Merge pull request #137 from psychoinformatics-de/ddist

Reorganize to versioned, multiple schemas

Makefile

@@ -11,34 +11,23 @@ endif
 try:
 	${FAILIF_STDERR} bash -c 'exit 12'
 
-all: mkdocs-site build/context.jsonld
-
-build/context.jsonld: src/linkml/schemas/ontology.yaml
-	mkdir -p build
-	gen-jsonld-context \
-		--prefixes \
-		--model \
-		--mergeimports \
-		$< > $@
+all: build/mkdocs-site
 
 build/linkml-docs: \
-	build/linkml-docs/data-distribution \
-	build/linkml-docs/derived-example \
-	build/linkml-docs/dataset-version \
-	build/linkml-docs/ontology
-build/linkml-docs/%: src/linkml/schemas/%.yaml src/extra-docs/%-schema
-	export OUTDIR=$$([ "$*" = "ontology" ] && echo $@ || echo build/linkml-docs/schemas/$*) && \
+	build/linkml-docs/s/distribution/unreleased
+#	build/linkml-docs/derived-example/unreleased
+build/linkml-docs/s/%: src/%.yaml src/%/extra-docs
 	gen-doc \
 		--hierarchical-class-view \
 		--include-top-level-diagram \
 		--diagram-type er_diagram \
 		--metadata \
 		--format markdown \
-		--example-directory src/examples/$* \
-		-d $$OUTDIR \
+		--example-directory src/$*/examples/ \
+		-d $@ \
 		$< \
-	&& (cp -r src/extra-docs/$*-schema/*.md $$OUTDIR || true) \
-	&& cp $< $${OUTDIR}.yaml
+	&& (cp -r src/$*/extra-docs/*.md $@ || true) \
+	&& cp $< $@.yaml
 	# try to inject any extra-docs (if any exist)
 
 build/mkdocs-site: build/linkml-docs src/extra-docs/*.md
@@ -50,11 +39,9 @@ check: check-models check-validation
 
 # add additional schemas to lint here
 check-models: \
-	check-model-data-distribution \
-	check-model-derived-example \
-	check-model-dataset-version \
-	check-model-ontology
-check-model-%: src/linkml/schemas/%.yaml
+	checkmodel/distribution/unreleased
+#	check-model-derived-example-unreleased
+checkmodel/%: src/%.yaml
 	@echo [Check $<]
 	@echo "Run linter"
 	@linkml-lint \
@@ -80,32 +67,27 @@ check-model-%: src/linkml/schemas/%.yaml
 # respective validation targets, because some tests rely on these
 # converted formats
 check-validation: \
-	convert-examples-data-distribution \
-	check-validation-data-distribution \
-	convert-examples-derived-example \
-	check-validation-derived-example \
-	convert-examples-dataset-version \
-	check-validation-dataset-version \
-	convert-examples-ontology
-check-validation-%:
-	$(MAKE) check-valid-validation-$* check-invalid-validation-$*
-check-valid-validation-%: tests/%-schema/validation src/linkml/schemas/%.yaml
+	convertexamples/distribution/unreleased \
+	checkvalidation/distribution/unreleased
+#	convert-examples-derived-example-unreleased \
+#	check-validation-derived-example-unreleased
+checkvalidation/%:
+	$(MAKE) checkvalid/$* checkinvalid/$*
+checkvalid/%: src/%/validation src/%.yaml
 	@for ex in $</*.valid.cfg.yaml; do \
 		echo "Validate $$ex" ; \
 		linkml-validate --config "$$ex" || exit 5 ; \
 	done
-check-invalid-validation-%: tests/%-schema/validation src/linkml/schemas/%.yaml
+checkinvalid/%: src/%/validation src/%.yaml
 	@for ex in $</*.invalid.cfg.yaml; do \
 		echo "(In)validate $$ex" ; \
 		linkml-validate --config "$$ex" && exit 5 || true; \
 	done
 
 convert-examples: \
-	convert-examples-data-distribution \
-	convert-examples-derived-example \
-	convert-examples-dataset-version \
-	convert-examples-ontology
-convert-examples-%: src/linkml/schemas/%.yaml src/examples/%
+	convertexamples/distribution/unreleased
+#	convert-examples-derived-example-unreleased
+convertexamples/%: src/%.yaml src/%/examples
 	# loop over all examples, skip the schema file itself
 	for ex in $^/*.yaml; do \
 		[ "$$ex" = "$<" ] && continue; \
@@ -133,4 +115,4 @@ clean:
 	rm -rf build
 	rm -f *-stamp
 
-.PHONY: clean check check-models check-examples convert-examples
+.PHONY: clean check check-models check-validation convert-examples

src/linkml/schemas/derived-example.yaml → src/derived-example/unreleased.yaml

@@ -19,9 +19,8 @@ prefixes:
   DCAT: http://www.w3.org/ns/dcat#
   datalad-ds: https://concepts.datalad.org/ns/dataset-uuid/
   dcterms: http://purl.org/dc/terms/
-  dlco: https://concepts.datalad.org/ontology/
-  # TODO homogenize with base schema
-  dlco1: https://concepts.datalad.org/
+  dlco: https://concepts.datalad.org/
+  dldist: https://concepts.datalad.org/s/distribution/unreleased/
   dex: https://example.org/ns/ex/terms/
   dpv: https://w3id.org/dpv#
   foaf: http://xmlns.com/foaf/0.1/
@@ -50,14 +49,14 @@ default_prefix: dex
 emit_prefixes:
   - CiTO
   - DCAT
-  - dlco
+  - dldist
   - licenses
   - marcrel
   - obo
   - prov
 
 imports:
-  - dlco1:schemas/data-distribution
+  - dlco:s/distribution/unreleased
 
 classes:
   DExResearchContributor:

src/derived-example/unreleased/examples/AgentInfluence-std.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/AgentInfluence-std.yaml

src/derived-example/unreleased/examples/DExDistribution-annexkey.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-annexkey.yaml

src/derived-example/unreleased/examples/DExDistribution-basic.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-basic.yaml

src/examples/derived-example/DExDistribution-customlicense.json → src/derived-example/unreleased/examples/DExDistribution-customlicense.json

@@ -4,7 +4,7 @@
   "relation": [
     {
       "id": "exthisds:#customlicense",
-      "meta_type": "dlco:LicenseDocument",
+      "meta_type": "dldist:LicenseDocument",
       "license_text": "Highly custom terms, never seen before."
     }
   ],

src/derived-example/unreleased/examples/DExDistribution-customlicense.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-customlicense.yaml

src/examples/derived-example/DExDistribution-datatypes.json → src/derived-example/unreleased/examples/DExDistribution-datatypes.json

@@ -4,7 +4,7 @@
   "has_property": [
     {
       "is_defined_by": "obo:NCIT_C95650",
-      "meta_type": "dlco:Property",
+      "meta_type": "dldist:Property",
       "name": "data type",
       "type": "obo:NCIT_C42645",
       "value": "encapsulated image data"

src/derived-example/unreleased/examples/DExDistribution-datatypes.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-datatypes.yaml

src/examples/derived-example/DExDistribution-formats.json → src/derived-example/unreleased/examples/DExDistribution-formats.json

@@ -5,12 +5,12 @@
   "has_part": [
     {
       "id": "exthisdsver:./dataset_description.json",
-      "meta_type": "dlco:Distribution",
+      "meta_type": "dldist:Distribution",
       "media_type": "application/json"
     },
     {
       "id": "exthisdsver:./participants.tsv",
-      "meta_type": "dlco:Distribution",
+      "meta_type": "dldist:Distribution",
       "format": "http://edamontology.org/format_3475"
     }
   ],

src/derived-example/unreleased/examples/DExDistribution-formats.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-formats.yaml

src/derived-example/unreleased/examples/DExDistribution-gitblob.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-gitblob.yaml

src/derived-example/unreleased/examples/DExDistribution-gittree.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-gittree.yaml

src/examples/derived-example/DExDistribution-parts.json → src/derived-example/unreleased/examples/DExDistribution-parts.json

@@ -5,12 +5,12 @@
     {
       "id": "exthisdsver:./archive.zip/subdir",
       "description": "A subdirectory",
-      "meta_type": "dlco:Distribution",
+      "meta_type": "dldist:Distribution",
       "has_part": [
         {
           "id": "exthisdsver:./archive.zip/subdir/file.txt",
           "description": "A file",
-          "meta_type": "dlco:Distribution"
+          "meta_type": "dldist:Distribution"
         }
       ],
       "qualified_part": [

src/derived-example/unreleased/examples/DExDistribution-parts.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-parts.yaml

src/examples/derived-example/DExDistribution-penguins.json → src/derived-example/unreleased/examples/DExDistribution-penguins.json

@@ -11,7 +11,7 @@
           "schema_agency": "https://doi.org"
         }
       ],
-      "meta_type": "dlco:Resource",
+      "meta_type": "dldist:Resource",
       "name": "penguins",
       "same_as": [
         "https://doi.org/10.5281/zenodo.3960218"
@@ -101,7 +101,7 @@
           "schema_agency": "https://ror.org/021nxhr62"
         }
       ],
-      "meta_type": "dlco:Grant",
+      "meta_type": "dldist:Grant",
       "name": "LTER: PALMER, ANTARCTICA LTER: Climate Change, Ecosystem Migration and Teleconnections in an Ice-Dominated Environment",
       "sponsor": "https://ror.org/05nwjp114",
       "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282"
@@ -114,7 +114,7 @@
           "schema_agency": "https://ror.org/021nxhr62"
         }
       ],
-      "meta_type": "dlco:Grant",
+      "meta_type": "dldist:Grant",
       "name": "Palmer, Antarctica Long Term Ecological Research Project",
       "sponsor": "https://ror.org/05nwjp114",
       "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0823101"
@@ -127,7 +127,7 @@
           "schema_agency": "https://ror.org/021nxhr62"
         }
       ],
-      "meta_type": "dlco:Grant",
+      "meta_type": "dldist:Grant",
       "name": "Collaborative Research: Possible Climate-induced Change in the Distribution of Pleuragramma Antarcticum on the Western Antarctic Peninsula Shelf",
       "sponsor": "https://ror.org/05nwjp114",
       "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0741351"
@@ -140,7 +140,7 @@
           "schema_agency": "https://doi.org"
         }
       ],
-      "meta_type": "dlco:Publication",
+      "meta_type": "dldist:Publication",
       "qualified_attribution": [
         {
           "had_role": [
@@ -162,7 +162,7 @@
           "schema_agency": "https://orcid.org"
         }
       ],
-      "meta_type": "dlco:ResearchContributor",
+      "meta_type": "dldist:ResearchContributor",
       "name": "Allison Horst",
       "same_as": [
         "https://orcid.org/0000-0002-6047-5564"
@@ -180,7 +180,7 @@
           "schema_agency": "https://orcid.org"
         }
       ],
-      "meta_type": "dlco:ResearchContributor",
+      "meta_type": "dldist:ResearchContributor",
       "name": "Allison Hill",
       "email": "[email protected]",
       "affiliation": [
@@ -195,7 +195,7 @@
           "schema_agency": "https://orcid.org"
         }
       ],
-      "meta_type": "dlco:ResearchContributor",
+      "meta_type": "dldist:ResearchContributor",
       "name": "Kirsten Gorman",
       "email": "[email protected]",
       "affiliation": [
@@ -204,12 +204,12 @@
     },
     {
       "id": "exthisds:#UCSB",
-      "meta_type": "dlco:Organization",
+      "meta_type": "dldist:Organization",
       "name": "UC Santa Barbara: Santa Barbara, CA, US"
     },
     {
       "id": "exthisds:#RStudio",
-      "meta_type": "dlco:Organization",
+      "meta_type": "dldist:Organization",
       "name": "RStudio: Boston, MA, US"
     },
     {
@@ -220,7 +220,7 @@
           "schema_agency": "https://ror.org"
         }
       ],
-      "meta_type": "dlco:Organization",
+      "meta_type": "dldist:Organization",
       "name": "University of Alaska Fairbanks: Fairbanks, AK, US"
     },
     {
@@ -231,7 +231,7 @@
           "schema_agency": "https://ror.org"
         }
       ],
-      "meta_type": "dlco:Agent",
+      "meta_type": "dldist:Agent",
       "name": "NSF Office of Polar Programs"
     },
     {
@@ -242,7 +242,7 @@
           "schema_agency": "https://ror.org"
         }
       ],
-      "meta_type": "dlco:Agent",
+      "meta_type": "dldist:Agent",
       "name": "US National Science Foundation",
       "same_as": [
         "https://www.nsf.org"
@@ -252,7 +252,7 @@
   "has_part": [
     {
       "id": "exthisdsver:./adelie.csv",
-      "meta_type": "dlco:Distribution",
+      "meta_type": "dldist:Distribution",
       "byte_size": 23755,
       "checksum": [
         {
@@ -265,7 +265,7 @@
     },
     {
       "id": "exthisdsver:./gentoo.csv",
-      "meta_type": "dlco:Distribution",
+      "meta_type": "dldist:Distribution",
       "byte_size": 11263,
       "checksum": [
         {
@@ -278,7 +278,7 @@
     },
     {
       "id": "exthisdsver:./chinstrap.csv",
-      "meta_type": "dlco:Distribution",
+      "meta_type": "dldist:Distribution",
       "byte_size": 18872,
       "checksum": [
         {

src/derived-example/unreleased/examples/DExDistribution-penguins.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-penguins.yaml

src/examples/derived-example/DExDistribution-resource.json → src/derived-example/unreleased/examples/DExDistribution-resource.json

@@ -5,19 +5,19 @@
     {
       "id": "exthisdsver:#some/path",
       "description": "Some tabular data",
-      "meta_type": "dlco:Resource",
+      "meta_type": "dldist:Resource",
       "is_part_of": "exthisdsver:#"
     },
     {
       "id": "exthisdsver:#",
       "description": "A version of a collection of some data",
-      "meta_type": "dlco:Resource",
+      "meta_type": "dldist:Resource",
       "is_version_of": "exthisds:#"
     },
     {
       "id": "exthisds:#",
       "description": "A collection of some data",
-      "meta_type": "dlco:Resource"
+      "meta_type": "dldist:Resource"
     }
   ],
   "is_distribution_of": "exthisdsver:#some/path",

src/derived-example/unreleased/examples/DExDistribution-resource.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/Distribution-resource.yaml

src/examples/data-distribution/EntityInfluence-std.json → src/derived-example/unreleased/examples/EntityInfluence-std.json

@@ -1,6 +1,6 @@
 {
   "had_role": [
-    "dlco:is_about"
+    "dldist:is_about"
   ],
   "entity": [
     "https://en.wikipedia.org/wiki/Vulcan_(Star_Trek)#Mind_melds"

src/derived-example/unreleased/examples/EntityInfluence-std.yaml

@@ -0,0 +1 @@
+../../../distribution/unreleased/examples/EntityInfluence-std.yaml