Better fix for the bids_validator regression (https://github.com/bids…

…-standard/bids-validator/issues/2113)

bidscoin/bids.py

@@ -47,19 +47,28 @@
 
 # Read the BIDS schema data
 with (schemafolder/'objects'/'datatypes.yaml').open('r') as _stream:
-    bidsdatatypesdef = yaml.load(_stream)                                       # The valid BIDS datatypes, along with their full names and descriptions
+    bidsdatatypesdef = yaml.load(_stream)
+    "The valid BIDS datatypes, along with their full names and descriptions"
 datatyperules = {}
+"The entities that can/should be present for each BIDS data type"
 for _datatypefile in (schemafolder/'rules'/'files'/'raw').glob('*.yaml'):
     with _datatypefile.open('r') as _stream:
-        datatyperules[_datatypefile.stem] = yaml.load(_stream)                  # The entities that can/should be present for each BIDS data type
+        datatyperules[_datatypefile.stem] = yaml.load(_stream)
 with (schemafolder/'objects'/'suffixes.yaml').open('r') as _stream:
-    suffixes = yaml.load(_stream)                                               # The descriptions of the valid BIDS file suffixes
+    suffixes = yaml.load(_stream)
+    "The descriptions of the valid BIDS file suffixes"
 with (schemafolder/'objects'/'entities.yaml').open('r') as _stream:
-    entities = yaml.load(_stream)                                               # The descriptions of the entities present in BIDS filenames
+    entities = yaml.load(_stream)
+    "The descriptions of the entities present in BIDS filenames"
+with (schemafolder/'objects'/'extensions.yaml').open('r') as _stream:
+    extensions = [val['value'] for key,val in yaml.load(_stream).items() if val['value'] not in ('.json','.tsv','.bval','.bvec')]
+    "The possible extensions of BIDS data files"
 with (schemafolder/'rules'/'entities.yaml').open('r') as _stream:
-    entitiesorder = yaml.load(_stream)                                          # The order in which the entities should appear within filenames
+    entitiesorder = yaml.load(_stream)
+    "The order in which the entities should appear within filenames"
 with (schemafolder/'objects'/'metadata.yaml').open('r') as _stream:
-    metafields = yaml.load(_stream)                                             # The descriptions of the valid BIDS metadata fields
+    metafields = yaml.load(_stream)
+    "The descriptions of the valid BIDS metadata fields"
 
 
 class DataSource:
@@ -1093,7 +1102,8 @@ def validate_bidsmap(bidsmap: Bidsmap, level: int=1) -> bool:
                 ignore   = check_ignore(datatype, bidsignore) or check_ignore(bidsname+'.json', bidsignore, 'file')
                 ignore_1 = datatype in ignoretypes or ignore
                 ignore_2 = datatype in ignoretypes
-                bidstest = bids_validator.BIDSValidator().is_bids(f"/sub-{sanitize(dataformat)}/{datatype}/{bidsname}.nii") # NB: This used to be '.json', which is more generic (but see https://github.com/bids-standard/bids-validator/issues/2113)
+                for ext in extensions:      # NB: `ext` used to be '.json', which is more generic (but see https://github.com/bids-standard/bids-validator/issues/2113)
+                    if bidstest := bids_validator.BIDSValidator().is_bids(f"/sub-{sanitize(dataformat)}/{datatype}/{bidsname}{ext}"): break
                 if level==3 or (abs(level)==2 and not ignore_2) or (-2<level<2 and not ignore_1):
                     valid = valid and bidstest
                 if (level==0 and not bidstest) or (level==1 and not ignore_1) or (level==2 and not ignore_2) or level==3:

bidscoin/bidseditor.py

@@ -24,7 +24,7 @@
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[1]))
 from bidscoin import bcoin, bids, bidsversion, check_version, trackusage, bidsmap_template, __version__
-from bidscoin.bids import Bidsmap, Plugin, Run
+from bidscoin.bids import Bidsmap, Plugin, Run, extensions
 
 
 ROW_HEIGHT       = 22
@@ -1532,12 +1532,12 @@ def accept_run(self):
         """Save the changes to the target_bidsmap and send it back to the main window: Finished!"""
 
         # Check if the bidsname is valid
-        bidsname = Path(self.bidsname_textbox.toPlainText())
-        validrun = False not in bids.check_run(self.target_datatype, self.target_run, checks=(False, False, False))[1:3]
+        bidsname  = Path(self.bidsname_textbox.toPlainText())
+        validrun  = False not in bids.check_run(self.target_datatype, self.target_run, checks=(False, False, False))[1:3]
+        bidsvalid = validrun
         if not (bids.check_ignore(self.target_datatype,self.bidsignore) or bids.check_ignore(bidsname.name,self.bidsignore,'file') or self.target_datatype in self.ignoredatatypes):
-            bidsvalid = BIDSValidator().is_bids((Path('/')/self.subid/self.sesid/bidsname).with_suffix('.json').as_posix())
-        else:
-            bidsvalid = validrun
+            for ext in extensions:      # NB: `ext` used to be '.json', which is more generic (but see https://github.com/bids-standard/bids-validator/issues/2113)
+                if bidsvalid := BIDSValidator().is_bids((Path('/')/self.subid/self.sesid/bidsname).with_suffix(ext).as_posix()): break
 
         # If the bidsname is not valid, ask the user if that's OK
         message = ''

bidscoin/plugins/dcm2niix2bids.py

@@ -297,7 +297,7 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> Union[N
         targets  = set()        # -> A store for all fullpath output targets (.nii/.tsv) for this bidsname
 
         # Check if the bidsname is valid
-        bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.json').as_posix()
+        bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.nii').as_posix()
         isbids   = BIDSValidator().is_bids(bidstest)
         if not isbids and not ignore:
             LOGGER.warning(f"The '{bidstest}' output name did not pass the bids-validator test")

bidscoin/plugins/nibabel2bids.py

@@ -222,7 +222,7 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> None:
         target     = (outfolder/bidsname).with_suffix(ext)
 
         # Check if the bidsname is valid
-        bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.json').as_posix()
+        bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.nii').as_posix()
         isbids   = BIDSValidator().is_bids(bidstest)
         if not isbids and not bidsignore:
             LOGGER.warning(f"The '{bidstest}' output name did not pass the bids-validator test")

bidscoin/plugins/spec2nii2bids.py

@@ -231,7 +231,7 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> Union[N
         target     = (outfolder/bidsname).with_suffix('.nii.gz')
 
         # Check if the bidsname is valid
-        bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.json').as_posix()
+        bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.nii').as_posix()
         isbids   = BIDSValidator().is_bids(bidstest)
         if not isbids and not bidsignore:
             LOGGER.warning(f"The '{bidstest}' output name did not pass the bids-validator test")