Makefile

GPMLS := ${shell cat pathways.txt | sed -e 's/\(.*\)/gpml\/\1.gpml/' }
WPRDFS := ${shell cat pathways.txt | sed -e 's/\(.*\)/wp\/Human\/\1.ttl/' }
GPMLRDFS := ${shell cat pathways.txt | sed -e 's/\(.*\)/wp\/gpml\/Human\/\1.ttl/' }
REPORTS := ${shell cat pathways.txt | sed -e 's/\(.*\)/reports\/\1.md/' }
SBMLS := ${shell cat pathways.txt | sed -e 's/\(.*\)/sbml\/\1.sbml/' } ${shell cat pathways.txt | sed -e 's/\(.*\)/sbml\/\1.txt/' }
SVGS := ${shell cat pathways.txt | sed -e 's/\(.*\)/sbml\/\1.svg/' }

all: wikipathways-SARS-CoV-2-rdf-authors.zip wikipathways-SARS-CoV-2-rdf-wp.zip \
     wikipathways-SARS-CoV-2-rdf-gpml.zip

rdf: ${WPRDFS} ${GPMLRDFS}
sbml: ${SBMLS}
svg: ${SVGS}

fetch:clean ${GPMLS}

clean:
	@rm -f ${GPMLS}

gpml/%.gpml:
	@echo "Git fetching $@ ..."
	@echo '$@' | sed -e 's/gpml\/\(.*\)\.gpml/\1/' | xargs bash getPathway.sh

wikipathways-SARS-CoV-2-rdf-authors.zip: authors/*
	@rm -f wikipathways-SARS-CoV-2-rdf-authors.zip
	@zip wikipathways-SARS-CoV-2-rdf-authors.zip authors/*

wikipathways-SARS-CoV-2-rdf-wp.zip: ${WPRDFS}
	@rm -f wikipathways-SARS-CoV-2-rdf-wp.zip
	@zip wikipathways-SARS-CoV-2-rdf-wp.zip wp/Human/*

wikipathways-SARS-CoV-2-rdf-gpml.zip: ${GPMLRDFS}
	@rm -f wikipathways-SARS-CoV-2-rdf-gpml.zip
	@zip wikipathways-SARS-CoV-2-rdf-gpml.zip wp/gpml/Human/*

sbml/%.sbml: gpml/%.gpml
	@mkdir -p sbml
	@echo "Fetching SBML for $< ..."
	curl -H "Content-Type: application/octet-stream" -X POST --data-binary @$< https://minerva-service.lcsb.uni.lu/minerva/api/convert/GPML:SBML > $@
	@sleep 1

sbml/%.txt: sbml/%.sbml
	@echo "Extracting notes for $@ ..."
	@xpath -e "/sbml/model/notes/body/p/text()" $< > $@ || :

sbml/%.svg: sbml/%.sbml
	@echo "Fetching SVG for $@ ..."
	@curl -H "Content-Type: application/octet-stream" -X POST --data-binary @$< https://minerva-service.lcsb.uni.lu/minerva/api/convert/image/SBML:svg > $@

wp/Human/%.ttl: gpml/%.gpml src/java/main/org/wikipathways/covid/CreateRDF.class
	@mkdir -p wp/Human
	@cat "$<.rev" | xargs java -cp src/java/main/.:libs/GPML2RDF-3.0.0-SNAPSHOT.jar:libs/slf4j-simple-1.7.32.jar org.wikipathways.covid.CreateRDF $< $@

wp/gpml/Human/%.ttl: gpml/%.gpml src/java/main/org/wikipathways/covid/CreateGPMLRDF.class
	@mkdir -p wp/gpml/Human
	cat "$<.rev" | xargs java -cp src/java/main/.:libs/GPML2RDF-3.0.0-SNAPSHOT.jar:libs/slf4j-simple-1.7.32.jar org.wikipathways.covid.CreateGPMLRDF $< $@

src/java/main/org/wikipathways/covid/CreateRDF.class: src/java/main/org/wikipathways/covid/CreateRDF.java
	@echo "Compiling $@ ..."
	@javac -cp libs/GPML2RDF-3.0.0-SNAPSHOT.jar src/java/main/org/wikipathways/covid/CreateRDF.java

src/java/main/org/wikipathways/covid/CreateGPMLRDF.class: src/java/main/org/wikipathways/covid/CreateGPMLRDF.java
	@echo "Compiling $@ ..."
	@javac -cp libs/GPML2RDF-3.0.0-SNAPSHOT.jar src/java/main/org/wikipathways/covid/CreateGPMLRDF.java

src/java/main/org/wikipathways/covid/CheckRDF.class: src/java/main/org/wikipathways/covid/CheckRDF.java libs/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar
	@echo "Compiling $@ ..."
	@javac -cp libs/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar src/java/main/org/wikipathways/covid/CheckRDF.java

check: ${REPORTS} index.md

reports/%.md: wp/Human/%.ttl wp/gpml/Human/%.ttl src/java/main/org/wikipathways/covid/CheckRDF.class
	@echo "Detection curation events for $@ ..."
	@mkdir -p reports
	@java -cp src/java/main/:libs/slf4j-simple-1.7.32.jar:libs/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar org.wikipathways.covid.CheckRDF $< $@

index.md: ${REPORTS}
	@echo "<img style=\"float: right; width: 200px\" src=\"logo.png\" />" > index.md
	@echo "# Validation Reports\n" >> index.md
	@echo "\nThe pathways evaluated here are part of the [COVID-19 Disease Map](https://www.embopress.org/doi/full/10.15252/msb.202110387).\n" >> index.md
	@for report in $(REPORTS) ; do \
		echo -n "* [$$report]($$report) " >> index.md ; \
		echo -n "<img alt=\"pathway status\" src=\"https://img.shields.io/endpoint?url=https://wikipathways.org/SARS-CoV-2-WikiPathways/reports/" >> index.md ; \
		echo -n "`echo "$$report" | sed -e 's/.md//; s/reports\///'`" >> index.md ; \
                echo ".json\">" >> index.md ; \
	done

update:
	@wget -O src/java/main/org/wikipathways/covid/CheckRDF.java https://raw.githubusercontent.com/wikipathways/wikipathways-curation-template/main/src/java/main/org/wikipathways/covid/CheckRDF.java

updateTests:
	@jar tf libs/wikipathways.curator-1-SNAPSHOT.jar | grep '.class' \
	  | grep 'nl.unimaas.bigcat.wikipathways.curator.tests' | tr / . \
	  | sed 's/\.class//' | xargs javap -public -cp libs/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar \
	  > tests.tmp
	@groovy extractTests.groovy > tests.tmp2
	@mv tests.tmp2 tests.txt