Merge pull request #368 from will-0/fix-multilayer-relative-imports

Fix multilayer relative imports

Author: sierra-moxon

linkml_runtime/utils/schemaview.py

@@ -10,6 +10,7 @@
 from typing import Optional, TypeVar
 from collections.abc import Mapping
 import warnings
+from urllib.parse import urlparse
 
 from linkml_runtime.utils.namespaces import Namespaces
 from deprecated.classic import deprecated
@@ -107,6 +108,25 @@ def is_absolute_path(path: str) -> bool:
     drive, tail = os.path.splitdrive(norm_path)
     return bool(drive and tail)
 
+def _resolve_import(source_sch: str, imported_sch: str) -> str:
+    if os.path.isabs(imported_sch):
+        # Absolute import paths are not modified
+        return imported_sch
+    if urlparse(imported_sch).scheme:
+        # File with URL schemes are not modified
+        return imported_sch
+    
+    if WINDOWS:
+        path = PurePath(os.path.normpath(PurePath(source_sch).parent / imported_sch)).as_posix()
+    else:
+        path = os.path.normpath(str(Path(source_sch).parent / imported_sch))
+
+    if imported_sch.startswith(".") and not path.startswith("."):
+        # Above condition handles cases where both source schema and imported schema are relative paths: these should remain relative
+        return f"./{path}"
+
+    return path
+
 
 @dataclass
 class SchemaUsage:
@@ -306,12 +326,7 @@ def imports_closure(self, imports: bool = True, traverse: Optional[bool] = None,
                     # - subdir/types.yaml
                     # we should treat the two `types.yaml` as separate schemas from the POV of the
                     # origin schema.
-                    if sn.startswith('.') and ':' not in i:
-                        if WINDOWS:
-                            # This cannot be simplified. os.path.normpath() must be called before .as_posix()
-                            i = PurePath(os.path.normpath(PurePath(sn).parent / i)).as_posix()
-                        else:
-                            i = os.path.normpath(str(Path(sn).parent / i))
+                    i = _resolve_import(sn, i)
                     todo.append(i)
 
             # add item to closure

tests/test_utils/input/imports_relative/L0_2/L2_2_0/L3_2_0_0/L4_2_0_0_0/greatgrandchild.yaml

@@ -0,0 +1,5 @@
+id: greatgrandchild
+name: greatgrandchild
+title: greatgrandchild
+imports:
+  - linkml:types

tests/test_utils/input/imports_relative/L0_2/L2_2_0/L3_2_0_0/grandchild.yaml

@@ -0,0 +1,6 @@
+id: grandchild
+name: grandchild
+title: grandchild
+imports:
+  - linkml:types
+  - ./L4_2_0_0_0/greatgrandchild

tests/test_utils/input/imports_relative/L0_2/L2_2_0/child.yaml

@@ -0,0 +1,6 @@
+id: child
+name: child
+title: child
+imports:
+  - linkml:types
+  - ./L3_2_0_0/grandchild

tests/test_utils/input/imports_relative/L0_2/main.yaml

@@ -0,0 +1,6 @@
+id: main
+name: main
+title: main
+imports:
+  - linkml:types
+  - ./L2_2_0/child

tests/test_utils/test_schemaview.py

@@ -22,6 +22,8 @@
 SCHEMA_WITH_STRUCTURED_PATTERNS = Path(INPUT_DIR) / "pattern-example.yaml"
 SCHEMA_IMPORT_TREE = Path(INPUT_DIR) / 'imports' / 'main.yaml'
 SCHEMA_RELATIVE_IMPORT_TREE = Path(INPUT_DIR) / 'imports_relative' / 'L0_0' / 'L1_0_0' / 'main.yaml'
+SCHEMA_RELATIVE_IMPORT_TREE2 = Path(INPUT_DIR) / 'imports_relative' / 'L0_2' / 'main.yaml'
+
 
 yaml_loader = YAMLLoader()
 IS_CURRENT = 'is current'
@@ -553,6 +555,11 @@ def test_imports_relative():
     assert 'L2100Index' in classes
     assert 'L2101Index' in classes
 
+def test_imports_relative_load():
+    """Relative imports from relative imports should load without FileNotFoundError."""
+    sv = SchemaView(SCHEMA_RELATIVE_IMPORT_TREE2)
+    sv.imports_closure(imports=True)
+
 
 def test_direct_remote_imports():
     """Tests that building a SchemaView directly from a remote URL works."""