Pubmed Reflist is a great little plugin. I’ve been running it on a site for a few years now without a problem—until recently, when query results ceased to appear. I don’t yet know what’s causing the problem.
I’m wondering whether the plugin continues to work for folks out there or has required workarounds to stay functional after updating to WP 6.2.
Hello! first, let me say I love your plugin! Thank you for creating this.
I’ve made a reference list for someone using the key=”LASTNAME+FIRSTNAME+MIDDLEINITIAL” — however, it turns out that some publications aren’t listed because he’s credited with just his first and last name. The problem is, there are other authors with his first and last name. My problem is: If the key is too strict, I don’t get all of his publications, and if the key isn’t strict enough, I get his publications plus others’.
My question is: Do you have any ideas for ensuring that all publications from this author are included in the list without including other authors’ works?
thanks!
]]>Hi,
The author list is trunkated and the media title of the publication is not displayed.
So the informations are different from pubmed site.
Is there a way to display the same information than pubmed site does ?
Thanks
]]>Hi there! Nice plugin. I am trying to edit a webpage that already had it installed but can’t find where to modify the querry. According to the instrucctions that should be in “settings” but in the plugin section there is no settings in the WP Pubmed Reflist
line, nor a WP Pubmed Reflist item no the left general column as with other plugins. Any help would be very much appreciated.
Hi,
I want to change the “author limit,” and to do this, presumably I have to add a new style and then enter the author limit for it in the “style data” table. When I entered a new style name and clicked on save, nothing happened. I expected a new row for the new style to be created in the style data table, but the table remained unchanged.
David
]]>Hi,
Is there a way to keep the same order as defined in the key argument.
Now, publications are displayed sort by PMID inverted.
But I would like to choose the most interesting publications displayed first.
Thanks for help
]]>Is there any way to edit the author list that is being returned from the pubmed scrape? I want to remove the comma between the last names and first/middle initials. I can’t seem to figure out how to do this. As far as I can tell, the entire author list is being returned from Pubmed as _Author, with no way to edit the format of the author list.
Citations currently read as: Petersen, NH, Silverman, A, Strander, SM, Kodali, S…etc
I need them to read as: Petersen NH, Silverman A, Stander SM, Kodali S, etc
Thanks in advance for any help you can provide!
]]>I just went to add a new query in the backend for a new lab member, and instead of showing me my list of queries with their associated keys, I now have a large block of text reading “2000pubs contains characters not allowed in the key2001pubs contains characters not allowed in the key2002pubs contains characters not allowed in the key2003pubs contains characters not allowed in the key” etc. for every query I’ve ever created. I can’t add, remove, or edit my queries.
]]>Sry – my site is currently not publicly available…
I built my WP site with an external developer and on my faculty pages I used the WP Pubmed Reflist plugin v1.2 to display pubs, it worked awesomely. This is what I use on each faculty page:
[pmid-refs key=John+Doe limit=20]
Well, the developer has handed over the WP site to me and I now host it on my own web server, but, now my faculty pages barely even show any content; header & footer is gone, text nearly all gone. Wasn’t sure what was the prob – until I removed the WP Pubmed Reflist shortcode from a faculty page and all their content reappeared.
So it seems the WP Pubmed Reflist is now causing issues and I would like help with resolving this. Please let me know what info you need and I will be happy to provide.
Thank you!!
]]>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.
]]>First, let me say I love the simplicity and flexibility of this plugin – it “just works”.
My specific query is about whether there is any way of introducing pagination into the output, either through the plugin itself or through the pubmed query. I have a reference list of around 500 entries and this won’t display – not sure whether this is a server query limit or a pubmed search limit, but in any case I don’t particularly want 500 references on one page, but would prefer to paginate. The only thing that has occurred to me is including year of publication in the pubmed query and displaying queries on different pages, but this would then need annual updates. Is there any way of doing this or any workaround that occurs to you? Thanks a lot!
I create a new key called “Profs” and then an associated query, but the plugin is using the KEY as the query and not what is in the query field.
The results that show are for the KEY and not the query. Please assist to resolve this issue.
Thanks
]]>I am testing the plugin with both quoted and unquoted samples shortcakes:
[pmid-refs key=smith]
[pmid-refs key="smith"]However, I receive an SSL connection error.
Warning: file_get_contents(): SSL: Connection reset by peer in wordpress/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 196
Warning: file_get_contents(): Failed to enable crypto in wordpress/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 196
Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=smith&retmax=20): failed to open stream: operation failed in wordpress/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 196Hello, I have a problem with the plugin not displaying titles with superscripted numbers correctly. These are abundant in my field and it makes the plugin unusable.
Superscript is separated by <sup></sup> tags in xml, but this does not seem to survive the conversion to html.
Example list of articles with alot of superscript:
https://www.ncbi.nlm.nih.gov/pmc/?term=Velikyan
What should display like this:
Comparison of 68Ga-DOTA-Siglec-9 and 18F-Fluorodeoxyribose-Siglec-9: Inflammation Imaging and Radiation Dosimetry.
Is instead like this:
Comparison of Ga-DOTA-Siglec-9 and F-Fluorodeoxyribose-Siglec-9: Inflammation Imaging and Radiation Dosimetry.
was working the other day – now it is not working….
pagesource:
2018
[pmid-refs key=”wittrup-2018″ limit=”75″ showlink=’false’]
2017
[pmid-refs key=”wittrup-2017″ limit=”75″ showlink=’false’]
2016
[pmid-refs key=”wittrup-2016″ limit=”75″ showlink=’false’]
etc. etc.
]]>sorry – wrong thread!
]]>I tested this on 4.9.4 using php 7.2. I have not tested it back to older versions since I don’t have the right development environment.
The biggest change is that I switched to making the queries to NCBI E-Utilities to use https instead of http. I found that this required the openSSL module in php, which may cause problems for some people.
Please report bugs and feature requests. I know I’m slow, but I want this plugin to remain useful to people.
]]>It was working fine on WordPress v4.9.2 I remember. But stop working correctly on v4.9.4. It only displays 3 articles on the list, and not the most recent ones either. Any way to fix?
]]>Hi! It has been years since I first contacted you about this plugin and you were a great help then. I am revamping a site right now (cannot show you a link yet, sorry) and I tried to use this plugin to generate a pubmed list where I search by grant number. The search works in PubMed, but not in your plugin.
The search term is:
U54AR055073[Grant Number]
If you try this in pubmed you get 73 results. But when I include the shortcode in a page I get only a blank list of 1-20.
Can you help?
Thanks,
Linda
I sometimes get this error when using the plugin. I think maybe i need to add a issec somewhere on line 180 ? If I refresh the page after getting this error, the problem goes away.
Notice: Undefined variable: bold_list in /var/www/html/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefListViews.php on line 180
wpPubMedReflistViews::bold
]]>on this page:
https://christlab.org/publications/
getting this error:
Warning: simplexml_load_file(): http%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fefetch.fcgi%3Fdb%3Dpubmed%26id%3D27768064%2C27718091%2C26042793%2C25914643%2C24909508%2C24066899%2C24051181%2C24012523%2C23991116%2C23818131%2C23059002%2C22917043%2C22442207%2C22439962%2C22133601%2C21687500%2C21548710%2C21518418%2C21290230%2C20934837%2C20683344%2C20639056%2C19888972%2C19846131%2C19720749%2C19447440%2C19290806%2C19267388%2C19167152%2C19147270%2C18804802%2C18400295%2C18355864%2C18337374%2C18200069%2C17696159%2C17493553%2C17468388%2C17313427%2C17150299%2C16899553%2C16643495%2C16465183%2C16406945%2C16368968%2C16093962%2C15821587%2C15794773%2C15784596%2C15758814%2C15471904%2C15371262%2C15322023%2C15146085%2C15088908%2C14733838%2C14713860%2C14551575%2C12973386%2C12937650%2C12879115%2C12796707%2C12686874%2C12676745%2C12448695%2C12427590%2C12409880%2C12392915%2C12236168%2C12193101%2C12147185%2C12138167%2C12050569%2C11992099%2C11884617%2C11641143%2C11550787%2C11465535%2C11457855%2C11426343%2C11404303%2C11402576%2C11401829% in /home/christla/www/www/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 191
Warning: simplexml_load_file(): <!DOCTYPE HTML PUBLIC “-//IETF//DTD HTML 2.0//EN”> in /home/christla/www/www/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 191
Warning: simplexml_load_file(): ^ in /home/christla/www/www/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 191
]]>Just wondering if you will be updating the plugin to use HTTPS vs HTTP as per the recent change at NCBI (https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml).
]]>Hi,
I’m trying to use your plug-in for a lab website but I am having trouble getting citations to appear. The only thing that appears is a list that begins and ends at 1 as well as the Search PubMed link.
Also, every now and then I also get this compilation error on the website:
Warning: simplexml_load_file(): http%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fesearch.fcgi%3Fdb%3Dpubmed%26term%3DCalhoun%2BPS%26retmax%3D10:1: parser error : Document is empty in /home/beckha6/public_html/wordpress/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 191
Warning: simplexml_load_file(): in /home/beckha6/public_html/wordpress/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 191
Warning: simplexml_load_file(): ^ in /home/beckha6/public_html/wordpress/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 191
Warning: simplexml_load_file(): http%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fesearch.fcgi%3Fdb%3Dpubmed%26term%3DCalhoun%2BPS%26retmax%3D10:1: parser error : Start tag expected, ‘<‘ not found in /home/beckha6/public_html/wordpress/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 191
Warning: simplexml_load_file(): in /home/beckha6/public_html/wordpress/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 191
Warning: simplexml_load_file(): ^ in /home/beckha6/public_html/wordpress/wp-content/plugins/wp-pubmed-reflist/class.wpPubMedRefList.php on line 191
Thanks a lot and I really look forward to using this plug-in.
]]>Hi,
I create a query and saved under the key “chef”. As query text I put the name of autor: “Rassaf T[au]”. In the html site I put the shortcode: [pmid-refs key=”chef” limit=10] and the query is working.
Now I am trying to get the author name in bold.
So I am using the references styles to get it in bold.
I put the author name under the option “highlighted words” in the same form like in PubMed, but in the list of publications his name is still normally (not bold).
Have you an idea what I am doing wrong?
Best regards
Fatmir
]]>Hello,
I wan to create a query of all publications of my institution. I must create some pages with publications list per year. How can I search pubmed by using institution name? How can combine this search with years?
Best regards
Fatmir
Hi, running WordPress 4.5 and just installed this plugin today.
Really love the idea of this plugin, extremely useful. But, like the two recent posts, I am getting a list of numbers but no citation listed next to them. Here is the HTML being generated on the page:
<div class="wpb_wrapper">
<!-- load from cache -->
<ol>
<li></li>
<li></li>
<li></li>
<li></li>
<li></li>
</ol>
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=GM103533[gr]">Search PubMed</a>
</div>I have tried making changes (changing default style and adding a new style) and saving in the “Reference Styles” settings page–but it had no effect.
Any ideas? Thanks.
]]>reflist does not work with 4.5 – numbers appear but no entries – any suggestions?
]]>Hi, I just downloaded your plugin and added a simple query with an authors first and last name. On pubmed, the query returns 13 results. When I view the page on my site, it displays a list of 1-13, but no citations/references – just an empty list of 13
elements. I tried changing the publication styles – nothing … can you assist? thanks.
Desrciption says tested up to 4.2.5, anyone have any trouble with this plugin in 4.3.1?
Thanks!
]]>Hi,
I’m somewhat flabbergasted by one specific pubmed reference not being retrieved. Hoping that you can replicate this query and confirm the same experience.
21250388[pmid]
The record is in pubmed: https://www.ncbi.nlm.nih.gov/pubmed/?term=21250388%5Bpmid%5D
Thank you for a wonderful plugin.
(using version 1.0)