Merge pull request #66 from linkml/linkml-issue-450

linkml issue 450
linkml · Nov 4, 2021 · ab780db · ab780db
2 parents 6c222b2 + ba6f709
commit ab780db
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Showing 7 changed files with 106 additions and 12 deletions.
diff --git a/linkml_runtime/dumpers/rdflib_dumper.py b/linkml_runtime/dumpers/rdflib_dumper.py
@@ -68,12 +68,14 @@ def inject_triples(self, element: Any, schemaview: SchemaView, graph: Graph, tar
             t = schemaview.get_type(target_type)
             dt_uri = t.uri
             if dt_uri:
-                if dt_uri == 'xsd:string':
+                if dt_uri == 'rdfs:Resource':
+                    return URIRef(schemaview.expand_curie(element))
+                elif dt_uri == 'xsd:string':
                     return Literal(element)
                 else:
                     return Literal(element, datatype=namespaces.uri_for(dt_uri))
             else:
-                logging.error(f'NO DT: {t}')
+                logging.warning(f'No datatype specified for : {t.name}, using plain Literal')
                 return Literal(element)
         element_vars = {k: v for k, v in vars(element).items() if not k.startswith('_')}
         if len(element_vars) == 0:

diff --git a/tests/test_issues/input/linkml_issue_450.yaml b/tests/test_issues/input/linkml_issue_450.yaml
@@ -0,0 +1,19 @@
+id: https://w3id.org/linkml/examples/test
+prefixes:
+  linkml: https://w3id.org/linkml/
+default_range: my_str
+default_curi_maps:
+  - semweb_context
+
+types:
+  entity:
+    base: str
+    uri: rdfs:Resource
+
+classes:
+  C1:
+    attributes:
+      a:
+        range: entity
+
+
diff --git a/tests/test_loaders_dumpers/input/example_personinfo_data.ttl b/tests/test_loaders_dumpers/input/example_personinfo_data.ttl
@@ -25,7 +25,7 @@ P:002 a ns3:Person ;
             ns2:employed_at ROR:1 ;
             ns2:is_current true ] ;
     ns2:has_familial_relationships [ a ns2:FamilialRelationship ;
-            ns2:related_to "P:001" ;
+            ns2:related_to P:001 ;
             ns2:type <https://example.org/FamilialRelations#01> ] ;
     ns2:has_medical_history [ a ns2:MedicalEvent ;
             ns1:startedAtTime "2019-01-01"^^xsd:date ;

diff --git a/tests/test_loaders_dumpers/input/example_personinfo_data.yaml b/tests/test_loaders_dumpers/input/example_personinfo_data.yaml
@@ -4,6 +4,7 @@ persons:
     primary_email: [email protected]
     age_in_years: 33
     gender: cisgender man
+    depicted_by: https://example.org/pictures/fred.jpg
   - id: P:002
     name: joe schmoe
     primary_email: [email protected]
@@ -21,6 +22,10 @@ persons:
           id: CODE:D0001
           name: headache
           code_system: CODE:D
+          mappings:
+            - HP:0002315
+            - http://purl.obolibrary.org/obo/SYMP_0000504
+            - http://www.wikidata.org/entity/Q86
         procedure:
           id: CODE:P0001
           name: trepanation

diff --git a/tests/test_loaders_dumpers/input/personinfo.yaml b/tests/test_loaders_dumpers/input/personinfo.yaml
@@ -16,6 +16,8 @@ prefixes:
   GSSO: http://purl.obolibrary.org/obo/GSSO_
   famrel: https://example.org/FamilialRelations#
   bizcodes: https://example.org/bizcodes/
+  HP: http://purl.obolibrary.org/obo/HP_
+  skos: http://www.w3.org/2004/02/skos/core#
 default_prefix: personinfo
 default_range: string
 
@@ -25,6 +27,19 @@ emit_prefixes:
   - xsd
   - skos
 
+types:
+
+  CrossReference:
+    typeof: uriorcurie
+    description: A string URI or CURIE representation of an external identifier, modeled as a Resource in RDF
+    base: str
+    uri: rdfs:Resource
+
+  ImageURL:
+    typeof: uri
+    base: str
+    uri: xsd:anyURI
+
 classes:
 
   NamedThing:
@@ -35,6 +50,7 @@ classes:
       - name
       - description
       - image
+      - depicted_by
     close_mappings:
      - schema:Thing
 
@@ -91,6 +107,7 @@ classes:
     slots:
       - id
       - name
+      - depicted_by
 
   Address:
     class_uri: schema:PostalAddress
@@ -113,6 +130,10 @@ classes:
     attributes:
       code system:
         range: code system
+      mappings:
+        slot_uri: skos:exactMatch
+        multivalued: true
+        range: CrossReference
 
   DiagnosisConcept:
     is_a: Concept
@@ -217,6 +238,9 @@ slots:
     minimum_value: 0
     maximum_value: 999
   related_to:
+    range: NamedThing
+  depicted_by:
+    range: ImageURL
   type:
   street:
   city:

diff --git a/tests/test_loaders_dumpers/models/personinfo.py b/tests/test_loaders_dumpers/models/personinfo.py
@@ -1,5 +1,5 @@
 # Auto generated from personinfo.yaml by pythongen.py version: 0.9.0
-# Generation date: 2021-10-20 18:50
+# Generation date: 2021-11-03 18:00
 # Schema: personinfo
 #
 # id: https://w3id.org/linkml/examples/personinfo
@@ -22,8 +22,8 @@
 from linkml_runtime.utils.enumerations import EnumDefinitionImpl
 from rdflib import Namespace, URIRef
 from linkml_runtime.utils.curienamespace import CurieNamespace
-from linkml_runtime.linkml_model.types import Boolean, Date, Float, Integer, String
-from linkml_runtime.utils.metamodelcore import Bool, XSDDate
+from linkml_runtime.linkml_model.types import Boolean, Date, Float, Integer, String, Uri, Uriorcurie
+from linkml_runtime.utils.metamodelcore import Bool, URI, URIorCURIE, XSDDate
 
 metamodel_version = "1.7.0"
 
@@ -32,6 +32,7 @@
 
 # Namespaces
 GSSO = CurieNamespace('GSSO', 'http://purl.obolibrary.org/obo/GSSO_')
+HP = CurieNamespace('HP', 'http://purl.obolibrary.org/obo/HP_')
 BIZCODES = CurieNamespace('bizcodes', 'https://example.org/bizcodes/')
 FAMREL = CurieNamespace('famrel', 'https://example.org/FamilialRelations#')
 LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
@@ -40,12 +41,26 @@
 RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#')
 RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#')
 SCHEMA = CurieNamespace('schema', 'http://schema.org/')
-SKOS = CurieNamespace('skos', 'http://example.org/UNKNOWN/skos/')
+SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#')
 XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
 DEFAULT_ = PERSONINFO
 
 
 # Types
+class CrossReference(Uriorcurie):
+    """ A string URI or CURIE representation of an external identifier, modeled as a Resource in RDF """
+    type_class_uri = RDFS.Resource
+    type_class_curie = "rdfs:Resource"
+    type_name = "CrossReference"
+    type_model_uri = PERSONINFO.CrossReference
+
+
+class ImageURL(Uri):
+    type_class_uri = XSD.anyURI
+    type_class_curie = "xsd:anyURI"
+    type_name = "ImageURL"
+    type_model_uri = PERSONINFO.ImageURL
+
 
 # Class references
 class NamedThingId(extended_str):
@@ -96,6 +111,7 @@ class NamedThing(YAMLRoot):
     name: Optional[str] = None
     description: Optional[str] = None
     image: Optional[str] = None
+    depicted_by: Optional[Union[str, ImageURL]] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.id):
@@ -112,6 +128,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.image is not None and not isinstance(self.image, str):
             self.image = str(self.image)
 
+        if self.depicted_by is not None and not isinstance(self.depicted_by, ImageURL):
+            self.depicted_by = ImageURL(self.depicted_by)
+
         super().__post_init__(**kwargs)
 
 
@@ -254,6 +273,7 @@ class Place(YAMLRoot):
 
     id: Union[str, PlaceId] = None
     name: Optional[str] = None
+    depicted_by: Optional[Union[str, ImageURL]] = None
     aliases: Optional[Union[str, List[str]]] = empty_list()
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
@@ -265,6 +285,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.name is not None and not isinstance(self.name, str):
             self.name = str(self.name)
 
+        if self.depicted_by is not None and not isinstance(self.depicted_by, ImageURL):
+            self.depicted_by = ImageURL(self.depicted_by)
+
         if not isinstance(self.aliases, list):
             self.aliases = [self.aliases] if self.aliases is not None else []
         self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases]
@@ -339,6 +362,7 @@ class Concept(NamedThing):
 
     id: Union[str, ConceptId] = None
     code_system: Optional[Union[str, CodeSystemId]] = None
+    mappings: Optional[Union[Union[str, CrossReference], List[Union[str, CrossReference]]]] = empty_list()
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.id):
@@ -349,6 +373,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.code_system is not None and not isinstance(self.code_system, CodeSystemId):
             self.code_system = CodeSystemId(self.code_system)
 
+        if not isinstance(self.mappings, list):
+            self.mappings = [self.mappings] if self.mappings is not None else []
+        self.mappings = [v if isinstance(v, CrossReference) else CrossReference(v) for v in self.mappings]
+
         super().__post_init__(**kwargs)
 
 
@@ -427,7 +455,7 @@ class Relationship(YAMLRoot):
 
     started_at_time: Optional[Union[str, XSDDate]] = None
     ended_at_time: Optional[Union[str, XSDDate]] = None
-    related_to: Optional[str] = None
+    related_to: Optional[Union[str, NamedThingId]] = None
     type: Optional[str] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
@@ -437,8 +465,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.ended_at_time is not None and not isinstance(self.ended_at_time, XSDDate):
             self.ended_at_time = XSDDate(self.ended_at_time)
 
-        if self.related_to is not None and not isinstance(self.related_to, str):
-            self.related_to = str(self.related_to)
+        if self.related_to is not None and not isinstance(self.related_to, NamedThingId):
+            self.related_to = NamedThingId(self.related_to)
 
         if self.type is not None and not isinstance(self.type, str):
             self.type = str(self.type)
@@ -674,7 +702,10 @@ class slots:
                    model_uri=PERSONINFO.age_in_years, domain=None, range=Optional[int])
 
 slots.related_to = Slot(uri=PERSONINFO.related_to, name="related_to", curie=PERSONINFO.curie('related_to'),
-                   model_uri=PERSONINFO.related_to, domain=None, range=Optional[str])
+                   model_uri=PERSONINFO.related_to, domain=None, range=Optional[Union[str, NamedThingId]])
+
+slots.depicted_by = Slot(uri=PERSONINFO.depicted_by, name="depicted_by", curie=PERSONINFO.curie('depicted_by'),
+                   model_uri=PERSONINFO.depicted_by, domain=None, range=Optional[Union[str, ImageURL]])
 
 slots.type = Slot(uri=PERSONINFO.type, name="type", curie=PERSONINFO.curie('type'),
                    model_uri=PERSONINFO.type, domain=None, range=Optional[str])
@@ -721,6 +752,9 @@ class slots:
 slots.concept__code_system = Slot(uri=PERSONINFO.code_system, name="concept__code_system", curie=PERSONINFO.curie('code_system'),
                    model_uri=PERSONINFO.concept__code_system, domain=None, range=Optional[Union[str, CodeSystemId]])
 
+slots.concept__mappings = Slot(uri=SKOS.exactMatch, name="concept__mappings", curie=SKOS.curie('exactMatch'),
+                   model_uri=PERSONINFO.concept__mappings, domain=None, range=Optional[Union[Union[str, CrossReference], List[Union[str, CrossReference]]]])
+
 slots.container__persons = Slot(uri=PERSONINFO.persons, name="container__persons", curie=PERSONINFO.curie('persons'),
                    model_uri=PERSONINFO.container__persons, domain=None, range=Optional[Union[Dict[Union[str, PersonId], Union[dict, Person]], List[Union[dict, Person]]]])
 

diff --git a/tests/test_loaders_dumpers/test_rdflib_dumper.py b/tests/test_loaders_dumpers/test_rdflib_dumper.py
@@ -4,7 +4,7 @@
 import logging
 
 from rdflib import Graph, Literal
-from rdflib.namespace import RDF
+from rdflib.namespace import RDF, SKOS, XSD
 from rdflib import Namespace
 
 from linkml_runtime.loaders import json_loader
@@ -44,14 +44,24 @@ def test_rdflib_dumper(self):
         INFO = Namespace('https://w3id.org/linkml/examples/personinfo/')
         SDO = Namespace('http://schema.org/')
         GSSO = Namespace('http://purl.obolibrary.org/obo/GSSO_')
+        HP = Namespace('http://purl.obolibrary.org/obo/HP_')
+        SYMP = Namespace('http://purl.obolibrary.org/obo/SYMP_')
+        WD = Namespace('http://www.wikidata.org/entity/')
         self.assertIn((P['001'], RDF.type, SDO.Person), g)
         self.assertIn((P['001'], SDO.name, Literal("fred bloggs")), g)
         self.assertIn((P['001'], SDO.email, Literal("[email protected]")), g)
         self.assertIn((P['001'], INFO.age_in_years, Literal(33)), g)
         self.assertIn((P['001'], SDO.gender, GSSO['000371']), g)
+        self.assertIn((P['001'], INFO.depicted_by, Literal('https://example.org/pictures/fred.jpg', datatype=XSD.anyURI)), g)
+        self.assertNotIn((P['001'], INFO.depicted_by, Literal('https://example.org/pictures/fred.jpg', datatype=XSD.string)), g)
         #for (s,p,o) in g.triples((None, None, None)):
         #    print(f'{s} {p} {o}')
         self.assertIn((CODE['D0001'], RDF.type, INFO.DiagnosisConcept), g)
+        self.assertIn((CODE['D0001'], RDF.type, INFO.DiagnosisConcept), g)
+        self.assertIn((CODE['D0001'], SKOS.exactMatch, HP['0002315']), g)
+        self.assertIn((CODE['D0001'], SKOS.exactMatch, WD.Q86), g)
+        self.assertIn((CODE['D0001'], SKOS.exactMatch, SYMP['0000504']), g)
+        self.assertNotIn((CODE['D0001'], SKOS.exactMatch, Literal(HP['0002315'])), g)
         [container] = g.subjects(RDF.type, INFO.Container)
         self.assertIn((container, INFO.organizations, ROR['1']), g)
         self.assertIn((container, INFO.organizations, ROR['2']), g)