[Bioperl-l] No error message is given for a warning (EUtilities)

Peng Yu pengyu.ut at gmail.com
Sat Jul 10 21:40:47 EDT 2010


Hi,

I have the following warnings and perl program. I don't understand why
there is a warning and what the error is. The ncbi's eutils url seems
OK. If shrink $term (see the code), then the warning is gone. Could
somebody let me know what the problem is with my bioperl code?

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000

$ ./main.pl |head

--------------------- WARNING ---------------------
MSG: NCBI esearch Errors/Warnings:
Error :
---------------------------------------------------
241
<?xml version="1.0" ?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May
2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">
<eSearchResult><Count>241</Count><RetMax>241</RetMax><RetStart>0</RetStart><IdList>
		<Id>20616305</Id>
		<Id>20581223</Id>
		<Id>20572313</Id>
		<Id>20564721</Id>
		<Id>20554763</Id>
		<Id>20542744</Id>
$ cat main.pl
#!/usr/bin/env perl

use strict;
use warnings;
use Bio::DB::EUtilities;

my $factory = Bio::DB::EUtilities->new(
  -eutil => 'esearch',
  -db => 'pubmed',
  -email => 'mymail at foo.bar',
  #-term => 'anoxia[mh] AND neoplasms[mh]',
  #-term => 'small ubiquitin-related modifier proteins[mh]',
  -term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab]
OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR
hCaCC-1[tiab]',
  #-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink
$term, then the warning is gone.
  -retmode => 'xml',
  -retmax => 1000000,
);

print $factory->get_retmax,"\n";
print $factory->get_Response->content;


-- 
Regards,
Peng


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