Fix dlite.Instance.from_dict() to correctly parse ref-type properti…

…es (#983)

Make it possible to correctly parse YAML files with ref-type properties.
* Parse ref-type in yaml files
* Update bindings/python/tests/test_ref_type.py
* Only test ref-type for yaml if yaml is installed

---------

Co-authored-by: Francesca L. Bleken <[email protected]>

bindings/python/tests/input/test_ref_type_middle.yaml

@@ -0,0 +1,11 @@
+http://onto-ns.com/meta/0.2/Middle:
+  description: Middle-level nested data structure.
+  dimensions: []
+  properties:
+  - name: name
+    type: string
+    description: Value of this structure.
+  - name: leaf
+    type: ref
+    $ref: http://onto-ns.com/meta/0.1/Leaf
+    description: Reference to low-level structure.

bindings/python/tests/test_ref_type.py

@@ -1,15 +1,24 @@
 from pathlib import Path
 
 import dlite
+from dlite.testutils import importcheck
+
+yaml = importcheck("yaml")
 
 
 thisdir = Path(__file__).resolve().parent
 indir = thisdir / "input"
 
-dlite.storage_path.append(indir / "test_ref_type.json")
+dlite.storage_path.append(indir)
+dlite.storage_path.append(indir / "test_ref_type_middle.yaml")
+
+# If yaml is available, we read Middle v0.2, which is defined in
+# `test_ref_type_middle.yaml`.  Otherwise, we read Middle v0.1, which
+# is defined together with the other datamodels in `test_ref_type.json`.
+version = "0.2" if yaml else "0.1"
 
 Top = dlite.get_instance("http://onto-ns.com/meta/0.1/Top")
-Middle = dlite.get_instance("http://onto-ns.com/meta/0.1/Middle")
+Middle = dlite.get_instance(f"http://onto-ns.com/meta/{version}/Middle")
 Leaf = dlite.get_instance("http://onto-ns.com/meta/0.1/Leaf")
 Linked = dlite.get_instance("http://onto-ns.com/meta/0.1/Linked")
 Tree = dlite.get_instance("http://onto-ns.com/meta/0.1/Tree")
@@ -78,6 +87,8 @@
 assert cyclic.subtree[0].subtree[0] == cyclic
 assert cyclic.subtree[0].subtree[0].subtree[0] == cyclic
 
-# Instantiate nested from dict
-# For issue #515
-# middle = Middle(properties={"name": "nested", "leaf": {"a": 1, "b": True}})
+# For isue #982: ref-type in yaml
+assert Middle.getprop("leaf").ref == "http://onto-ns.com/meta/0.1/Leaf"
+
+# For issue #515: Instantiate nested from dict
+#middle = Middle(properties={"name": "nested", "leaf": {"a": 1, "b": True}})

bindings/python/utils.py

@@ -136,8 +136,16 @@ def instance_from_dict(d, id=None, single=None, check_storages=True):
     if meta.is_metameta:
         if "uri" in d:
             uri = d["uri"]
-        else:
+        elif "identity" in d:
+            uri = d["identity"]
+        elif "name" in d and "version" in d and "namespace" in d:
             uri = dlite.join_meta_uri(d["name"], d["version"], d["namespace"])
+        elif id and dlite.urlparse(id).scheme:
+            uri = id
+        else:
+            raise TypeError(
+                "`id` required for metadata when the URI is not in the dict"
+            )
 
         if check_storages:
             try:
@@ -169,6 +177,7 @@ def instance_from_dict(d, id=None, single=None, check_storages=True):
                     dlite.Property(
                         name=p["name"],
                         type=p["type"],
+                        ref=p.get("$ref", p.get("ref")),
                         shape=p.get("shape", p.get("dims")),
                         unit=p.get("unit"),
                         description=p.get("description"),
@@ -180,6 +189,7 @@ def instance_from_dict(d, id=None, single=None, check_storages=True):
                     dlite.Property(
                         name=k,
                         type=v["type"],
+                        ref=v.get("$ref", v.get("ref")),
                         shape=v.get("shape", v.get("dims")),
                         unit=v.get("unit"),
                         description=v.get("description"),