Minor fixes

Author: marcelzwiers

bidscoin/bids.py

@@ -1136,11 +1136,8 @@ def __init__(self, yamlfile: Path, folder: Path=templatefolder, plugins: Iterabl
                                 if entitykey not in runitem.bids and entitykey not in ('sub', 'ses'):
                                     LOGGER.info(f"Adding missing {dataformat}>{datatype}>{suffix} bidsmap entity key: {entitykey}")
                                     runitem.bids[entitykey] = ''
-                                if entitykey == 'part' and not isinstance(runitem.bids['part'], list):
-                                    if runitem.bids['part'] in ('', 'mag', 'phase', 'real', 'imag', None):
-                                        runitem.bids['part'] = ['', 'mag', 'phase', 'real', 'imag', ('', 'mag', 'phase', 'real', 'imag').index(runitem.bids['part'] or '')]
-                                    else:
-                                        runitem.bids['part'] = ['', 'mag', 'phase', 'real', 'imag', runitem.bids['part'], 5]
+                                if entitykey == 'part' and not isinstance(runitem.bids['part'], list) and runitem.bids['part'] in ('', 'mag', 'phase', 'real', 'imag', None):
+                                    runitem.bids['part'] = ['', 'mag', 'phase', 'real', 'imag', ('', 'mag', 'phase', 'real', 'imag').index(runitem.bids['part'] or '')]
 
         # Validate the bidsmap entries
         self.check(checks)
@@ -1258,7 +1255,7 @@ def validate(self, 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
-                    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)
+                    for ext in extensions + ['.tsv' if runitem.bids['suffix']=='events' else '.dum']:      # 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

bidscoin/bidseditor.py

@@ -1808,7 +1808,7 @@ def accept_run(self):
         bidsvalid = validrun
         datatype  = self.target_run.datatype
         if not (bids.check_ignore(datatype,self.bidsignore) or bids.check_ignore(bidsname.name,self.bidsignore,'file') or datatype in self.ignoredatatypes):
-            for ext in bids.extensions:     # NB: `ext` used to be '.json', which is more generic (but see https://github.com/bids-standard/bids-validator/issues/2113)
+            for ext in bids.extensions + ['.tsv' if self.target_run.bids['suffix']=='events' else '.dum']:     # 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

bidscoin/bidsmapper.py

@@ -56,8 +56,6 @@ def bidsmapper(sourcefolder: str, bidsfolder: str, bidsmap: str, template: str,
         LOGGER.bcdebug(f"Regular expression metacharacters found in {sesprefix}, this may cause errors later on...")
     if not rawfolder.is_dir():
         raise SystemExit(f"\n[ERROR] Exiting the program because your sourcefolder argument '{sourcefolder}' was not found")
-    if not templatefile.is_file():
-        raise SystemExit(f"\n[ERROR] Exiting the program because your template bidsmap '{templatefile}' was not found")
 
     # Start logging
     if force:
@@ -75,6 +73,8 @@ def bidsmapper(sourcefolder: str, bidsfolder: str, bidsmap: str, template: str,
     bidsmap_old = BidsMap(bidsmapfile,  bidscoinfolder, plugins)
     bidsmapfile = bidsmap_old.filepath
     template    = BidsMap(templatefile, plugins=plugins, checks=(True, True, False))
+    if not template.filepath.is_file():
+        raise SystemExit(f"\n[ERROR] Exiting the program because your template bidsmap '{templatefile}' was not found")
     template.check_template()
 
     # Create the new bidsmap as a copy / bidsmap skeleton with only data types without run-items (i.e. empty lists)

bidscoin/heuristics/bidsmap_bids2bids.yaml

@@ -471,7 +471,7 @@ Nibabel:
       dir: <filename:sub-.*_dir-(.*?)_.*\.nii.*>
       run: <<>>
       echo:
-      part: ['', mag, phase, real, imag, 0]
+      part: <filename:sub-.*_part-(.*?)_.*\.nii.*>
       suffix: asl
     meta: &perf_meta
       ArterialSpinLabelingType: "CASL / PCASL / PASL"
@@ -647,7 +647,7 @@ Nibabel:
       dir: <filename:sub-.*_dir-(.*?)_.*\.nii.*>
       run: <<>>
       chunk: <filename:sub-.*_chunk-(.*?)_.*\.nii.*>
-      part: ['', mag, phase, real, imag, 0]
+      part: <filename:sub-.*_part-(.*?)_.*\.nii.*>
       suffix: epi
     meta: *fmap_meta
   - properties: