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Release date: 2016-07-01

The Apache Taverna (incubating) team is pleased to announce the release of:

  • apache-taverna-commandline 3.1.0-incubating
  • apache-taverna-engine 3.1.0-incubating
  • apache-taverna-commonactivities 2.1.0-incubating


This is the first major release of Apache Taverna since joining the Apache Software Foundation incubator.

 

This announcement is also available at: https://s.apache.org/taverna-commandline-3.1.0

Taverna Command-line

Apache Taverna Command-line Tool 3.1.0-incubating enables you to run Taverna workflows from a command prompt or shell script. Workflow results can be saved either to a folder or to a Research Object bundle that include detailed provenance.

The Command-line Tool can run workflows defined with Apache Taverna Language in SCUFL2 format (.wfbundle). It can also execute many Taverna 2 workflows (.t2flow) , depending on which activities they require.

Download apache-taverna-commandline 3.1.0-incubating: https://taverna.incubator.apache.org/download/commandline/

Taverna Engine

Apache Taverna Engine 3.1.0-incubating is a Java library to execute Taverna workflows, defined using Apache Taverna Language or Taverna 2's .t2flow format. The engine provides OSGi services for monitoring and controlling the detailed execution of workflows.  

Download apache-taverna-engine 3.1.0-incubating: https://taverna.incubator.apache.org/download/engine/

Taverna Common Activities

Apache Taverna Common Activities 2.1.0-incubating are Java libraries for the Taverna Engine to invoke specific activities such as command-line tools (local/ssh), Beanshell scripts, REST and WSDL services, spreadsheet import, and user interactions.

This also includes the Apache Taverna WSDL Generic library, which can be used separately to parse and invoke WSDL SOAP services.

Download apache-taverna-commonactivities 2.1.0-incubating: https://taverna.incubator.apache.org/download/common-activities/

Taverna Java libraries

In addition to the above, Apache Taverna Command-line relies on these libraries which have been released earlier:

Changes

Changes since Taverna Command-line 3.0a2 are described below. Developers should note the significant back-end changes since Taverna 2.5, including a new OSGi-based plugin system and support for SCUFL2 workflow definitions.

Improved WSDL support

This release adds improved WSDL support using Apache Woden. The code has two parsers (wsdl 1.1 based on WSDL4j and 2.0 based on Woden) that implement a common interface from taverna-wsdl-generic.

Source Code Name Changes

Package names have changed to be under org.apache.taverna.* and source code modules have been reorganized. See the Javadoc for details.

Data bundle input/output

The Command-line now supports the -inputbundle option to provide structured inputs (e.g. list of lists or lists of URLs). The input bundle can be prepared as a ZIP file or using the Taverna Language API.

The Command-line now supports the -bundle option to save the Research Object Bundle ZIP file of the workflow run, which include inputs, outputs, intermediate values and the executed workflow. Note that for this release the bundle only includes provenance in JSON format.

Removed / Retired Features

Activity types

These activities are no longer supported directly by Apache Taverna:

  • RShell
  • Soaplab
  • Biomart

For interested developers, the source code for the above are available separately as part of the Taverna Plugin Bioinformatics and Taverna Extras.

Database storage

The Command-line no longer supports the -embedded or -startdb options for database storage.

Intermediate data values are stored within a Research Object Data Bundle, which can be saved for provenance purposes using the -bundle option.

Baclava format

The Command-line no longer supports the Baclava options -inputdoc  or -outputdoc.

Bug Fixes

For details of bug fixes since 3.0a2, see:

Installation Information

Prerequisites

Java 1.8 or newer (tested with OpenJDK 1.8)
Apache Maven 3.2.5 or newer

Installation

Version 3.1.0 is the first release of the Apache Taverna Command-line Tool. It is only available as source code, as we think this release is mainly useful for development and testing.

Apache Taverna is planning to include a binary distribution of the Taverna Command-line Tool with its next release. Please contact the dev@taverna mailing list for details.

See the included taverna-commandline README for details on how to build the source code. 

Stay Informed

Please subscribe to and contact the dev@taverna mailing list for any questions, suggestions, and discussions about Apache Taverna.

Bugs and feature plans are tracked in the JIRA Issue tracker under the corresponding components. Anyone may add, comment or work on an issue!

 

SHA1 checksums

cccbdaf2cac2a05df55c62d03d6308ac75f72a58 apache-taverna-engine-3.1.0-incubating-source-release.zip
94d15c4c1dbd1021b8726e584810a6030e90a16c apache-taverna-common-activities-2.1.0-incubating-source-release.zip 
71ba1a84cf1cb7293de3fef5bbeb81b353634698 apache-taverna-commandline-3.1.0-incubating-source-release.zip

 

Disclaimer

Apache Taverna is an effort undergoing incubation at The Apache Software Foundation (ASF) sponsored by the Apache Incubator PMC. Incubation is required of all newly accepted projects until a further review indicates that the infrastructure, communications, and decision making process have stabilized in a manner consistent with other successful ASF projects. While incubation status is not necessarily a reflection of the completeness or stability of the code, it does indicate that the project has yet to be fully endorsed by the ASF.

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