Decomp – WebService

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BiBiServ -
Bielefeld University Bioinformatic Service

Decomp – WebService

This is a short introduction using decomp WebServices offered by BiBiServ. If you're not familiar with using webservices in general you should have a closer look at our webservice-related link list.

WSDL – methods, parameters and datatypes

If you've a closer look at the WSDL file describing the decomp webservice, you can see two 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 decomp WebService we use a technique called Request and Reply with polling based on BiBiWS. First the client side (e.g. your program) requests a Decomp 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 Decomp job is not finished, the user gets back a status code with an enhanced description of current status (see HOBIT status codes for more information).

array_params parameter in request_orig

Key	Type	Accepted values	Default	Description
masses	string	`([\\.\\d, -]+)`		-
alphabet	string	`(upload\|custom\|nucleotide\|aminoacid\|atom)`		-
tool	string	`(imsdecomp\|imsintdecomp)`		What tool should be called: imsdecomp is the regular, real-valued decomposition tool and imsintdecomp is for the integer decomposition problem.
task	string	`(findall\|findone\|getnumber\|isdecomposable)`		If the parameter 'tool' is imsintdecomp, this gives the type of task to perform.
precision	float			The computational precision. This parameter is ignored if the parameter 'autoprecision' is true.
error	float		0.0	Allowed mass error.
errorunit	string	`(Da\|ppm)`	Da	Unit in which the allowed mass error is given.
massmode	string	`(mono\|average)`	average	Choose between monoisotopic and average isotopic masses.
autoprecision	boolean		false	Whether to determine the precision automatically or not.
minconstraints	string	`[A-Za-z0-9_']*`		Minimum constraints.
maxconstraints	string	`[A-Za-z0-9_']*`		Maximum constraints.
modifications	string			Modifications (Note: this is work in progress)
showmass	boolean		false	Show actual mass in output.
showdeviation	boolean		false	Show deviation from actual mass in output.
showplausible	boolean		false	Show only chemically plausible decompositions.
maxdecomps	int		1000	Maximum number of decompositions to show (sorted by mass error).

response_orig
The response method gets the id returned by the request method as input parameter and returns the calculated result as String