Makefile

# Makefile

BLAZEGRAPH_RUNNER_URL ?= https://github.com/balhoff/blazegraph-runner/releases/download/v1.7/blazegraph-runner-1.7.tgz
BLAZEGRAPH_RUNNER_TGZ ?= blazegraph-runner-1.7.tgz
BLAZEGRAPH_RUNNER_DIR ?= blazegraph-runner-1.7
BG_JNL ?= blazegraph-production.jnl
JAVA_OPTS ?= -Xmx64G

%/$(BLAZEGRAPH_RUNNER_TGZ):
	mkdir -p $*
	@echo "Downloading blazegraph-runner..."
	curl -L $(BLAZEGRAPH_RUNNER_URL) -o $@

.PRECIOUS: %/$(BLAZEGRAPH_RUNNER_DIR)/bin/blazegraph-runner
%/$(BLAZEGRAPH_RUNNER_DIR)/bin/blazegraph-runner: %/$(BLAZEGRAPH_RUNNER_TGZ)
	@echo "Decompressing blazegraph-runner..."
	cd $* && tar -xzf $(BLAZEGRAPH_RUNNER_TGZ)

%/run_query: %/$(BLAZEGRAPH_RUNNER_DIR)/bin/blazegraph-runner
	@if [ ! -f $(BG_JNL) ]; then echo "Error: Journal '$(BG_JNL)' does not exist"; exit 1; fi
	JAVA_OPTS=$(JAVA_OPTS) ./$< select --journal=$(BG_JNL) --outformat=tsv $(QUERY_FILE) $(OUT_FILE)

.PRECIOUS: %/pthwy_gocams_count_mf_roots.tsv
%/pthwy_gocams_count_mf_roots.tsv:
	QUERY_FILE=sparql/pthwy_gocams_count_mf_roots.rq OUT_FILE=$@ $(MAKE) $*/run_query

.PRECIOUS: %/metabolic_pthwy_gocams_count_mf_roots.tsv
%/metabolic_pthwy_gocams_count_mf_roots.tsv:
	QUERY_FILE=sparql/metabolic_pthwy_gocams_count_mf_roots.rq OUT_FILE=$@ $(MAKE) $*/run_query

.PRECIOUS: %/multi_connected_cc_gocams.tsv
%/multi_connected_cc_gocams.tsv:
	QUERY_FILE=sparql/multi_connected_cc_gocams.rq OUT_FILE=$@ $(MAKE) $*/run_query

.PRECIOUS: %/multi_connected_bp_gocams.tsv
%/multi_connected_bp_gocams.tsv:
	QUERY_FILE=sparql/multi_connected_bp_gocams.rq OUT_FILE=$@ $(MAKE) $*/run_query

.PRECIOUS: %/non_mf_causal_gocams.tsv
%/non_mf_causal_gocams.tsv:
	QUERY_FILE=sparql/non_mf_causal_gocams.rq OUT_FILE=$@ $(MAKE) $*/run_query

.PRECIOUS: %/pathway_like_go_cams.tsv
%/pathway_like_go_cams.tsv: %/pthwy_gocams_count_mf_roots.tsv %/metabolic_pthwy_gocams_count_mf_roots.tsv %/multi_connected_cc_gocams.tsv %/multi_connected_bp_gocams.tsv %/non_mf_causal_gocams.tsv
	./scripts/compile_pathway_like_gocams.sh $*

# NOCTUA_MODELS_PATH is the repo root
%/cp_model_ttl_to_new_dir.touch: %/pathway_like_go_cams.tsv
	mkdir -p $*/pathway_like_go_cams
	./scripts/cp_model_ttl_to_new_dir.sh $< $(NOCTUA_MODELS_PATH) $*/pathway_like_go_cams
	touch $@

.PRECIOUS: %/pathway-like_go-cams.tar.gz
%/pathway-like_go-cams.tar.gz: %/cp_model_ttl_to_new_dir.touch
	cd $* && tar -czf pathway-like_go-cams.tar.gz pathway_like_go_cams

%/all: %/pathway_like_go_cams.tsv %/pathway-like_go-cams.tar.gz
	@echo "Done"

%/clean:
	rm -f $*/pathway-like_go-cams.tar.gz
	rm -f $*/*.touch
	rm -f $*/*.tsv
	rm -f $*/pathway_like_go_cams/*
	if [ -d $*/pathway_like_go_cams ]; then rmdir $*/pathway_like_go_cams; fi