Changes to /analysis-runner API point (#690)

* Added ar_guid query parameter to GET /analysis-runner API point.

* Commenting out author from getAnalysisRunnerLog as it is not currently implemented.

api/routes/analysis.py

@@ -79,19 +79,25 @@ class AnalysisQueryModel(BaseModel):
     def to_filter(self, project_id_map: dict[str, int]) -> AnalysisFilter:
         """Convert to internal analysis filter"""
         return AnalysisFilter(
-            sample_id=GenericFilter(
-                in_=sample_id_transform_to_raw_list(self.sample_ids)
-            )
-            if self.sample_ids
-            else None,
-            sequencing_group_id=GenericFilter(
-                in_=sequencing_group_id_transform_to_raw_list(self.sequencing_group_ids)
-            )
-            if self.sequencing_group_ids
-            else None,
-            project=GenericFilter(in_=[project_id_map.get(p) for p in self.projects])
-            if self.projects
-            else None,
+            sample_id=(
+                GenericFilter(in_=sample_id_transform_to_raw_list(self.sample_ids))
+                if self.sample_ids
+                else None
+            ),
+            sequencing_group_id=(
+                GenericFilter(
+                    in_=sequencing_group_id_transform_to_raw_list(
+                        self.sequencing_group_ids
+                    )
+                )
+                if self.sequencing_group_ids
+                else None
+            ),
+            project=(
+                GenericFilter(in_=[project_id_map.get(p) for p in self.projects])
+                if self.projects
+                else None
+            ),
             type=GenericFilter(eq=self.type) if self.type else None,
         )
 
@@ -241,8 +247,9 @@ async def query_analyses(
 @router.get('/analysis-runner', operation_id='getAnalysisRunnerLog')
 async def get_analysis_runner_log(
     project_names: list[str] = Query(None),  # type: ignore
-    author: str = None,
+    # author: str = None, # not implemented yet, uncomment when we do
     output_dir: str = None,
+    ar_guid: str = None,
     connection: Connection = get_projectless_db_connection,
 ) -> list[AnalysisInternal]:
     """
@@ -257,7 +264,10 @@ async def get_analysis_runner_log(
         )
 
     results = await atable.get_analysis_runner_log(
-        project_ids=project_ids, author=author, output_dir=output_dir
+        project_ids=project_ids,
+        # author=author,
+        output_dir=output_dir,
+        ar_guid=ar_guid,
     )
     return [a.to_external() for a in results]
 

db/python/layers/analysis.py

@@ -441,9 +441,9 @@ async def get_cram_sizes_between_range(
         sample_create_dates = await sglayer.get_samples_create_date_from_sgs(
             list(crams.keys())
         )
-        by_date: dict[
-            SequencingGroupInternalId, list[tuple[datetime.date, int]]
-        ] = defaultdict(list)
+        by_date: dict[SequencingGroupInternalId, list[tuple[datetime.date, int]]] = (
+            defaultdict(list)
+        )
 
         for sg_id, analyses in crams.items():
             if len(analyses) == 1:
@@ -531,7 +531,9 @@ async def get_sgs_added_by_day_by_es_indices(
 
         return by_day
 
-    async def get_audit_logs_by_analysis_ids(self, analysis_ids: list[int]) -> dict[int, list[AuditLogInternal]]:
+    async def get_audit_logs_by_analysis_ids(
+        self, analysis_ids: list[int]
+    ) -> dict[int, list[AuditLogInternal]]:
         """Get audit logs for analysis IDs"""
         return await self.at.get_audit_log_for_analysis_ids(analysis_ids)
 
@@ -594,12 +596,16 @@ async def update_analysis(
     async def get_analysis_runner_log(
         self,
         project_ids: list[int] = None,
-        author: str = None,
+        # author: str = None,
         output_dir: str = None,
+        ar_guid: str = None,
     ) -> list[AnalysisInternal]:
         """
         Get log for the analysis-runner, useful for checking this history of analysis
         """
         return await self.at.get_analysis_runner_log(
-            project_ids, author=author, output_dir=output_dir
+            project_ids,
+            # author=author,
+            output_dir=output_dir,
+            ar_guid=ar_guid,
         )

db/python/tables/analysis.py

@@ -486,8 +486,9 @@ async def get_sample_cram_path_map_for_seqr(
     async def get_analysis_runner_log(
         self,
         project_ids: List[int] = None,
-        author: str = None,
+        # author: str = None,
         output_dir: str = None,
+        ar_guid: str = None,
     ) -> List[AnalysisInternal]:
         """
         Get log for the analysis-runner, useful for checking this history of analysis
@@ -501,15 +502,15 @@ async def get_analysis_runner_log(
             wheres.append('project in :project_ids')
             values['project_ids'] = project_ids
 
-        if author:
-            wheres.append('audit_log_id = :audit_log_id')
-            values['audit_log_id'] = await self.audit_log_id()
-
         if output_dir:
             wheres.append('(output = :output OR output LIKE :output_like)')
             values['output'] = output_dir
             values['output_like'] = f'%{output_dir}'
 
+        if ar_guid:
+            wheres.append('JSON_EXTRACT(meta, "$.ar_guid") = :ar_guid')
+            values['ar_guid'] = ar_guid
+
         wheres_str = ' AND '.join(wheres)
         _query = f'SELECT * FROM analysis WHERE {wheres_str}'
         rows = await self.connection.fetch_all(_query, values)