completed at to None if force storage

Clinical-Genomics · Jul 29, 2024 · 0e1140e · 0e1140e
1 parent 36c50aa
commit 0e1140e
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Showing 4 changed files with 15 additions and 12 deletions.
diff --git a/cg/cli/workflow/balsamic/base.py b/cg/cli/workflow/balsamic/base.py
@@ -135,7 +135,7 @@ def report_deliver(context: CGConfig, case_id: str, dry_run: bool, force: bool):
     analysis_api: AnalysisAPI = context.meta_apis["analysis_api"]
     try:
         analysis_api.status_db.verify_case_exists(case_id)
-        analysis_api.verify_case_config_file_exists(case_id=case_id)
+        analysis_api.verify_case_config_file_exists(case_id=case_id, dry_run=dry_run)
         analysis_api.trailblazer_api.verify_latest_analysis_is_completed(
             case_id=case_id, force=force
         )
@@ -151,8 +151,9 @@ def report_deliver(context: CGConfig, case_id: str, dry_run: bool, force: bool):
 @balsamic.command("store-housekeeper")
 @ARGUMENT_CASE_ID
 @FORCE
+@DRY_RUN
 @click.pass_obj
-def store_housekeeper(context: CGConfig, case_id: str, force: bool):
+def store_housekeeper(context: CGConfig, case_id: str, dry_run: bool, force: bool):
     """Store a finished analysis in Housekeeper and StatusDB."""
 
     analysis_api: AnalysisAPI = context.meta_apis["analysis_api"]
@@ -161,11 +162,11 @@ def store_housekeeper(context: CGConfig, case_id: str, force: bool):
 
     try:
         analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
-        analysis_api.verify_case_config_file_exists(case_id=case_id)
+        analysis_api.verify_case_config_file_exists(case_id=case_id, dry_run=dry_run)
         analysis_api.verify_deliverables_file_exists(case_id=case_id)
-        analysis_api.upload_bundle_housekeeper(case_id=case_id, force=force)
-        analysis_api.upload_bundle_statusdb(case_id=case_id)
-        analysis_api.set_statusdb_action(case_id=case_id, action=None)
+        analysis_api.upload_bundle_housekeeper(case_id=case_id, dry_run=dry_run, force=force)
+        analysis_api.upload_bundle_statusdb(case_id=case_id, dry_run=dry_run, force=force)
+        analysis_api.set_statusdb_action(case_id=case_id, action=None, dry_run=dry_run)
     except ValidationError as error:
         LOG.warning("Deliverables file is malformed")
         raise error

diff --git a/cg/cli/workflow/commands.py b/cg/cli/workflow/commands.py
@@ -106,9 +106,9 @@ def store(context: CGConfig, case_id: str, dry_run: bool, force: bool):
         LOG.info(f"Dry run: Would have stored deliverables for {case_id}")
         return
     try:
-        analysis_api.upload_bundle_housekeeper(case_id=case_id, force=force)
-        analysis_api.upload_bundle_statusdb(case_id=case_id)
-        analysis_api.set_statusdb_action(case_id=case_id, action=None)
+        analysis_api.upload_bundle_housekeeper(case_id=case_id, dry_run=dry_run, force=force)
+        analysis_api.upload_bundle_statusdb(case_id=case_id, dry_run=dry_run, force=force)
+        analysis_api.set_statusdb_action(case_id=case_id, action=None, dry_run=dry_run)
     except Exception as exception_object:
         housekeeper_api.rollback()
         status_db.session.rollback()

diff --git a/cg/meta/workflow/analysis.py b/cg/meta/workflow/analysis.py
@@ -241,7 +241,9 @@ def upload_bundle_housekeeper(
             f"Analysis successfully stored in Housekeeper: {case_id} ({bundle_version.created_at})"
         )
 
-    def upload_bundle_statusdb(self, case_id: str, dry_run: bool = False) -> None:
+    def upload_bundle_statusdb(
+        self, case_id: str, dry_run: bool = False, force: bool = False
+    ) -> None:
         """Storing an analysis bundle in StatusDB for a provided case."""
         LOG.info(f"Storing analysis in StatusDB for {case_id}")
         case_obj: Case = self.status_db.get_case_by_internal_id(case_id)
@@ -250,7 +252,7 @@ def upload_bundle_statusdb(self, case_id: str, dry_run: bool = False) -> None:
         new_analysis: Case = self.status_db.add_analysis(
             workflow=self.workflow,
             version=workflow_version,
-            completed_at=datetime.now(),
+            completed_at=datetime.now() if not force else None,
             primary=(len(case_obj.analyses) == 0),
             started_at=analysis_start,
         )

diff --git a/cg/meta/workflow/nf_analysis.py b/cg/meta/workflow/nf_analysis.py
@@ -789,7 +789,7 @@ def store_analysis_housekeeper(
             self.trailblazer_api.verify_latest_analysis_is_completed(case_id=case_id, force=force)
             self.verify_deliverables_file_exists(case_id)
             self.upload_bundle_housekeeper(case_id=case_id, dry_run=dry_run, force=force)
-            self.upload_bundle_statusdb(case_id=case_id, dry_run=dry_run)
+            self.upload_bundle_statusdb(case_id=case_id, dry_run=dry_run, force=force)
             self.set_statusdb_action(case_id=case_id, action=None, dry_run=dry_run)
         except ValidationError as error:
             raise HousekeeperStoreError(f"Deliverables file is malformed: {error}")