additional test for % encoding

linkml · Jan 18, 2023 · fcbd2cb · fcbd2cb
1 parent 546f53c
commit fcbd2cb
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Showing 9 changed files with 27 additions and 5 deletions.
diff --git a/tests/test_loaders_dumpers/input/phenopackets/base.yaml b/tests/test_loaders_dumpers/input/phenopackets/base.yaml
@@ -48,6 +48,7 @@ classes:
         range: string
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: "e.g. ISBN, PMID:123456, DOI:..., FHIR mapping: Reference.identifier"
         range: string

diff --git a/tests/test_loaders_dumpers/input/phenopackets/biosample.yaml b/tests/test_loaders_dumpers/input/phenopackets/biosample.yaml
@@ -36,6 +36,7 @@ classes:
         range: OntologyClass
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: biosamples SAMN08666232 Human Cell Atlas The Biosample id This is unique in the context of the server instance. ARGO mapping specimen::submitter_specimen_id
         exact_mappings: 

diff --git a/tests/test_loaders_dumpers/input/phenopackets/individual.yaml b/tests/test_loaders_dumpers/input/phenopackets/individual.yaml
@@ -21,6 +21,7 @@ classes:
         range: OntologyClass
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: An identifier for the individual. This must be unique within the record. ARGO mapping donor::submitter_donor_id
         exact_mappings: 

diff --git a/tests/test_loaders_dumpers/input/phenopackets/interpretation.yaml b/tests/test_loaders_dumpers/input/phenopackets/interpretation.yaml
@@ -61,6 +61,7 @@ classes:
         range: Diagnosis
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: id of the interpretation
         range: string

diff --git a/tests/test_loaders_dumpers/input/phenopackets/meta_data.yaml b/tests/test_loaders_dumpers/input/phenopackets/meta_data.yaml
@@ -46,8 +46,10 @@ classes:
     description: ''
   Resource: 
     attributes: 
-      id: 
+      id:
+        identifier: true
         annotations: 
+          percent_encoded: true
           rank: 1
         description: "for OBO Ontologies, the value of this string MUST always be the official OBO ID, which is always equivalent to the ID prefix in lower case. Examples: hp, go, mp, mondo Consult http://obofoundry.org for a complete list For other ontologies (e.g. SNOMED), use the prefix in identifiers.org"
         range: string

diff --git a/tests/test_loaders_dumpers/input/phenopackets/phenopackets.yaml b/tests/test_loaders_dumpers/input/phenopackets/phenopackets.yaml
@@ -16,6 +16,7 @@ classes:
         range: File
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: ''
         range: string
@@ -49,6 +50,7 @@ classes:
         range: File
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: An identifier specific for this family.
         range: string
@@ -101,6 +103,7 @@ classes:
         range: File
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: An identifier specific for this phenopacket.
         range: string

diff --git a/tests/test_loaders_dumpers/input/phenopackets/vrs.yaml b/tests/test_loaders_dumpers/input/phenopackets/vrs.yaml
@@ -35,6 +35,7 @@ classes:
         range: DerivedSequenceExpression
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: ''
         range: string
@@ -79,6 +80,7 @@ classes:
         range: string
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: ''
         range: string
@@ -128,6 +130,7 @@ classes:
         range: Haplotype
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: ''
         range: string
@@ -305,6 +308,7 @@ classes:
         range: Haplotype
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: ''
         range: string
@@ -518,6 +522,7 @@ classes:
     attributes: 
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: ''
         range: string
@@ -586,6 +591,7 @@ classes:
         range: string
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: ''
         range: string

diff --git a/tests/test_loaders_dumpers/input/phenopackets/vrsatile.yaml b/tests/test_loaders_dumpers/input/phenopackets/vrsatile.yaml
@@ -110,6 +110,7 @@ classes:
         range: GeneDescriptor
       id: 
         annotations: 
+          percent_encoded: true
           rank: 1
         description: ''
         range: string
@@ -175,6 +176,7 @@ classes:
         range: string
       id: 
         annotations: 
+          percent_encoded: true
           rank: 4
         description: ''
         range: string

diff --git a/tests/test_loaders_dumpers/test_rdflib_dumper.py b/tests/test_loaders_dumpers/test_rdflib_dumper.py
@@ -16,7 +16,8 @@
 from tests.test_loaders_dumpers import INPUT_DIR, OUTPUT_DIR
 from tests.test_loaders_dumpers.models.personinfo import Container, Person, Address, Organization, OrganizationType
 from tests.test_loaders_dumpers.models.node_object import NodeObject, Triple
-from tests.test_loaders_dumpers.models.phenopackets import PhenotypicFeature, OntologyClass, Phenopacket, MetaData
+from tests.test_loaders_dumpers.models.phenopackets import PhenotypicFeature, OntologyClass, Phenopacket, MetaData, \
+    Resource
 
 SCHEMA = os.path.join(INPUT_DIR, 'personinfo.yaml')
 DATA = os.path.join(INPUT_DIR, 'example_personinfo_data.yaml')
@@ -351,7 +352,8 @@ def test_phenopackets(self):
             rdflib_dumper.dumps(c, view)
         cases = [
             ("HP:1", "http://purl.obolibrary.org/obo/HP_1", None),
-            ("FOO:1", "http://example.org/FOO_1", {'FOO': 'http://example.org/FOO_'}),
+            ("FOO:1", "http://example.org/FOO_1", {'FOO': 'http://example.org/FOO_',
+                                                   "@base": "http://example.org/base/"}),
         ]
         for id, expected_uri, prefix_map in cases:
 
@@ -364,14 +366,17 @@ def test_phenopackets(self):
                           f'Expected label {test_label} for {expected_uri} in {ttl}')
             pf = PhenotypicFeature(type=c)
             pkt = Phenopacket(id='id with spaces',
-                              metaData=MetaData(),
+                              metaData=MetaData(resources=[Resource(id='id with spaces')]),
                               phenotypicFeatures=[pf])
             ttl = rdflib_dumper.dumps(pkt, view, prefix_map=prefix_map)
-            print(ttl)
             g = Graph()
             g.parse(data=ttl, format='ttl')
             self.assertIn(Literal(test_label), list(g.objects(URIRef(expected_uri))),
                           f'Expected label {test_label} for {expected_uri} in {ttl}')
+            if prefix_map and "@base" in prefix_map:
+                resource_uri = URIRef(prefix_map["@base"] + "id%20with%20spaces")
+                self.assertEqual(1, len(list(g.objects(resource_uri))))
+