update test fixtures

tests/fixtures/failed_job_state.json

@@ -208,7 +208,7 @@
         },
         "activity_id": "nmdc:wfmag-11-g7msr323.1",
         "last_status": "Failed",
-        "done": true,
+        "done": false,
         "failed_count": 2,
         "start": "2024-09-16T19:33:32.562412+00:00",
         "end": "2024-09-16T21:52:12.873101+00:00",

tests/fixtures/mags_workflow_state.json

@@ -208,7 +208,7 @@
       },
       "activity_id": "nmdc:wfmag-11-g7msr323.1",
       "last_status": "Succeeded",
-      "done": true,
+      "done": false,
       "failed_count": 0,
       "start": "2024-09-16T19:33:32.562412+00:00",
       "end": "2024-09-16T21:52:12.873101+00:00",

tests/test_watch_nmdc.py

@@ -264,11 +264,13 @@ def test_job_manager_prepare_and_cache_new_job_force(site_config, initial_state_
 
 
 def test_job_manager_get_finished_jobs(site_config, initial_state_file, fixtures_dir):
+    # Mock the URL and response
+
     # Arrange - initial state has 1 failure and is not done
     fh = FileHandler(site_config, initial_state_file)
     jm = JobManager(site_config, fh)
 
-    # Add a job to the cache - mags is done and successful
+    # Add a finished job: finished job is not done, but has a last_status of Succeeded
     new_job_state = json.load(open(fixtures_dir / "mags_workflow_state.json"))
     assert new_job_state
     new_job = WorkflowJob(site_config, new_job_state)
@@ -295,22 +297,29 @@ def test_job_manager_get_finished_jobs(site_config, initial_state_file, fixtures
 
 
 def test_job_manager_process_successful_job(site_config, initial_state_file, fixtures_dir):
-    # Arrange
-    fh = FileHandler(site_config, initial_state_file)
-    jm = JobManager(site_config, fh)
-    new_job_state = json.load(open(fixtures_dir / "mags_workflow_state.json"))
-    assert new_job_state
-    new_job = WorkflowJob(site_config, new_job_state)
-    jm.job_cache.append(new_job)
-    # Act
-    db = jm.process_successful_job(new_job)
-    # Assert
-    assert db
-    assert isinstance(db, Database)
-    assert new_job.done
-    assert new_job.job_status == "Succeeded"
-    # cleanup
-    jm.job_cache = []
+    # mock job.job.get_job_metadata - use fixture cromwell/succeded_metadata.json
+    job_metadata = json.load(open(fixtures_dir / "mags_job_metadata.json"))
+    with patch("nmdc_automation.workflow_automation.wfutils.CromwellRunner.get_job_metadata") as mock_get_metadata:
+        mock_get_metadata.return_value = job_metadata
+
+
+
+        # Arrange
+        fh = FileHandler(site_config, initial_state_file)
+        jm = JobManager(site_config, fh)
+        new_job_state = json.load(open(fixtures_dir / "mags_workflow_state.json"))
+        assert new_job_state
+        new_job = WorkflowJob(site_config, new_job_state)
+        jm.job_cache.append(new_job)
+        # Act
+        db = jm.process_successful_job(new_job)
+        # Assert
+        assert db
+        assert isinstance(db, Database)
+        assert new_job.done
+        assert new_job.job_status == "Succeeded"
+        # cleanup
+        jm.job_cache = []
 
 
 def test_job_manager_process_failed_job(site_config, initial_state_file, fixtures_dir):

tests/test_wfutils.py

@@ -13,8 +13,18 @@
 import requests
 import tempfile
 from unittest import mock
+import importlib.resources
+import yaml
+from functools import lru_cache
+import linkml.validator
+from linkml_runtime.dumpers import yaml_dumper
 
 
+@lru_cache(maxsize=None)
+def get_nmdc_materialized():
+    with importlib.resources.open_text("nmdc_schema", "nmdc_materialized_patterns.yaml") as f:
+        return yaml.safe_load(f)
+
 
 def test_workflow_job(site_config, fixtures_dir):
     workflow_state = json.load(open(fixtures_dir / "mags_workflow_state.json"))
@@ -75,9 +85,6 @@ def test_cromwell_job_runner_get_job_metadata(site_config, fixtures_dir, mock_cr
     assert job_runner.metadata == metadata
 
 
-
-
-
 def test_workflow_job_as_workflow_execution_dict(site_config, fixtures_dir):
     workflow_state = json.load(open(fixtures_dir / "mags_workflow_state.json"))
     job_metadata = json.load(open(fixtures_dir / "mags_job_metadata.json"))
@@ -275,8 +282,7 @@ def test_workflow_job_data_objects_and_execution_record_mags(site_config, fixtur
     assert data_objects
     for data_object in data_objects:
         assert isinstance(data_object, DataObject)
-    wfe_dict = job.make_workflow_execution_record(data_objects)
-    wfe = workflow_process_factory(wfe_dict)
+    wfe = job.make_workflow_execution(data_objects)
     assert isinstance(wfe, MagsAnalysis)
     # attributes from final_stats_json
     assert wfe.mags_list
@@ -286,7 +292,9 @@ def test_workflow_job_data_objects_and_execution_record_mags(site_config, fixtur
         assert mag.eukaryotic_evaluation
         assert isinstance(mag.eukaryotic_evaluation, EukEval)
         assert mag.eukaryotic_evaluation.completeness
+        assert isinstance(mag.eukaryotic_evaluation.completeness, float)
         assert mag.eukaryotic_evaluation.contamination
+        assert isinstance(mag.eukaryotic_evaluation.contamination, float)
         assert mag.eukaryotic_evaluation.ncbi_lineage
         assert mag.eukaryotic_evaluation.ncbi_lineage
     # check that the other final_stats props are there