Plugin is not using the query field

You mean it’s searching pubmed for the word “Profs”? I need more information to understand how that might have happened.

One thing to try, though. Is to make another test key-query pair and save. Use something simple, like one author. Just saving it should flush the previous cached query and might cause it to reload.

Also, you use that to test if there is something weird about the Profs query itself, or if there’s a more general problem with your installation.

I created a new key called test and randomly chose an author “safe s”

Have a look at this page and hover over the Search PubMed at the bottom. It is searching for test and not the author safe s.
https://ultimatevision.ca/DAG/new-publications/

I removed the plugin, re-installed. I have created numerous keys and queries and nothing changes.

Any new suggestions?

That’s looking like what I feared you were describing. I’m going to review the code to see if I can figure out how this could have happened… but it’s hard to diagnose things if I can’t reproduce them on my sites, and I only work on the code intermittently so it often takes a while for me to remember how it works.

Some of other questions:

• Do you know if your site is using curl or allow_url_fopen?
• Do you have access to the underlying mysql database? If so, can you search the wp_options table for an option named “wp_pubmed_reflist”
• Do you see anything in the error logs for the webserver?
• Do you have edit access to the site code? I’m wondering if I can have you put some diagnostic statements in the plugin code to help trace what the problem is once I get an idea of what it might be… if I get an idea.

I believe the web hosting has curl activated automatically.

Yes I can put some diagnostic statements in the plugin.

I have access to the mysql database and here is what wp_pubmed_reflist shows:

a:2:{s:7:"faclist";a:3:{i:0;s:5:"profs";i:1;s:4:"test";i:2;s:0:"";}s:8:"facprops";a:4:{s:5:"profs";a:3:{s:5:"query";s:1:"1";s:6:"extras";s:0:"";s:11:"last_update";s:1:"0";}s:4:"test";a:3:{s:5:"query";s:6:"safe s";s:6:"extras";s:0:"";s:11:"last_update";s:1:"0";}s:18:"”profs”.20..ol";a:2:{s:7:"reflist";s:13:"<ol><li></ol>";s:11:"last_update";i:1528214026;}s:17:"”test”.20..ol";a:2:{s:7:"reflist";s:7675:"<ol><li>Froyman, W, Wynants, L, Landolfo, C, Bourne, T, Valentin, L, Testa, A <i>et al.</i>. Validation of the Performance of International Ovarian Tumor Analysis (IOTA) Methods in the Diagnosis of Early Stage Ovarian Cancer in a Non-Screening Population. Diagnostics (Basel). 2017;7 (2):. doi: <a href='https://dx.doi.org/10.3390/diagnostics7020032'>10.3390/diagnostics7020032</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/28574444'>PMID:28574444</a> PubMed Central <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5489952'>PMC5489952</a>.</li><li>Guienne, V, Parahy, S, Testa, A. [Conservative management option in elderly patients]. Nephrol. Ther. 2016;12 (2):98-103. doi: <a href='https://dx.doi.org/10.1016/j.nephro.2015.09.002'>10.1016/j.nephro.2015.09.002</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/26725173'>PMID:26725173</a> .</li><li>Testa, AC, Ludovisi, M, Mascilini, F, Di Legge, A, Malaggese, M, Fagotti, A <i>et al.</i>. Ultrasound evaluation of intra-abdominal sites of disease to predict likelihood of suboptimal cytoreduction in advanced ovarian cancer: a prospective study. Ultrasound Obstet Gynecol. 2012;39 (1):99-105. doi: <a href='https://dx.doi.org/10.1002/uog.10100'>10.1002/uog.10100</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/21913276'>PMID:21913276</a> .</li><li>Testa, AC, Timmerman, D, Van Holsbeke, C, Zannoni, GF, Fransis, S, Moerman, P <i>et al.</i>. Ovarian cancer arising in endometrioid cysts: ultrasound findings. Ultrasound Obstet Gynecol. 2011;38 (1):99-106. doi: <a href='https://dx.doi.org/10.1002/uog.8970'>10.1002/uog.8970</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/21351179'>PMID:21351179</a> .</li><li>Testa, A, Dejoie, T, Lecarrer, D, Wratten, M, Sereni, L, Renaux, JL <i>et al.</i>. Reduction of free immunoglobulin light chains using adsorption properties of hemodiafiltration with endogenous reinfusion. Blood Purif. 2010;30 (1):34-6. doi: <a href='https://dx.doi.org/10.1159/000316684'>10.1159/000316684</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/20588010'>PMID:20588010</a> .</li><li>Testa, AC, Timmerman, D, Van Belle, V, Fruscella, E, Van Holsbeke, C, Savelli, L <i>et al.</i>. Intravenous contrast ultrasound examination using contrast-tuned imaging (CnTI) and the contrast medium SonoVue for discrimination between benign and malignant adnexal masses with solid components. Ultrasound Obstet Gynecol. 2009;34 (6):699-710. doi: <a href='https://dx.doi.org/10.1002/uog.7464'>10.1002/uog.7464</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/19924735'>PMID:19924735</a> .</li><li>Testa, AC, Ludovisi, M, Manfredi, R, Zannoni, G, Gui, B, Basso, D <i>et al.</i>. Transvaginal ultrasonography and magnetic resonance imaging for assessment of presence, size and extent of invasive cervical cancer. Ultrasound Obstet Gynecol. 2009;34 (3):335-44. doi: <a href='https://dx.doi.org/10.1002/uog.7325'>10.1002/uog.7325</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/19705403'>PMID:19705403</a> .</li><li>Testa, AC, Van Holsbeke, C, Mascilini, F, Timmerman, D. Dynamic and interactive gynecological ultrasound examination. Ultrasound Obstet Gynecol. 2009;34 (2):225-9. doi: <a href='https://dx.doi.org/10.1002/uog.7309'>10.1002/uog.7309</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/19644933'>PMID:19644933</a> .</li><li>Testa, AC, Bourne, TH. Characterising pelvic masses using ultrasound. Best Pract Res Clin Obstet Gynaecol. 2009;23 (5):725-38. doi: <a href='https://dx.doi.org/10.1016/j.bpobgyn.2009.02.002'>10.1016/j.bpobgyn.2009.02.002</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/19303367'>PMID:19303367</a> .</li><li>Testa, AC, Gaurilcikas, A, Licameli, A, Mancari, R, Di Legge, A, Malaggese, M <i>et al.</i>. Sonographic features of primary ovarian fibrosarcoma: a report of two cases. Ultrasound Obstet Gynecol. 2009;33 (1):112-5. doi: <a href='https://dx.doi.org/10.1002/uog.6291'>10.1002/uog.6291</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/19072774'>PMID:19072774</a> .</li><li>Testa, AC, Mancari, R, Di Legge, A, Mascilini, F, Salutari, V, Scambia, G <i>et al.</i>. The 'lead vessel': a vascular ultrasound feature of metastasis in the ovaries. Ultrasound Obstet Gynecol. 2008;31 (2):218-21. doi: <a href='https://dx.doi.org/10.1002/uog.5251'>10.1002/uog.5251</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/18254156'>PMID:18254156</a> .</li><li>Testa, A. [Sodium intake and interdialytic weight gain]. Nephrol. Ther. 2007;3 Suppl 2 :S133-6. . PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/17939969'>PMID:17939969</a> .</li><li>Testa, AC, Ferrandina, G, Timmerman, D, Savelli, L, Ludovisi, M, Van Holsbeke, C <i>et al.</i>. Imaging in gynecological disease (1): ultrasound features of metastases in the ovaries differ depending on the origin of the primary tumor. Ultrasound Obstet Gynecol. 2007;29 (5):505-11. doi: <a href='https://dx.doi.org/10.1002/uog.4020'>10.1002/uog.4020</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/17444565'>PMID:17444565</a> .</li><li>Testa, AC, Timmerman, D, Exacoustos, C, Fruscella, E, Van Holsbeke, C, Bokor, D <i>et al.</i>. The role of CnTI-SonoVue in the diagnosis of ovarian masses with papillary projections: a preliminary study. Ultrasound Obstet Gynecol. 2007;29 (5):512-6. doi: <a href='https://dx.doi.org/10.1002/uog.4013'>10.1002/uog.4013</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/17444549'>PMID:17444549</a> .</li><li>Testa, A, Gentilhomme, H, Le Carrer, D, Orsonneau, JL. In vivo removal of high- and low-molecular-weight compounds in hemodiafiltration with on-line regeneration of ultrafiltrate. Nephron Clin Pract. 2006;104 (1):c55-60. doi: <a href='https://dx.doi.org/10.1159/000093671'>10.1159/000093671</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/16741371'>PMID:16741371</a> .</li><li>Testa, AC, Ludovisi, M, Savelli, L, Fruscella, E, Ghi, T, Fagotti, A <i>et al.</i>. Ultrasound and color power Doppler in the detection of metastatic omentum: a prospective study. Ultrasound Obstet Gynecol. 2006;27 (1):65-70. doi: <a href='https://dx.doi.org/10.1002/uog.2673'>10.1002/uog.2673</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/16374750'>PMID:16374750</a> .</li><li>Testa, AC, Fruscella, E, Ludovisi, M, De Vincenzo, R, Malaggese, M, Corrado, G <i>et al.</i>. The role of sonographic examination in the follow-up of gynecological neoplasms. Gynecol. Oncol. 2005;99 (3):696-703. doi: <a href='https://dx.doi.org/10.1016/j.ygyno.2005.07.116'>10.1016/j.ygyno.2005.07.116</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/16140365'>PMID:16140365</a> .</li><li>Testa, AC, Ferrandina, G, Fruscella, E, Van Holsbeke, C, Ferrazzi, E, Leone, FP <i>et al.</i>. The use of contrasted transvaginal sonography in the diagnosis of gynecologic diseases: a preliminary study. J Ultrasound Med. 2005;24 (9):1267-78. . PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/16123187'>PMID:16123187</a> .</li><li>Testa, AC, Ferrandina, G, Distefano, M, Fruscella, E, Mansueto, D, Basso, D <i>et al.</i>. Color Doppler velocimetry and three-dimensional color power angiography of cervical carcinoma. Ultrasound Obstet Gynecol. 2004;24 (4):445-52. doi: <a href='https://dx.doi.org/10.1002/uog.1703'>10.1002/uog.1703</a>. PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/15343602'>PMID:15343602</a> .</li><li>Testa, AC, Mansueto, D, Lorusso, D, Fruscella, E, Basso, D, Scambia, G <i>et al.</i>. Angiographic power 3-dimensional quantitative analysis in gynecologic solid tumors: feasibility and reproducibility. J Ultrasound Med. 2004;23 (6):821-8. . PubMed <a href='https://www.ncbi.nlm.nih.gov/pubmed/15244306'>PMID:15244306</a> .</ol>";s:11:"last_update";i:1528214032;}}}

• This reply was modified 6 years, 5 months ago by Steven Stern (sterndata).
• This reply was modified 6 years, 5 months ago by Steven Stern (sterndata).

I believe the web hosting has curl activated automatically.

Yes I can put some diagnostic statements in the plugin.

I have access to the mysql database and here is what wp_pubmed_reflist shows:

a:2:{s:7:”faclist”;a:3:{i:0;s:5:”profs”;i:1;s:4:”test”;i:2;s:0:””;}s:8:”facprops”;a:4:{s:5:”profs”;a:3:{s:5:”query”;s:1:”1″;s:6:”extras”;s:0:””;s:11:”last_update”;s:1:”0″;}s:4:”test”;a:3:{s:5:”query”;s:6:”safe s”;s:6:”extras”;s:0:””;s:11:”last_update”;s:1:”0″;}s:18:””profs”.20..ol”;a:2:{s:7:”reflist”;s:13:”

“;s:11:”last_update”;i:1528214026;}s:17:””test”.20..ol”;a:2:{s:7:”reflist”;s:7675:”

*** THE 20 RESULTS GO HERE ***

“;s:11:”last_update”;i:1528214032;}}}

• This reply was modified 6 years, 5 months ago by Steven Stern (sterndata).

Just fyi, I’ve been looking at the code. Nothing to suggest yet.

Thanks for letting me know!

Based on what’s in your database, it looks like the correct query is in the database, but it’s either not being fetched from wp_options or it’s being overwritten after being fetched.

To see if it ever gets found, put this line above the return on line 187 of class.wpPubMedRefList.php

echo __METHOD__.': '.$this->options['facprops'][$key]['query']."<hr>";

it should print something like

wpPubMedRefList::getQueryFromOptions:safe s <hr>

You could also uncomment the echo statement on line 174.

• This reply was modified 6 years, 5 months ago by jimhu.

The line of code is giving an error: syntax error, unexpected end of file, expecting ‘`’

I did uncomment line 174 and now on the page you can see it is outputting “test” at the top and not the query for “safe s”

Sorry, the backtick doesn’t belong. It’s an unclosed tag from the markup here.

Fixed the post above.

• This reply was modified 6 years, 5 months ago by jimhu.

Thanks. Code is inserted.

I see no output from the new line of code.

OK, that means it’s not seeing what’s in the wp_options. The wp_options data is supposed to get loaded when the object is created on line 9

Try adding this after that line:
echo __METHOD__."<pre>".print_r($this->options['facprops'], true)."</pre>"; die();

Note, you might want to remove diagnostics after testing them so we don’t get the line numbers all messed up.

Line of code has been inserted. You can see the results on the page.

OK got it. I have a meeting now, so I’ll get back to you later. It looks like the data is loaded, though.

question: what version of php is running on your install?