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 <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” 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

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