update sub schemas and fix tests

Makefile

@@ -0,0 +1,40 @@
+PYV:=3.12
+VEDIR=venv/${PYV}
+
+############################################################################
+#= SETUP, INSTALLATION, PACKAGING
+
+#=> venv: make a Python 3 virtual environment
+.PHONY: venv/%
+venv/%:
+	python$* -m venv $@; \
+	source $@/bin/activate; \
+	python -m ensurepip --upgrade; \
+	pip install --upgrade pip setuptools
+
+#=> develop: install package in develop mode
+.PHONY: develop setup
+develop setup:
+	pip install -r .requirements.txt
+
+#=> devready: create venv, install prerequisites, install pkg in develop mode
+.PHONY: devready
+devready:
+	make ${VEDIR} && source ${VEDIR}/bin/activate && make develop
+	@echo '#################################################################################'
+	@echo '###  Do not forget to `source ${VEDIR}/bin/activate` to use this environment  ###'
+	@echo '#################################################################################'
+
+############################################################################
+#= TESTING
+# see test configuration in pyproject.toml
+
+#=> test: execute tests
+.PHONY: test
+test:
+	pytest tests/
+
+#=> doctest: execute documentation tests (requires extra data)
+.PHONY: doctest
+doctest:
+	pytest tests/ --doctest-modules

examples/proteinSequenceConsequence-ex1.yaml

@@ -1,13 +1,13 @@
 id: civic.mpid:33
 type: ProteinSequenceConsequence
 description: >-
-  EGFR L858R has long been recognized as a functionally significant mutation in cancer, 
-  and is one of the most prevalent single mutations in lung cancer. Best described in 
-  non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first 
-  and second generation TKI's like gefitinib and neratinib. NSCLC patients with this 
-  mutation treated with TKI's show increased overall and progression-free survival, as 
-  compared to chemotherapy alone. Third generation TKI's are currently in clinical trials 
-  that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in 
+  EGFR L858R has long been recognized as a functionally significant mutation in cancer,
+  and is one of the most prevalent single mutations in lung cancer. Best described in
+  non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first
+  and second generation TKI's like gefitinib and neratinib. NSCLC patients with this
+  mutation treated with TKI's show increased overall and progression-free survival, as
+  compared to chemotherapy alone. Third generation TKI's are currently in clinical trials
+  that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in
   treating patients that failed to respond to earlier generation TKI therapies.
 label: EGFR L858R
 definingContext: vrs.json#/ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA
@@ -16,7 +16,7 @@ members:
   - vrs.json#/ga4gh:VA.3_FsKSUHEdurPIw5gqpw6g0_Ga0TEXQh
   - vrs.json#/ga4gh:VA.zpv3dW34z8jioKL-NtbGc0fa9clsgAZT
   - vrs.json#/ga4gh:VA.BJOtfUhZMooMJUO4FjxHXTEimrKXtF0i
-aliases:
+alternativeLabels:
   - LEU858ARG
   - rs121434568
 mappings:

schema/catvrs/catvrs-source.yaml

@@ -5,12 +5,12 @@ type: object
 strict: true
 
 imports:
-  gks.common: ../gks-common/common-source.yaml
+  gks.core: ../gks-core-im/core-im-source.yaml
   vrs: ../vrs/vrs-source.yaml
 
 namespaces:
   vrs: ../vrs/vrs.yaml#/$defs/
-  gks.common: ../gks-common/common.yaml#/$defs/
+  gks.core: ../gks-core-im/core-im.yaml#/$defs/
 
 $defs:
   # Categorical Variation are presented top-down. Everything rolls up to
@@ -22,7 +22,7 @@ $defs:
   # =============================================================================
 
   CategoricalVariation:
-    inherits: gks.common:DomainEntity
+    inherits: gks.core:DomainEntity
     description: >-
       A representation of a categorically-defined domain for variation, in which individual 
       contextual variation instances may be members of the domain.
@@ -41,7 +41,7 @@ $defs:
         items:
           oneOf:
             - $refCurie: vrs:Variation
-            - $refCurie: gks.common:IRI
+            - $refCurie: gks.core:IRI
 
   ProteinSequenceConsequence:
     maturity: draft
@@ -62,7 +62,7 @@ $defs:
       definingContext:
         oneOf:
           - $refCurie: vrs:Allele
-          - $refCurie: gks.common:IRI
+          - $refCurie: gks.core:IRI
         description: >-
           The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_
           object that is congruent with (projects to the same codons) as alleles on other protein reference 
@@ -88,7 +88,7 @@ $defs:
       definingContext:
         oneOf:
           - $refCurie: vrs:Allele
-          - $refCurie: gks.common:IRI
+          - $refCurie: gks.core:IRI
         description: >-
           The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_
           object that is congruent with variants on alternate reference sequences.
@@ -342,7 +342,7 @@ $defs:
   # =============================================================================
 
   CategoricalVariant:
-    inherits: gks.common:DomainEntity
+    inherits: gks.core:DomainEntity
     description: >-
       A top-level representation of a categorically-defined domain for variation across one or multiple biological levels in which individual contextual variants may be members of the domain.
     # type: object

schema/catvrs/def/CanonicalAllele.rst

@@ -28,27 +28,27 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`.
           - string
           - 0..1
           - A free-text description of the entity.
-       *  - mappings
-          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
+       *  - alternativeLabels
+          - string
           - 0..m
-          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
+          - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-common/common.json#/$defs/Extension>`_
+          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
        *  - type
           - string
           - 1..1
           - MUST be "CanonicalAllele"
-       *  - aliases
-          - string
+       *  - mappings
+          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
           - 0..m
-          - Aliases are alternate names for a Domain Entity.
+          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
        *  - definingContext
-          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
+          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
           - 1..1
           - The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_ object that is congruent with variants on alternate reference sequences.

schema/catvrs/def/CategoricalCnv.rst

@@ -28,24 +28,24 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`.
           - string
           - 0..1
           - A free-text description of the entity.
-       *  - mappings
-          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
+       *  - alternativeLabels
+          - string
           - 0..m
-          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
+          - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-common/common.json#/$defs/Extension>`_
+          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
        *  - type
           - string
           - 1..1
           - MUST be "CategoricalCnv"
-       *  - aliases
-          - string
+       *  - mappings
+          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
           - 0..m
-          - Aliases are alternate names for a Domain Entity.
+          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
        *  - location

schema/catvrs/def/CategoricalVariation.rst

@@ -4,7 +4,7 @@ A representation of a categorically-defined domain for variation, in which indiv
 
     **Information Model**
 
-Some CategoricalVariation attributes are inherited from :ref:`gks.common:DomainEntity`.
+Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEntity`.
 
     .. list-table::
        :class: clean-wrap
@@ -28,23 +28,23 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.common:DomainE
           - string
           - 0..1
           - A free-text description of the entity.
-       *  - mappings
-          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
+       *  - alternativeLabels
+          - string
           - 0..m
-          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
+          - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-common/common.json#/$defs/Extension>`_
+          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
        *  - type
           - string
           - 1..1
           - 
-       *  - aliases
-          - string
+       *  - mappings
+          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
           - 0..m
-          - Aliases are alternate names for a Domain Entity.
+          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.

schema/catvrs/def/DescribedVariation.rst

@@ -20,24 +20,24 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation
           - string
           - 0..1
           - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
-       *  - mappings
-          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
+       *  - alternativeLabels
+          - string
           - 0..m
-          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
+          - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-common/common.json#/$defs/Extension>`_
+          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
        *  - type
           - string
           - 1..1
           - MUST be "DescribedVariation"
-       *  - aliases
-          - string
+       *  - mappings
+          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
           - 0..m
-          - Aliases are alternate names for a Domain Entity.
+          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
        *  - label

schema/catvrs/def/ProteinSequenceConsequence.rst

@@ -28,27 +28,27 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV
           - string
           - 0..1
           - A free-text description of the entity.
-       *  - mappings
-          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
+       *  - alternativeLabels
+          - string
           - 0..m
-          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
+          - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-common/common.json#/$defs/Extension>`_
+          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
        *  - type
           - string
           - 1..1
           - MUST be "ProteinSequenceConsequence"
-       *  - aliases
-          - string
+       *  - mappings
+          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
           - 0..m
-          - Aliases are alternate names for a Domain Entity.
+          - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
        *  - definingContext
-          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
+          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
           - 1..1
           - The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_ object that is congruent with (projects to the same codons) as alleles on other protein reference  sequences.

schema/catvrs/json/CanonicalAllele

@@ -18,19 +18,19 @@
          "type": "string",
          "description": "A free-text description of the entity."
       },
-      "mappings": {
+      "alternativeLabels": {
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/json/ConceptMapping"
+            "type": "string"
          },
-         "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation."
+         "description": "Alternative name(s) for the Entity."
       },
       "extensions": {
          "type": "array",
          "ordered": true,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core-im/1.x/json/Extension"
          },
          "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
       },
@@ -40,13 +40,13 @@
          "default": "CanonicalAllele",
          "description": "MUST be \"CanonicalAllele\""
       },
-      "aliases": {
-         "description": "Aliases are alternate names for a Domain Entity.",
-         "ordered": false,
+      "mappings": {
          "type": "array",
+         "ordered": false,
          "items": {
-            "type": "string"
-         }
+            "$ref": "/ga4gh/schema/gks-core-im/1.x/json/ConceptMapping"
+         },
+         "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation."
       },
       "members": {
          "type": "array",
@@ -55,7 +55,7 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI"
                },
                {
                   "$ref": "/ga4gh/schema/vrs/2.x/json/Variation"
@@ -66,7 +66,7 @@
       "definingContext": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI"
+               "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI"
             },
             {
                "$ref": "/ga4gh/schema/vrs/2.x/json/Allele"