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services:sfc:readseq_rest [2012/09/05 09:23]
hpm (172.22.68.212) created
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-====== Readseq (REST) ====== 
-===== Important ==== 
- 
-Please note that this is a **beta service**, so please avoid using it in production environments. Please report any feedback or issues encountered to us via. [[http://www.ebi.ac.uk/support/index.php?query=WebServices|EMBL-EBI Support]]. 
- 
-We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 25 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime. 
- 
-Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the [[http://www.ebi.ac.uk/Information/termsofuse.html|EBI's Terms of Use]]. 
- 
-===== Description ===== 
- 
-Readseq reads and converts biosequences between a selection of common biological sequence formats, including EMBL, GenBank and fasta sequence formats. 
- 
-For more information see: 
-  * Web form: [[http://www.ebi.ac.uk/Tools/sfc/readseq/]] 
-  * [[.:Readseq (SOAP)|Document/literal SOAP service]] 
-  * [[http://iubio.bio.indiana.edu/soft/molbio/readseq/java/|Readseq home]] 
- 
-===== 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 ^ 
-^ Perl | ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/perl/lwp/readseq_lwp.pl|readseq_lwp.pl]]'' | [[http://search.cpan.org/perldoc?LWP|LWP]] and [[http://search.cpan.org/perldoc?XML::Simple|XML::Simple]] | 
- 
-For further details of these tool-kits and workflow platforms see our [[:tutorials:00_Contents|Guide to Web Services]]. 
- 
-===== Resources ===== 
- 
-==== parameters ==== 
- 
-List parameter names. 
- 
-**Request** 
- 
-^ URL        | http://www.ebi.ac.uk/Tools/services/rest/readseq/parameters/ | 
-^ Parameters  | //none// | 
- 
-**Response** 
- 
-An XML document containing a list of parameter names. 
- 
-For example: http://www.ebi.ac.uk/Tools/services/rest/readseq/parameters/ 
- 
-==== parameterdetails ==== 
- 
-Get detailed information about a parameter. 
- 
-**Request** 
- 
-^ URL        | http://www.ebi.ac.uk/Tools/services/rest/readseq/parameterdetails/$parameterId | 
-^ Parameters  | ''$parameterId'': the name of the parameter | 
- 
-**Response** 
- 
-An XML document providing details about the parameter. 
- 
-For example: http://www.ebi.ac.uk/Tools/services/rest/readseq/parameterdetails/inputformat. 
- 
-==== run ==== 
- 
-Submit a job with the specified parameters. 
- 
-**Request** 
- 
-^ URL        | http://www.ebi.ac.uk/Tools/services/rest/readseq/run/ || 
-^ POST        | ''email''        | User e-mail address. | 
-^            | ''title''        | an optional title for the job. | 
-^            | ''inputformat''  | sequence format for input data | 
-^            | ''outputformat'' | sequence format for output data | 
-^            | ''outputcase''  | character case for output sequence data | 
-^            | ''reverse''      | output reverse complement of input nucleotide sequence | 
-^            | ''degap''        | remove gap symbols from sequence | 
-^            | ''transymbol''  | replace specified base/residue symbol(s) in input sequence with specified base/residue symbol(s) | 
-^            | ''feature''      | set of selected features to process | 
-^            | ''fthandle''    | action to perform on selected features | 
-^            | ''subrange''    | region of input sequence on which feature processing is performed | 
-^            | ''sequence''    | input sequence data to process  | 
- 
-More detailed information about each parameter, including valid values can be obtained using the [[#getParameterDetails(parameterId)]] operation. 
- 
-**Response** 
- 
-A plain text document containing the job identifier. 
- 
-==== status ==== 
- 
-Get the status of a submitted job. 
- 
-**Request** 
- 
-^ URL        | http://www.ebi.ac.uk/Tools/services/rest/readseq/status/$jobId | 
-^ Parameters  | ''$jobId'': job identifier | 
- 
-**Response** 
- 
-A plain text document containing the job status. 
- 
-The values for the status are: 
-  * ''RUNNING'': the job is currently being processed. 
-  * ''FINISHED'': job has finished, and the results can then be retrieved. 
-  * ''ERROR'': an error occurred attempting to get the job status. 
-  * ''FAILURE'': the job failed. 
-  * ''NOT_FOUND'': the job cannot be found. 
-Further details can be found in [[:tutorials:01_intro#jdispatcher|Synchronous and Asynchronous Access: JDispatcher]]. 
- 
- 
-==== resulttypes ==== 
- 
-Get available result types for a finished job. 
- 
-**Request** 
- 
-^ URL        | http://www.ebi.ac.uk/Tools/services/rest/readseq/resulttypes/$jobId | 
-^ Parameters  | ''$jobId'': job identifier | 
- 
-**Response** 
- 
-An XML document detailing the available result types. 
- 
-==== result ==== 
- 
-Get the job result of the specified type. 
- 
-**Request** 
- 
-^ URL        | http://www.ebi.ac.uk/Tools/services/rest/readseq/result/$jobId/$resultType | 
-^ Parameters  | ''$jobId'': job identifier | 
-^            | ''$resultType'': type of result to retrieve. See [[#resulttypes]]. | 
- 
-**Response** 
- 
-A document containing the result in the requested format. The MIME type of the returned document is set according to the format. 
 
services/sfc/readseq_rest.1346833414.txt · Last modified: 2012/09/05 09:23 by hpm
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