Fix analysis started at assignment (#3195)

- Analysis started_at assignment. Now set at the creation date of the slurm jobs YAML file.

cg/meta/workflow/analysis.py

@@ -1,7 +1,7 @@
-import datetime as dt
 import logging
 import os
 import shutil
+from datetime import datetime
 from pathlib import Path
 from subprocess import CalledProcessError
 from typing import Any, Iterator
@@ -233,17 +233,21 @@ def upload_bundle_housekeeper(self, case_id: str, dry_run: bool = False) -> None
             f"Analysis successfully stored in Housekeeper: {case_id} : {bundle_version.created_at}"
         )
 
+    def get_analysis_started_date(self, case_id: str) -> datetime.date:
+        """Return the start date of the analysis for a given case."""
+        return self.get_date_from_file_path(self.get_job_ids_path(case_id))
+
     def upload_bundle_statusdb(self, case_id: str, dry_run: bool = False) -> None:
         """Storing analysis bundle in StatusDB for CASE_ID"""
 
         LOG.info(f"Storing analysis in StatusDB for {case_id}")
         case_obj: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
-        analysis_start: dt.datetime = self.get_bundle_created_date(case_id=case_id)
+        analysis_start: datetime.date = self.get_analysis_started_date(case_id)
         workflow_version: str = self.get_workflow_version(case_id=case_id)
         new_analysis: Case = self.status_db.add_analysis(
             workflow=self.workflow,
             version=workflow_version,
-            completed_at=dt.datetime.now(),
+            completed_at=datetime.now(),
             primary=(len(case_obj.analyses) == 0),
             started_at=analysis_start,
         )
@@ -300,7 +304,7 @@ def get_hermes_transformed_deliverables(self, case_id: str) -> dict:
             created=self.get_bundle_created_date(case_id),
         ).model_dump()
 
-    def get_bundle_created_date(self, case_id: str) -> dt.datetime:
+    def get_bundle_created_date(self, case_id: str) -> datetime.date:
         return self.get_date_from_file_path(self.get_deliverables_file_path(case_id=case_id))
 
     def get_workflow_version(self, case_id: str) -> str:
@@ -331,7 +335,7 @@ def set_statusdb_action(self, case_id: str, action: str | None, dry_run: bool =
             f"Action '{action}' not permitted by StatusDB and will not be set for case {case_id}"
         )
 
-    def get_analyses_to_clean(self, before: dt.datetime) -> list[Analysis]:
+    def get_analyses_to_clean(self, before: datetime) -> list[Analysis]:
         analyses_to_clean = self.status_db.get_analyses_to_clean(
             before=before, workflow=self.workflow
         )
@@ -500,11 +504,11 @@ def resolve_decompression(self, case_id: str, dry_run: bool) -> None:
         self.prepare_fastq_api.add_decompressed_fastq_files_to_housekeeper(case_id)
 
     @staticmethod
-    def get_date_from_file_path(file_path: Path) -> dt.datetime.date:
+    def get_date_from_file_path(file_path: Path) -> datetime.date:
         """
         Get date from deliverables path using date created metadata.
         """
-        return dt.datetime.fromtimestamp(int(os.path.getctime(file_path)))
+        return datetime.fromtimestamp(int(os.path.getctime(file_path)))
 
     def get_lims_naming_metadata(self, sample: Sample) -> str | None:
         return None
@@ -532,7 +536,7 @@ def clean_analyses(self, case_id: str) -> None:
         analyses: list = self.status_db.get_case_by_internal_id(internal_id=case_id).analyses
         LOG.info(f"Adding a cleaned at date for case {case_id}")
         for analysis_obj in analyses:
-            analysis_obj.cleaned_at = analysis_obj.cleaned_at or dt.datetime.now()
+            analysis_obj.cleaned_at = analysis_obj.cleaned_at or datetime.now()
             self.status_db.session.commit()
 
     def clean_run_dir(self, case_id: str, yes: bool, case_path: list[Path] | Path) -> int:

tests/cli/workflow/balsamic/test_compound_commands.py

@@ -1,4 +1,5 @@
 import logging
+from datetime import datetime
 from pathlib import Path
 
 from click.testing import CliRunner
@@ -12,6 +13,7 @@
     store,
     store_available,
 )
+from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI
 from cg.models.cg_config import CGConfig
 
@@ -48,7 +50,7 @@ def test_start(
     case_id = "balsamic_case_wgs_single"
 
     # WHEN dry running and config case already exists
-    mocker.patch("cg.meta.workflow.balsamic.BalsamicAnalysisAPI.config_case", return_value=None)
+    mocker.patch.object(BalsamicAnalysisAPI, "config_case", return_value=None)
     result = cli_runner.invoke(start, [case_id, "--dry-run"], obj=balsamic_context)
 
     # THEN command should execute successfully
@@ -82,7 +84,8 @@ def test_store(
     # Make sure analysis not already stored in ClinicalDB
     assert not balsamic_context.status_db.get_case_by_internal_id(internal_id=case_id).analyses
 
-    # GIVEN that HermesAPI returns a deliverables output
+    # GIVEN a started analysis and a HermesAPI returning a deliverables output
+    mocker.patch.object(AnalysisAPI, "get_analysis_started_date", return_value=datetime.now())
     mocker.patch.object(HermesApi, "convert_deliverables")
     HermesApi.convert_deliverables.return_value = CGDeliverables(**hermes_deliverables)
 
@@ -122,10 +125,8 @@ def test_start_available(
     )
 
     # GIVEN decompression is not needed and config case performed
-    mocker.patch(
-        "cg.meta.workflow.balsamic.BalsamicAnalysisAPI.resolve_decompression", return_value=None
-    )
-    mocker.patch("cg.meta.workflow.balsamic.BalsamicAnalysisAPI.config_case", return_value=None)
+    mocker.patch.object(BalsamicAnalysisAPI, "resolve_decompression", return_value=None)
+    mocker.patch.object(BalsamicAnalysisAPI, "config_case", return_value=None)
 
     # WHEN running command
     result = cli_runner.invoke(start_available, ["--dry-run"], obj=balsamic_context)
@@ -172,11 +173,11 @@ def test_store_available(
 
     # GIVEN that HermesAPI returns a deliverables output and config case performed
     hermes_deliverables["bundle_id"] = case_id_success
-    mocker.patch(
-        "cg.apps.hermes.hermes_api.HermesApi.convert_deliverables",
-        return_value=CGDeliverables(**hermes_deliverables),
+    mocker.patch.object(AnalysisAPI, "get_analysis_started_date", return_value=datetime.now())
+    mocker.patch.object(
+        HermesApi, "convert_deliverables", return_value=CGDeliverables(**hermes_deliverables)
     )
-    mocker.patch("cg.meta.workflow.balsamic.BalsamicAnalysisAPI.config_case", return_value=None)
+    mocker.patch.object(BalsamicAnalysisAPI, "config_case", return_value=None)
 
     # Ensure case was successfully picked up by start-available and status set to running
     result = cli_runner.invoke(start_available, ["--dry-run"], obj=balsamic_context)

tests/cli/workflow/balsamic/test_store_housekeeper.py

@@ -1,4 +1,5 @@
 import logging
+from datetime import datetime
 from pathlib import Path
 
 import pytest
@@ -12,6 +13,7 @@
 from cg.constants import EXIT_SUCCESS
 from cg.constants.constants import FileFormat
 from cg.io.controller import WriteStream
+from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.utils import Process
@@ -141,6 +143,7 @@ def test_valid_case(
     assert not balsamic_context.status_db.get_case_by_internal_id(internal_id=case_id).analyses
 
     # GIVEN that HermesAPI returns a deliverables output
+    mocker.patch.object(AnalysisAPI, "get_analysis_started_date", return_value=datetime.now())
     mocker.patch.object(HermesApi, "convert_deliverables")
     HermesApi.convert_deliverables.return_value = CGDeliverables(**hermes_deliverables)
 

tests/cli/workflow/nf_analysis/test_cli_store_housekeeper.py

@@ -1,6 +1,7 @@
 """Tests CLI common methods to store deliverable files into Housekeeper for NF analyses."""
 
 import logging
+from datetime import datetime
 
 import pytest
 from _pytest.fixtures import FixtureRequest
@@ -15,6 +16,7 @@
 from cg.constants import EXIT_SUCCESS, Workflow
 from cg.constants.constants import FileFormat
 from cg.io.controller import WriteStream
+from cg.meta.workflow.analysis import AnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.store.store import Store
 from cg.utils import Process
@@ -161,6 +163,7 @@ def test_store_housekeeper_valid_case(
     assert not store.get_case_by_internal_id(internal_id=case_id).analyses
 
     # GIVEN that HermesAPI returns a deliverables output
+    mocker.patch.object(AnalysisAPI, "get_analysis_started_date", return_value=datetime.now())
     mocker.patch.object(HermesApi, "convert_deliverables")
     HermesApi.convert_deliverables.return_value = CGDeliverables(**hermes_deliverables)
 
@@ -210,6 +213,7 @@ def test_valid_case_already_added(
     assert not context.status_db.get_case_by_internal_id(internal_id=case_id).analyses
 
     # GIVEN that HermesAPI returns a deliverables output
+    mocker.patch.object(AnalysisAPI, "get_analysis_started_date", return_value=datetime.now())
     mocker.patch.object(HermesApi, "convert_deliverables")
     HermesApi.convert_deliverables.return_value = CGDeliverables(**hermes_deliverables)
 
@@ -257,6 +261,7 @@ def test_dry_run(
     context.meta_apis["analysis_api"].housekeeper_api = real_housekeeper_api
 
     # GIVEN that HermesAPI returns a deliverables output
+    mocker.patch.object(AnalysisAPI, "get_analysis_started_date", return_value=datetime.now())
     mocker.patch.object(HermesApi, "convert_deliverables")
     HermesApi.convert_deliverables.return_value = CGDeliverables(**hermes_deliverables)