🙅🏻‍♂️ add REJECTED choice and cli to reject analyses

isabl_cli/api.py

@@ -628,7 +628,7 @@ def patch_analysis_status(analysis, status):
     analysis["status"] = status  # make sure that the analysis status is updated
     _set_analysis_permissions(analysis)
 
-    if status in {"FAILED", "SUCCEEDED", "IN_PROGRESS"}:
+    if status in {"FAILED", "SUCCEEDED", "IN_PROGRESS", "REJECTED"}:
         data["storage_usage"] = utils.get_tree_size(storage_url)
 
     if status == "STARTED":

isabl_cli/app.py

@@ -99,7 +99,7 @@ class AbstractApplication:  # pylint: disable=too-many-public-methods
     # Analyses in these status won't be prepared for submission. To re-rerun SUCCEEDED
     # analyses see unique_analysis_per_individual. To re-rerun failed analyses use
     # either --force or --restart.
-    skip_status = {"FAILED", "FINISHED", "STARTED", "SUBMITTED", "SUCCEEDED"}
+    skip_status = {"FAILED", "FINISHED", "STARTED", "SUBMITTED", "SUCCEEDED", "REJECTED"}
 
     # If any of these errors is raised during the command generation process, the
     # submission will continue. Errors or valdation messages are presented at the end.
@@ -957,7 +957,7 @@ def run_analyses(self, analyses, commit, force, restart, local):
                     api.patch_analysis_status(i, "STAGED")
 
                 # trash analysis and create outdir again
-                elif force and i["status"] not in {"SUCCEEDED", "FINISHED"}:
+                elif force and i["status"] not in {"SUCCEEDED", "FINISHED", "REJECTED"}:
                     system_settings.TRASH_ANALYSIS_STORAGE(i)
                     utils.makedirs(i["storage_url"])
 

isabl_cli/commands.py

@@ -468,3 +468,13 @@ def run_signals(endpoint, filters, signals):
 
     for i in api.get_instances(endpoint, **filters):
         api._run_signals(endpoint, i, signals, raise_error=True, create_record=False)
+
+
+@click.command(hidden=True)
+@options.ANALYSIS_PRIMARY_KEY
+@click.option("--reason", help="Rejection reason. (Will be stored in Analysis.notes)")
+def reject_analysis(key, reason):
+    """Patch an analysis status as REJECTED, providing the rejection reason."""
+    analysis = api.get_instance("analyses", key)
+    api.patch_analysis_status(analysis, "REJECTED")
+    api.patch_instance("analyses", key, notes=reason)

isabl_cli/factories.py

@@ -22,6 +22,7 @@ class ProjectFactory(BaseFactory):
     owner = factory.Sequence(lambda n: f"owner-{n}@test.com")
     principal_investigator = factory.Sequence(lambda n: f"pi-{n}@test.com")
     title = fuzzy.FuzzyText(length=20, chars=string.ascii_lowercase + " ")
+    sharing = {"can_share": [], "can_read": [], "is_public": True}
 
 
 class CenterFactory(BaseFactory):

isabl_cli/options.py

@@ -49,6 +49,7 @@ def _get_experiments(filter_tuples):
             "STARTED",
             "SUBMITTED",
             "SUCCEEDED",
+            "REJECTED",
         ]
     ),
 )

isabl_cli/settings.py

@@ -56,12 +56,13 @@
         "isabl_cli.commands.get_reference",
         "isabl_cli.commands.get_results",
         "isabl_cli.commands.login",
-        "isabl_cli.commands.merge_project_analyses",
         "isabl_cli.commands.merge_individual_analyses",
+        "isabl_cli.commands.merge_project_analyses",
         "isabl_cli.commands.patch_status",
+        "isabl_cli.commands.reject_analysis",
         "isabl_cli.commands.rerun_signals",
-        "isabl_cli.commands.run_web_signals",
         "isabl_cli.commands.run_signals",
+        "isabl_cli.commands.run_web_signals",
     ],
     "EXTRA_RAW_DATA_FORMATS": [],
 }

tests/test_commands.py

@@ -1,6 +1,4 @@
 from click.testing import CliRunner
-import pytest
-import click
 
 from isabl_cli import api
 from isabl_cli import commands
@@ -180,7 +178,7 @@ def test_get_bams():
     assert "/hello/mars" in result.output
 
 
-def test_get_data(tmpdir):
+def test_get_data():
     runner = CliRunner()
     experiment = api.create_instance("experiments", **factories.ExperimentFactory())
     experiment = data.update_storage_url("experiments", experiment.pk)
@@ -287,7 +285,7 @@ def test_run_web_signals():
 
 
 def test_process_finished_tags(tmpdir):
-    # check that a tagged analysis does NOT get processed to FINISHED
+    """Check that a tagged analysis does NOT get processed to FINISHED."""
     analysis = api.create_instance(
         "analyses",
         project_level_analysis=factories.ProjectFactory(),
@@ -310,7 +308,7 @@ def test_process_finished_tags(tmpdir):
 
 
 def test_force_process_finished_tags(tmpdir):
-    # check that a tagged analysis does get processed to FINISHED when forced
+    """Check that a tagged analysis does get processed to FINISHED when forced."""
     analysis = api.create_instance(
         "analyses",
         project_level_analysis=factories.ProjectFactory(),
@@ -324,3 +322,20 @@ def test_force_process_finished_tags(tmpdir):
     print(result.output)
     analysis = api.get_instance("analyses", analysis["pk"])
     assert analysis["status"] == "SUCCEEDED"
+
+
+def test_rejected_analysis(tmpdir):
+    """Check an analysis can be rejected using the command cli."""
+    analysis = api.create_instance(
+        "analyses",
+        status="FINISHED",
+        storage_url=tmpdir.strpath,
+        **factories.AnalysisFactory(ran_by=None),
+    )
+    runner = CliRunner()
+    rejection_reason = "This analysis is FAKE."
+    args = ["--key", analysis["pk"], "--reason", rejection_reason]
+    runner.invoke(commands.reject_analysis, args, catch_exceptions=False)
+    analysis = api.get_instance("analyses", analysis["pk"])
+    assert analysis["status"] == "REJECTED"
+    assert analysis["notes"] == rejection_reason