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EBIEBI Web Servicesservicesdbfetch

WSDbfetch (SOAP)

Description

WSDbfetch allows you to retrieve entries from various up-to-date biological databases using entry identifiers or accession numbers. This is equivalent to the CGI based dbfetch service. Like the CGI service a request can return a maximum of 200 entries.

For more information see:

Clients

Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language Download Requirements
C# .NET Executable: wsdbfetch.exe; Source: wsdbfetch.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: WSDbfetch.jar; Source: WSDbfetchClient.java Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in lib-1.4.zip.
Perl dbfetch.pl SOAP::Lite
PHP wsdbfetch_cli_nusoap.php nuSOAP/nusoap-for-php5
wsdbfetch_cli_pear_soap.php PEAR SOAP
wsdbfetch_cli_php_soap.php PHP SOAP
Python wsdbfetch.py SOAPpy
wsdbfetch_zsi.py ZSI 2.0
Ruby wsdbfetch.rb soap4r
VB.NET .NET Executable: wsdbfetch.exe; Source: wsdbfetch.vb A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.

For further details see WSDbfetch Clients.

WSDL

http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl

Service API

fetchBatch(db, ids, format, style)

Fetch a set of entries in a defined format and style.

Arguments:

  • db: the name of the database to obtain the entries from. For example: “uniprotkb”
  • query: a string containing a comma separated list of entry identifiers. For example: “WAP_MOUSE,WAP_RAT”
  • format: the name of the format required. To get the default format for the database use the value “default”.
  • style: the name of the style required. To get the default style for the database use the value “default”.

Returns: an array of strings containing the entries. Generally this will contain only one item which contains the set of entries.

Throws:

fetchData(query, format, style)

Fetch an entry in a defined format and style.

Arguments:

  • query: the entry identifier in db:id format. For example: “UniProtKB:WAP_RAT”
  • format: the name of the format required. To get the default format for the database use the value “default”.
  • style: the name of the style required. To get the default style for the database use the value “default”.

Returns: an array of strings containing the entry. Generally this will contain only one item which contains the whole entry.

Throws:

getDbFormats(db)

Get a list of format names for a given database.

Arguments:

  • db: database name to get available formats for. For example: “uniprotkb”

Returns: an array of strings containing the format names.

Throws:

getFormatStyles(db, format)

Get a list of style names available for a given database and format.

Arguments:

  • db: database name to get available styles for. For example: “uniprotkb”
  • format: the data format to get available styles for. For example: “fasta”

Returns: an array of strings containing the style names.

Throws:

getSupportedDBs()

Get a list of database names usable with WSDbfetch.

Arguments: none

Returns: an array of strings containing the database names.

getSupportedFormats()

Get a list of database and format names usable with WSDbfetch.

Arguments: none

Returns: an array of strings containing the database and format names. For example: 

uniprotkb       default,fasta,uniprot,uniprotxml

getSupportedStyles()

Get a list of database and style names usable with WSDbfetch.

Arguments: none

Returns: an array of strings containing the database and style names. For example: 

uniprotkb       default,html,raw

DbfException

Generic exception used for errors thrown by the WSDbfetch service.

Subclasses:

DbfParamsException

Exception indicating that the input parameters failed to validate. The message contains specific information about the cause. For example: 

  • uk.ac.ebi.jdbfetch.exceptions.DbfParamsException: Database, wibble , not found!
  • uk.ac.ebi.jdbfetch.exceptions.DbfParamsException: No database found for the job:
Job: 
        Database name: wibble
        Style: raw
        Format: default
        IDs:    blah

Parent class: DbfException

DbfConnException

Exception indicating that there was a problem contacting the database to retrieve the requested data. For example: 

uk.ac.ebi.jdbfetch.exceptions.DbfConnException: Unexpected error when opening stream on the URL, please contact support@ebi.ac.uk

Parent class: DbfException

DbfNoEntryFoundException

Exception indicating that no entries were found in the database which matches the request. For example: 

uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException: No result found

Common causes of the error include:

  • Invalid identifier used for the specified database. For example: EMBL-Bank does not contain entries with RefSeq identifiers (e.g. XM_002123246).
  • Use of an identifier which is not supported for the specified database. For example: the EMBL-Bank query used by WSDbfetch does not support sequence versions (e.g. L12345.1) instead the accession (e.g. L12345) should be used, or the archive database EMBL-SVA, which does support sequence versions, should be queried.

Parent class: DbfException

InputException

Exception indicating that required parameters were not specified, or were in an incorrect format. For example: 

  • uk.ac.ebi.jdbfetch.ws.wsdbfetch.InputException: The 'query' argument doesn't contain ':'. Proper format= DBNAME:ID
  • uk.ac.ebi.jdbfetch.ws.wsdbfetch.InputException: No database found in the query
  • uk.ac.ebi.jdbfetch.ws.wsdbfetch.InputException: No ID found in the query

Contact

If you have any questions, comments, if you plan to use this service as part of a course or for a high number of submissions, please contact us via EBI Support.

 
services/dbfetch.txt · Last modified: 2009/12/14 10:49 (external edit)
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