Make stripping the suffix from bids-values in run-items optional (GitHub issue #265)

Author: marcelzwiers

bidscoin/bids.py

@@ -545,7 +545,7 @@ def strip_suffix(self):
 
         # See if we have a suffix for this datatype
         bids = self.bids
-        if 'suffix' in bids and bids['suffix']:
+        if 'suffix' in bids and bids['suffix'] and self.options.get('stripsuffix','y').lower() in ('y', 'yes'):
             suffix = bids['suffix'].lower()
         else:
             return

bidscoin/heuristics/bidsmap_bids2bids.yaml

@@ -27,6 +27,7 @@ Options:
     unknowntypes: [extra_data]      # A list of datatypes that are converted to BIDS-like datatype folders
     ignoretypes: [exclude]          # A list of datatypes that are excluded / not converted to BIDS
     anon: y                         # Set this anonymization flag to 'y' to round off age and discard acquisition date from the metadata
+    stripsuffix: y                  # Strips off the suffix from bids-values (to reduce redundancy within filenames)
     unzip:                          # Wildcard pattern to select tarball/zip-files in the source folders that need to be unzipped (in a tempdir) to expose the data, e.g. '*.tar.gz'
   plugins:                          # List of plugins with plugin-specific key-value pairs (that can be used by the plugin)
     nibabel2bids:

bidscoin/heuristics/bidsmap_dccn.yaml

@@ -28,6 +28,7 @@ Options:
     unknowntypes: [extra_data]      # A list of datatypes that are converted to BIDS-like datatype folders
     ignoretypes: [exclude]          # A list of datatypes that are excluded / not converted to BIDS
     anon: y                         # Set this anonymization flag to 'y' to round off age and discard acquisition date from the metadata
+    stripsuffix: y                  # Strips off the suffix from bids-values (to reduce redundancy within filenames)
     unzip:                          # Wildcard pattern to select tarball/zip-files in the source folders that need to be unzipped (in a tempdir) to expose the data, e.g. '*.tar.gz'
   plugins:                          # List of plugins with plugin-specific key-value pairs (that can be used by the plugin)
     dcm2niix2bids:                  # See dcm2niix -h and https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage for more info

bidscoin/heuristics/bidsmap_sst.yaml

@@ -27,6 +27,7 @@ Options:
     unknowntypes: [extra_data]      # A list of datatypes that are converted to BIDS-like datatype folders
     ignoretypes: [exclude]          # A list of datatypes that are excluded / not converted to BIDS
     anon: y                         # Set this anonymization flag to 'y' to round off age and discard acquisition date from the metadata
+    stripsuffix: y                  # Strips off the suffix from bids-values (to reduce redundancy within filenames)
     unzip:                          # Wildcard pattern to select tarball/zip-files in the source folders that need to be unzipped (in a tempdir) to expose the data, e.g. '*.tar.gz'
   plugins:                          # List of plugins with plugin-specific key-value pairs (that can be used by the plugin)
     dcm2niix2bids:                  # See dcm2niix -h and https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage for more info

bidscoin/heuristics/schema.json

@@ -23,6 +23,7 @@
                   "unknowntypes": { "type": ["array"] },
                   "ignoretypes": { "type": ["array"] },
                   "anon": { "type": ["string", "null"] },
+                  "stripsuffix": { "type": ["string", "null"] },
                   "unzip": { "type": ["string", "null"] }
                },
                "additionalProperties": false