Fix bidsmap filepath resolving

bidscoin/bids.py

@@ -876,7 +876,7 @@ def __init__(self, yamlfile: Path, folder: Path=templatefolder, plugins: Iterabl
         has precedence over folder and bidsmap.yaml has precedence over the bidsmap_template.
 
         :param yamlfile:    The full pathname or basename of the bidsmap yaml-file
-        :param folder:      Used when yamlfile=basename and not in the pwd: yamlfile is then assumed to be in the (bidscoin)folder. A bidsignore file in folder will be added to the bidsmap bidsignore items
+        :param folder:      Used when yamlfile=basename and not in the pwd: yamlfile is then assumed to be in the (bids/code/bidscoin)folder. A bidsignore file in folder will be added to the bidsmap bidsignore items
         :param plugins:     List of plugins to be used (with default options, overrules the plugin list in the study/template bidsmaps). Leave empty to use all plugins in the bidsmap
         :param checks:      Booleans to check if all (bidskeys, bids-suffixes, bids-values) in the run are present according to the BIDS schema specifications
         """
@@ -893,8 +893,7 @@ def __init__(self, yamlfile: Path, folder: Path=templatefolder, plugins: Iterabl
             yamlfile = yamlfile.with_suffix('.yaml')                # Add a standard file-extension if needed
         if len(yamlfile.parents) == 1 and not yamlfile.is_file():
             yamlfile = folder/yamlfile                              # Get the full path to the bidsmap yaml-file
-        yamlfile = yamlfile.resolve()
-        self.filepath = yamlfile if yamlfile.is_file() else Path()
+        self.filepath = yamlfile = yamlfile.resolve()
         """The full path to the bidsmap yaml-file"""
         if not yamlfile.is_file():
             if yamlfile.name: LOGGER.info(f"No bidsmap file found: {yamlfile}")

bidscoin/bidsapps/fixmeta.py

@@ -54,7 +54,7 @@ def fixmeta(bidsfolder: str, pattern: str, metadata: dict, participant: list, bi
 
     # Load the bidsmap data (-> plugins)
     bidsmap = bids.BidsMap(Path(bidsmap or 'bidsmap.yaml'), bidsdir/'code'/'bidscoin', checks=(False, False, False))
-    if not bidsmap.filepath:
+    if not bidsmap.filepath.is_file():
         bidsmap = bids.BidsMap(bidsmap_template, checks=(False, False, False))
     plugins  = bidsmap.plugins
     provdata = bids.bidsprov(bidsdir)

bidscoin/bidseditor.py

@@ -85,7 +85,7 @@ def __init__(self, bidsfolder: Path, input_bidsmap: BidsMap, template_bidsmap: B
             self.setWindowIcon(QtGui.QIcon(str(BIDSCOIN_ICON)))
             self.set_menu_statusbar()
 
-        if not input_bidsmap.filepath.name:
+        if not input_bidsmap.filepath.is_file():
             filename, _ = QFileDialog.getOpenFileName(self, 'Open a bidsmap file', str(bidsfolder), 'YAML Files (*.yaml *.yml);;All Files (*)')
             if filename:
                 input_bidsmap = BidsMap(Path(filename))
@@ -868,7 +868,7 @@ def save_bidsmap(self):
         """Check and save the bidsmap to file"""
 
         for dataformat in self.dataformats:
-            if 'fmap' in self.output_bidsmap.dataformat(dataformat):
+            if 'fmap' in self.output_bidsmap.dataformat(dataformat).datatypes:
                 for runitem in self.output_bidsmap.dataformat(dataformat).datatype('fmap').runitems:
                     if not (runitem.meta.get('B0FieldSource') or runitem.meta.get('B0FieldIdentifier') or runitem.meta.get('IntendedFor')):
                         LOGGER.warning(f"B0FieldIdentifier/IntendedFor fieldmap value is empty for {dataformat} run-item: {runitem}")

bidscoin/bidsmapper.py

@@ -73,17 +73,18 @@ def bidsmapper(sourcefolder: str, bidsfolder: str, bidsmap: str, template: str,
 
     # Get the heuristics for filling the new bidsmap (NB: plugins are stored in the bidsmaps)
     bidsmap_old = BidsMap(bidsmapfile,  bidscoinfolder, plugins)
+    bidsmapfile = bidsmap_old.filepath
     template    = BidsMap(templatefile, plugins=plugins, checks=(True, True, False))
     template.check_template()
 
     # Create the new bidsmap as a copy / bidsmap skeleton with only data types without run-items (i.e. empty lists)
-    if force and bidsmap_old.filepath.name:
+    if force and bidsmap_old.filepath.is_file():
         LOGGER.info(f"Deleting previous bidsmap: {bidsmap_old.filepath}")
         bidsmap_old.filepath.unlink()
         bidsmap_old.filepath = Path()
-    bidsmap_new          = copy.deepcopy(bidsmap_old if bidsmap_old.filepath.name else template)
+    bidsmap_new          = copy.deepcopy(bidsmap_old if bidsmap_old.filepath.is_file() else template)
     bidsmap_new.delete_runs()
-    bidsmap_new.filepath = bidsmapfile.resolve()
+    bidsmap_new.filepath = bidsmapfile
     template.options     = bidsmap_new.options      # Always use the options of the new bidsmap
     template.plugins     = bidsmap_new.plugins      # Always use the plugins of the new bidsmap
     if unzip:
@@ -95,7 +96,7 @@ def bidsmapper(sourcefolder: str, bidsfolder: str, bidsmap: str, template: str,
     subprefix, sesprefix = setprefix(bidsmap_new, subprefix, sesprefix, rawfolder, update = not no_update)
 
     # Start with an empty skeleton if we don't have an old bidsmap (due to loading failure or deletion by force)
-    if not bidsmap_old.filepath.name:
+    if not bidsmap_old.filepath.is_file():
         bidsmap_old = copy.deepcopy(bidsmap_new)
 
     # Import the data scanning plugins
@@ -156,7 +157,7 @@ def bidsmapper(sourcefolder: str, bidsfolder: str, bidsmap: str, template: str,
         mainwin = bidseditor.MainWindow(bidsfolder, bidsmap_new, template)
         mainwin.show()
 
-        if not bidsmap_new.filepath.name or not uptodate:
+        if not bidsmap_new.filepath.is_file() or not uptodate:
             messagebox = QMessageBox(mainwin)
             messagebox.setText(f"The bidsmapper has finished scanning {rawfolder}\n\n"
                                f"Please carefully check all the different BIDS output names "

bidscoin/utilities/bidsparticipants.py

@@ -84,7 +84,7 @@ def bidsparticipants(sourcefolder: str, bidsfolder: str, keys: list, bidsmap: st
 
     # Get the bidsmap sub-/ses-prefix from the bidsmap YAML-file
     bidsmap = BidsMap(Path(bidsmap), bidsfolder/'code'/'bidscoin', checks=(False, False, False))
-    if not bidsmap.filepath.name:
+    if not bidsmap.filepath.is_file():
         LOGGER.info('Make sure to run "bidsmapper" first, exiting now')
         return
     subprefix = bidsmap.options['subprefix']