Question: get() function fatal error while using Entrez Eutilities
0
gravatar for vigprasud
4.9 years ago by
vigprasud60
United States
vigprasud60 wrote:

I am trying to use Entrez'z Eutilitiy for a text mining module. I tried using the sample snippets from the pubmed website.

use LWP::Simple;

# Download PubMed records that are indexed in MeSH for both asthma and 
# leukotrienes and were also published in 2009.

$db = 'pubmed';
$query = 'asthma[mesh]+AND+leukotrienes[mesh]+AND+2009[pdat]';

#assemble the esearch URL
$base = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/';
$url = $base . "esearch.fcgi?db=$db&term=$query&usehistory=y";

#post the esearch URL
$output = get($url);

 

I got get() function Fatal Error. I have the perl LWD module installed But I am still unable to solve this error. Can someone suggest me any error checking pointers?

ADD COMMENTlink modified 16 months ago by c0mput3rxz0 • written 4.9 years ago by vigprasud60

a problem with the proxy ?

ADD REPLYlink written 4.9 years ago by Pierre Lindenbaum119k

I dont see a problem with proxy..I let all the proxys access while installing the module and the firewall is also off. 

ADD REPLYlink written 4.9 years ago by vigprasud60

Also If I check in the command line with this command 

perl -MLWP::Simple -e 'getprint "http://www.sn.no"'

I get the XML version of the page. It is installed correctly but not working with php

ADD REPLYlink written 4.9 years ago by vigprasud60
0
gravatar for c0mput3rxz
16 months ago by
c0mput3rxz0
c0mput3rxz0 wrote:

NCBI updates to https. It is important to update calls to use https for example your base would be

$base = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/';
ADD COMMENTlink modified 16 months ago • written 16 months ago by c0mput3rxz0
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