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myExperimentBeanshellCollection

Workflow Entry: myExperimentBeanshellCollection

Created at: 06/03/08 @ 11:46:11 Last updated: 25/03/08 @ 16:23:24

Version 2 (latest) (of 2)

Version created on: 06/03/08 @ 11:46:11 by: Pieter Neerincx | Revision comments Expand

Last edited on: 25/03/08 @ 16:23:24 by: Pieter Neerincx

Title: myExperimentBeanshellCollection

Type: Taverna 1

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Description

Public collection of generic Beanshells curated by the myExperimentBeanshellCollection group on myExperiment. Visit http://www.myexperiment.org for details and updates.

To use this collection of beanshells in Taverna:

Right click "Available Processors" in the "Design Perspective"
Choose "Add new Workflow scavenger..."
Provide the URL to this beanshell collection on www.myExperiment.org or if you downloaded this to your hard disk, provide a "file" URL to the absolute path of this file (On Linux/Unix/Mac: file:///some/path/on/my/disk/myExperimentBeanshellCollection.xml) (On Windows: file:///drive_letter:/My%20Documents/myExperimentBeanshellCollection.xml)

* You can select Beanshells from this scavenger now and add them to your workflow like any other processor.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/169/download?version=2
[ More Info Expand ]

Workflow Components

Inputs (0)

Processors (3)

Name	Type	Description
DecodeBase64EncodedSVGZ	beanshell	This Beanshell script first decodes the Base64 encoded input followed by unzipping. Originally designed for extracting SVG images from Base64 encoded SVGZ service outputs, but it could be used for parsing any other zipped and afterwards base64 encoded service output.
DownloadToDiskFromURLWithBasicAuth	beanshell	This Beanshell downloads a file to disk. The standard download local Java widgets don't handle URLs with HTTP(S) Basic Authentication, but this Beanshell can. When a webserver uses BasicAuth, a login and password can be coded as part of the URL using the following syntax: http(s)://login:password@www.some.website/my/great/tool/result.xml. This beanshel extracts the login and password from the URL and supplies them automatically to the webserver. This prevents Taverna from showing popup dialogs requesting the login and password from the user as this will be problematic for large workflows. Please note that the path where the downloaded file will be stored must be an absolute path to a folder ended with a slash. (Slash backward on Windows or a slash forward on Linux/Unix/Mac OS X.) The filename for the result is automatically extracted from the URL.
SelectItemsFromList	beanshell	Allows the user to select items from a given list to be analysed by processors downstream from this Beanshell script as a step of the workflow.

Beanshells (3)

Name	Description	Inputs	Outputs
DecodeBase64EncodedSVGZ	This Beanshell script first decodes the Base64 encoded input followed by unzipping. Originally designed for extracting SVG images from Base64 encoded SVGZ service outputs, but it could be used for parsing any other zipped and afterwards base64 encoded service output.	Base64EncSVGZ	Message Decoded SVG
DownloadToDiskFromURLWithBasicAuth	This Beanshell downloads a file to disk. The standard download local Java widgets don't handle URLs with HTTP(S) Basic Authentication, but this Beanshell can. When a webserver uses BasicAuth, a login and password can be coded as part of the URL using the following syntax: http(s)://login:password@www.some.website/my/great/tool/result.xml. This beanshel extracts the login and password from the URL and supplies them automatically to the webserver. This prevents Taverna from showing popup dialogs requesting the login and password from the user as this will be problematic for large workflows. Please note that the path where the downloaded file will be stored must be an absolute path to a folder ended with a slash. (Slash backward on Windows or a slash forward on Linux/Unix/Mac OS X.) The filename for the result is automatically extracted from the URL.	URL Path	Downloaded Message
SelectItemsFromList	Allows the user to select items from a given list to be analysed by processors downstream from this Beanshell script as a step of the workflow.	inputList	outputList

Outputs (0)

Links (0)

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Pieter Neerincx

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

myExperimentBeanshellCollection

Information Attributions (0)

(Workflows/Files)

None

Information Tags (2)

Original Uploader tags

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Information Shared with Groups (1)

myExperimentBeanshellCollection

Information Featured In Packs (0)

None

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Information Ratings (1)

Current:

5.0 / 5

(1 rating)

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Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (1)

Sven

Information Statistics

1075 viewings

1289 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - myExperimentBeanshellCollection

Created on: Thursday 06 March 2008 @ 11:46:11 (GMT)

Created by: Pieter Neerincx

Last edited on: Thursday 06 March 2008 @ 11:46:12 (GMT)

Last edited by: Pieter Neerincx

Revision comments:

None

Latest Version:
[2] - myExperimentBeanshellCollection

Created on: Thursday 06 March 2008 @ 11:46:11 (GMT)

Created by: Pieter Neerincx

Last edited on: Tuesday 25 March 2008 @ 16:23:24 (GMT)

Last edited by: Pieter Neerincx

Revision comments:

Added a new beanshell script which provides a basic form of user interaction in a workflow. The beanshell script pops up a window which allows the user to select items from a given input list for further analysis by downstream processors.