Merge pull request #30 from bids-standard/schema_entities

Change get_metadata to return long-name

Author: adelavega

bids/layout/layout.py

@@ -18,7 +18,7 @@
 )
 
 from ancpbids import CustomOpExpr, EntityExpr, AllExpr, ValidationPlugin, load_dataset, validate_dataset, \
-    write_derivative
+    write_derivative, DatasetOptions
 from ancpbids.query import query, query_entities, FnMatchExpr, AnyExpr
 from ancpbids.utils import deepupdate, resolve_segments, convert_to_relative, parse_bids_name
 
@@ -274,7 +274,6 @@ def __init__(
             root = root.absolute()
 
         if ignore is None:
-            # If there is no .bidsignore file, apply default ignore patterns
             if not (Path(root) / '.bidsignore').exists():
                 ignore = ['.*', 'models', 'stimuli', 'code', 'sourcedata']
                 warnings.warn(
@@ -290,7 +289,9 @@ def __init__(
                 DeprecationWarning
             )
 
-        self.dataset = load_dataset(root, ignore=ignore)
+        options = DatasetOptions(ignore=ignore)
+
+        self.dataset = load_dataset(root, options=options)
         self.schema = self.dataset.get_schema()
         self.validationReport = None
 
@@ -420,7 +421,7 @@ def parse_file_entities(self, filename, scope=None, entities=None,
         results = parse_bids_name(filename)
 
         entities = results.pop('entities')
-        schema_entities = {e.literal_: e.name for e in list(self.schema.EntityEnum)}
+        schema_entities = {e.value['name']: e.name for e in list(self.schema.EntityEnum)}
         entities = {schema_entities[k]: v for k, v in entities.items()}
         results = {**entities, **results}
 
@@ -601,19 +602,19 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
 
         # Provide some suggestions if target is specified and invalid.
         if return_type in ("dir", "id"):
-            # Resolve proper target names to their "key", e.g., session to ses
-            # XXX should we allow ses?
-            target_match = [e for e in self.dataset._schema.EntityEnum 
-                if target in [e.name, e.literal_]]
-            potential = list(self.get_entities().keys())
-            if (not target_match) or target_match[0].name not in potential:
+            if target is None:
+                raise TargetError(f'If return_type is "id" or "dir", a valid target '
+                                  'entity must also be specified.')
+            self_entities = self.get_entities()
+            if target not in self_entities:
+                potential = list(self_entities.keys())
                 suggestions = difflib.get_close_matches(target, potential)
                 if suggestions:
                     message = "Did you mean one of: {}?".format(suggestions)
                 else:
                     message = "Valid targets are: {}".format(potential)
                 raise TargetError(f"Unknown target '{target}'. {message}")  
-            target = target_match[0].name
+
         folder = self.dataset
         result = query(folder, return_type, target, scope, extension, suffix, regex_search, **entities)
         if return_type == 'file':

bids/layout/models.py

@@ -4,7 +4,7 @@
 from typing import Union
 from pathlib import Path
 import json
-from ancpbids.model_v1_8_0 import Artifact
+from ancpbids.model_v1_8_0 import Artifact, Dataset
 from ancpbids.utils import parse_bids_name
 
 from ..utils import listify
@@ -37,12 +37,14 @@ def from_filename(cls, filename):
                 break
         return cls(path)
 
-    def __init__(self, file_ref: Union[str, os.PathLike, Artifact]):
+    def __init__(self, file_ref: Union[str, os.PathLike, Artifact], schema = None):
         self._path = None
         self._artifact = None
+        self._schema = schema
         if isinstance(file_ref, (str, os.PathLike)):
             self._path = Path(file_ref)
         elif isinstance(file_ref, Artifact):
+            self._schema = file_ref.get_schema()
             self._artifact = file_ref
 
     @property
@@ -105,7 +107,7 @@ def get_associations(self, kind=None, include_parents=False):
     def get_metadata(self):
         """Return all metadata associated with the current file. """
         md = BIDSMetadata(self.path)
-        md.update(self.get_entities(metadata=True))
+        md.update(self._artifact.get_metadata())
         return md
 
     @property
@@ -138,10 +140,9 @@ def get_entities(self, metadata=False, values='tags'):
         """
         try:
             entities = self._artifact.get_entities()
-
             # Convert literal entity values to their names
-            # schema_entities = {e.literal_: e.name for e in list(self.schema.EntityEnum)}
-            # entities = {schema_entities[k]: v for k, v in entities.items()}
+            known_entities = {e.value['name']: e.name for e in list(self._schema.EntityEnum)}
+            entities = {known_entities[k] if k in known_entities else k: v for k, v in entities.items()}
             entities['suffix'] = self._artifact.suffix
             entities['extension'] = self._artifact.extension
 

bids/layout/tests/test_layout.py

@@ -236,7 +236,7 @@ def test_get_with_bad_target(layout_7t_trt):
     msg = str(exc.value)
     assert 'subject' in msg and 'reconstruction' in msg and 'proc' in msg
     with pytest.raises(TargetError) as exc:
-        layout_7t_trt.get(target='sub')
+        layout_7t_trt.get(target='subject')
     msg = str(exc.value)
     assert 'subject' in msg and 'reconstruction' not in msg
 
@@ -282,7 +282,7 @@ def test_bids_json(layout_7t_trt):
 
 
 def test_get_return_type_dir(layout_7t_trt):
-    res_relpath = layout_7t_trt.get(target='sub', return_type='dir')
+    res_relpath = layout_7t_trt.get(target='subject', return_type='dir')
     target_relpath = ["sub-{:02d}".format(i) for i in range(1, 11)]
     assert all([tp in res_relpath for tp in target_relpath])
 
@@ -322,7 +322,7 @@ def test_get_val_enum_any_optional(layout_7t_trt, layout_ds005):
 
 
 def test_get_return_sorted(layout_7t_trt):
-    paths = layout_7t_trt.get(target='sub', return_type='file')
+    paths = layout_7t_trt.get(target='subject', return_type='file')
     assert natural_sort(paths) == paths
 
 
@@ -335,8 +335,8 @@ def test_layout_with_derivs(layout_ds005_derivs):
     event_file = "sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv"
     deriv_files = [f.name for f in files]
     assert event_file in deriv_files
-    entities = deriv.query_entities()
-    assert 'sub' in entities
+    entities = deriv.query_entities(long_form=True)
+    assert 'subject' in entities
 
 
 def test_layout_with_multi_derivs(layout_ds005_multi_derivs):

pyproject.toml

@@ -31,6 +31,7 @@ dependencies = [
   "bids-validator",
   "num2words",
   "click >=8.0",
+  "ancpbids @ git+https://github.com/adelavega/ancp-bids.git",
 ]
 dynamic = ["version"]