Perform a schema validation when reading a template bidsmap (Github i…

…ssue #225)

bidscoin/bids.py

@@ -16,6 +16,7 @@
 import pandas as pd
 import ast
 import datetime
+import jsonschema
 from functools import lru_cache
 from pathlib import Path
 from typing import List, Set, Tuple, Union, Dict, Any, Iterable, NewType
@@ -1156,7 +1157,7 @@ def check_template(bidsmap: Bidsmap) -> bool:
     bidsignore  = bidsmap['Options']['bidscoin'].get('bidsignore', [])
 
     # Check all the datatypes in the bidsmap
-    LOGGER.info('Checking the bidsmap datatypes:')
+    LOGGER.verbose('Checking the template bidsmap datatypes:')
     for dataformat in bidsmap:
         if dataformat in ('$schema', 'Options'): continue
         for datatype in bidsmap[dataformat]:
@@ -1182,10 +1183,19 @@ def check_template(bidsmap: Bidsmap) -> bool:
                         LOGGER.warning(f"Missing '{suffix}' run-item in: bidsmap[{dataformat}][{datatype}] (NB: this may be fine / a deprecated item)")
                         valid = False
 
+    # Validate against the json schema
+    with (templatefolder/'schema.json').open('r') as stream:
+        schema = json.load(stream)
+    try:
+        jsonschema.validate(bidsmap, schema)
+    except jsonschema.ValidationError as bidsmaperror:
+        LOGGER.warning(f"Invalid template bidsmap:\n{bidsmaperror}")
+        valid = False
+
     if valid:
-        LOGGER.success('All datatypes in the bidsmap are valid')
+        LOGGER.success('All datatypes and options in the template bidsmap are valid')
     else:
-        LOGGER.warning('Not all datatypes in the bidsmap are valid')
+        LOGGER.warning('Not all datatypes and options in the template bidsmap are valid')
 
     return valid
 

bidscoin/bidseditor.py

@@ -1669,6 +1669,7 @@ def bidseditor(bidsfolder: str, bidsmapfile: str='', templatefile: str=bidsmap_t
     # Obtain the initial bidsmap info
     template_bidsmap, templatefile = bids.load_bidsmap(templatefile, checks=(True, True, False))
     input_bidsmap, bidsmapfile     = bids.load_bidsmap(bidsmapfile,  bidsfolder/'code'/'bidscoin')
+    bids.check_template(template_bidsmap)
     if input_bidsmap.get('Options'):
         template_bidsmap['Options'] = input_bidsmap['Options']      # Always use the options of the input bidsmap
 

bidscoin/bidsmapper.py

@@ -73,6 +73,7 @@ def bidsmapper(rawfolder: str, bidsfolder: str, bidsmapfile: str, templatefile:
     # Get the heuristics for filling the new bidsmap (NB: plugins are stored in the bidsmaps)
     bidsmap_old, bidsmapfile = bids.load_bidsmap(bidsmapfile,  bidscoinfolder, plugins)
     template, _              = bids.load_bidsmap(templatefile, plugins=plugins, checks=(True, True, False))
+    bids.check_template(template)
 
     # Create the new bidsmap as a copy / bidsmap skeleton with no data type entries (i.e. bidsmap with empty lists)
     if force and bidsmapfile.is_file():

bidscoin/heuristics/schema.json

@@ -96,6 +96,9 @@
                "meta": {
                   "description": "The meta-data that will be appended to the json sidecar files produced by the plugin",
                   "type": "object"
+               },
+               "datasource": {
+                  "description": "The data source that will be appended when loading the bidsmap"
                }
             },
             "additionalProperties": false

docs/CHANGELOG.md

@@ -15,9 +15,10 @@
 - A `--cluster` option for running bidscoiner in parallel on a (DRMAA enabled) HPC
 - Option to exclude datatypes from being saved in bids/derivatives
 - A `bidsmap_bids2bids` template bidsmap for nibabel2bids to edit existing BIDS datasets
-- A `bidscoiner.tsv` logfile containing a concise overview of all input to output file conversions
+- A `bidscoiner.tsv` log-file containing a concise overview of all input to output file conversions
 - Integrated fslmaths preprocessing on slicereport input images
 - BIDScoin duecredit reports
+- A new environment variable `BIDSCOIN_CONFIG=/writable/path/to/config.toml` for using a non-default config file
 
 ### Changed
 - `bidscoiner_plugin()` API: you can (should) return a personals dict (instead of writing it to `participants.tsv`)

pyproject.toml

@@ -30,6 +30,7 @@ dependencies     = ['pandas',
                     'python-dateutil',
                     'nibabel',
                     'bids-validator',
+                    'jsonschema',
                     'drmaa',
                     'duecredit']