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From Stian Soiland-Reyes <st...@apache.org>
Subject [ANNOUNCE] Apache Taverna Command-line 3.1.0-incubating
Date Fri, 01 Jul 2016 14:01:26 GMT
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 with additional hyperlinks 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:

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.

See:
https://taverna.incubator.apache.org/download/


# Changes

The below highlights changes since Taverna Command-line 3.0a2.
Developers should note that there are as well significant changes in
the back-end 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 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 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:

- https://s.apache.org/changelog-engine-3.1.0
- https://s.apache.org/changelog-commonactivities-2.1.0
- https://s.apache.org/changelog-commandine-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!



# 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


-- 
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718

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