Some queries not being displayed

  • Hi and thank you again for your great plugin. We’ve been using it for years now!

    I have pages that have multiple shortcodes each. Each shortcode is for a different key and query. I’m doing this mostly to display our publications by year.

    Recently, I found that only some of the shortcodes actually list results. I’m sorry I can’t be more specific, it seems that the first one always returns results, more than one can return results and the number of the publilcations doesn’t affect whether they will be returned or not. Sometimes a query of one pubmed id doesn’t work and a query of 19 does.

    Here’s an example of usage that doesn’t work:
    Page:
    <h2>2018</h2>
    [pmid-refs key=”2018″ wrap=ul showlink=’false’]
    <h2>2017</h2>
    [pmid-refs key=”2017″ wrap=ul showlink=’false’]

    Queries:
    2018: 29030841[pmid] OR 29030853[pmid] OR 29138120[pmid] OR 29186503[pmid] OR 29219214[pmid] OR 29229607[pmid] OR 29593348[pmid]

    2017: 27879434[pmid] OR 28108659[pmid] OR 28203700[pmid] OR 28206648[pmid] OR 28220888[pmid] OR 28242812[pmid] OR 28344153[pmid] OR 28495225[pmid] OR 28535802[pmid] OR 28601227[pmid] OR 28645172[pmid] OR 28646211[pmid] OR 28652247[pmid] OR 28687616[pmid] OR 28730153[pmid] OR 28810144[pmid] OR 29138120[pmid] OR 29156127[pmid] OR 29219214[pmid]

    Please let me know if I can provide anything that could be more helpful than the above.

    The page I need help with: [log in to see the link]

Viewing 5 replies - 16 through 20 (of 20 total)
  • Plugin Author jimhu

    (@jimhu)

    Before talking to them, there are a couple of things I’d look at:

    Is the problem dependent on what theme you’re using?
    Is the problem dependent on the other plugins that are active on the site?

    Do you have a test site at idcsoft.com that is just a basic WP theme with no other plugins? That would allow you to tell whether it’s a problem on the host or with the themes or plugins.

    I assume that the version of WP is recent. I should note that my testing has been on a single install on GoDaddy (my host for historical reasons, not because I like them) and I don’t know if you’re using a multisite installation. My dept. has a multisite installation on WP-engine, which I may be able to test.

    If it comes down to more in depth debugging, the two things you’d want are the ability to look at the mysql database back end and the ability to check error logs.

    I’m hoping it turns out to be a theme or plugin incompatibility.

    After flushing the queue, I get a ‘too many queries’ error. This problem occurs when multiple shortcodes appear on one page.

    Here is a very bare site: https://source.academicwebpages.com/pubs/

    reflist is the sole plugin enabled.

    The theme is Enfold and the site does not work.

    I changed the theme to Twenty Nineteen the site still does not work.

    Seems to be something with the server.

    If you want to poke around, u/p is awp-admin / @c@demic-cascais

    Do you want FTP?

    Plugin Author jimhu

    (@jimhu)

    This is what I’m seeing on the bare site. Having the error messages display may be helpful.

    Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=28160848,26744909&retmode=xml): failed to open stream: HTTP request failed! HTTP/1.1 429 Too Many Requests in /home/academic/www/source/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 196

    Warning: Invalid argument supplied for foreach() in /home/academic/www/source/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 109

    Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=redenti+s%5Bau%5D+AND+2016%5Bdp%5D&retmax=20): failed to open stream: HTTP request failed! HTTP/1.1 429 Too Many Requests in /home/academic/www/source/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 196

    This is potentially useful.

    It looks like I will need to do some revamping to deal with changes in how NCBI provides the EUtils

    https://www.ncbi.nlm.nih.gov/books/NBK25497/#_chapter2_Usage_Guidelines_and_Requiremen_

    On December 1, 2018, NCBI will begin enforcing the use of API keys that will offer enhanced levels of supported access to the E-utilities. After that date, any site (IP address) posting more than 3 requests per second to the E-utilities without an API key will receive an error message. By including an API key, a site can post up to 10 requests per second by default. Higher rates are available by request (vog.hin.mln.ibcn@seitilitue). Users can obtain an API key now from the Settings page of their NCBI account (to create an account, visit https://www.ncbi.nlm.nih.gov/account/). After creating the key, users should include it in each E-utility request by assigning it to the new api_key parameter.

    Example request including an API key:
    esummary.fcgi?db=pubmed&id=123456&api_key=ABCDE12345

    Example error message if rates are exceeded:
    {“error”:”API rate limit exceeded”,”count”:”11″}
    Only one API key is allowed per NCBI account; however, a user may request a new key at any time. Such a request will invalidate any existing API key associated with that NCBI account.

    So it looks like when you have too many shortcodes on the same page, NCBI blocks the service after some number of them have run. But I’m still not sure why this is happening to you but not to me or to your other site hosted at MIT.

    Not sure how fast I can fix this. I’ll probably have to spend some time reaching out to NCBI tech support.

    Thanks for your work.

    As a workaround to the problem you discovered, I have re-created pages that are broken into year with static HTML except the most recent year.

    I noticed that even mit.edu breaks but it allows a lot more calls to pubmed than icdsoft.com

    If you do fix this, please let me know.

Viewing 5 replies - 16 through 20 (of 20 total)
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