ENH: a little pythonisation + ensure no bad entities provided

Author: yarikoptic

heudiconv/bids/consts.py

@@ -0,0 +1,31 @@
+#emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*- 
+#ex: set sts=4 ts=4 sw=4 noet:
+"""
+
+ COPYRIGHT: Yaroslav Halchenko 2014
+
+ LICENSE: MIT
+
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to deal
+  in the Software without restriction, including without limitation the rights
+  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+  copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included in
+  all copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+  THE SOFTWARE.
+"""
+
+__author__ = 'yoh'
+__license__ = 'MIT'
+
+BIDS_VERSION = "1.7.0"

heudiconv/bids/schema.py

@@ -6,6 +6,8 @@
 
 from heudiconv.utils import remove_prefix
 
+from .consts import BIDS_VERSION
+
 lgr = logging.getLogger(__name__)
 
 
@@ -31,21 +33,21 @@ class BIDSFile:
     _known_entities = _load_entities_order()
 
     def __init__(self, entities, suffix, extension):
+        unknown_entities = set(entities).difference(self._known_entities)
+        if unknown_entities:
+            raise ValueError(f"Unknown to BIDS {BIDS_VERSION} entities provided: {', '.join(unknown_entities)}")
         self._entities = entities
         self._suffix = suffix
         self._extension = extension
 
     def __eq__(self, other):
         if not isinstance(other, self.__class__):
             return False
-        if (
+        return (
             all([other[k] == v for k, v in self._entities.items()])
             and self.extension == other.extension
             and self.suffix == other.suffix
-        ):
-            return True
-        else:
-            return False
+        )
 
     @classmethod
     def parse(cls, filename):

heudiconv/bids/tests/test_schema.py

@@ -11,6 +11,10 @@ def test_BIDSFile_known_entries():
     assert len(BIDSFile._known_entities) > 10  # we do have many
     assert 'run' in BIDSFile._known_entities
 
+    good_entities = dict(sub='me')
+    BIDSFile(good_entities, None, None)  # just to ensure we are good
+    with pytest.raises(ValueError):
+        BIDSFile(dict(good_entities, badentity="good"), None, None)
 
 def test_BIDSFile():
     """ Tests for the BIDSFile class """

heudiconv/bids/utils.py

@@ -10,10 +10,10 @@
 from collections import OrderedDict
 from datetime import datetime
 from glob import glob
-from random import sample
 
 import numpy as np
 
+from .consts import BIDS_VERSION
 from .. import __version__
 from ..external.pydicom import dcm
 from ..parser import find_files
@@ -55,8 +55,6 @@ class BIDSError(Exception):
     pass
 
 
-BIDS_VERSION = "1.7.0"
-
 # List defining allowed parameter matching for fmap assignment:
 SHIM_KEY = 'ShimSetting'
 AllowedFmapParameterMatching = [

heudiconv/convert.py

@@ -31,8 +31,8 @@
     tuneup_bids_json_files,
     add_participant_record,
     BIDSError,
-    BIDS_VERSION,
 )
+from .bids.consts import BIDS_VERSION
 from .dicoms import (
     group_dicoms_into_seqinfos,
     embed_metadata_from_dicoms,