Get tests running.

Author: tsalo

cubids/tests/test_apply.py

@@ -42,7 +42,6 @@
         },
     ],
 }
-
 bidsuri_longitudinal_intendedfor = {
     '01': [
         {
@@ -81,11 +80,85 @@
         },
     ],
 }
+relpath_cs_intendedfor = {
+    '01': [
+        {
+            'anat': [{'suffix': 'T1w', 'metadata': {'EchoTime': 1}}],
+            'fmap': [
+                {
+                    'dir': 'AP',
+                    'suffix': 'epi',
+                    'metadata': {
+                        'IntendedFor': [
+                            'dwi/sub-01_dir-AP_run-01_dwi.nii.gz'
+                        ]
+                    }
+                },
+                {
+                    'dir': 'PA',
+                    'suffix': 'epi',
+                    'metadata': {
+                        'IntendedFor': [
+                            'dwi/sub-01_dir-AP_run-01_dwi.nii.gz'
+                        ]
+                    }
+                },
+            ],
+            'dwi': [
+                {
+                    'dir': 'AP',
+                    'run': '01',
+                    'suffix': 'dwi',
+                    'metadata': {
+                        'RepetitionTime': 0.8,
+                    },
+                }
+            ],
+        },
+    ],
+}
+bidsuri_cs_intendedfor = {
+    '01': [
+        {
+            'anat': [{'suffix': 'T1w', 'metadata': {'EchoTime': 1}}],
+            'fmap': [
+                {
+                    'dir': 'AP',
+                    'suffix': 'epi',
+                    'metadata': {
+                        'IntendedFor': [
+                            'bids::sub-01/dwi/sub-01_dir-AP_run-01_dwi.nii.gz'
+                        ]
+                    }
+                },
+                {
+                    'dir': 'PA',
+                    'suffix': 'epi',
+                    'metadata': {
+                        'IntendedFor': [
+                            'bids::sub-01/dwi/sub-01_dir-AP_run-01_dwi.nii.gz'
+                        ]
+                    }
+                },
+            ],
+            'dwi': [
+                {
+                    'dir': 'AP',
+                    'run': '01',
+                    'suffix': 'dwi',
+                    'metadata': {
+                        'RepetitionTime': 0.8,
+                    },
+                }
+            ],
+        },
+    ],
+}
 
 summary_data = {
     'RenameEntitySet': [
         None,
-        "acquisition-VARIANT_datatype-dwi_direction-AP_run-01_suffix-dwi",
+        "acquisition-VAR_datatype-dwi_direction-AP_run-01_suffix-dwi",
         None,
         None
     ],
@@ -107,14 +180,14 @@
     'ParamGroup': [1, 1, 1, 1]
 }
 
-files_data = {
+files_data_longitudinal = {
     'ParamGroup': [1, 1, 1, 1],
     'EntitySet': [
         "datatype-anat_suffix-T1w",
         "datatype-dwi_direction-AP_run-01_suffix-dwi",
         "datatype-fmap_direction-AP_fmap-epi_suffix-epi",
         "datatype-fmap_direction-PA_fmap-epi_suffix-epi"
-    ], 
+    ],
     'FilePath': [
         "/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz",
         "/sub-01/ses-01/dwi/sub-01_ses-01_dir-AP_run-01_dwi.nii.gz",
@@ -129,20 +202,46 @@
     ]
 }
 
+files_data_cs = {
+    'ParamGroup': [1, 1, 1, 1],
+    'EntitySet': [
+        "datatype-anat_suffix-T1w",
+        "datatype-dwi_direction-AP_run-01_suffix-dwi",
+        "datatype-fmap_direction-AP_fmap-epi_suffix-epi",
+        "datatype-fmap_direction-PA_fmap-epi_suffix-epi"
+    ],
+    'FilePath': [
+        "/sub-01/anat/sub-01_T1w.nii.gz",
+        "/sub-01/dwi/sub-01_dir-AP_run-01_dwi.nii.gz",
+        "/sub-01/fmap/sub-01_dir-AP_epi.nii.gz",
+        "/sub-01/fmap/sub-01_dir-PA_epi.nii.gz"
+    ],
+    'KeyParamGroup': [
+        "datatype-anat_suffix-T1w__1",
+        "datatype-dwi_direction-AP_run-01_suffix-dwi__1",
+        "datatype-fmap_direction-AP_fmap-epi_suffix-epi__1",
+        "datatype-fmap_direction-PA_fmap-epi_suffix-epi__1"
+    ]
+}
+
 @pytest.mark.parametrize(
     ('name', 'skeleton', 'summary_data', 'files_data', 'expected'),
     [
-        ('relpath_longitudinal', relpath_longitudinal_intendedfor, summary_data, files_data, 'pass'),
-        ('bidsuri_longitudinal', bidsuri_longitudinal_intendedfor, summary_data, files_data, 'error'),
+        ('relpath_longitudinal', relpath_longitudinal_intendedfor, summary_data, files_data_longitudinal, 'ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-001_dwi.nii.gz'),
+        ('bidsuri_longitudinal', bidsuri_longitudinal_intendedfor, summary_data, files_data_longitudinal, 'bids::sub-01/ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-001_dwi.nii.gz'),
+        ('relpath_cs', relpath_cs_intendedfor, summary_data, files_data_cs, 'dwi/sub-01_acq-VAR_dir-AP_run-001_dwi.nii.gz'),
+        ('bidsuri_cs', bidsuri_cs_intendedfor, summary_data, files_data_cs, 'bids::sub-01/dwi/sub-01_acq-VAR_dir-AP_run-001_dwi.nii.gz'),
     ],
 )
 def test_cubids_apply_intendedfor(tmpdir, name, skeleton, summary_data, files_data, expected):
     """Test cubids apply with different IntendedFor types."""
+    import json
+
     from cubids.workflows import apply
 
     # Generate a BIDS dataset
-    bids_dir = str(tmpdir / name)
-    generate_bids_skeleton(bids_dir, skeleton)
+    bids_dir = tmpdir / name
+    generate_bids_skeleton(str(bids_dir), skeleton)
 
     # Create a summary tsv
     summary_tsv = tmpdir / 'summary.tsv'
@@ -155,22 +254,22 @@ def test_cubids_apply_intendedfor(tmpdir, name, skeleton, summary_data, files_da
 
     # Run cubids apply
     apply(
-        bids_dir=bids_dir,
+        bids_dir=str(bids_dir),
         use_datalad=False,
         acq_group_level='subject',
         config=None,
         edited_summary_tsv=summary_tsv,
         files_tsv=files_tsv,
         new_tsv_prefix=None,
-        container=False,
+        container=None,
     )
-
-    # Check the results
-    if expected == 'pass':
-        # Look at the IntendedFor in the renamed files and it should be correct
-        assert True
-    elif expected == 'error':
-        # Look at the IntendedFor in the renamed files and it should NOT be correct
-        assert False
+    if 'longitudinal' in name:
+        fmap_json = bids_dir / 'sub-01/ses-01/fmap/sub-01_ses-01_dir-AP_epi.json'
     else:
-        raise ValueError(f'Unknown expected value: {expected}')
+        fmap_json = bids_dir / 'sub-01/fmap/sub-01_dir-AP_epi.json'
+
+    with open(fmap_json) as f:
+        metadata = json.load(f)
+
+    # XXX: Should not have extra leading zero in run entity, but that's a known bug.
+    assert metadata['IntendedFor'] == [expected]

cubids/workflows.py

@@ -467,7 +467,7 @@ def apply(
             str(new_tsv_prefix),
             raise_on_error=False,
         )
-        sys.exit(0)
+        return
 
     # Run it through a container
     container_type = _get_container_type(container)