Merge pull request #114 from PennLINC/accept-string-IntendedFor

Accept string intended for

bond/bond.py

@@ -5,6 +5,7 @@
 import bids.layout
 import json
 import csv
+import os
 from pathlib import Path
 from bids.layout import parse_file_entities
 from bids.utils import listify
@@ -26,7 +27,7 @@ class BOnD(object):
 
     def __init__(self, data_root, use_datalad=False, grouping_config=None):
 
-        self.path = data_root
+        self.path = os.path.abspath(data_root)
         self._layout = None
         self.keys_files = {}
         self.fieldmaps_cached = False
@@ -420,14 +421,27 @@ def change_filename(self, filepath, entities):
             data = json_file.get_dict()
 
             if 'IntendedFor' in data.keys():
-                for item in data['IntendedFor']:
-                    if item in _get_intended_for_reference(filepath):
-
-                        # remove old filename
-                        data['IntendedFor'].remove(item)
-                        # add new filename
-                        data['IntendedFor'].append(_get_intended_for_reference
-                                                   (new_path))
+                # check if IntendedFor field is a str or list
+                if isinstance(data['IntendedFor'], str):
+                    if data['IntendedFor'] == \
+                            _get_intended_for_reference(filepath):
+                        # replace old filename with new one (overwrite string)
+                        data['IntendedFor'] = \
+                                _get_intended_for_reference(new_path)
+
+                        # update the json with the new data dictionary
+                        _update_json(json_file.path, data)
+
+                if isinstance(data['IntendedFor'], list):
+                    for item in data['IntendedFor']:
+                        if item in _get_intended_for_reference(filepath):
+
+                            # remove old filename
+                            data['IntendedFor'].remove(item)
+                            # add new filename
+                            data['IntendedFor'].append(
+                                    _get_intended_for_reference(new_path))
+
                         # update the json with the new data dictionary
                         _update_json(json_file.path, data)
 
@@ -517,13 +531,21 @@ def _purge_associations(self, scans):
             # remove scan references in the IntendedFor
 
             if 'IntendedFor' in data.keys():
-                for item in data['IntendedFor']:
-                    if item in if_scans:
-                        data['IntendedFor'].remove(item)
-
+                # check if IntendedFor field value is a list or a string
+                if isinstance(data['IntendedFor'], str):
+                    if data['IntendedFor'] in if_scans:
+                        data['IntendedFor'] = []
                         # update the json with the new data dictionary
                         _update_json(json_file.path, data)
 
+                if isinstance(data['IntendedFor'], list):
+                    for item in data['IntendedFor']:
+                        if item in if_scans:
+                            data['IntendedFor'].remove(item)
+
+                            # update the json with the new data dictionary
+                            _update_json(json_file.path, data)
+
         # save IntendedFor purges so that you can datalad run the
         # remove association file commands on a clean dataset
         if self.use_datalad:

bond/testdata/complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.json

@@ -1,7 +1,6 @@
 {
-  "IntendedFor": [
-    "ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz"
-  ],
+  "IntendedFor":
+    "ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz",
   "AcquisitionMatrixPE": 64,
   "AcquisitionNumber": 1,
   "BaseResolution": 64,

tests/test_bond.py

@@ -115,23 +115,35 @@ def test_purge_no_datalad(tmp_path):
     json_name = data_root / "complete" / "sub-03" / "ses-phdiff" \
         / "func" / "sub-03_ses-phdiff_task-rest_bold.json"
     scans.append(scan_name)
-    purge_path = str(tmp_path / "purge_scans.txt")
+    scans.append(data_root / "complete" / "sub-01" / "ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz")
 
+    # create and save .txt with list of scans
+    purge_path = str(tmp_path / "purge_scans.txt")
     with open(purge_path, 'w') as filehandle:
         for listitem in scans:
             filehandle.write('%s\n' % listitem)
     bod = BOnD(data_root / "complete", use_datalad=False)
-    #bod.datalad_save()
 
-    #assert bod.is_datalad_clean()
     assert Path(scan_name).exists()
     assert Path(json_name).exists()
 
-    # create and save .txt with list of scans
+    # Check that IntendedFor purge worked
+    with open(str(data_root / "complete" / "sub-01" / "ses-phdiff" / "fmap" / "sub-01_ses-phdiff_acq-v4_phasediff.json")) as f:
+        j_dict = json.load(f)
+
+    assert "ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz" in j_dict.values()
+    assert isinstance(j_dict['IntendedFor'], str)
+    # PURGE
     bod.purge(purge_path)
 
+    with open(str(data_root / "complete" / "sub-01" / "ses-phdiff" / "fmap" / "sub-01_ses-phdiff_acq-v4_phasediff.json")) as f:
+        purged_dict = json.load(f)
+
     assert not Path(scan_name).exists()
     assert not Path(json_name).exists()
+    assert "ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz" not in purged_dict.values()
+    assert isinstance(purged_dict['IntendedFor'], list)
+    assert purged_dict['IntendedFor'] == []
 
 def test_purge(tmp_path):
     data_root = get_data(tmp_path)
@@ -926,6 +938,7 @@ def test_validator(tmp_path):
     # test the validator in valid dataset
     call = build_validator_call(str(data_root) + "/complete")
     ret = run_validator(call)
+    print(ret)
 
     assert ret.returncode == 0