Migrate from Sesame to RDF4J

trustyuri · Feb 8, 2019 · 049c24e · 049c24e
1 parent 0f1c224
commit 049c24e
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Showing 26 changed files with 310 additions and 305 deletions.
diff --git a/pom.xml b/pom.xml
@@ -23,9 +23,19 @@
     <maven.compiler.target>1.7</maven.compiler.target>
     <!-- 1.6 does not work because of java.nio.file dependency -->
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <sesame.version>2.9.0</sesame.version>
+    <rdf4j.version>2.4.4</rdf4j.version>
   </properties>
   <dependencies>
+    <dependency>
+      <groupId>com.sun.activation</groupId>
+      <artifactId>javax.activation</artifactId>
+      <version>1.2.0</version>
+    </dependency>
+    <dependency>
+      <groupId>javax.xml.bind</groupId>
+      <artifactId>jaxb-api</artifactId>
+      <version>2.3.1</version>
+    </dependency>
     <dependency>
       <groupId>junit</groupId>
       <artifactId>junit</artifactId>
@@ -48,39 +58,39 @@
       <version>1.7.2</version>
     </dependency>
     <dependency>
-      <groupId>org.openrdf.sesame</groupId>
-      <artifactId>sesame-rio-trig</artifactId>
-      <version>${sesame.version}</version>
+      <groupId>org.eclipse.rdf4j</groupId>
+      <artifactId>rdf4j-rio-trig</artifactId>
+      <version>${rdf4j.version}</version>
     </dependency>
     <dependency>
-      <groupId>org.openrdf.sesame</groupId>
-      <artifactId>sesame-rio-rdfxml</artifactId>
-      <version>${sesame.version}</version>
+      <groupId>org.eclipse.rdf4j</groupId>
+      <artifactId>rdf4j-rio-rdfxml</artifactId>
+      <version>${rdf4j.version}</version>
     </dependency>
     <dependency>
-      <groupId>org.openrdf.sesame</groupId>
-      <artifactId>sesame-rio-turtle</artifactId>
-      <version>${sesame.version}</version>
+      <groupId>org.eclipse.rdf4j</groupId>
+      <artifactId>rdf4j-rio-turtle</artifactId>
+      <version>${rdf4j.version}</version>
     </dependency>
     <dependency>
-      <groupId>org.openrdf.sesame</groupId>
-      <artifactId>sesame-rio-ntriples</artifactId>
-      <version>${sesame.version}</version>
+      <groupId>org.eclipse.rdf4j</groupId>
+      <artifactId>rdf4j-rio-ntriples</artifactId>
+      <version>${rdf4j.version}</version>
     </dependency>
     <dependency>
-      <groupId>org.openrdf.sesame</groupId>
-      <artifactId>sesame-rio-trix</artifactId>
-      <version>${sesame.version}</version>
+      <groupId>org.eclipse.rdf4j</groupId>
+      <artifactId>rdf4j-rio-trix</artifactId>
+      <version>${rdf4j.version}</version>
     </dependency>
     <dependency>
-      <groupId>org.openrdf.sesame</groupId>
-      <artifactId>sesame-rio-nquads</artifactId>
-      <version>${sesame.version}</version>
+      <groupId>org.eclipse.rdf4j</groupId>
+      <artifactId>rdf4j-rio-nquads</artifactId>
+      <version>${rdf4j.version}</version>
     </dependency>
     <dependency>
-      <groupId>org.openrdf.sesame</groupId>
-      <artifactId>sesame-repository-sparql</artifactId>
-      <version>${sesame.version}</version>
+      <groupId>org.eclipse.rdf4j</groupId>
+      <artifactId>rdf4j-repository-sparql</artifactId>
+      <version>${rdf4j.version}</version>
     </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>

diff --git a/src/main/java/net/trustyuri/AbstractTrustyUriModule.java b/src/main/java/net/trustyuri/AbstractTrustyUriModule.java
@@ -1,6 +1,6 @@
 package net.trustyuri;
 
-import org.openrdf.model.URI;
+import org.eclipse.rdf4j.model.IRI;
 
 /**
  * A partial implementation of a trusty URI module.
@@ -18,7 +18,7 @@ public AbstractTrustyUriModule() {
 		pattern = ".*[^A-Za-z0-9\\-_]" + getModuleId() + "[A-Za-z0-9\\-_]{" + getDataPartLength() + "}";
 	}
 
-	public boolean matches(URI uri) {
+	public boolean matches(IRI uri) {
 		return uri.stringValue().matches(pattern);
 	}
 

diff --git a/src/main/java/net/trustyuri/Run.java b/src/main/java/net/trustyuri/Run.java
@@ -3,7 +3,7 @@
 import java.io.IOException;
 import java.util.Arrays;
 
-import org.openrdf.OpenRDFException;
+import org.eclipse.rdf4j.RDF4JException;
 
 import net.trustyuri.file.ProcessFile;
 import net.trustyuri.rdf.CheckLargeRdf;
@@ -27,7 +27,7 @@ private Run() {}  // no instances allowed
 	 *
 	 * @param args the command
 	 */
-	public static void main(String[] args) throws IOException, OpenRDFException, TrustyUriException {
+	public static void main(String[] args) throws IOException, RDF4JException, TrustyUriException {
 		run(args);
 	}
 
@@ -36,7 +36,7 @@ public static void main(String[] args) throws IOException, OpenRDFException, Tru
 	 *
 	 * @param command the command, as a String array
 	 */
-	public static void run(String[] command) throws IOException, OpenRDFException, TrustyUriException {
+	public static void run(String[] command) throws IOException, RDF4JException, TrustyUriException {
 		String cmd = command[0];
 		String[] cmdArgs = Arrays.copyOfRange(command, 1, command.length);
 		if (cmd.equals("CheckFile")) {

diff --git a/src/main/java/net/trustyuri/RunBatch.java b/src/main/java/net/trustyuri/RunBatch.java
@@ -8,13 +8,13 @@
 import java.nio.charset.Charset;
 import java.nio.file.Files;
 
-import org.openrdf.OpenRDFException;
+import org.eclipse.rdf4j.RDF4JException;
 
 public class RunBatch {
 
 	private RunBatch() {}  // no instances allowed
 
-	public static void main(String[] args) throws IOException, OpenRDFException, TrustyUriException {
+	public static void main(String[] args) throws IOException, RDF4JException, TrustyUriException {
 		String batchFile = args[0];
 
 		BufferedReader reader = new BufferedReader(new FileReader(batchFile));

diff --git a/src/main/java/net/trustyuri/TrustyUriModule.java b/src/main/java/net/trustyuri/TrustyUriModule.java
@@ -3,7 +3,7 @@
 import java.io.File;
 import java.io.IOException;
 
-import org.openrdf.model.URI;
+import org.eclipse.rdf4j.model.IRI;
 
 /**
  * A trusty URI module handles a particular type of content (such as RDF graphs or the byte content
@@ -51,6 +51,6 @@ public interface TrustyUriModule {
 	 * @param uri the URI
 	 * @return true if the URI matches the format of this module
 	 */
-	public boolean matches(URI uri);
+	public boolean matches(IRI uri);
 
 }
diff --git a/src/main/java/net/trustyuri/TrustyUriResource.java b/src/main/java/net/trustyuri/TrustyUriResource.java
@@ -8,10 +8,11 @@
 import java.net.URL;
 import java.net.URLConnection;
 import java.nio.charset.Charset;
+import java.util.Optional;
 import java.util.zip.GZIPInputStream;
 
-import org.openrdf.rio.RDFFormat;
-import org.openrdf.rio.Rio;
+import org.eclipse.rdf4j.rio.RDFFormat;
+import org.eclipse.rdf4j.rio.Rio;
 
 public class TrustyUriResource {
 
@@ -106,11 +107,14 @@ public String getModuleId() {
 	}
 
 	public RDFFormat getFormat(RDFFormat defaultFormat) {
-		RDFFormat format = Rio.getParserFormatForMIMEType(getMimetype());
-		if (format == null) {
-			format = Rio.getParserFormatForFileName(getFilename(), defaultFormat);
+		Optional<RDFFormat> format = Rio.getParserFormatForMIMEType(getMimetype());
+		if (!format.isPresent()) {
+			format = Rio.getParserFormatForFileName(getFilename());
 		}
-		return format;
+		if (format.isPresent()) {
+			return format.get();
+		}
+		return null;
 	}
 
 }
diff --git a/src/main/java/net/trustyuri/rdf/CheckLargeRdf.java b/src/main/java/net/trustyuri/rdf/CheckLargeRdf.java
@@ -10,20 +10,18 @@
 import java.util.Comparator;
 import java.util.List;
 
-import net.trustyuri.TrustyUriException;
-import net.trustyuri.TrustyUriResource;
-
-import org.openrdf.OpenRDFException;
-import org.openrdf.model.Statement;
-import org.openrdf.rio.RDFFormat;
-import org.openrdf.rio.RDFHandlerException;
-import org.openrdf.rio.RDFParser;
-import org.openrdf.rio.Rio;
-import org.openrdf.rio.helpers.RDFHandlerBase;
-import org.openrdf.rio.helpers.RDFaParserSettings;
+import org.eclipse.rdf4j.RDF4JException;
+import org.eclipse.rdf4j.model.Statement;
+import org.eclipse.rdf4j.rio.RDFFormat;
+import org.eclipse.rdf4j.rio.RDFHandlerException;
+import org.eclipse.rdf4j.rio.RDFParser;
+import org.eclipse.rdf4j.rio.helpers.AbstractRDFHandler;
 
 import com.google.code.externalsorting.ExternalSort;
 
+import net.trustyuri.TrustyUriException;
+import net.trustyuri.TrustyUriResource;
+
 public class CheckLargeRdf {
 
 	public static void main(String[] args) throws IOException, TrustyUriException {
@@ -52,12 +50,11 @@ public boolean check() throws IOException, TrustyUriException {
 		md = RdfHasher.getDigest();
 		RDFFormat format = r.getFormat(RDFFormat.TURTLE);
 
-		RDFParser p = Rio.createParser(format);
-		p.getParserConfig().set(RDFaParserSettings.FAIL_ON_RDFA_UNDEFINED_PREFIXES, true);
+		RDFParser p = RdfUtils.getParser(format);
 		File sortInFile = new File(dir, fileName + ".temp.sort-in");
 		final FileOutputStream preOut = new FileOutputStream(sortInFile);
-		p.setRDFHandler(new RdfPreprocessor(new RDFHandlerBase() {
-			
+		p.setRDFHandler(new RdfPreprocessor(new AbstractRDFHandler() {
+
 			@Override
 			public void handleStatement(Statement st) throws RDFHandlerException {
 				String s = SerStatementComparator.toString(st) + "\n";
@@ -72,7 +69,7 @@ public void handleStatement(Statement st) throws RDFHandlerException {
 		BufferedReader reader = new BufferedReader(r.getInputStreamReader(), 64*1024);
 		try {
 			p.parse(reader, "");
-		} catch (OpenRDFException ex) {
+		} catch (RDF4JException ex) {
 			throw new TrustyUriException(ex);
 		} finally {
 			reader.close();

diff --git a/src/main/java/net/trustyuri/rdf/CheckRdfGraph.java b/src/main/java/net/trustyuri/rdf/CheckRdfGraph.java
@@ -7,14 +7,14 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import org.eclipse.rdf4j.model.IRI;
+import org.eclipse.rdf4j.model.Statement;
+import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
+
 import net.trustyuri.TrustyUriException;
 import net.trustyuri.TrustyUriResource;
 import net.trustyuri.TrustyUriUtils;
 
-import org.openrdf.model.Statement;
-import org.openrdf.model.URI;
-import org.openrdf.model.impl.URIImpl;
-
 public class CheckRdfGraph {
 
 	public static void main(String[] args) throws IOException, TrustyUriException {
@@ -30,7 +30,7 @@ public static void main(String[] args) throws IOException, TrustyUriException {
 			c = new CheckRdfGraph(new File(fileName));
 		}
 		for (int i = 1 ; i < args.length ; i++) {
-			URI graphUri = new URIImpl(args[i]);
+			IRI graphUri = SimpleValueFactory.getInstance().createIRI(args[i]);
 			boolean valid = c.check(graphUri);
 			if (valid) {
 				System.out.println("Correct hash: " + getArtifactCode(graphUri));
@@ -57,7 +57,7 @@ private void init() throws IOException, TrustyUriException {
 		content = RdfUtils.load(r);
 	}
 
-	public boolean check(URI graphUri) throws TrustyUriException {
+	public boolean check(IRI graphUri) throws TrustyUriException {
 		String artifactCode = getArtifactCode(graphUri);
 		if (artifactCode == null) {
 			throw new TrustyUriException("Not a trusty URI: " + graphUri);
@@ -74,7 +74,7 @@ public boolean check(URI graphUri) throws TrustyUriException {
 		return artifactCode.equals(ac);
 	}
 
-	private static String getArtifactCode(URI graphUri) {
+	private static String getArtifactCode(IRI graphUri) {
 		return TrustyUriUtils.getArtifactCode(graphUri.stringValue());
 	}
 

diff --git a/src/main/java/net/trustyuri/rdf/CheckSortedRdf.java b/src/main/java/net/trustyuri/rdf/CheckSortedRdf.java
@@ -5,18 +5,16 @@
 import java.io.IOException;
 import java.security.MessageDigest;
 
+import org.eclipse.rdf4j.RDF4JException;
+import org.eclipse.rdf4j.model.Statement;
+import org.eclipse.rdf4j.rio.RDFFormat;
+import org.eclipse.rdf4j.rio.RDFHandlerException;
+import org.eclipse.rdf4j.rio.RDFParser;
+import org.eclipse.rdf4j.rio.helpers.AbstractRDFHandler;
+
 import net.trustyuri.TrustyUriException;
 import net.trustyuri.TrustyUriResource;
 
-import org.openrdf.OpenRDFException;
-import org.openrdf.model.Statement;
-import org.openrdf.rio.RDFFormat;
-import org.openrdf.rio.RDFHandlerException;
-import org.openrdf.rio.RDFParser;
-import org.openrdf.rio.Rio;
-import org.openrdf.rio.helpers.RDFHandlerBase;
-import org.openrdf.rio.helpers.RDFaParserSettings;
-
 public class CheckSortedRdf {
 
 	public static void main(String[] args) throws IOException, TrustyUriException {
@@ -54,10 +52,9 @@ public boolean check() throws IOException, TrustyUriException {
 		}
 		RDFFormat format = r.getFormat(RDFFormat.TURTLE);
 
-		RDFParser p = Rio.createParser(format);
+		RDFParser p = RdfUtils.getParser(format);
 		previous = null;
-		p.getParserConfig().set(RDFaParserSettings.FAIL_ON_RDFA_UNDEFINED_PREFIXES, true);
-		p.setRDFHandler(new RdfPreprocessor(new RDFHandlerBase() {
+		p.setRDFHandler(new RdfPreprocessor(new AbstractRDFHandler() {
 
 			@Override
 			public void handleStatement(Statement st) throws RDFHandlerException {
@@ -74,7 +71,7 @@ public void handleStatement(Statement st) throws RDFHandlerException {
 		BufferedReader reader = new BufferedReader(r.getInputStreamReader(), 64*1024);
 		try {
 			p.parse(reader, "");
-		} catch (OpenRDFException ex) {
+		} catch (RDF4JException ex) {
 			throw new TrustyUriException(ex);
 		} finally {
 			reader.close();