Scufl2 has moved to Apache (incubator)

Information in this section is out of date!

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

Table of Contents

Overview

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

Modules

Official modules:

scufl2-api Java Beans for working with SCUFL2 workflow structure
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 cases 4codes. (Replaced by https://github.com/myGrid/scufl2-examples)
scufl2-rdf Pure RDF export/import (out of date)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

Maven

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 to your pom.xml:

Code Block

	xml

<properties>
	<scufl2.version>0.14.0</scufl2.version>
</properties>
<repositories>
	<repository>
		<releases />
		<snapshots>
			<enabled>false</enabled>
		</snapshots>
		<id>mygrid-repository</id>
		<name>myGrid Repository</name>
		<url>http://www.mygrid.org.uk/maven/repository</url>
	</repository>
</repositories>
<dependencies>
	<dependency>
		<groupId>uk.org.taverna.scufl2</groupId>
		<artifactId>scufl2-api</artifactId>
		<version>${scufl2.version}</version>
	</dependency>
	<dependency>
		<groupId>uk.org.taverna.scufl2</groupId>
		<artifactId>scufl2-t2flow</artifactId>
		<version>${scufl2.version}</version>
	</dependency>
	<dependency>
		<groupId>uk.org.taverna.scufl2</groupId>
		<artifactId>scufl2-rdfxml</artifactId>
		<version>${scufl2.version}</version>
	</dependency>
</dependencies>

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.

Releases

0.14.0

2014-04-30: This release adds the methods WorkflowBundleIO.getSupportedReaderMediaTypes() and getSupportedWriterMediaTypes(). This version will not allow invalid names of workflow beans (e.g. containing /, :or ASCII controll characters).

Maven version: 0.14.0 (see Maven section) - Jenkins build 4140
Git tag: 0.14.0
Source code as tar-ball or zip-ball (see Source code section below)
Javadoc: http://mygrid.github.com/scufl2/api/0.14/

Changes: (commit log)

ReaderException if nested workflow uuid is not found
SCUFL2-87: Disallow certain invalid characters in name
use Accept headers for readBundle(URL)
t2flow parser: Updated error msg if missing dispatch layer
Log warning if multiple mediatypes are detected
Escape \ in annotations to \\ in Turtle
Content type "content/unknown" (as returned by OpenJDK 7 URLConnection) ignored

0.13.1

2013-11-18: This patch release updates SCUFL2's t2flow parser to correctly set the @base for any SemanticAnnotation's, e.g. from Taverna 2's Component Plugin. This is used by scufl2-wfdesc which now embeds any annotations on workflows, processors and ports.

Maven version: 0.13.1 (see Maven section) - Jenkins build 4021
Git tag: 0.13.1
Source code as tar-ball or zip-ball (see Source code section below)
Javadoc: http://mygrid.github.com/scufl2/api/0.13/

Changes: (commit log)

Correct @base for semantic annotations (e.g. so that <> annotates the correct processor)

0.13.0

2013-11-07: This release changes the API for the Processor dispatch stack. Retry, failover and looping are now set by configuring the Processor. The Dispatch Stack is now not directly exposed in SCUFL2. Custom dispatch stack layers can however still be added to the Processor configuration by using the keywords _below and _type within the processor configuration.

Maven version: 0.13.0 (see Maven section) - Jenkins build 4004
Git tag: 0.13.0
Source code as tar-ball or zip-ball (see Source code section below)
Javadoc: http://mygrid.github.com/scufl2/api/0.13/

Changes: (commit log)

SCUFL2-126: Removed dispatch stack, Processor is Configurable
Added Scufl2Tools.createConfigurationFor()
Workflow Bundle version is bumped to manifest:version 0.4.0
- Bundles v0.3.0, used by T3 alpha 1, still parses, but its dispatch stack configuration is ignored

0.12.1

2013-10-07: This patch release primarily adds a manifest:version attribute in the Workflow Bundle's META-INF/manifest.xml, version 0.3.0 indicates the modified bundle format with JSON configurations as of SCUFL2 API 0.12.0.

Maven version: 0.12.1 (see Maven section)
Git tag: 0.12.1
Source code as tar-ball or zip-ball (see Source code section below)
Javadoc: http://mygrid.github.com/scufl2/api/0.12/

Changes: (commit log)

Indicate rootfile version with manifest:version (0.3.0)
scufl2-t2flow: Spreadsheet Import uses correct start/end and avoids JSON array for column/row ranges

0.12.0

2013-10-07: This release changes the API for Configurations. PropertyResource and friends have been replaced with JSON configurations, accessible using Jackson. Note that this means that the configuration for all the default Taverna activities also have changed. The motivation for this was to simplify the flexibility of configurations within the SCUFL2 API, Taverna 3 activities and third-party read/write of Workflow Bundles.

Maven version: 0.12.0 (see Maven section)
Git tag: 0.12.0
Source code as tar-ball or zip-ball (see Source code section below)
Javadoc: http://mygrid.github.com/scufl2/api/0.12/

Changes: (commit log)

Configuration done as JSON objects instead of PropertyResource. JSON is saved separately in Workflow Bundle.
- Note: t2flow translation of External Tool activity is temporarily disabled as it has not yet been updated to JSON
PropertyResource, PropertyObject, etc. have been removed
Available as OSGi bundles
Scufl2Tools adds methods createConstant, createConfigurationFor, getConstantStringValue, getConstants
Workflows/profiles with "Escaped names" (e.g. with spaces) now saved with correct (unescaped) filename inside workflow bundle
set/getConfigurableType -> set/getType

0.11.0

2013-04-25: A "silent" release which updates annotation support, used by scufl2-wfdesc.

Maven version: 0.11.0 (see Maven section)
Git tag: 0.11.0
Source code as tar-ball or zip-ball (see Source code section below)
Javadoc: http://mygrid.github.com/scufl2/api/0.11/

Changes: (commit log)

Support for annotations (experimental)
Revision API refactored
Nested workflow help in Scufl2Tools
Any workflow bean can be .clone()d
WorkflowBundleIO.save*() now always set the parents first

Fixes (from Jira):

Bug

[SCUFL2-81] - BlockingControlLink compare method fails to handle null block or untilFinished
[SCUFL2-82] - DataLink.compareTo(Object o) does not handle nulls
[SCUFL2-97] - Configuration.getConfigurableType() and setConfigurableType(URI) throw NullPointerException
[SCUFL2-120] - Stack overflow when parsing profile with nodes of type collection
[SCUFL2-121] - EmptyStackException when writing workflow bundle
[SCUFL2-123] - NPE on parsing Loop activity configuration

Improvement

[SCUFL2-96] - compareTo in AbstractNamed takes account of parent

New Feature

[SCUFL2-56] - Parse loop layer configuration

0.10-SNAPSHOT-biovel

2012-07-13: Internal snapshot release for the BioVel project

Maven version: 0.10-biovel-SNAPSHOT (see Maven section)
Git tag: 0.10-biovel-SNAPSHOT
Source code as tar-ball or zip-ball (see Source code section below)

Changes: (commit log)

Improved parsing of External Tool activity
Fixes bugs SCUFL2-81, SCUFL2-82, SCUFL2-120, SCUFL2-121, SCUFL2-122
Read revision log of previous versions of workflow from t2flow (adds Workflow.getCurrentRevision() and uk.org.taverna.scufl2.api.annotation.Revision). Bump to new major version 0.10.x due to API addition.
When converting from t2flow, embeds original t2flow under history/

0.9.2

2012-06-12: First public release.

Maven version: 0.9.2 (see Maven section) - Jenkins build 3445
Git tag: 0.9.2
SVN tag (legacy): scufl2-0.9.2
Download source Source code : as tar-ball or zip-ball (see Source code section below)
Javadoc: http://mygrid.github.com/scufl2/api/0.9/

Changes: (commit log)

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

...

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

0.9

Git tag: 0.9
Javadoc: http://mygrid.github.com/scufl2/api/0.9/

Changes: (commit log)

Important changes:

...

Changes: (commit log)

First internal release.

Maven

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:

...


<properties>
	<scufl2.version>0.9.2</scufl2.version>
</properties>
<repositories>
	<repository>
		<releases />
		<snapshots>
			<enabled>false</enabled>
		</snapshots>
		<id>mygrid-repository</id>
		<name>myGrid Repository</name>
		<url>http://www.mygrid.org.uk/maven/repository</url>
	</repository>
</repositories>
<dependencies>
	<dependency>
		<groupId>uk.org.taverna.scufl2</groupId>
		<artifactId>scufl2-api</artifactId>
		<version>${scufl2.version}</version>
	</dependency>
	<dependency>
		<groupId>uk.org.taverna.scufl2</groupId>
		<artifactId>scufl2-t2flow</artifactId>
		<version>${scufl2.version}</version>
	</dependency>
	<dependency>
		<groupId>uk.org.taverna.scufl2</groupId>
		<artifactId>scufl2-rdfxml</artifactId>
		<version>${scufl2.version}</version>
	</dependency>
</dependencies>

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.

...

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

No Format


: stain@ralph /tmp/93/scufl2; git tag
0.10-biovel-SNAPSHOT
0.11.0
0.5
0.9
0.9.1
0.9.2
eclipse-xsd-bug

: 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 ;

...

Note

title	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 Usage below on how to use the JARs independently.

...

Some of the experimental modules are not built automatically, to build them separately, run the same command from within their folder.

Example output:

No Format


: stain@ralph /tmp/93/scufl2; mvn clean install
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]

[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] ------------------------------------------------------------------------
[INFO] Building Taverna Scufl 2 0.9.2
[INFO] ------------------------------------------------------------------------
...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]

[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] BUILD SUCCESS
[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 Maven above.

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

...

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

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

JavaDocs

See the JavaDoc at:

http://mygrid.github.com/scufl2/api/0.9/

...

title	Other modules

...

Javadocs

The SCUFL2 Javadocs document the core classes and functions of the SCUFL2 API. A good starting point is the package uk.org.taverna.scufl2.api.

If you are using Eclipse we recommend also using the m2e plugin for Maven support - which can , then the built-in Maven support (m2e plugin) is able to provide both JavaDocs and source code from within the editor. After adding the #Maven Maven dependencies for SCUFL2, try Open declaration or Open Type on a class like uk.org.taverna.scufl2.api.io.WorkflowBundleIO. (You can open the class with Navigate -> Open Type).

Examples

Examples of using the Scufl2 API are available as a separate Github project scufl2-examples. Also see If you don't use Git you can download the example project as a ZIP fie.

See the scufl2-validationusecases folder of the SCUFL2 API source code for examples of Workflow Bundle usage in other programming languages like Python or Ruby.

The best classes to start using would be uk.org.taverna.scufl2.api.io.WorkflowBundleIO and uk.org.taverna.scufl2.api.container.WorkflowBundle.

Example of converting .t2flow to .wfbundle:

Code Block

	java

     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");

Command line

The Github project scufl2-examples includes experimental SCUFL2 command line tools:

processornames - print list of processor names
servicetypes - print URIs of service types
t2flowtowfbundle - convert a Taverna 2 .t2flow to a SCUFL2 Workflow Bundle
jsonexport - show a simple JSON structure of workflow content

Other projects

These projects extend, use or relate to the SCUFL2 api:

scufl2-wfdesc - translate t2flow and scufl2 workflows to Wf4Ever wfdesc RDF Turtle
databundle - used by taverna-prov for including the executed workflow in Taverna's provenance bundle
scufl2-clojure - prototype Clojure interface to the SCUFL2 API
scufl2-info - a web service that resolves SCUFL2 URIs like http://ns.taverna.org.uk/2010/workflowBundle/2f0e94ef-b5c4-455d-aeab-1e9611f46b8b/workflow/HelloWorld/processor/hello/
scufl2-awf - SCUFL2 Reader for importing MG-RAST AWE workflows as SCUFL2
scufl2-iwir - SCUFL2 Writer for writing SCUFL2 workflows as SHIWA IWIR workflow definitions
Taverna 3 - SCUFL2 is the workflow definition language for Taverna 3, using the SCUFL2 API for designing workflows and using the Taverna 3 Platform API.

SCUFL2 API

Versions Compared

Old Version 26

New Version Current

Key

Scufl2 has moved to Apache (incubator)

Overview

Modules

Maven

Releases

0.14.0

0.13.1

0.13.0

0.12.0

0.11.0

Bug

Improvement

New Feature

0.10-SNAPSHOT-biovel

0.9.2

0.9

Maven

Source code

JavaDocs

Javadocs

Examples

Command line

Other projects