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feat: add bfo-diff, stamp-version, build-ccom targets #790

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7 changes: 3 additions & 4 deletions .github/workflows/manage_release.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,10 @@ name: Build, Test, Draft Release

on:
push:
branches:
- develop
- feature/*
branches:
- develop
pull_request:
branches:
branches:
- master

permissions:
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86 changes: 85 additions & 1 deletion Makefile
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Expand Up @@ -63,7 +63,7 @@ REQUIRED_DIRS = $(config.LIBRARY_DIR) $(config.SOURCE_DIR) $(config.QUERIES_DIR)
# ----------------------------------------
#### Targets / main "goals" of this Makefile
.PHONY: all
all: setup reason-individual test-individual build-combined reason-combined test-combined
all: setup bfo-diff stamp-version reason-individual test-individual build-combined reason-combined test-combined build-ccom

# Setup target for creating necessary directories
.PHONY: setup
Expand Down Expand Up @@ -169,3 +169,87 @@ clean:
@[ "${config.REPORTS_DIR}" ] || ( echo ">> config.REPORTS_DIR is not set"; exit 1 )
rm -rf $(config.REPORTS_DIR)
rm -rf $(combined-file)

BFO_LOCAL := src/cco-imports/bfo-core.ttl
BFO_UPSTREAM_URL := http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl
BFO_UPSTREAM_TMP := $(config.TEMP_DIR)/bfo-upstream-latest.ttl
BFO_DIFF_OUT := $(config.TEMP_DIR)/bfo-upstream-diff.txt

.PHONY: bfo-diff
bfo-diff: | $(config.TEMP_DIR)
@echo "Fetching BFO upstream from $(BFO_UPSTREAM_URL)..."
curl -sSL -o $(BFO_UPSTREAM_TMP) $(BFO_UPSTREAM_URL)
@echo "Diffing local $(BFO_LOCAL) against upstream..."
@if diff -u $(BFO_LOCAL) $(BFO_UPSTREAM_TMP) > $(BFO_DIFF_OUT) 2>&1; then \
echo "BFO DIFF: No changes — local copy is in sync with upstream."; \
else \
echo "BFO DIFF: Changes detected! Review $(BFO_DIFF_OUT) before release."; \
echo "--- Summary (added/removed lines) ---"; \
echo " Lines added : $$(grep -c '^+[^+]' $(BFO_DIFF_OUT) || echo 0)"; \
echo " Lines removed: $$(grep -c '^-[^-]' $(BFO_DIFF_OUT) || echo 0)"; \
fi
@echo "Full diff written to $(BFO_DIFF_OUT)"

# ---------------------------------------------------------------------------
# T11 — stamp-version: Update owl:versionIRI and owl:versionInfo on all modules
# ---------------------------------------------------------------------------

VERSION ?=
DATE ?= $(TODAY)

.PHONY: stamp-version
stamp-version:
@if [ -z '$(VERSION)' ]; then \
echo 'ERROR: VERSION is required. Usage: make stamp-version VERSION=2.1 [DATE=YYYY-MM-DD]'; \
exit 1; \
fi
@echo "Stamping v$(VERSION) ($(DATE)) on all module files..."
@for f in $(DEV_FILES); do \
echo " $$f"; \
sed -i '' \
-e 's|<https://www\.commoncoreontologies\.org/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]/|<https://www.commoncoreontologies.org/$(DATE)/|g' \
-e 's|"Version [^"]*"@en|"Version $(VERSION)"@en|g' \
"$$f"; \
done
@echo " src/cco-merged/CommonCoreOntologiesMerged.ttl"
@sed -i '' \
-e 's|<https://www\.commoncoreontologies\.org/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]/|<https://www.commoncoreontologies.org/$(DATE)/|g' \
-e 's|"Version [^"]*"@en|"Version $(VERSION)"@en|g' \
src/cco-merged/CommonCoreOntologiesMerged.ttl
@echo "stamp-version complete: v$(VERSION) / $(DATE)"

# ---------------------------------------------------------------------------
# T12 — build-ccom: Rebuild CommonCoreOntologiesMerged.ttl via ROBOT merge
# ---------------------------------------------------------------------------
CCOM_MERGED := src/cco-merged/CommonCoreOntologiesMerged.ttl
CCOM_IRI := https://www.commoncoreontologies.org/CommonCoreOntologiesMerged
CCOM_COMMENT := A stand-alone file containing the eleven mid-level Common Core Ontologies plus BFO. Provided for use-cases where one file representing a specific release of CCO and its imports is desirable.
CCOM_LICENSE := BSD 3-Clause: https://github.com/CommonCoreOntology/CommonCoreOntologies/blob/master/LICENSE
CCOM_RIGHTS := CUBRC Inc., see full license.

.PHONY: build-ccom
build-ccom: $(ROBOT_FILE) | $(config.TEMP_DIR)
@if [ -z '$(VERSION)' ]; then \
echo 'ERROR: VERSION is required. Usage: make build-ccom VERSION=2.1 [DATE=YYYY-MM-DD]'; \
exit 1; \
fi
@echo "Merging 11 CCO modules + BFO via ROBOT merge..."
java -jar $(ROBOT_FILE) merge \
$(foreach f,$(DEV_FILES),--input $(f)) \
--input $(BFO_LOCAL) \
--catalog src/cco-merged/catalog-v001.xml \
--output $(config.TEMP_DIR)/ccom-raw.ttl
@echo "Applying CCOM ontology header (IRI, version, metadata)..."
java -jar $(ROBOT_FILE) annotate \
--input $(config.TEMP_DIR)/ccom-raw.ttl \
--remove-annotations \
--ontology-iri $(CCOM_IRI) \
--version-iri https://www.commoncoreontologies.org/$(DATE)/CommonCoreOntologiesMerged \
--language-annotation rdfs:label "Common Core Ontologies Merged" en \
--language-annotation rdfs:comment "$(CCOM_COMMENT)" en \
--language-annotation http://purl.org/dc/terms/license "$(CCOM_LICENSE)" en \
--language-annotation http://purl.org/dc/terms/rights "$(CCOM_RIGHTS)" en \
--language-annotation owl:versionInfo "Version $(VERSION)" en \
--language-annotation owl:versionInfo "Depends on http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl, obtained $(DATE)." en \
--output $(CCOM_MERGED)
@echo "build-ccom complete: $(CCOM_MERGED)"