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.PHONY: dependencies
dependencies:
@command -v uv >/dev/null 2>&1 || \
(echo "Install uv: https://docs.astral.sh/uv/getting-started/installation"; exit 1)
uv venv .venv
uv pip install -e ".[dev]"
uv pip install --no-deps "ucumvert>=0.3.0"
examples/linkml-map/personinfo/agent.instance.yml: \
examples/linkml-map/personinfo/personinfo.transform.yml \
examples/linkml-map/personinfo/personinfo.schema.yml \
examples/linkml-map/personinfo/personinfo.instance.yaml \
dependencies
.venv/bin/linkml-map map-data \
-T examples/linkml-map/personinfo/personinfo.transform.yml \
-s examples/linkml-map/personinfo/personinfo.schema.yml \
--source-type Person \
examples/linkml-map/personinfo/personinfo.instance.yaml \
-o $@
examples/linkml-map/datacite-dcat/dcat-dataset.instance.yml: \
examples/linkml-map/datacite-dcat/datacite-to-dcat-ap.transform.yml \
examples/linkml-map/datacite-dcat/datacite.schema.yml \
examples/linkml-map/datacite-dcat/datacite-resource.instance.yml \
dependencies
.venv/bin/linkml-map map-data \
-T examples/linkml-map/datacite-dcat/datacite-to-dcat-ap.transform.yml \
-s examples/linkml-map/datacite-dcat/datacite.schema.yml \
--source-type Resource \
--unrestricted-eval \
examples/linkml-map/datacite-dcat/datacite-resource.instance.yml \
-o $@
examples/linkml-map/datacite-dcat-date/dcat-date.instance.yml: \
examples/linkml-map/datacite-dcat-date/datacite-dcat-date.transform.yml \
examples/linkml-map/datacite-dcat-date/datacite.schema.yml \
examples/linkml-map/datacite-dcat-date/datacite-date.instance.yml \
dependencies
.venv/bin/linkml-map map-data \
-T examples/linkml-map/datacite-dcat-date/datacite-dcat-date.transform.yml \
-s examples/linkml-map/datacite-dcat-date/datacite.schema.yml \
--source-type DatasetInstance \
--unrestricted-eval \
examples/linkml-map/datacite-dcat-date/datacite-date.instance.yml \
-o $@
LINKMAP_SCHEMA="https://raw.githubusercontent.com/linkml/linkml-map/refs/heads/main/src/linkml_map/datamodel/transformer_model.yaml"
tmp/linkml-map.yml:
wget $(LINKMAP_SCHEMA) -O $@
examples/linkml-map/personinfo/personinfo.transform.jsonld: tmp/linkml-map.yml examples/linkml-map/personinfo/personinfo.transform.yml
uv run linkml-convert -t json-ld -f yaml -C TransformationSpecification -s $^ -o $@
examples/linkml-map/personinfo/personinfo.transform.json: tmp/linkml-map.yml examples/linkml-map/personinfo/personinfo.transform.yml
uv run linkml-convert -t json -f yaml -C TransformationSpecification -s $^ -o $@
examples/linkml-map/datacite-dcat/datacite-to-dcat-ap.transform.jsonld: tmp/linkml-map.yml examples/linkml-map/datacite-dcat/datacite-to-dcat-ap.transform.yml
uv run linkml-convert -t json-ld -f yaml -C TransformationSpecification -s $^ -o $@
examples/linkml-map/datacite-dcat/datacite-to-dcat-ap.transform.json: tmp/linkml-map.yml examples/linkml-map/datacite-dcat/datacite-to-dcat-ap.transform.yml
uv run linkml-convert -t json -f yaml -C TransformationSpecification -s $^ -o $@
examples/linkml-map/datacite-dcat-date/datacite-dcat-date.transform.jsonld: tmp/linkml-map.yml examples/linkml-map/datacite-dcat-date/datacite-dcat-date.transform.yml
uv run linkml-convert -t json-ld -f yaml -C TransformationSpecification -s $^ -o $@
examples/linkml-map/datacite-dcat-date/datacite-dcat-date.transform.json: tmp/linkml-map.yml examples/linkml-map/datacite-dcat-date/datacite-dcat-date.transform.yml
uv run linkml-convert -t json -f yaml -C TransformationSpecification -s $^ -o $@
examples/linkml-map/datacite-dcat-date/datacite-date.instance.jsonld: examples/linkml-map/datacite-dcat-date/datacite.schema.yml examples/linkml-map/datacite-dcat-date/datacite-date.instance.yml
uv run linkml-convert -t json-ld -f yaml -C DatasetInstance -s $^ -o $@
examples/linkml-map/datacite-dcat-date/datacite-date.instance.json: examples/linkml-map/datacite-dcat-date/datacite.schema.yml examples/linkml-map/datacite-dcat-date/datacite-date.instance.yml
uv run linkml-convert -t json -f yaml -C DatasetInstance -s $^ -o $@
examples/linkml-map/datacite-dcat-date/datacite-date.instance.ttl: examples/linkml-map/datacite-dcat-date/datacite.schema.yml examples/linkml-map/datacite-dcat-date/datacite-date.instance.yml
uv run linkml-convert -t ttl -f yaml -C DatasetInstance -s $^ -o $@
examples/linkml-map/datacite-dcat-date/dcat-date.instance.jsonld: examples/linkml-map/datacite-dcat-date/dcat.schema.yml examples/linkml-map/datacite-dcat-date/dcat-date.instance.yml
uv run linkml-convert -t json-ld -f yaml -C DatasetMetadata -s $^ -o $@
examples/linkml-map/datacite-dcat-date/dcat-date.instance.json: examples/linkml-map/datacite-dcat-date/dcat.schema.yml examples/linkml-map/datacite-dcat-date/dcat-date.instance.yml
uv run linkml-convert -t json -f yaml -C DatasetMetadata -s $^ -o $@
examples/linkml-map/datacite-dcat-date/dcat-date.instance.ttl: examples/linkml-map/datacite-dcat-date/dcat.schema.yml examples/linkml-map/datacite-dcat-date/dcat-date.instance.yml
uv run linkml-convert -t ttl -f yaml -C DatasetMetadata -s $^ -o $@
.PHONY: serialisations
serialisations: \
examples/linkml-map/personinfo/personinfo.transform.jsonld \
examples/linkml-map/personinfo/personinfo.transform.json \
examples/linkml-map/datacite-dcat/datacite-to-dcat-ap.transform.jsonld \
examples/linkml-map/datacite-dcat/datacite-to-dcat-ap.transform.json \
examples/linkml-map/datacite-dcat-date/datacite-dcat-date.transform.jsonld \
examples/linkml-map/datacite-dcat-date/datacite-dcat-date.transform.json \
examples/linkml-map/datacite-dcat-date/datacite-date.instance.jsonld \
examples/linkml-map/datacite-dcat-date/datacite-date.instance.json \
examples/linkml-map/datacite-dcat-date/datacite-date.instance.ttl \
examples/linkml-map/datacite-dcat-date/dcat-date.instance.jsonld \
examples/linkml-map/datacite-dcat-date/dcat-date.instance.json \
examples/linkml-map/datacite-dcat-date/dcat-date.instance.ttl | dependencies
.PHONY: examples
examples: \
examples/linkml-map/personinfo/agent.instance.yml \
examples/linkml-map/datacite-dcat-date/dcat-date.instance.yml
# ==========================================
# FAIR Mappings Schema Transformation Examples
# ==========================================
# These demonstrate transforming LinkML-Map and SSSOM metadata to FAIR Mappings Schema
FAIR_EXAMPLE_DIR = examples/linkml-map/fair-mappings-schema
# Download SSSOM schema (similar to linkml-map schema)
SSSOM_SCHEMA_URL = "https://raw.githubusercontent.com/mapping-commons/sssom/refs/heads/master/src/sssom_schema/schema/sssom_schema.yaml"
tmp/sssom-schema.yaml:
mkdir -p tmp
wget $(SSSOM_SCHEMA_URL) -O $@
# Download LinkML-Map schema
LINKMLMAP_SCHEMA_URL = "https://raw.githubusercontent.com/linkml/linkml-map/refs/heads/main/src/linkml_map/datamodel/transformer_model.yaml"
tmp/linkml-map-schema.yaml:
mkdir -p tmp
wget $(LINKMLMAP_SCHEMA_URL) -O $@
# Transform LinkML-Map TransformationSpecification to FAIR Mappings Schema
examples/linkml-map/fair-mappings-schema/linkmlmap-fair-mappings.yaml: \
$(FAIR_EXAMPLE_DIR)/data/sample-linkmlmap-spec.yaml \
$(FAIR_EXAMPLE_DIR)/transform/linkmlmap-to-fair.transformation.yaml \
tmp/linkml-map-schema.yaml \
dependencies
.venv/bin/linkml-map map-data \
-T $(FAIR_EXAMPLE_DIR)/transform/linkmlmap-to-fair.transformation.yaml \
-s tmp/linkml-map-schema.yaml \
--source-type TransformationSpecification \
--unrestricted-eval \
$(FAIR_EXAMPLE_DIR)/data/sample-linkmlmap-spec.yaml \
-o $@
# Transform SSSOM Mapping Set to FAIR Mappings Schema
examples/linkml-map/fair-mappings-schema/sssom-fair-mappings.yaml: \
$(FAIR_EXAMPLE_DIR)/data/sample-sssom-mapping-set.yaml \
$(FAIR_EXAMPLE_DIR)/transform/sssom-to-fair.transformation.yaml \
tmp/sssom-schema.yaml \
dependencies
.venv/bin/linkml-map map-data \
-T $(FAIR_EXAMPLE_DIR)/transform/sssom-to-fair.transformation.yaml \
-s tmp/sssom-schema.yaml \
--source-type 'mapping set' \
--unrestricted-eval \
$(FAIR_EXAMPLE_DIR)/data/sample-sssom-mapping-set.yaml \
-o $@
.PHONY: fair-mappings-transforms
fair-mappings-transforms: \
examples/linkml-map/fair-mappings-schema/linkmlmap-fair-mappings.yaml \
examples/linkml-map/fair-mappings-schema/sssom-fair-mappings.yaml