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DIALIGN - WebService

This is a short introduction using DIALIGN 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 DIALIGN webservice, you can see two pairs of methods belonging together.

request and response
request_orig and response_orig

Bioinformatics 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 DIALIGN WebService we use a technique called Request and Reply with polling based on BiBiWS. First the client side (e.g. your program) requests a DIALIGN 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 DIALIGN 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).

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

key type value description
sequenceMode String n|nt n : Nucleotide Sequence (w/o translation)
nt : Nucleotide Sequence (with translation) (optional)
threshold Integer 0 - 10 see manual (optional)
stars Integer 0 - 15, 5 maximum number of `*' characters indicating
degree of local similarity among sequences (optional)

response_orig
The response_orig gets the id returned by the request and request_orig methods as input parameter and returns the original DIALIGN result as ASCII text.

request
The request method has the same parameters and return value as the request_orig method except the sequences which have to be in SequenceML xml format (http://hobit.sourceforge.net/xsds/20060201/sequenceML.xsd).

response
The response method gets the id returned by the request and request_orig methods as input parameter and returns the calculated result as a AlignmentML xml document (http://hobit.sourceforge.net/xsds/20060201/alignmentML.xsd).

Example Perl client

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

request_orig (download)
The implementation of the request_orig method is quite simple. Simply call request_orig.pl with a filname as a parameter. If no error occured, a bibiid will be printed to STDOUT.

response_orig (download)
If you want to recieve the result of your DIALIGN run, call response_orig.pl with a valid bibiid (retrieved by request_orig) as a parameter. If no error occured, the DIALIGN result will be printed to STDOUT.

Example Java client

The example Java client implements the request/replywith polling technique using the XML based methods (response and request) and is based on Apache Axis (tested with Version 1.3)
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Fri Dec 14 12:50:24 2012