TAVERNA-1017 Use Commons RDF API instead of Jena
diff --git a/pom.xml b/pom.xml
index 01cd73a..67c98bf 100644
--- a/pom.xml
+++ b/pom.xml
@@ -31,6 +31,9 @@
<description>Taverna Language API for workflow definitions (SCUFL2)
and workflow inputs/outputs/run (DataBundle).
</description>
+ <properties>
+ <commons.rdf.version>0.4.0-incubating-SNAPSHOT</commons.rdf.version>
+ </properties>
<build>
<plugins>
<plugin>
diff --git a/taverna-scufl2-annotation/pom.xml b/taverna-scufl2-annotation/pom.xml
index b5d7ea2..23e2875 100644
--- a/taverna-scufl2-annotation/pom.xml
+++ b/taverna-scufl2-annotation/pom.xml
@@ -44,12 +44,11 @@
<version>${project.version}</version>
<scope>test</scope>
</dependency>
- <dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>jena-osgi</artifactId>
- <version>${jena.version}</version>
- </dependency>
-
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-rdf-jena</artifactId>
+ <version>${commons.rdf.version}</version>
+ </dependency>
</dependencies>
</project>
diff --git a/taverna-scufl2-annotation/src/main/java/org/apache/taverna/scufl2/annotation/AnnotationTools.java b/taverna-scufl2-annotation/src/main/java/org/apache/taverna/scufl2/annotation/AnnotationTools.java
index 9e8a157..4a5de12 100644
--- a/taverna-scufl2-annotation/src/main/java/org/apache/taverna/scufl2/annotation/AnnotationTools.java
+++ b/taverna-scufl2-annotation/src/main/java/org/apache/taverna/scufl2/annotation/AnnotationTools.java
@@ -26,12 +26,19 @@
import java.net.URI;
import java.util.Calendar;
import java.util.GregorianCalendar;
-import java.util.Iterator;
+import java.util.Optional;
+import java.util.concurrent.ExecutionException;
import java.util.logging.Logger;
-import org.apache.jena.riot.Lang;
-import org.apache.jena.riot.RDFDataMgr;
-import org.apache.jena.riot.RDFLanguages;
+import org.apache.commons.rdf.api.Dataset;
+import org.apache.commons.rdf.api.Graph;
+import org.apache.commons.rdf.api.IRI;
+import org.apache.commons.rdf.api.Literal;
+import org.apache.commons.rdf.api.Quad;
+import org.apache.commons.rdf.jena.JenaIRI;
+import org.apache.commons.rdf.jena.JenaLiteral;
+import org.apache.commons.rdf.jena.JenaRDF;
+import org.apache.commons.rdf.jena.experimental.JenaRDFParser;
import org.apache.taverna.scufl2.api.annotation.Annotation;
import org.apache.taverna.scufl2.api.common.Child;
import org.apache.taverna.scufl2.api.common.Scufl2Tools;
@@ -39,24 +46,14 @@
import org.apache.taverna.scufl2.api.container.WorkflowBundle;
import org.apache.taverna.scufl2.ucfpackage.UCFPackage.ResourceEntry;
-
-import org.apache.jena.graph.Node;
-import org.apache.jena.graph.NodeFactory;
-import org.apache.jena.query.Dataset;
-import org.apache.jena.query.DatasetFactory;
-import org.apache.jena.rdf.model.Model;
-import org.apache.jena.rdf.model.ModelFactory;
-import org.apache.jena.sparql.core.Quad;
-
public class AnnotationTools {
- private static final String EXAMPLE_DATA_PREDICATE = "http://biocatalogue.org/attribute/exampleData";
- public static final URI EXAMPLE_DATA = URI.create(EXAMPLE_DATA_PREDICATE);
- private static final String TITLE_PREDICATE = "http://purl.org/dc/terms/title";
- public static final URI TITLE = URI.create(TITLE_PREDICATE);
- private static final String DESCRIPTION_PREDICATE = "http://purl.org/dc/terms/description";
- public static final URI DESCRIPTION = URI.create(DESCRIPTION_PREDICATE);
- private static final String CREATOR_PREDICATE = "http://purl.org/dc/elements/1.1/creator";
- public static final URI CREATOR = URI.create(CREATOR_PREDICATE);
+
+ private static JenaRDF rdf = new JenaRDF();
+
+ public static final IRI EXAMPLE_DATA = rdf.createIRI("http://biocatalogue.org/attribute/exampleData");
+ public static final IRI TITLE = rdf.createIRI("http://purl.org/dc/terms/title");
+ public static final IRI DESCRIPTION = rdf.createIRI("http://purl.org/dc/terms/description");
+ public static final IRI CREATOR = rdf.createIRI("http://purl.org/dc/elements/1.1/creator");
private static Logger logger = Logger.getLogger(AnnotationTools.class
.getCanonicalName());
@@ -65,7 +62,7 @@
private URITools uritools = new URITools();
public Dataset annotationDatasetFor(Child<?> workflowBean) {
- Dataset dataset = DatasetFactory.createMem();
+ Dataset dataset = rdf.createDataset();
for (Annotation ann : scufl2Tools.annotationsFor(workflowBean)) {
WorkflowBundle bundle = ann.getParent();
URI annUri = uritools.uriForBean(ann);
@@ -87,57 +84,79 @@
continue;
}
String contentType = resourceEntry.getMediaType();
- Lang lang = RDFLanguages.contentTypeToLang(contentType);
- if (lang == null) {
- lang = RDFLanguages.filenameToLang(path);
- }
- if (lang == null) {
- logger.warning("Can't find media type of annotation body: "
- + ann.getBody());
- continue;
- }
- Model model = ModelFactory.createDefaultModel();
+
try (InputStream inStream = bundle.getResources()
.getResourceAsInputStream(path)) {
- RDFDataMgr.read(model, inStream, bodyUri, lang);
+
+ Optional<Graph> graph = graphForAnnotation(dataset, annUri);
+
+
+ JenaRDFParser parser = new JenaRDFParser()
+ .base(bodyUri).source(inStream)
+ .contentType(contentType)
+ .target(graph.get());
+ // TODO: Do multiple parsings in one go to speed up outer
+ // for-loop? Would need thread-safe Dataset backed by say TDB in memory
+ try {
+ parser.parse().get();
+ } catch (IllegalStateException | InterruptedException | ExecutionException e) {
+ logger.warning("Can't parse annotation body: " + path);
+ continue;
+ }
} catch (IOException e) {
logger.warning("Can't read annotation body: " + path);
continue;
}
- dataset.addNamedModel(annUri.toString(), model);
}
return dataset;
}
+ private Optional<Graph> graphForAnnotation(Dataset dataset, URI annUri) {
+ IRI graphUri = uritools.asIRI(annUri);
+ Optional<Graph> graph = dataset.getGraph(graphUri);
+
+ if (! graph.isPresent()) {
+ // Need a dummy quad first?
+ JenaIRI example = rdf.createIRI("http://example.com/");
+ dataset.add(graphUri, example, example, example);
+ graph = dataset.getGraph(graphUri);
+ if (! graph.isPresent()) {
+ logger.severe("Can't create named graph: " + graphUri.getIRIString());
+ }
+ // Remove dummy triple :) This will crash if the above can't create graph.
+ graph.get().remove(example, example, example);
+ }
+
+ return graph;
+ }
+
public String getTitle(Child<?> workflowBean) {
- return getLiteral(workflowBean, TITLE_PREDICATE);
+ return getLiteral(workflowBean, TITLE).orElse(null);
}
- private String getLiteral(Child<?> workflowBean, String propertyUri) {
+ private Optional<String> getLiteral(Child<?> workflowBean, IRI property) {
+ // TODO: Cache dataset PARSING!
Dataset annotations = annotationDatasetFor(workflowBean);
- URI beanUri = uritools.uriForBean(workflowBean);
- Node subject = NodeFactory.createURI(beanUri.toString());
- Node property = NodeFactory.createURI(propertyUri);
-
- Iterator<Quad> found = annotations.asDatasetGraph().find(null, subject,
- property, null);
- if (!found.hasNext()) {
- return null;
- }
- return found.next().getObject().toString(false);
+ IRI beanIRI = uritools.asIRI(uritools.uriForBean(workflowBean));
+ return annotations.stream(null, beanIRI, property, null).map(Quad::getObject)
+ // Pick any Literal property value, if it exist
+ .filter(Literal.class::isInstance).map(Literal.class::cast)
+ .map(Literal::getLexicalForm).findAny();
}
public String getCreator(Child<?> workflowBean) {
- return getLiteral(workflowBean, CREATOR_PREDICATE);
+ // TODO: Also support dcterms:creator and foaf:name ?
+ return getLiteral(workflowBean, CREATOR).orElse(null);
}
public String getExampleValue(Child<?> workflowBean) {
- return getLiteral(workflowBean, EXAMPLE_DATA_PREDICATE);
+ // TODO: Also support example value as a path?
+ return getLiteral(workflowBean, EXAMPLE_DATA).orElse(null);
}
- public String getDescription(Child<?> workflowBean) {
- return getLiteral(workflowBean, DESCRIPTION_PREDICATE);
+ public String getDescription(Child<?> workflowBean) {
+ return getLiteral(workflowBean, DESCRIPTION).orElse(null);
}
/**
@@ -150,7 +169,7 @@
* @throws IOException
*/
public Annotation createNewAnnotation(WorkflowBundle workflowBundle,
- Child<?> subject, URI predicate, String value) throws IOException {
+ Child<?> subject, IRI predicate, String value) throws IOException {
Object parent = subject.getParent();
while (parent instanceof Child)
parent = ((Child<?>) parent).getParent();
@@ -176,25 +195,22 @@
annotation.setAnnotatedAt(now);
// annotation.setAnnotator();//FIXME
annotation.setSerializedAt(now);
- URI annotatedSubject = uritools.relativeUriForBean(subject, annotation);
+ IRI annotatedSubject = uritools.asIRI(uritools.relativeUriForBean(subject, annotation));
+
+
StringBuilder turtle = new StringBuilder();
- turtle.append("<");
- turtle.append(annotatedSubject.toASCIIString());
- turtle.append("> ");
+ turtle.append(annotatedSubject.ntriplesString());
- turtle.append("<");
- turtle.append(predicate.toASCIIString());
- turtle.append("> ");
+ turtle.append(" ");
+ turtle.append(predicate.ntriplesString());
- // A potentially multi-line string
- turtle.append("\"\"\"");
- // Escape existing \ to \\
- String escaped = value.replace("\\", "\\\\");
- // Escape existing " to \" (beware Java's escaping of \ and " below)
- escaped = escaped.replace("\"", "\\\"");
- turtle.append(escaped);
- turtle.append("\"\"\"");
- turtle.append(" .");
+ turtle.append(" ");
+ JenaLiteral literal = rdf.createLiteral(value);
+ turtle.append(literal.ntriplesString());
+
+ turtle.append(" .\n");
+
+ // TODO: Save with Jena instead
try {
workflowBundle.getResources().addResource(turtle.toString(), path,
"text/turtle");
diff --git a/taverna-scufl2-api/pom.xml b/taverna-scufl2-api/pom.xml
index 2930371..6efa903 100644
--- a/taverna-scufl2-api/pom.xml
+++ b/taverna-scufl2-api/pom.xml
@@ -50,6 +50,11 @@
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-rdf-simple</artifactId>
+ <version>${commons.rdf.version}</version>
+ </dependency>
</dependencies>
<build>
<plugins>
diff --git a/taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/URITools.java b/taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/URITools.java
index 85d96ac..dff04b4 100644
--- a/taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/URITools.java
+++ b/taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/URITools.java
@@ -27,6 +27,9 @@
import java.util.List;
import java.util.Map;
+import org.apache.commons.rdf.api.IRI;
+import org.apache.commons.rdf.api.RDF;
+import org.apache.commons.rdf.simple.SimpleRDF;
import org.apache.taverna.scufl2.api.annotation.Annotation;
import org.apache.taverna.scufl2.api.annotation.Revision;
import org.apache.taverna.scufl2.api.common.Visitor.VisitorWithPath;
@@ -53,6 +56,18 @@
private static final String DATALINK = "datalink";
private static final URI DOT = URI.create(".");
+ private RDF rdf = new SimpleRDF();
+
+ public IRI asIRI(URI uri) {
+ // TODO: Handle internationalization?
+ return rdf.createIRI(uri.toString());
+ }
+
+ public URI asURI(IRI iri) {
+ // TODO: Handle internationalization?
+ return URI.create(iri.getIRIString());
+ }
+
public URI relativePath(URI base, URI uri) {
URI root = base.resolve("/");
if (!root.equals(uri.resolve("/")))
