Better support for external links

pipeline/src/base.py

@@ -232,9 +232,14 @@ def __init__(self, **properties):
 class Link:
     """Representation of a metadata node for which only the identifier is currently known."""
 
-    def __init__(self, identifier):
+    def __init__(self, identifier, allowed_types=None):
         self.identifier = identifier
+        self.allowed_types = allowed_types
 
+    def to_jsonld(self):
+        return {
+            "@id": self.identifier
+        }
 
 class IRI:
     """

pipeline/src/init_template.py.txt

@@ -6,6 +6,6 @@ openMINDS Python package
 
 __version__ = "{{version}}"
 
-from .base import Node, EmbeddedMetadata, LinkedMetadata, IRI
+from .base import Node, EmbeddedMetadata, LinkedMetadata, IRI, Link
 from .collection import Collection
 from .properties import Property

pipeline/src/properties.py

@@ -10,7 +10,14 @@
 from typing import Optional, Union, Iterable
 
 from .registry import lookup
-from .base import Node, IRI, Link, Node
+from .base import Node, IRI, Link
+
+
+def _could_be_instance(value, types):
+    """
+    True if a Link's allowed types are consistent with the given types
+    """
+    return isinstance(value, Link) and value.allowed_types and set(value.allowed_types).issubset(types)
 
 
 class Property:
@@ -89,6 +96,10 @@ def types(self):
             self._resolved_types = True
         return self._types
 
+    @property
+    def is_link(self) -> bool:
+        return issubclass(self.types[0], Node)
+
     def validate(self, value, ignore=None):
         """
         Check whether `value` satisfies all constraints.
@@ -113,7 +124,7 @@ def validate(self, value, ignore=None):
                 if not isinstance(value, (list, tuple)):
                     value = [value]
                 for item in value:
-                    if not isinstance(item, self.types):
+                    if not (isinstance(item, self.types) or _could_be_instance(item, self.types)):
                         if "type" not in ignore:
                             failures["type"].append(
                                 f"{self.name}: Expected {', '.join(t.__name__ for t in self.types)}, "
@@ -145,7 +156,7 @@ def validate(self, value, ignore=None):
                     failures["multiplicity"].append(
                         f"{self.name} does not accept multiple values, but contains {len(value)}"
                     )
-            elif not isinstance(value, self.types):
+            elif not (isinstance(value, self.types) or _could_be_instance(value, self.types)):
                 if "type" not in ignore:
                     failures["type"].append(
                         f"{self.name}: Expected {', '.join(t.__name__ for t in self.types)}, "
@@ -163,8 +174,9 @@ def deserialize(self, data):
         Args:
             data: the JSON-LD data
         """
-
         # todo: check data type
+        link_keys = set(("@id", "@type"))
+
         def deserialize_item(item):
             if self.types == (str,):
                 if self.formatting != "text/plain":
@@ -188,9 +200,18 @@ def deserialize_item(item):
                 if "@type" in item:
                     for cls in self.types:
                         if cls.type_ == item["@type"]:
-                            return cls.from_jsonld(item)
+                            if set(item.keys()) == link_keys:
+                                # if we only have @id and @type, it's a Link
+                                return Link(item["@id"], allowed_types=[cls])
+                            else:
+                                # otherwise it's a Node
+                                return cls.from_jsonld(item)
+                    raise TypeError(
+                        f"Mismatched types. Data has '{item['@type']}' "
+                        f"but property only allows {[cls.type_ for cls in self.types]}"
+                    )
                 else:
-                    return Link(item["@id"])
+                    return Link(item["@id"], allowed_types=self.types)
             else:
                 raise NotImplementedError()
 

pipeline/tests/test_instantiation.py

@@ -4,7 +4,7 @@
 
 import pytest
 
-from openminds.base import Node, IRI
+from openminds.base import Node, IRI, Link
 from openminds.latest import (
     chemicals,
     computation,
@@ -33,7 +33,9 @@
 
 def classes_in_module(module):
     contents = [getattr(module, name) for name in dir(module)]
-    return [item for item in contents if isinstance(item, type) and issubclass(item, Node)]
+    return [
+        item for item in contents if isinstance(item, type) and issubclass(item, Node)
+    ]
 
 
 def test_instantiation_random_data():
@@ -55,7 +57,10 @@ def test_json_roundtrip():
 
 
 def test_IRI():
-    valid_iris = ["https://example.com/path/to/my/file.txt", "file:///path/to/my/file.txt"]
+    valid_iris = [
+        "https://example.com/path/to/my/file.txt",
+        "file:///path/to/my/file.txt",
+    ]
     for value in valid_iris:
         iri = IRI(value)
         assert iri.value == value
@@ -69,3 +74,43 @@ def test_IRI():
         with pytest.raises(ValueError) as exc_info:
             iri = IRI(value)
         assert exc_info.value.args[0] == "Invalid IRI"
+
+
+def test_link():
+    from openminds.v4.controlled_terms import Species
+    from openminds.v4.core import DatasetVersion
+
+    maybe_mouse = Link("https://openminds.om-i.org/instances/species/musMusculus")
+
+    definitely_mouse = Link(
+        "https://openminds.om-i.org/instances/species/musMusculus",
+        allowed_types=[Species],
+    )
+
+    my_dsv1 = DatasetVersion(study_targets=[maybe_mouse])
+    failures1 = my_dsv1.validate(ignore=["required"])
+    assert len(failures1["type"]) == 1
+    assert "study_targets" in failures1["type"][0]
+
+    my_dsv2 = DatasetVersion(study_targets=[definitely_mouse])
+    failures2 = my_dsv2.validate(ignore=["required"])
+    assert len(failures2) == 0
+
+    expected = {
+        "@context": {
+            "@vocab": "https://openminds.om-i.org/props/",
+        },
+        "@type": "https://openminds.om-i.org/types/DatasetVersion",
+        "studyTarget": [
+            {
+                "@id": "https://openminds.om-i.org/instances/species/musMusculus",
+            },
+        ],
+    }
+    assert my_dsv1.to_jsonld(
+        include_empty_properties=False,
+        embed_linked_nodes=False
+    ) == my_dsv2.to_jsonld(
+        include_empty_properties=False,
+        embed_linked_nodes=False
+    ) == expected