Workflow Entry: Download Entries from PubChem

Created at: 30/03/09 @ 09:20:42 Last updated: 30/03/09 @ 09:34:37

Version 1 (of 1)

Version created on: 30/03/09 @ 09:20:42 by: Michael Gerlich | Revision comments Expand

Last edited on: 30/03/09 @ 09:34:38 by: Michael Gerlich

Title: Download Entries from PubChem

Type: Taverna 1

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Description

Given a list of identifiers (e.g. CID) and their appropriate type (eID_CID - note that these differ slightly from the original identifier name -> CID <-> eID_CID), this workflow queries PubChem via PUG to retrieve a download URL for the resulting XML file containing the results.

Adding support for downloading this XML file and writing it to filesystem is planned.

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/737/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
ID	1, 2, 3, 4, 5, 6, 7, 8, 9, 10
idType	eID_CID

Processors (12)

Name	Type	Description
Compression	stringconstant
Format	stringconstant
Download_out	local
GetDownloadUrl_in	local
InputListText_in	local
GetDownloadUrl_out	local
InputListText_out	local
Download_in	local
GetDownloadUrl	arbitrarywsdl	Given a download key, return an FTP URL that may be used to download the requested file. Synchronous.
InputListText	arbitrarywsdl	Input a set of identifiers for a PubChem database, as a simple string of integer values separated by commas and/or whitespace. Returns a list key. Synchronous.
Download	arbitrarywsdl	Given a list key, prepare for download a file containing those records in the selected format. See the web download service documentation (http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html) for more detail on the supported formats and file types. Returns a download key. Asynchronous.
Status_Check	workflow

Beanshells (1)

Name	Description	Inputs	Outputs
CheckForSuccess		status	success

Outputs (1)

Name	Description
URL

Links (14)

Source	Sink
Compression:value	Download_in:eCompress
Download:parameters	Download_out:input
Download_in:output	Download:parameters
Download_out:DownloadKey	Status_Check:KeyIn
Format:value	Download_in:eFormat
GetDownloadUrl:parameters	GetDownloadUrl_out:input
GetDownloadUrl_in:output	GetDownloadUrl:parameters
ID	InputListText_in:ids
InputListText:parameters	InputListText_out:input
InputListText_in:output	InputListText:parameters
InputListText_out:ListKey	Download_in:ListKey
Status_Check:KeyOut	GetDownloadUrl_in:DownloadKey
idType	InputListText_in:idType
GetDownloadUrl_out:url	URL