Download Entries from PubChem

Created: 2009-03-30 09:20:42 Last updated: 2009-03-30 09:34:37

Download Workflow

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.

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Option 1:

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http://www.myexperiment.org/workflows/737/download?version=1
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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

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Michael Gerlich

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Michael Gerlich

Information Attributions (0)

(Workflows/Files)

None

Information Tags (4)

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Information Attributed By (1)

(Workflows/Files)

Download Structures from PubChem given chemical names

Information Favourited By (0)

No one

Information Statistics

2952 viewings

2132 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Download Entries from PubChem

Created by Michael Gerlich on Monday 30 March 2009 09:20:42 (UTC)

Last edited by Michael Gerlich on Monday 30 March 2009 09:34:38 (UTC)

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