Checkpoint commit with test cases

Author: sneakers-the-rat

linkml_runtime/utils/schemaview.py

@@ -1,4 +1,5 @@
 import os
+import pdb
 import uuid
 import logging
 import collections
@@ -231,6 +232,7 @@ def imports_closure(self, imports: bool = True, traverse=True, inject_metadata=T
                 self.schema_map[sn] = imported_schema
             s = self.schema_map[sn]
             if sn not in closure:
+                #closure.insert(0, sn)
                 closure.append(sn)
             for i in s.imports:
                 if i not in visited:
@@ -434,6 +436,7 @@ def all_elements(self, imports=True) -> Dict[ElementName, Element]:
     def _get_dict(self, slot_name: str, imports=True) -> Dict:
         schemas = self.all_schema(imports)
         d = {}
+        # pdb.set_trace()
         # iterate through all schemas and merge the list together
         for s in schemas:
             # get the value of element name from the schema, if empty, return empty dictionary.

tests/test_utils/input/imports/README.md

@@ -0,0 +1,33 @@
+A tree of imports like:
+
+```
+main
+|- linkml:types
+|- s1
+|  |- s1_1
+|  |- s1_2
+|     |- s1_2_1
+|        |- s1_2_1_1
+|           |- s1_2_1_1_1
+|           |- s1_2_1_1_2
+|- s2
+|  |- s2_1
+|  |- s2_2
+|- s3
+   |- s3_1
+   |- s3_2
+```
+
+This is used to test SchemaView's logic for complex import hierarchies,
+eg.
+- overrides
+- imports closure completeness
+- (at some point) monotonicity
+- etc. 
+
+Currently, each schema...
+- Contains one `Main` class with a value whose default is overridden to indicate which module defined it, this is used to test overrides.
+- Contains a class like `S2` that carries the name of the module to ensure that unique classes are gotten from the whole tree
+- Each node in the tree outwards from `main` will carry the 'special classes' from the parents, overriding them as with `main` to
+  get a more detailed picture of override order: eg. `s1_2_1` will also define `S1_2` and override its `ifabsent` field, 
+  which `S1_2` should override since it's the importing schema.

tests/test_utils/input/imports/main.yaml

@@ -0,0 +1,15 @@
+id: main
+name: main
+title: main
+imports:
+  - linkml:types
+  - s1
+  - s2
+  - s3
+classes:
+  Main:
+    description: "The class we use to test overrides on imports!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "Main"

tests/test_utils/input/imports/s1.yaml

@@ -0,0 +1,20 @@
+id: s1
+name: s1
+title: s1
+imports:
+  - linkml:types
+  - s1_1
+  - s1_2
+classes:
+  Main:
+    description: "The class we use to test overrides on imports!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1"
+  S1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1"

tests/test_utils/input/imports/s1_1.yaml

@@ -0,0 +1,24 @@
+id: s1_1
+name: s1_1
+title: s1_1
+imports:
+  - linkml:types
+classes:
+  Main:
+    description: "The class we use to test overrides on imports!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_1"
+  S1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_1"
+  S1_1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_1"

tests/test_utils/input/imports/s1_2.yaml

@@ -0,0 +1,25 @@
+id: s1_2
+name: s1_2
+title: s1_2
+imports:
+  - linkml:types
+  - s1_2_1
+classes:
+  Main:
+    description: "The class we use to test overrides on imports!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2"
+  S1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2"
+  S1_2:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2"

tests/test_utils/input/imports/s1_2_1.yaml

@@ -0,0 +1,31 @@
+id: s1_2_1
+name: s1_2_1
+title: s1_2_1
+imports:
+  - linkml:types
+  - s1_2_1_1
+classes:
+  Main:
+    description: "The class we use to test overrides on imports!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1"
+  S1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1"
+  S1_2:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1"
+  S1_2_1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1"

tests/test_utils/input/imports/s1_2_1_1.yaml

@@ -0,0 +1,38 @@
+id: s1_2_1_1
+name: s1_2_1_1
+title: s1_2_1_1
+imports:
+  - linkml:types
+  - s1_2_1_1_1
+  - s1_2_1_1_2
+classes:
+  Main:
+    description: "The class we use to test overrides on imports!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1"
+  S1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1"
+  S1_2:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1"
+  S1_2_1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1"
+  S1_2_1_1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1"

tests/test_utils/input/imports/s1_2_1_1_1.yaml

@@ -0,0 +1,42 @@
+id: s1_2_1_1_1
+name: s1_2_1_1_1
+title: s1_2_1_1_1
+imports:
+  - linkml:types
+classes:
+  Main:
+    description: "The class we use to test overrides on imports!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_1"
+  S1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_1"
+  S1_2:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_1"
+  S1_2_1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_1"
+  S1_2_1_1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_1"
+  S1_2_1_1_1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_1"

tests/test_utils/input/imports/s1_2_1_1_2.yaml

@@ -0,0 +1,42 @@
+id: s1_2_1_1_2
+name: s1_2_1_1_2
+title: s1_2_1_1_2
+imports:
+  - linkml:types
+classes:
+  Main:
+    description: "The class we use to test overrides on imports!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_2"
+  S1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_2"
+  S1_2:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_2"
+  S1_2_1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_2"
+  S1_2_1_1:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_2"
+  S1_2_1_1_2:
+    description: "A class from one of the imported classes!"
+    attributes:
+      value:
+        range: string
+        ifabsent: "S1_2_1_1_2"