Linting fixes

populationgenomics · Sep 19, 2024 · e5661d6 · e5661d6
1 parent d9b732e
commit e5661d6
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Showing 3 changed files with 30 additions and 18 deletions.
diff --git a/db/python/layers/project_insights.py b/db/python/layers/project_insights.py
@@ -276,14 +276,15 @@ def get_sg_web_report_links(
             }
 
         return report_links
-
-    def get_cram_record(
-        self, cram_row: AnalysisRow | None
-    ):
+
+    def get_cram_record(self, cram_row: AnalysisRow | None):
+        """Get the CRAM record for a sequencing group"""
         return {
             'id': cram_row.id if cram_row else None,
             'output': cram_row.output if cram_row else None,
-            'timestamp_completed': cram_row.timestamp_completed.strftime('%d-%m-%y') if cram_row else None,
+            'timestamp_completed': cram_row.timestamp_completed.strftime('%d-%m-%y')
+            if cram_row
+            else None,
         }
 
     def get_analysis_stats_internal_from_record(
@@ -569,10 +570,12 @@ async def _crams_by_project_id_and_seq_fields(
         return self.parse_project_seqtype_technology_keyed_rows(
             _query_results, 'sequencing_group_ids'
         )
-        
+
     async def _sg_crams_by_project_id_and_seq_fields(
         self, project_ids: list[ProjectId], sequencing_types: list[str]
-    ) -> dict[ProjectSeqTypeTechnologyKey, dict[SequencingGroupInternalId, AnalysisRow]]:
+    ) -> dict[
+        ProjectSeqTypeTechnologyKey, dict[SequencingGroupInternalId, AnalysisRow]
+    ]:
         _query = """
 SELECT
     a.project,
@@ -613,9 +616,9 @@ async def _sg_crams_by_project_id_and_seq_fields(
                 'sequencing_types': sequencing_types,
             },
         )
-        
+
         cram_timestamps_by_project_id_and_seq_fields: dict[
-            ProjectSeqTypeKey, dict[SequencingGroupInternalId, AnalysisRow]
+            ProjectSeqTypeTechnologyKey, dict[SequencingGroupInternalId, AnalysisRow]
         ] = {}
         for row in _query_results:
             key = ProjectSeqTypeTechnologyKey(
@@ -634,7 +637,6 @@ async def _sg_crams_by_project_id_and_seq_fields(
             cram_timestamps_by_project_id_and_seq_fields[key][sg_id] = cram_row
         return cram_timestamps_by_project_id_and_seq_fields
 
-
     async def _latest_annotate_dataset_by_project_id_and_seq_type(
         self, project_ids: list[ProjectId], sequencing_types: list[str]
     ) -> dict[ProjectSeqTypeKey, AnalysisRow]:
@@ -661,7 +663,7 @@ async def _latest_annotate_dataset_by_project_id_and_seq_type(
 ) max_timestamps ON a.project = max_timestamps.project
 AND a.timestamp_completed = max_timestamps.max_timestamp
 AND JSON_UNQUOTE(JSON_EXTRACT(a.meta, '$.sequencing_type')) = max_timestamps.sequencing_type
-WHERE 
+WHERE
     a.type = 'CUSTOM'
     AND a.status = 'COMPLETED'
     AND a.project IN :projects
@@ -711,7 +713,7 @@ async def _latest_es_indices_by_project_id_and_seq_type_and_stage(
 AND a.timestamp_completed = max_timestamps.max_timestamp
 AND JSON_UNQUOTE(JSON_EXTRACT(a.meta, '$.sequencing_type')) = max_timestamps.sequencing_type
 AND JSON_EXTRACT(a.meta, '$.stage') = max_timestamps.stage
-WHERE 
+WHERE
     a.project IN :projects
     AND JSON_UNQUOTE(JSON_EXTRACT(a.meta, '$.sequencing_type')) in :sequencing_types;
         """
@@ -1104,8 +1106,10 @@ async def get_project_insights_details(
             ):
                 continue
 
-            sequencing_groups_crams: dict[SequencingGroupInternalId, AnalysisRow] = crams_by_project_id_and_seq_fields.get(
-                (project.id, seq_type, seq_tech), {}
+            sequencing_groups_crams: dict[SequencingGroupInternalId, AnalysisRow] = (
+                crams_by_project_id_and_seq_fields.get(
+                    (project.id, seq_type, seq_tech), {}
+                )
             )
             (
                 latest_annotate_dataset_row,

diff --git a/test/data/generate_seqr_project_data.py b/test/data/generate_seqr_project_data.py
@@ -626,17 +626,23 @@ async def main():
                 body={'meta': {'is_seqr': 'true'}},
             )
             logging.info(f'Set {project} as seqr project')
-
-        project_id_query_result = await query_async(QUERY_PROJECT_ID, {'project': project})
+
+        project_id_query_result = await query_async(
+            QUERY_PROJECT_ID, {'project': project}
+        )
         project_id = project_id_query_result['project']['id']
 
         participant_id_map = await generate_project_pedigree(project)
 
         await generate_sample_entries(project, participant_id_map, metamist_enums, sapi)
 
-        aligned_sgs = await generate_cram_analyses(project, project_id, analyses_to_insert)
+        aligned_sgs = await generate_cram_analyses(
+            project, project_id, analyses_to_insert
+        )
 
-        await generate_web_report_analyses(project, project_id, aligned_sgs, analyses_to_insert)
+        await generate_web_report_analyses(
+            project, project_id, aligned_sgs, analyses_to_insert
+        )
 
         await generate_joint_called_analyses(project, aligned_sgs, analyses_to_insert)
 

diff --git a/web/package.json b/web/package.json
@@ -4,6 +4,8 @@
     "private": true,
     "dependencies": {
         "@apollo/client": "^3.7.3",
+        "@emotion/react": "^11.13.3",
+        "@emotion/styled": "^11.13.0",
         "@monaco-editor/react": "^4.6.0",
         "@mui/icons-material": "^5.10.9",
         "@mui/material": "^5.10.9",