Save schema version in JSON-LD files

pipeline/src/base.py

@@ -68,11 +68,14 @@ def to_jsonld(self, include_empty_properties=True, embed_linked_nodes=True, with
         """
 
         data = {"@type": self.type_}
+        if isinstance(self, LinkedMetadata):
+            data["schema:schemaVersion"] = self.schema_version
         if with_context:
             if self.type_.startswith("https://openminds.ebrains.eu/"):
                 data["@context"] = {"@vocab": "https://openminds.ebrains.eu/vocab/"}
             else:
                 data["@context"] = {"@vocab": "https://openminds.om-i.org/props/"}
+            data["@context"]["schema"] = "https://schema.org/"
         if hasattr(self, "id") and self.id:
             data["@id"] = self.id
         for property in self.__class__.properties:
@@ -122,6 +125,10 @@ def from_jsonld(cls, data, ignore_unexpected_keys=False):
         """
         data_copy = data.copy()
         context = data_copy.pop("@context", None)
+        schema_version = data_copy.pop("schema:schemaVersion", None)
+        # todo: also handle an expanded key, i.e., "https://schema.org/schemaVersion"
+        # todo: check major part of schema_version against self.schema_version
+        #       i.e. v4.1 and v4.0 would be ok, v5.0 and v4.0 would not
         type_ = data_copy.pop("@type")
         if isinstance(type_, list) and len(type_) == 1:
             type_ = type_[0]
@@ -138,7 +145,7 @@ def from_jsonld(cls, data, ignore_unexpected_keys=False):
             else:
                 # todo: implement or import a function that does a full JSON-LD expansion
                 #       not just this special case
-                expanded_path  = f"{cls.context['@vocab']}{property.path}"
+                expanded_path = f"{cls.context['@vocab']}{property.path}"
                 if expanded_path in data_copy:
                     value = data_copy.pop(expanded_path)
                     found = True
@@ -278,9 +285,8 @@ def __init__(self, identifier, allowed_types=None):
         self.allowed_types = allowed_types
 
     def to_jsonld(self):
-        return {
-            "@id": self.identifier
-        }
+        return {"@id": self.identifier}
+
 
 class IRI:
     """

pipeline/src/collection.py

@@ -91,9 +91,14 @@ def save(self, path, individual_files=False, include_empty_properties=False):
         for node in tuple(self.nodes.values()):
 
             if node.type_.startswith("https://openminds.ebrains.eu/"):
-                data_context = {"@vocab": "https://openminds.ebrains.eu/vocab/"}
+                data_context = {
+                    "@vocab": "https://openminds.ebrains.eu/vocab/"
+                }
             else:
-                data_context = {"@vocab": "https://openminds.om-i.org/props/"}
+                data_context = {
+                    "@vocab": "https://openminds.om-i.org/props/"
+                }
+            data_context["schema"] = "https://schema.org/"
 
             for linked_node in node.links:
                 self._add_node(linked_node)
@@ -169,12 +174,15 @@ def load(self, *paths):
                 data = json.load(fp)
             if "@graph" in data:
                 if data["@context"]["@vocab"].startswith("https://openminds.ebrains.eu/"):
-                    version = "v3"
+                    default_version = "v3"
                 else:
-                    version = "latest"
+                    default_version = "v4"
                 for item in data["@graph"]:
                     if "@type" in item:
-                        cls = lookup_type(item["@type"], version=version)
+                        version = default_version
+                        if "schema:schemaVersion" in item:  # todo: expand this using the context
+                            version = item["schema:schemaVersion"]
+                        cls = lookup_type(item["@type"], version=version.split(".")[0])
                         node = cls.from_jsonld(item)
                     else:
                         # allow links to metadata instances outside this collection
@@ -245,4 +253,3 @@ def sort_nodes_for_upload(self):
                     newly_sorted.append(node_id)
             unsorted -= set(newly_sorted)
         return [self.nodes[node_id] for node_id in sorted]
-

pipeline/tests/test_collections.py

@@ -96,17 +96,22 @@ def test_collection_sort_by_id():
     os.remove("test_collection_sort_by_id.jsonld")
 
     expected_saved_data = {
-        "@context": {"@vocab": "https://openminds.om-i.org/props/"},
+        "@context": {
+            "@vocab": "https://openminds.om-i.org/props/",
+            "schema": "https://schema.org/",
+        },
         "@graph": [
             {
                 "@id": "_:001",
                 "@type": "https://openminds.om-i.org/types/Organization",
                 "fullName": "University of That Place",
+                "schema:schemaVersion": "latest"
             },
             {
                 "@id": "_:002",
                 "@type": "https://openminds.om-i.org/types/Organization",
                 "fullName": "University of This Place",
+                "schema:schemaVersion": "latest"
             },
             {
                 "@id": "_:004",
@@ -117,6 +122,7 @@ def test_collection_sort_by_id():
                 ],
                 "familyName": "Professor",
                 "givenName": "A",
+                "schema:schemaVersion": "latest"
             },
         ],
     }

pipeline/tests/test_instantiation.py

@@ -104,8 +104,10 @@ def test_link():
     expected = {
         "@context": {
             "@vocab": "https://openminds.om-i.org/props/",
+            "schema": "https://schema.org/"
         },
         "@type": "https://openminds.om-i.org/types/DatasetVersion",
+        "schema:schemaVersion": "v4.0",
         "studyTarget": [
             {
                 "@id": "https://openminds.om-i.org/instances/species/musMusculus",

pipeline/tests/test_regressions.py

@@ -2,7 +2,7 @@
 import json
 import os
 from openminds import Collection, IRI
-from openminds.latest import core as omcore
+import openminds.v4.core as omcore
 from utils import build_fake_node
 
 
@@ -38,18 +38,24 @@ def test_issue_0003():
     )
     # on export, a single item should be wrapped in a list, where the property expects an array
     expected = {
-        "@context": {"@vocab": "https://openminds.om-i.org/props/"},
+        "@context": {
+            "@vocab": "https://openminds.om-i.org/props/",
+            "schema": "https://schema.org/"
+        },
         "@type": "https://openminds.om-i.org/types/FileArchive",
         "IRI": "http://example.com/archive.zip",
         "format": {
             "@type": "https://openminds.om-i.org/types/ContentType",
             "name": "application/zip",
+            "schema:schemaVersion": "v4.0",
         },
+        "schema:schemaVersion": "v4.0",
         "sourceData": [
             {
                 "@type": "https://openminds.om-i.org/types/File",
                 "IRI": "http://example.com/some_file.txt",
                 "name": "some_file.txt",
+                "schema:schemaVersion": "v4.0",
             }
         ],
     }
@@ -90,11 +96,15 @@ def test_issue0007():
 
     actual = person.to_jsonld(include_empty_properties=False, embed_linked_nodes=False, with_context=True)
     expected = {
-        "@context": {"@vocab": "https://openminds.om-i.org/props/"},
+        "@context": {
+            "@vocab": "https://openminds.om-i.org/props/",
+            "schema": "https://schema.org/"
+        },
         "@id": "_:001",
         "@type": "https://openminds.om-i.org/types/Person",
         "familyName": "Professor",
         "givenName": "A",
+        "schema:schemaVersion": "v4.0",
         "affiliation": [
             {
                 "@type": "https://openminds.om-i.org/types/Affiliation",
@@ -105,6 +115,7 @@ def test_issue0007():
                 "memberOf": {"@id": "_:003"},
             },
         ],
+
     }
     assert actual == expected
 
@@ -116,7 +127,10 @@ def test_issue0007():
         saved_data = json.load(fp)
     os.remove("issue0007.jsonld")
     expected_saved_data = {
-        "@context": {"@vocab": "https://openminds.om-i.org/props/"},
+        "@context": {
+            "@vocab": "https://openminds.om-i.org/props/",
+            "schema": "https://schema.org/"
+        },
         "@graph": [
             {
                 "@id": "_:001",
@@ -133,16 +147,19 @@ def test_issue0007():
                 ],
                 "familyName": "Professor",
                 "givenName": "A",
+                "schema:schemaVersion": "v4.0",
             },
             {
                 "@id": "_:002",
                 "@type": "https://openminds.om-i.org/types/Organization",
                 "fullName": "University of This Place",
+                "schema:schemaVersion": "v4.0",
             },
             {
                 "@id": "_:003",
                 "@type": "https://openminds.om-i.org/types/Organization",
                 "fullName": "University of That Place",
+                "schema:schemaVersion": "v4.0",
             },
         ],
     }
@@ -163,7 +180,10 @@ def test_issue0008():
     )
     actual = person.to_jsonld(include_empty_properties=False, embed_linked_nodes=False, with_context=True)
     expected = {
-        "@context": {"@vocab": "https://openminds.om-i.org/props/"},
+        "@context": {
+            "@vocab": "https://openminds.om-i.org/props/",
+            "schema": "https://schema.org/"
+        },
         "@id": "_:002",
         "@type": "https://openminds.om-i.org/types/Person",
         "affiliation": [
@@ -175,6 +195,7 @@ def test_issue0008():
         ],
         "familyName": "Professor",
         "givenName": "A",
+        "schema:schemaVersion": "v4.0",
     }
     assert actual == expected
 
@@ -261,12 +282,12 @@ def test_issue0073():
     # Infinite recursion in validate()
     ds1 = omcore.DatasetVersion(
         short_name="ds1",
-        is_variant_of=None
+        is_alternative_version_of=None
     )
     ds2 = omcore.DatasetVersion(
         short_name="ds2",
-        is_variant_of=ds1
+        is_alternative_version_of=ds1
     )
-    ds1.is_variant_of = ds2
+    ds1.is_alternative_version_of = ds2
 
     failures = ds1.validate()