TAVERNA-1044: Use RDFParser.create builder
..for more control of warnings
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/combine/CombineManifest.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/combine/CombineManifest.java
index 854667a..b171835 100644
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/combine/CombineManifest.java
+++ b/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/combine/CombineManifest.java
@@ -1,5 +1,14 @@
package org.apache.taverna.robundle.manifest.combine;
+import static java.nio.file.Files.createDirectories;
+import static java.nio.file.Files.exists;
+import static java.nio.file.Files.isRegularFile;
+import static java.nio.file.Files.newInputStream;
+import static java.nio.file.Files.newOutputStream;
+import static java.nio.file.Files.setLastModifiedTime;
+import static java.util.logging.Level.FINE;
+import static java.util.logging.Level.WARNING;
+
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -8,9 +17,9 @@
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -21,16 +30,6 @@
import static org.apache.jena.rdf.model.ModelFactory.createDefaultModel;
-import static java.nio.file.Files.createDirectories;
-import static java.nio.file.Files.exists;
-import static java.nio.file.Files.isRegularFile;
-import static java.nio.file.Files.newInputStream;
-import static java.nio.file.Files.newOutputStream;
-import static java.nio.file.Files.setLastModifiedTime;
-import static java.util.logging.Level.FINE;
-import static java.util.logging.Level.WARNING;
-import static org.apache.jena.riot.RDFDataMgr.read;
-import static org.apache.jena.riot.RDFLanguages.RDFXML;
import static org.apache.taverna.robundle.utils.RDFUtils.literalAsFileTime;
import java.io.IOException;
@@ -54,17 +53,6 @@
import javax.xml.transform.Source;
import javax.xml.transform.sax.SAXSource;
-import org.apache.jena.riot.RiotException;
-import org.apache.taverna.robundle.Bundle;
-import org.apache.taverna.robundle.manifest.Agent;
-import org.apache.taverna.robundle.manifest.PathAnnotation;
-import org.apache.taverna.robundle.manifest.PathMetadata;
-
-import org.apache.taverna.robundle.xml.combine.Content;
-import org.apache.taverna.robundle.xml.combine.ObjectFactory;
-import org.apache.taverna.robundle.xml.combine.OmexManifest;
-import org.xml.sax.InputSource;
-
import org.apache.commons.lang3.tuple.Pair;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
@@ -76,11 +64,23 @@
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.riot.Lang;
+import org.apache.jena.riot.RDFParser;
+import org.apache.jena.riot.RiotException;
+import org.apache.taverna.robundle.Bundle;
+import org.apache.taverna.robundle.manifest.Agent;
+import org.apache.taverna.robundle.manifest.PathAnnotation;
+import org.apache.taverna.robundle.manifest.PathMetadata;
+import org.apache.taverna.robundle.xml.combine.Content;
+import org.apache.taverna.robundle.xml.combine.ObjectFactory;
+import org.apache.taverna.robundle.xml.combine.OmexManifest;
+import org.xml.sax.InputSource;
+
import com.sun.xml.bind.marshaller.NamespacePrefixMapper;
/**
* Parse and generate COMBINE Archive OMEX manifest
- *
+ *
* @author Stian Soiland-Reyes
*/
public class CombineManifest {
@@ -238,19 +238,26 @@
private static Model parseRDF(Path metadata) throws IOException {
Model model = createDefaultModel();
try (InputStream in = newInputStream(metadata)) {
- // TAVERNA-1027: Workaround for JENA-1462 -
- // RO Bundle URIs like
- // app://fad6e1b4-c0d1-45be-a978-7a570b62aa8d/manifest.xml
- // can't be used as base URI when parsing RDF/XML
- read(model, in, fakeFileURI(metadata), RDFXML);
+ RDFParser.create()
+ .base(fakeFileURI(metadata))
+ .lang(Lang.RDFXML)
+ .source(in)
+ .parse(model.getGraph());
}
return model;
}
+ /**
+ * Convert Path's URI to a fake file:/// URI
+ * <p>
+ * TAVERNA-1027: Workaround for JENA-1462 - RO Bundle URIs like
+ * app://fad6e1b4-c0d1-45be-a978-7a570b62aa8d/manifest.xml can't be used as base
+ * URI when parsing RDF/XML in Jena 3.6.0 or earlier
+ */
private static String fakeFileURI(Path path) {
return fakeFileURI(path.toAbsolutePath().toUri());
}
-
+
private static String fakeFileURI(URI uri) {
// Assume path starts with "/"
return "file://" + uri.getPath();
@@ -404,14 +411,14 @@
// add the COMBINE "creators" as RO "authors"
List<Agent> authors = pathMetadata.getAuthoredBy ();
-
+
for (RDFNode s : creatingAgentsFor(resource)) {
if (authors == null)
{
authors = new ArrayList<Agent> ();
pathMetadata.setAuthoredBy (authors);
}
-
+
if (s.isLiteral()) {
authors.add (new Agent(s.asLiteral()
.getLexicalForm()));
@@ -436,7 +443,7 @@
// if there is a single COMBINE "creator" it is also the RO "creator"
if (authors != null && authors.size () == 1)
pathMetadata.setCreatedBy (authors.get (0));
-
+
if (pathMetadata.getFile().equals(bundle.getRoot())
|| pathMetadata.getFile().equals(metadataRdf)) {
// Statements where about the RO itself
@@ -505,6 +512,7 @@
}
if (!manifest.getManifest().contains(manifestXml))
manifest.getManifest().add(manifestXml);
+
for (Content c : omexManifest.getContent()) {
PathMetadata metadata;
if (c.getLocation().contains(":")) {
