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[bioontology-support] problem doing large queries

Xin.H hxin87 at gmail.com
Thu Oct 24 09:14:23 PDT 2013


Hi,

I was using the Annotator to map some text into Human Disease Ontology.
There are about 55000 rows' text and I need to do it for every row so it
takes a long time. During the query, I noticed some errors that appear
occasionally which are hard to make an example to repeat. The script is
still running so I assume that it just ignore this problem rows?

Here are the different errors I got:

<h1>Internal Server Error</h1> at Thu Oct 24 00:04:27 2013

Status read failed: Connection reset by peer at
/usr/share/perl5/Net/HTTP/Methods.pm line 269.
 at Thu Oct 24 01:36:17 2013

Server closed connection without sending any data back at
/usr/share/perl5/Net/HTTP/Methods.pm line 345.
 at Thu Oct 24 13:14:25 2013

Can't connect to data.bioontology.org:80 (No route to host)
LWP::Protocol::http::Socket: connect: No route to host at
/usr/share/perl5/LWP/Protocol/http.pm line 51.
 at Thu Oct 24 16:17:54 2013

These seem to be connection problem so I was wondering if this is
caused losing connection during the long time query? I once used ENSEMBL
API to do large queries and there provide a method to allow reconnecting if
time out without breaking the script. I was wondering if the Annotator
provide similar API? Or is that another way to do big queries?

Many thanks,
Xin
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