The following tool has been running without problem for years:
https://tools.wmflabs.org/citation-template-filling/cgi-bin/index.cgi https://tools.wmflabs.org/citation-template-filling/cgi-bin/index.cgi Recently the tool has started generating the following error message:
Can't call method "findnodes" on an undefined value at /data/project/citation-template-filling/perl/ActivePerl-5.26/site/lib/WWW/Search/PubMedLite.pm line 117.
PubMedLite.pm in turn makes a request to “'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi” for data. For debugging, I queried the entrez server using an equivalent command in curl which generated the following error messages:
curl 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=1... https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=12345&retmode=xml'
curl: (6) Could not resolve host: eutils.ncbi.nlm.nih.gov http://eutils.ncbi.nlm.nih.gov/ I also tried replacing “eutils.ncbi.nlm.nih.gov http://eutils.ncbi.nlm.nih.gov/” with its IP address:
curl 'https://130.14.29.110/entrez/eutils/efetch.fcgi?db=pubmed&id=12345 https://130.14.29.110/entrez/eutils/efetch.fcgi?db=pubmed&id=12345'
curl: (51) SSL: no alternative certificate subject name matches target host name '130.14.29.110'
The same curl command runs without problem on my local workstation:
curl 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=1... https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=12345&retmode=xml’
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2019//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd <https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd>"> …
Anyone have an idea how to fix this? Thanks,
Boghog
I looked at `dig eutils.ncbi.nlm.nih.gov +trace` and at `strace -f dig eutils.ncbi.nlm.nih.gov +trace` - it looks to me like NIH's nameservers are not willing to serve labs?
On Fri, 14 Jun 2019 at 05:59, Konrad Koehler via Cloud < cloud@lists.wikimedia.org> wrote:
The following tool has been running without problem for years:
https://tools.wmflabs.org/citation-template-filling/cgi-bin/index.cgi
Recently the tool has started generating the following error message:
Can't call method "findnodes" on an undefined value at /data/project/citation-template-filling/perl/ActivePerl-5.26/site/lib/WWW/Search/PubMedLite.pm line 117.
PubMedLite.pm in turn makes a request to “' https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi%E2%80%9D for data. For debugging, I queried the entrez server using an equivalent command in curl which generated the following error messages:
curl ' https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=1... '
curl: (6) Could not resolve host: eutils.ncbi.nlm.nih.gov
I also tried replacing “eutils.ncbi.nlm.nih.gov” with its IP address:
curl 'https://130.14.29.110/entrez/eutils/efetch.fcgi?db=pubmed&id=12345'
curl: (51) SSL: no alternative certificate subject name matches target host name '130.14.29.110'
The same curl command runs without problem on my local workstation:
curl ' https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=1... ’
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2019//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd"> …
Anyone have an idea how to fix this? Thanks,
Boghog _______________________________________________ Wikimedia Cloud Services mailing list Cloud@lists.wikimedia.org (formerly labs-l@lists.wikimedia.org) https://lists.wikimedia.org/mailman/listinfo/cloud
FWIW, I am running a service that queries eutils.
They have a rate limitation, but I do stay under that, AFAICT. Maybe multiple bots from the same host, together, triggered a rate limiting mechanism?
On Fri, Jun 14, 2019 at 5:56 PM Alex Monk krenair@gmail.com wrote:
I looked at `dig eutils.ncbi.nlm.nih.gov +trace` and at `strace -f dig eutils.ncbi.nlm.nih.gov +trace` - it looks to me like NIH's nameservers are not willing to serve labs?
On Fri, 14 Jun 2019 at 05:59, Konrad Koehler via Cloud < cloud@lists.wikimedia.org> wrote:
The following tool has been running without problem for years:
https://tools.wmflabs.org/citation-template-filling/cgi-bin/index.cgi
Recently the tool has started generating the following error message:
Can't call method "findnodes" on an undefined value at /data/project/citation-template-filling/perl/ActivePerl-5.26/site/lib/WWW/Search/PubMedLite.pm line 117.
PubMedLite.pm in turn makes a request to “' https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi%E2%80%9D for data. For debugging, I queried the entrez server using an equivalent command in curl which generated the following error messages:
curl ' https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=1... '
curl: (6) Could not resolve host: eutils.ncbi.nlm.nih.gov
I also tried replacing “eutils.ncbi.nlm.nih.gov” with its IP address:
curl 'https://130.14.29.110/entrez/eutils/efetch.fcgi?db=pubmed&id=12345'
curl: (51) SSL: no alternative certificate subject name matches target host name '130.14.29.110'
The same curl command runs without problem on my local workstation:
curl ' https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=1... ’
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2019//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd"> …
Anyone have an idea how to fix this? Thanks,
Boghog _______________________________________________ Wikimedia Cloud Services mailing list Cloud@lists.wikimedia.org (formerly labs-l@lists.wikimedia.org) https://lists.wikimedia.org/mailman/listinfo/cloud
Wikimedia Cloud Services mailing list Cloud@lists.wikimedia.org (formerly labs-l@lists.wikimedia.org) https://lists.wikimedia.org/mailman/listinfo/cloud