Skip to end of metadata
Go to start of metadata
You are viewing an old version of this page. View the current version. Compare with Current ·  View Page History

The SCUFL2 API provides Java classes that can be used independently from Taverna to inspect, modify and generate SCUFL2 workflows.


The code and definitions for SCUFL2 are kept in the GitHub project scufl2.


Official modules:

  • scufl2-api Java Beans for working with SCUFL2
  • scufl2-t2flow .t2flow import from Taverna 2
  • scufl2-rdfxml .wfbundle import/export (RDF/XML)
  • scufl2-ucfpackage Structured ZIP-file support (used by scufl2-rdfxml)

Experimental modules:

  • scufl2-usecases Example code covering SCUFL2 use cases4
  • scufl2-rdf Pure RDF export/import (out of date)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



First public release.

Changes: (commit log)

  • scufl2-usecases: Java examples moved to separate GitHub project:
  • scufl2-ucfpackage: Workflow Bundles handling of relative paths
  • scufl2-rdfxml: URIs for Nested workflows should be relative to profile, not bundle


Changes: (commit log)

  • scufl2-api: Error messages for missing JAXB now less intrusive
  • scufl2-rdfxml: File locking issues on Windows resolved


Changes: (commit log)

Important changes:

  • scufl2-rdf: Ontology updated to reflect scufl2-rdfxml serialisation
  • scufl2-t2flow: Parses almost all standard Taverna 2.3 activities. (Beanshell, API consumer, Biomart, Dataflow, RShell, Soaplab, Spreadshheet, String constant, WSDL, XML splitter, External Tool, REST, XPath). Matches configuration properties in Taverna 3 platform. Missing: BioMoby
  • scufl2-validation: New experimental modules for validating correctness and soundness of a SCUFL2 workflow bundle
  • scufl2-scufl: New experimental module for parsing Taverna 1 workflows (SCUFL 1).
  • scufl2-t2flow: Dispatch stack layers translated
  • scufl2-api: WorkflowBundleIO.readBundle() media type parameter can now be null to make a mime-magic like guess
  • scufl2-rdfxml: Workflow bundle file extension is .wfbundle, not .scufl2
  • scufl2-api: Added various add/get convenience methods in PropertyResource
  • scufl2-api: WorkflowBean.accept() can be used to traverse the whole WorkflowBundle
  • scufl2-rdfxml: scufl2:sameBaseAs renamed to scufl2:globalBaseURI SCUFL2-95


Changes: (commit log)

First internal release.


The simplest way to use the SCUFL2 API is to use Maven 3 (Maven 2 should also work) and the myGrid Maven repository. See the example pom.xml.

In short, add:

The <property>scufl2.version</property> used above allows you to consistently upgrade to later versions of SCUFL2. Note that the version number above might not be the latest, see #Release notes.

Source code

You should not need to compile the SCUFL2 API for most uses, as the Maven deployment even includes the source code for retrieval by tools like Eclipse using the m2e plugin.

The simplest way to retrieve the current version of the SCUFL2 API is using git:

Note that this will by default check out the master branch, which represents the latest SNAPSHOT version of the API, which might not be stable or backwards-compatible.

To inspect the code of the latest release, use git tag and git checkout:

: stain@ralph /tmp/93/scufl2; git tag

: stain@ralph /tmp/93/scufl2; git checkout 0.9.2
Note: checking out '0.9.2'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 1a50c07... [maven-release-plugin]  copy for tag scufl2-0.9.2

: stain@ralph /tmp/93/scufl2 ;

Alternatively you can download a tagged release as a ZIP or TAR ball from:

Unpack using your favourite archiver, but don't use the ZIP support of Windows Explorer, as it occasionally don't unpack all files.


After installing Java JDK (6 or later) and Maven (2.2 or later), simply run:

  • mvn clean install

This will build each module and run their tests, producing JARs like `scufl2-api/target/scufl2-api-0.9.2.jar`.

Separate JARs

The build does not yet produce a single scufl2.jar for non-Maven users. This is planned for the 1.0 release. See #Usage below on how to use the JARs independently.

First time you build Scufl2 this might download dependencies needed for compilation. 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.

Example output:

: stain@ralph /tmp/93/scufl2; mvn clean install
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] Taverna Scufl 2
[INFO] Taverna Scufl 2 UCF Package
[INFO] Taverna Scufl 2 API
[INFO] Taverna Scufl 2 RDF/XML
[INFO] Taverna Scufl 2 t2Flow parser
[INFO] Taverna Scufl 2 SCUFL parser
[INFO] Taverna Scufl 2 use cases
[INFO] Taverna Scufl 2 validation
[INFO] Taverna Scufl 2 validation structural
[INFO] Taverna Scufl 2 validation correctness
[INFO] ------------------------------------------------------------------------
[INFO] Building Taverna Scufl 2 0.9.2
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] Taverna Scufl 2 ................................... SUCCESS [13.881s]
[INFO] Taverna Scufl 2 UCF Package ....................... SUCCESS [32.924s]
[INFO] Taverna Scufl 2 API ............................... SUCCESS [29.490s]
[INFO] Taverna Scufl 2 RDF/XML ........................... SUCCESS [1:20.551s]
[INFO] Taverna Scufl 2 t2Flow parser ..................... SUCCESS [1:37.902s]
[INFO] Taverna Scufl 2 SCUFL parser ...................... SUCCESS [11.911s]
[INFO] Taverna Scufl 2 use cases ......................... SUCCESS [15.337s]
[INFO] Taverna Scufl 2 validation ........................ SUCCESS [2.799s]
[INFO] Taverna Scufl 2 validation structural ............. SUCCESS [7.488s]
[INFO] Taverna Scufl 2 validation correctness ............ SUCCESS [12.120s]
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5:07.591s
[INFO] Finished at: Tue Jan 31 15:56:50 WET 2012
[INFO] Final Memory: 67M/176M
[INFO] ------------------------------------------------------------------------


The simplest way to use the SCUFL2 API is as Maven dependencies. See #Maven above.

Typical use of the Scufl2 API will depend on the three modules scufl2-api, scufl2-t2flow and scufl2-rdfxml.

All Scufl2 modules are also valid OSGi bundles.

If you don't use Maven, you can alternatively copy and add the JARs from these modules to your classpath:

  • scufl2-api/target/scufl2-api-0.9.2.jar
  • scufl2-rdfxml/target/scufl2-rdfxml-0.9.2.jar
  • scufl2-t2flow/target/scufl2-t2flow-0.9.2.jar

Note that version numbers above might not be the latest, see #Release notes


See the JavaDoc at:

Other modules

Note that these JavaDocs does not show the other modules, as they are generally extensions to the core API. For instance, to load a .t2flow file, include scufl2-t2flow as a Maven dependency, and use the media type "application/vnd.taverna.t2flow+xml" as an argument to WorkflowBundleIO.readBundle.

If you are using Eclipse we recommend also using the m2e plugin for Maven support - which can provide both JavaDocs and source code from within the editor. After adding the #Maven dependencies for SCUFL2, try Open declaration or Open Type on a class like


Examples of using the Scufl2 API are available as a separate Github project scufl2-examples.

Also see the scufl2-validation folder of the SCUFL2 API source code for examples of usage.

The best classes to start using would be and

Example of converting .t2flow to .wfbundle:

  • None