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EricMaeker / dokuwiki-plugin-pubmed

PubMed data integrator plugin for dokuwiki
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No showing of pubmed records #2

Closed whytong closed 4 years ago

whytong commented 5 years ago

Anyone has an issue with the latest copy? I installed manually and configurated. It seems it is not working. The default Vancouver style showed only ;:, changed the setting to long style, it says "No author listed. . . ;:." Also, the preview does not work.

EricMaeker commented 5 years ago

Hello, Can you paste the dokuwiki code of your page here please.

EricMaeker commented 5 years ago

Please install and test this new version (sept-2019). Thanks

cbso-uc commented 4 years ago

Same problem encountered. Works when using PMID in your example: {{pubmed>24073682}}, I get "Maher Robert L, Hanlon Joseph, Hajjar Emily R. Clinical consequences of polypharmacy in elderly. Expert Opin Drug Saf. 2014 Jan;13(1):57-65. PMID : 24073682" If I try to use my own PMID: 30644303 {{pubmed>30644303}}, I end up with " ;:" I guess it it the parsing routine that is not working for some different citations.

EricMaeker commented 4 years ago

Hello, thanks for reporting. Please try to upgrade the plugin manually, purge your cache and test {{pubmed>vancouver:30644303}}

You should read : Chompoosang T, D'Apolito R, Lacagnina C, Peretti G, Zagra L. Total hip arthroplasty in rapidly progressive osteoarthritis of the hip: clinical and radiological outcome of a consecutive series of patients. J Biol Regul Homeost Agents. 2018 Nov-Dec;32(6 Suppl. 1):201-207

I've just tested on my configuration. Please confirm this issue.

Le dim. 27 oct. 2019 à 02:03, cbso-uc notifications@github.com a écrit :

Same problem encountered. Works when using PMID in your example: {{pubmed>24073682}}, I get "Maher Robert L, Hanlon Joseph, Hajjar Emily R. Clinical consequences of polypharmacy in elderly. Expert Opin Drug Saf. 2014 Jan;13(1):57-65. PMID : 24073682" If I try to use my own PMID: 30644303 {{pubmed>30644303}}, I end up with " ;:" I guess it it the parsing routine that is not working for some different citations.

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cbso-uc commented 4 years ago

No luck. See screenshot below,

Github shows no new commit since Sep 6 though. Any changes made in the code?

Capture

EricMaeker commented 4 years ago

Do your website has access to internet ? It seems like the plugins did not retrieve the citation XML file from NCBI.

Please, follow these steps :

Le dim. 27 oct. 2019 à 16:44, cbso-uc notifications@github.com a écrit :

No luck. See screenshot below,

Github shows no new commit since Sep 6 though. Any changes made in the code?

[image: Capture] https://user-images.githubusercontent.com/57051636/67637235-f8d87500-f89d-11e9-8cec-9fbc7645d812.JPG

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cbso-uc commented 4 years ago

That is not the problem as summaryxml and search works. See screenshots.

Capture2 Capture

cbso-uc commented 4 years ago

Checked the media/ncbi_esummary directory. Permission and ownership is fine. No files inside at all. Same results and no luck.

EricMaeker commented 4 years ago

This is a simple checking I have done :

Do you have any error from your server ? Did you purge your cache ?

Le dim. 27 oct. 2019 à 17:30, cbso-uc notifications@github.com a écrit :

Checked the media/ncbi_esummary directory. Permission and ownership is fine. No files inside at all. Same results and no luck.

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cbso-uc commented 4 years ago

I'd followed dokuwiki's instructions to purge cache and tried with different browsers.

I will try to disable other plugins and try again.

EricMaeker commented 4 years ago

Did you check user owner of the media/ncbi_esummary dir ? Use ls -al There should be four files : all your three pubmed_PMDI.xml.gz and crossref.xml.gz

Le dim. 27 oct. 2019 à 17:45, Eric Maeker eric@maeker.fr a écrit :

This is a simple checking I have done :

  • download latest Dokuwiki (without any plugin)
  • install pubmed freshly downloaded from github
  • create start from the dokuwiki UI
  • added {{pubmed>vancouver:30644303}}
  • result : Chompoosang T, D'Apolito R, Lacagnina C, Peretti G, Zagra L. Total hip arthroplasty in rapidly progressive osteoarthritis of the hip: clinical and radiological outcome of a consecutive series of patients. J Biol Regul Homeost Agents. 2018 Nov-Dec;32(6 Suppl. 1):201-207

Do you have any error from your server ? Did you purge your cache ?

Le dim. 27 oct. 2019 à 17:30, cbso-uc notifications@github.com a écrit :

Checked the media/ncbi_esummary directory. Permission and ownership is fine. No files inside at all. Same results and no luck.

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EricMaeker commented 4 years ago

Can you send the full code of your page ?

Le dim. 27 oct. 2019 à 17:48, cbso-uc notifications@github.com a écrit :

I'd followed dokuwiki's instructions https://www.dokuwiki.org/faq:pluginproblems to purge cache and tried with different browsers.

I will try to disable other plugins and try again.

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cbso-uc commented 4 years ago

ls -la data/media/ncbi_esummary is totally empty total 8 drwxrwxr-x 2 www-data www-data 4096 Jan 6 2019 . drwxrwsr-x 6 bso www-data 4096 Oct 27 09:59 ..

`====== Rapidly Progressive Osteoarthritis (RPOA) ======

===== References =====

NOCACHE`

EricMaeker commented 4 years ago

Absolutely no problem here with this wiki code !

What is the output of ls -la data/*

and ls -la data/media/*

Le dim. 27 oct. 2019 à 17:54, cbso-uc notifications@github.com a écrit :

ls -la data/media/ncbi_esummary is totally empty total 8 drwxrwxr-x 2 www-data www-data 4096 Jan 6 2019 . drwxrwsr-x 6 bso www-data 4096 Oct 27 09:59 ..

`====== Rapidly Progressive Osteoarthritis (RPOA) ======

  • Distinct from Primary OA by features and progression (({{pubmed>long:28328832}}))
    • older female more common {{pubmed>30644303}}
    • less ROM limitation compared with primary OA
    • pain onset average 3 years vs 5 years
    • 9.5% of a series of 863 patients who undergone THR (Primary OA 52.8%)
    • may be distinct from Primary OA
    • most commonly the hips but can occur in the shoulders
  • Two Stages (({{pubmed>long:28689367}}))
    • Early Chondrolysis Stage
      • MRI
        • bone edema
        • subchondral fracture
      • Late-Subchondral Destruction Stage
  • Two grading systems
    • Type 1-2 : no collapse vs collapse
    • Grades 1-3
      • Grade 1 - jt space narrowed
      • Grade 2 - deformed femoral head with <= 5mm ascension above teardrop
      • Grade 3 - complete loss of jt space, osteolysis, > 5mm ascension {{ :msk:rpoa_grades.jpg?400 |}}
    • Distinct feature vs Primary OA
    • presences of geodes at all stages
    • osteophytes absent or not prominent
    • absence of a demarcation between healthy and necrotic tissue cf. AVN
  • corticosteroid injection - less likely to be effective to manage pain in advanced stages
  • Definitive treatment - THR
  • Added surgical difficulties - opinion varies
    • intra and postoperative blood loss was similar in one series but higher blood loss reported in another series
    • immediate postop complication - not significant
    • prosthesis take and complications concerns raised - no hard evidence as far as reported (({{pubmed>long:30644303}}))

===== References =====

NOCACHE`

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EricMaeker commented 4 years ago

Did you set a different path in the config file of your site for the pubmed plugin ?

cbso-uc commented 4 years ago

tried disabling all plugins except farmer and pubmed, still no luck.

bso@R3SSD:/var/www/dokuwiki $ ls -la data/ total 96 drwxrwsr-x 12 bso www-data 4096 Jan 6 2019 . drwxrws--- 8 bso www-data 4096 Jan 6 2019 .. drwxrwsr-x 2 bso www-data 4096 Jan 6 2019 attic drwxrwsr-x 17 bso www-data 4096 Oct 27 10:49 cache -rwxrwsr-x 1 bso www-data 19724 Jan 6 2019 deleted.files -rwxrwsr-x 1 bso www-data 6516 Jan 6 2019 dont-panic-if-you-see-this-in-your-logs-it-means-your-directory-permissions-are-correct.png -rwxrwsr-x 1 bso www-data 12093 Jan 6 2019 dont-panic-if-you-see-this-in-your-logs-it-means-your-directory-permissions-are-correct.xcf -rwxrwsr-x 1 bso www-data 32 Jan 6 2019 _dummy -rwxrwsr-x 1 bso www-data 139 Jan 6 2019 .htaccess drwxrwsr-x 2 bso www-data 4096 Jan 6 2019 index drwxrwsr-x 2 bso www-data 4096 Oct 27 10:58 locks drwxrwsr-x 6 bso www-data 4096 Oct 27 09:59 media drwxrwsr-x 2 bso www-data 4096 Jan 6 2019 media_attic drwxrwsr-x 2 bso www-data 4096 Jan 6 2019 media_meta drwxrwsr-x 4 bso www-data 4096 Mar 17 2019 meta drwxrwsr-x 4 bso www-data 4096 Jan 6 2019 pages drwxrwsr-x 2 bso www-data 4096 Oct 26 19:08 tmp bso@R3SSD:/var/www/dokuwiki $ ls -la data/media total 24 drwxrwsr-x 6 bso www-data 4096 Oct 27 09:59 . drwxrwsr-x 12 bso www-data 4096 Jan 6 2019 .. drwxrwxr-x 2 www-data www-data 4096 Jan 6 2019 ncbi_esummary drwxrwxr-x 2 www-data www-data 4096 Oct 27 09:59 ncbi_esummary_doi_pdf drwxrwxr-x 2 www-data www-data 4096 Oct 27 09:59 ncbi_esummary_pmid_pdf drwxrwsr-x 2 bso www-data 4096 Jan 6 2019 wiki

cbso-uc commented 4 years ago

bso@R3SSD:/var/www/dokuwiki $ ls -la lib/plugins/pubmed/conf total 16 drwxrws--- 2 www-data www-data 4096 Oct 27 09:28 . drwxr-sr-x 7 www-data www-data 4096 Oct 27 09:28 .. -rwxrwx--- 1 www-data www-data 314 Oct 27 09:28 default.php -rwxrwx--- 1 www-data www-data 509 Oct 27 09:28 metadata.php

EricMaeker commented 4 years ago

Try in dokuwiki path

sudo chown bso:www-data -R *

And if this does not correct the plugin functions, please have a look at your server log file and php log file. Check any error found.

cbso-uc commented 4 years ago

Apache2 error.log

[Sun Oct 27 11:23:56.818193 2019] [php7:warn] [pid 20055] [client 184.64.172.33:12222] PHP Warning: Declaration of syntax_plugin_pubmed::handle($match, $state, $pos, &$handler) should be compatible with DokuWiki_Syntax_Plugin::handle($match, $state, $pos, Doku_Handler $handler) in /var/www/dokuwiki/lib/plugins/pubmed/syntax.php on line 14 [Sun Oct 27 11:23:56.818340 2019] [php7:warn] [pid 20055] [client 184.64.172.33:12222] PHP Warning: Declaration of syntax_plugin_pubmed::render($mode, &$renderer, $data) should be compatible with DokuWiki_Syntax_Plugin::render($format, Doku_Renderer $renderer, $data) in /var/www/dokuwiki/lib/plugins/pubmed/syntax.php on line 14

EricMaeker commented 4 years ago

What is your PHP version ?

Éric

Le dim. 27 oct. 2019 à 18:27, cbso-uc notifications@github.com a écrit :

Apache2 error.log

[Sun Oct 27 11:23:56.818193 2019] [php7:warn] [pid 20055] [client 184.64.172.33:12222] PHP Warning: Declaration of syntax_plugin_pubmed::handle($match, $state, $pos, &$handler) should be compatible with DokuWiki_Syntax_Plugin::handle($match, $state, $pos, Doku_Handler $handler) in /var/www/dokuwiki/lib/plugins/pubmed/syntax.php on line 14 [Sun Oct 27 11:23:56.818340 2019] [php7:warn] [pid 20055] [client 184.64.172.33:12222] PHP Warning: Declaration of syntax_plugin_pubmed::render($mode, &$renderer, $data) should be compatible with DokuWiki_Syntax_Plugin::render($format, Doku_Renderer $renderer, $data) in /var/www/dokuwiki/lib/plugins/pubmed/syntax.php on line 14

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cbso-uc commented 4 years ago

PHP7.3

EricMaeker commented 4 years ago

Ah ok, give me few hours to test with PHP 7.3 please.

Le dim. 27 oct. 2019 à 18:31, cbso-uc notifications@github.com a écrit :

PHP7.3

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EricMaeker commented 4 years ago

What is the version of dokuwiki ?

Le dim. 27 oct. 2019 à 18:35, Eric Maeker eric@maeker.fr a écrit :

Ah ok, give me few hours to test with PHP 7.3 please.

Le dim. 27 oct. 2019 à 18:31, cbso-uc notifications@github.com a écrit :

PHP7.3

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EricMaeker commented 4 years ago

Can you update the pubmed plugin, I've just pushed new code and test please ?

Le dim. 27 oct. 2019 à 18:46, Eric Maeker eric@maeker.fr a écrit :

What is the version of dokuwiki ?

Le dim. 27 oct. 2019 à 18:35, Eric Maeker eric@maeker.fr a écrit :

Ah ok, give me few hours to test with PHP 7.3 please.

Le dim. 27 oct. 2019 à 18:31, cbso-uc notifications@github.com a écrit :

PHP7.3

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cbso-uc commented 4 years ago

2018-04-22b "Greebo"

manually reinstalled plugin from your updated files in GitHub. Still the same issue. there are no files in data/media/ncbi_esummary

Sorry to have taken up your evening.

EricMaeker commented 4 years ago

No problem. Can you send the new php error please.

Le dim. 27 oct. 2019 à 19:13, cbso-uc notifications@github.com a écrit :

2018-04-22b "Greebo"

manually reinstalled plugin from your updated files in GitHub. Still the same issue. there are no files in data/media/ncbi_esummary

Sorry to have taken up your evening.

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EricMaeker commented 4 years ago

Ok code updated. Seems ok with PHP7. Can you update and test please

Le dim. 27 oct. 2019 à 19:41, Eric Maeker eric@maeker.fr a écrit :

No problem. Can you send the new php error please.

Le dim. 27 oct. 2019 à 19:13, cbso-uc notifications@github.com a écrit :

2018-04-22b "Greebo"

manually reinstalled plugin from your updated files in GitHub. Still the same issue. there are no files in data/media/ncbi_esummary

Sorry to have taken up your evening.

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cbso-uc commented 4 years ago

Updated, checked permissions and cleared cache. Re-saved dokuwiki configuration. Restarted apache2. No luck. Checked error.log - no longer flag previous error. No new error item in log.

EricMaeker commented 4 years ago

Mmmm. Do you have apache errors ?

cbso-uc commented 4 years ago

Nothing suggestive in the Apache log. Could be a configuration issue but too hard for me to figure out. I will revert to Ikuo Obataya’s more basic version of the plugin for now. Thanks for taking the time to look into this.

EricMaeker commented 4 years ago

Ok i will make some tests on debian10 and send back a small report asap.

EricMaeker commented 4 years ago

Ok Test done :

Perfect result without any error... Please check your configuration. I can help you to find what is wrong on your server

Le lun. 28 oct. 2019 à 17:35, Eric Maeker eric@maeker.fr a écrit :

Ok i will make some tests on debian10 and send back a small report asap.

EricMaeker commented 4 years ago

Also done a chmod 777 -R * at dokuwiki root before running dokuwiki install.php

Le mar. 29 oct. 2019 à 13:01, Eric Maeker eric@maeker.fr a écrit :

Ok Test done :

  • Freshly installed Debian10 desktop gnome
  • Installed Apache2
  • Installed PHP7 + PHP extensions
  • Nothing more
  • Dokuwiki freshly downloaded from the dokuwiki site
  • Pubmed plugin freshly downloaded from the github
  • Testing {{pubmed>vancouver:30644303}}

Perfect result without any error... Please check your configuration. I can help you to find what is wrong on your server

Le lun. 28 oct. 2019 à 17:35, Eric Maeker eric@maeker.fr a écrit :

Ok i will make some tests on debian10 and send back a small report asap.

cbso-uc commented 4 years ago

I have also done a similar test with a minimal os install and ran into the same issues which leads me to think Debian on the Raspberry Pi (Raspbian) seems to be responsible.

Observations:

The steps were as follows :

cbso-uc commented 4 years ago

May be you can figure out what is wrong from the phpinfo() output attached.

PHP 7.3.11-1_deb10u1 - phpinfo().pdf

EricMaeker commented 4 years ago

Thanks for this report. Did you install PHP extensions ?

sudo apt-get install -y php7.3-dom php7.3-simplexml php7.3-ssh2 php7.3-xml php7.3-xmlreader php7.3-curl php7.3-exif php7.3-ftp php7.3-gd php7.3-iconv php7.3-imagick php7.3-json php7.3-mbstring php7.3-posix php7.3-sockets php7.3-tokenizer

Le mer. 30 oct. 2019 à 03:56, cbso-uc notifications@github.com a écrit :

May be you can figure out what is wrong from the phpinfo() output attached.

PHP 7.3.11-1_deb10u1 - phpinfo().pdf https://github.com/EricMaeker/dokuwiki-plugin-pubmed/files/3786710/PHP.7.3.11-1_deb10u1.-.phpinfo.pdf

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EricMaeker commented 4 years ago

Also summaryxml bug corrected and commited

cbso-uc commented 4 years ago

Thanks for the pointers. Finally worked out where the problem is: need to install php-xml

After reinstalling Raspbian several times and testing PHP extensions one at a time, narrowed down to php-xml.

For anyone using Raspbian on a Raspberry Pi as a webserver, these are the steps from a basic install starting from scratch (substitute dokuwiki version as applicable):

sudo apt update; sudo apt install apache2 -y sudo apt install php libapache2-mod-php -y sudo apt install php-xml -y sudo systemctl restart apache2 cd /var/www/html sudo wget https://download.dokuwiki.org/src/dokuwiki/dokuwiki-stable.tgz sudo tar xzf dokuwiki-stable.tgz sudo mv dokuwiki-2018-04-22b dokuwiki sudo chown www-data:www-data -R dokuwiki sudo chmod 2775 -R dokuwiki cd dokuwiki/lib/plugins/

now download the current pubmed plugin files from GitHub and place in the plugins folder. Make sure they are in a directory named pubmed. Then change ownership and permission

sudo chown www-data:www-data -R pubmed sudo chmod 2775 -R pubmed

Goto your webbrowser and connect to dokuwiki to finish installation: http://your-server.ip.address/dokuwiki/install.php

To test pubmed plugin, create a new page with the following markup: ====== PlayGround ====== {{pubmed>clear_summary:28328832}} {{pubmed>long:28328832}}

cbso-uc commented 4 years ago

Pubmed_Success

EricMaeker commented 4 years ago

Yes only one extension is necessary. php-xml Thanks for your report and documentation I will add a notice in the readme file

Le mer. 30 oct. 2019 21:32, cbso-uc notifications@github.com a écrit :

[image: Pubmed_Success] https://user-images.githubusercontent.com/57051636/67896482-0ef66780-fb22-11e9-915e-0a4bc80d5130.JPG

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