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 <[email protected]> Authored: Wed Feb 10 16:30:21 2016 +0000 Committer: Stian Soiland-Reyes <[email protected]> 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" .
