I files a bug report on toolforge: https://phabricator.wikimedia.org/T226088
On Wed, Jun 19, 2019 at 9:29 AM boghog@me.com wrote:
Thanks for your replies.
I contacted the NIH to register the citation-template-filling tool and my e-mail address and added both as parameters to the query url (i.e., “&email=my@email“ and “&tool=ciation-filling-tool") to the PubMedLite.pm module that citation-template-filling tool calls. They also assured me that “tools.wmflabs.org” has not been blocked from accessing the NIH site.
I have done a few more tests:
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
does not work on the tool server, but does work on my local workstation. The following
curl -k ' 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
also does not work. But
curl -k ' https://130.14.29.110/entrez/eutils/efetch.fcgi?db=pubmed&id=12345'
works.
I am not sure what to do next. Is the problem on the “tools.wmflabs.org” or “eutils.ncbi.nlm.nih.gov” side? Also what precisely is the problem, so that I can accurately describe the issue to server administrators?
Thanks,
Boghog
On Jun 14, 2019, at 11:07 PM, Magnus Manske via Cloud < cloud@lists.wikimedia.org> wrote:
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
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