feat(refactor): Analysis failed jobs

tests/cli/test_cli_core.py

@@ -2,13 +2,13 @@
 from typing import Dict
 
 import pytest
-import trailblazer
-
 from click.testing import CliRunner
+
+import trailblazer
 from tests.mocks.store_mock import MockStore
 from trailblazer.cli.core import (
-    archive_user,
     add_user_to_db,
+    archive_user,
     base,
     cancel,
     delete,
@@ -138,7 +138,7 @@ def test_cancel_ongoing(cli_runner, trailblazer_context, caplog):
         )
 
         # Analysis should have jobs that can be cancelled
-        assert analysis_obj.failed_jobs
+        assert analysis_obj.jobs
 
         # WHEN running cancel command
         result = cli_runner.invoke(cancel, [str(analysis_obj.id)], obj=trailblazer_context)

tests/store/crud/test_delete.py

@@ -9,15 +9,15 @@ def test_delete_analysis_jobs(analysis_store: MockStore, tower_jobs: List[dict],
 
     # GIVEN an analysis without failed jobs
     analysis: Analysis = analysis_store.get_latest_analysis(case_id=case_id)
-    assert not analysis.failed_jobs
+    assert not analysis.jobs
 
     # WHEN jobs are updated
     analysis_store.update_analysis_jobs(analysis=analysis, jobs=tower_jobs[:2])
 
-    assert analysis.failed_jobs
+    assert analysis.jobs
 
     # WHEN jobs are deleted
     analysis_store.delete_analysis_jobs(analysis=analysis)
 
     # THEN analysis object should have no jobs
-    assert not analysis.failed_jobs
+    assert not analysis.jobs

tests/store/crud/test_update.py

@@ -4,22 +4,22 @@
 from trailblazer.apps.slurm.api import get_squeue_result
 from trailblazer.apps.slurm.models import SqueueResult
 from trailblazer.constants import TrailblazerStatus
-from trailblazer.store.filters.user_filters import apply_user_filter, UserFilter
-from trailblazer.store.models import User, Analysis
+from trailblazer.store.filters.user_filters import UserFilter, apply_user_filter
+from trailblazer.store.models import Analysis, User
 
 
 def test_update_analysis_jobs(analysis_store: MockStore, tower_jobs: List[dict], case_id: str):
     """Test jobs are successfully updated."""
 
     # GIVEN an analysis without failed jobs
     analysis: Analysis = analysis_store.get_latest_analysis(case_id=case_id)
-    assert not analysis.failed_jobs
+    assert not analysis.jobs
 
     # WHEN jobs are updated
     analysis_store.update_analysis_jobs(analysis=analysis, jobs=tower_jobs[:2])
 
     # THEN there should be jobs
-    assert analysis.failed_jobs
+    assert analysis.jobs
 
 
 def test_update_user_is_archived(user_store: MockStore, user_email: str):
@@ -49,7 +49,7 @@ def test_update_analysis_jobs_from_slurm_jobs(analysis_store: MockStore, squeue_
     """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.failed_jobs
+    assert not analysis.jobs
 
     squeue_result: SqueueResult = get_squeue_result(squeue_response=squeue_stream_jobs)
 
@@ -62,4 +62,4 @@ def test_update_analysis_jobs_from_slurm_jobs(analysis_store: MockStore, squeue_
     )
 
     # THEN it should update the analysis jobs
-    assert updated_analysis.failed_jobs
+    assert updated_analysis.jobs

tests/store/test_store_api.py

@@ -22,7 +22,7 @@ def test_update_analysis_from_slurm_run_status(analysis_store: MockStore, squeue
     """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.failed_jobs
+    assert not analysis.jobs
 
     # WHEN updating the analysis
     analysis_store.update_analysis_from_slurm_run_status(analysis_id=analysis.id)
@@ -33,7 +33,7 @@ def test_update_analysis_from_slurm_run_status(analysis_store: MockStore, squeue
     )
 
     # THEN it should update the analysis jobs
-    assert updated_analysis.failed_jobs
+    assert updated_analysis.jobs
 
 
 @pytest.mark.parametrize(
@@ -218,19 +218,19 @@ def test_update_tower_jobs(analysis_store: MockStore, tower_jobs: List[dict], ca
 
     # GIVEN an analysis without failed jobs
     analysis: Analysis = analysis_store.get_latest_analysis(case_id=case_id)
-    assert not analysis.failed_jobs
+    assert not analysis.jobs
 
     # WHEN analysis jobs are deleted
     analysis_store.delete_analysis_jobs(analysis=analysis)
 
     # THEN analysis object should have no failed jobs
-    assert not analysis.failed_jobs
+    assert not analysis.jobs
 
     # WHEN jobs are updated
     analysis_store.update_analysis_jobs(analysis=analysis, jobs=tower_jobs[:2])
 
     # THEN failed jobs should be updated
-    assert len(analysis.failed_jobs) == 2
+    assert len(analysis.jobs) == 2
 
 
 @pytest.mark.parametrize(

trailblazer/server/api.py

@@ -2,14 +2,18 @@
 import multiprocessing
 import os
 from http import HTTPStatus
-from typing import Dict, Mapping, List, Union
+from typing import Dict, List, Mapping, Union
 
 from flask import Blueprint, Response, abort, g, jsonify, make_response, request
 from google.auth import jwt
 
-from trailblazer.constants import TrailblazerStatus, ONE_MONTH_IN_DAYS, TRAILBLAZER_TIME_STAMP
+from trailblazer.constants import (
+    ONE_MONTH_IN_DAYS,
+    TRAILBLAZER_TIME_STAMP,
+    TrailblazerStatus,
+)
 from trailblazer.server.ext import store
-from trailblazer.store.models import Info, User, Analysis
+from trailblazer.store.models import Analysis, Info, User
 from trailblazer.utils.datetime import get_date_number_of_days_ago
 
 blueprint = Blueprint("api", __name__, url_prefix="/api/v1")
@@ -59,7 +63,7 @@ def analyses():
     for analysis_obj in query_page.items:
         analysis_data = analysis_obj.to_dict()
         analysis_data["user"] = analysis_obj.user.to_dict() if analysis_obj.user else None
-        analysis_data["failed_jobs"] = [job_obj.to_dict() for job_obj in analysis_obj.failed_jobs]
+        analysis_data["failed_jobs"] = [job_obj.to_dict() for job_obj in analysis_obj.jobs]
         data.append(analysis_data)
 
     return jsonify(analyses=data)
@@ -77,7 +81,7 @@ def analysis(analysis_id):
         store.commit()
 
     data = analysis_obj.to_dict()
-    data["failed_jobs"] = [job_obj.to_dict() for job_obj in analysis_obj.failed_jobs]
+    data["failed_jobs"] = [job_obj.to_dict() for job_obj in analysis_obj.jobs]
     data["user"] = analysis_obj.user.to_dict() if analysis_obj.user else None
     return jsonify(**data)
 

trailblazer/store/api.py

@@ -12,13 +12,17 @@
 from trailblazer.apps.slurm.api import get_current_analysis_status, get_squeue_result
 from trailblazer.apps.slurm.models import SqueueResult
 from trailblazer.apps.tower.api import TowerAPI
-from trailblazer.constants import FileFormat, SlurmJobStatus, TrailblazerStatus, WorkflowManager
+from trailblazer.constants import (
+    FileFormat,
+    SlurmJobStatus,
+    TrailblazerStatus,
+    WorkflowManager,
+)
 from trailblazer.exc import TowerRequirementsError, TrailblazerError
 from trailblazer.io.controller import ReadFile
 from trailblazer.store.core import CoreHandler
 from trailblazer.store.models import Analysis, Model
 
-
 LOG = logging.getLogger(__name__)
 
 
@@ -318,7 +322,7 @@ def cancel_analysis(self, analysis_id: int, email: str = None, ssh: bool = False
         if analysis.status not in TrailblazerStatus.ongoing_statuses():
             raise TrailblazerError(f"Analysis {analysis_id} is not running")
 
-        for job_obj in analysis.failed_jobs:
+        for job_obj in analysis.jobs:
             if job_obj.status in SlurmJobStatus.ongoing_statuses():
                 LOG.info(f"Cancelling job {job_obj.slurm_id} - {job_obj.name}")
                 self.cancel_slurm_job(job_obj.slurm_id, ssh=ssh)

trailblazer/store/crud/delete.py

@@ -7,6 +7,6 @@ class DeleteHandler(BaseHandler_2):
 
     def delete_analysis_jobs(self, analysis: Analysis) -> None:
         """Delete all jobs linked to the given analysis."""
-        for job in analysis.failed_jobs:
+        for job in analysis.jobs:
             job.delete()
         self.commit()

trailblazer/store/crud/update.py

@@ -1,18 +1,17 @@
-from trailblazer.apps.slurm.api import reformat_squeue_result_job_step
-from trailblazer.apps.slurm.models import SqueueResult
 from typing import List
 
+from trailblazer.apps.slurm.api import reformat_squeue_result_job_step
+from trailblazer.apps.slurm.models import SqueueResult
 from trailblazer.store.base import BaseHandler_2
-from trailblazer.store.models import User, Analysis, Job
+from trailblazer.store.models import Analysis, Job, User
 
 
 class UpdateHandler(BaseHandler_2):
     """Class for updating items in the database."""
 
     def update_analysis_jobs(self, analysis: Analysis, jobs: List[dict]) -> None:
         """Update jobs in the analysis."""
-        # failed_jobs is misnamed and actually contains all jobs irrespective of status
-        analysis.failed_jobs = [Job(**job) for job in jobs]
+        analysis.jobs = [Job(**job) for job in jobs]
         self.commit()
 
     def update_user_is_archived(self, user: User, archive: bool = True) -> None:
@@ -23,7 +22,7 @@ def update_user_is_archived(self, user: User, archive: bool = True) -> None:
     def update_analysis_jobs_from_slurm_jobs(
         self, analysis: Analysis, squeue_result: SqueueResult
     ) -> None:
-        """Update analysis failed jobs from supplied squeue results."""
+        """Update analysis jobs from supplied squeue results."""
         if len(squeue_result.jobs) == 0:
             return
         for job in squeue_result.jobs:
@@ -32,7 +31,7 @@ def update_analysis_jobs_from_slurm_jobs(
             )
 
         self.delete_analysis_jobs(analysis=analysis)
-        analysis.failed_jobs = [
+        analysis.jobs = [
             Job(
                 analysis_id=analysis.id,
                 slurm_id=job.id,

trailblazer/store/models.py

@@ -78,7 +78,7 @@ class Analysis(Model):
         types.Enum(*WorkflowManager.list()), default=WorkflowManager.SLURM.value
     )
 
-    failed_jobs = orm.relationship("Job", cascade="all,delete", backref="analysis")
+    jobs = orm.relationship("Job", cascade="all,delete", backref="analysis")
 
     @property
     def has_ongoing_status(self) -> bool: