THIS IS A TEST INSTANCE. ALL YOUR CHANGES WILL BE LOST!!!!
Release date: 2016-06-31
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 incubator, following two library releases which this relies on.
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 a Research Object bundle including 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.
Support for executing Common Workflow Language workflows and invoking Docker services is under development and is not included in this release. Please contact the dev@taverna mailing list for details.
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/
Other Taverna
In addition to the above, Apache Taverna Command-line relies on these libraries which have been released earlier:
- Apache Taverna OSGi 0.2.1-incubating is a plugin system for Java console and desktop applications using OSGi, including an online update mechanism.
- Apache Taverna Language 0.15.1-incubating is a Java API that gives programmatic access to inspecting, modifying and converting SCUFL2 workflow definitions and Research Object Bundles.
Changes
The below highlights changes since Taverna Commandline 3.0a2. Developers should note that there are as well significant changes in the backend 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 (inherited from “wsdl-generic” based on AXIS 1.4). The service execution part is based on embedded JAX-WS API, but given that this part is calling the abstract interface, there shouldn’t be a significant change.
Source Code Name Changes
Package names have changed to be under org.apache.taverna.* and source code modules has 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 of the workflow run, including inputs, outputs, intermediate values and the executed workflow. Note that for this release the bundle only includes provenance in JSON format.
Removed / Retired Features
Unsupported 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 an 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:
- Changelog for Taverna Engine 3.1.0
- Changelog for Taverna Common Activities 2.1.0
- Changelog for Taverna Commandline 3.1.0
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!
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