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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 11:05:36 UTC
[51/79] [partial] incubator-taverna-language git commit: Revert
"temporarily empty repository"
Revert "temporarily empty repository"
This reverts commit 316e4a8a8871a09cb9e7986ed2ef99570a16cfd6.
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/c08405cb
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/c08405cb
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/c08405cb
Branch: refs/heads/master
Commit: c08405cb90018170a8c214702523b142ebfa10cb
Parents: 316e4a8
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sat Feb 21 19:26:44 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sat Feb 21 19:26:44 2015 +0000
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615 files changed, 127445 insertions(+)
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/.gitignore
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diff --git a/.gitignore b/.gitignore
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--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,5 @@
+.project
+.settings
+.classpath
+target
+.gitignore
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
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--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,15 @@
+# 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.
+language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/LICENSE
----------------------------------------------------------------------
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..68c771a
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,176 @@
+
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+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..4c543f7
--- /dev/null
+++ b/README.md
@@ -0,0 +1,230 @@
+<!---
+ 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.
+--->
+# Apache Taverna Language
+
+[](https://travis-ci.org/taverna-incubator/incubator-taverna-language)
+[](http://dx.doi.org/10.5281/zenodo.10651)
+
+
+## SCUFL2
+
+
+See also the [SCUFL2 wiki][1]
+
+(c) 2009-2014 University of Manchester, UK
+
+Licensed under the [GNU Lesser General Public License (LGPL) 2.1][6].
+See LICENSE.txt for the full terms of LGPL 2.1.
+
+This is the [API][9], model and format of [SCUFL2][1], which replaces
+[Taverna][5]'s workflow format .t2flow. This API allows
+JVM applications to inspect, generate and modify Taverna workflow
+definitions without depending on the Taverna runtime.
+
+A new format, called [Scufl2 Workflow Bundle][7] is defined alongside this
+API. This format can be inspected, generated and modified independently
+of this API.
+
+Note that the ability for Scufl2 API to read a workflow bundle (using
+the `scufl2-rdfxml` module) does not guarantee it is valid or
+structurally sound. The experimental modules `scufl2-validation-*` will
+in the future be able to provide such verification.
+
+For more information, see the [SCUFL2 API][9] pages, the
+[Javadoc][10] and the [SCUFL2 examples][8].
+
+Requisites
+----------
+
+* Java 1.6 or newer (tested with Java 1.7)
+* Maven 2.2.2 or newer (for building, tested with Maven 3.0.5)
+
+
+Building
+--------
+
+* `mvn clean install`
+
+This will build each module and run their tests, producing JARs like
+`scufl2-api/target/scufl2-api-0.14.0.jar`.
+
+First time you build Scufl2 this might download dependencies needed for
+compliation. These have separate open source licenses, but should be
+compatible with LGPL. None of the dependencies are neccessary for
+using the compiled SCUFL2 API.
+
+Some of the experimental modules are not built automatically, to build
+them separately, run the same command from within their folder.
+
+
+
+Usage
+-----
+
+Scufl2 is built as a Maven project, and the easiest way to use it is
+from other Maven projects.
+
+Typical users of the Scufl2 API will depend on the three modules
+*scufl2-api*, *scufl2-t2flow* and *scufl2-rdfxml*. In your Maven
+project's POM file, add this to your `<dependencies>` section:
+
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-api</artifactId>
+ <version>0.14.0</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-rdfxml</artifactId>
+ <version>0.14.0</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-t2flow</artifactId>
+ <version>0.14.0</version>
+ </dependency>
+
+All Scufl2 modules are also valid OSGi bundles, see the OSGi section
+below.
+
+You can alternatively copy and add the JARs from these modules to your
+classpath:
+
+* scufl2-api/target/scufl2-api-0.14.0.jar
+* scufl2-rdfxml/target/scufl2-rdfxml-0.14.0.jar
+* scufl2-t2flow/target/scufl2-t2flow-0.14.0.jar
+
+See the [SCUFL2 Javadoc](http://mygrid.github.io/scufl2/api/0.14/) for
+documentation of classes and methods of SCUFL2. The package
+[uk.o.rg.taverna.scufl2.api](http://mygrid.github.io/scufl2/api/0.14/uk/org/taverna/scufl2/api/package-summary.html)
+is a good starting point.
+
+See the *scufl2-validation* folder for examples of
+usage. The best classes to start exploring would be
+`uk.org.taverna.scufl2.api.io.WorkflowBundleIO` and
+`uk.org.taverna.scufl2.api.container.WorkflowBundle`.
+
+Example of converting .t2flow to .wfbundle:
+
+ import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+ import uk.org.taverna.scufl2.api.io.ReaderException;
+ import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
+ import uk.org.taverna.scufl2.api.io.WriterException;
+
+ // ..
+
+ WorkflowBundleIO io = new WorkflowBundleIO();
+ File t2File = new File("workflow.t2flow");
+ File scufl2File = new File("workflow.wfbundle");
+ WorkflowBundle wfBundle = io.readBundle(t2File, "application/vnd.taverna.t2flow+xml");
+ io.writeBundle(wfBundle, scufl2File, "application/vnd.taverna.scufl2.workflow-bundle");
+
+Check out the GitHub project scufl2-examples[8] for examples of using Scufl2,
+including the above code.
+
+Supported file formats with WorkflowBundleIO and their required modules:
+
+<table>
+ <tr><th>Media type</th> <th>Support</th> <th>JAR</th> <th>Description</th> </tr>
+ <tr><td>application/vnd.taverna.t2flow+xml</td><td>read</td><td>scufl2-t2flow</td><td>Taverna 2 t2flow</td></tr>
+ <tr><td>application/vnd.taverna.scufl2.workflow-bundle</td><td>read/write</td><td>scufl2-rdfxml</td><td>Taverna 3 workflow bundle</td></tr>
+ <tr><td>application/vnd.taverna.scufl+xml</td><td>read</td><td>scufl2-scufl</td><td>Taverna 1 SCUFL (experimental)</td></tr>
+ <tr><td>text/vnd.taverna.scufl2.structure</td><td>read/write</td><td>scufl2-api</td><td>Textual format for testing/debugging</td></tr>
+ <tr><td>text/vnd.wf4ever.wfdesc+turtle</td><td>write</td><td><a href="https://github.com/wf4ever/scufl2-wfdesc">scufl2-wfdesc</a></td><td>Abstract workflow structure in <a href="http://www.w3.org/TR/turtle/">RDF Turtle</a> according to the <a href="http://purl.org/wf4ever/model#wfdesc">Wf4Ever wfdesc ontology</a></td></tr>
+ <tr><td>text/vnd.mgrast.awe.awf+json</td><td>read</td><td><a href="https://github.com/stain/scufl2-awf">scufl2-awf</a></td> <td>Workflow definition of the MG-RAST <a href="https://github.com/MG-RAST/AWE">AWE</a> workflow engine. (experimental)</td></tr>
+ <tr><td>application/vnd.shiwa.iwir+xml</td><td>read/write</td> <td><a href="https://github.com/stain/scufl2-iwir/">scufl2-iwir</a></td> <td><a href="http://www.shiwa-workflow.eu/">SHIWA</a>'s <a href="https://www.shiwa-workflow.eu/documents/10753/55350/IWIR+v1.1+Specification">IWIR</a> interoperabile workflow language (experimental)</td></tr>
+ <tr><td>application/json</td> <td>write</td> <td><a href="https://github.com/myGrid/scufl2-examples">scufl2-examples</a></td> <td>Abstract workflow as JSON (experimental)</td></tr>
+</table>
+
+
+OSGi services
+-------------
+To use SCUFL2 from OSGi, use the following OSGi Services. Example, from
+META-INF/spring/run-context.osgi.xml:
+
+ <?xml version="1.0" encoding="UTF-8"?>
+ <beans:beans xmlns="http://www.springframework.org/schema/osgi"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="myService" interface="com.example.MyService"/>
+
+ <reference id="workflowBundleIO" interface="uk.org.taverna.scufl2.api.io.WorkflowBundleIO" />
+
+ </beans:beans>
+
+And in run-context.xml:
+
+ <?xml version="1.0" encoding="UTF-8"?>
+ <beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="myService" class="com.example.impl.MyServiceImpl" >
+ <property name="workflowBundleIO" ref="workflowBundleIO"/>
+ </bean>
+
+ </beans>
+
+This will provide a WorkflowBundleIO instance with its readers and
+writers loaded through OSGi, which when the bundles for scufl2-t2flow
+and scufl2-rdfxml are loaded, would include support for the Taverna 2
+t2flow format and the Taverna 3 wfbundle format.
+
+Note that you do not need to use OSGi services to instantiate
+Scufl2Tools or URITools, but may do so if you wish.
+
+
+Modules
+-------
+
+Official modules:
+
+* *scufl2-api* Java Beans for working with SCUFL2
+* *scufl2-t2flow* .t2flow import from Taverna 2
+* *scufl2-rdfxml* .wfbundle import/export (RDF/XML)
+
+Experimental modules:
+
+* *scufl2-usecases* Example code covering [SCUFL2 use cases][4] (out of date)
+* *scufl2-rdf* Pure RDF export/import (out of date)
+* *scufl2-scufl* SCUFL 1 .xml import from Taverna 1
+* *scufl2-validation* API for validating a Scufl2 workflow bundle
+* *scufl2-validation-correctness*
+ Validate correctness of Scufl2 workflow definition
+* *scufl2-validation-structural*
+ Validate that a Scufl2 workflow definition is structurally sound
+* *scufl2-validation-integration*
+ Integration tests for scufl2-validation modules
+
+
+
+[1]: http://www.mygrid.org.uk/dev/wiki/display/developer/SCUFL2
+[2]: http://www.mygrid.org.uk/
+[3]: http://www.mygrid.org.uk/dev/wiki/display/story/Dataflow+serialization
+[4]: http://www.mygrid.org.uk/dev/wiki/display/developer/SCUFL2+use+cases
+[5]: http://www.taverna.org.uk/
+[6]: http://www.gnu.org/licenses/lgpl-2.1.html
+[7]: http://www.mygrid.org.uk/dev/wiki/display/developer/Taverna+Workflow+Bundle
+[8]: https://github.com/mygrid/scufl2-examples
+[9]: http://www.mygrid.org.uk/dev/wiki/display/developer/SCUFL2+API
+[10]: http://mygrid.github.io/scufl2/api/0.14/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..030d92f
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,350 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ 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.
+-->
+<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>taverna-parent</artifactId>
+ <version>1-incubating-SNAPSHOT</version>
+ </parent>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-language</artifactId>
+ <version>0.16.1-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.rat</groupId>
+ <artifactId>apache-rat-plugin</artifactId>
+ <executions>
+ <execution>
+ <id>rat-checks</id>
+ <phase>verify</phase>
+ <goals>
+ <goal>check</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <useDefaultExcludes>true</useDefaultExcludes>
+ <excludes>
+ <!-- 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>
+ <!-- The following schemas are W3C; automatic retrieval during build is
+ blocked by their administrative processes, yet they are explicitly
+ standardised documents intended for wide use. Their licenses should
+ be standard W3C ones, but that's never stated explicitly by the W3C.
+ "Thanks!" -->
+ <exclude>**/xml.xsd</exclude>
+ <exclude>**/xenc-schema.xsd</exclude>
+ <exclude>**/xmldsig-core-schema.xsd</exclude>
+ <!-- This refers to the FOAF spec, which is available online at
+ http://xmlns.com/foaf/spec/ and which uses the CC-BY-SA 1.0
+ license. The RDF downloadable from the site, of which this is a copy,
+ has no copyright statement at all in it. -->
+ <exclude>**/foaf.rdf</exclude>
+ <!-- The following contain a mix of licenses. PROBLEM! -->
+ <exclude>/src/main/resources/ontologies/*.owl</exclude>
+ <exclude>/src/main/resources/ontologies/*.rdf</exclude>
+ <exclude>/src/main/resources/org/purl/wf4ever/wfdesc/roterms.ttl</exclude>
+ <exclude>/src/main/resources/org/purl/wf4ever/wfdesc/wf4ever.ttl</exclude>
+ <exclude>/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl</exclude>
+ <exclude>/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl</exclude>
+ <exclude>/src/main/resources/org/w3/prov-o.ttl</exclude>
+ <!-- Various files used for testing and test support only. -->
+ <!-- THESE SUPPORT COMMENTS with # --><!--taverna-integration-test-->
+ <exclude>/src/test/resources/t172starterpacklist</exclude>
+ <exclude>/src/test/resources/t230starterpacklist</exclude>
+ <!-- THESE ARE XML AND SUPPORT COMMENTS -->
+ <exclude>/src/test/resources/annotation_with_backslash.t2flow</exclude>
+ <exclude>/src/test/resources/beanshell-deps.t2flow</exclude>
+ <exclude>/src/test/resources/component_simple.t2flow</exclude>
+ <exclude>/src/test/resources/dataflow_link_then_merge.t2flow</exclude>
+ <exclude>/src/test/resources/dispatchlayers-xsd.t2flow</exclude>
+ <exclude>/src/test/resources/dispatchlayers.t2flow</exclude>
+ <exclude>/src/test/resources/fasta_and_pscan.t2flow</exclude>
+ <exclude>/src/test/resources/fasta_pscan_and_dbfetch.t2flow</exclude>
+ <exclude>/src/test/resources/interaction-with-strange-loop.t2flow</exclude>
+ <exclude>/src/test/resources/interaction_multiple_choice.t2flow</exclude>
+ <exclude>/src/test/resources/interaction_simple_tell.t2flow</exclude>
+ <exclude>/src/test/resources/iterationstrategies.t2flow</exclude><!-- TOM -->
+ <exclude>/src/test/resources/merge_fun.t2flow</exclude>
+ <exclude>/src/test/resources/merge_then_dataflow_link.t2flow</exclude>
+ <exclude>/src/test/resources/missing_merge.t2flow</exclude>
+ <exclude>/src/test/resources/missing_produced_by_941.t2flow</exclude>
+ <exclude>/src/test/resources/rest-2-2.t2flow</exclude>
+ <exclude>/src/test/resources/rshell-2-2.t2flow</exclude>
+ <exclude>/src/test/resources/simple_fasta.t2flow</exclude>
+ <exclude>/src/test/resources/sleepers.t2flow</exclude>
+ <exclude>/src/test/resources/apiconsumer.t2flow</exclude>
+ <exclude>/src/test/resources/rest.t2flow</exclude>
+ <exclude>/src/test/resources/valid_component_imagemagickconvert.t2flow</exclude>
+ <exclude>/src/test/resources/enm-v21.t2flow</exclude>
+ <exclude>/src/test/resources/helloworld.wfdesc.ttl</exclude>
+ <exclude>/src/test/resources/localdependency.t2flow</exclude>
+ <exclude>/src/test/resources/nested.t2flow</exclude>
+ <exclude>/src/test/resources/rdf-in-example-annotation.t2flow</exclude>
+ <exclude>/src/test/resources/workflow10.xml</exclude>
+ <exclude>/src/test/resources/full-example/ebi_interproscan_newservices_900329.t2flow</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>
+ </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.codehaus.mojo</groupId>
+ <artifactId>jaxb2-maven-plugin</artifactId>
+ <version>1.6</version>
+ <configuration>
+ <target>2.2</target>
+ <enableIntrospection>true</enableIntrospection>
+ <!--
+ Needed for consistency across Java 6 and Java 7 on optional Booleans.
+ http://www.olivergierke.de/wordpress/2011/03/a-jaxb-or-rather-xjc-odyssey/
+ http://www.mojavelinux.com/blog/archives/2006/09/the_great_jaxb_api_blunder/
+ http://java.net/jira/browse/JAXB-131
+ -->
+ <!--
+ <arguments>-disableXmlSecurity</arguments>
+ -->
+ <!--
+ Needed to read schemas from file: (!!)
+ https://github.com/stianh/gradle-jaxb-plugin/issues/20
+ -->
+ </configuration>
+ <dependencies>
+ <!--
+ <dependency>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-xjc</artifactId>
+ <version>${jaxb.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>${jaxb.version}</version>
+ </dependency>
+ -->
+ </dependencies>
+ </plugin>
+ <plugin>
+ <groupId>org.jvnet.jaxb2.maven2</groupId>
+ <artifactId>maven-jaxb2-plugin</artifactId>
+ <version>0.11.0</version>
+ <configuration>
+ <enableIntrospection>true</enableIntrospection>
+ <specVersion>2.2</specVersion>
+ <schemaDirectory>src/main/xsd</schemaDirectory>
+ </configuration>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+<!-- TODO: Update -->
+ <scm>
+ <!-- TODO: Replace with git.apache.org details :
+ <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://git-wip-us.apache.org/repos/asf/incubator-taverna-language.git</url>
+ -->
+ <connection>scm:git:https://github.com/taverna-incubator/incubator-taverna-language.git</connection>
+ <developerConnection>scm:git:git@github.com:taverna-incubator/incubator-taverna-language.git</developerConnection>
+ <url>https://github.com/taverna-incubator/incubator-taverna-language</url>
+ <tag>HEAD</tag>
+ </scm>
+
+ <repositories>
+ <!--
+ <repository>
+ <id>com.springsource.repository.bundles.release</id>
+ <name>SpringSource Enterprise Bundle Repository - SpringSource Bundle Releases</name>
+ <url>http://repository.springsource.com/maven/bundles/release</url>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ </repository>
+ <repository>
+ <id>com.springsource.repository.bundles.external</id>
+ <name>SpringSource Enterprise Bundle Repository - External Bundle Releases</name>
+ <url>http://repository.springsource.com/maven/bundles/external</url>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ </repository>
+ -->
+
+<!-- TODO: Remove myGrid repositories -->
+ <repository>
+ <id>taverna-incubating</id>
+ <name>Apache Taverna incubating Repository</name>
+ <url>http://repository.mygrid.org.uk/artifactory/incubator-snapshot-local/</url>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ </repository>
+ <repository>
+<!-- TODO: Use Apache snapshot repo instead -->
+ <id>taverna-incubating-release</id>
+ <name>Taverna incubating test release</name>
+ <url>http://repository.mygrid.org.uk/artifactory/incubator-release-test/</url>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ </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>
+ <modules>
+ <module>taverna-scufl2-ucfpackage</module>
+ <module>taverna-scufl2-api</module>
+ <module>taverna-scufl2-examples</module>
+ <module>taverna-scufl2-rdfxml</module>
+ <module>taverna-scufl2-t2flow</module>
+ <module>taverna-scufl2-scufl</module>
+ <module>taverna-scufl2-validation</module>
+ <module>taverna-scufl2-validation-structural</module>
+ <module>taverna-scufl2-validation-correctness</module>
+ <module>taverna-scufl2-validation-integration</module>
+ <module>taverna-scufl2-integration-tests</module>
+ <module>taverna-scufl2-annotation</module>
+ <module>taverna-scufl2-schemas</module>
+ <module>taverna-scufl2-wfdesc</module>
+ <module>taverna-robundle</module>
+ <module>taverna-databundle</module>
+ <module>taverna-baclava-language</module>
+ </modules>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-baclava-language/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/pom.xml b/taverna-baclava-language/pom.xml
new file mode 100644
index 0000000..36b5f7d
--- /dev/null
+++ b/taverna-baclava-language/pom.xml
@@ -0,0 +1,66 @@
+<?xml version='1.0'?>
+<!--
+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.
+-->
+
+<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/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-language</artifactId>
+ <version>0.16.1-incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>baclava-language</artifactId>
+ <version>0.0.1-SNAPSHOT</version>
+ <name>baclava</name>
+ <packaging>bundle</packaging>
+ <description>Support for reading and writing Baclava files</description>
+ <build>
+ <plugins>
+
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>jaxb2-maven-plugin</artifactId>
+ <executions>
+ <execution>
+ <goals>
+ <goal>xjc</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <packageName>org.apache.taverna.baclava</packageName>
+ <schemaDirectory>src/main/resources/xsd/</schemaDirectory>
+ </configuration>
+ </plugin>
+
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <configuration>
+ <source>1.7</source>
+ <target>1.7</target>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.rat</groupId>
+ <artifactId>apache-rat-plugin</artifactId>
+ </plugin>
+ </plugins>
+ </build>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaReader.java
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaReader.java b/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaReader.java
new file mode 100644
index 0000000..8b78826
--- /dev/null
+++ b/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaReader.java
@@ -0,0 +1,42 @@
+package org.apache.taverna.baclava;
+
+/*
+ * 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.Reader;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+
+
+public class BaclavaReader {
+
+ private static JAXBContext jaxbContext;
+ private static Unmarshaller unmarshaller;
+
+ public static DataThingMapType readBaclava(Reader r) throws JAXBException {
+ jaxbContext = JAXBContext.newInstance("org.apache.taverna.baclava");
+ unmarshaller = jaxbContext.createUnmarshaller();
+ JAXBElement<?> jb = (JAXBElement<?>) unmarshaller.unmarshal(r);
+ return (DataThingMapType) jb.getValue();
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaWriter.java
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaWriter.java b/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaWriter.java
new file mode 100644
index 0000000..cf8917d
--- /dev/null
+++ b/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaWriter.java
@@ -0,0 +1,47 @@
+/**
+ *
+ */
+package org.apache.taverna.baclava;
+
+/*
+ * 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.Writer;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+
+/**
+ * @author alanrw
+ *
+ */
+public class BaclavaWriter {
+
+ public static void writeBaclava(DataThingMapType d, Writer w) throws JAXBException {
+ JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class);
+ Marshaller marshaller = jaxbContext.createMarshaller();
+ marshaller.setProperty("jaxb.formatted.output", true);
+
+ ObjectFactory of = new ObjectFactory();
+ marshaller.marshal(of.createDataThingMap(d), w);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-baclava-language/src/main/resources/xsd/baclava.xsd
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/src/main/resources/xsd/baclava.xsd b/taverna-baclava-language/src/main/resources/xsd/baclava.xsd
new file mode 100644
index 0000000..de1afa9
--- /dev/null
+++ b/taverna-baclava-language/src/main/resources/xsd/baclava.xsd
@@ -0,0 +1,183 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+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.
+-->
+<schema targetNamespace="http://org.embl.ebi.escience/baclava/0.1alpha"
+ elementFormDefault="qualified" xmlns="http://www.w3.org/2001/XMLSchema"
+ xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha"
+ xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"
+ xmlns:jaxb="http://java.sun.com/xml/ns/jaxb"
+ jaxb:version="2.0">
+
+ <import schemaLocation="xscufl.xsd" namespace="http://org.embl.ebi.escience/xscufl/0.1alpha"></import>
+ <element name="dataThingMap" type="b:DataThingMapType"></element>
+
+ <complexType name="DataThingMapType">
+ <sequence>
+ <element ref="b:dataThing" minOccurs="1"
+ maxOccurs="unbounded">
+ </element>
+ </sequence>
+ </complexType>
+
+ <complexType name="DataThingType">
+ <sequence>
+ <element ref="b:myGridDataDocument" minOccurs="1"
+ maxOccurs="1">
+ </element>
+ </sequence>
+ <attribute name="key" use="required">
+ <simpleType>
+ <restriction base="string">
+ <minLength value="1"></minLength>
+ <whiteSpace value="collapse"></whiteSpace>
+ </restriction>
+ </simpleType>
+ </attribute>
+ </complexType>
+
+ <element name="dataThing" type="b:DataThingType"></element>
+
+ <complexType name="MyGridDataDocumentType">
+ <sequence>
+ <element ref="s:metadata" minOccurs="1" maxOccurs="1"></element>
+ <choice minOccurs="1" maxOccurs="1">
+ <element ref="b:partialOrder"></element>
+ <element ref="b:dataElement"></element>
+ </choice>
+ </sequence>
+ <attribute name="lsid" use="required">
+ <simpleType>
+ <restriction base="string">
+ <minLength value="0"></minLength>
+ <whiteSpace value="collapse"></whiteSpace>
+ </restriction>
+ </simpleType>
+ </attribute>
+ <attribute name="syntactictype" use="required">
+ <simpleType>
+ <restriction base="string">
+ <minLength value="1"></minLength>
+ <whiteSpace value="collapse"></whiteSpace>
+ </restriction>
+ </simpleType>
+ </attribute>
+ </complexType>
+
+ <element name="myGridDataDocument"
+ type="b:MyGridDataDocumentType">
+ </element>
+
+
+ <complexType name="PartialOrderType">
+ <sequence>
+ <element ref="b:relationList" minOccurs="0" maxOccurs="1"></element>
+ <element ref="b:itemList" minOccurs="0" maxOccurs="1"></element>
+ </sequence>
+ <attribute name="lsid" use="required">
+ <simpleType>
+ <restriction base="string">
+ <minLength value="0"></minLength>
+ <whiteSpace value="collapse"></whiteSpace>
+ </restriction>
+ </simpleType>
+ </attribute>
+ <attribute name="type" type="string" use="required"
+ fixed="list">
+ </attribute>
+ <attribute name="index" use="optional">
+ <simpleType>
+ <restriction base="int">
+ <minExclusive value="0"></minExclusive>
+ <whiteSpace value="collapse"></whiteSpace>
+ </restriction>
+ </simpleType>
+ </attribute>
+ </complexType>
+
+ <complexType name="RelationListType">
+ <sequence>
+ <element ref="b:relation" minOccurs="0" maxOccurs="unbounded"></element>
+ </sequence>
+ </complexType>
+
+ <complexType name="ItemListType">
+ <sequence>
+ <element ref="b:dataElement" minOccurs="0"
+ maxOccurs="unbounded">
+ </element>
+ </sequence>
+ </complexType>
+
+
+
+ <element name="partialOrder" type="b:PartialOrderType"></element>
+
+ <element name="relationList" type="b:RelationListType"></element>
+
+ <element name="itemList" type="b:ItemListType"></element>
+
+ <element name="dataElement" type="b:DataElementType"></element>
+
+ <element name="dataElementData" type="string"></element>
+
+ <complexType name="DataElementType">
+ <sequence>
+ <element ref="b:dataElementData" minOccurs="1"
+ maxOccurs="1">
+ </element>
+ </sequence>
+ <attribute name="lsid" use="required">
+ <simpleType>
+ <restriction base="string">
+ <minLength value="0"></minLength>
+ <whiteSpace value="collapse"></whiteSpace>
+ </restriction>
+ </simpleType>
+ </attribute>
+ <attribute name="index" use="optional">
+ <simpleType>
+ <restriction base="int">
+ <minInclusive value="0"></minInclusive>
+ <whiteSpace value="collapse"></whiteSpace>
+ </restriction>
+ </simpleType>
+ </attribute>
+ </complexType>
+
+ <complexType name="RelationType">
+ <attribute name="parent" use="required">
+ <simpleType>
+ <restriction base="int">
+ <minInclusive value="0"></minInclusive>
+ <whiteSpace value="collapse"></whiteSpace>
+ </restriction>
+ </simpleType>
+ </attribute>
+ <attribute name="child">
+ <simpleType>
+ <restriction base="int">
+ <minExclusive value="0"></minExclusive>
+ <whiteSpace value="collapse"></whiteSpace>
+ </restriction>
+ </simpleType>
+ </attribute>
+ </complexType>
+
+ <element name="relation" type="b:RelationType"></element>
+</schema>
\ No newline at end of file