I files a bug report on toolforge: https://phabricator.wikimedia.org/T226088
On Wed, Jun 19, 2019 at 9:29 AM <[email protected]> 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=12345 > ' > 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=12345 > ' > 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 < > [email protected]> 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 <[email protected]> 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 < >> [email protected]> 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” 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=12345&retmode=xml >>> ' >>> >>> 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=12345&retmode=xml >>> ’ >>> >>> <!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 >>> [email protected] (formerly [email protected]) >>> https://lists.wikimedia.org/mailman/listinfo/cloud >> >> _______________________________________________ >> Wikimedia Cloud Services mailing list >> [email protected] (formerly [email protected]) >> https://lists.wikimedia.org/mailman/listinfo/cloud > > _______________________________________________ > Wikimedia Cloud Services mailing list > [email protected] (formerly [email protected]) > https://lists.wikimedia.org/mailman/listinfo/cloud > > >
_______________________________________________ Wikimedia Cloud Services mailing list [email protected] (formerly [email protected]) https://lists.wikimedia.org/mailman/listinfo/cloud
