add bids sort to bids.models from bids.utils

Author: bendhouseart

src/bids/layout/models.py

@@ -25,7 +25,7 @@
 except ImportError:  # sqlalchemy < 1.4
     from sqlalchemy.ext.declarative import declarative_base
 
-from ..utils import listify
+from ..utils import listify, bids_sort
 from .writing import build_path, write_to_file
 from ..config import get_option
 from .utils import BIDSMetadata, PaddedInt
@@ -541,8 +541,8 @@ def get_entities(self, metadata=False, values='tags'):
 
         results = query.all()
         if values.startswith('obj'):
-            return {t.entity_name: t.entity for t in results}
-        return {t.entity_name: t.value for t in results}
+            return bids_sort({t.entity_name: t.entity for t in results})
+        return bids_sort({t.entity_name: t.value for t in results})
 
     def copy(self, path_patterns, symbolic_link=False, root=None,
              conflicts='fail'):

src/bids/layout/tests/test_layout.py

@@ -15,7 +15,7 @@
 from bids.layout.models import Config
 from bids.layout.index import BIDSLayoutIndexer, _check_path_matches_patterns, _regexfy
 from bids.layout.utils import PaddedInt
-from bids.utils import natural_sort
+from bids.utils import natural_sort, bids_sort
 
 from bids.exceptions import (
     BIDSChildDatasetError,
@@ -1268,3 +1268,34 @@ def test_get_return_type_dir_with_legacy_config_no_template():
         # because task entity has no directory template
         with pytest.raises(ValueError, match='Return type set to directory'):
             layout.get(target='task', return_type='dir')
+
+def test_bids_sort(layout_7t_trt):
+    files = layout_7t_trt.get(task='rest', extension='.nii.gz')
+    assert len(files) > 0
+    from bidsschematools.schema import load_schema
+    import random
+    import copy
+    # we apply bids_sort at the model level, but just to be extra sure
+    # we sort here one more time
+    first_file_ents_sorted = bids_sort(files[0].get_entities())
+    schema_order = list(load_schema().rules.entities) + ['suffix', 'extension', 'datatype']
+
+    # collect keys from file entity then unsort them
+    sorted_keys = list(first_file_ents_sorted.keys())
+    unsorted_keys = copy.copy(sorted_keys)
+    while unsorted_keys == sorted_keys:
+        random.shuffle(unsorted_keys)
+
+    first_file_ents_unsorted = {}
+    for key in unsorted_keys:
+        first_file_ents_unsorted[key] = first_file_ents_sorted[key] 
+    
+    # check order of sorted entities against schema
+    for i, entity in enumerate(sorted_keys):
+        for j in sorted_keys[i + 1:]:
+            if entity in schema_order and j in schema_order:
+                assert schema_order.index(entity) < schema_order.index(j)
+
+    assert list(first_file_ents_unsorted.keys()) != sorted_keys
+    assert list(bids_sort(first_file_ents_unsorted).keys()) == sorted_keys
+    

src/bids/utils.py

@@ -187,3 +187,28 @@ def validate_multiple(val, retval=None):
     if len(val) == 1:
         return val[0]
     return val
+
+def bids_sort(unsorted: dict):
+    f"""
+    Sorts filename entity dictionaries according to their order as defined in 
+    schema.rules.entities as well as suffix, extension. Lastly, appends datatype
+    to the end of the sort to accomodate pybids datastructures.
+
+    Parameters
+    ----------
+    unsorted: dict
+        A dictionary containing bids file entities and their values.
+    
+    Returns
+    -------
+    sorted_bids: dict
+
+    """
+    from bidsschematools.schema import load_schema
+    from bidsschematools.types.namespace import Namespace
+    _schema = load_schema()
+    entity_order = list(_schema.rules.entities) + ['suffix', 'extension', 'datatype']
+    
+    sorted_bids = {k: unsorted[k] for k in sorted(unsorted, key=lambda k: entity_order.index(k) if k in entity_order else len(entity_order))}
+
+    return sorted_bids