feat(refactor):

tests/store/crud/test_update.py

@@ -1,12 +1,13 @@
+import subprocess
 from datetime import datetime
-from typing import List, Optional
+from typing import Dict, List, Optional
 
 import pytest
 
 from tests.mocks.store_mock import MockStore
 from trailblazer.apps.slurm.api import get_squeue_result
 from trailblazer.apps.slurm.models import SqueueResult
-from trailblazer.constants import TrailblazerStatus
+from trailblazer.constants import CharacterFormat, TrailblazerStatus
 from trailblazer.exc import MissingAnalysis, TrailblazerError
 from trailblazer.store.filters.user_filters import UserFilter, apply_user_filter
 from trailblazer.store.models import Analysis, User
@@ -242,3 +243,35 @@ def test_update_analysis_comment_when_existing(analysis_store: MockStore, case_i
 
     # THEN comments should have been added
     assert analysis.comment == f"{first_comment} {second_comment}"
+
+
+def test_update_analysis_from_slurm_run_status(
+    analysis_store: MockStore,
+    squeue_stream_jobs: str,
+    mocker,
+    ongoing_analysis_case_id: str,
+    slurm_squeue_output: Dict[str, str],
+):
+    """Test updating analysis jobs when given squeue results."""
+    # GIVEN an analysis and a squeue stream
+    analysis: Analysis = analysis_store.get_query(table=Analysis).first()
+    assert not analysis.jobs
+
+    # GIVEN SLURM squeue output for an analysis
+    mocker.patch(
+        "trailblazer.store.crud.update.get_slurm_squeue_output",
+        return_value=subprocess.check_output(
+            ["cat", slurm_squeue_output.get(ongoing_analysis_case_id)]
+        ).decode(CharacterFormat.UNICODE_TRANSFORMATION_FORMAT_8),
+    )
+
+    # WHEN updating the analysis
+    analysis_store.update_analysis_from_slurm_output(
+        analysis_id=analysis.id, analysis_host="a_host"
+    )
+    updated_analysis: Analysis = analysis_store.get_analysis(
+        case_id=analysis.family, started_at=analysis.started_at, status=TrailblazerStatus.RUNNING
+    )
+
+    # THEN it should update the analysis jobs
+    assert updated_analysis.jobs

tests/store/test_store_api.py

@@ -20,38 +20,6 @@ def test_setup_db(store: MockStore):
     assert store.engine.table_names()
 
 
-def test_update_analysis_from_slurm_run_status(
-    analysis_store: MockStore,
-    squeue_stream_jobs: str,
-    mocker,
-    ongoing_analysis_case_id: str,
-    slurm_squeue_output: Dict[str, str],
-):
-    """Test updating analysis jobs when given squeue results."""
-    # GIVEN an analysis and a squeue stream
-    analysis: Analysis = analysis_store.get_query(table=Analysis).first()
-    assert not analysis.jobs
-
-    # GIVEN SLURM squeue output for an analysis
-    mocker.patch(
-        FUNC_GET_SLURM_SQUEUE_OUTPUT_PATH,
-        return_value=subprocess.check_output(
-            ["cat", slurm_squeue_output.get(ongoing_analysis_case_id)]
-        ).decode(CharacterFormat.UNICODE_TRANSFORMATION_FORMAT_8),
-    )
-
-    # WHEN updating the analysis
-    analysis_store.update_analysis_from_slurm_output(
-        analysis_id=analysis.id, analysis_host="a_host"
-    )
-    updated_analysis: Analysis = analysis_store.get_analysis(
-        case_id=analysis.family, started_at=analysis.started_at, status=TrailblazerStatus.RUNNING
-    )
-
-    # THEN it should update the analysis jobs
-    assert updated_analysis.jobs
-
-
 @pytest.mark.parametrize(
     "case_id, status",
     [

trailblazer/store/api.py

@@ -100,22 +100,6 @@ def update_run_status(self, analysis_id: int, analysis_host: Optional[str] = Non
                 analysis_id=analysis_id, analysis_host=analysis_host
             )
 
-    def update_analysis_from_slurm_output(
-        self, analysis_id: int, analysis_host: Optional[str] = False
-    ) -> None:
-        """Query SLURM for entries related to given analysis, and update the analysis in the database."""
-        analysis: Optional[Analysis] = self.get_analysis_with_id(analysis_id=analysis_id)
-        try:
-            self._update_analysis_from_slurm_squeue_output(
-                analysis=analysis, analysis_host=analysis_host
-            )
-        except Exception as exception:
-            LOG.error(
-                f"Error updating analysis for: case - {analysis.family} : {exception.__class__.__name__}"
-            )
-            analysis.status = TrailblazerStatus.ERROR
-            self.commit()
-
     @staticmethod
     def query_tower(config_file: str, case_id: str) -> TowerAPI:
         """Parse a config file to extract a NF Tower workflow ID and return a TowerAPI.

trailblazer/store/crud/update.py

@@ -79,6 +79,22 @@ def _update_analysis_from_slurm_squeue_output(
         analysis.logged_at = datetime.now()
         self.commit()
 
+    def update_analysis_from_slurm_output(
+        self, analysis_id: int, analysis_host: Optional[str] = False
+    ) -> None:
+        """Query SLURM for entries related to given analysis, and update the analysis in the database."""
+        analysis: Optional[Analysis] = self.get_analysis_with_id(analysis_id=analysis_id)
+        try:
+            self._update_analysis_from_slurm_squeue_output(
+                analysis=analysis, analysis_host=analysis_host
+            )
+        except Exception as exception:
+            LOG.error(
+                f"Error updating analysis for: case - {analysis.family} : {exception.__class__.__name__}"
+            )
+            analysis.status = TrailblazerStatus.ERROR
+            self.commit()
+
     def update_case_analyses_as_deleted(self, case_id: str) -> Optional[List[Analysis]]:
         """Mark analyses connected to a case as deleted."""
         analyses: Optional[List[Analysis]] = self.get_analyses_for_case(case_id=case_id)