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REPuter - WebService

This is a short introduction using REPuter WebServices offered by BiBiServ. If you're not familiar with using webservices in general you should have a closer look to our webservice related linklist.

WSDL - methods, parameters and datatypes

If you've a closer look at the WSDL file describing the REPuter webservice, you can see two pairs of methods belonging together.

request and response
request_orig and response_orig

Bioinformatic programs often perform computation on large data sets and therefore require much CPU time. This can cause problems like http connection timeouts (usually after 5 minutes) during online usage. To avoid such problems when using REPuter WebService we use a technique called Request and Reply with polling based on BiBiWS. First the client side (e.g. your program) requests a REPuter job submitting the necessary data (parameter and data) and gets an id after the job is started. Afterwards the client can request the result by calling the corresponding response method with the id returned earlier. If the REPuter job is not finished, the user gets a status code with an enhanced description of current status back (see HOBIT status codes for more information).

The request method gets three parameters as input - a parameter array with key/value pairs as described in the following table , a (multiple) sequence file in FASTA format and a email address (optional) - and returns either a unique id or in case of an error a fault message.

key value description
sequencetype dna|protein|smap type of input sequences
smap String optional
direct true|false compute direct matches
palindromic true|false computes palindromic (reverse complemented) matches
length > 7 minimal match length
hamming 0..5 allowed hamming distance
edit 0..5 allowed edit distance
best 5000 show the best matches
content true|false show the alignment of matching sequences
identity 60..100 minimum identity of match
evalue double maximum E-value of a match

The response method gets the id returned by the request method as input parameter and returns the calculated result as EBI application xml document ( aware). The current version of the schema defines some tags as "must have", which are not needed by REPuter:

  • xml output is generated from REPuter output on the fly, so the attribut total of tag hits contains -1 and NOT the real number of computed repeats
  • Without switch content (see above table), the tags querySeq, pattern and matchSeq contain no sequence/pattern data
  • If switch content is set (see above table) and the repeat identity is 100%, only querySeq is returned to save space (pattern and matchSeq contains no data)

The request_orig method has the same parameter and return value as the request method.

The response_orig gets the id returned by the request_orig method as input parameter returns the result as original ascii text.

Example Perl client

The example perl client implementation for both methods request and response is based on SOAP::Lite.

REPuter_request (download)
The implementation of the request method is quite simple. The sequence data and all necessary parameters are hard coded in the script - we search for all direct and palindromic repeats of length 8 with hamming distance of 1. The returned id will be printed to STDOUT.

REPuter_response (download)
The response method gets the previous returned id and returns an xml document containing the result or, if the job is not finished yet, a statuscode with description.

sample run

ID - bibiwsserv_2005-03-02_123113_D0oFZ

>./ bibiwsserv_2005-03-02_123113_D0oFZ
Description:602: PreProcessing
>./ bibiwsserv_2005-03-02_123113_D0oFZ
Description:603: Processing: Pending
>./ bibiwsserv_2005-03-02_123113_D0oFZ
Description:604: Processing: Running
>./ bibiwsserv_2005-03-02_123113_D0oFZ
<?xml version="1.0"?>
<EBIApplicationResult xmlns="" 

Example Java client

The Example Java client (download)is based on Apache Axis and combines both methods (request and response) through active waiting. The example needs following libs installed:
project download url tested release
Apache AXIS download 1.2RC3
JavaBeans Activation Framework (JAF) download 1.0.2
JavaMail download 1.3.2

$Date: 2006/04/05 10:28:01 $

Wed Apr 3 16:19:55 2013