Support » Plugin: WP Pubmed Reflist » 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 15 replies - 1 through 15 (of 20 total)
  • Update, it’s not true that the first query is always displayed. Also queries that were displayed at one point are displayed when I change a different query.

    I’m looking at the page source code and I see that there are comments like this:

    <!– updating from pubmed last update:1970-01-01 00:00:00 –>

    Which does look wrong.

    Plugin Author jimhu

    (@jimhu)

    The comment is there for debugging purposes. But the date is clearly messed up. I need to do some tests and get back to you.

    Thank you so much!

    Note, please check the page https://cm.jefferson.edu/publications-2018-2017/ if you need to look at our website. I, temporarily, removed the shortcodes from the page I linked to earlier.

    Plugin Author jimhu

    (@jimhu)

    I think the problem may be the quotes around the keys. I think they’re MS “curly quotes”.

    When I copied your tags into my test site and substituted key names I got very strange results. They went back to normal when I deleted the quote marks.

    Thank you very much for your reply.

    I checked some code without quotes and that doesn’t seem to work either:

    [pmid-refs key=26387536 wrap=ul]</p>

    [pmid-refs key=27153631 wrap=ul]</p>

    [pmid-refs key=27590350 wrap=ul]</p>

    [pmid-refs key=27630665 wrap=ul]</p>

    That returns only the first publication (tried a couple of pubmeds).

    Interestingly, if I change only one of the pubmeds on the shortcodes, update the page and refresh, I see the new result too.

    So, if I’m looking at https://cm.jefferson.edu/publications-2018-2017/ and I have the code from my previous comment, I see only the first publication.

    If I change the last one to:

    [pmid-refs key=26387536 wrap=ul]

    [pmid-refs key=27153631 wrap=ul]

    [pmid-refs key=27590350 wrap=ul]

    [pmid-refs key=27879490 wrap=ul]

    I see the first and the last one. From the page source:

    <!– load from cache<br> –>

    • Blanco, FF, Jimbo, M, Wulfkuhle, J, Gallagher, I, Deng, J, Enyenihi, L, Meisner-Kober, N, Londin, E, Rigoutsos, I, Sawicki, JA, Risbud, MV, Witkiewicz, AK, McCue, PA, Jiang, W, Rui, H, Yeo, CJ, Petricoin, E, Winter, JM, Brody, JR. The mRNA-binding protein HuR promotes hypoxia-induced chemoresistance through posttranscriptional regulation of the proto-oncogene PIM1 in pancreatic cancer cells. Oncogene. 2016;35 (19):2529-41. doi: 10.1038/onc.2015.325. PubMed PMID:26387536 .

    Search PubMed
    <!– load from cache<br> –>

    Search PubMed
    <!– load from cache<br> –>

    Search PubMed
    <!– load from cache<br> –>

    • Stephens, M, Kim, DI, Shepherd, B, Gustafson, S, Thomas, P. Intense Uptake in Amyloidosis of the Seminal Vesicles on 68Ga-PSMA PET Mimicking Locally Advanced Prostate Cancer. Clin Nucl Med. 2017;42 (2):147-148. doi: 10.1097/RLU.0000000000001460. PubMed PMID:27879490 .

    Search PubMed

    Note that I’ve never tried the last pubmed id before. It’s a random one, not from my group.

    <!-- load from cache<br> --><ul><li>Blanco, FF, Jimbo, M, Wulfkuhle, J, Gallagher, I, Deng, J, Enyenihi, L, Meisner-Kober, N, Londin, E, Rigoutsos, I, Sawicki, JA, Risbud, MV, Witkiewicz, AK, McCue, PA, Jiang, W, Rui, H, Yeo, CJ, Petricoin, E, Winter, JM, Brody, JR. The mRNA-binding protein HuR promotes hypoxia-induced chemoresistance through posttranscriptional regulation of the proto-oncogene PIM1 in pancreatic cancer cells. Oncogene. 2016;35 (19):2529-41. doi: <a href='http://dx.doi.org/10.1038/onc.2015.325'>10.1038/onc.2015.325</a>. PubMed <a href='http://www.ncbi.nlm.nih.gov/pubmed/26387536'>PMID:26387536</a> .</ul><a href='http://www.ncbi.nlm.nih.gov/pubmed?term=26387536'>Search PubMed</a>
    <!-- load from cache<br> --><ul><li></ul><a href='http://www.ncbi.nlm.nih.gov/pubmed?term=27153631'>Search PubMed</a>
    <!-- load from cache<br> --><ul><li></ul><a href='http://www.ncbi.nlm.nih.gov/pubmed?term=27590350'>Search PubMed</a>
    <!-- load from cache<br> --><ul><li>Stephens, M, Kim, DI, Shepherd, B, Gustafson, S, Thomas, P. Intense Uptake in Amyloidosis of the Seminal Vesicles on 68Ga-PSMA PET Mimicking Locally Advanced Prostate Cancer. Clin Nucl Med. 2017;42 (2):147-148. doi: <a href='http://dx.doi.org/10.1097/RLU.0000000000001460'>10.1097/RLU.0000000000001460</a>. PubMed <a href='http://www.ncbi.nlm.nih.gov/pubmed/27879490'>PMID:27879490</a> .</ul><a href='http://www.ncbi.nlm.nih.gov/pubmed?term=27879490'>Search PubMed</a>
    Plugin Author jimhu

    (@jimhu)

    I just tried your example

    [pmid-refs key=26387536 wrap=ul]

    [pmid-refs key=27153631 wrap=ul]

    [pmid-refs key=27590350 wrap=ul]

    [pmid-refs key=27879490 wrap=ul]

    I get

    Blanco, FF, Jimbo, M, Wulfkuhle, J, Gallagher, I, Deng, J, Enyenihi, L et al.. The mRNA-binding protein HuR promotes hypoxia-induced chemoresistance through posttranscriptional regulation of the proto-oncogene PIM1 in pancreatic cancer cells. Oncogene. 2016;35 (19):2529-41. doi: 10.1038/onc.2015.325. PubMed PMID:26387536 .
    Search PubMed
    Pliatsika, V, Loher, P, Telonis, AG, Rigoutsos, I. MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. Bioinformatics. 2016;32 (16):2481-9. doi: 10.1093/bioinformatics/btw194. PubMed PMID:27153631 PubMed Central PMC4978933.
    Search PubMed
    Oran, AR, Adams, CM, Zhang, XY, Gennaro, VJ, Pfeiffer, HK, Mellert, HS et al.. Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. Oncotarget. 2016;7 (45):72395-72414. doi: 10.18632/oncotarget.11718. PubMed PMID:27590350 PubMed Central PMC5340124.
    Search PubMed
    Stephens, M, Kim, DI, Shepherd, B, Gustafson, S, Thomas, P. Intense Uptake in Amyloidosis of the Seminal Vesicles on 68Ga-PSMA PET Mimicking Locally Advanced Prostate Cancer. Clin Nucl Med. 2017;42 (2):147-148. doi: 10.1097/RLU.0000000000001460. PubMed PMID:27879490 .

    with bullets and links that don’t show here.

    it’s weird because the handling of multiple shortcodes in the same post should be part of the WP codebase unrelated to anything in the plugin.

    edit to add: here’s where I’m testing

    http://jimhu.org/wp-pubmed-reflist-tests/

    • This reply was modified 9 months, 2 weeks ago by  .
    moeuf

    (@moeuf)

    I’m having a similar issue – I had all our lab publications in two (tabbed) tables on one page, with the second tab containing a table of shortcodes. It worked fine last time I looked at it a few months ago, but when I went to update our list of selected pubs, I found that the full list is no longer working. After some half-random playing around with the shortcodes, three of them are working (the first two and the last), but none of the others. My site is here: https://guttman.csb.utoronto.ca/publications/ and the table in question is in the “all publications” tab.

    Plugin Author jimhu

    (@jimhu)

    I assume you already checked for smart quotes problem in the shortcode content?

    Can you post the markup?

    edit to add: I’m also wondering if there is another incompatible plugin involved.

    • This reply was modified 9 months ago by  .
    moeuf

    (@moeuf)

    Yes, I actually didn’t need any quotes (and I use a plain text editor exclusively specifically to avoid that sort of annoyance).

    I managed to get them all working but there’s no logic to it. Originally I had them all set up as [pmid-refs key=<year> limit=20 wrap=p] (the year varied, was simple alphanumeric). After they failed I got three working by stripping the wrap=p, then two of them stopped working the next time I looked. I tried wrap=ul, wrap=p, with and without a limit, and nothing was working. Then I stripped the limit from all of them and the last one stopped working. Then I added the limit and a wrap=ul to each one individually, saving between and checking, and now they all work. Makes no reasonable sense at all, which makes me think it’s either a failure at the call to pubmed (maybe too many simultaneous calls? Don’t know if that makes sense) or a plugin incompatibility. I do have them embedded in a TablePress table, and the ones that aren’t embedded (on individual lab member pages) seem to be so far unaffected.

    i am seeing this peculiar result, suddenly, too

    https://redentilab.org/pubs-test/

    if you compare to this listing (of all) you can see that many are missing.

    https://redentilab.org/publications/

    I have removed all quotes.

    Suggestions?

    Plugin Author jimhu

    (@jimhu)

    That’s weird because some are working for you and others aren’t.

    I used the tools query panel to make a set of queries that look like this:

    key: redenti_18
    query: redenti s[au] AND 2018[dp]

    for 2016-18

    Then I put these on my test page like this:

    2018

    [pmid-refs key=redenti_18 wrap=ol showlink=false]

    2017

    [pmid-refs key=redenti_17 wrap=ol showlink=false]

    2016

    [pmid-refs key=redenti_16 wrap=ol showlink=false]

    See it here: http://jimhu.org/wp-pubmed-reflist-tests/

    So, the big question is: did I do it differently from you or is there something different about our installations?

    I copied your text and created this page: https://redentilab.org/pubs-2/

    I created the keys as per your direction:

    SO as you can see it is not working. It is definitely some setting at my server company icdsoft.com because it is working on your site, plus it is working with multiple shortcodes at another of my clients that is hosted at mit.edu: https://kdw-lab.mit.edu/publication-list/

    What should I ask my server company?

    Nancy

Viewing 15 replies - 1 through 15 (of 20 total)
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