Question: Using NCBIs EDirect to download pubmed abstract
0
gravatar for zorn21g
20 months ago by
zorn21g0
zorn21g0 wrote:

This is what I have done:

esearch -db pubmed -query "lycopene cyclase" | efetch -format abstract

I was struck by this error:

500 Can't connect to eutils.be-md.ncbi.nlm.nih.gov:443 (certificate verify failed)
No do_post output returned from 'https://eutils.be-md.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_67454450_130.14.18.34_9001_1529992046_810451412_0MetA0_S_MegaStore&rettype=abstract&retmode=text&retstart=0&retmax=100&edirect_os=linux&edirect=9.20&tool=edirect&email=zorn@ubuntu'
Result of do_post http request is
$VAR1 = bless( {
                 '_content' => 'Can\'t connect to eutils.be-md.ncbi.nlm.nih.gov:443 (certificate verify failed)

LWP::Protocol::https::Socket: SSL connect attempt failed with unknown errorerror:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed at /usr/share/perl5/LWP/Protocol/http.pm line 51, <STDIN> line 7.
',
                 '_rc' => 500,
                 '_headers' => bless( {
                                        'client-warning' => 'Internal response',
                                        'client-date' => 'Tue, 26 Jun 2018 05:47:26 GMT',
                                        'content-type' => 'text/plain'
                                      }, 'HTTP::Headers' ),
                 '_msg' => 'Can\'t connect to eutils.be-md.ncbi.nlm.nih.gov:443 (certificate verify failed)',
                 '_request' => bless( {
                                        '_content' => 'db=pubmed&query_key=1&WebEnv=NCID_1_67454450_130.14.18.34_9001_1529992046_810451412_0MetA0_S_MegaStore&rettype=abstract&retmode=text&retstart=0&retmax=100&edirect_os=linux&edirect=9.20&tool=edirect&email=zorn@ubuntu',
                                        '_uri' => bless( do{\(my $o = 'https://eutils.be-md.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi')}, 'URI::https' ),
                                        '_headers' => bless( {
                                                               'user-agent' => 'libwww-perl/6.03',
                                                               'content-type' => 'application/x-www-form-urlencoded'
                                                             }, 'HTTP::Headers' ),
                                        '_method' => 'POST'
                                      }, 'HTTP::Request' )
               }, 'HTTP::Response' );
pubmed tool edirect ncbi • 731 views
ADD COMMENTlink modified 20 months ago by finswimmer13k • written 20 months ago by zorn21g0

Hmm,

works here. Just a temporary problem?

fin swimmer

ADD REPLYlink written 20 months ago by finswimmer13k

I have try many times. T_T

ADD REPLYlink written 20 months ago by zorn21g0

Works here too. From where did you try this?

ADD REPLYlink written 20 months ago by WouterDeCoster42k

network failure? I work in China.

ADD REPLYlink written 20 months ago by zorn21g0

You should ensure that you're using the most recent version of the eutils. Do you get the same error when you try searching against any other databases?

ADD REPLYlink written 20 months ago by Sej Modha4.6k

The same error when I try SRA database

ADD REPLYlink written 19 months ago by zorn21g0
1

This could be related to some local firewall restrictions (which you may have no control over). Perhaps you could talk with your network people. eUtils are working as expected.

ADD REPLYlink written 19 months ago by genomax78k

Thanks. I will change networks and try again.

ADD REPLYlink written 19 months ago by zorn21g0
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