Using NCBIs EDirect to download pubmed abstract
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0
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3.0 years ago
zorn21g • 0

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' );
NCBI edirect pubmed Tool • 1.2k views
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Hmm,

works here. Just a temporary problem?

fin swimmer

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I have try many times. T_T

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Works here too. From where did you try this?

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network failure? I work in China.

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0
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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?

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The same error when I try SRA database

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1
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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.

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Thanks. I will change networks and try again.

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