Bugfix for random sorting of the unknowntypes (set() -> list())

bidscoin/bids.py

@@ -936,10 +936,10 @@ def __init__(self, yamlfile: Path, folder: Path=templatefolder, plugins: Iterabl
         bidsignorefile = folder.parents[1]/'.bidsignore'
         if bidsignorefile.is_file():
             self.options['bidsignore'] = list(set(list(self.options['bidsignore']) + bidsignorefile.read_text().splitlines()))
-        self.options['bidsignore']     = list(set(self.options.get('bidsignore')    or []))
-        self.options['unknowntypes']   = list(set(self.options.get('unknowntypes')  or []))
-        self.options['ignoretypes']    = list(set(self.options.get('ignoretypes')   or []))
-        self.options['notderivative']  = list(set(self.options.get('notderivative') or []))
+        self.options['bidsignore']     = sorted(set(self.options.get('bidsignore'))) or []
+        self.options['unknowntypes']   = self.options.get('unknowntypes')  or []
+        self.options['ignoretypes']    = self.options.get('ignoretypes')   or []
+        self.options['notderivative']  = self.options.get('notderivative') or []
 
         # Make sure we get a proper plugin options and dataformat sections (use plugin default bidsmappings when a template bidsmap is loaded)
         if plugins:
@@ -1536,7 +1536,7 @@ def unpack(sesfolder: Path, wildcard: str='', workfolder: Path='', _subprefix: U
     :param wildcard:    A glob search pattern to select the tarball/zipped files (leave empty to skip unzipping)
     :param workfolder:  A root folder for temporary data
     :param _subprefix:  A pytest helper variable that is passed to dicomsort.sortsessions(args, subprefix=_subprefix)
-    :return:            Either ([unpacked and sorted session folders], True), or ([sourcefolder], False)
+    :return:            Either ({a set of unpacked session folders}, True), or ({sourcefolder}, False)
     """
 
     # Search for zipped/tarball files
@@ -2560,7 +2560,7 @@ def updatemetadata(datasource: DataSource, targetmeta: Path, usermeta: Meta, ext
 
     # Add the source metadata to the metadict or copy it over
     if sourcemeta.name:
-        for ext in set(extensions):
+        for ext in extensions:
             for sourcefile in sourcemeta.parent.glob(sourcemeta.with_suffix('').with_suffix(ext).name):
                 LOGGER.verbose(f"Copying source data from: '{sourcefile}''")
 

bidscoin/utilities/dicomsort.py

@@ -149,7 +149,7 @@ def sortsessions(sourcefolder: Path, subprefix: Union[str,None]='', sesprefix: s
     :param recursive:    Boolean to search for DICOM files recursively in a session folder
     :param force:        Sort the DICOM data even the DICOM fields of the folder/name scheme are not in the data
     :param dryrun:       Boolean to just display the action
-    :return:             List of sorted sessions
+    :return:             A set of sessions
     """
 
     # Input checking

tests/conftest.py

@@ -21,6 +21,7 @@ def raw_dicomdir(tmp_path_factory):
     dicomsort.sortsessions(raw/'DICOMDIR', None)                        # The bidsmapper/coiner are NOT picking up the multi-subject DICOMDIR data properly :-(
     dicomfile = sorted((raw/'Doe^Peter'/'03-Brain'/'002-TSC RF FAST PILOT/').iterdir())[0]   # Make sure this is the first file
     with dicomfile.with_suffix('.json').open('w') as sidecar:
+        print(f"Saving extended metadata file: {dicomfile.with_suffix('.json')}")           # = raw_dicomdir0/Doe^Peter/03-Brain/002-TSC RF FAST PILOT/4950.json
         json.dump({'SeriesDescription': 'TestExtAtrributes',  'Comment': 'TestExtComment'}, sidecar)
     return raw
 

tests/test_bidscoiner.py

@@ -1,6 +1,7 @@
 import os
 import json
 from bidscoin import bcoin, bidsmapper, bidscoiner, bidsmap_template, __version__
+from bidscoin.bids import BidsMap
 from duecredit.io import load_due, DUECREDIT_FILE
 
 bcoin.setup_logging()
@@ -14,8 +15,11 @@ def test_bidscoiner(raw_dicomdir, bids_dicomdir, bidsmap_dicomdir):
         except Exception:
             pass
     bidscoiner.bidscoiner(raw_dicomdir, bids_dicomdir)
-    logs     = (bidsmap_dicomdir.parent/'bidscoiner.errors').read_text()
-    sidecars = sorted((bids_dicomdir/'sub-Peter'/'ses-03Brain'/'extra_data').glob('*TestExtAtrributes*.json'))
+    logs    = (bidsmap_dicomdir.parent/'bidscoiner.errors').read_text()
+    sidecar = sorted((bids_dicomdir/'sub-Peter'/'ses-03Brain').rglob('*TestExtAtrributes*.json'))[0]
+    bidsmap = BidsMap(bidsmap_dicomdir)
+    assert bidsmap.options['unknowntypes'][-1]           == 'extra_data'
+    assert sidecar.relative_to(bids_dicomdir).as_posix() == 'sub-Peter/ses-03Brain/extra_data/sub-Peter_ses-03Brain_acq-TSCRFFASTPILOTi00001_mod-TestExtAtrributes_GR.json'
     try:
         (bidsmap_dicomdir.parent/'bidscoiner.errors').unlink(missing_ok=True)
     except Exception:
@@ -27,7 +31,7 @@ def test_bidscoiner(raw_dicomdir, bids_dicomdir, bidsmap_dicomdir):
     assert (bids_dicomdir/'sub-Peter'/'ses-01').is_dir()
     assert (bids_dicomdir/'sub-Peter'/'ses-04BrainMRA').is_dir()
     assert len(list(bids_dicomdir.rglob('*.nii*'))) > 3             # Exact number (10) is a bit arbitrary (depends on what dcm2niix can convert)
-    with sidecars[0].open('r') as json_fid:
+    with sidecar.open('r') as json_fid:
         metadict = json.load(json_fid)
     assert metadict.get('ProtocolName')      == 'T/S/C RF FAST PILOT'
     assert metadict.get('SeriesDescription') == 'TestExtAtrributes'
@@ -45,5 +49,6 @@ def test_bidscoiner(raw_dicomdir, bids_dicomdir, bidsmap_dicomdir):
 
 
 # def test_addmetadata(bids_dicomdir, bidsmap_dicomdir):
-#     bidsmap, _ = bids.load_bidsmap(bidsmap_dicomdir)
+#     """WIP"""
+#     bidsmap = BidsMap(bidsmap_dicomdir)
 #     bidscoiner.addmetadata(bids_dicomdir/'sub-something'/'ses-else', '*', '*')

tests/test_bidsmapper.py

@@ -1,7 +1,6 @@
 import pytest
 import re
 from bidscoin import bcoin, bidsmapper, bidsmap_template
-from pathlib import Path
 
 bcoin.setup_logging()