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Posted to commits@taverna.apache.org by st...@apache.org on 2016/10/31 17:37:51 UTC
[1/3] incubator-taverna-language git commit: indentation fix of
pom.xml
Repository: incubator-taverna-language
Updated Branches:
refs/heads/TAVERNA-1017 [created] a748e824f
indentation fix of pom.xml
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/66d74f7c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/66d74f7c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/66d74f7c
Branch: refs/heads/TAVERNA-1017
Commit: 66d74f7c10c50e730ee1eb68ffcfc23ed85f93e6
Parents: 7b70e67
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon Oct 31 17:03:03 2016 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon Oct 31 17:03:03 2016 +0000
----------------------------------------------------------------------
pom.xml | 338 ++++++++++++++++++++++++++++++-----------------------------
1 file changed, 171 insertions(+), 167 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/66d74f7c/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index af5f393..d6908df 100644
--- a/pom.xml
+++ b/pom.xml
@@ -15,7 +15,8 @@
See the License for the specific language governing permissions and
limitations under the License.
-->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.apache.taverna</groupId>
@@ -34,31 +35,31 @@
<build>
<plugins>
<plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <executions>
- <execution>
- <id>attach-javadocs</id>
- <goals>
- <goal>jar</goal>
- </goals>
- <configuration>
- <additionalparam>-Xdoclint:none</additionalparam>
- </configuration>
- </execution>
- </executions>
-</plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <executions>
+ <execution>
+ <id>attach-javadocs</id>
+ <goals>
+ <goal>jar</goal>
+ </goals>
+ <configuration>
+ <additionalparam>-Xdoclint:none</additionalparam>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
<plugin>
<groupId>org.apache.rat</groupId>
<artifactId>apache-rat-plugin</artifactId>
<configuration>
<useDefaultExcludes>true</useDefaultExcludes>
<excludes>
- <!--Just a META-INF file -->
- <exclude>DEPENDENCIES</exclude>
- <!-- Following excludes needed for taverna-scufl2-rdf,
- taverna-scufl2-integration-tests and taverna-scufl2-validation-integration
- subfolders that should be modules but are not. -->
+ <!--Just a META-INF file -->
+ <exclude>DEPENDENCIES</exclude>
+ <!-- Following excludes needed for taverna-scufl2-rdf, taverna-scufl2-integration-tests
+ and taverna-scufl2-validation-integration subfolders that should be modules
+ but are not. -->
<exclude>**/.classpath</exclude>
<exclude>**/.project</exclude>
<exclude>**/.settings/</exclude>
@@ -83,80 +84,87 @@
<!-- Expanded data bundle. Generated. -->
<exclude>/src/test/resources/full-example/ebi-wfrun-2013-05-31/</exclude>
- <!-- Test COMBINE archives. Skeleton only (files empty) -->
- <exclude>/src/test/resources/combine/aslanidi_purkinje_model_skeleton.zip</exclude>
- <exclude>/src/test/resources/combine/Boris-skeleton.omex</exclude>
- <exclude>/src/test/resources/combine/DirectoryMadnessZipped-skeleton.omex</exclude>
- <exclude>/src/test/resources/combine/DirectoryMadness-skeleton.omex</exclude>
+ <!-- Test COMBINE archives. Skeleton only (files empty) -->
+ <exclude>/src/test/resources/combine/aslanidi_purkinje_model_skeleton.zip</exclude>
+ <exclude>/src/test/resources/combine/Boris-skeleton.omex</exclude>
+ <exclude>/src/test/resources/combine/DirectoryMadnessZipped-skeleton.omex</exclude>
+ <exclude>/src/test/resources/combine/DirectoryMadness-skeleton.omex</exclude>
- <!-- Our own test documents - contains LICENSE -->
- <exclude>src/test/resources/document.odt</exclude>
- <exclude>src/test/resources/workflowrun.bundle.zip</exclude>
+ <!-- Our own test documents - contains LICENSE -->
+ <exclude>src/test/resources/document.odt</exclude>
+ <exclude>src/test/resources/workflowrun.bundle.zip</exclude>
- <!-- Created by Maven Shade plugin -->
- <exclude>dependency-reduced-pom.xml</exclude>
+ <!-- Created by Maven Shade plugin -->
+ <exclude>dependency-reduced-pom.xml</exclude>
- <!--
- Below exclusions are for
- externally sourced/derived files
- that must be acknowledged in
- NOTICE (and/or */src/*/resources/META-INF/NOTICE)
- -->
+ <!-- Below exclusions are for externally sourced/derived files that
+ must be acknowledged in NOTICE (and/or */src/*/resources/META-INF/NOTICE) -->
- <!-- W3C license -->
+ <!-- W3C license -->
<exclude>**/xml.xsd</exclude>
<exclude>**/xenc-schema.xsd</exclude>
<exclude>**/xmldsig-core-schema.xsd</exclude>
- <exclude>**/prov-o.rdf</exclude>
- <exclude>**/prov-o.ttl</exclude>
- <exclude>**/prov-aq.rdf</exclude>
- <!-- W3C Community license -->
- <!-- FOAF, Creative Commons Attribution 1.0 -->
- <exclude>**/oa.rdf</exclude>
+ <exclude>**/prov-o.rdf</exclude>
+ <exclude>**/prov-o.ttl</exclude>
+ <exclude>**/prov-aq.rdf</exclude>
+ <!-- W3C Community license -->
+ <!-- FOAF, Creative Commons Attribution 1.0 -->
+ <exclude>**/oa.rdf</exclude>
<exclude>**/foaf.rdf</exclude>
- <!-- Research Object Model, Creative Commons Attribution 3.0 -->
+ <!-- Research Object Model, Creative Commons Attribution 3.0 -->
<exclude>**/roterms.ttl</exclude>
- <exclude>**/wf4ever.ttl</exclude>
- <exclude>**/wfdesc.ttl</exclude>
- <exclude>**/wfprov.ttl</exclude>
+ <exclude>**/wf4ever.ttl</exclude>
+ <exclude>**/wfdesc.ttl</exclude>
+ <exclude>**/wfprov.ttl</exclude>
- <!-- Dublin Core, Creative Commons Attribution 3.0 -->
- <exclude>**/dcam.owl</exclude>
- <exclude>**/dcterms_od.owl</exclude>
+ <!-- Dublin Core, Creative Commons Attribution 3.0 -->
+ <exclude>**/dcam.owl</exclude>
+ <exclude>**/dcterms_od.owl</exclude>
</excludes>
</configuration>
</plugin>
-
- <!--
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>license-maven-plugin</artifactId>
- <version>1.7</version>
- <executions>
- <execution>
- <id>add-licenses</id>
- <phase>generate-sources</phase>
- <goals>
- <goal>aggregate-add-third-party</goal>
- </goals>
- <configuration>
- <excludedGroups>.*(mygrid|taverna).*</excludedGroups>
- <useMissingFile>true</useMissingFile>
- <missingFile>src/license/THIRD-PARTY.properties</missingFile>
- <licenseMerges>
- <licenseMerge>The Apache Software License, Version 2.0|Apache 2|Apache License|Apache License, Version 2.0|Apache Public License 2.0|Apache License Version 2.0|Apache Software License 2.0|Apache Software License - Version 2.0</licenseMerge>
- <licenseMerge>The BSD License|BSD|BSD License|BSD-style license|BSD style|Aduna BSD license|Aduna BSD-style license</licenseMerge>
- <licenseMerge>MIT License|The MIT License|MIT license</licenseMerge>
- <licenseMerge>GNU Lesser General Public License|GNU LESSER GENERAL PUBLIC LICENSE|GNU Library or Lesser General Public License|LGPL</licenseMerge>
- <licenseMerge>Common Development and Distribution License (CDDL) v1.0|CDDL 1.1|COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0</licenseMerge>
- <licenseMerge>Eclipse Public License, Version 1.0|Eclipse Public License</licenseMerge>
- </licenseMerges>
- </configuration>
- </execution>
- </executions>
- </plugin>
- -->
+<!--
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>license-maven-plugin</artifactId>
+ <version>1.7</version>
+ <executions>
+ <execution>
+ <id>add-licenses</id>
+ <phase>generate-sources</phase>
+ <goals>
+ <goal>aggregate-add-third-party</goal>
+ </goals>
+ <configuration>
+ <excludedGroups>.*(mygrid|taverna).*</excludedGroups>
+ <useMissingFile>true</useMissingFile>
+ <missingFile>src/license/THIRD-PARTY.properties</missingFile>
+ <licenseMerges>
+ <licenseMerge>The Apache Software License, Version 2.0|Apache
+ 2|Apache License|Apache License, Version 2.0|Apache Public
+ License 2.0|Apache
+ License Version 2.0|Apache Software License 2.0|Apache Software License
+ -
+ Version 2.0</licenseMerge>
+ <licenseMerge>The BSD License|BSD|BSD License|BSD-style
+ license|BSD style|Aduna BSD license|Aduna BSD-style license</licenseMerge>
+ <licenseMerge>MIT License|The MIT License|MIT license</licenseMerge>
+ <licenseMerge>GNU
+ Lesser General Public License|GNU LESSER GENERAL PUBLIC LICENSE|GNU
+ Library
+ or Lesser General Public License|LGPL</licenseMerge>
+ <licenseMerge>Common
+ Development and Distribution License (CDDL) v1.0|CDDL 1.1|COMMON DEVELOPMENT
+ AND DISTRIBUTION LICENSE (CDDL) Version 1.0</licenseMerge>
+ <licenseMerge>Eclipse
+ Public License, Version 1.0|Eclipse Public License</licenseMerge>
+ </licenseMerges>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ -->
</plugins>
<pluginManagement>
<plugins>
@@ -179,15 +187,15 @@
<tag>HEAD</tag>
</scm>
- <repositories>
- <repository>
- <id>apache.snapshots</id>
- <name>Apache Snapshot Repository</name>
- <url>https://repository.apache.org/snapshots</url>
- <releases>
- <enabled>false</enabled>
- </releases>
- </repository>
+ <repositories>
+ <repository>
+ <id>apache.snapshots</id>
+ <name>Apache Snapshot Repository</name>
+ <url>https://repository.apache.org/snapshots</url>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ </repository>
</repositories>
<dependencyManagement>
@@ -234,7 +242,8 @@
<dependency>
<groupId>org.jaxen</groupId>
<artifactId>com.springsource.org.jaxen</artifactId>
- <!-- Was 1.1.4. as "1.1.3 has missing dependencies" but 1.1.1 appears to work fine -->
+ <!-- Was 1.1.4. as "1.1.3 has missing dependencies" but 1.1.1 appears
+ to work fine -->
<version>${jaxen.version}</version>
<type>jar</type>
</dependency>
@@ -245,83 +254,78 @@
</dependency>
</dependencies>
</dependencyManagement>
-<dependencies>
- <!-- Common dependencies on jena-osgi, which requires some
-additional dependencies to be a happy OSGi bundle -->
-
- <dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>jena-osgi</artifactId>
- <version>${jena.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.servicemix.bundles</groupId>
- <artifactId>org.apache.servicemix.bundles.xerces</artifactId>
- <version>${servicemix.xerces.version}</version>
- </dependency>
- <!-- JENA-1178 workaround: Upgrade jsonlld-java -->
- <dependency>
- <groupId>com.github.jsonld-java</groupId>
- <artifactId>jsonld-java</artifactId>
- <version>${jsonldjava.version}</version>
- </dependency>
- <!-- Needed by Jena -->
- <dependency>
- <groupId>com.github.andrewoma.dexx</groupId>
- <artifactId>collection</artifactId>
- <version>${dexx.collection.version}</version>
- </dependency>
+ <dependencies>
+ <!-- Common dependencies on jena-osgi, which requires some additional dependencies
+ to be a happy OSGi bundle -->
-</dependencies>
-<profiles>
-<profile>
-<id>all</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- <modules>
- <module>taverna-baclava-language</module>
- <module>taverna-databundle</module>
- <module>taverna-robundle</module>
- <module>taverna-scufl2-annotation</module>
- <module>taverna-scufl2-api</module>
- <module>taverna-scufl2-examples</module>
- <module>taverna-scufl2-integration-tests</module>
- <module>taverna-scufl2-schemas</module>
- <module>taverna-scufl2-scufl</module>
- <module>taverna-scufl2-t2flow</module>
- <module>taverna-scufl2-ucfpackage</module>
- <module>taverna-scufl2-wfbundle</module>
- <module>taverna-tavlang-tool</module>
- <module>taverna-scufl2-wfdesc</module>
- </modules>
-</profile>
- <profile>
- <id>android</id>
- <!-- <activation>
- <property>
- <name>environment</name>
- <value>android</value>
- </property>
- </activation>-->
- <properties>
-<maven.compiler.source>1.7</maven.compiler.source>
-<maven.compiler.target>1.7</maven.compiler.target>
-</properties>
- <modules>
- <module>taverna-baclava-language</module>
- <module>taverna-scufl2-annotation</module>
- <module>taverna-scufl2-api</module>
- <module>taverna-scufl2-examples</module>
- <module>taverna-scufl2-integration-tests</module>
- <module>taverna-scufl2-schemas</module>
- <module>taverna-scufl2-scufl</module>
- <module>taverna-scufl2-t2flow</module>
- <module>taverna-scufl2-ucfpackage</module>
- <module>taverna-scufl2-wfbundle</module>
- <module>taverna-tavlang-tool</module>
- </modules>
- </profile>
-</profiles>
+ <dependency>
+ <groupId>org.apache.jena</groupId>
+ <artifactId>jena-osgi</artifactId>
+ <version>${jena.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.servicemix.bundles</groupId>
+ <artifactId>org.apache.servicemix.bundles.xerces</artifactId>
+ <version>${servicemix.xerces.version}</version>
+ </dependency>
+ <!-- JENA-1178 workaround: Upgrade jsonlld-java -->
+ <dependency>
+ <groupId>com.github.jsonld-java</groupId>
+ <artifactId>jsonld-java</artifactId>
+ <version>${jsonldjava.version}</version>
+ </dependency>
+ <!-- Needed by Jena -->
+ <dependency>
+ <groupId>com.github.andrewoma.dexx</groupId>
+ <artifactId>collection</artifactId>
+ <version>${dexx.collection.version}</version>
+ </dependency>
+ </dependencies>
+ <profiles>
+ <profile>
+ <id>all</id>
+ <activation>
+ <activeByDefault>true</activeByDefault>
+ </activation>
+ <modules>
+ <module>taverna-baclava-language</module>
+ <module>taverna-databundle</module>
+ <module>taverna-robundle</module>
+ <module>taverna-scufl2-annotation</module>
+ <module>taverna-scufl2-api</module>
+ <module>taverna-scufl2-examples</module>
+ <module>taverna-scufl2-integration-tests</module>
+ <module>taverna-scufl2-schemas</module>
+ <module>taverna-scufl2-scufl</module>
+ <module>taverna-scufl2-t2flow</module>
+ <module>taverna-scufl2-ucfpackage</module>
+ <module>taverna-scufl2-wfbundle</module>
+ <module>taverna-tavlang-tool</module>
+ <module>taverna-scufl2-wfdesc</module>
+ </modules>
+ </profile>
+ <profile>
+ <id>android</id>
+ <!-- <activation> <property> <name>environment</name> <value>android</value>
+ </property> </activation> -->
+ <properties>
+ <maven.compiler.source>1.7</maven.compiler.source>
+ <maven.compiler.target>1.7</maven.compiler.target>
+ </properties>
+ <modules>
+ <module>taverna-baclava-language</module>
+ <module>taverna-scufl2-annotation</module>
+ <module>taverna-scufl2-api</module>
+ <module>taverna-scufl2-examples</module>
+ <module>taverna-scufl2-integration-tests</module>
+ <module>taverna-scufl2-schemas</module>
+ <module>taverna-scufl2-scufl</module>
+ <module>taverna-scufl2-t2flow</module>
+ <module>taverna-scufl2-ucfpackage</module>
+ <module>taverna-scufl2-wfbundle</module>
+ <module>taverna-tavlang-tool</module>
+ </modules>
+ </profile>
+ </profiles>
</project>
[3/3] incubator-taverna-language git commit: TAVERNA-1017 Use Commons
RDF API instead of Jena
Posted by st...@apache.org.
TAVERNA-1017 Use Commons RDF API instead of 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/a748e824
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/a748e824
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/a748e824
Branch: refs/heads/TAVERNA-1017
Commit: a748e824fb43616bedf60c299934744c8eec98e1
Parents: 3002424
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon Oct 31 17:37:11 2016 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon Oct 31 17:37:37 2016 +0000
----------------------------------------------------------------------
pom.xml | 21 ++-
taverna-scufl2-annotation/pom.xml | 11 +-
.../scufl2/annotation/AnnotationTools.java | 154 ++++++++++---------
taverna-scufl2-api/pom.xml | 5 +
.../taverna/scufl2/api/common/URITools.java | 15 ++
5 files changed, 126 insertions(+), 80 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a748e824/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index d5acb9b..43132cb 100644
--- a/pom.xml
+++ b/pom.xml
@@ -28,10 +28,14 @@
<version>0.16.0-incubating-SNAPSHOT</version>
<packaging>pom</packaging>
- <name>Apache Taverna Language APIs (Scufl2, Databundle)</name>
+ <name>Apache Taverna Language APIs (Scufl2, Databundle)</name>
<description>Taverna Language API for workflow definitions (SCUFL2)
and workflow inputs/outputs/run (DataBundle).
</description>
+ <properties>
+ <!-- TODO: Use 0.3.0-incubating once it is released -->
+ <commons.rdf.version>0.4.0-incubating-SNAPSHOT</commons.rdf.version>
+ </properties>
<build>
<plugins>
<plugin>
@@ -252,11 +256,12 @@
<artifactId>commons-beanutils</artifactId>
<version>${commons.beanutils.version}</version>
</dependency>
+
</dependencies>
</dependencyManagement>
<dependencies>
<!-- Common dependencies on jena-osgi, which requires some additional dependencies
- to be a happy OSGi bundle -->
+ to be a happy OSGi bundle
<dependency>
<groupId>org.apache.jena</groupId>
@@ -268,17 +273,23 @@
<artifactId>org.apache.servicemix.bundles.xerces</artifactId>
<version>${servicemix.xerces.version}</version>
</dependency>
- <!-- JENA-1178 workaround: Upgrade jsonlld-java -->
+ -->
+ <!-- JENA-1178 workaround: Upgrade jsonlld-java
<dependency>
<groupId>com.github.jsonld-java</groupId>
<artifactId>jsonld-java</artifactId>
<version>${jsonldjava.version}</version>
- </dependency>
- <!-- Needed by Jena -->
+ </dependency>-->
+ <!-- Needed by Jena
<dependency>
<groupId>com.github.andrewoma.dexx</groupId>
<artifactId>collection</artifactId>
<version>${dexx.collection.version}</version>
+ </dependency>-->
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-rdf-api</artifactId>
+ <version>${commons.rdf.version}</version>
</dependency>
</dependencies>
<profiles>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a748e824/taverna-scufl2-annotation/pom.xml
----------------------------------------------------------------------
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>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a748e824/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 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.io.InputStream;
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.common.URITools;
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 @@ public class AnnotationTools {
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 @@ public class AnnotationTools {
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 @@ public class AnnotationTools {
* @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 @@ public class AnnotationTools {
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("<");
- turtle.append(predicate.toASCIIString());
- turtle.append("> ");
-
- // 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(annotatedSubject.ntriplesString());
+
+ turtle.append(" ");
+ turtle.append(predicate.ntriplesString());
+
+ 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");
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a748e824/taverna-scufl2-api/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-api/pom.xml b/taverna-scufl2-api/pom.xml
index 4c0052a..a7ea442 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>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a748e824/taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/URITools.java
----------------------------------------------------------------------
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.HashMap;
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 @@ public class URITools {
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("/")))
[2/3] incubator-taverna-language git commit: tab -> 4 spaces
Posted by st...@apache.org.
tab -> 4 spaces
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/30024242
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/30024242
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/30024242
Branch: refs/heads/TAVERNA-1017
Commit: 300242422cfe22fc80350034fc256f351401c8f5
Parents: 66d74f7
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon Oct 31 17:03:34 2016 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon Oct 31 17:03:34 2016 +0000
----------------------------------------------------------------------
pom.xml | 598 +++++++++++++++++++++++++++++------------------------------
1 file changed, 299 insertions(+), 299 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/30024242/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index d6908df..d5acb9b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -16,316 +16,316 @@
limitations under the License.
-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>org.apache.taverna</groupId>
- <artifactId>apache-taverna-parent</artifactId>
- <version>3-incubating-SNAPSHOT</version>
- </parent>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>apache-taverna-language</artifactId>
- <version>0.16.0-incubating-SNAPSHOT</version>
- <packaging>pom</packaging>
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna</groupId>
+ <artifactId>apache-taverna-parent</artifactId>
+ <version>3-incubating-SNAPSHOT</version>
+ </parent>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>apache-taverna-language</artifactId>
+ <version>0.16.0-incubating-SNAPSHOT</version>
+ <packaging>pom</packaging>
- <name>Apache Taverna Language APIs (Scufl2, Databundle)</name>
- <description>Taverna Language API for workflow definitions (SCUFL2)
- and workflow inputs/outputs/run (DataBundle).
- </description>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <executions>
- <execution>
- <id>attach-javadocs</id>
- <goals>
- <goal>jar</goal>
- </goals>
- <configuration>
- <additionalparam>-Xdoclint:none</additionalparam>
- </configuration>
- </execution>
- </executions>
- </plugin>
- <plugin>
- <groupId>org.apache.rat</groupId>
- <artifactId>apache-rat-plugin</artifactId>
- <configuration>
- <useDefaultExcludes>true</useDefaultExcludes>
- <excludes>
- <!--Just a META-INF file -->
- <exclude>DEPENDENCIES</exclude>
- <!-- Following excludes needed for taverna-scufl2-rdf, taverna-scufl2-integration-tests
- and taverna-scufl2-validation-integration subfolders that should be modules
- but are not. -->
- <exclude>**/.classpath</exclude>
- <exclude>**/.project</exclude>
- <exclude>**/.settings/</exclude>
- <exclude>**/target/</exclude>
- <!-- Text and Markdown files are typically used only for documentation
- purposes and license declarations are usually spurious in these files since
- often they will refer to the LICENSE/NOTICE for users to find the actual
- licenses -->
- <exclude>**/*.md</exclude>
- <!-- META-INF services files can include comments but a license header
- would be unecessarily clutter so we exclude these -->
- <exclude>**/META-INF/services/*</exclude>
- <!-- No headers in JSON which haven't got comments ... -->
- <exclude>**/*.json</exclude>
- <!-- Really a binary format, but must look like text -->
- <exclude>**/mimetype</exclude>
- <!-- Effectively a binary format -->
- <exclude>**/*.url</exclude>
- <!-- Cannot contain comments; content must match program output. -->
- <exclude>/src/test/resources/org/apache/taverna/scufl2/api/io/HelloWorld.txt</exclude>
- <exclude>/src/test/resources/as.txt</exclude>
- <!-- Expanded data bundle. Generated. -->
- <exclude>/src/test/resources/full-example/ebi-wfrun-2013-05-31/</exclude>
+ <name>Apache Taverna Language APIs (Scufl2, Databundle)</name>
+ <description>Taverna Language API for workflow definitions (SCUFL2)
+ and workflow inputs/outputs/run (DataBundle).
+ </description>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <executions>
+ <execution>
+ <id>attach-javadocs</id>
+ <goals>
+ <goal>jar</goal>
+ </goals>
+ <configuration>
+ <additionalparam>-Xdoclint:none</additionalparam>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.rat</groupId>
+ <artifactId>apache-rat-plugin</artifactId>
+ <configuration>
+ <useDefaultExcludes>true</useDefaultExcludes>
+ <excludes>
+ <!--Just a META-INF file -->
+ <exclude>DEPENDENCIES</exclude>
+ <!-- Following excludes needed for taverna-scufl2-rdf, taverna-scufl2-integration-tests
+ and taverna-scufl2-validation-integration subfolders that should be modules
+ but are not. -->
+ <exclude>**/.classpath</exclude>
+ <exclude>**/.project</exclude>
+ <exclude>**/.settings/</exclude>
+ <exclude>**/target/</exclude>
+ <!-- Text and Markdown files are typically used only for documentation
+ purposes and license declarations are usually spurious in these files since
+ often they will refer to the LICENSE/NOTICE for users to find the actual
+ licenses -->
+ <exclude>**/*.md</exclude>
+ <!-- META-INF services files can include comments but a license header
+ would be unecessarily clutter so we exclude these -->
+ <exclude>**/META-INF/services/*</exclude>
+ <!-- No headers in JSON which haven't got comments ... -->
+ <exclude>**/*.json</exclude>
+ <!-- Really a binary format, but must look like text -->
+ <exclude>**/mimetype</exclude>
+ <!-- Effectively a binary format -->
+ <exclude>**/*.url</exclude>
+ <!-- Cannot contain comments; content must match program output. -->
+ <exclude>/src/test/resources/org/apache/taverna/scufl2/api/io/HelloWorld.txt</exclude>
+ <exclude>/src/test/resources/as.txt</exclude>
+ <!-- Expanded data bundle. Generated. -->
+ <exclude>/src/test/resources/full-example/ebi-wfrun-2013-05-31/</exclude>
- <!-- Test COMBINE archives. Skeleton only (files empty) -->
- <exclude>/src/test/resources/combine/aslanidi_purkinje_model_skeleton.zip</exclude>
- <exclude>/src/test/resources/combine/Boris-skeleton.omex</exclude>
- <exclude>/src/test/resources/combine/DirectoryMadnessZipped-skeleton.omex</exclude>
- <exclude>/src/test/resources/combine/DirectoryMadness-skeleton.omex</exclude>
+ <!-- Test COMBINE archives. Skeleton only (files empty) -->
+ <exclude>/src/test/resources/combine/aslanidi_purkinje_model_skeleton.zip</exclude>
+ <exclude>/src/test/resources/combine/Boris-skeleton.omex</exclude>
+ <exclude>/src/test/resources/combine/DirectoryMadnessZipped-skeleton.omex</exclude>
+ <exclude>/src/test/resources/combine/DirectoryMadness-skeleton.omex</exclude>
- <!-- Our own test documents - contains LICENSE -->
- <exclude>src/test/resources/document.odt</exclude>
- <exclude>src/test/resources/workflowrun.bundle.zip</exclude>
+ <!-- Our own test documents - contains LICENSE -->
+ <exclude>src/test/resources/document.odt</exclude>
+ <exclude>src/test/resources/workflowrun.bundle.zip</exclude>
- <!-- Created by Maven Shade plugin -->
- <exclude>dependency-reduced-pom.xml</exclude>
+ <!-- Created by Maven Shade plugin -->
+ <exclude>dependency-reduced-pom.xml</exclude>
- <!-- Below exclusions are for externally sourced/derived files that
- must be acknowledged in NOTICE (and/or */src/*/resources/META-INF/NOTICE) -->
+ <!-- Below exclusions are for externally sourced/derived files that
+ must be acknowledged in NOTICE (and/or */src/*/resources/META-INF/NOTICE) -->
- <!-- W3C license -->
- <exclude>**/xml.xsd</exclude>
- <exclude>**/xenc-schema.xsd</exclude>
- <exclude>**/xmldsig-core-schema.xsd</exclude>
- <exclude>**/prov-o.rdf</exclude>
- <exclude>**/prov-o.ttl</exclude>
- <exclude>**/prov-aq.rdf</exclude>
- <!-- W3C Community license -->
- <!-- FOAF, Creative Commons Attribution 1.0 -->
- <exclude>**/oa.rdf</exclude>
- <exclude>**/foaf.rdf</exclude>
- <!-- Research Object Model, Creative Commons Attribution 3.0 -->
- <exclude>**/roterms.ttl</exclude>
- <exclude>**/wf4ever.ttl</exclude>
- <exclude>**/wfdesc.ttl</exclude>
- <exclude>**/wfprov.ttl</exclude>
+ <!-- W3C license -->
+ <exclude>**/xml.xsd</exclude>
+ <exclude>**/xenc-schema.xsd</exclude>
+ <exclude>**/xmldsig-core-schema.xsd</exclude>
+ <exclude>**/prov-o.rdf</exclude>
+ <exclude>**/prov-o.ttl</exclude>
+ <exclude>**/prov-aq.rdf</exclude>
+ <!-- W3C Community license -->
+ <!-- FOAF, Creative Commons Attribution 1.0 -->
+ <exclude>**/oa.rdf</exclude>
+ <exclude>**/foaf.rdf</exclude>
+ <!-- Research Object Model, Creative Commons Attribution 3.0 -->
+ <exclude>**/roterms.ttl</exclude>
+ <exclude>**/wf4ever.ttl</exclude>
+ <exclude>**/wfdesc.ttl</exclude>
+ <exclude>**/wfprov.ttl</exclude>
- <!-- Dublin Core, Creative Commons Attribution 3.0 -->
- <exclude>**/dcam.owl</exclude>
- <exclude>**/dcterms_od.owl</exclude>
+ <!-- Dublin Core, Creative Commons Attribution 3.0 -->
+ <exclude>**/dcam.owl</exclude>
+ <exclude>**/dcterms_od.owl</exclude>
- </excludes>
- </configuration>
- </plugin>
+ </excludes>
+ </configuration>
+ </plugin>
<!--
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>license-maven-plugin</artifactId>
- <version>1.7</version>
- <executions>
- <execution>
- <id>add-licenses</id>
- <phase>generate-sources</phase>
- <goals>
- <goal>aggregate-add-third-party</goal>
- </goals>
- <configuration>
- <excludedGroups>.*(mygrid|taverna).*</excludedGroups>
- <useMissingFile>true</useMissingFile>
- <missingFile>src/license/THIRD-PARTY.properties</missingFile>
- <licenseMerges>
- <licenseMerge>The Apache Software License, Version 2.0|Apache
- 2|Apache License|Apache License, Version 2.0|Apache Public
- License 2.0|Apache
- License Version 2.0|Apache Software License 2.0|Apache Software License
- -
- Version 2.0</licenseMerge>
- <licenseMerge>The BSD License|BSD|BSD License|BSD-style
- license|BSD style|Aduna BSD license|Aduna BSD-style license</licenseMerge>
- <licenseMerge>MIT License|The MIT License|MIT license</licenseMerge>
- <licenseMerge>GNU
- Lesser General Public License|GNU LESSER GENERAL PUBLIC LICENSE|GNU
- Library
- or Lesser General Public License|LGPL</licenseMerge>
- <licenseMerge>Common
- Development and Distribution License (CDDL) v1.0|CDDL 1.1|COMMON DEVELOPMENT
- AND DISTRIBUTION LICENSE (CDDL) Version 1.0</licenseMerge>
- <licenseMerge>Eclipse
- Public License, Version 1.0|Eclipse Public License</licenseMerge>
- </licenseMerges>
- </configuration>
- </execution>
- </executions>
- </plugin>
- -->
- </plugins>
- <pluginManagement>
- <plugins>
- <plugin>
- <groupId>org.jvnet.jaxb2.maven2</groupId>
- <artifactId>maven-jaxb2-plugin</artifactId>
- <configuration>
- <enableIntrospection>true</enableIntrospection>
- <specVersion>2.2</specVersion>
- <schemaDirectory>src/main/xsd</schemaDirectory>
- </configuration>
- </plugin>
- </plugins>
- </pluginManagement>
- </build>
- <scm>
- <connection>scm:git:https://git-wip-us.apache.org/repos/asf/incubator-taverna-language.git</connection>
- <developerConnection>scm:git:https://git-wip-us.apache.org/repos/asf/incubator-taverna-language.git</developerConnection>
- <url>https://github.com/apache/incubator-taverna-language</url>
- <tag>HEAD</tag>
- </scm>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>license-maven-plugin</artifactId>
+ <version>1.7</version>
+ <executions>
+ <execution>
+ <id>add-licenses</id>
+ <phase>generate-sources</phase>
+ <goals>
+ <goal>aggregate-add-third-party</goal>
+ </goals>
+ <configuration>
+ <excludedGroups>.*(mygrid|taverna).*</excludedGroups>
+ <useMissingFile>true</useMissingFile>
+ <missingFile>src/license/THIRD-PARTY.properties</missingFile>
+ <licenseMerges>
+ <licenseMerge>The Apache Software License, Version 2.0|Apache
+ 2|Apache License|Apache License, Version 2.0|Apache Public
+ License 2.0|Apache
+ License Version 2.0|Apache Software License 2.0|Apache Software License
+ -
+ Version 2.0</licenseMerge>
+ <licenseMerge>The BSD License|BSD|BSD License|BSD-style
+ license|BSD style|Aduna BSD license|Aduna BSD-style license</licenseMerge>
+ <licenseMerge>MIT License|The MIT License|MIT license</licenseMerge>
+ <licenseMerge>GNU
+ Lesser General Public License|GNU LESSER GENERAL PUBLIC LICENSE|GNU
+ Library
+ or Lesser General Public License|LGPL</licenseMerge>
+ <licenseMerge>Common
+ Development and Distribution License (CDDL) v1.0|CDDL 1.1|COMMON DEVELOPMENT
+ AND DISTRIBUTION LICENSE (CDDL) Version 1.0</licenseMerge>
+ <licenseMerge>Eclipse
+ Public License, Version 1.0|Eclipse Public License</licenseMerge>
+ </licenseMerges>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ -->
+ </plugins>
+ <pluginManagement>
+ <plugins>
+ <plugin>
+ <groupId>org.jvnet.jaxb2.maven2</groupId>
+ <artifactId>maven-jaxb2-plugin</artifactId>
+ <configuration>
+ <enableIntrospection>true</enableIntrospection>
+ <specVersion>2.2</specVersion>
+ <schemaDirectory>src/main/xsd</schemaDirectory>
+ </configuration>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+ <scm>
+ <connection>scm:git:https://git-wip-us.apache.org/repos/asf/incubator-taverna-language.git</connection>
+ <developerConnection>scm:git:https://git-wip-us.apache.org/repos/asf/incubator-taverna-language.git</developerConnection>
+ <url>https://github.com/apache/incubator-taverna-language</url>
+ <tag>HEAD</tag>
+ </scm>
- <repositories>
- <repository>
- <id>apache.snapshots</id>
- <name>Apache Snapshot Repository</name>
- <url>https://repository.apache.org/snapshots</url>
- <releases>
- <enabled>false</enabled>
- </releases>
- </repository>
- </repositories>
+ <repositories>
+ <repository>
+ <id>apache.snapshots</id>
+ <name>Apache Snapshot Repository</name>
+ <url>https://repository.apache.org/snapshots</url>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ </repository>
+ </repositories>
- <dependencyManagement>
- <dependencies>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-core</artifactId>
- <version>${jackson.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>${jackson.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.module</groupId>
- <artifactId>jackson-module-jsonSchema</artifactId>
- <version>${jackson.version}</version>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>${commons.io.version}</version>
- </dependency>
- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>com.springsource.org.jdom</artifactId>
- <version>${jdom.version}</version>
- <type>jar</type>
- </dependency>
- <dependency>
- <groupId>com.sun.xml.bind</groupId>
- <artifactId>jaxb-impl</artifactId>
- <version>${jaxb.version}</version>
- <type>jar</type>
- <optional>true</optional>
- </dependency>
- <dependency>
- <groupId>org.jaxen</groupId>
- <artifactId>com.springsource.org.jaxen</artifactId>
- <!-- Was 1.1.4. as "1.1.3 has missing dependencies" but 1.1.1 appears
- to work fine -->
- <version>${jaxen.version}</version>
- <type>jar</type>
- </dependency>
- <dependency>
- <groupId>commons-beanutils</groupId>
- <artifactId>commons-beanutils</artifactId>
- <version>${commons.beanutils.version}</version>
- </dependency>
- </dependencies>
- </dependencyManagement>
- <dependencies>
- <!-- Common dependencies on jena-osgi, which requires some additional dependencies
- to be a happy OSGi bundle -->
+ <dependencyManagement>
+ <dependencies>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-core</artifactId>
+ <version>${jackson.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>${jackson.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.module</groupId>
+ <artifactId>jackson-module-jsonSchema</artifactId>
+ <version>${jackson.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>${commons.io.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>com.springsource.org.jdom</artifactId>
+ <version>${jdom.version}</version>
+ <type>jar</type>
+ </dependency>
+ <dependency>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>${jaxb.version}</version>
+ <type>jar</type>
+ <optional>true</optional>
+ </dependency>
+ <dependency>
+ <groupId>org.jaxen</groupId>
+ <artifactId>com.springsource.org.jaxen</artifactId>
+ <!-- Was 1.1.4. as "1.1.3 has missing dependencies" but 1.1.1 appears
+ to work fine -->
+ <version>${jaxen.version}</version>
+ <type>jar</type>
+ </dependency>
+ <dependency>
+ <groupId>commons-beanutils</groupId>
+ <artifactId>commons-beanutils</artifactId>
+ <version>${commons.beanutils.version}</version>
+ </dependency>
+ </dependencies>
+ </dependencyManagement>
+ <dependencies>
+ <!-- Common dependencies on jena-osgi, which requires some additional dependencies
+ to be a happy OSGi bundle -->
- <dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>jena-osgi</artifactId>
- <version>${jena.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.servicemix.bundles</groupId>
- <artifactId>org.apache.servicemix.bundles.xerces</artifactId>
- <version>${servicemix.xerces.version}</version>
- </dependency>
- <!-- JENA-1178 workaround: Upgrade jsonlld-java -->
- <dependency>
- <groupId>com.github.jsonld-java</groupId>
- <artifactId>jsonld-java</artifactId>
- <version>${jsonldjava.version}</version>
- </dependency>
- <!-- Needed by Jena -->
- <dependency>
- <groupId>com.github.andrewoma.dexx</groupId>
- <artifactId>collection</artifactId>
- <version>${dexx.collection.version}</version>
- </dependency>
- </dependencies>
- <profiles>
- <profile>
- <id>all</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- <modules>
- <module>taverna-baclava-language</module>
- <module>taverna-databundle</module>
- <module>taverna-robundle</module>
- <module>taverna-scufl2-annotation</module>
- <module>taverna-scufl2-api</module>
- <module>taverna-scufl2-examples</module>
- <module>taverna-scufl2-integration-tests</module>
- <module>taverna-scufl2-schemas</module>
- <module>taverna-scufl2-scufl</module>
- <module>taverna-scufl2-t2flow</module>
- <module>taverna-scufl2-ucfpackage</module>
- <module>taverna-scufl2-wfbundle</module>
- <module>taverna-tavlang-tool</module>
- <module>taverna-scufl2-wfdesc</module>
- </modules>
- </profile>
- <profile>
- <id>android</id>
- <!-- <activation> <property> <name>environment</name> <value>android</value>
- </property> </activation> -->
- <properties>
- <maven.compiler.source>1.7</maven.compiler.source>
- <maven.compiler.target>1.7</maven.compiler.target>
- </properties>
- <modules>
- <module>taverna-baclava-language</module>
- <module>taverna-scufl2-annotation</module>
- <module>taverna-scufl2-api</module>
- <module>taverna-scufl2-examples</module>
- <module>taverna-scufl2-integration-tests</module>
- <module>taverna-scufl2-schemas</module>
- <module>taverna-scufl2-scufl</module>
- <module>taverna-scufl2-t2flow</module>
- <module>taverna-scufl2-ucfpackage</module>
- <module>taverna-scufl2-wfbundle</module>
- <module>taverna-tavlang-tool</module>
- </modules>
- </profile>
- </profiles>
+ <dependency>
+ <groupId>org.apache.jena</groupId>
+ <artifactId>jena-osgi</artifactId>
+ <version>${jena.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.servicemix.bundles</groupId>
+ <artifactId>org.apache.servicemix.bundles.xerces</artifactId>
+ <version>${servicemix.xerces.version}</version>
+ </dependency>
+ <!-- JENA-1178 workaround: Upgrade jsonlld-java -->
+ <dependency>
+ <groupId>com.github.jsonld-java</groupId>
+ <artifactId>jsonld-java</artifactId>
+ <version>${jsonldjava.version}</version>
+ </dependency>
+ <!-- Needed by Jena -->
+ <dependency>
+ <groupId>com.github.andrewoma.dexx</groupId>
+ <artifactId>collection</artifactId>
+ <version>${dexx.collection.version}</version>
+ </dependency>
+ </dependencies>
+ <profiles>
+ <profile>
+ <id>all</id>
+ <activation>
+ <activeByDefault>true</activeByDefault>
+ </activation>
+ <modules>
+ <module>taverna-baclava-language</module>
+ <module>taverna-databundle</module>
+ <module>taverna-robundle</module>
+ <module>taverna-scufl2-annotation</module>
+ <module>taverna-scufl2-api</module>
+ <module>taverna-scufl2-examples</module>
+ <module>taverna-scufl2-integration-tests</module>
+ <module>taverna-scufl2-schemas</module>
+ <module>taverna-scufl2-scufl</module>
+ <module>taverna-scufl2-t2flow</module>
+ <module>taverna-scufl2-ucfpackage</module>
+ <module>taverna-scufl2-wfbundle</module>
+ <module>taverna-tavlang-tool</module>
+ <module>taverna-scufl2-wfdesc</module>
+ </modules>
+ </profile>
+ <profile>
+ <id>android</id>
+ <!-- <activation> <property> <name>environment</name> <value>android</value>
+ </property> </activation> -->
+ <properties>
+ <maven.compiler.source>1.7</maven.compiler.source>
+ <maven.compiler.target>1.7</maven.compiler.target>
+ </properties>
+ <modules>
+ <module>taverna-baclava-language</module>
+ <module>taverna-scufl2-annotation</module>
+ <module>taverna-scufl2-api</module>
+ <module>taverna-scufl2-examples</module>
+ <module>taverna-scufl2-integration-tests</module>
+ <module>taverna-scufl2-schemas</module>
+ <module>taverna-scufl2-scufl</module>
+ <module>taverna-scufl2-t2flow</module>
+ <module>taverna-scufl2-ucfpackage</module>
+ <module>taverna-scufl2-wfbundle</module>
+ <module>taverna-tavlang-tool</module>
+ </modules>
+ </profile>
+ </profiles>
</project>