Draft Taverna Language Release Notes

 

This is a DRAFT article for discussion purposes only.

Apache Taverna (Incubating) Taverna Language 3.1.0 Release Notes

2016-02-01 DRAFT  Revised 2016-02-10

Introduction

These are the release notes for the first Apache release of Taverna Language. This release is an update that fixes bugs (TAVERNA-874) only one bug? and adds the Tavlang Tool, contributed by Menaka Madushanka and sponsored by Google Summer of Code 2015.

Continue reading “Draft Taverna Language Release Notes”

References and Publications

This is a DRAFT article for discussion purposes only. (Revised to change reference links to refer to dx.doi.org. 2016-01-12.) See live citationpublications, and references pages.

Referencing Taverna

Reference Taverna in a paper

If you wish to reference Taverna in a paper, please use:

Katherine Wolstencroft, Robert Haines, Donal Fellows, Alan Williams, David Withers, Stuart Owen, Stian Soiland-Reyes, Ian Dunlop, Aleksandra Nenadic, Paul Fisher, Jiten Bhagat, Khalid Belhajjame, Finn Bacall, Alex Hardisty, Abraham Nieva de la Hidalga, Maria P. Balcazar Vargas, Shoaib Sufi, and Carole Goble (2013):
“The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud”Nucleic Acids Research, 41(W1): W557-W561.
doi:10.1093/nar/gkt328

Reference the Apache Taverna Website

If you want to reference the Taverna website, please use http://taverna.incubator.apache.org/

Publications List

The following is a partial list of publications that reference the Taverna Workflow Management System.

2015

Sonja Holl, Yassene Mohammed, Olav Zimmermann, and Magnus Palmblad (2015): “Scientific workflow optimization for improved peptide and protein identification.” BMC Bioinformatics 16, no. 1: 1-13. doi:10.1186/s12859-015-0714-x

2014

Ahmet Yildiz, Erkan Dilaveroglu, Ilhami Visne, Bilal Günay, Emrah Sefer, Andreas Weinhausel, Frank Rattay, Carole A Goble, Ram Vinay Pandey, and Albert Kriegner (2014): “BIFI: a Taverna plugin for a simplified and user-friendly workflow platform.” BMC Research Notes 7, 740. doi:10.1186/1756-0500-7-740

Structured List of Taverna (Workbench) Documentation Files

The following document is based on the index.md file contained in https://github.com/apache/incubator-taverna-site/tree/trunk/content/documentation. The index.md file is a structured document, and contains links to most of the *.md files in the /documentation directory, as well as external links, as described below.

This document follows the same format as index.md, but includes a brief description of each link and identifies files that are not linked (orphaned) in the index.md file. The purpose is to gain a better understanding of the Taverna documentation structure.

Taverna Workbench Documentation

Contents

  • Introduction
  • Available Documentation
  • Tools and Services
  • Orphaned Folders
    (Included in /documentation folder, but not described in index.md)
  • Questions/Comments

Introduction

See also Taverna Roadmap

Taverna Workbench is a redesign of the Taverna Workbench 1.7.x
series from the ground up. It has a greater emphasis on scalability
to enable the manipulation of larger and more diverse data.

In addition to the improvements to the engine, Taverna Workbench
provides more support for workflow design with a graphical workflow
editor for direct manipulation of the workflow diagram, context-
specific views over Web services and other resources, and standard
editing facilities such as copy/paste and undo/redo.

Available Documentation

Glossary

glossary
Glossary of terms and relevant links.

Quick Start Guide

quick-start-guide –Taverna 2.x
Brief summmary of how to use the Taverna Workbench to create, open,
and run workflows.

FAQ (Non-Apache Wiki)

http://dev.mygrid.org.uk/wiki/display/tav250/Frequently+Asked+Questions

User Manual (Non-Apache Wiki)

http://dev.mygrid.org.uk/wiki/display/tav250/User+Manual

components (since Taverna 2.5)
components — integrated feature of Taverna since Workbench 2.5.0 and Server 2.5.4
Creates shareable, reusable, encapsulated sub-workflows.
Folder contains component-profile-editor and component-validator.
(See Tools and Services)

interaction service (since Taverna 2.5)
interaction
Supports user interaction with workflows running on a server.

Tutorials

tutorials — Taverna 2
Links to introductory Taverna 2 tutorial, a webinar, and old video tutorials and wiki.

Videos

videos
Provides links to several videos.

Example Workflows to Help You Get Started with Taverna

example-workflows
Links to workflow examples on myexperiment.org website for Taverna 2.5,
2.4, 2.3, and 2.2.

Service Sets for Various Domains

service sets
Brief description of service sets and list of available service sets.

10 Best Practices for Workflow Design

http://www.slideshare.net/khettne/10-best-practices-for-workflow-design

Paper: How to Prevent Workflow Decay #####
http://ceur-ws.org/Vol-952/paper_23.pdf

Provenance Management in Taverna

provenance
Defines provenance, describes how provenance is handled in Taverna, and
discusses historical development of provenance and related research.

Taverna Command Line Tool and How To Use It

command-line-tool — latest non-Apache version 2.5
Runs Taverna 2.x workflows from terminal.

Taverna Server (REST API, SOAP API Explained)

and How To Use It
server — latest non-Apache release 2.5
Link to documentation for Taverna server 2.5 release.

Taverna Player

taverna-player
Web-based interface for executing existing workflows through the Taverna server.
Data supplied can be from creator or user, but workflows cannot be altered. Also
describes integration of Taverna Player into Web apps.

Various Plugins for Taverna

plugins — Taverna 2
Describes available Taverna 2 plugins and how to install.

Developer’s Wiki Containing Developer’s Guide and More

(Non-Apache Wiki)
http://dev.mygrid.org.uk/wiki/display/developer/Home

Tools and Services

There are a number of non-Apache tools and services available to use
with Taverna. (Some of these are in the incubator-taverna-site, so
shouldn’t they be Apache “tools” ?)

Component Profile Editor

component-profile-editor
Simple tool for creating and editing profiles for Taverna Components.
(See Available Documentation.)

Component Validator

component-validator
Tool for validating Taverna Components.

Data Viewer Tool for Viewing Result Data

dataviewer-tool — EXPERIMENTAL TBR
Utility for viewing Baclava files.

API Consumer Tool

api-consumer-tool — current version 1.1
Wraps Java for use in Taverna.

Taverna Galaxy

taverna-galaxy — Taverna 2
Describes initial integration of Taverna 2 with the Galaxy biomedical
research platform.

Taverna Online

online
Info about Russian Academy of Sciences (IITP) project to create and run
Taverna workflows from a browser.

Orphaned Folders in /documentation

command-line
(Appears to be describing the same item as the above command line tool,
but in more detail.)

Runs Taverna workflows from a terminal. Describes command in some detail.

scufl2 — Taverna 3
New mechanism for specifying Taverna workflows. Defines a model,
workflow bundle file format (wfbundle), and a Java API for working with
workflow structures. SCUFL2 is the workflow language for Taverna 3,
and replaces Taverna 2’s t2flow format. (Folder contains many additional
documentation files. See separate list – not yet started.)

training-and-workshops
Lists ways to get training and provides contact information.

web-services-developers
How to create web services that are compatible with Taverna.

Questions/Comments

  1. Is there a way to isolate old/experimental documentation on the incubator-taverna-site?

Apache Taverna Language Command Line – Conversion File Type Mapping

UNOFFICIAL, PUBLIC WORKING DRAFT.

The Apache Taverna Language Command Line tool development is in progress. Currently, the supported file type conversions are as follows:

Input File Type Allowable Output File Types Comments
.t2flow .iwir Taverna 2 input.
.t2flow .json Taverna 2 input.
.t2flow .structure Taverna 2 input.
.t2flow .wfbundle Taverna 2 input.
.t2flow .wfdesc.ttl Taverna 2 input. Development in progress.
.wfbundle .iwir Taverna 3 input.
.wfbundle .json Taverna 3 input.
.wfbundle .structure Taverna 3 input.
COMBINE Archive (OMEX) .robundle See [1] below.

[1] When converting COMBINE Archive (OMEX) files, the support for recursive conversion or for selecting the output file directory in not yet included.

[Updated 2015-06-29]

Apache Taverna Language Command Line – Convert Examples

UNOFFICIAL, PUBLIC WORKING DRAFT.

Please see convert command description blog post.

Examples 1 – 4 are for non-recursive (simple) conversions and examples 5 – 7 are for recursive conversions.

Example 1: Simple conversion, single input file, no options

$tavlang convert –-json /someFile1.t2flow

Converts /someFile1.t2flow into .json format and saves the output file to the /converted folder in the current working directory.

Resulting output file:
/converted/someFile1.json

Example 2: Simple conversion, multiple input files, no options

$tavlang convert –-structure /someFile1.t2flow /someFile2.t2flow

Converts /someFile1.t2flow and /someFile2.t2flow into .structure format and saves the output files to the /converted folder in the current working directory.

Resulting output files:
/converted/someFile1.structure
/converted/someFile2.structure

Example 3: Simple conversion, single file, specify output directory

$tavlang convert –-structure –o /output-dir /someFile1.t2flow

Converts /someFile1.t2flow into .structure format and saves the output file to the specified output directory.

Resulting output file:
/output-dir/someFile1.structure

Example 4: Simple conversion, single file, validate before conversion, specify output directory

$tavlang convert –-iwir –V –o /output-dir /someFile1.t2flow

Validates and then converts /someFile1.t2flow into .iwir format and saves the output file to the specified output directory.

Resulting output file:
/output-dir/someFile1.iwir

Example 5: Recursive conversion & specify input file directory, no output directory

$tavlang convert –-wfbundle –r –i /home/username/toConvert/

Converts all files in the /home/username/toConvert/ directory into .wfbundle format and saves the output files to the /converted folder in the input file directory.

Resulting output files:
/home/username/toConvert/converted/someFile1.wfbundle
/home/username/toConvert/converted/someFile2.wfbundle
/home/username/toConvert/converted/someFile3.wfbundle

etc. for all files in the input file directory.

Example 6: Recursive conversion & specify input file directory, specify output directory

$tavlang convert –-wfdesc –r –i /home/username/toConvert/
-o /home/username/convertedFiles/

Converts all files in the /home/username/toConvert/ directory into .wfdesc.ttl format and saves the output files to the specified output file directory.

Resulting output files:
/home/username/convertedFiles/someFile1.wfdesc.ttl
/home/username/convertedFiles/someFile2.wfdesc.ttl
/home/username/convertedFiles/someFile3.wfdesc.ttl

etc. for all files in the input file directory.

Example 7: Same as Example 6, with validation (Recursive conversion & specify input file directory, specify output directory, with validation)

$tavlang convert –-json –V –r –i /home/username/toConvert/ -o /home/username/convertedFiles/

Validates and then converts all files in the /home/username/toConvert/ directory into .json format and saves the output files to the specified output file directory.

Resulting output files:
/home/username/convertedFiles/someFile1.json
/home/username/convertedFiles/someFile2.json
/home/username/convertedFiles/someFile3.json

etc. for all files in the input file directory.

[Edited 2015-06-26]

Apache Taverna Language Command Line — Convert Command

UNOFFICIAL, PUBLIC WORKING DRAFT.

The following conversion options are available when running the Taverna Language Command Line tool.

usage: tavlang convert output-format [options] [input-file-list]

Options:
-i,--input Specify input file directory
-o,--output Specify output file directory
-r,--recursive Execute command recursively
-V,--validate Validate workflow before conversion
-- Indicate end of options list (optional)
Output-format:
--iwir Output workflow as .iwir
--json Output workflow as .json
--robundle Output bundle as .robundle
--structure Output workflow as .structure
--wfbundle Output bundle as .wfbundle
--wfdesc Output workflow as .wfdesc.ttl

The Apache Taverna Language provides a set of APIs for converting and managing workflow bundles and Research Object bundles. The Taverna Language Command Line tool invokes those methods in a console interface.

The command line tool converts .t2flow and .wfbundle file formats into either .structure, .json, .iwir, .wfbundle, .wfdesc.ttl (in progress), or .robundle (in progress) file formats. The convert command can be invoked on single or multiple files. Input files are specified two ways: (1) by listing the file(s) in the command line – separated by spaces – or (2) by specifying the input file directory (recursive option). (The input file type is auto-guessed by WorkflowBundleIO.)

Option Usage
-i Specifies the input file directory for recursive conversions.
Example:

 $tavlang convert --json –r –i /inputdir
-o Specifies the output file directory. If not used, converted files will be saved to the /converted folder in the current working directory.
Example:

 $tavlang convert --structure –o/outputdir /input.t2flow
-r Executes the command recursively on all workflows.
Example:

$tavlang convert --wfbundle –r –i /inputdir
-V Validates the workflow before conversion.
Example:

 $tavlang convert –-json –V /input.t2flow
--
Separates command line options from argument lists.

See separate post for examples. [Edited, 2015-06-26]