Merge branch 'master' into dependabot/pip/ci/dependabot-updates/pydan…

…tic-gte-1.10.0-and-lt-2.10.2

bindings/python/scripts/CMakeLists.txt

@@ -25,6 +25,12 @@ function(test_failure name)
   set_property(TEST ${name} PROPERTY WILL_FAIL true)
 endfunction()
 
+# Check for yaml
+execute_process(
+  COMMAND ${Python3_EXECUTABLE} -c "import yaml"
+  RESULT_VARIABLE missing_yaml
+)
+
 
 # Install
 install(
@@ -83,13 +89,35 @@ test_success(
   dlite-validate-empty
   dlite-validate Empty.json
 )
-# Test valid yaml
-test_success(
-  dlite-validate-valid1-yaml
-  dlite-validate ../tests/entities/ValidYaml1.yaml
-)
-# Test invalid yaml
-test_failure(
-  dlite-validate-invalid1-yaml
-  dlite-validate ../tests/entities/InvalidYaml1.yaml
-)
+
+# Tests depending on yaml
+if(NOT ${missing_yaml})
+  # Test valid yaml
+  test_success(
+    dlite-validate-valid1-yaml
+    dlite-validate ../tests/entities/ValidYaml1.yaml
+  )
+  # Test invalid yaml
+  test_failure(
+    dlite-validate-invalid1-yaml
+    dlite-validate ../tests/entities/InvalidYaml1.yaml
+  )
+
+  # Test invalid yaml with ref-type
+  test_failure(
+    dlite-validate-ref-invalid1-yaml
+    dlite-validate ../tests/entities/Ref_invalid1.json
+  )
+
+  # Test valid yaml with invalid ref-type
+  test_failure(
+    dlite-validate-invalidref-yaml
+    dlite-validate ../tests/entities/ValidYaml_invalidref.yaml
+  )
+
+  # Test invalid yaml
+  test_failure(
+    dlite-validate-invalid2-yaml
+    dlite-validate ../tests/entities/InvalidYaml2.yaml
+  )
+endif()

bindings/python/scripts/dlite-validate

@@ -22,10 +22,23 @@ def parse(url, driver=None, options="mode=r", id=None):
         List of new instances.
     """
     import dlite
-
     loc = url.split("#", 1)[0].split("?",1)[0]
     if driver is None:
         driver = Path(loc).suffix.lstrip('.').lower()
+
+
+    # Validate all instances if `id` is None
+    if id is None:
+        try:
+            uuids = dlite.Instance.get_uuids(driver, url, options=options)
+        #except dlite.DLiteError:
+        except dlite.DLiteUnsupportedError:
+            pass
+        else:
+            insts = []
+            for uuid in uuids:
+                insts.extend(parse(url, driver=driver, options=options, id=uuid))
+            return insts
 
     # Validate all instances if `id` is None
     if id is None:
@@ -102,8 +115,9 @@ def main():
     parser.add_argument(
         '--storage-path', '-p', action='append', default=[],
         help='URL or path to storage path to look up metadata. '
-        'Only needed when validating data instances. '
-        'This option can be given multiple times.'
+        'Only needed when validating data instances, or datamodels '
+        'referring to other datamodels as properties. '
+        'This option can be given multiple times.' 
     )
     parser.add_argument(
         '--show', '-s', action='store_true',
@@ -140,6 +154,23 @@ def main():
     for inst in insts:
         if inst.is_meta:
             check_dimensions(args.url, inst)
+            # Check that datamodels for properties that refer to
+            # a specific datamodel can be loaded.
+            for prop in inst.properties['properties']:
+                if prop.type == 'ref':
+                    if prop.ref == 'ref':
+                        print(f'Property "{prop.name}" is of type "ref", the value '
+                                'is ref and not a uri. Check that the property '
+                                '"$ref" is given, the "$" is a strict requirement.')
+                        sys.exit(1)
+                    # Add the path of the original url to storage_path
+                    # since it is likely that referenced data models are 
+                    # in the same folder.
+                    dlite.storage_path.append(Path(args.url).resolve().parent)
+                    propmeta = dlite.get_instance(prop.ref)
+                    print(f"Datamodel for property '{prop.name}' was loaded successfully, and "
+                        " not further validated.")
+
 
     print(f'{args.url}: validated')
 

bindings/python/tests/entities/InvalidYaml2.yaml

@@ -0,0 +1,8 @@
+# An invalid version of datamodel Valid1.yaml
+uri: http://onto-ns.com/meta/0.1/InvalidYaml2
+description: A datamodel wiht invalid dimension (empty).
+dimensions:
+properties:
+  name:
+    type: str
+    description: Name of the item.

bindings/python/tests/entities/Ref_invalid1.json

@@ -0,0 +1,27 @@
+{
+  "uri": "http://onto-ns.com/meta/0.2/Ref",
+  "description": "A datamodel with ref-types...",
+  "dimensions": {
+    "nitems": "Number of items.",
+    "nrefs": "Number of references to Ref datamodels."
+  },
+  "properties": {
+    "item": {
+      "type": "ref",
+      "ref": "http://onto-ns.com/meta/0.1/Item",
+      "description": "Single item."
+    },
+    "items": {
+      "type": "ref",
+      "$ref": "http://onto-ns.com/meta/0.1/Item",
+      "shape": ["nitems"],
+      "description": "List of items."
+    },
+    "refs": {
+      "type": "ref",
+      "$ref": "http://onto-ns.com/meta/0.1/Ref",
+      "shape": ["nrefs"],
+      "description": "List of references to Ref datamodels.  This may become very cyclic, but DLite should cope with it..."
+    }
+  }
+}

bindings/python/tests/entities/ValidYaml_invalidref.yaml

@@ -0,0 +1,9 @@
+# An valid version of datamodel Invalid1.yaml
+uri: http://onto-ns.com/meta/0.1/ValidYaml1
+description: An datamodel for an item with float type and invalid shape name.
+dimensions: []
+properties:
+  name:
+    type: ref
+    description: Name of the item.
+    $ref: http://onto-ns.com/meta/0.1/InvalidYaml2

src/dlite-json.c

@@ -725,6 +725,8 @@ static DLiteInstance *parse_instance(const char *src, jsmntok_t *obj,
           if (dlite_property_jscan(src, t, p->name, ptr, p, pdims, 0) < 0)
             goto fail;
         } else {
+          if (!ptr)
+            FAIL1("cannot assign property with NULL destination: %s", p->name);
           if (dlite_type_scan(src+t->start, t->end - t->start, ptr, p->type,
                               p->size, 0) < 0)
             goto fail;