WIP: update to new build structure

.requirements.txt

@@ -1,8 +1,8 @@
 pytest
-python-jsonschema-objects>=0.4.0
-jsonschema==3.2.0
+jsonschema
+referencing
 ipython
 pyyaml
-ga4gh.gks.metaschema==0.3.0b1
+ga4gh.gks.metaschema==0.3.0b4
 sphinx ~= 7.2
 sphinx-rtd-theme ~= 1.2

schema/.gitignore

@@ -0,0 +1 @@
+build/

schema/Makefile

@@ -1,27 +1,40 @@
-.PHONY: defs FORCE
 .SECONDARY:
-.SUFFIXES:
 .DELETE_ON_ERROR:
 
-JSYAMLS:=vrs.yaml
-JSONS:=${JSYAMLS:.yaml=.json}
+BUILD_DIR := build
+IMPORT_DIR := import
 
-all: ${JSONS} merged.json defs
+vpath %tag $(BUILD_DIR)
+vpath %.classes $(BUILD_DIR)
 
-%.json: %.yaml
-	jsy2js.py <$< >$@
+SOURCES := $(wildcard *-source.yaml)
+TAGS := $(SOURCES:-source.yaml=.tag)
+IMPORTS := $(wildcard $(IMPORT_DIR)/*-source.yaml)
 
-%.yaml: %-source.yaml
-	source2jsy.py $< >$@
+all: build-ordered ${TAGS} prune.tag
 
-merged.yaml: vrs-source.yaml
-	source2mergedjsy.py $< >$@
+build-ordered: | $(BUILD_DIR)
 
-defs:
-	rm -rf defs
-	y2t.py vrs-source.yaml
-	ln -s ../../submodules/gks-common/schema/defs/gks.common defs/gks.common
+$(BUILD_DIR):
+	mkdir $(BUILD_DIR)
 
+%.tag: %.classes %.json-tag %.defs-tag
+	touch $(BUILD_DIR)/$@
 
-watch:
-	-while true; do ls -1 *.yaml | entr -dn make ${JSONS}; done
+%.classes: %-source.yaml
+	source2classes.py $< >${BUILD_DIR}/$@
+
+%.json-tag: %-source.yaml ${IMPORTS}
+	source2splitjs.py $<
+	touch $(BUILD_DIR)/$@
+
+%.defs-tag: %-source.yaml ${IMPORTS}
+	y2t.py $<
+	touch $(BUILD_DIR)/$@
+
+prune.tag: ${TAGS}
+	$(MAKE) -f prune.mk
+	touch $(BUILD_DIR)/$@
+
+clean:
+	rm $(BUILD_DIR)/*

schema/def/Adjacency.rst

@@ -0,0 +1,54 @@
+**Computational Definition**
+
+The `Adjacency` class can represent either the termination of a sequence or the adjoining of the end of a sequence with the beginning of an adjacent sequence, potentially with an intervening linker sequence.
+
+    **Information Model**
+
+Some Adjacency attributes are inherited from :ref:`Variation`.
+
+    .. list-table::
+       :class: clean-wrap
+       :header-rows: 1
+       :align: left
+       :widths: auto
+
+       *  - Field
+          - Type
+          - Limits
+          - Description
+       *  - id
+          - 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).
+       *  - label
+          - string
+          - 0..1
+          - A primary label for the entity.
+       *  - description
+          - string
+          - 0..1
+          - A free-text description of the entity.
+       *  - extensions
+          - `Extension <import/gks-common/core.json#/$defs/Extension>`_
+          - 0..m
+          - 
+       *  - type
+          - string
+          - 0..1
+          - MUST be "Adjacency".
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
+       *  - expressions
+          - :ref:`Expression`
+          - 0..m
+          - 
+       *  - adjoinedSequences
+          - `IRI.json <import/gks-common/json/IRI.json>`_ | :ref:`Location`
+          - 1..2
+          - The terminal sequence or pair of adjoined sequences that defines in the adjacency.
+       *  - linker
+          - :ref:`SequenceExpression`
+          - 0..1
+          - The sequence found between adjoined sequences.

schema/def/Allele.rst

@@ -0,0 +1,54 @@
+**Computational Definition**
+
+The state of a molecule at a :ref:`Location`.
+
+    **Information Model**
+
+Some Allele attributes are inherited from :ref:`Variation`.
+
+    .. list-table::
+       :class: clean-wrap
+       :header-rows: 1
+       :align: left
+       :widths: auto
+
+       *  - Field
+          - Type
+          - Limits
+          - Description
+       *  - id
+          - 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).
+       *  - label
+          - string
+          - 0..1
+          - A primary label for the entity.
+       *  - description
+          - string
+          - 0..1
+          - A free-text description of the entity.
+       *  - extensions
+          - `Extension <import/gks-common/core.json#/$defs/Extension>`_
+          - 0..m
+          - 
+       *  - type
+          - string
+          - 0..1
+          - MUST be "Allele"
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
+       *  - expressions
+          - :ref:`Expression`
+          - 0..m
+          - 
+       *  - location
+          - `IRI.json <import/gks-common/json/IRI.json>`_ | :ref:`Location`
+          - 1..1
+          - The location of the Allele
+       *  - state
+          - :ref:`SequenceExpression`
+          - 1..1
+          - An expression of the sequence state

schema/def/CopyNumber.rst

@@ -0,0 +1,50 @@
+**Computational Definition**
+
+A measure of the copies of a :ref:`Location` within a system (e.g. genome, cell, etc.)
+
+    **Information Model**
+
+Some CopyNumber attributes are inherited from :ref:`Variation`.
+
+    .. list-table::
+       :class: clean-wrap
+       :header-rows: 1
+       :align: left
+       :widths: auto
+
+       *  - Field
+          - Type
+          - Limits
+          - Description
+       *  - id
+          - 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).
+       *  - label
+          - string
+          - 0..1
+          - A primary label for the entity.
+       *  - description
+          - string
+          - 0..1
+          - A free-text description of the entity.
+       *  - extensions
+          - `Extension <import/gks-common/core.json#/$defs/Extension>`_
+          - 0..m
+          - 
+       *  - type
+          - string
+          - 0..1
+          - 
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
+       *  - expressions
+          - :ref:`Expression`
+          - 0..m
+          - 
+       *  - location
+          - `IRI.json <import/gks-common/json/IRI.json>`_ | :ref:`Location`
+          - 1..1
+          - A location for which the number of systemic copies is described.

schema/def/CopyNumberChange.rst

@@ -0,0 +1,54 @@
+**Computational Definition**
+
+An assessment of the copy number of a :ref:`Location` or a :ref:`Gene` within a system (e.g. genome, cell, etc.) relative to a baseline ploidy.
+
+    **Information Model**
+
+Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
+
+    .. list-table::
+       :class: clean-wrap
+       :header-rows: 1
+       :align: left
+       :widths: auto
+
+       *  - Field
+          - Type
+          - Limits
+          - Description
+       *  - id
+          - 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).
+       *  - label
+          - string
+          - 0..1
+          - A primary label for the entity.
+       *  - description
+          - string
+          - 0..1
+          - A free-text description of the entity.
+       *  - extensions
+          - `Extension <import/gks-common/core.json#/$defs/Extension>`_
+          - 0..m
+          - 
+       *  - type
+          - string
+          - 0..1
+          - MUST be "CopyNumberChange"
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
+       *  - expressions
+          - :ref:`Expression`
+          - 0..m
+          - 
+       *  - location
+          - `IRI.json <import/gks-common/json/IRI.json>`_ | :ref:`Location`
+          - 1..1
+          - A location for which the number of systemic copies is described.
+       *  - copyChange
+          - string
+          - 1..1
+          - MUST be one of "efo:0030069" (complete genomic loss), "efo:0020073" (high-level loss), "efo:0030068" (low-level loss), "efo:0030067" (loss), "efo:0030064" (regional base ploidy), "efo:0030070" (gain), "efo:0030071" (low-level gain), "efo:0030072" (high-level gain).

schema/def/CopyNumberCount.rst

@@ -0,0 +1,54 @@
+**Computational Definition**
+
+The absolute count of discrete copies of a :ref:`Location` or :ref:`Gene`, within a system (e.g. genome, cell, etc.).
+
+    **Information Model**
+
+Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
+
+    .. list-table::
+       :class: clean-wrap
+       :header-rows: 1
+       :align: left
+       :widths: auto
+
+       *  - Field
+          - Type
+          - Limits
+          - Description
+       *  - id
+          - 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).
+       *  - label
+          - string
+          - 0..1
+          - A primary label for the entity.
+       *  - description
+          - string
+          - 0..1
+          - A free-text description of the entity.
+       *  - extensions
+          - `Extension <import/gks-common/core.json#/$defs/Extension>`_
+          - 0..m
+          - 
+       *  - type
+          - string
+          - 0..1
+          - MUST be "CopyNumberCount"
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
+       *  - expressions
+          - :ref:`Expression`
+          - 0..m
+          - 
+       *  - location
+          - `IRI.json <import/gks-common/json/IRI.json>`_ | :ref:`Location`
+          - 1..1
+          - A location for which the number of systemic copies is described.
+       *  - copies
+          - integer | :ref:`Range`
+          - 1..1
+          - The integral number of copies of the subject in a system

schema/def/Expression.rst

@@ -0,0 +1,28 @@
+**Computational Definition**
+
+Representation of a variation by a specified nomenclature or syntax for a Variation object.  Common examples of expressions for the description of molecular variation include the HGVS  and ISCN nomenclatures.
+
+    **Information Model**
+
+    .. list-table::
+       :class: clean-wrap
+       :header-rows: 1
+       :align: left
+       :widths: auto
+
+       *  - Field
+          - Type
+          - Limits
+          - Description
+       *  - syntax
+          - string
+          - 1..1
+          - 
+       *  - value
+          - string
+          - 1..1
+          - 
+       *  - syntax_version
+          - string
+          - 0..1
+          -