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@egonw
egonw committed May 21, 2022
1 parent c9020f9 commit 2f6d512
Showing 1 changed file with 17 additions and 16 deletions.
33 changes: 17 additions & 16 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ SBMLS := ${shell cat pathways.txt | sed -e 's/\(.*\)/sbml\/\1.sbml/' } ${shell c
SVGS := ${shell cat pathways.txt | sed -e 's/\(.*\)/sbml\/\1.svg/' }

FRAMEWORKVERSION=release-3
JENAVERSION=4.3.0

WEBSITE := ${shell cat website.txt }

Expand All @@ -15,7 +16,7 @@ install:
@wget -O libs/GPML2RDF-3.0.0-SNAPSHOT.jar https://github.com/wikipathways/wikipathways-curation-template/releases/download/${FRAMEWORKVERSION}/GPML2RDF-3.0.0-SNAPSHOT.jar
@wget -O libs/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar https://github.com/wikipathways/wikipathways-curation-template/releases/download/${FRAMEWORKVERSION}/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar
@wget -O libs/slf4j-simple-1.7.32.jar https://search.maven.org/remotecontent?filepath=org/slf4j/slf4j-simple/1.7.32/slf4j-simple-1.7.32.jar
@wget -O libs/jena-arq-4.3.0.jar https://repo1.maven.org/maven2/org/apache/jena/jena-arq/4.3.0/jena-arq-4.3.0.jar
@wget -O libs/jena-arq-${JENAVERSION}.jar https://repo1.maven.org/maven2/org/apache/jena/jena-arq/${JENAVERSION}/jena-arq-${JENAVERSION}.jar

sbml: ${SBMLS}

Expand Down Expand Up @@ -54,32 +55,32 @@ sbml/%.svg: sbml/%.sbml
@echo "Fetching SVG for $@ ..."
@curl -X POST --data-binary @$< -H "Content-Type: text/plain" 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
wp/Human/%.ttl: gpml/%.gpml src/java/main/org/wikipathways/curator/CreateRDF.class
@mkdir -p wp/Human
@cat "$<.rev" | xargs java -cp src/java/main/.:libs/GPML2RDF-3.0.0-SNAPSHOT.jar:libs/derby-10.14.2.0.jar:libs/slf4j-simple-1.7.32.jar org.wikipathways.covid.CreateRDF $< $@
@cat "$<.rev" | xargs java -cp src/java/main/.:libs/GPML2RDF-3.0.0-SNAPSHOT.jar:libs/derby-10.14.2.0.jar:libs/slf4j-simple-1.7.32.jar org.wikipathways.curator.CreateRDF $< $@

wp/gpml/Human/%.ttl: gpml/%.gpml src/java/main/org/wikipathways/covid/CreateGPMLRDF.class
wp/gpml/Human/%.ttl: gpml/%.gpml src/java/main/org/wikipathways/curator/CreateGPMLRDF.class
@mkdir -p wp/gpml/Human
@cat "$<.rev" | xargs java -cp src/java/main/.:libs/GPML2RDF-3.0.0-SNAPSHOT.jar:libs/derby-10.14.2.0.jar:libs/slf4j-simple-1.7.32.jar org.wikipathways.covid.CreateGPMLRDF $< $@
@cat "$<.rev" | xargs java -cp src/java/main/.:libs/GPML2RDF-3.0.0-SNAPSHOT.jar:libs/derby-10.14.2.0.jar:libs/slf4j-simple-1.7.32.jar org.wikipathways.curator.CreateGPMLRDF $< $@

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

src/java/main/org/wikipathways/covid/CreateGPMLRDF.class: src/java/main/org/wikipathways/covid/CreateGPMLRDF.java
src/java/main/org/wikipathways/curator/CreateGPMLRDF.class: src/java/main/org/wikipathways/curator/CreateGPMLRDF.java
@echo "Compiling $@ ..."
@javac -cp libs/GPML2RDF-3.0.0-SNAPSHOT.jar src/java/main/org/wikipathways/covid/CreateGPMLRDF.java
@javac -cp libs/GPML2RDF-3.0.0-SNAPSHOT.jar src/java/main/org/wikipathways/curator/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
src/java/main/org/wikipathways/curator/CheckRDF.class: src/java/main/org/wikipathways/curator/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
@javac -cp libs/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar src/java/main/org/wikipathways/curator/CheckRDF.java

check: ${REPORTS} index.md

reports/%.md: wp/Human/%.ttl wp/gpml/Human/%.ttl src/java/main/org/wikipathways/covid/CheckRDF.class tests.txt
reports/%.md: wp/Human/%.ttl wp/gpml/Human/%.ttl src/java/main/org/wikipathways/curator/CheckRDF.class tests.txt
@echo "Detection curation events for $@ ..."
@mkdir -p reports
@java -cp libs/slf4j-simple-1.7.32.jar:libs/jena-arq-4.2.0.jar:src/java/main/:libs/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar org.wikipathways.covid.CheckRDF $< $@
@java -cp libs/slf4j-simple-1.7.32.jar:libs/jena-arq-${JENAVERSION}.jar:src/java/main/:libs/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar org.wikipathways.curator.CheckRDF $< $@

index.md: ${REPORTS}
@echo "<img style=\"float: right; width: 200px\" src=\"logo.png\" />" > index.md
Expand All @@ -93,6 +94,6 @@ index.md: ${REPORTS}

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

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