Merge pull request #279 from owlcollab/issue-276-url_bending

changing URLs for files in gaf checking
owlcollab · Apr 2, 2019 · dbd5871 · dbd5871
2 parents 3ffa1cb + e216ac1
commit dbd5871
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Showing 3 changed files with 14 additions and 9 deletions.
diff --git a/OWLTools-Annotation/src/main/java/owltools/gaf/rules/AnnotationRulesFactoryImpl.java b/OWLTools-Annotation/src/main/java/owltools/gaf/rules/AnnotationRulesFactoryImpl.java
@@ -72,7 +72,7 @@ public synchronized void init() {
 		Document doc = null;
 		try {
 			URI uri;
-			if(!(path.startsWith("http://") || path.startsWith("file:///"))){
+			if(!(path.startsWith("http://") || path.startsWith("file://") || path.startsWith("https://"))){
 				File f = new File(path);
 				uri = f.toURI();
 			}

diff --git a/OWLTools-Annotation/src/main/java/owltools/gaf/rules/go/BasicChecksRule.java b/OWLTools-Annotation/src/main/java/owltools/gaf/rules/go/BasicChecksRule.java
@@ -12,6 +12,7 @@
 import java.util.List;
 import java.util.Set;
 
+import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.LineIterator;
 import org.apache.log4j.Logger;
@@ -68,13 +69,15 @@ private static Set<String> buildAbbreviations(String path){
 		InputStream is = null;
 		LineIterator it = null;
 		try{
-			if(path.startsWith("http://") || path.startsWith("file:/")){
-				is = new URL(path).openStream();
+			File destination = new File("/tmp/tmp.xrf_abbs");
+			destination.deleteOnExit();
+			if(path.startsWith("http://") || path.startsWith("https://")){
+				FileUtils.copyURLToFile(new URL(path), destination, 10000, 10000);
+			} else {
+				destination = new File(path);
 			}
-			else {
-				is = new FileInputStream(new File(path));
-			}
-
+			// Copy from destination, always a file now.
+			is = new FileInputStream(destination);
 			it = new LineIterator(new InputStreamReader(is));
 
 			while (it.hasNext()) {
@@ -95,6 +98,7 @@ private static Set<String> buildAbbreviations(String path){
 		finally {
 			IOUtils.closeQuietly(is);
 			LineIterator.closeQuietly(it);
+
 		}
 
 		return set;

diff --git a/OWLTools-Annotation/src/main/java/owltools/gaf/rules/go/GoAnnotationRulesFactoryImpl.java b/OWLTools-Annotation/src/main/java/owltools/gaf/rules/go/GoAnnotationRulesFactoryImpl.java
@@ -1,5 +1,6 @@
 package owltools.gaf.rules.go;
 
+import java.io.InputStream;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -45,8 +46,8 @@ public GoAnnotationRulesFactoryImpl(String qcfile, String xrfabbslocation, Parse
 	}
 
 	public GoAnnotationRulesFactoryImpl(OWLGraphWrapper graph, TraversingEcoMapper eco, String taxonModule) {
-		this("http://www.geneontology.org/quality_control/annotation_checks/annotation_qc.xml",
-				"http://www.geneontology.org/doc/GO.xrf_abbs", graph, eco, taxonModule);
+		this("https://raw.githubusercontent.com/owlcollab/owltools/master/docs/legacy/annotation_qc.xml",
+				"http://current.geneontology.org/metadata/GO.xrf_abbs", graph, eco, taxonModule);
 	}
 
 	@Override