rename

.gitignore

@@ -1,3 +1,10 @@
 *.old
 venv/
 target/
+Pipfile
+target/
+site/
+venv/
+docs/*md
+docs/types/
+*/my_schema.*

Makefile

@@ -1,29 +1,109 @@
-SHELL=/bin/bash -o pipefail
+SRC_DIR = src
+SCHEMA_DIR = $(SRC_DIR)/schema
+SOURCE_FILES := $(shell find $(SCHEMA_DIR) -name '*.yaml')
+SCHEMA_NAMES = $(patsubst $(SCHEMA_DIR)/%.yaml, %, $(SOURCE_FILES))
 
-EXTS = _datamodel.py .graphql .schema.json .owl -docs .shex
+SCHEMA_NAME = kgcl
+SCHEMA_SRC = $(SCHEMA_DIR)/$(SCHEMA_NAME).yaml
+TGTS = graphql jsonschema docs shex owl csv graphql python
 
-all: $(patsubst %,src/schema/ocl%, $(EXTS))
+#GEN_OPTS = --no-mergeimports
+GEN_OPTS = 
+
+all: gen stage
+gen: $(patsubst %,gen-%,$(TGTS))
+clean:
+	rm -rf target/
+	rm -rf docs/
+
+t:
+	echo $(SCHEMA_NAMES)
+
+echo:
+	echo $(patsubst %,gen-%,$(TGTS))
 
 test: all
 
-OUT = > $@.tmp && mv $@.tmp $@
-
-src/schema/%_datamodel.py: src/schema/%.yaml
-	gen-py-classes $< $(OUT)
-src/schema/%.graphql: src/schema/%.yaml
-	gen-graphql $< $(OUT)
-src/schema/%.schema.json: src/schema/%.yaml
-	gen-json-schema -t transaction $< $(OUT)
-src/schema/%.shex: src/schema/%.yaml
-	gen-shex $< $(OUT)
-src/schema/%.csv: src/schema/%.yaml
-	gen-csv $< $(OUT)
-src/schema/%.owl: src/schema/%.yaml
-	gen-owl $< $(OUT)
-src/schema/%.ttl: src/schema/%.owl
-	cp $< $@
-src/schema/%-docs: src/schema/%.yaml
-	pipenv run gen-markdown --dir $@ $<
-
-deploy-docs:
-	cp src/schema/ocl-docs/*md docs/
+install:
+	. environment.sh
+	pip install -r requirements.txt
+
+tdir-%:
+	mkdir -p target/$*
+docs:
+	mkdir $@
+
+stage: $(patsubst %,stage-%,$(TGTS))
+stage-%: gen-%
+	cp -pr target/$* .
+
+
+###  -- MARKDOWN DOCS --
+# Generate documentation ready for mkdocs
+# TODO: modularize imports
+gen-docs: target/docs/index.md copy-src-docs
+.PHONY: gen-docs
+copy-src-docs:
+	cp $(SRC_DIR)/docs/*md target/docs/
+target/docs/%.md: $(SCHEMA_SRC) tdir-docs
+	gen-markdown $(GEN_OPTS) --dir target/docs $<
+stage-docs: gen-docs
+	cp -pr target/docs .
+
+###  -- MARKDOWN DOCS --
+# TODO: modularize imports
+gen-python: $(patsubst %, target/python/%.py, $(SCHEMA_NAMES))
+.PHONY: gen-python
+target/python/%.py: $(SCHEMA_DIR)/%.yaml  tdir-python
+	gen-py-classes --no-mergeimports $(GEN_OPTS) $< > $@
+
+###  -- MARKDOWN DOCS --
+# TODO: modularize imports. For now imports are merged.
+gen-graphql:target/graphql/$(SCHEMA_NAME).graphql 
+target/graphql/%.graphql: $(SCHEMA_DIR)/%.yaml tdir-graphql
+	gen-graphql $(GEN_OPTS) $< > $@
+
+###  -- JSON schema --
+# TODO: modularize imports. For now imports are merged.
+gen-jsonschema: target/jsonschema/$(SCHEMA_NAME).schema.json
+target/jsonschema/%.schema.json: $(SCHEMA_DIR)/%.yaml tdir-jsonschema
+	gen-json-schema $(GEN_OPTS) -t transaction $< > $@
+
+###  -- Shex --
+# one file per module
+gen-shex: $(patsubst %, target/shex/%.shex, $(SCHEMA_NAMES))
+target/shex/%.shex: $(SCHEMA_DIR)/%.yaml tdir-shex
+	gen-shex --no-mergeimports $(GEN_OPTS) $< > $@
+
+###  -- CSV --
+# one file per module
+gen-csv: $(patsubst %, target/csv/%.csv, $(SCHEMA_NAMES))
+target/csv/%.csv: $(SCHEMA_DIR)/%.yaml tdir-csv
+	gen-csv $(GEN_OPTS) $< > $@
+
+###  -- OWL --
+# TODO: modularize imports. For now imports are merged.
+gen-owl: target/owl/$(SCHEMA_NAME).owl.ttl
+.PHONY: gen-owl
+target/owl/%.owl.ttl: $(SCHEMA_DIR)/%.yaml tdir-owl
+	gen-owl $(GEN_OPTS) $< > $@
+
+###  -- RDF (direct mapping) --
+# TODO: modularize imports. For now imports are merged.
+gen-rdf: target/rdf/$(SCHEMA_NAME).ttl
+target/rdf/%.ttl: $(SCHEMA_DIR)/%.yaml tdir-rdf
+	gen-rdf $(GEN_OPTS) $< > $@
+
+###  -- LinkML --
+# linkml (copy)
+# one file per module
+gen-linkml: target/linkml/$(SCHEMA_NAME).yaml
+target/linkml/%.yaml: $(SCHEMA_DIR)/%.yaml tdir-limkml
+	cp $< > $@
+
+# test docs locally.
+docserve:
+	mkdocs serve
+
+gh-deploy:
+	mkdocs gh-deploy

README.md

@@ -1,40 +1,8 @@
 # Ontology Change Language
 
-This repo includes schema and code for an Ontology Change Language
+This repo includes schema and code for an Ontology Change Language.
 
-The overall idea is laid out in:
+For full documentation, see:
 
-https://docs.google.com/document/d/1__7p64FOI5ZhiZ6F2TXtUc8JN1XXGwglOiVRrlg9G_c/edit#heading=h.xadk0a3ee8g
+[http://cmungall.github.io/knowledge-graph-change-language](http://cmungall.github.io/knowledge-graph-change-language)
 
-The goal is to provide a high level abstracted graph-oriented change
-language that is intended for describing changes in ontologies and
-ontology-like artefacts. The level of abstraction is intentionally at
-a higher level than either RDF or OWL. It currently does not attempt
-to encapsulate all of OWL. Instead it focuses on the majority of
-operations performed on ontologies.
-
-## Schema
-
-Browse the schema here: [http://cmungall.github.io/ontology-change-language](http://cmungall.github.io/ontology-change-language)
-
-See the [schema/](schema/) folder
-
-The source is in YAML (biolinkml)
-
-Currently the main derived artefacts of interest are:
-
- - [JSON Schema](src/schema/ocl.schema.json)
- - [Python dataclasses](src/schema/ocl_datamodel.py)
- - [GraphQL](src/schema/ocl.graphql)
-
-Note there is also an OWL vocabulary rendering, and a schema in ShEx (TODO: fix issues with namespaces)
-
- - [JSON Schema](src/schema/ocl.schema.json)
- - [Python dataclasses](src/schema/ocl_datamodel.py)
-
-
-It is likely we will bind this into [owl-diff](https://github.com/balhoff/owl-diff) so compilation to scala traits likely in future.
-
-Note that transactions can themselves be represented in RDF. This can
-be either JSON-LD following the schema above or native. The [ShEx
-Schema](src/schema/ocl.shex) constrains the shape of the RDF graph.

docs/Activity.md

@@ -4,7 +4,7 @@
 
 a provence-generating activity
 
-URI: [ocl:Activity](http://w3id.org/oclActivity)
+URI: [kgcl:Activity](http://w3id.org/kgclActivity)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Agent],[Agent]<was%20associated%20with%200..1-++[Activity&#124;activity_id:string;started_at_time:string%20%3F;ended_at_time:string%20%3F;used:string%20%3F],[Activity]<was%20informed%20by%200..1-%20[Activity],[Change]-%20was%20generated%20by%200..1>[Activity],[Change])

docs/AddNodeToSubset.md

@@ -4,10 +4,10 @@
 
 Places a node inside a subset, by annotating that node
 
-URI: [ocl:AddNodeToSubset](http://w3id.org/oclAddNodeToSubset)
+URI: [kgcl:AddNodeToSubset](http://w3id.org/kgclAddNodeToSubset)
 
 
-![img](http://yuml.me/diagram/nofunky;dir:TB/class/[NodeChange],[AddToSubset],[AddNodeToSubset|about(i):string%20%3F;old_value(i):string%20%3F;new_value(i):string%20%3F]uses%20-.->[AddToSubset],[NodeChange]^-[AddNodeToSubset],[Activity])
+![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Subset],[NodeChange],[AddToSubset],[AddNodeToSubset|about(i):string%20%3F;old_value(i):string%20%3F;new_value(i):string%20%3F]uses%20-.->[AddToSubset],[NodeChange]^-[AddNodeToSubset],[Activity])
 
 ## Parents
 
@@ -33,6 +33,12 @@ URI: [ocl:AddNodeToSubset](http://w3id.org/oclAddNodeToSubset)
  * [was generated by](was_generated_by.md)  <sub>OPT</sub>
     * range: [Activity](Activity.md)
 
+### Mixed in from add to subset:
+
+ * [add to subset➞in subset](add_to_subset_in_subset.md)  <sub>OPT</sub>
+    * Description: subset that the element is being placed inside.
+    * range: [Subset](Subset.md)
+
 ## Other properties
 
 |  |  |  |

docs/AddToSubset.md

@@ -4,10 +4,10 @@
 
 placing an element inside a subset
 
-URI: [ocl:AddToSubset](http://w3id.org/oclAddToSubset)
+URI: [kgcl:AddToSubset](http://w3id.org/kgclAddToSubset)
 
 
-![img](http://yuml.me/diagram/nofunky;dir:TB/class/[ChangeMixin],[AddNodeToSubset]uses%20-.->[AddToSubset],[ChangeMixin]^-[AddToSubset],[AddNodeToSubset])
+![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Subset],[ChangeMixin],[Subset]<in%20subset%200..1-++[AddToSubset],[AddNodeToSubset]uses%20-.->[AddToSubset],[ChangeMixin]^-[AddToSubset],[AddNodeToSubset])
 
 ## Parents
 
@@ -22,3 +22,9 @@ URI: [ocl:AddToSubset](http://w3id.org/oclAddToSubset)
 
 ## Attributes
 
+
+### Own
+
+ * [add to subset➞in subset](add_to_subset_in_subset.md)  <sub>OPT</sub>
+    * Description: subset that the element is being placed inside.
+    * range: [Subset](Subset.md)

docs/Agent.md

@@ -4,7 +4,7 @@
 
 a provence-generating agent
 
-URI: [ocl:Agent](http://w3id.org/oclAgent)
+URI: [kgcl:Agent](http://w3id.org/kgclAgent)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Activity]<was%20informed%20by%200..1-%20[Agent],[Agent]<acted%20on%20behalf%20of%200..1-++[Agent],[Activity]++-%20was%20associated%20with%200..1>[Agent],[Activity])

docs/Annotation.md

@@ -4,7 +4,7 @@
 
 owl annotations. Not to be confused with annotations sensu GO
 
-URI: [ocl:Annotation](http://w3id.org/oclAnnotation)
+URI: [kgcl:Annotation](http://w3id.org/kgclAnnotation)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[PropertyValue],[Node],[Node]<property(i)%200..1-%20[Annotation&#124;filler(i):string%20%3F],[Annotation]<annotation%20set%200..1-++[Annotation],[PropertyValue]^-[Annotation])

docs/Change.md

@@ -4,7 +4,7 @@
 
 Any change perform on an ontology or knowledge graph
 
-URI: [ocl:Change](http://w3id.org/oclChange)
+URI: [kgcl:Change](http://w3id.org/kgclChange)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SimpleChange],[ComplexChange],[Activity]<was%20generated%20by%200..1-%20[Change],[ComplexChange]++-%20change%20set%200..*>[Change],[Transaction]++-%20change%20set%200..*>[Change],[Change]^-[SimpleChange],[Change]^-[ComplexChange],[Transaction],[Activity])

docs/ChangeMixin.md

@@ -4,7 +4,7 @@
 
 root class for all change mixins
 
-URI: [ocl:ChangeMixin](http://w3id.org/oclChangeMixin)
+URI: [kgcl:ChangeMixin](http://w3id.org/kgclChangeMixin)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Unobsoletion],[RemoveFromSubset],[Obsoletion],[Deletion],[Creation],[ChangeMixin]^-[Unobsoletion],[ChangeMixin]^-[RemoveFromSubset],[ChangeMixin]^-[Obsoletion],[ChangeMixin]^-[Deletion],[ChangeMixin]^-[Creation],[ChangeMixin]^-[AddToSubset],[AddToSubset])

docs/ChangeSetSummaryStatistic.md

@@ -4,10 +4,10 @@
 
 A summary statistic for a set of changes of the same type, grouped by zero or more node properties
 
-URI: [ocl:ChangeSetSummaryStatistic](http://w3id.org/oclChangeSetSummaryStatistic)
+URI: [kgcl:ChangeSetSummaryStatistic](http://w3id.org/kgclChangeSetSummaryStatistic)
 
 
-![img](http://yuml.me/diagram/nofunky;dir:TB/class/[PropertyValue],[PropertyValue]<property%20value%20set%200..*-++[ChangeSetSummaryStatistic])
+![img](http://yuml.me/diagram/nofunky;dir:TB/class/[PropertyValue],[PropertyValue]<property%20value%20set%200..*-++[ChangeSetSummaryStatistic&#124;change_type:change_class_type%20%3F;count:integer%20%3F])
 
 ## Referenced by class
 
@@ -17,6 +17,10 @@ URI: [ocl:ChangeSetSummaryStatistic](http://w3id.org/oclChangeSetSummaryStatisti
 
 ### Own
 
+ * [change set summary statistic➞change type](change_set_summary_statistic_change_type.md)  <sub>OPT</sub>
+    * range: [ChangeClassType](types/ChangeClassType.md)
+ * [change set summary statistic➞count](change_set_summary_statistic_count.md)  <sub>OPT</sub>
+    * range: [Integer](types/Integer.md)
  * [change set summary statistic➞property value set](change_set_summary_statistic_property_value_set.md)  <sub>0..*</sub>
     * Description: Summary statistic is grouped by these constraints
     * range: [PropertyValue](PropertyValue.md)

docs/ClassNode.md

@@ -4,7 +4,7 @@
 
 A node that is a class
 
-URI: [ocl:ClassNode](http://w3id.org/oclClassNode)
+URI: [kgcl:ClassNode](http://w3id.org/kgclClassNode)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Node],[Node]^-[ClassNode|id(i):string;name(i):string%20%3F],[Annotation])

docs/ComplexChange.md

@@ -4,7 +4,7 @@
 
 A change that is is a composition of other changes
 
-URI: [ocl:ComplexChange](http://w3id.org/oclComplexChange)
+URI: [kgcl:ComplexChange](http://w3id.org/kgclComplexChange)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Change]<change%20set%200..*-++[ComplexChange],[Change]^-[ComplexChange],[Change],[Activity])

docs/Creation.md

@@ -4,7 +4,7 @@
 
 Creation of an element.
 
-URI: [ocl:Creation](http://w3id.org/oclCreation)
+URI: [kgcl:Creation](http://w3id.org/kgclCreation)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[NodeCreation]uses%20-.->[Creation],[EdgeCreation]uses%20-.->[Creation],[ChangeMixin]^-[Creation],[NodeCreation],[EdgeCreation],[ChangeMixin])

docs/DatatypeChange.md

@@ -4,7 +4,7 @@
 
 
 
-URI: [ocl:DatatypeChange](http://w3id.org/oclDatatypeChange)
+URI: [kgcl:DatatypeChange](http://w3id.org/kgclDatatypeChange)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SimpleChange],[SimpleChange]^-[DatatypeChange|about(i):string%20%3F;old_value(i):string%20%3F;new_value(i):string%20%3F],[Activity])

docs/Deletion.md

@@ -4,7 +4,7 @@
 
 Removal of an element.
 
-URI: [ocl:Deletion](http://w3id.org/oclDeletion)
+URI: [kgcl:Deletion](http://w3id.org/kgclDeletion)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[NodeDeletion]uses%20-.->[Deletion],[EdgeDeletion]uses%20-.->[Deletion],[ChangeMixin]^-[Deletion],[NodeDeletion],[EdgeDeletion],[ChangeMixin])

docs/Edge.md

@@ -4,7 +4,7 @@
 
 A relationship between two nodes. We assume owlstar or similar for existential restrictions
 
-URI: [ocl:Edge](http://w3id.org/oclEdge)
+URI: [kgcl:Edge](http://w3id.org/kgclEdge)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement],[Node],[Annotation]<annotation%20set%200..1-++[Edge],[Node]<object%200..1-%20[Edge],[Node]<edge%20label%200..1-%20[Edge],[Node]<subject%200..1-%20[Edge],[OntologyElement]^-[Edge],[Annotation])

docs/EdgeChange.md

@@ -4,7 +4,7 @@
 
 A change in which the entity changes is an edge
 
-URI: [ocl:EdgeChange](http://w3id.org/oclEdgeChange)
+URI: [kgcl:EdgeChange](http://w3id.org/kgclEdgeChange)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[SimpleChange],[NodeMove],[EdgeObsoletion],[EdgeLogicalInterpretationChange],[EdgeLabelChange],[EdgeDeletion],[EdgeCreation],[EdgeChange|about:string%20%3F;old_value(i):string%20%3F;new_value(i):string%20%3F]^-[NodeMove],[EdgeChange]^-[EdgeObsoletion],[EdgeChange]^-[EdgeLogicalInterpretationChange],[EdgeChange]^-[EdgeLabelChange],[EdgeChange]^-[EdgeDeletion],[EdgeChange]^-[EdgeCreation],[SimpleChange]^-[EdgeChange],[Activity])

docs/EdgeCreation.md

@@ -4,7 +4,7 @@
 
 An edge change in which a de-novo edge is created. The edge is potentially annotated in the same action.
 
-URI: [ocl:EdgeCreation](http://w3id.org/oclEdgeCreation)
+URI: [kgcl:EdgeCreation](http://w3id.org/kgclEdgeCreation)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Node],[Annotation]<annotation%20set%200..1-++[EdgeCreation&#124;change_description:string%20%3F;about(i):string%20%3F;old_value(i):string%20%3F;new_value(i):string%20%3F],[Node]<object%200..1-%20[EdgeCreation],[Node]<edge%20label%200..1-%20[EdgeCreation],[Node]<subject%200..1-%20[EdgeCreation],[EdgeCreation]uses%20-.->[Creation],[EdgeChange]^-[EdgeCreation],[EdgeChange],[Creation],[Annotation],[Activity])

docs/EdgeDeletion.md

@@ -4,7 +4,7 @@
 
 An edge change in which an edge is removed. All edge annotations/properies are removed in the same action.
 
-URI: [ocl:EdgeDeletion](http://w3id.org/oclEdgeDeletion)
+URI: [kgcl:EdgeDeletion](http://w3id.org/kgclEdgeDeletion)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[Node],[Annotation]<annotation%20set%200..1-++[EdgeDeletion&#124;change_description:string%20%3F;about(i):string%20%3F;old_value(i):string%20%3F;new_value(i):string%20%3F],[Node]<object%200..1-%20[EdgeDeletion],[Node]<edge%20label%200..1-%20[EdgeDeletion],[Node]<subject%200..1-%20[EdgeDeletion],[EdgeDeletion]uses%20-.->[Deletion],[EdgeChange]^-[EdgeDeletion],[EdgeChange],[Deletion],[Annotation],[Activity])

docs/EdgeLabelChange.md

@@ -4,7 +4,7 @@
 
 An edge change where the edge label (relationship type) is modified.
 
-URI: [ocl:EdgeLabelChange](http://w3id.org/oclEdgeLabelChange)
+URI: [kgcl:EdgeLabelChange](http://w3id.org/kgclEdgeLabelChange)
 
 
 ![img](http://yuml.me/diagram/nofunky;dir:TB/class/[EdgeChange]^-[EdgeLabelChange|change_description:string%20%3F;about(i):string%20%3F;old_value(i):string%20%3F;new_value(i):string%20%3F],[EdgeChange],[Activity])