Reorganize code

Importantly, strictly separate ontology components from schema
definitions.

The rest is the changes are largely a consequence of the renaming/move.

Makefile

@@ -13,7 +13,7 @@ try:
 
 all: mkdocs-site build/context.jsonld
 
-build/context.jsonld: src/linkml/ontology.yaml
+build/context.jsonld: src/linkml/schemas/ontology.yaml
 	mkdir -p build
 	gen-jsonld-context \
 		--prefixes \
@@ -23,22 +23,21 @@ build/context.jsonld: src/linkml/ontology.yaml
 
 build/linkml-docs: \
 	build/linkml-docs/ontology \
-	build/linkml-docs/data-access-schema \
-	build/linkml-docs/datalad-dataset-version-schema
+	build/linkml-docs/data-access \
+	build/linkml-docs/datalad-dataset-version
 #   build/linkml-docs/git-provenance-schema
-build/linkml-docs/%: src/linkml/%.yaml src/extra-docs/%
+build/linkml-docs/%: src/linkml/schemas/%.yaml src/extra-docs/%-schema
 	gen-doc \
-		--mergeimports \
 		--hierarchical-class-view \
 		--include-top-level-diagram \
 		--diagram-type er_diagram \
 		--metadata \
 		--format markdown \
-		--example-directory src/examples/$$(basename $@) \
-		-d $@ \
+		--example-directory src/examples/$$(basename $@)-schema \
+		-d $$([ "$*" = "ontology" ] && echo $@ || echo $@-schema) \
 		$<
 	# try to inject any extra-docs (if any exist)
-	-cp -r src/extra-docs/$$(basename $@)/*.md $@
+	-cp -r src/extra-docs/$$(basename $@)-schema/*.md $@
 
 build/mkdocs-site: build/linkml-docs src/extra-docs/*.md
 	# top-level content
@@ -49,11 +48,11 @@ check: check-models check-validation
 
 # add additional schemas to lint here
 check-models: \
-	check-model-data-access-schema \
-	check-model-datalad-dataset-version-schema \
+	check-model-data-access \
+	check-model-datalad-dataset-version \
 	check-model-ontology
-#	check-model-git-provenance-schema
-check-model-%: src/linkml/%.yaml
+#	check-model-git-provenance
+check-model-%: src/linkml/schemas/%.yaml
 	@echo [Check $<]
 	@echo "Run linter"
 	@linkml-lint \
@@ -79,32 +78,32 @@ check-model-%: src/linkml/%.yaml
 # respective validation targets, because some tests rely on these
 # converted formats
 check-validation: \
-	convert-examples-data-access-schema \
-	check-validation-data-access-schema \
-	convert-examples-datalad-dataset-version-schema \
-	check-validation-datalad-dataset-version-schema \
+	convert-examples-data-access \
+	check-validation-data-access \
+	convert-examples-datalad-dataset-version \
+	check-validation-datalad-dataset-version \
 	convert-examples-ontology
-#	convert-examples-git-provenance-schema
-#	check-validation-git-provenance-schema
+#	convert-examples-git-provenance
+#	check-validation-git-provenance
 check-validation-%:
 	$(MAKE) check-valid-validation-$* check-invalid-validation-$*
-check-valid-validation-%: tests/%/validation src/linkml/%.yaml
+check-valid-validation-%: tests/%-schema/validation src/linkml/schemas/%.yaml
 	@for ex in $</*.valid.cfg.yaml; do \
 		echo "Validate $$ex" ; \
 		linkml-validate --config "$$ex" ; \
 	done
-check-invalid-validation-%: tests/%/validation src/linkml/%.yaml
+check-invalid-validation-%: tests/%-schema/validation src/linkml/schemas/%.yaml
 	@for ex in $</*.invalid.cfg.yaml; do \
 		echo "(In)validate $$ex" ; \
 		linkml-validate --config "$$ex" && UNEXPECTEDLY VALID || true; \
 	done
 
 convert-examples: \
-	convert-examples-data-access-schema \
-	convert-examples-datalad-dataset-version-schema \
+	convert-examples-data-access \
+	convert-examples-datalad-dataset-version \
 	convert-examples-ontology
-#	convert-examples-git-provenance-schema
-convert-examples-%: src/linkml/%.yaml src/examples/%
+#	convert-examples-git-provenance
+convert-examples-%: src/linkml/schemas/%.yaml src/examples/%
 	# loop over all examples, skip the schema file itself
 	for ex in $^/*.yaml; do \
 		[ "$$ex" = "$<" ] && continue; \

src/linkml/checksumming.yaml → src/linkml/ontology/checksumming.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/checksumming
+id: https://concepts.datalad.org/ontology/checksumming
 name: checksumming
 title: Concepts for describing checksums of digital content
 description: >
@@ -13,8 +13,8 @@ prefixes:
   spdx: http://spdx.org/rdf/terms#
 
 imports:
-  - properties
-  - types
+  - ../ontology/properties
+  - ../ontology/types
   - linkml:types
 default_prefix: dlco
 

src/linkml/datalad-datasets.yaml → src/linkml/ontology/datalad-datasets.yaml

@@ -1,16 +1,16 @@
 # models for DataLad datasets
 
-id: https://concepts.datalad.org/datalad-datasets
+id: https://concepts.datalad.org/ontology/datalad-datasets
 name: datalad-datasets
 prefixes:
   dlco: https://concepts.datalad.org/ontology/
   dcterms: http://purl.org/dc/terms/
   rdfs: http://www.w3.org/2000/01/rdf-schema#
 imports:
-  - datasets
-  - labeling
-  - meta_utils
-  - types
+  - ../ontology/datasets
+  - ../ontology/labeling
+  - ../ontology/meta_utils
+  - ../ontology/types
 default_prefix: dlco
 
 

src/linkml/datalad.yaml → src/linkml/ontology/datalad.yaml

@@ -1,6 +1,6 @@
 # models for DataLad datasets
 
-id: https://concepts.datalad.org/datalad
+id: https://concepts.datalad.org/ontology/datalad
 name: datalad
 title: DataLad concepts
 description: >
@@ -10,13 +10,13 @@ prefixes:
   dcterms: http://purl.org/dc/terms/
   rdfs: http://www.w3.org/2000/01/rdf-schema#
 imports:
-  - datasets
-  - properties
-default_prefix: dlco
+  - ../ontology/datasets
+  - ../ontology/properties
 
 
 classes:
   DataladDatasetVersion:
+    class_uri: dlco:DataladDatasetVersion
     mixin: true
     is_a: Dataset
     description: >-
@@ -26,6 +26,7 @@ classes:
         range: DataladDataset
 
   DataladDataset:
+    class_uri: dlco:DataladDataset
     mixin: true
     description: >-
       Concept class for linking `DataladDatasetVersion` instances.

src/linkml/datasets.yaml → src/linkml/ontology/datasets.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/datasets
+id: https://concepts.datalad.org/ontology/datasets
 name: datasets
 title: Concepts for describing datasets
 description: >
@@ -28,11 +28,11 @@ prefixes:
   schema: http://schema.org/
 
 imports:
-  - checksumming
-  - meta_utils
-  - properties
-  - provenance
-  - types
+  - ../ontology/checksumming
+  - ../ontology/meta_utils
+  - ../ontology/properties
+  - ../ontology/provenance
+  - ../ontology/types
   - linkml:types
 default_prefix: dlco
 
@@ -239,6 +239,7 @@ classes:
         that cannot be inferred from a standard `DCAT:Distribution`.
 
   DataService:
+    class_uri: dlco:DataService
     mixin: true
     description: >-
       A collection of operations that provides access to one or more

src/linkml/git-annex.yaml → src/linkml/ontology/git-annex.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/git-annex
+id: https://concepts.datalad.org/ontology/git-annex
 name: git-annex
 title: Git-annex concepts
 description: >
@@ -7,9 +7,9 @@ prefixes:
   annex: https://concepts.datalad.org/namespace/annex-uuid/
   dlco: https://concepts.datalad.org/ontology/
 imports:
-  - datasets
-  - git
-  - properties
+  - ../ontology/datasets
+  - ../ontology/git
+  - ../ontology/properties
 default_prefix: dlco
 
 

src/linkml/git.yaml → src/linkml/ontology/git.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/git
+id: https://concepts.datalad.org/ontology/git
 name: git
 title: Git concepts
 description: >
@@ -7,9 +7,9 @@ prefixes:
   gitsha: https://concepts.datalad.org/namespace/gitsha/
   dlco: https://concepts.datalad.org/ontology/
 imports:
-  - datasets
-  - meta_utils
-  - types
+  - ../ontology/datasets
+  - ../ontology/meta_utils
+  - ../ontology/types
 default_prefix: dlco
 
 

src/linkml/labeling.yaml → src/linkml/ontology/labeling.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/labeling
+id: https://concepts.datalad.org/ontology/labeling
 name: labeling
 title: Utilities for labeling objects
 description: >-

src/linkml/meta_utils.yaml → src/linkml/ontology/meta_utils.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/meta_utils
+id: https://concepts.datalad.org/ontology/meta_utils
 name: meta_utils
 title: Utilities for identifying and typing metadata objects
 description: >-

src/linkml/properties.yaml → src/linkml/ontology/properties.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/properties
+id: https://concepts.datalad.org/ontology/properties
 name: properties
 title: Common properties
 description: >
@@ -12,7 +12,7 @@ prefixes:
   spdx: http://spdx.org/rdf/terms#
 
 imports:
-  - types
+  - ../ontology/types
 default_prefix: dlco
 
 slots:

src/linkml/provenance.yaml → src/linkml/ontology/provenance.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/provenance
+id: https://concepts.datalad.org/ontology/provenance
 name: provenance
 title: Concepts for ascribing provenance to entities
 description: >-

src/linkml/types.yaml → src/linkml/ontology/types.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/types
+id: https://concepts.datalad.org/ontology/types
 name: types
 prefixes:
   afo: http://purl.allotrope.org/ontologies/result#

src/linkml/data-access-schema.yaml → src/linkml/schemas/data-access.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/data-access-schema
+id: https://concepts.datalad.org/schemas/data-access
 name: data-access-schema
 title: Data access schema
 description: >-
@@ -13,8 +13,8 @@ prefixes:
   schema: http://schema.org/
   linkml: https://w3id.org/linkml/
 imports:
-  - types
-  - meta_utils
+  - ../ontology/types
+  - ../ontology/meta_utils
   - linkml:types
 default_prefix: dlco
 

src/linkml/datalad-dataset-version-schema.yaml → src/linkml/schemas/datalad-dataset-version.yaml

@@ -1,6 +1,6 @@
 # models for DataLad datasets
 
-id: https://concepts.datalad.org/datalad-dataset-version-schema
+id: https://concepts.datalad.org/schemas/datalad-dataset-version
 name: datalad-dataset-version-schema
 title: DataLad dataset version schema
 description: >-
@@ -20,8 +20,8 @@ prefixes:
   prov: http://www.w3.org/ns/prov#
   spdx: http://spdx.org/rdf/terms#
 imports:
-  - datalad
-  - git-annex
+  - ../ontology/datalad
+  - ../ontology/git-annex
 default_prefix: dlco
 
 classes:

src/linkml/git-provenance-schema.yaml → src/linkml/schemas/git-provenance.yaml

@@ -1,4 +1,4 @@
-id: https://concepts.datalad.org/git-provenance-schema
+id: https://concepts.datalad.org/schemas/git-provenance
 name: git-provenance-schema
 title: Git provenance schema
 description: >-
@@ -14,11 +14,11 @@ prefixes:
   linkml: https://w3id.org/linkml/
   prov: http://www.w3.org/ns/prov#
 imports:
-  - git
-  - labeling
-  - meta_utils
-  - provenance
-  - types
+  - ../ontology/git
+  - ../ontology/labeling
+  - ../ontology/meta_utils
+  - ../ontology/provenance
+  - ../ontology/types
 default_prefix: dlco
 
 

src/linkml/schemas/ontology.yaml

@@ -0,0 +1,21 @@
+id: https://concepts.datalad.org/schemas/ontology
+name: datalad-concepts-ontology
+title: DataLad Concepts Ontology (DLCO)
+description: |-
+  [DataLad Concepts Ontology](https://concepts.datalad.org) (DLCO)
+license: MIT
+
+prefixes:
+  linkml: https://w3id.org/linkml/
+  dlco: https://concepts.datalad.org/ontology/
+
+imports:
+  - ../ontology/checksumming
+  - ../ontology/datalad
+  - ../ontology/datasets
+  - ../ontology/git-annex
+  - ../ontology/labeling
+  - ../ontology/meta_utils
+  - ../ontology/properties
+  - ../ontology/provenance
+  - ../ontology/types

tests/data-access-schema/validation/annexremote.valid.cfg.yaml

@@ -1,7 +1,7 @@
-schema: src/linkml/data-access-schema.yaml
+schema: src/linkml/schemas/data-access.yaml
 target_class: ObjectAvailability
 data_sources:
-  - src/examples/data-access-schema/ObjectAvailability-annexwebdav.yaml
+  - src/examples/data-access/ObjectAvailability-annexwebdav.yaml
 plugins:
   JsonschemaValidationPlugin:
     closed: true

tests/data-access-schema/validation/annexremote_missing_type.invalid.cfg.yaml

@@ -1,4 +1,4 @@
-schema: src/linkml/data-access-schema.yaml
+schema: src/linkml/schemas/data-access.yaml
 target_class: DataObject
 data_sources:
   - tests/data-access-schema/validation/GitAnnexSpecialRemote-missing_type.yaml