EB-eye getAllResultIds and WSDbfetch fetchBatch

Created: 2013-03-28 12:34:14

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Get database entries for a query using EB-eye to perform the initial query against the database to get entry identifiers and using the identifiers with WSDbfetch to retrieve the entry data in the desired format.

Note: this particular implementation is not suitable for queries which return large numbers of results.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
Database_name	Name of database to query and fetch entry data from.
Query_string	Query to perform in database to find entries to retrieve.
Entry_data_format	Data format for the entries retrieved.

Processors (7)

Name	Type	Description
getAllResultsIds	wsdl	Query the database using EB-eye and get the entry identifiers matching the query. Note: should not be used for large query results. Wsdl http://www.ebi.ac.uk/ebisearch/service.ebi?wsdl Wsdl Operation getAllResultsIds
getAllResultsIds_input	xmlsplitter
getAllResultsIds_output	xmlsplitter
fetchBatch	wsdl	Retrieve the entries for the identifier(s). Wsdl http://www.ebi.ac.uk/ws/services/WSDbfetchDoclit?wsdl Wsdl Operation fetchBatch
fetchBatch_input	xmlsplitter
fetchBatch_output	xmlsplitter
style_value	stringconstant	Value raw

Beanshells (0)

Outputs (2)

Name	Description
Entry_data	Data entries retrived for entry identifiers found by query.
Identifiers	Identifiers found by query in database.

Datalinks (12)

Source	Sink
getAllResultsIds_input:output	getAllResultsIds:parameters
Database_name	getAllResultsIds_input:domain
Query_string	getAllResultsIds_input:query
getAllResultsIds:parameters	getAllResultsIds_output:input
fetchBatch_input:output	fetchBatch:parameters
Database_name	fetchBatch_input:db
getAllResultsIds_output:arrayOfIds	fetchBatch_input:ids
style_value:value	fetchBatch_input:style
Entry_data_format	fetchBatch_input:format
fetchBatch:parameters	fetchBatch_output:input
fetchBatch_output:fetchBatchReturn	Entry_data
getAllResultsIds_output:arrayOfIds	Identifiers

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Information Workflow Type

Taverna 2

Information Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Apache License v2.0

Information Version 1 (of 1)

Information Credits (1)

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Hamish McWilliam

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Information Featured In Packs (1)

EMBL-EBI Web Services

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Information Statistics

719 viewings

614 downloads

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Version History

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EB-eye getAllResultIds and WSDbfetch fetchBatch

Created by Hamish McWilliam on Thursday 28 March 2013 12:34:14 (UTC)

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