[MOBY-dev] question to ask

[Chunyan Wang]

Hi Mark,
I have a question to ask you:
I made my service can take a large input sequences (1000 to 5000 DNA) in 
XML format. I use "./build/run/run-cmdline-client -scall search_Pfam 
../../../JMOBY2/DNASEQ/input_1000" to test this service. The input_1000 
contains 1000 DNA sequences in XML format. This service takes 3 mins and 
34 seconds to parse the input file, and terminated after 3 mins and 41 
seconds, then I got the error message as the following:

===ERROR===
org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[string: null]
Fault string: (0)null
Fault code:   {http://xml.apache.org/axis/}HTTP
Fault actor:  null
When calling:
    http://moby.ucalgary.ca/cgi-bin/MobyEd_dispatcher.cgi
===========

    at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:196)
    at org.biomoby.client.CentralImpl.call(CentralImpl.java:1422)
    at MobyCmdLineClient.main(MobyCmdLineClient.java:641)
===========

I thought the service got time out, so I changed "call.setTimeout(new 
Integer (0)" to "call.setTimeout(new Integer (600000)" in the 
"CentralImpl.java", then recompiled and I tested the service again, but 
still got same message. However,  the big problem which I have right now 
is the service will be terminated after around 4 mins. I want to delay 
the timeout time. If you can, could you let me know is there anyway 
which I can solve this problem. Now I just tested on 800 and 1000 
sequences. The 800 sequences worked fine, but not 1000 sequences. please 
help me if you can. I know you are very busy.
Thanks so much!

Joyce