FIX: Associate "is_metadata" with Tag, not Entity; and only return non-metadata entries for core Entities in get(return_type='id')

bids/layout/index.py

@@ -445,9 +445,9 @@ def create_association_pair(src, dst, kind, kind2=None):
                             md_val))
                     continue
                 if md_key not in all_entities:
-                    all_entities[md_key] = Entity(md_key, is_metadata=True)
+                    all_entities[md_key] = Entity(md_key)
                     self.session.add(all_entities[md_key])
-                tag = Tag(bf, all_entities[md_key], md_val)
+                tag = Tag(bf, all_entities[md_key], md_val, is_metadata=True)
                 self.session.add(tag)
 
             if len(self.session.new) >= 1000:

bids/layout/layout.py

@@ -296,7 +296,7 @@ def files(self):
 
     @classmethod
     def load(cls, database_path):
-        """ Load index from database path. Initialization parameters are set to
+        """ Load index from database path. Initiget_entitiesalization parameters are set to
         those found in database_path JSON sidecar.
 
         Parameters
@@ -313,7 +313,7 @@ def save(self, database_path, replace_connection=True):
 
         Note: This is only necessary if a database_path was not specified
         at initialization, and the user now wants to save the index.
-        If a database_path was specified originally, there is no need to
+        If a database_path was specified originaquery = l.session.query(Entity)lly, there is no need to
         re-save using this method.
 
         Parameters
@@ -369,7 +369,7 @@ def get_entities(self, scope='all', metadata=None):
         for l in layouts:
             query = l.session.query(Entity)
             if metadata is not None:
-                query = query.filter_by(is_metadata=metadata)
+                query = query.join(Tag).filter_by(is_metadata=metadata)
             results = query.all()
             entities.update({e.name: e for e in results})
         return entities
@@ -513,7 +513,7 @@ def to_df(self, metadata=False, **filters):
         query = self.session.query(Tag).filter(Tag.file_path.in_(file_paths))
 
         if not metadata:
-            query = query.join(Entity).filter(Entity.is_metadata == False)
+            query = query.join(Entity).filter(Tag.is_metadata == False)
 
         tags = query.all()
 
@@ -675,13 +675,13 @@ def get(self, return_type='object', target=None, scope='all',
                 raise TargetError('If return_type is "id" or "dir", a valid '
                                  'target entity must also be specified.')
 
-            results = [x for x in results if target in x.entities]
+            metadata = target not in self.get_entities(metadata=False)
 
             if return_type == 'id':
-                results = list(set(
-                    [x.entities[target] for x in results 
-                     if type(x.entities[target]) is not dict]))
-                results = natural_sort(results)
+                ent_iter = (x.get_entities(metadata=metadata) for x in results)
+                results = list({
+                    ents[target] for ents in ent_iter if target in ents
+                })
 
             elif return_type == 'dir':
                 template = entities[target].directory
@@ -879,7 +879,7 @@ def get_metadata(self, path, include_entities=False, scope='all'):
                      .filter(BIDSFile.path == path))
 
             if not include_entities:
-                query = query.join(Entity).filter(Entity.is_metadata == True)
+                query = query.join(Entity).filter(Tag.is_metadata == True)
 
             results = query.all()
             if results:

bids/layout/models.py

@@ -319,8 +319,9 @@ def get_entities(self, metadata=False, values='tags'):
         query = (session.query(Tag)
                  .filter_by(file_path=self.path)
                  .join(Entity))
+
         if metadata not in (None, 'all'):
-            query = query.filter(Entity.is_metadata == metadata)
+            query = query.filter(Tag.is_metadata == metadata)
 
         results = query.all()
         if values.startswith('obj'):
@@ -517,28 +518,22 @@ class Entity(Base):
         one of 'int', 'float', 'bool', or 'str'. If None, no type
         enforcement will be attempted, which means the dtype of the
         value may be unpredictable.
-    is_metadata : bool
-        Indicates whether or not the Entity is derived
-        from JSON sidecars (True) or is a predefined Entity from a
-        config (False).
     """
     __tablename__ = 'entities'
 
     name = Column(String, primary_key=True)
     mandatory = Column(Boolean, default=False)
     pattern = Column(String)
     directory = Column(String, nullable=True)
-    is_metadata = Column(Boolean, default=False)
     _dtype = Column(String, default='str')
     files = association_proxy("tags", "value")
 
     def __init__(self, name, pattern=None, mandatory=False, directory=None,
-                 dtype='str', is_metadata=False):
+                 dtype='str'):
         self.name = name
         self.pattern = pattern
         self.mandatory = mandatory
         self.directory = directory
-        self.is_metadata = is_metadata
 
         if not isinstance(dtype, str):
             dtype = dtype.__name__
@@ -640,25 +635,32 @@ class Tag(Base):
         value. If passed, must be one of str, int, float, bool, or json.
         Any other value will be treated as json (and will fail if the
         value can't be serialized to json).
+    is_metadata : bool
+        Indicates whether or not the Entity is derived
+        from JSON sidecars (True) or is a predefined Entity from a
+        config (False).
     """
     __tablename__ = 'tags'
 
     file_path = Column(String, ForeignKey('files.path'), primary_key=True)
     entity_name = Column(String, ForeignKey('entities.name'), primary_key=True)
     _value = Column(String, nullable=False)
     _dtype = Column(String, default='str')
+    is_metadata = Column(Boolean, default=False)
+
 
     file = relationship('BIDSFile', backref=backref(
         "tags", collection_class=attribute_mapped_collection("entity_name")))
     entity = relationship('Entity', backref=backref(
         "tags", collection_class=attribute_mapped_collection("file_path")))
 
-    def __init__(self, file, entity, value, dtype=None):
+    def __init__(self, file, entity, value, dtype=None, is_metadata=False):
 
         if dtype is None:
             dtype = type(value)
 
         self.value = value
+        self.is_metadata = is_metadata
 
         if not isinstance(dtype, str):
             dtype = dtype.__name__