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Posted to commits@taverna.apache.org by st...@apache.org on 2016/05/04 10:55:58 UTC
[3/3] incubator-taverna-language git commit: Don't list missing
text/turtle files
Don't list missing text/turtle files
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/cfe263c9
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/cfe263c9
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/cfe263c9
Branch: refs/heads/master
Commit: cfe263c9600f28a97ff04e58e4d3b6e2bce46ced
Parents: 9add077
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed May 4 11:54:52 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed May 4 11:55:30 2016 +0100
----------------------------------------------------------------------
.../scufl2/rdfxml/WorkflowBundleParser.java | 6 +-
.../taverna/scufl2/rdfxml/example.wfbundle | Bin 40331 -> 51844 bytes
.../taverna/scufl2/rdfxml/example/LICENSE | 430 +++++++++++++++++++
.../rdfxml/example/META-INF/container.xml | 2 -
.../scufl2/rdfxml/example/META-INF/manifest.xml | 7 -
.../apache/taverna/scufl2/rdfxml/example/NOTICE | 11 +
6 files changed, 444 insertions(+), 12 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfe263c9/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java b/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java
index 362be52..dfaa34e 100644
--- a/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java
+++ b/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java
@@ -154,8 +154,8 @@ public class WorkflowBundleParser extends AbstractParser {
// Not a semantic annotation
continue;
}
- System.out.println(resource.getPath());
- System.out.println(resource.getMediaType());
+ //System.out.println(resource.getPath());
+ //System.out.println(resource.getMediaType());
Annotation ann = new Annotation();
// Hackish way to generate a name from the annotation filename
// as these typically are UUIDs
@@ -169,7 +169,7 @@ public class WorkflowBundleParser extends AbstractParser {
Model model = ModelFactory.createDefaultModel();
InputStream inputStream = resource.getUcfPackage().getResourceAsInputStream(path);
if (inputStream == null) {
- System.out.println("Eh..?");
+ // Not found!
continue;
}
RDFDataMgr.read(model, inputStream,
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfe263c9/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example.wfbundle
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example.wfbundle b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example.wfbundle
index 5e01a49..8e33e51 100644
Binary files a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example.wfbundle and b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example.wfbundle differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfe263c9/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/LICENSE
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/LICENSE b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/LICENSE
new file mode 100644
index 0000000..6e202da
--- /dev/null
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/LICENSE
@@ -0,0 +1,430 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
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+ "License" shall mean the terms and conditions for use, reproduction,
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+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
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+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
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+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
+ or by an individual or Legal Entity authorized to submit on behalf of
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+ to the Licensor or its representatives, including but not limited to
+ communication on electronic mailing lists, source code control systems,
+ and issue tracking systems that are managed by, or on behalf of, the
+ Licensor for the purpose of discussing and improving the Work, but
+ excluding communication that is conspicuously marked or otherwise
+ designated in writing by the copyright owner as "Not a Contribution."
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+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
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+ 2. Grant of Copyright License. Subject to the terms and conditions of
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+ Work and such Derivative Works in Source or Object form.
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+ 3. Grant of Patent License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
+ use, offer to sell, sell, import, and otherwise transfer the Work,
+ where such license applies only to those patent claims licensable
+ by such Contributor that are necessarily infringed by their
+ Contribution(s) alone or by combination of their Contribution(s)
+ with the Work to which such Contribution(s) was submitted. If You
+ institute patent litigation against any entity (including a
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
+ or a Contribution incorporated within the Work constitutes direct
+ or contributory patent infringement, then any patent licenses
+ granted to You under this License for that Work shall terminate
+ as of the date such litigation is filed.
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+ 4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
+ modifications, and in Source or Object form, provided that You
+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
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+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
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+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
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+ 7. Disclaimer of Warranty. Unless required by applicable law or
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+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
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+ 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.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
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+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed 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
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+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
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+ 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.
+
+
+
+
+---------------------------------------------------------
+./taverna-scufl2-wfdesc/src/main/resources/org/w3/prov-o.ttl
+./taverna-robundle/src/main/resources/ontologies/prov-aq.rdf
+./taverna-robundle/src/main/resources/ontologies/prov-o.rdf
+
+W3C PROVenance Interchange Ontology (PROV-O)
+http://www.w3.org/ns/prov-o.rdf
+http://www.w3.org/TR/2013/REC-prov-o-20130430/
+
+W3C PROV Access and Query Ontology (PROV-AQ)
+http://www.w3.org/ns/prov-aq.owl
+http://www.w3.org/TR/2013/NOTE-prov-aq-20130430/
+
+Copyright (c) 2011-2013 W3C(R) (MIT, ERCIM, Keio, Beihang), All Rights Reserved.
+W3C liability, trademark and document use rules apply.
+http://www.w3.org/Consortium/Legal/2015/doc-license
+
+
+---------------------------------------------------------
+./taverna-robundle/src/main/xsd/xenc-schema.xsd
+
+XML Encryption Syntax and Processing
+W3C Recommendation 10 December 2002
+http://www.w3.org/TR/xmlenc-core/xenc-schema.xsd
+http://www.w3.org/TR/xmlenc-core/
+
+Copyright (c) 2002 World Wide Web Consortium, (Massachusetts
+Institute of Technology, Institut National de Recherche en Informatique et en
+Automatique, Keio University). All Rights Reserved.
+http://www.w3.org/Consortium/Legal/
+
+
+---------------------------------------------------------
+./taverna-robundle/src/main/xsd/xmldsig-core-schema.xsd
+
+Schema for XML Signatures
+http://www.w3.org/2000/09/xmldsig#
+$Revision: 1.1 $ on $Date: 2002/02/08 20:32:26 $ by $Author: reagle $
+
+Copyright 2001 The Internet Society and W3C (Massachusetts Institute
+of Technology, Institut National de Recherche en Informatique et en
+Automatique, Keio University). All Rights Reserved.
+http://www.w3.org/Consortium/Legal/
+
+This document is governed by the W3C Software License [1] as described
+in the FAQ [2].
+
+[1] http://www.w3.org/Consortium/Legal/copyright-software-19980720
+[2] http://www.w3.org/Consortium/Legal/IPR-FAQ-20000620.html#DTD
+
+
+---------------------------------------------------------
+./taverna-scufl2-wfdesc/src/main/resources/com/xmlns/foaf/foaf.rdf
+./taverna-robundle/src/main/resources/ontologies/foaf.rdf
+
+Friend of a Friend (FOAF) RDF vocabulary
+http://xmlns.com/foaf/spec/20140114.rdf
+
+Copyright (c) 2000-2014 Dan Brickley and Libby Miller
+This work is licensed under a Creative Commons Attribution License.
+http://creativecommons.org/licenses/by/1.0/
+
+
+---------------------------------------------------------
+./taverna-robundle/src/main/resources/ontologies/dcterms_od.owl
+
+DCMI metadata terms
+http://purl.org/wf4ever/dcterms_od
+Modified to reduce owl:imports
+
+Adapted from Dublin Core in OWL 2
+http://purl.org/NET/dc_owl2dl/terms_od
+Modified for OWL compliance
+
+Adapted from Dublin Core
+http://purl.org/dc/terms/
+
+Copyright (c) 2012-2015 University of Manchester
+Copyright (c) 2009-2014 Simon Reinhardt (http://simon-reinhardt.de/)
+Copyright (c) 1995-2012 DCMI, the Dublin Core Metadata Initiative (http://dublincore.org/)
+
+Licensed under a Creative Commons Attribution 3.0 Unported License (CC BY 3.0).
+http://creativecommons.org/licenses/by/3.0/
+
+
+---------------------------------------------------------
+./taverna-robundle/src/main/resources/ontologies/dcam.owl
+
+DCMI Abstract model
+http://purl.org/wf4ever/dcam
+Modified URI of the owl:Ontology
+
+Adapted from Dublin Core in OWL 2
+http://purl.org/NET/dc_owl2dl/dcam
+Modified for OWL compliance
+
+Adapted from Dublin Core
+http://purl.org/dc/dcam/
+
+Copyright (c) 2012-2015 University of Manchester
+Copyright (c) 2009-2014 Simon Reinhardt (http://simon-reinhardt.de/)
+Copyright (c) 1995-2012 DCMI, the Dublin Core Metadata Initiative (http://dublincore.org/)
+
+Licensed under a Creative Commons Attribution 3.0 Unported License (CC BY 3.0).
+http://creativecommons.org/licenses/by/3.0/
+
+
+---------------------------------------------------------
+./taverna-robundle/src/main/resources/ontologies/oa.rdf
+
+Open Annotation Data Model 0.9.20130208
+http://www.w3.org/ns/oa
+
+Copyright (c) 2012-2013 the Contributors to the Open Annotation Core Data Model
+Specification, published by the Open Annotation Community Group under the W3C
+Community Contributor License Agreement (CLA). A human-readable summary is
+available.
+
+http://www.w3.org/community/about/agreements/cla/
+
+---------------------------------------------------------
+./taverna-robundle/src/main/xsd/OpenDocument-v1.2-os-manifest-schema.rng
+./taverna-robundle/src/main/xsd/OpenDocument-v1.2-os-manifest-schema.xsd
+
+Open Document Format for Office Applications (OpenDocument) Version 1.2
+OASIS Standard, 29 September 2011
+Manifest Relax-NG Schema
+Source: http://docs.oasis-open.org/office/v1.2/os/
+Copyright (c) OASIS Open 2002-2011. All Rights Reserved.
+
+ All capitalized terms in the following text have the meanings assigned to them
+ in the OASIS Intellectual Property Rights Policy (the "OASIS IPR Policy"). The
+ full Policy may be found at the OASIS website.
+
+ This document and translations of it may be copied and furnished to others, and
+ derivative works that comment on or otherwise explain it or assist in its
+ implementation may be prepared, copied, published, and distributed, in whole or
+ in part, without restriction of any kind, provided that the above copyright
+ notice and this section are included on all such copies and derivative works.
+ However, this document itself may not be modified in any way, including by
+ removing the copyright notice or references to OASIS, except as needed for the
+ purpose of developing any document or deliverable produced by an OASIS
+ Technical Committee (in which case the rules applicable to copyrights, as set
+ forth in the OASIS IPR Policy, must be followed) or as required to translate it
+ into languages other than English.
+
+ The limited permissions granted above are perpetual and will not be revoked by
+ OASIS or its successors or assigns.
+
+ This document and the information contained herein is provided on an "AS IS"
+ basis and OASIS DISCLAIMS ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT
+ LIMITED TO ANY WARRANTY THAT THE USE OF THE INFORMATION HEREIN WILL NOT
+ INFRINGE ANY OWNERSHIP RIGHTS OR ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR
+ FITNESS FOR A PARTICULAR PURPOSE.
+
+
+---------------------------------------------------------
+./taverna-robundle/src/main/resources/ontologies/ro.owl
+./taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl
+./taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl
+./taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/roterms.ttl
+./taverna-scufl2-wfdesc/src/main/resources/org/purl/wf4ever/wfdesc/wf4ever.ttl
+
+Wf4Ever Research Object Model 1.0
+https://w3id.org/ro/
+
+wfdesc ontology
+https://w3id.org/ro/wfdesc
+
+wfprov ontology
+https://w3id.org/ro/wfprov
+
+roterms ontology
+http://purl.org/wf4ever/roterms
+
+wf4ever ontology
+https://w3id.org/ro/wf4ever
+
+Copyright (c) 2011-2014
+ Stian Soiland-Reyes, University of Manchester
+ Sean Bechhofer, University of Manchester
+ Khalid Belhajjame, University of Manchester
+ Graham Klyne, University of Oxford
+ Daniel Garijo, UPM
+ Oscar Corcho, UPM
+ Esteban Garcia Cuesta, iSOCO
+ Raul Palma, PSNC
+
+Licensed under a Creative Commons Attribution 3.0 License.
+http://creativecommons.org/licenses/by/3.0/
+
+
+------------------------------------------------------
+./taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
+
+xml.xsd
+Extensible Markup Language (XML) 1.0 (Fifth Edition)
+W3C Recommendation 26 November 2008
+http://www.w3.org/2001/xml.xsd
+http://www.w3.org/TR/xml/
+
+Copyright (c) 2015 W3C(R) (MIT, ERCIM, Keio, Beihang). This software or
+document includes material copied from or derived from:
+
+W3C liability, trademark and document use rules apply.
+http://www.w3.org/Consortium/Legal/2015/doc-license
+
+
+------------------------------------------------------
+./taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd
+
+roevo.xsd derived from
+Research Object Evolution Ontology (roevo)
+http://w3id.org/ro/roevo
+
+Copyright (c) 2011-2014
+ Raul Palma, PSNC
+ Jun Zhao, University of Oxford
+ Khalid Belhajjame, University of Manchester
+ Stian Soiland-Reyes, University of Manchester
+ Oscar Corcho, UPM
+
+Creative Commons Attribution 3.0 License
+http://creativecommons.org/licenses/by/3.0
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfe263c9/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/container.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/container.xml b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/container.xml
index 8d064af..0f48202 100644
--- a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/container.xml
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/container.xml
@@ -23,8 +23,6 @@
<container version="1.0"
xmlns="urn:oasis:names:tc:opendocument:xmlns:container">
<rootfiles>
- <rootfile full-path="workflowBundle.ttl"
- media-type="text/turtle" />
<rootfile full-path="workflowBundle.rdf"
media-type="application/rdf+xml" />
</rootfiles>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfe263c9/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/manifest.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/manifest.xml b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/manifest.xml
index f30dd2b..c355e13 100644
--- a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/manifest.xml
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/manifest.xml
@@ -23,13 +23,6 @@
<manifest:manifest xmlns:manifest="urn:oasis:names:tc:opendocument:xmlns:manifest:1.0">
<manifest:file-entry manifest:media-type="application/vnd.taverna.scufl2.workflowBundle" manifest:full-path="/"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="workflowBundle.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="workflow/HelloWorld.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="annotation/workflow/HelloWorld.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="annotation/workflowBundle.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="profile/tavernaWorkbench.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="profile/tavernaServer.ttl"/>
-
<manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="workflowBundle.rdf"/>
<manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="workflow/HelloWorld.rdf"/>
<manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="annotation/workflow/HelloWorld.rdf"/>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfe263c9/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/NOTICE
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/NOTICE b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/NOTICE
new file mode 100644
index 0000000..750b5d3
--- /dev/null
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/NOTICE
@@ -0,0 +1,11 @@
+Apache Taverna Language
+Copyright 2014-2016 The Apache Software Foundation
+
+This product includes software developed at
+The Apache Software Foundation (http://www.apache.org/).
+
+Portions of this software were originally based on the following:
+- Copyright 2010-2014 University of Manchester, UK
+These have been licensed to the Apache Software Foundation under a software grant.
+
+-----------------------------------------------------------------------------------