertEqual(response.status_code, 200)
 
-    def _assert_expected_read_vcf_header_subprocess_calls(self, body):
-        return True
-
     def test_validate_callset(self):
         url = reverse(validate_callset)
         self.check_pm_login(url)