feat: add language and datatype support when converting rdflib.terms.…

linkml_runtime/utils/yamlutils.py

@@ -7,8 +7,9 @@
 
 import yaml
 from deprecated.classic import deprecated
-from jsonasobj2 import JsonObj, JsonObjTypes, as_dict, as_json, items
-from rdflib import Graph, URIRef
+from jsonasobj2 import JsonObj, as_json, as_dict, JsonObjTypes, items
+import jsonasobj2
+from rdflib import Graph, URIRef, Literal
 from yaml.constructor import ConstructorError
 
 from linkml_runtime.utils.context_utils import CONTEXTS_PARAM_TYPE, merge_contexts
@@ -85,6 +86,17 @@ def _default(self, obj, filtr: Callable[[dict], dict] = None):
                     # elif isinstance(v, EnumDefinition):
                     elif isinstance(v, EnumDefinitionImpl):
                         rval[k] = v.code
+                    elif isinstance(v, Literal):
+                        if v.datatype:
+                            # use v and not not v.value to not serialize the python object (datetime, xml, html, ...)
+                            rval[k] = {
+                                '@value': str(v), '@type': v.datatype}
+                        elif v.language:
+                            # language tag format https://www.rfc-editor.org/rfc/rfc5646#section-2.1.1
+                            rval[k] = {
+                                '@value': v.value, '@language': v.language}
+                        else:
+                            rval[k] = v
                     else:
                         rval[k] = v
             return rval

pyproject.toml

@@ -71,6 +71,27 @@ enable = true
 vcs = "git"
 style = "pep440"
 
+[tool.poetry.scripts]
+comparefiles = "linkml_runtime.utils.comparefiles:cli"
+linkml-normalize = "linkml_runtime.processing.referencevalidator:cli"
+
+[tool.poetry.dependencies]
+python = "^3.8"
+click = "*"
+deprecated = "*"
+hbreader = "*"
+json-flattener = ">=0.1.9"
+jsonasobj2 = "==1.*,>=1.0.0,>=1.0.4"
+jsonschema = ">=3.2.0"
+prefixcommons = ">=0.1.12"
+pyyaml = "*"
+rdflib = ">=6.0.0"
+requests = "*"
+prefixmaps = ">=0.1.4"
+curies = ">=0.5.4"
+pydantic = ">=1.10.2, <3.0.0"
+html5lib = "^1.1"
+
 [tool.poetry.group.dev.dependencies]
 coverage = "^6.2"
 requests-cache = "^1.2.0"

tests/test_issues/test_linkml_runtime_issue_2475.py

@@ -0,0 +1,200 @@
+import dataclasses
+from dataclasses import dataclass
+import json
+from linkml_runtime import SchemaView
+from linkml_runtime.dumpers import rdflib_dumper
+from linkml_runtime.utils.metamodelcore import XSDDateTime
+from linkml_runtime.utils.yamlutils import YAMLRoot, as_rdf
+from linkml_runtime.utils.slot import Slot
+from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
+from linkml_runtime.utils.curienamespace import CurieNamespace
+from rdflib import Graph, Literal, URIRef
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Optional,
+    Union
+)
+import unittest
+
+
+schema_content = """
+id: Literal2JsonLD
+name: Literal2JsonLD
+prefixes:
+  ex: http://example.org/
+  linkml: https://w3id.org/linkml/
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+  rdfs: http://www.w3.org/2000/01/rdf-schema#
+  vcard: http://www.w3.org/2006/vcard/ns#
+default_prefix: ex
+default_range: string
+imports:
+- linkml:types
+classes:
+  Person:
+    class_uri: vcard:Individual
+    slots:
+      - comment
+      - nickname
+slots:
+  comment:
+    slot_uri: rdfs:comment
+  nickname:
+    slot_uri: vcard:nickname
+"""
+
+
+#
+# below was generated with gen-python using the above schema
+#
+
+# Auto generated from Literal2JsonLD.yaml by pythongen.py version: 0.0.1
+# Generation date: 2025-01-01T22:37:07
+# Schema: Literal2JsonLD
+#
+# id: Literal2JsonLD
+# description:
+# license: https://creativecommons.org/publicdomain/zero/1.0/
+
+
+metamodel_version = "1.7.0"
+version = None
+
+# Overwrite dataclasses _init_fn to add **kwargs in __init__
+dataclasses._init_fn = dataclasses_init_fn_with_kwargs
+
+# Namespaces
+EX = CurieNamespace('ex', 'http://example.org/')
+LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
+RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#')
+RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#')
+VCARD = CurieNamespace('vcard', 'http://www.w3.org/2006/vcard/ns#')
+DEFAULT_ = EX
+
+
+# Types
+
+# Class references
+
+
+@dataclass(repr=False)
+class Person(YAMLRoot):
+    _inherited_slots: ClassVar[List[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = VCARD["Individual"]
+    class_class_curie: ClassVar[str] = "vcard:Individual"
+    class_name: ClassVar[str] = "Person"
+    class_model_uri: ClassVar[URIRef] = EX.Person
+
+    comment: Optional[str] = None
+    nickname: Optional[str] = None
+
+    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+        if self.comment is not None and not isinstance(self.comment, str):
+            self.comment = str(self.comment)
+
+        if self.nickname is not None and not isinstance(self.nickname, str):
+            self.nickname = str(self.nickname)
+
+        super().__post_init__(**kwargs)
+
+
+# Enumerations
+
+
+# Slots
+class slots:
+    pass
+
+
+slots.comment = Slot(uri=RDFS.comment, name="comment", curie=RDFS.curie('comment'),
+                     model_uri=EX.comment, domain=None, range=Optional[str])
+
+slots.nickname = Slot(uri=VCARD.nickname, name="nickname", curie=VCARD.curie('nickname'),
+                      model_uri=EX.nickname, domain=None, range=Optional[str])
+
+#
+# below was generated with gen-jsonld-context using the above schema
+#
+
+context = {
+    "comments": {
+        "description": "Auto generated by LinkML jsonld context generator",
+        "generation_date": "2025-01-01T23:08:58",
+        "source": "Literal2JsonLD.yaml"
+    },
+    "@context": {
+        "xsd": "http://www.w3.org/2001/XMLSchema#",
+        "ex": "http://example.org/",
+        "linkml": "https://w3id.org/linkml/",
+        "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+        "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+        "vcard": "http://www.w3.org/2006/vcard/ns#",
+        "@vocab": "http://example.org/",
+        "comment": {
+            "@id": "rdfs:comment"
+        },
+        "nickname": {
+            "@id": "vcard:nickname"
+        },
+        "Person": {
+            "@id": "vcard:Individual"
+        }
+    }
+}
+
+
+#
+# the tests start here
+#
+
+
+class TestConvertingRDFLibLiteral(unittest.TestCase):
+    """
+    See https://github.com/linkml/linkml/issues/2475
+    """
+
+    def setUp(self) -> None:
+        self.schemaview = SchemaView(schema_content)
+        self.person = Person(
+            nickname=Literal("Bob", lang="en"),
+            comment=Literal("Bob is <b>strong</b>", datatype=RDF.HTML))
+
+    def _test_jsonld_has_tags(self, person: dict):
+        self.assertIn('@type', person)
+        self.assertIn(
+            'http://www.w3.org/2006/vcard/ns#Individual', person['@type'])
+        self.assertIn('http://www.w3.org/2000/01/rdf-schema#comment', person)
+        self.assertIn({'@type': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#HTML',
+                      '@value': 'Bob is <b>strong</b>'}, person['http://www.w3.org/2000/01/rdf-schema#comment'])
+        self.assertIn('http://www.w3.org/2006/vcard/ns#nickname', person)
+        self.assertIn({'@language': 'en', '@value': 'Bob'},
+                      person['http://www.w3.org/2006/vcard/ns#nickname'])
+
+    def test_rdflib_dumper_with_schemaview(self):
+        g = Graph()
+        g += rdflib_dumper.as_rdf_graph(element=self.person,
+                                        schemaview=self.schemaview)
+        self.assertEqual(len(g), 3)
+        jsonld = json.loads(g.serialize(format="json-ld"))
+        print(jsonld)
+        self.assertEqual(len(jsonld), 1)
+        person = jsonld[0]
+        self._test_jsonld_has_tags(person)
+
+    def test_rdflib_dumper_with_context(self):
+        g = Graph()
+        g += as_rdf(self.person, contexts=context)
+        self.assertEqual(len(g), 3)
+        jsonld = json.loads(g.serialize(format="json-ld"))
+        print(jsonld)
+        self.assertEqual(len(jsonld), 1)
+        person = jsonld[0]
+        self._test_jsonld_has_tags(person)
+
+
+if __name__ == "__main__":
+    unittest.main()