Additional tests for percent encoding of IDs for rdflib_dumper

Author: cmungall

linkml_runtime/dumpers/rdflib_dumper.py

@@ -160,8 +160,8 @@ def dumps(self, element: YAMLRoot, schemaview: SchemaView = None,
         return self.as_rdf_graph(element, schemaview, prefix_map=prefix_map).\
             serialize(format=fmt)
 
-    def _as_uri(self, element_id: str, id_slot: SlotDefinition, schemaview: SchemaView) -> URIRef:
-        if schemaview.is_slot_percent_encoded(id_slot):
+    def _as_uri(self, element_id: str, id_slot: Optional[SlotDefinition], schemaview: SchemaView) -> URIRef:
+        if id_slot and schemaview.is_slot_percent_encoded(id_slot):
             return URIRef(urllib.parse.quote(element_id))
         else:
             return schemaview.namespaces().uri_for(element_id)

tests/test_loaders_dumpers/input/phenopackets/any.yaml

@@ -0,0 +1,37 @@
+ 
+classes: 
+  Any: 
+    attributes: 
+      typeUrl: 
+        annotations: 
+          rank: 1
+        description: "A URL/resource name that uniquely identifies the type of the serialized protocol buffer message. This string must contain at least one \"/\" character. The last segment of the URL's path must represent the fully qualified name of the type (as in `path/google.protobuf.Duration`). The name should be in a canonical form (e.g., leading \".\" is not accepted).  In practice, teams usually precompile into the binary all types that they expect it to use in the context of Any. However, for URLs which use the scheme `http`, `https`, or no scheme, one can optionally set up a type server that maps type URLs to message definitions as follows:  * If no scheme is provided, `https` is assumed. * An HTTP GET on the URL must yield a [google.protobuf.Type][] value in binary format, or produce an error. * Applications are allowed to cache lookup results based on the URL, or have them precompiled into a binary to avoid any lookup. Therefore, binary compatibility needs to be preserved on changes to types. (Use versioned type names to manage breaking changes.)  Note: this functionality is not currently available in the official protobuf release, and it is not used for type URLs beginning with type.googleapis.com.  Schemes other than `http`, `https` (or the empty scheme) might be used with implementation specific semantics. "
+        range: string
+      value: 
+        annotations: 
+          rank: 2
+        description: Must be a valid serialized protocol buffer of the above specified type.
+        range: string
+    description: "`Any` contains an arbitrary serialized protocol buffer message along with a URL that describes the type of the serialized message.  Protobuf library provides support to pack/unpack Any values in the form of utility functions or additional generated methods of the Any type.  Example 1: Pack and unpack a message in C++.  Foo foo = ...; Any any; any.PackFrom(foo); ... if (any.UnpackTo(&foo)) { ... }  Example 2: Pack and unpack a message in Java.  Foo foo = ...; Any any = Any.pack(foo); ... if (any.is(Foo.class)) { foo = any.unpack(Foo.class); }  Example 3: Pack and unpack a message in Python.  foo = Foo(...) any = Any() any.Pack(foo) ... if any.Is(Foo.DESCRIPTOR): any.Unpack(foo) ...  Example 4: Pack and unpack a message in Go  foo := &pb.Foo{...} any, err := anypb.New(foo) if err != nil { ... } ... foo := &pb.Foo{} if err := any.UnmarshalTo(foo); err != nil { ... }  The pack methods provided by protobuf library will by default use 'type.googleapis.com/full.type.name' as the type URL and the unpack methods only use the fully qualified type name after the last '/' in the type URL, for example \"foo.bar.com/x/y.z\" will yield type name \"y.z\".   JSON ==== The JSON representation of an `Any` value uses the regular representation of the deserialized, embedded message, with an additional field `@type` which contains the type URL. Example:  package google.profile; message Person { string first_name = 1; string last_name = 2; }  { \"@type\": \"type.googleapis.com/google.profile.Person\", \"firstName\": <string>, \"lastName\": <string> }  If the embedded message type is well-known and has a custom JSON representation, that representation will be embedded adding a field `value` which holds the custom JSON in addition to the `@type` field. Example (for message [google.protobuf.Duration][]):  { \"@type\": \"type.googleapis.com/google.protobuf.Duration\", \"value\": \"1.212s\" } "
+default_prefix: any
+description: "Automatic translation of phenopackets protobuf to LinkML. Status: EXPERIMENTAL."
+enums: {}
+
+id: https://w3id.org/linkml/phenopackets/any
+imports: 
+  - linkml:types
+name: any
+prefixes: 
+  GENO: http://purl.obolibrary.org/obo/GENO_
+  HP: http://purl.obolibrary.org/obo/HP_
+  LOINC: https://loinc.org/
+  MONDO: http://purl.obolibrary.org/obo/MONDO_
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  UBERON: http://purl.obolibrary.org/obo/UBERON_
+  UCUM: http://unitsofmeasure.org/
+  UO: http://purl.obolibrary.org/obo/UO_
+  any: https://w3id.org/linkml/phenopackets/any/
+  argo: https://docs.icgc-argo.org/dictionary/
+  linkml: https://w3id.org/linkml/
+slots: {}
+

tests/test_loaders_dumpers/input/phenopackets/base.yaml

@@ -0,0 +1,227 @@
+ 
+classes: 
+  Age: 
+    attributes: 
+      iso8601duration: 
+        annotations: 
+          rank: 1
+        description: The :ref:`ISO 8601<metadata_date_time>` age of this object as ISO8601 duration or time intervals. e.g. P40Y10M05D)
+        range: string
+    description: See http://build.fhir.org/datatypes and http://build.fhir.org/condition-definitions.html#Condition.onset_x_ In FHIR this is represented as a UCUM measurement - http://unitsofmeasure.org/trac/
+  AgeRange: 
+    attributes: 
+      end: 
+        annotations: 
+          rank: 2
+        description: ''
+        range: Age
+      start: 
+        annotations: 
+          rank: 1
+        description: ''
+        range: Age
+    description: ''
+  Dictionary: 
+    comments: 
+      - TODO
+  Evidence: 
+    attributes: 
+      evidenceCode: 
+        annotations: 
+          rank: 1
+        description: "The encoded evidence type using, for example the Evidence & Conclusion Ontology (ECO - http://purl.obolibrary.org/obo/eco.owl) FHIR mapping: Condition.evidence.code"
+        inlined: true
+        range: OntologyClass
+      reference: 
+        annotations: 
+          rank: 2
+        description: "FHIR mapping: Condition.evidence.detail"
+        inlined: true
+        range: ExternalReference
+    description: "FHIR mapping: Condition.evidence (https://www.hl7.org/fhir/condition-definitions.html#Condition.evidence)"
+  ExternalReference: 
+    attributes: 
+      description: 
+        annotations: 
+          rank: 3
+        description: "Human readable title or display string for the reference FHIR mapping: Reference.display"
+        range: string
+      id: 
+        annotations: 
+          rank: 1
+        description: "e.g. ISBN, PMID:123456, DOI:..., FHIR mapping: Reference.identifier"
+        range: string
+      reference: 
+        annotations: 
+          rank: 2
+        description: A full or partial URL pointing to the external reference if no commonly resolvable identifier can be used in the `id` field FHIR mapping Reference.reference
+        range: string
+    description: "FHIR mapping: Reference (https://www.hl7.org/fhir/references.html)"
+  File: 
+    attributes: 
+      fileAttributes: 
+        annotations: 
+          rank: 3
+        description: Map of attributes describing the file. For example the File format or genome assembly would be defied here. For genomic data files there MUST be a 'genomeAssembly' key.
+        inlined: true
+        range: Dictionary
+      individualToFileIdentifiers: 
+        annotations: 
+          rank: 2
+        description: A map of identifiers mapping an individual to a sample in the file. The key values must correspond to the Individual::id for the individuals in the message, the values must map to the samples in the file.
+        inlined: true
+        range: Dictionary
+      uri: 
+        annotations: 
+          rank: 1
+        description: URI for the file e.g. file://data/genomes/file1.vcf.gz or https://opensnp.org/data/60.23andme-exome-vcf.231?1341012444
+        range: string
+    description: ''
+  GestationalAge: 
+    attributes: 
+      days: 
+        annotations: 
+          rank: 2
+        description: ''
+        range: integer
+      weeks: 
+        annotations: 
+          rank: 1
+        description: ''
+        range: integer
+    description: ''
+  OntologyClass: 
+    attributes: 
+      id: 
+        annotations: 
+          rank: 1
+        description: a CURIE-style identifier e.g. HP:0100024, MP:0001284, UBERON:0001690. This is the primary key for the ontology class REQUIRED!
+        identifier: true
+        range: string
+        required: true
+      label: 
+        annotations: 
+          rank: 2
+        description: class label, aka name. E.g. "Abnormality of cardiovascular system"
+        range: string
+    description: "A class (aka term, concept) in an ontology. FHIR mapping: CodeableConcept (http://www.hl7.org/fhir/datatypes.html#CodeableConcept) see also Coding (http://www.hl7.org/fhir/datatypes.html#Coding)"
+  Procedure: 
+    attributes: 
+      bodySite: 
+        annotations: 
+          rank: 2
+        description: "FHIR mapping: Procedure.bodySite"
+        inlined: true
+        range: OntologyClass
+      code: 
+        annotations: 
+          rank: 1
+        description: "FHIR mapping: Procedure.code"
+        inlined: true
+        range: OntologyClass
+      performed: 
+        annotations: 
+          rank: 3
+        description: When the procedure was performed.
+        inlined: true
+        range: TimeElement
+    description: "A clinical procedure performed on a subject. By preference a single concept to indicate both the procedure and the body site should be used. In cases where this is not possible, the body site should be indicated using a separate ontology class. e.g. {\"code\":{\"NCIT:C51585\": \"Biopsy of Soft Palate\"}} {\"code\":{\"NCIT:C28743\": \"Punch Biopsy\"}, \"body_site\":{\"UBERON:0003403\": \"skin of forearm\"}} - a punch biopsy of the skin from the forearm FHIR mapping: Procedure (https://www.hl7.org/fhir/procedure.html)"
+  TimeElement: 
+    attributes: 
+      age: 
+        annotations: 
+          rank: 1
+        description: ''
+        range: Age
+      ageRange: 
+        annotations: 
+          rank: 2
+        description: ''
+        range: AgeRange
+      gestationalAge: 
+        annotations: 
+          rank: 6
+        description: ''
+        range: GestationalAge
+      interval: 
+        annotations: 
+          rank: 5
+        description: ''
+        inlined: true
+        range: TimeInterval
+      ontologyClass: 
+        annotations: 
+          rank: 3
+        description: ''
+        inlined: true
+        range: OntologyClass
+      timestamp: 
+        annotations: 
+          rank: 4
+        description: ''
+        range: string
+    description: ''
+    rules: 
+      - 
+        postconditions: 
+          exactly_one_of: 
+            - 
+              slot_conditions: 
+                gestationalAge: 
+                  required: true
+            - 
+              slot_conditions: 
+                age: 
+                  required: true
+            - 
+              slot_conditions: 
+                ageRange: 
+                  required: true
+            - 
+              slot_conditions: 
+                ontologyClass: 
+                  required: true
+            - 
+              slot_conditions: 
+                timestamp: 
+                  required: true
+            - 
+              slot_conditions: 
+                interval: 
+                  required: true
+  TimeInterval: 
+    attributes: 
+      end: 
+        annotations: 
+          rank: 2
+        description: ''
+        range: string
+      start: 
+        annotations: 
+          rank: 1
+        description: ''
+        range: string
+    description: ''
+default_prefix: base
+description: "Automatic translation of phenopackets protobuf to LinkML. Status: EXPERIMENTAL."
+enums: {}
+
+id: https://w3id.org/linkml/phenopackets/base
+imports: 
+  - linkml:types
+  - timestamp
+name: base
+prefixes: 
+  GENO: http://purl.obolibrary.org/obo/GENO_
+  HP: http://purl.obolibrary.org/obo/HP_
+  LOINC: https://loinc.org/
+  MONDO: http://purl.obolibrary.org/obo/MONDO_
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  UBERON: http://purl.obolibrary.org/obo/UBERON_
+  UCUM: http://unitsofmeasure.org/
+  UO: http://purl.obolibrary.org/obo/UO_
+  argo: https://docs.icgc-argo.org/dictionary/
+  base: https://w3id.org/linkml/phenopackets/base/
+  linkml: https://w3id.org/linkml/
+slots: {}
+