build triggered by submodule version

Author: openMINDS pipeline

openminds/base.py

@@ -47,7 +47,7 @@ def value_to_jsonld(value):
                 else:
                     if hasattr(value, "id") and value.id is None:
                         raise ValueError("Exporting as a stand-alone JSON-LD document requires @id to be defined.")
-                    item = {"@id": value.id, "@type": value.type_}
+                    item = {"@id": value.id}
             elif isinstance(value, EmbeddedMetadata):
                 item = value.to_jsonld(
                     with_context=False,
@@ -142,6 +142,14 @@ def links(self):
                 _links.extend(value.links)
         return _links
 
+    def _resolve_links(self, node_lookup):
+        """Replace `Link` attributes with typed Nodes where possible"""
+        for property in self.__class__.properties:
+            value = getattr(self, property.name)
+            if isinstance(value, Link):
+                resolved_value = node_lookup[value.identifier]
+                setattr(self, property.name, resolved_value)
+
 
 class LinkedMetadata(Node):
     """
@@ -181,9 +189,16 @@ def __init__(self, **properties):
             setattr(self, name, value)
 
 
+class Link:
+    """Representation of a metadata node for which only the identifier is currently known."""
+
+    def __init__(self, identifier):
+        self.identifier = identifier
+
+
 class IRI:
     """
-    Representation of an Internationalized Resource Identifier
+    Representation of an International Resource Identifier
     """
 
     def __init__(self, value: Union[str, IRI]):

openminds/collection.py

@@ -8,6 +8,7 @@
 import json
 import os
 from .registry import lookup_type
+from .base import Link
 
 
 class Collection:
@@ -147,15 +148,31 @@ def load(self, *paths):
                 data = json.load(fp)
             if "@graph" in data:
                 for item in data["@graph"]:
-                    cls = lookup_type(item["@type"])
-                    node = cls.from_jsonld(item)
+                    if "@type" in item:
+                        cls = lookup_type(item["@type"])
+                        node = cls.from_jsonld(item)
+                    else:
+                        # allow links to metadata instances outside this collection
+                        if not item["@id"].startswith("http"):
+                            raise ValueError("Local nodes must have @type specified")
+                        node = Link(item["@id"])
                     self.add(node)
             else:
-                if "@type" not in data:
-                    raise ValueError(f"Invalid file '{path}': no @type property")
-                cls = lookup_type(data["@type"])
-                node = cls.from_jsonld(data)
+                if "@type" in data:
+                    cls = lookup_type(data["@type"])
+                    node = cls.from_jsonld(data)
+                else:
+                    # allow links to metadata instances outside this collection
+                    if not data["@id"].startswith("http"):
+                        raise ValueError("Local nodes must have @type specified")
+                    node = Link(data["@id"])
                 self.add(node)
+        self._resolve_links()
+
+    def _resolve_links(self):
+        """Replace `Link` attributes with typed Nodes where possible"""
+        for node in self.nodes.values():
+            node._resolve_links(self.nodes)
 
     def validate(self):
         """

openminds/latest/publications/live_paper_version.py

@@ -4,9 +4,9 @@
 
 # this file was auto-generated!
 
+from datetime import datetime
 from openminds.base import IRI
 from datetime import date
-from datetime import datetime
 
 from openminds.base import LinkedMetadata
 from openminds.properties import Property

openminds/properties.py

@@ -7,7 +7,7 @@
 from datetime import datetime, date
 from collections import defaultdict
 from .registry import lookup
-from .base import Node, IRI
+from .base import Node, IRI, Link
 
 
 class Property:
@@ -146,7 +146,7 @@ def deserialize_item(item):
                         if cls.type_ == item["@type"]:
                             return cls.from_jsonld(item)
                 else:
-                    raise Exception("missing @type")
+                    return Link(item["@id"])
             else:
                 raise NotImplementedError()
 

openminds/v3/publications/live_paper_version.py

@@ -4,9 +4,9 @@
 
 # this file was auto-generated!
 
+from datetime import datetime
 from openminds.base import IRI
 from datetime import date
-from datetime import datetime
 
 from openminds.base import LinkedMetadata
 from openminds.properties import Property