In the
WSDL file describing
the pknotsRG webservice, there are five methods defined
(request,request_orig, response, response_orig and getVersion).
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
pknotsRG WebService we use a technique called Request and
Reply with polling based on BiBiWS. First the client side
(e.g. your program) requests a pknotsRG 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 pknotsRG 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).
Currently the pknotsRG WebService support two different pairs
of request/response methods, request/response using sequenceML as Input and RNAStructML as output format. Both
formats are supported by BioDOM. The
request_orig/response_orig pair deals with the original data
formats (Fasta as Input and a DotBracket Notation as
Output).
request/request_orig
The request method get two parameters as input - a parameter
array with key/value pairs as described in the following table
and a valid sequenceML document (request) or one or
more sequences in FASTA format (request_orig) - and returns
either a unique id or in case of an error a fault
message.
| key |
value |
description |
| strategy |
m,f,l |
strategy used by pknotsRG |
| s |
|
show suboptimals |
| c |
0.0 ≤ 3.0 |
set energy range for suboptimals (%) |
| n |
positive double value |
set npp-value |
| k |
positive integer value |
set maximal pknot-length |
| p |
positive integer value |
set pkinit-value |
response/response_orig
The response/response_orig methods gets the id returned by the
request method as input parameter and returns the calculated
result as
RNAStructML or in DotBracket notation (Vienna format).
