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Posted to commits@taverna.apache.org by st...@apache.org on 2015/06/11 17:24:21 UTC
[01/11] incubator-taverna-language git commit: less Sesame
Repository: incubator-taverna-language
Updated Branches:
refs/heads/wfdesc-jena [created] a0c10e624
less Sesame
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/a0c10e62
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/a0c10e62
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/a0c10e62
Branch: refs/heads/wfdesc-jena
Commit: a0c10e624bce477d2c17ebfe87d40204ea57f86c
Parents: a64c2d2
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 23:13:03 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
.../taverna/scufl2/wfdesc/WfdescSerialiser.java | 29 ++------------------
1 file changed, 3 insertions(+), 26 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a0c10e62/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescSerialiser.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescSerialiser.java b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescSerialiser.java
index 28a2c1b..ee541ff 100644
--- a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescSerialiser.java
+++ b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescSerialiser.java
@@ -76,7 +76,6 @@ import org.purl.wf4ever.wfdesc.Output;
import org.purl.wf4ever.wfdesc.Process;
import org.w3.prov.Entity;
-
import com.fasterxml.jackson.databind.JsonNode;
public class WfdescSerialiser {
@@ -97,42 +96,20 @@ public class WfdescSerialiser {
.create("http://ns.taverna.org.uk/2010/activity/tool");
private Scufl2Tools scufl2Tools = new Scufl2Tools();
- private SesameManager sesameManager;
private URITools uriTools = new URITools();
private WorkflowBundle wfBundle;
- public Repository getRepository() {
- return getSesameManager().getConnection().getRepository();
- }
public Scufl2Tools getScufl2Tools() {
return scufl2Tools;
}
- public SesameManager getSesameManager() {
- if (sesameManager == null) {
-
- // Raven workaround - register SPARQLParserFactory
- QueryParserRegistry.getInstance().add(new SPARQLParserFactory());
-
- ElmoModule module = new ElmoModule();
- module.addConcept(Labelled.class);
- SesameManagerFactory factory = new SesameManagerFactory(module);
- factory.setInferencingEnabled(true);
- sesameManager = factory.createElmoManager();
- }
- return sesameManager;
- }
-
public URITools getUriTools() {
return uriTools;
}
- private QName qnameForBean(WorkflowBean bean) {
- URI uri = uriTools.uriForBean(bean);
- org.openrdf.model.URI sesameUri = getRepository().getValueFactory()
- .createURI(uri.toASCIIString());
- return new QName(sesameUri.getNamespace(), sesameUri.getLocalName());
+ private String uriForBean(WorkflowBean bean) {
+ return uriTools.uriForBean(bean).toASCIIString();
}
protected void save(final WorkflowBundle bundle) {
@@ -319,7 +296,7 @@ public class WfdescSerialiser {
}
private <T> T entityForBean(WorkflowBean bean, Class<T> type) {
- return getSesameManager().create(qnameForBean(bean), type);
+ return getSesameManager().create(uriForBean(bean), type);
}
// @Override
[05/11] incubator-taverna-language git commit: jena dependency
Posted by st...@apache.org.
jena dependency
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/856fadc2
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/856fadc2
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/856fadc2
Branch: refs/heads/wfdesc-jena
Commit: 856fadc26bdf1a34ec71144c74eed6d054b1a616
Parents: 0f6bd20
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 17:27:09 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
taverna-scufl2-wfdesc/pom.xml | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/856fadc2/taverna-scufl2-wfdesc/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/pom.xml b/taverna-scufl2-wfdesc/pom.xml
index 2c0f24f..8dcba50 100755
--- a/taverna-scufl2-wfdesc/pom.xml
+++ b/taverna-scufl2-wfdesc/pom.xml
@@ -48,7 +48,7 @@
<fileOptions>
<source>
<input>default</input>
- <package-name>org.apache.taverna.scufl2.wfdesc.impl.ontologies</package-name>
+ <package-name>org.apache.taverna.scufl2.wfdesc.ontologies</package-name>
<ontology>true</ontology>
</source>
</fileOptions>
@@ -167,6 +167,11 @@
<type>test-jar</type>
<scope>test</scope>
</dependency>
+ <dependency>
+ <groupId>org.apache.jena</groupId>
+ <artifactId>jena-core</artifactId>
+ <version>${jena.version}</version>
+ </dependency>
<dependency>
<groupId>junit</groupId>
[02/11] incubator-taverna-language git commit: Test RoEvoSerializer
Posted by st...@apache.org.
Test RoEvoSerializer
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/fe8ad277
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/fe8ad277
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/fe8ad277
Branch: refs/heads/wfdesc-jena
Commit: fe8ad277ddc5a3a2a6f878d66da04882cfceccf6
Parents: e116209
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 22:00:43 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
.../scufl2/wfdesc/TestRoEvoSerializer.java | 26 +++++++++++++++++---
1 file changed, 23 insertions(+), 3 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/fe8ad277/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java
index 1e757ad..afe8cd5 100644
--- a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java
+++ b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java
@@ -21,9 +21,12 @@ package org.apache.taverna.scufl2.wfdesc;
*/
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
+import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
@@ -31,10 +34,14 @@ import java.io.InputStream;
import org.apache.taverna.scufl2.api.container.WorkflowBundle;
import org.apache.taverna.scufl2.api.io.ReaderException;
import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
-import org.apache.taverna.scufl2.wfdesc.ROEvoSerializer;
+import org.apache.taverna.scufl2.wfdesc.ontologies.Prov_o;
import org.junit.Before;
import org.junit.Test;
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Resource;
+
public class TestRoEvoSerializer {
private static final String HELLOWORLD_T2FLOW = "helloanyone.t2flow";
@@ -50,15 +57,28 @@ public class TestRoEvoSerializer {
assertNotNull(helloStream);
helloWorld = io.readBundle(helloStream, "application/vnd.taverna.t2flow+xml");
assertNotNull(helloWorld);
+ assertEquals("/2010/workflow/01348671-5aaa-4cc2-84cc-477329b70b0d/",
+ helloWorld.getMainWorkflow().getIdentifier().getPath());
}
-
@Test
public void workflowUUIDs() throws Exception {
ByteArrayOutputStream os = new ByteArrayOutputStream();
roEvo.workflowHistory(helloWorld.getMainWorkflow(), os);
+ System.out.write(os.toByteArray());
assertTrue(500 < os.size());
- assertTrue(os.toString("UTF-8").indexOf(" a roevo:VersionableResource , prov:Entity ;") > 0);
+ String ttl = os.toString("UTF-8");
+ assertTrue(ttl.contains("01348671-5aaa-4cc2-84cc-477329b70b0d"));
+ assertTrue(ttl.contains("VersionableResource"));
+ assertTrue(ttl.contains("Entity"));
+
+ OntModel m = ModelFactory.createOntologyModel();
+ m.read(new ByteArrayInputStream(os.toByteArray()), "http://example.com/", "Turtle");
+ Resource mainWf = m.getResource(helloWorld.getMainWorkflow().getIdentifier().toASCIIString());
+ Resource older = mainWf.getProperty(Prov_o.wasRevisionOf).getResource();
+ Resource oldest = older.getProperty(Prov_o.wasRevisionOf).getResource();
+ assertNull(oldest.getProperty(Prov_o.wasRevisionOf));
+
}
}
[08/11] incubator-taverna-language git commit: also jena-arq
Posted by st...@apache.org.
also jena-arq
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/f7b6a876
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/f7b6a876
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/f7b6a876
Branch: refs/heads/wfdesc-jena
Commit: f7b6a876e13501b7f8f7a2abc70e741e1c8fd59b
Parents: b180c12
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 17:40:34 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
taverna-scufl2-wfdesc/pom.xml | 5 +++++
1 file changed, 5 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/f7b6a876/taverna-scufl2-wfdesc/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/pom.xml b/taverna-scufl2-wfdesc/pom.xml
index 8dcba50..228f917 100755
--- a/taverna-scufl2-wfdesc/pom.xml
+++ b/taverna-scufl2-wfdesc/pom.xml
@@ -172,6 +172,11 @@
<artifactId>jena-core</artifactId>
<version>${jena.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.apache.jena</groupId>
+ <artifactId>jena-arq</artifactId>
+ <version>${jena.version}</version>
+ </dependency>
<dependency>
<groupId>junit</groupId>
[11/11] incubator-taverna-language git commit: Correct rdf.write()
argument for "Turtle"
Posted by st...@apache.org.
Correct rdf.write() argument for "Turtle"
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/e1162095
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/e1162095
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/e1162095
Branch: refs/heads/wfdesc-jena
Commit: e1162095c80fb87841a6338ce549107b7d3c5975
Parents: f289179
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 22:00:21 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
.../java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e1162095/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
index 4d09d4d..0ed58fe 100644
--- a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
+++ b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
@@ -57,7 +57,7 @@ public class ROEvoSerializer {
model.setNsPrefix("rdfs",
"http://www.w3.org/2000/01/rdf-schema#");
- model.write(output, "turtle", baseURI.toASCIIString());
+ model.write(output, "Turtle", baseURI.toASCIIString());
// throw new WriterException("Can't write to output", e);
[03/11] incubator-taverna-language git commit: serialize revisions
with Jena instead of Sesame
Posted by st...@apache.org.
serialize revisions with Jena instead of Sesame
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/3c775388
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/3c775388
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/3c775388
Branch: refs/heads/wfdesc-jena
Commit: 3c77538817f3016be71799e2c1f04906347d0fe2
Parents: f7b6a87
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 17:40:42 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
.../taverna/scufl2/wfdesc/ROEvoSerializer.java | 65 ++++++++------------
1 file changed, 25 insertions(+), 40 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3c775388/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
index b58d8bb..f0ee289 100644
--- a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
+++ b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
@@ -28,6 +28,7 @@ import java.io.OutputStream;
import org.apache.taverna.scufl2.api.annotation.Revision;
import org.apache.taverna.scufl2.api.core.Workflow;
import org.apache.taverna.scufl2.api.io.WriterException;
+import org.apache.taverna.scufl2.wfdesc.ontologies.Prov_o;
import org.openrdf.OpenRDFException;
import org.openrdf.model.URI;
import org.openrdf.model.ValueFactory;
@@ -39,32 +40,24 @@ import org.openrdf.repository.sail.SailRepository;
import org.openrdf.rio.helpers.OrganizedRDFWriter;
import org.openrdf.sail.memory.MemoryStore;
+import com.hp.hpl.jena.ontology.Individual;
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Resource;
+
public class ROEvoSerializer {
//private URITools uriTools = new URITools();
public void workflowHistory(Workflow mainWorkflow, OutputStream output) throws WriterException {
- Repository repository = new SailRepository(new MemoryStore());
- try {
- repository.initialize();
- } catch (RepositoryException e1) {
- throw new IllegalStateException("Can't initialize memory SAIL repository", e1);
- }
- ValueFactory factory = repository.getValueFactory();
-
-
- RepositoryConnection con;
- try {
- con = repository.getConnection();
- } catch (RepositoryException e1) {
- throw new IllegalStateException("Can't get repository connection", e1);
- }
+ OntModel model = ModelFactory.createOntologyModel();
Revision revision = mainWorkflow.getCurrentRevision();
Revision previous = revision.getPreviousRevision();
- addRevision(factory, con, revision);
+ addRevision(model, revision);
while (previous != null) {
- addRevision(factory, con, previous);
- addPrevious(factory, con, revision, previous);
+ addRevision(model, previous);
+ addPrevious(model, revision, previous);
revision = previous;
previous = revision.getPreviousRevision();
}
@@ -90,33 +83,25 @@ public class ROEvoSerializer {
}
- private void addRevision(ValueFactory factory, RepositoryConnection con,
+ private void addRevision(OntModel model,
Revision revision) {
- URI revisionURI = factory.createURI(revision.getIdentifier().toASCIIString());
-
- URI version = factory.createURI("http://purl.org/wf4ever/roevo#VersionableResource");
- URI entity = factory.createURI("http://www.w3.org/ns/prov#Entity");
- try {
- con.add(revisionURI, RDF.TYPE, version);
- con.add(revisionURI, RDF.TYPE, entity);
- } catch (RepositoryException e1) {
- throw new IllegalStateException("Can't add triple to repository", e1);
- }
-
+ OntClass VersionableResource = model.createClass("http://purl.org/wf4ever/roevo#VersionableResource");
+ VersionableResource.addSuperClass(Prov_o.Entity);
+ Individual revisionResource = model.createIndividual(revision.getIdentifier().toASCIIString(),
+ VersionableResource);
+ revisionResource.addRDFType(Prov_o.Entity);
}
- private void addPrevious(ValueFactory factory, RepositoryConnection con,
+ private void addPrevious(OntModel model,
Revision revision, Revision previous) {
- URI revisionURI = factory.createURI(revision.getIdentifier().toASCIIString());
- URI previousURI = factory.createURI(previous.getIdentifier().toASCIIString());
+ OntClass VersionableResource = model.createClass("http://purl.org/wf4ever/roevo#VersionableResource");
+ VersionableResource.addSuperClass(Prov_o.Entity);
- URI prev = factory.createURI("http://www.w3.org/ns/prov#wasRevisionOf");
-
- try {
- con.add(revisionURI, prev, previousURI);
- } catch (RepositoryException e1) {
- throw new IllegalStateException("Can't add triple to repository", e1);
- }
+ Individual revisionResource = model.createIndividual(revision.getIdentifier().toASCIIString(),
+ VersionableResource);
+ Individual previousResource = model.createIndividual(previous.getIdentifier().toASCIIString(),
+ VersionableResource);
+ revisionResource.addProperty(Prov_o.wasRevisionOf, previousResource);
}
}
[06/11] incubator-taverna-language git commit: Removed classes for
Elmo/Sesame
Posted by st...@apache.org.
Removed classes for Elmo/Sesame
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/b180c122
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/b180c122
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/b180c122
Branch: refs/heads/wfdesc-jena
Commit: b180c1226e02138d7dc3a0bb8c7c93ac2c62c857
Parents: 856fadc
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 17:28:02 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
.../apache/taverna/scufl2/wfdesc/Labelled.java | 36 ----------
.../scufl2/wfdesc/TurtleWriterWithBase.java | 71 --------------------
2 files changed, 107 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/b180c122/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/Labelled.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/Labelled.java b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/Labelled.java
deleted file mode 100644
index 203be79..0000000
--- a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/Labelled.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package org.apache.taverna.scufl2.wfdesc;
-
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * 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
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-
-import java.util.Set;
-
-import org.openrdf.elmo.annotations.rdf;
-
-@rdf("http://purl.org/wf4ever/wfdesc#Description")
-public interface Labelled {
-
- @rdf("http://www.w3.org/2000/01/rdf-schema#label")
- Set<String> getLabel();
- void setLabel(Set<String> label);
-}
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/b180c122/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/TurtleWriterWithBase.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/TurtleWriterWithBase.java b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/TurtleWriterWithBase.java
deleted file mode 100644
index 05f484d..0000000
--- a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/TurtleWriterWithBase.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package org.apache.taverna.scufl2.wfdesc;
-
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * 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
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-import java.io.IOException;
-import java.io.OutputStream;
-import java.net.URI;
-
-import org.apache.taverna.scufl2.api.common.URITools;
-import org.openrdf.rio.RDFHandlerException;
-import org.openrdf.rio.turtle.TurtleUtil;
-import org.openrdf.rio.turtle.TurtleWriter;
-import org.openrdf.sail.memory.model.MemURI;
-
-
-public class TurtleWriterWithBase extends TurtleWriter {
- private URITools uriTools = new URITools();
- private final URI baseURI;
-
- TurtleWriterWithBase(OutputStream out, URI baseURI) {
- super(out);
- this.baseURI = baseURI;
- }
-
- @Override
- public void startRDF() throws RDFHandlerException {
- super.startRDF();
- try {
- writeBase();
- } catch (IOException e) {
- throw new RDFHandlerException(e);
- }
- }
-
- @Override
- protected void writeURI(org.openrdf.model.URI uri) throws IOException {
-
- final String uriString = uriTools.relativePath(baseURI,
- URI.create(uri.toString())).toASCIIString();
- super.writeURI(new MemURI(null, uriString, ""));
- }
-
- protected void writeBase() throws IOException {
- writer.write("@base ");
- writer.write("<");
- writer.write(TurtleUtil.encodeURIString(baseURI.toASCIIString()));
- writer.write("> .");
- writer.writeEOL();
- }
-
-
-}
[07/11] incubator-taverna-language git commit: roevo serialization
with jena
Posted by st...@apache.org.
roevo serialization with jena
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/518d7ce5
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/518d7ce5
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/518d7ce5
Branch: refs/heads/wfdesc-jena
Commit: 518d7ce525dade5b68c8025d9c62de7128279532
Parents: 3c77538
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 21:40:01 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
taverna-scufl2-wfdesc/pom.xml | 6 ----
.../taverna/scufl2/wfdesc/ROEvoSerializer.java | 35 +++++---------------
2 files changed, 8 insertions(+), 33 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/518d7ce5/taverna-scufl2-wfdesc/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/pom.xml b/taverna-scufl2-wfdesc/pom.xml
index 228f917..6eb231a 100755
--- a/taverna-scufl2-wfdesc/pom.xml
+++ b/taverna-scufl2-wfdesc/pom.xml
@@ -173,12 +173,6 @@
<version>${jena.version}</version>
</dependency>
<dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>jena-arq</artifactId>
- <version>${jena.version}</version>
- </dependency>
-
- <dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.4</version>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/518d7ce5/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
index f0ee289..4d09d4d 100644
--- a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
+++ b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ROEvoSerializer.java
@@ -29,22 +29,11 @@ import org.apache.taverna.scufl2.api.annotation.Revision;
import org.apache.taverna.scufl2.api.core.Workflow;
import org.apache.taverna.scufl2.api.io.WriterException;
import org.apache.taverna.scufl2.wfdesc.ontologies.Prov_o;
-import org.openrdf.OpenRDFException;
-import org.openrdf.model.URI;
-import org.openrdf.model.ValueFactory;
-import org.openrdf.model.vocabulary.RDF;
-import org.openrdf.repository.Repository;
-import org.openrdf.repository.RepositoryConnection;
-import org.openrdf.repository.RepositoryException;
-import org.openrdf.repository.sail.SailRepository;
-import org.openrdf.rio.helpers.OrganizedRDFWriter;
-import org.openrdf.sail.memory.MemoryStore;
import com.hp.hpl.jena.ontology.Individual;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Resource;
public class ROEvoSerializer {
@@ -63,23 +52,15 @@ public class ROEvoSerializer {
}
java.net.URI baseURI = Workflow.WORKFLOW_ROOT;
-
- try {
- con.setNamespace("roevo", "http://purl.org/wf4ever/roevo#");
- con.setNamespace("prov", "http://www.w3.org/ns/prov#");
-// con.setNamespace("wfdesc",
-// "http://purl.org/wf4ever/wfdesc#");
-// con.setNamespace("wf4ever",
-// "http://purl.org/wf4ever/wf4ever#");
- con.setNamespace("rdfs",
- "http://www.w3.org/2000/01/rdf-schema#");
-
+ model.setNsPrefix("roevo", "http://purl.org/wf4ever/roevo#");
+ model.setNsPrefix("prov", "http://www.w3.org/ns/prov#");
+ model.setNsPrefix("rdfs",
+ "http://www.w3.org/2000/01/rdf-schema#");
- con.export(new OrganizedRDFWriter(
- new TurtleWriterWithBase(output, baseURI)));
- } catch (OpenRDFException e) {
- throw new WriterException("Can't write to output", e);
- }
+ model.write(output, "turtle", baseURI.toASCIIString());
+
+// throw new WriterException("Can't write to output", e);
+
}
[10/11] incubator-taverna-language git commit: Avoid @prefix : as it
confuses Jena schemagen
Posted by st...@apache.org.
Avoid @prefix : as it confuses Jena schemagen
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/a64c2d27
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/a64c2d27
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/a64c2d27
Branch: refs/heads/wfdesc-jena
Commit: a64c2d27a9f1f4006ee0ffc84b4fa5fb2972e53c
Parents: fe8ad27
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 23:12:42 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
.../src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl | 1 -
.../src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl | 1 -
2 files changed, 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a64c2d27/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl b/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl
index 2a87996..6087ffc 100644
--- a/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl
+++ b/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl
@@ -19,7 +19,6 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix parrot: <http://vocab.ctic.es/parrot#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix : <http://www.semanticweb.org/owl/owlapi/turtle#> .
@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a64c2d27/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl b/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl
index f6e0eef..193f29d 100644
--- a/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl
+++ b/taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl
@@ -19,7 +19,6 @@
@prefix wfprov: <http://purl.org/wf4ever/wfprov#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix : <http://www.semanticweb.org/owl/owlapi/turtle#> .
@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
[04/11] incubator-taverna-language git commit: Draft: Using
Jena/schemagen instead of sesame/elmo
Posted by st...@apache.org.
Draft: Using Jena/schemagen instead of sesame/elmo
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/0f6bd203
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/0f6bd203
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/0f6bd203
Branch: refs/heads/wfdesc-jena
Commit: 0f6bd203c995dfd72de53fe0f9710cf86eeba784
Parents: b1a77b3
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 01:55:05 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
taverna-scufl2-wfdesc/pom.xml | 219 +++++--------------------------------
1 file changed, 27 insertions(+), 192 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/0f6bd203/taverna-scufl2-wfdesc/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/pom.xml b/taverna-scufl2-wfdesc/pom.xml
index 88d8bd3..2c0f24f 100755
--- a/taverna-scufl2-wfdesc/pom.xml
+++ b/taverna-scufl2-wfdesc/pom.xml
@@ -35,89 +35,34 @@
<build>
<plugins>
<plugin>
- <artifactId>maven-antrun-plugin</artifactId>
- <version>1.6</version>
- <executions>
- <execution>
- <phase>generate-sources</phase>
- <configuration>
- <target>
- <property name="compile_classpath" refid="maven.compile.classpath" />
- <property name="runtime_classpath" refid="maven.runtime.classpath" />
- <property name="test_classpath" refid="maven.test.classpath" />
- <property name="plugin_classpath" refid="maven.plugin.classpath" />
-
- <!-- inspired by http://openprovenance.org/java/maven-releases/org/openprovenance/opm-elmo/1.1.1/opm-elmo-1.1.1.pom -->
-
- <mkdir dir="${project.build.directory}" />
- <mkdir dir="${project.build.directory}/generated-sources" />
- <mkdir dir="${project.build.directory}/generated-sources/elmo" />
-
- <java classname="org.openrdf.elmo.codegen.OntologyConverter" fork="true" failonerror="true" maxmemory="128m">
- <arg value="-b" />
- <arg value="org.purl.wf4ever.wfdesc=http://purl.org/wf4ever/wfdesc#" />
- <arg value="-b" />
- <arg value="org.purl.wf4ever.wf4ever=http://purl.org/wf4ever/wf4ever#" />
- <arg value="-b" />
- <arg value="org.purl.wf4ever.wfprov=http://purl.org/wf4ever/wfprov#" />
- <arg value="-b" />
- <arg value="org.w3.prov=http://www.w3.org/ns/prov#" />
- <arg value="-b" />
- <arg value="org.purl.wf4ever.roterms=http://purl.org/wf4ever/roterms#" />
- <arg value="-b" />
- <arg value="org.w3.rdfs=http://www.w3.org/2000/01/rdf-schema#" />
-
-
-
- <!-- <arg value="-p" /> <arg value="wfdesc" /> -->
- <arg value="-j" />
- <arg value="target/wfdesc-ontology.jar" />
-
- <arg value="-p" />
- <arg value="wf" /> <!-- Windows freaks out if this is really empty -->
-
- <!-- <arg value="http://purl.org/wf4ever/wfdesc" /> -->
- <arg value="src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl" />
- <arg value="src/main/resources/org/purl/wf4ever/wfdesc/wf4ever.ttl" />
- <arg value="src/main/resources/com/xmlns/foaf/foaf.rdf" />
- <arg value="src/main/resources/org/w3/prov-o.ttl" />
-
- <!--
- -->
- <arg value="src/main/resources/org/purl/wf4ever/wfdesc/roterms.ttl" />
-
-
- <classpath refid="maven.plugin.classpath" />
- <classpath>
- <pathelement path="." />
- </classpath>
- project.name
- </java>
- <unzip src="${project.build.directory}/wfdesc-ontology.jar" dest="${project.build.directory}/generated-sources/elmo">
- <patternset>
- <exclude name="**/*.class" />
- </patternset>
- </unzip>
- </target>
- </configuration>
- <goals>
- <goal>run</goal>
- </goals>
- </execution>
- </executions>
- <dependencies>
- <dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-codegen</artifactId>
- <version>1.5</version>
- </dependency>
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-log4j12</artifactId>
- <version>1.5.2</version> <!-- note old version required for elmo! -->
- </dependency>
- </dependencies>
+ <groupId>org.apache.jena</groupId>
+ <artifactId>jena-maven-tools</artifactId>
+ <version>0.8-SNAPSHOT</version>
+ <configuration>
+ <includes>
+ <include>src/main/resources/org/purl/wf4ever/wfdesc/*.ttl</include>
+ <include>src/main/resources/org/purl/wf4ever/wfdesc/*.ttl</include>
+ <include>src/main/resources/com/xmlns/foaf/foaf.rdf</include>
+ <include>src/main/resources/org/w3/prov-o.ttl</include>
+ </includes>
+ <fileOptions>
+ <source>
+ <input>default</input>
+ <package-name>org.apache.taverna.scufl2.wfdesc.impl.ontologies</package-name>
+ <ontology>true</ontology>
+ </source>
+ </fileOptions>
+ </configuration>
+ <executions>
+ <execution>
+ <id>schemagen</id>
+ <goals>
+ <goal>translate</goal>
+ </goals>
+ </execution>
+ </executions>
</plugin>
+
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
@@ -195,51 +140,6 @@
</executions>
</plugin>
</plugins>
- <pluginManagement>
- <plugins>
- <!--This plugin's configuration is used to store Eclipse
- m2e settings only. It has no influence on the Maven build itself. -->
- <plugin>
- <groupId>org.eclipse.m2e</groupId>
- <artifactId>lifecycle-mapping</artifactId>
- <version>1.0.0</version>
- <configuration>
- <lifecycleMappingMetadata>
- <pluginExecutions>
- <pluginExecution>
- <pluginExecutionFilter>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-antrun-plugin</artifactId>
- <versionRange>[1.6,)</versionRange>
- <goals>
- <goal>run</goal>
- </goals>
- </pluginExecutionFilter>
- <action>
- <execute>
- <runOnIncremental>false</runOnIncremental>
- </execute>
- </action>
- </pluginExecution>
- <pluginExecution>
- <pluginExecutionFilter>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>build-helper-maven-plugin</artifactId>
- <versionRange>[1.5,)</versionRange>
- <goals>
- <goal>add-source</goal>
- </goals>
- </pluginExecutionFilter>
- <action>
- <execute />
- </action>
- </pluginExecution>
- </pluginExecutions>
- </lifecycleMappingMetadata>
- </configuration>
- </plugin>
- </plugins>
- </pluginManagement>
</build>
<dependencies>
@@ -278,51 +178,12 @@
<artifactId>commons-beanutils</artifactId>
<version>1.7.0</version>
</dependency>
-
- <dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-api</artifactId>
- <version>${elmo.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-sesame</artifactId>
- <version>${elmo.version}</version>
- <exclusions>
- <exclusion>
- <groupId>org.slf4j</groupId>
- <artifactId>jcl104-over-slf4j</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
-
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.4.3</version>
</dependency>
<dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-dynabean</artifactId>
- <version>${elmo.version}</version>
- </dependency>
- <dependency>
- <groupId>org.openrdf.sesame</groupId>
- <artifactId>sesame-repository-sail</artifactId>
- <version>${sesame.version}</version>
- </dependency>
- <dependency>
- <groupId>org.openrdf.sesame</groupId>
- <artifactId>sesame-sail-memory</artifactId>
- <version>${sesame.version}</version>
- </dependency>
- <dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-codegen</artifactId>
- <version>${elmo.version}</version>
- </dependency>
- <dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.1</version>
@@ -342,30 +203,4 @@
<scope>compile</scope>
</dependency>
</dependencies>
- <repositories>
- <repository>
- <releases>
- <enabled>true</enabled>
- </releases>
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>aduna-opensource.releases</id>
- <name>Apache Taverna Half-a-mirror of http://repo.aduna-software.org/maven2/releases/</name>
- <url>http://repository.mygrid.org.uk/artifactory/aduna/</url>
- </repository>
- </repositories>
- <pluginRepositories>
- <pluginRepository>
- <releases>
- <enabled>true</enabled>
- </releases>
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>aduna-opensource.releases</id>
- <name>Apache Taverna Half-a-mirror of http://repo.aduna-software.org/maven2/releases/</name>
- <url>http://repository.mygrid.org.uk/artifactory/aduna/</url>
- </pluginRepository>
- </pluginRepositories>
</project>
[09/11] incubator-taverna-language git commit: avoid outdated
slf4j-log4j
Posted by st...@apache.org.
avoid outdated slf4j-log4j
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/f2891796
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/f2891796
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/f2891796
Branch: refs/heads/wfdesc-jena
Commit: f289179659ce6e443f5d56a7ace5e9c67e422e1c
Parents: 518d7ce
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Feb 26 22:00:05 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 5 22:52:22 2015 +0100
----------------------------------------------------------------------
taverna-scufl2-wfdesc/pom.xml | 5 -----
1 file changed, 5 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/f2891796/taverna-scufl2-wfdesc/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/pom.xml b/taverna-scufl2-wfdesc/pom.xml
index 6eb231a..662b1c1 100755
--- a/taverna-scufl2-wfdesc/pom.xml
+++ b/taverna-scufl2-wfdesc/pom.xml
@@ -183,11 +183,6 @@
<version>1.7.0</version>
</dependency>
<dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-log4j12</artifactId>
- <version>1.4.3</version>
- </dependency>
- <dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.1</version>