add monkeypatch to schemaview

nwb_linkml/src/nwb_linkml/monkeypatch.py

@@ -38,6 +38,63 @@ def patch_npytyping():
     dataframe.DataFrameMeta.__module__ = property(new_module_dataframe)
     base_meta_classes.SubscriptableMeta._get_module = new_get_module
 
+def patch_schemaview():
+    """
+    Patch schemaview to correctly resolve multiple layers of relative imports.
+
+    References:
+
+    Returns:
+
+    """
+    from typing import List
+    from functools import lru_cache
+    from linkml_runtime.utils.schemaview import SchemaView
+
+    from linkml_runtime.linkml_model import SchemaDefinitionName
+    @lru_cache()
+    def imports_closure(self, imports: bool = True, traverse=True, inject_metadata=True) -> List[SchemaDefinitionName]:
+        """
+        Return all imports
+
+        :param traverse: if true, traverse recursively
+        :return: all schema names in the transitive reflexive imports closure
+        """
+        if not imports:
+            return [self.schema.name]
+        if self.schema_map is None:
+            self.schema_map = {self.schema.name: self.schema}
+        closure = []
+        visited = set()
+        todo = [self.schema.name]
+        if not traverse:
+            return todo
+        while len(todo) > 0:
+            sn = todo.pop()
+            visited.add(sn)
+            if sn not in self.schema_map:
+                imported_schema = self.load_import(sn)
+                self.schema_map[sn] = imported_schema
+            s = self.schema_map[sn]
+            if sn not in closure:
+                closure.append(sn)
+            for i in s.imports:
+                if sn.startswith('.') and ':' not in i:
+                    # prepend the relative part
+                    i = '/'.join(sn.split('/')[:-1]) + '/' + i
+                if i not in visited:
+                    todo.append(i)
+        if inject_metadata:
+            for s in self.schema_map.values():
+                for x in {**s.classes, **s.enums, **s.slots, **s.subsets, **s.types}.values():
+                    x.from_schema = s.id
+                for c in s.classes.values():
+                    for a in c.attributes.values():
+                        a.from_schema = s.id
+        return closure
+
+    SchemaView.imports_closure = imports_closure
 
 def apply_patches():
     patch_npytyping()
+    patch_schemaview()

nwb_linkml/src/nwb_linkml/providers/schema.py

@@ -7,10 +7,9 @@ an NWB file, we need a bit of infrastructure for generating and caching
 pydantic models on the fly.
 
 Relationship to other modules:
-- :mod:`.adapters` manage the conversion from NWB schema language to linkML.
-- :mod:`.generators` create models like pydantic models from the linkML schema
-- :mod:`.providers` then use ``adapters`` and ``generators`` to provide models
-  from generated schema!
+* :mod:`.adapters` manage the conversion from NWB schema language to linkML.
+* :mod:`.generators` create models like pydantic models from the linkML schema
+* :mod:`.providers` then use ``adapters`` and ``generators`` to provide models from generated schema!
 """
 import pdb
 from typing import Dict, TypedDict, List, Optional, Literal, TypeVar, Any, Dict
@@ -155,7 +154,7 @@ class LinkMLProvider(Provider):
     Like other :class:`.Provider` classes, this model is not a singleton but
     behaves a bit like one in that when instantiated without arguments
     it is stateless (except for configuration by environment-level variables).
-    So we don't use ``@classmethod``s here, but instantiating the class should remain
+    So we don't use ``@classmethod`` s here, but instantiating the class should remain
     cheap.
 
     Namespaces can be built from:
@@ -164,6 +163,7 @@ class LinkMLProvider(Provider):
     * dictionaries, as are usually packaged in nwb files: :meth:`.build_from_dicts`
 
     All of which feed into...
+
     * :class:`~.adapters.NamespacesAdapter` used throughout the rest of ``nwb_linkml`` - :meth:`.build`
 
     After a namespace is built, it can be accessed using :meth:`.LinkMLProvider.get`, which