merged data-types to core-im (tests and schemas)

schema/Makefile

@@ -1,7 +1,4 @@
-all: gks-data-types gks-core-im gks-domain-entities
-
-gks-data-types:
-	(cd data-types; make all)
+all: gks-core-im gks-domain-entities
 
 gks-core-im:
 	(cd core-im; make all)
@@ -10,6 +7,5 @@ gks-domain-entities:
 	(cd domain-entities; make all)
 
 clean:
-	(cd data-types; make clean)
 	(cd core-im; make clean)
 	(cd domain-entities; make clean)

schema/core-im/core-im-source.yaml

@@ -2,8 +2,6 @@ $schema: "https://json-schema.org/draft/2020-12/schema"
 $id: "https://w3id.org/ga4gh/schema/gks-common/1.x/core-im/core-im-source.yaml"
 title: GKS Commons Core Information Class Definitions
 
-imports:
-  gks.data-types: ../data-types/data-types-source.yaml
 
 $defs:
   Entity:
@@ -48,7 +46,7 @@ $defs:
         type: array
         ordered: false
         items:
-          $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+          $ref: "#/$defs/Extension"
         description: >-
           A list of extensions to the Entity, that allow for capture of information not directly
           supported by elements defined in the model.
@@ -72,7 +70,7 @@ $defs:
         type: array
         ordered: false
         items:
-          $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping"
+          $ref: "#/$defs/ConceptMapping"
         description: >-
           A list of mappings to concepts in terminologies or code systems. Each mapping should
           include a coding and a relation.
@@ -98,7 +96,7 @@ $defs:
       specifiedBy:
         oneOf:
         - $ref: "#/$defs/Method"
-        - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+        - $ref: "#/$defs/IRI"
         description: >-
           A specification that describes all or part of the process that led to creation of the
           Information Entity
@@ -126,7 +124,7 @@ $defs:
         items:
           oneOf:
           - $ref: "#/$defs/Document"
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "#/$defs/IRI"
         description: A document in which the the Information Entity is reported.
       dateAuthored:
         type: string
@@ -171,7 +169,7 @@ $defs:
         default: Method
         description: MUST be "Method".
       subtype:
-        $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
+        $ref: "#/$defs/Coding"
         description: >-
           A specific type of method that a Method instance represents (e.g. 'Variant Interpretation
           Guideline', or 'Experimental Protocol').
@@ -207,7 +205,7 @@ $defs:
         default: Document
         description: Must be "Document"
       subtype:
-        $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
+        $ref: "#/$defs/Coding"
         description: >-
           A specific type of document that a Document instance represents (e.g.  'publication',
           'patent', 'pathology report')
@@ -273,7 +271,7 @@ $defs:
       Activities may use, generate, modify, move, or destroy one or more entities.
     heritableProperties:
       subtype:
-        $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
+        $ref: "#/$defs/Coding"
         description: >-
           A specific type of activity the Activity instance represents.
         $comment: >-
@@ -328,7 +326,7 @@ $defs:
           If multiple Agents contributed to an entity, a separate Contribution instances MUST be
           created for each.
       activityType:
-        $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
+        $ref: "#/$defs/Coding"
         description: >-
           The specific type of activity performed or role played by an agent in making the contribution
           (e.g. for a publication, agents may contribute as a primary author, editor, figure designer,
@@ -446,8 +444,8 @@ $defs:
           (supports, disputes, neutral)
       strengthOfEvidenceProvided:
         oneOf:
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "#/$defs/Coding"
+          - $ref: "#/$defs/IRI"
         description: >-
           The strength of support that an Evidence Line is determined to provide for or against its target Proposition,
           evaluated relative to the direction indicated by the directionOfEvidenceProvided value.
@@ -580,8 +578,8 @@ $defs:
           values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs
           'medium' vs 'low').
         oneOf:
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "#/$defs/Coding"
+          - $ref: "#/$defs/IRI"
       score:
         type: number
         description: >-
@@ -619,8 +617,8 @@ $defs:
       #     using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself.
       classification:
         oneOf:
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "#/$defs/Coding"
+          - $ref: "#/$defs/IRI"
         description: >-
           A single term or phrase summarizing the outcome of direction and strength
           assessments of a Statement's proposition, in terms of a classification of
@@ -678,7 +676,7 @@ $defs:
         default: DataSet
         description: MUST be "DataSet".
       subtype:
-        $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
+        $ref: "#/$defs/Coding"
         description: >-
           A specific type of data set the DataSet instance represents (e.g. a
           'clinical data set', a 'sequencing data set', a 'gene expression data set',
@@ -732,8 +730,8 @@ $defs:
       focus:
         oneOf:
           - $ref: "#/$defs/DomainEntity"
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "#/$defs/Coding"
+          - $ref: "#/$defs/IRI"
         description: >-
           The specific subject or experimental unit in a Study that data in the StudyResult object is about -
           e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD.
@@ -914,7 +912,7 @@ $defs:
   #       description: The Entity or concept about which the Proposition is made.
   #     predicate:
   #       type:
-  #         $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
+  #         $ref: "#/$defs/Coding"
   #       description: The relationship asserted to hold between the subject and the object of the Proposition.
   #     object:
   #       type:
@@ -929,3 +927,107 @@ $defs:
   #     - subject
   #     - predicate
   #     - object
+
+
+  Coding:
+    type: object
+    maturity: draft
+    description: >-
+      A structured representation of a code for a defined concept in a terminology or code system.
+    properties:
+      label:
+        type: string
+        description: The human-readable name for the coded concept, as defined by the code system.
+      system:
+        type: string
+        description: >-
+          The terminology/code system that defined the code. May be reported as a free-text name
+          (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system.
+          When the 'code' is reported as a CURIE, the 'system' should be reported as the uri that
+          the CURIE's prefix expands to (e.g. 'http://purl.obofoundry.org/so.owl/' for the
+          Sequence Ontology).
+      systemVersion:
+        type: string
+        description: Version of the terminology or code system that provided the code.
+      code:
+        $ref: '#/$defs/Code'
+        description: >-
+          A symbol uniquely identifying the concept, as in a syntax defined by the code system.
+          CURIE format is preferred where possible (e.g. 'SO:0000704' is the CURIE form of the
+          Sequence Ontology code for 'gene').
+    required:
+      - system
+      - code
+
+  ConceptMapping:
+    type: object
+    maturity: draft
+    description: >-
+      A mapping to a concept in a terminology or code system.
+    properties:
+      coding:
+        $ref: '#/$defs/Coding'
+        description: >-
+          A structured representation of a code for a defined concept in a terminology or code system.
+      relation:
+        description: >-
+          A mapping relation between concepts as defined by the Simple Knowledge Organization System (SKOS).
+        type: string
+        enum:
+          - closeMatch
+          - exactMatch
+          - broadMatch
+          - narrowMatch
+          - relatedMatch
+    required:
+      - relation
+      - coding
+
+  Extension:
+    type: object
+    maturity: draft
+    description: >-
+      The Extension class provides entities with a means to include
+      additional attributes that are outside of the specified standard
+      but needed by a given content provider or system implementer.
+      These extensions are not expected to be natively understood, but
+      may be used for pre-negotiated exchange of message attributes
+      between systems.
+    properties:
+      name:
+        type: string
+        description: >-
+          A name for the Extension. Should be indicative of its meaning and/or the type of
+          information it value represents.
+      value:
+        type: [ "number", "string", "boolean", "object", "array", "null" ]
+        description: The value of the Extension - can be any primitive or structured object
+        additionalProperties: true
+      description:
+        type: string
+        description: >-
+          A description of the meaning or utility of the Extension, to explain
+          the type of information it is meant to hold.
+    required:
+      - name
+      - value
+
+  Code:    
+    type: string
+    maturity: draft
+    description: >-
+      Indicates that the value is taken from a set of controlled strings defined elsewhere.
+      Technically, a code is restricted to a string which has at least one character and no leading or
+      trailing whitespace, and where there is no whitespace other than single spaces in the contents.
+    pattern: '\S+( \S+)*'
+    example: ENSG00000139618
+
+  IRI:
+    type: string
+    maturity: draft
+    description: >-
+      An IRI Reference (either an IRI or a relative-reference), according to `RFC3986 section 4.1
+      <https://datatracker.ietf.org/doc/html/rfc3986#section-4.1>`_ and `RFC3987 section 2.1
+      <https://datatracker.ietf.org/doc/html/rfc3987#section-2.1>`_. MAY be a JSON Pointer as an IRI fragment, as
+      described by `RFC6901 section 6 <https://datatracker.ietf.org/doc/html/rfc6901#section-6>`_.
+    format: iri-reference

schema/core-im/def/StudyResult.rst

@@ -79,8 +79,8 @@ Some StudyResult attributes are inherited from :ref:`InformationEntity`.
    *  - ancillaryResults
       - object
       - 0..1
-      -
+      - 
    *  - qualityMeasures
       - object
       - 0..1
-      -
+      - 

schema/core-im/json/Agent

@@ -31,7 +31,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."

schema/data-types/json/Code → schema/core-im/json/Code

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/data-types/json/Code",
+   "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/core-im/json/Code",
    "title": "Code",
    "type": "string",
    "maturity": "draft",

schema/data-types/json/Coding → schema/core-im/json/Coding

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/data-types/json/Coding",
+   "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/core-im/json/Coding",
    "title": "Coding",
    "type": "object",
    "maturity": "draft",
@@ -19,13 +19,12 @@
          "description": "Version of the terminology or code system that provided the code."
       },
       "code": {
-         "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Code",
+         "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Code",
          "description": "A symbol uniquely identifying the concept, as in a syntax defined by the code system. CURIE format is preferred where possible (e.g. 'SO:0000704' is the CURIE form of the Sequence Ontology code for 'gene')."
       }
    },
    "required": [
       "code",
       "system"
-   ],
-   "additionalProperties": false
+   ]
 }

schema/data-types/json/ConceptMapping → schema/core-im/json/ConceptMapping

@@ -1,13 +1,13 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping",
+   "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/core-im/json/ConceptMapping",
    "title": "ConceptMapping",
    "type": "object",
    "maturity": "draft",
    "description": "A mapping to a concept in a terminology or code system.",
    "properties": {
       "coding": {
-         "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Coding",
+         "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding",
          "description": "A structured representation of a code for a defined concept in a terminology or code system."
       },
       "relation": {
@@ -25,6 +25,5 @@
    "required": [
       "coding",
       "relation"
-   ],
-   "additionalProperties": false
+   ]
 }

schema/core-im/json/Contribution

@@ -31,13 +31,13 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
       },
       "subtype": {
-         "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Coding",
+         "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding",
          "description": "A specific type of activity the Activity instance represents.",
          "$comment": "This attribute can be used to report a specific type for the Activity, in cases where a model does not define Activity subclasses for this purpose. Implementers can define their own set of data set type codes/terms, to match the needs of the domain or application."
       },
@@ -74,7 +74,7 @@
          "$comment": "Note that this must be a single agent (which can be a Person, or an Organization). If multiple Agents contributed to an entity, a separate Contribution instances MUST be created for each."
       },
       "activityType": {
-         "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Coding",
+         "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding",
          "description": "The specific type of activity performed or role played by an agent in making the contribution (e.g. for a publication, agents may contribute as a primary author, editor, figure designer, data generator, etc. . Values of this property may be framed as activities or as contribution roles (e.g. using terms from the Contribution Role Ontology (CRO))."
       }
    },