add cli command for status update

tests/cli/test_cli_core.py

@@ -1,7 +1,16 @@
 import pytest
 
 import trailblazer
-from trailblazer.cli.core import base, cancel, delete, ls_cmd, scan, set_analysis_completed, user
+from trailblazer.cli.core import (
+    base,
+    cancel,
+    delete,
+    ls_cmd,
+    scan,
+    set_analysis_completed,
+    set_analysis_status,
+    user,
+)
 
 
 def test_base(cli_runner):
@@ -36,6 +45,47 @@ def test_set_analysis_completed(cli_runner, trailblazer_context, caplog):
     assert analysis_obj.status == "completed"
 
 
+def test_set_analysis_status(cli_runner, trailblazer_context, caplog) -> None:
+    """Test that the lastest analysis status is updated for a given case ID."""
+
+    # GIVEN an analysis with status FAILED
+    failed_analysis = "crackpanda"
+    analysis_obj = trailblazer_context["trailblazer"].get_latest_analysis(case_id=failed_analysis)
+
+    # Make sure status is not "completed"
+    assert analysis_obj.status != "qc"
+
+    # WHEN running command
+    result = cli_runner.invoke(
+        set_analysis_status, ["--status", "qc", failed_analysis], obj=trailblazer_context
+    )
+
+    # THEN command runs successfully
+    assert result.exit_code == 0
+
+    # THEN status will be set to COMPLETED
+    analysis_obj = trailblazer_context["trailblazer"].get_latest_analysis(case_id=failed_analysis)
+    assert analysis_obj.status == "qc"
+
+
+def test_set_analysis_status_error(cli_runner, trailblazer_context, caplog) -> None:
+    """Test that setting the status to a non-accepted value raises an error."""
+
+    # GIVEN an analysis with status FAILED
+    failed_analysis = "crackpanda"
+
+    # WHEN running command
+    result = cli_runner.invoke(
+        set_analysis_status,
+        ["--status", "non_existing_status", failed_analysis],
+        obj=trailblazer_context,
+    )
+
+    # THEN an error should be raised
+    assert result.exit_code != 0
+    assert "Invalid status" in caplog.text
+
+
 def test_cancel_nonexistent(cli_runner, trailblazer_context, caplog):
     with caplog.at_level("ERROR"):
         # GIVEN Trailblazer database with analyses and jobs

trailblazer/cli/core.py

@@ -167,6 +167,30 @@ def set_analysis_completed(context, analysis_id):
         LOG.error(e)
 
 
+@base.command("set-status")
+@click.option(
+    "--status",
+    is_flag=False,
+    type=str,
+    help=f"Status to be set. Can take the values:{STATUS_OPTIONS}",
+)
+@click.argument("case_id", type=str)
+@click.pass_context
+def set_analysis_status(
+    context,
+    case_id: str,
+    status: str,
+):
+    """Set the status of the latest analysis for a given CASE_ID."""
+    try:
+        context.obj["trailblazer"].set_analysis_status(case_id=case_id, status=status)
+    except ValueError as e:
+        LOG.error(e)
+        raise click.Abort from e
+    except Exception as e:
+        LOG.error(e)
+
+
 @base.command()
 @click.option("--force", is_flag=True, help="Force delete if analysis ongoing")
 @click.option("--cancel-jobs", is_flag=True, help="Cancel all ongoing jobs before deleting")

trailblazer/store/api.py

@@ -19,13 +19,14 @@
     ONGOING_STATUSES,
     SLURM_ACTIVE_CATEGORIES,
     STARTED_STATUSES,
+    STATUS_OPTIONS,
+    FileFormat,
     TrailblazerStatus,
     WorkflowManager,
-    FileFormat,
 )
 from trailblazer.exc import EmptySqueueError, TowerRequirementsError, TrailblazerError
 from trailblazer.io.controller import ReadFile
-from trailblazer.store.models import Model, User, Analysis, Job, Info
+from trailblazer.store.models import Analysis, Info, Job, Model, User
 from trailblazer.store.utils import formatters
 
 LOG = logging.getLogger(__name__)
@@ -249,6 +250,7 @@ def mark_analyses_deleted(self, case_id: str) -> Query:
         return old_analyses
 
     def set_analysis_completed(self, analysis_id: int) -> None:
+        """Set an analysis status to completed."""
         analysis_obj = self.analysis(analysis_id=analysis_id)
         analysis_obj.status = "completed"
         self.commit()
@@ -262,10 +264,13 @@ def set_analysis_uploaded(self, case_id: str, uploaded_at: dt.datetime) -> None:
 
     def set_analysis_status(self, case_id: str, status: str):
         """Setting analysis status."""
+        status = status.lower()
+        if status not in set(STATUS_OPTIONS):
+            raise ValueError(f"Invalid status. Allowed values are: {STATUS_OPTIONS}")
         analysis_obj: Analysis = self.get_latest_analysis(case_id=case_id)
         analysis_obj.status: str = status
         self.commit()
-        LOG.info(f"{analysis_obj.family} - Status set to {status}")
+        LOG.info(f"{analysis_obj.family} - Status set to {status.upper()}")
 
     def add_comment(self, case_id: str, comment: str):
         analysis_obj: Analysis = self.get_latest_analysis(case_id=case_id)
@@ -494,7 +499,7 @@ def query_tower(config_file: str, case_id: str) -> TowerAPI:
         Currently only one tower ID is supported."""
         workflow_id: int = ReadFile.get_content_from_file(
             file_format=FileFormat.YAML, file_path=Path(config_file)
-        ).get(case_id)[0]
+        ).get(case_id)[-1]
         tower_api = TowerAPI(workflow_id=workflow_id)
         if not tower_api.tower_client.meets_requirements:
             raise TowerRequirementsError