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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:40:42 UTC
[51/51] [partial] incubator-taverna-language git commit: temporarily
empty repository
temporarily empty repository
.. as Software Grant is not yet formally on file
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/316e4a8a
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/316e4a8a
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/316e4a8a
Branch: refs/heads/master
Commit: 316e4a8a8871a09cb9e7986ed2ef99570a16cfd6
Parents: aa46364
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 17 20:39:33 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 17 20:39:33 2015 +0000
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/LICENSE
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- 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/316e4a8a/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
deleted file mode 100644
index 4c543f7..0000000
--- a/README.md
+++ /dev/null
@@ -1,230 +0,0 @@
-<!---
- 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.
---->
-# 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/316e4a8a/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 030d92f..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,350 +0,0 @@
-<?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/316e4a8a/taverna-baclava-language/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/pom.xml b/taverna-baclava-language/pom.xml
deleted file mode 100644
index 36b5f7d..0000000
--- a/taverna-baclava-language/pom.xml
+++ /dev/null
@@ -1,66 +0,0 @@
-<?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/316e4a8a/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
deleted file mode 100644
index 8b78826..0000000
--- a/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaReader.java
+++ /dev/null
@@ -1,42 +0,0 @@
-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/316e4a8a/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
deleted file mode 100644
index cf8917d..0000000
--- a/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaWriter.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/**
- *
- */
-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/316e4a8a/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
deleted file mode 100644
index de1afa9..0000000
--- a/taverna-baclava-language/src/main/resources/xsd/baclava.xsd
+++ /dev/null
@@ -1,183 +0,0 @@
-<?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