Fix empty datasource.dataformat attribute values

bidscoin/bids.py

@@ -1274,6 +1274,9 @@ def get_matching_run(self, datasource: DataSource, runtime=False) -> Tuple[RunIt
                             If there is a match, the provenance of the bidsmap entry is returned, otherwise it will be ''
         """
 
+        if not datasource.dataformat and not datasource.has_plugin():
+            LOGGER.bcdebug(f"No dataformat/plugin support found when getting a matching run for: {datasource}")
+
         unknowndatatypes = self.options.get('unknowntypes') or ['unknown_data']
         ignoredatatypes  = self.options.get('ignoretypes') or []
         normaldatatypes  = [dtype.datatype for dtype in self.dataformat(datasource.dataformat).datatypes if dtype not in unknowndatatypes + ignoredatatypes]
@@ -1366,6 +1369,9 @@ def get_run(self, datatype: Union[str, DataType], suffix_idx: Union[int, str], d
                             otherwise an empty dict
         """
 
+        if not datasource.dataformat and not datasource.has_plugin():
+            LOGGER.bcdebug(f"No dataformat/plugin support found when getting a run for: {datasource}")
+
         datatype = str(datatype)
 
         for index, _runitem in enumerate(self.dataformat(datasource.dataformat).datatype(datatype).runitems):

bidscoin/plugins/nibabel2bids.py

@@ -129,7 +129,7 @@ def bidsmapper_plugin(session: Path, bidsmap_new: BidsMap, bidsmap_old: BidsMap,
     for sourcefile in [file for file in session.rglob('*') if has_support(file)]:
 
         # See if we can find a matching run in the old bidsmap
-        datasource = bids.DataSource(sourcefile, plugins, datasource.dataformat)
+        datasource = bids.DataSource(sourcefile, plugins, has_support(sourcefile))
         run, match = bidsmap_old.get_matching_run(datasource)
 
         # If not, see if we can find a matching run in the template
@@ -185,7 +185,7 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> None:
     # Collect the different Nibabel source files for all files in the session
     for source in sourcefiles:
 
-        datasource = bids.DataSource(source, {'nibabel2bids': options})
+        datasource = bids.DataSource(source, {'nibabel2bids': options}, has_support(source))
         run, runid = bidsmap.get_matching_run(datasource, runtime=True)
 
         # Check if we should ignore this run

bidscoin/plugins/spec2nii2bids.py

@@ -123,7 +123,7 @@ def bidsmapper_plugin(session: Path, bidsmap_new: BidsMap, bidsmap_old: BidsMap,
     # Update the bidsmap with the info from the source files
     for sourcefile in [file for file in session.rglob('*') if has_support(file)]:
 
-        datasource = bids.DataSource(sourcefile, plugins)
+        datasource = bids.DataSource(sourcefile, plugins, has_support(sourcefile))
 
         # Input checks
         if datasource.dataformat not in template.dataformats + bidsmap_old.dataformats:
@@ -192,7 +192,7 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[N
     for source in sourcefiles:
 
         # Get a data source, a matching run from the bidsmap
-        datasource = bids.DataSource(source, {'spec2nii2bids': options})
+        datasource = bids.DataSource(source, {'spec2nii2bids': options}, has_support(source))
         run, runid = bidsmap.get_matching_run(datasource, runtime=True)
 
         # Check if we should ignore this run