update tests of bids command

bagel/cli.py

@@ -338,8 +338,7 @@ def bids(
  hasFilePath=session_path,
  hasAcquisition=image_list,
  )
-
- existing_subject.hasSession.append(new_imaging_session)
+ existing_subject.hasSession.append(new_imaging_session)
 
  context = generate_context()
  merged_dataset = {**context, **jsonld_dataset.dict(exclude_none=True)}

bagel/tests/test_cli_bids.py

@@ -36,14 +36,14 @@ def test_bids_valid_inputs_run_successfully(
  ).exists(), "The pheno_bids.jsonld output was not created."
 
 
-def test_bids_sessions_have_correct_labels(
+def test_imaging_sessions_have_expected_labels(
  runner,
  test_data_upload_path,
  bids_synthetic,
  default_pheno_bids_output_path,
  load_test_json,
 ):
- """Check that sessions added to pheno_bids.jsonld have the expected labels."""
+ """Check that the imaging sessions in the JSONLD output have the expected session labels."""
  runner.invoke(
  bagel,
  [
@@ -57,21 +57,77 @@ def test_bids_sessions_have_correct_labels(
  ],
  )
 
- pheno_bids = load_test_json(default_pheno_bids_output_path)
- for sub in pheno_bids["hasSamples"]:
+ output = load_test_json(default_pheno_bids_output_path)
+
+ for sub in output["hasSamples"]:
+ # all subjects in the BIDS synthetic dataset are expected to have 4 sessions total
  assert 4 == len(sub["hasSession"])
 
- imaging_session = [
- ses
+ imaging_ses_labels = [
+ ses["hasLabel"]
  for ses in sub["hasSession"]
  if ses["schemaKey"] == "ImagingSession"
  ]
- assert 2 == len(imaging_session)
 
- # We also need to make sure that we do not have duplicate imaging session labels
- assert set(["ses-01", "ses-02"]) == set(
- [ses["hasLabel"] for ses in imaging_session]
- )
+ assert sorted(imaging_ses_labels) == ["ses-01", "ses-02"]
+
+
+@pytest.mark.parametrize(
+ "jsonld_path,expected_sessions_with_acq_and_pipe_metadata",
+ [
+ ("example_synthetic.jsonld", 0),
+ (
+ "pheno-derivatives-output/example_synthetic_pheno-derivatives.jsonld",
+ 3,
+ ),
+ ],
+)
+def test_imaging_sessions_have_expected_metadata(
+ runner,
+ test_data_upload_path,
+ bids_synthetic,
+ default_pheno_bids_output_path,
+ load_test_json,
+ jsonld_path,
+ expected_sessions_with_acq_and_pipe_metadata,
+):
+ """
+ Check that the JSONLD output contains the expected total number of imaging sessions with
+ acquisition and completed pipeline metadata, based on whether a phenotypic-only JSONLD or
+ JSONLD with both phenotypic and processing pipeline metadata is provided as input.
+ """
+ runner.invoke(
+ bagel,
+ [
+ "bids",
+ "--jsonld-path",
+ test_data_upload_path / jsonld_path,
+ "--bids-dir",
+ bids_synthetic,
+ "--output",
+ default_pheno_bids_output_path,
+ ],
+ )
+
+ output = load_test_json(default_pheno_bids_output_path)
+
+ sessions_with_acq_metadata = []
+ sessions_with_acq_and_pipe_metadata = []
+ for sub in output["hasSamples"]:
+ for ses in sub["hasSession"]:
+ if (
+ ses["schemaKey"] == "ImagingSession"
+ and ses.get("hasAcquisition") is not None
+ ):
+ sessions_with_acq_metadata.append(ses)
+ if ses.get("hasCompletedPipeline") is not None:
+ sessions_with_acq_and_pipe_metadata.append(ses)
+
+ assert len(sessions_with_acq_metadata) == 10
+ assert (
+ len(sessions_with_acq_and_pipe_metadata)
+ == expected_sessions_with_acq_and_pipe_metadata
+ )
 
 
 def test_bids_data_with_sessions_have_correct_paths(