follow paths in multi-layer relative imports

Author: sneakers-the-rat

linkml_runtime/utils/schemaview.py

@@ -279,8 +279,25 @@ def imports_closure(self, imports: bool = True, traverse: Optional[bool] = None,
             if sn not in visited:
                 for i in self.schema_map[sn].imports:
                     # no self imports ;)
-                    if i != sn:
-                        todo.append(i)
+                    if i == sn:
+                        continue
+
+                    # resolve relative imports relative to the importing schema, rather than the
+                    # origin schema. Imports can be a URI or Curie, and imports from the same
+                    # directory don't require a ./, so if the current (sn) import is a relative
+                    # path, and the target import doesn't have : (as in a curie or a URI)
+                    # we prepend the relative path. This WILL make the key in the `schema_map` not
+                    # equal to the literal text specified in the importing schema, but this is
+                    # essential to sensible deduplication: eg. for
+                    # - main.yaml (imports ./types.yaml, ./subdir/subschema.yaml)
+                    # - types.yaml
+                    # - subdir/subschema.yaml (imports ./types.yaml)
+                    # - 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:
+                        i = os.path.normpath(str(Path(sn).parent / i))
+                    todo.append(i)
 
             # add item to closure
             # append + pop (above) is FILO queue, which correctly extends tree leaves,

tests/test_utils/input/imports_relative/L0_0/L1_0_0/L2_0_0_0/child.yaml

@@ -0,0 +1,15 @@
+id: child
+name: child
+title: child
+description: |
+  Child class that shares the same name and ID as another child and should *not* be deduplicated, 
+  but imports the dupe schema which *should* be deduplicated
+imports:
+  - linkml:types
+  - ../../L1_0_1/dupe
+classes:
+  Child1:
+    attributes:
+      value:
+        range: string
+        ifabsent: "Child1"

tests/test_utils/input/imports_relative/L0_0/L1_0_0/L2_0_0_1/child.yaml

@@ -0,0 +1,15 @@
+id: child
+name: child
+title: child
+description: |
+  Child class that shares the same name and ID as another child and should *not* be deduplicated, 
+  but imports the dupe schema which *should* be deduplicated
+imports:
+  - linkml:types
+  - ../../L1_0_1/dupe
+classes:
+  Child2:
+    attributes:
+      value:
+        range: string
+        ifabsent: "Child2"

tests/test_utils/input/imports_relative/L0_0/L1_0_0/main.yaml

@@ -0,0 +1,17 @@
+id: main
+name: main
+title: main
+imports:
+  - linkml:types
+  - neighbor
+  - ../parent
+  - ../../L0_1/cousin
+  - ./L2_0_0_0/child
+  - ./L2_0_0_1/child
+classes:
+  Main:
+    description: "Our intrepid main class!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "Main"

tests/test_utils/input/imports_relative/L0_0/L1_0_0/neighbor.yaml

@@ -0,0 +1,13 @@
+id: neighbor
+name: neighbor
+title: neighbor
+description: neighbor class imported without ./, but has relative imports of its own
+imports:
+  - ../neighborhood_parent
+classes:
+  Neighbor:
+    description: "Our main class's best friend!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "Neighbor"

tests/test_utils/input/imports_relative/L0_0/L1_0_1/L2_0_1_0/grandchild.yaml

@@ -0,0 +1,13 @@
+id: grandchild
+name: grandchild
+title: grandchild
+description: Grandchild schema that should cause a cycle with parent if we are just naively concatenating paths
+imports:
+  - ../../parent
+classes:
+  Grandchild:
+    description: "spoiled rotten!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "Grandchild"

tests/test_utils/input/imports_relative/L0_0/L1_0_1/dupe.yaml

@@ -0,0 +1,11 @@
+id: dupe
+name: dupe
+title: dupe
+description: A Duplicate schema that is imported from multiple places (but should only actually be imported once)
+classes:
+  Dupe:
+    description: "A class from the duplicated import!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "Dupe"

tests/test_utils/input/imports_relative/L0_0/neighborhood_parent.yaml

@@ -0,0 +1,11 @@
+id: neighborhood_parent
+name: neighborhood_parent
+title: neighborhood_parent
+description: parent of same-directory import
+classes:
+  Neighborhood_Parent:
+    description: "Keeps the cul-de-sac fed and scolds the speeding traffic"
+    attributes:
+      value:
+        range: string
+        ifabsent: "Neighborhood_Parent"

tests/test_utils/input/imports_relative/L0_0/parent.yaml

@@ -0,0 +1,13 @@
+id: parent
+name: parent
+title: parent
+description: Parent of our main schema, imports two layers down in the grandchild
+imports:
+  - linkml:types
+  - ./L1_0_1/L2_0_1_0/grandchild
+classes:
+  Parent:
+    attributes:
+      value:
+        range: string
+        ifabsent: "Parent"

tests/test_utils/input/imports_relative/L0_1/L1_1_0/L2_1_0_0/apple.yaml

@@ -0,0 +1,9 @@
+id: apple
+name: apple
+title: apple
+classes:
+  Apple:
+    attributes:
+      value:
+        range: string
+        ifabsent: "Apple"