First (non-working) version of the new BidsMap, Format and Datatype c…

…lasses

bidscoin/bcoin.py

@@ -443,7 +443,7 @@ def test_plugin(plugin: Union[Path,str], options: dict) -> int:
     Performs runtime tests of the plug-in
 
     :param plugin:  The name of the plugin that is being tested
-    :param options: A dictionary with the plugin options, e.g. taken from the bidsmap['Options']['plugins'][plugin.stem]
+    :param options: A dictionary with the plugin options, e.g. taken from the bidsmap.plugins[plugin.stem]
     :return:        The result of the plugin test routine (e.g. 0 if it passed or 1 if there was a general plug-in error)
     """
 
@@ -493,12 +493,12 @@ def test_bidsmap(bidsmapfile: str):
     bidsmapfile = Path(bidsmapfile)
     if bidsmapfile.is_dir():
         bidsmapfile = bidsmapfile/'code'/'bidscoin'/'bidsmap.yaml'
-    bidsmap, _ = bids.load_bidsmap(bidsmapfile, checks=(True, True, True))
+    bidsmap = bids.BidsMap(bidsmapfile, checks=(True, True, True))
 
-    return bids.validate_bidsmap(bidsmap, 1)
+    return bidsmap.validate(1)
 
 
-def test_bidscoin(bidsmapfile: Union[Path,dict], options: dict=None, testplugins: bool=True, testgui: bool=True, testtemplate: bool=True) -> int:
+def test_bidscoin(bidsmapfile: Path, options: dict=None, testplugins: bool=True, testgui: bool=True, testtemplate: bool=True) -> int:
     """
     Performs a bidscoin installation test
 
@@ -521,7 +521,7 @@ def test_bidscoin(bidsmapfile: Union[Path,dict], options: dict=None, testplugins
         LOGGER.info(f"Running bidsmap checks:")
         try:            # Moving the import to the top of this module will cause circular import issues
             from bidscoin import bids
-            bidsmap, _ = bids.load_bidsmap(bidsmapfile, checks=(True, True, False))
+            bidsmap = bids.BidsMap(bidsmapfile, checks=(True, True, False))
         except Exception as bidsmaperror:
             LOGGER.error(f"An error occurred when loading {bidsmapfile}:\n{bidsmaperror}\nThis may be due to invalid YAML syntax. You can check this using a YAML validator (e.g. https://www.yamllint.com)")
             bidsmap = {'Options': {}}
@@ -533,7 +533,7 @@ def test_bidscoin(bidsmapfile: Union[Path,dict], options: dict=None, testplugins
     if testtemplate:
         try:                # Moving the import to the top of this module will cause circular import issues
             from bidscoin import bids
-            success = bids.check_template(bidsmap) and success
+            success = bidsmap.check_template() and success
         except ImportError:
             LOGGER.info(f"Could not fully test: {bidsmap}")
 

bidscoin/bidsapps/fixmeta.py

@@ -53,10 +53,10 @@ def fixmeta(bidsfolder: str, pattern: str, metadata: dict, participant: list, bi
     LOGGER.info(f"Command: fixmeta {' '.join(sys.argv[1:])}")
 
     # Load the bidsmap data (-> plugins)
-    bidsmap, _ = bids.load_bidsmap(Path(bidsmap or 'bidsmap.yaml'), bidsdir/'code'/'bidscoin', checks=(False, False, False))
+    bidsmap, _ = bids.BidsMap(Path(bidsmap or 'bidsmap.yaml'), bidsdir/'code'/'bidscoin', checks=(False, False, False))
     if not bidsmap:
-        bidsmap, _ = bids.load_bidsmap(bidsmap_template, checks=(False, False, False))
-    plugins  = bidsmap['Options']['plugins']
+        bidsmap, _ = bids.BidsMap(bidsmap_template, checks=(False, False, False))
+    plugins  = bidsmap.plugins
     provdata = bids.bidsprov(bidsdir)
 
     # Loop over the subject/session-directories
@@ -83,7 +83,7 @@ def fixmeta(bidsfolder: str, pattern: str, metadata: dict, participant: list, bi
                         if isinstance(row['targets'], str) and target.name in row['targets']:
                             sourcedir = source
                     datasource = bids.get_datasource(Path(sourcedir), plugins)
-                    LOGGER.bcdebug(f"Datasource provenance: '{target.name}' -> '{datasource.path}'")
+                    LOGGER.bcdebug(f"Datasource provenance: '{target.name}' -> '{datasource}'")
 
                     # Load/copy over the source meta-data
                     jsonfile = target.with_suffix('').with_suffix('.json')

bidscoin/bidscoiner.py

@@ -81,27 +81,25 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
 
     # Create a README file if it does not exist
     readme_file = bidsfolder/'README'
-    if not readme_file.is_file():
+    if not (readme_file.is_file() or next(bidsfolder.glob('README.*'))):
         LOGGER.info(f"Creating a template README file (adjust it to your needs): {readme_file}")
         try:
             urllib.request.urlretrieve('https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/README.MD', readme_file)
         except urllib.error.URLError:
-            readme_file.write_text(
-                f"A free form text ( README ) describing the dataset in more details that SHOULD be provided. For an example, see e.g.:\n"
-                f"https://github.com/bids-standard/bids-starter-kit/blob/main/templates/README.MD\n\n"
-                f"The raw BIDS data was created using BIDScoin {__version__}\n"
-                f"All provenance information and settings can be found in ./code/bidscoin\n"
-                f"For more information see: https://github.com/Donders-Institute/bidscoin\n")
+            readme_file.write_text(f"A free form text ( README ) describing the dataset in more details that SHOULD be provided. For an example, see e.g.:\n"
+                                   f"https://github.com/bids-standard/bids-starter-kit/blob/main/templates/README.MD\n\n"
+                                   f"The raw BIDS data was created using BIDScoin {__version__}\n"
+                                   f"All provenance information and settings can be found in ./code/bidscoin\n"
+                                   f"For more information see: https://github.com/Donders-Institute/bidscoin\n")
 
     # Get the bidsmap heuristics from the bidsmap YAML-file
-    bidsmap, bidsmapfile = bids.load_bidsmap(bidsmapfile, bidscoinfolder)
-    dataformats          = [dataformat for dataformat in bidsmap if dataformat and dataformat not in ('$schema','Options')]
-    if not bidsmap:
+    bidsmap = bids.BidsMap(bidsmapfile, bidscoinfolder)
+    if not bidsmap.filepath.is_file():
         LOGGER.error(f"No bidsmap file found in {bidsfolder}. Please run the bidsmapper first and/or use the correct bidsfolder")
         return
 
     # Load the data conversion plugins
-    plugins = [bcoin.import_plugin(plugin, ('bidscoiner_plugin',)) for plugin,options in bidsmap['Options']['plugins'].items()]
+    plugins = [bcoin.import_plugin(plugin, ('bidscoiner_plugin',)) for plugin,options in bidsmap.plugins.items()]
     plugins = [plugin for plugin in plugins if plugin]          # Filter the empty items from the list
     if not plugins:
         LOGGER.warning(f"The plugins listed in your bidsmap['Options'] did not have a usable `bidscoiner_plugin` function, nothing to do")
@@ -110,7 +108,7 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
         return
 
     # Append options to the .bidsignore file
-    bidsignore_items = bidsmap['Options']['bidscoin']['bidsignore']
+    bidsignore_items = bidsmap.options['bidsignore']
     bidsignore_file  = bidsfolder/'.bidsignore'
     if bidsignore_items:
         LOGGER.verbose(f"Writing {bidsignore_items} entries to {bidsignore_file}")
@@ -121,8 +119,8 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
                 bidsignore.write(item + '\n')
 
     # Get the list of subjects
-    subprefix = bidsmap['Options']['bidscoin']['subprefix'].replace('*','')
-    sesprefix = bidsmap['Options']['bidscoin']['sesprefix'].replace('*','')
+    subprefix = bidsmap.options['subprefix'].replace('*','')
+    sesprefix = bidsmap.options['sesprefix'].replace('*','')
     if not participant:
         subjects = lsdirs(rawfolder, (subprefix if subprefix!='*' else '') + '*')
         if not subjects:
@@ -151,7 +149,7 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
             for subject in subjects:
 
                 # Check if we should skip the session-folder
-                datasource = bids.get_datasource(subject, bidsmap['Options']['plugins'])
+                datasource = bids.get_datasource(subject, bidsmap.plugins)
                 subid,_    = datasource.subid_sesid(bidsmap[datasource.dataformat]['subject'], bidsmap[datasource.dataformat]['session'])
                 if (bidsfolder/subid).is_dir() and not force:
                     LOGGER.info(f">>> Skipping already processed subject: {bidsfolder/subid} (you can use the -f option to overrule)")
@@ -257,11 +255,11 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
             for session in sessions:
 
                 # Unpack the data in a temporary folder if it is tarballed/zipped and/or contains a DICOMDIR file
-                sesfolders, unpacked = bids.unpack(session, bidsmap['Options']['bidscoin'].get('unzip',''))
+                sesfolders, unpacked = bids.unpack(session, bidsmap.options.get('unzip',''))
                 for sesfolder in sesfolders:
 
                     # Check if we should skip the session-folder
-                    datasource = bids.get_datasource(sesfolder, bidsmap['Options']['plugins'])
+                    datasource = bids.get_datasource(sesfolder, bidsmap.plugins)
                     if not datasource.dataformat:
                         LOGGER.info(f">>> No datasources found in '{sesfolder}'")
                         continue