New framework release

wikipathways · Nov 28, 2021 · 656a92f · 656a92f
1 parent d08b904
commit 656a92f
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Showing 4 changed files with 30 additions and 28 deletions.
diff --git a/Makefile b/Makefile
@@ -5,17 +5,17 @@ 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/' }
 
-FRAMEWORKVERSION=release-1
+FRAMEWORKVERSION=release-2
 
 WEBSITE := ${shell cat website.txt }
 
 all: wikipathways-rdf-wp.zip wikipathways-rdf-gpml.zip
 
 install:
-	@wget -O libs/GPML2RDF-3.0.0-SNAPSHOT-jar-with-dependencies.jar https://github.com/wikipathways/wikipathways-curation-template/releases/download/${FRAMEWORKVERSION}/GPML2RDF-3.0.0-SNAPSHOT-jar-with-dependencies.jar
-	@wget -O libs/jena-arq-3.17.0.jar https://github.com/wikipathways/wikipathways-curation-template/releases/download/${FRAMEWORKVERSION}/jena-arq-3.17.0.jar
+	@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-4.2.0.jar.jar https://repo1.maven.org/maven2/org/apache/jena/jena-arq/4.2.0/jena-arq-4.2.0.jar
 
 sbml: ${SBMLS}
 
@@ -56,19 +56,19 @@ sbml/%.svg: sbml/%.sbml
 
 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-with-dependencies.jar:libs/derby-10.14.2.0.jar:libs/slf4j-simple-1.7.32.jar org.wikipathways.covid.CreateRDF $< | grep -v ".bridge" | grep -v "^WARNING" | grep -v "^TODO" | grep -v "^Unknown and unsupported" | grep -v "regulating line is reversible" > $@
+	@cat "$<.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 $< $@
 
 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-with-dependencies.jar:libs/derby-10.14.2.0.jar:libs/slf4j-simple-1.7.32.jar org.wikipathways.covid.CreateGPMLRDF $< | grep -v ".bridge" | grep -v "^WARNING" | grep -v "^TODO" > $@
+	@cat "$<.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 $< $@
 
 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-with-dependencies.jar src/java/main/org/wikipathways/covid/CreateRDF.java
+	@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-with-dependencies.jar src/java/main/org/wikipathways/covid/CreateGPMLRDF.java
+	@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 $@ ..."
@@ -91,6 +91,8 @@ index.md: ${REPORTS}
 		echo ".json\">" >> index.md ; \
 	done
 
-update:
+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
diff --git a/libs/README.md b/libs/README.md
@@ -1,13 +1,11 @@
 # Required libraries
 
 Java libraries needed for running the tests. They can be downloaded from
-https://github.com/wikipathways/wikipathways-curation-template/releases/tag/release-1
+https://github.com/wikipathways/wikipathways-curation-template/releases/
 
 Get the libraries with:
 
 ```
-wget https://github.com/wikipathways/wikipathways-curation-template/releases/download/release-1/GPML2RDF-3.0.0-SNAPSHOT-jar-with-dependencies.jar
-wget https://github.com/wikipathways/wikipathways-curation-template/releases/download/release-1/jena-arq-3.17.0.jar
-wget https://github.com/wikipathways/wikipathways-curation-template/releases/download/release-1/wikipathways.curator-1-SNAPSHOT-jar-with-dependencies.jar
-wget -O 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
+cd ..
+make install
 ```
diff --git a/src/java/main/org/wikipathways/covid/CreateGPMLRDF.java b/src/java/main/org/wikipathways/covid/CreateGPMLRDF.java
@@ -3,9 +3,9 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.ByteArrayOutputStream;
 import java.util.Collections;
 
 import org.bridgedb.DataSource;
@@ -18,25 +18,24 @@
 import org.wikipathways.wp2rdf.GpmlConverter;
 import org.wikipathways.wp2rdf.WPREST2RDF;
 
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Model;
 
 public class CreateGPMLRDF {
 
     public static void main(String[] args) throws Exception {
         String gpmlFile = args[0];
         String wpid     = gpmlFile.substring(5,11);
-        String rev      = args[1];
+        String rev      = args[2];
+        String outFile  = args[1];
 
         InputStream input = new FileInputStream(gpmlFile);
         Pathway pathway = PathwayReader.readPathway(input);
         input.close();
 
-        Model model = ModelFactory.createDefaultModel();
-        GpmlConverter.convertGpml(pathway, wpid, rev, model);
-        ByteArrayOutputStream output = new ByteArrayOutputStream();
+        Model model = GpmlConverter.convertGpml(pathway, wpid, rev, Collections.<String>emptyList());
+        FileOutputStream output = new FileOutputStream(outFile);
         model.write(output, "TURTLE");
-        System.out.print(new String(output.toByteArray()));
+        output.close();
     }
 
 }
diff --git a/src/java/main/org/wikipathways/covid/CreateRDF.java b/src/java/main/org/wikipathways/covid/CreateRDF.java
@@ -3,9 +3,9 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.ByteArrayOutputStream;
 import java.util.Collections;
 
 import org.bridgedb.DataSource;
@@ -18,24 +18,27 @@
 import org.wikipathways.wp2rdf.GpmlConverter;
 import org.wikipathways.wp2rdf.WPREST2RDF;
 
-import com.hp.hpl.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Model;
 
 public class CreateRDF {
 
     public static void main(String[] args) throws Exception {
         String gpmlFile = args[0];
         String wpid     = gpmlFile.substring(5,11);
-        String rev      = args[1];
+        String rev      = args[2];
+        String outFile  = args[1];
+
         DataSourceTxt.init();
-        // the next line is needed until BridgeDb gets updated
         InputStream input = new FileInputStream(gpmlFile);
         Pathway pathway = PathwayReader.readPathway(input);
+        input.close();
+
         IDMapperStack stack = WPREST2RDF.maps();
         Model model = GpmlConverter.convertWp(pathway, wpid, rev, stack, Collections.<String>emptyList());
-        input.close();
-        ByteArrayOutputStream output = new ByteArrayOutputStream();
+        FileOutputStream output = new FileOutputStream(outFile);
         model.write(output, "TURTLE");
-        System.out.print(new String(output.toByteArray()));
+        output.flush();
+        output.close();
     }
 
 }