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Posted to commits@taverna.apache.org by st...@apache.org on 2016/02/13 21:01:45 UTC
[21/26] incubator-taverna-language git commit: TAVERNA-892 Use Jena
3.0.1
TAVERNA-892 Use Jena 3.0.1
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/e22f7b5f
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/e22f7b5f
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/e22f7b5f
Branch: refs/heads/master
Commit: e22f7b5f473f6e72c4eb4dab3e0a82efa42daf24
Parents: f24046d
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed Feb 10 16:30:21 2016 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed Feb 10 16:30:25 2016 +0000
----------------------------------------------------------------------
pom.xml | 5 +-
.../robundle/manifest/RDFToManifest.java | 24 +++----
.../manifest/combine/CombineManifest.java | 22 +++---
.../apache/taverna/robundle/utils/RDFUtils.java | 10 +--
.../taverna/robundle/manifest/TestManifest.java | 16 ++---
.../scufl2/annotation/AnnotationTools.java | 14 ++--
.../scufl2/annotation/TestAnnotationTools.java | 8 +--
.../examples/converted/helloanyone.wfdesc.ttl | 70 ++++++++++++++++++++
8 files changed, 121 insertions(+), 48 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e22f7b5f/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 30baeb1..5aaa50e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -20,7 +20,7 @@
<parent>
<groupId>org.apache.taverna</groupId>
<artifactId>taverna-parent</artifactId>
- <version>1-incubating</version>
+ <version>2-incubating-SNAPSHOT</version>
</parent>
<groupId>org.apache.taverna.language</groupId>
<artifactId>taverna-language</artifactId>
@@ -31,6 +31,9 @@
<description>Taverna Language API for workflow definitions (SCUFL2)
and workflow inputs/outputs/run (DataBundle).
</description>
+ <properties>
+ <jena.version>3.0.1</jena.version> <!-- TAVERNA-892 -->
+ </properties>
<build>
<plugins>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e22f7b5f/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java
index 4413de9..663fd46 100644
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java
+++ b/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java
@@ -20,8 +20,8 @@ package org.apache.taverna.robundle.manifest;
*/
-import static com.hp.hpl.jena.ontology.OntModelSpec.OWL_DL_MEM_RULE_INF;
-import static com.hp.hpl.jena.rdf.model.ModelFactory.createOntologyModel;
+import static org.apache.jena.ontology.OntModelSpec.OWL_DL_MEM_RULE_INF;
+import static org.apache.jena.rdf.model.ModelFactory.createOntologyModel;
import static org.apache.taverna.robundle.utils.PathHelper.relativizeFromBase;
import static org.apache.taverna.robundle.utils.RDFUtils.literalAsFileTime;
@@ -42,16 +42,16 @@ import org.apache.jena.riot.RDFDataMgr;
import org.apache.jena.riot.RiotException;
import org.apache.taverna.robundle.Bundles;
-import com.hp.hpl.jena.ontology.DatatypeProperty;
-import com.hp.hpl.jena.ontology.Individual;
-import com.hp.hpl.jena.ontology.ObjectProperty;
-import com.hp.hpl.jena.ontology.OntClass;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntResource;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.util.iterator.ExtendedIterator;
+import org.apache.jena.ontology.DatatypeProperty;
+import org.apache.jena.ontology.Individual;
+import org.apache.jena.ontology.ObjectProperty;
+import org.apache.jena.ontology.OntClass;
+import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntResource;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.util.iterator.ExtendedIterator;
public class RDFToManifest {
public static class ClosableIterable<T> implements AutoCloseable,
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e22f7b5f/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/combine/CombineManifest.java
----------------------------------------------------------------------
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 16188b4..27012d2 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
@@ -20,7 +20,7 @@ package org.apache.taverna.robundle.manifest.combine;
*/
-import static com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel;
+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;
@@ -64,16 +64,16 @@ import org.identifiers.combine_specifications.omex_manifest.ObjectFactory;
import org.identifiers.combine_specifications.omex_manifest.OmexManifest;
import org.xml.sax.InputSource;
-import com.hp.hpl.jena.query.QueryExecution;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.QuerySolutionMap;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.query.QueryFactory;
+import org.apache.jena.query.QuerySolutionMap;
+import org.apache.jena.query.ResultSet;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.Statement;
import com.sun.xml.bind.marshaller.NamespacePrefixMapper;
/**
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e22f7b5f/taverna-robundle/src/main/java/org/apache/taverna/robundle/utils/RDFUtils.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/utils/RDFUtils.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/utils/RDFUtils.java
index ee3575e..5230827 100644
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/utils/RDFUtils.java
+++ b/taverna-robundle/src/main/java/org/apache/taverna/robundle/utils/RDFUtils.java
@@ -20,16 +20,16 @@ package org.apache.taverna.robundle.utils;
*/
-import static com.hp.hpl.jena.datatypes.xsd.XSDDatatype.XSDdateTime;
+import static org.apache.jena.datatypes.xsd.XSDDatatype.XSDdateTime;
import static java.nio.file.attribute.FileTime.fromMillis;
import java.nio.file.attribute.FileTime;
import java.util.logging.Logger;
-import com.hp.hpl.jena.datatypes.DatatypeFormatException;
-import com.hp.hpl.jena.datatypes.xsd.XSDDateTime;
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.RDFNode;
+import org.apache.jena.datatypes.DatatypeFormatException;
+import org.apache.jena.datatypes.xsd.XSDDateTime;
+import org.apache.jena.rdf.model.Literal;
+import org.apache.jena.rdf.model.RDFNode;
public class RDFUtils {
private static final Logger logger = Logger.getLogger(RDFUtils.class
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e22f7b5f/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
index 3ca4030..32d2048 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
@@ -46,14 +46,14 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import com.hp.hpl.jena.query.Query;
-import com.hp.hpl.jena.query.QueryExecution;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.QuerySolution;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Resource;
+import org.apache.jena.query.Query;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.query.QueryFactory;
+import org.apache.jena.query.QuerySolution;
+import org.apache.jena.query.ResultSet;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Resource;
@SuppressWarnings({ "deprecation", "unused" })
public class TestManifest {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e22f7b5f/taverna-scufl2-annotation/src/main/java/org/apache/taverna/scufl2/annotation/AnnotationTools.java
----------------------------------------------------------------------
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 ef169c3..9e8a157 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
@@ -40,13 +40,13 @@ import org.apache.taverna.scufl2.api.container.WorkflowBundle;
import org.apache.taverna.scufl2.ucfpackage.UCFPackage.ResourceEntry;
-import com.hp.hpl.jena.graph.Node;
-import com.hp.hpl.jena.graph.NodeFactory;
-import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.query.DatasetFactory;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.sparql.core.Quad;
+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";
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e22f7b5f/taverna-scufl2-annotation/src/test/java/org/apache/taverna/scufl2/annotation/TestAnnotationTools.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-annotation/src/test/java/org/apache/taverna/scufl2/annotation/TestAnnotationTools.java b/taverna-scufl2-annotation/src/test/java/org/apache/taverna/scufl2/annotation/TestAnnotationTools.java
index ef5dd94..9cced6d 100644
--- a/taverna-scufl2-annotation/src/test/java/org/apache/taverna/scufl2/annotation/TestAnnotationTools.java
+++ b/taverna-scufl2-annotation/src/test/java/org/apache/taverna/scufl2/annotation/TestAnnotationTools.java
@@ -34,10 +34,10 @@ import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
import org.junit.Before;
import org.junit.Test;
-import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QuerySolution;
-import com.hp.hpl.jena.query.ResultSet;
+import org.apache.jena.query.Dataset;
+import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.query.QuerySolution;
+import org.apache.jena.query.ResultSet;
public class TestAnnotationTools {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e22f7b5f/taverna-scufl2-examples/examples/converted/helloanyone.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/examples/converted/helloanyone.wfdesc.ttl b/taverna-scufl2-examples/examples/converted/helloanyone.wfdesc.ttl
new file mode 100644
index 0000000..bdf5cc7
--- /dev/null
+++ b/taverna-scufl2-examples/examples/converted/helloanyone.wfdesc.ttl
@@ -0,0 +1,70 @@
+@base <http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/> .
+@prefix : <#> .
+@prefix comp: <http://purl.org/DP/components#> .
+@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix roterms: <http://purl.org/wf4ever/roterms#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix biocat: <http://biocatalogue.org/attribute/> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+
+<datalink?from=processor/Concatenate_two_strings/out/output&to=out/greeting>
+ a wfdesc:DataLink ;
+ wfdesc:hasSink <out/greeting> ;
+ wfdesc:hasSource <processor/Concatenate_two_strings/out/output> .
+
+<processor/Concatenate_two_strings/in/string2>
+ a owl:Thing , wfdesc:Input ;
+ rdfs:label "string2" .
+
+<datalink?from=processor/hello/out/value&to=processor/Concatenate_two_strings/in/string1>
+ a wfdesc:DataLink ;
+ wfdesc:hasSink <processor/Concatenate_two_strings/in/string1> ;
+ wfdesc:hasSource <processor/hello/out/value> .
+
+<processor/Concatenate_two_strings/out/output>
+ a owl:Thing , wfdesc:Output ;
+ rdfs:label "output" .
+
+<processor/hello/out/value>
+ a owl:Thing , wfdesc:Output ;
+ rdfs:label "value" .
+
+<processor/hello/> a owl:Thing , wfdesc:Process ;
+ rdfs:label "hello" ;
+ wfdesc:hasOutput <processor/hello/out/value> .
+
+<> a wfdesc:Process , owl:Thing , wfdesc:Workflow ;
+ rdfs:label "Hello_Anyone" ;
+ wfdesc:hasDataLink <datalink?from=processor/hello/out/value&to=processor/Concatenate_two_strings/in/string1> , <datalink?from=processor/Concatenate_two_strings/out/output&to=out/greeting> , <datalink?from=in/name&to=processor/Concatenate_two_strings/in/string2> ;
+ wfdesc:hasInput <in/name> ;
+ wfdesc:hasOutput <out/greeting> ;
+ wfdesc:hasSubProcess <processor/Concatenate_two_strings/> , <processor/hello/> .
+
+<processor/Concatenate_two_strings/>
+ a wf4ever:BeanshellScript , owl:Thing , wfdesc:Process ;
+ rdfs:label "Concatenate_two_strings" ;
+ wf4ever:script "output = string1 + string2;" ;
+ wfdesc:hasInput <processor/Concatenate_two_strings/in/string2> , <processor/Concatenate_two_strings/in/string1> ;
+ wfdesc:hasOutput <processor/Concatenate_two_strings/out/output> .
+
+<datalink?from=in/name&to=processor/Concatenate_two_strings/in/string2>
+ a wfdesc:DataLink ;
+ wfdesc:hasSink <processor/Concatenate_two_strings/in/string2> ;
+ wfdesc:hasSource <in/name> .
+
+<processor/Concatenate_two_strings/in/string1>
+ a owl:Thing , wfdesc:Input ;
+ rdfs:label "string1" .
+
+<out/greeting> a wfdesc:Input , owl:Thing , wfdesc:Output ;
+ rdfs:label "greeting" .
+
+<in/name> a wfdesc:Output , owl:Thing , wfdesc:Input ;
+ rdfs:label "name" .