Upgrades and Changes

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This page documents changes in the installed software on the biowikifarm (new software, new version, new configuration, etc.), including notes on known problems. Upgrades and Changes from 2010 and 2011 are no longer shown and available through the page history. Older changes are occasionally archived



According to MediaWiki documentation on privilege rights to the wikiuser index, create, select, insert, update, delete, alter, lock tables should be set. But running the rebuildall.php maintenance script brings up the error DROP command denied to user 'wikiuser' for table 'smw_new'. So DROP must be activated for the wiki user to run the rebuildall.php script. Should be checked in phpmydamin if semantic mediawiki extensions are activated. --Andreas Plank (talk) 11:17, 14 December 2013 (CET)

Help:Installation General Notes for SMW states:
“For installation and upgrade, SMW needs the rights to create new tables (CREATE) and to alter tables (ALTER TABLE). You can remove both rights after SMW is set up. The script SMW_setup.php can use the DB credentials from AdminSettings.php for this purpose, avoiding the need of extra rights for the wiki DB user.”
Not sure whether table rights can stripped of the extended table rights or not. Running maintenance sudo rebuildall.php seems to need extended rights for SMW. --Andreas Plank (talk) 15:26, 8 January 2014 (CET)


Upgrade Semantic Forms to version 2.6 --Andreas Plank (talk) 22:36, 16 December 2013 (CET)


Falko Glöckler added WYSIWIG editor to MfN test wikis --WikiSysop (talk) 04:37, 24 December 2013 (CET)


Both storage and dump partitions increased to 350 GB each, content moved from old to new partition in Xen. Xen full VM export made. --Gregor Hagedorn (talk) 02:31, 15 January 2014 (CET)


Added Wiki http://www.mod-co.net/ --Andreas Plank (talk) 14:33, 28 April 2014 (CEST)


Disabled global inclusion of out of date Widgets extension in preparation for test of current Widgets Extension. There is a Widgets_Discussion page for discussion of the update and its use. It would be particularly helpful if sysops of affected farm wikis would mention what page on which wiki are affected. If brief, that can be done on this page. If not, please do so on Widgets_Discussion

When the new extension is in place, this page will carry a notice --BobMorris (talk) 17:02, 8 May 2014 (CEST) As of late on 8 May 2014 The Widgets extension is in place, but any wiki that wants to use it will have to enable it in its LocalSettings. At some future time to be decided by Gregor, Widgets will become available to all wikis in the farm, and a notice applied in this page. --BobMorris (talk) 23:02, 11 May 2014 (CEST)

In mediawiki20/extensions renamed Widgets Widgets.2012 --BobMorris (talk) 17:45, 8 May 2014 (CEST)


Fixed caching media. Adjusted path. --Andreas Plank (talk) 16:39, 11 May 2014 (CEST)


Fixed broken rsvg, maybe some libraryies were not up to date. Removed librsvg2-bin, updated package list installed it again librsvg2-bin. Works now. Still a problem https://bugzilla.wikimedia.org/show_bug.cgi?id=45054 (a blank between option height -h400 is needed) is fixed in MW 1.21. Current fix is

$wgSVGConverters ['rsvg'] ='$path/rsvg -w $width -h $height $input $output';// BUG resolved after MW 1.21 https://bugzilla.wikimedia.org/show_bug.cgi?id=45054

--Andreas Plank (talk) 18:23, 13 May 2014 (CEST)


Fixed missing cache directory (MWException) in OpenMedia and corrected symbolic links in following Wikis: all v-species, offene naturführer, studienstiftung, testwiki2, v-filteredpush, v-floramalesiana, v-fotoflora-bb, v-gbif-d, v-hypergarden, v-ibiosphere, v-ides, v-ispi, h = teachers handbook wiki, w = KeyToNature, v-lias (c = checklist, w= wiki), v-naturgucker/r, v-orowiki, v-phytomed, v-phytopathology, v-plantnet/terms/f, v-plantnet/uses/e, v-rosaceae, v-ukcounty, v-workbench, v-zsm --Andreas Plank (talk) 11:35, 30 May 2014 (CEST)


In the last week we had some problems as a result of incompatibility of the biowikifarm VM software and the virtualization host. The host has now been updated to Xen 6.2 with all patches. --Gregor Hagedorn (talk) 20:14, 7 June 2014 (CEST)


4 plantnet-project.org wikis fixed: Michel Chauvet reported the 4 plantnet-project.org wikis not working. When accessing the site, the error message "Fatal exception of type MWException" appeared. After setting $wgShowExceptionDetails = true;, the error message stated "Unable to create the localisation store directory '/var/www/v-plantnet/uses/e/cache'". This problem was easily fixed by running

cd /var/www/v-plantnet/uses/e/
sudo mkdir cache && sudo chown www-data:www-data cache

and repeating it in the other wiki directories. --David Fichtmueller (talk)


added new wikis:

  • GFBio Terms Wiki
  • Terminology Sandbox Wiki This wiki can be used by any BWF user to play around with the functionalities of SemanticMediaWiki without working on existing terminologies like on the TDWG Terms Wiki.

-- David Fichtmueller (talk) 10:40, 1 July 2014 (CEST)


After a crash some parts of the biowikifarm had to be recovered from backup. All database content is current to the last minute, media on our shared repositories (openmedia) are current to the last minute, but in some cases media uploaded to a local wiki between 2014-07-14 ca. 7:30 (last media backup) and ca. 18:00 may be missing. Similarly, the subversion repository was restored from the nightly backup, please report any errors you encounter. Our apologies for the service interruption! --Gregor Hagedorn (talk) 02:08, 15 July 2014 (CEST)


To improve long-term stability, a daily restart of nginx+php5-fpm was added to cron job (services-restart-php-nginx.sh) --Gregor Hagedorn (talk) 19:57, 23 July 2014 (CEST)


Changes for the Back-Ups: I changed some of the backup scripts:

  • All Wikis are now backed up automatically. Previously in order to back up a wiki it needed to be added to the corresponding file. This was forgotten when setting up some of the wikis in the recent past which is why some of the data was lost after the crash on 2014-07-14. Now all of the wikis within /var/www are backed up automatically with the possibility of blacklisting wikis that have a different backup strategy (e.g. practical plants). This makes setting up wikis easier and the backups more reliable.
  • The logs of the backup process are now stored in /var/log/backups/ so it is possible to determine what when wrong if somethings goes wrong.

--David Fichtmueller (talk) 16:17, 25 July 2014 (CEST)


Upgrade Django 1.4.2 to 1.6.5 for http://artenquiz.de. Additional python modules: django-registration, django_pyodbc (MSSQL database connections) --Andreas Plank (talk) 23:10, 7 August 2014 (CEST)


In the past days days, I encountered the Gateway Timeout issue several days. Restarting nginx helped, but it is still strange that it is happening several times a day. As a quick fix, I changed /etc/crontab to run the nginx-restart script not only once a day, but 5 times (6:15, 9:15, 12:15, 15:15 and 18:15). We still need to find the cause of this problem. --David Fichtmueller (talk) 16:13, 2 September 2014 (CEST)


Added configuration for http//artenquiz.bayernflora.de using http://diversityworkbench.net/Portal/DiversityDescriptions_Quiz_%28Artenquiz%29 --Andreas Plank (talk) 14:05, 28 September 2014 (CEST)


I updated a file in the ConfirmAccounts extensions, so it now shows on the Special:ConfirmAccounts page, the wiki in which the user has applied for an account. Also for the account requests that have been put on hold or rejected it shows the comment that was send to the user (if there is one). --David Fichtmueller (talk) 17:30, 21 November 2014 (CET)


  • Disabled the backup connection with the Bulgarian Key to Nature server as no longer required (BGBM backup working for 2 years now) --20:13, 23 November 2014 (CET)
  • 2014-11-28: (Alvaro) Checked if backups are still stored correctly in /var/backups (everything OK).


Running all apt-get updates, esp. updating php5. The latter required temporarily disabling the debian sources and relying only on dotdeb sources (else updates held back because versions got mixed). All sources re-enabled afterwards. --Gregor Hagedorn (talk) 02:05, 26 November 2014 (CET)


As the nginx configuration file was getting too large to handle, I split the config in 1 file per domain. See also: Nginx_Installation_and_Configuration#Virtual_hosts


sources.list updated, testing unstable were accidentially still active (from previous focussed install). Now all upgrades performed, all current, no packages held back any longer. --Gregor Hagedorn (talk) 23:29, 21 January 2015 (CET)


Since the nginx config file was split into one file for each domain, the first config file to be loaded was the one for abcd.biowikifarm.net. This however cause all requests from (sub)domains that are not mapped (e.g. http://example.biowikifarm.net or http://openbiodiversity.net) to display the ABCD wiki. I fixed this by renaming /etc/nginx/sites-enabled/default (config for the meta wiki) to 00_default, so it is now loaded first and all unmapped requests will show the meta wiki. --David Fichtmueller (talk) 15:19, 28 January 2015 (CET)


Applied Bugfix of api prop=imageinfo broken on PHP 5.4 with a patch manually generated from https://gerrit.wikimedia.org/r/#/c/28795/1/includes/api/ApiQueryImageInfo.php. Patch applied to all MW 1.20.7 wikis. --Andreas Plank (talk) 14:32, 5 February 2015 (CET)


NGINX conifg has globally locations for Openmedia, SpecialMedia. Because $wgForeignFileRepos ('fetchDescription') gets somehow only src="/o/media/thumb/3/3e/….jpg" without a full URL, so NGINX should have location settings vo /o/media or /s/media. So I guess symlinks in Web-Wiki-folders are not really necessary. --Andreas Plank (talk) 23:18, 7 February 2015 (CET)


I added a small script that will show some useful and commonly used shell commands to the user on the terminal. It is kind of like the small sibling of Selected Linux commands. Just type useful via the command line. It will currently prompt

#check if nginx config is valid (to be used before restarting)
sudo nginx -t 

#live view of the end (last 20 lines) of a log file
tail -f -n 20 /var/log/<log_file>

#gracefully restart apache, nginx and php-fpm
sudo /usr/sbin/apache2ctl -k graceful && sudo service nginx restart && sudo service php5-fpm restart

#update MediaWiki settings/tables/etc for a particular wiki (e.g. after enabling addons that require db tables)
cd /var/www/metawiki
php maintenance/update.php --conf /var/www/v-<wiki>/w/LocalSettings.php

I just added it, because I use such a script as well for another server I maintain and it proved to be useful. Feel free to add you own commands by calling edit-useful (or just open /var/lib/useful/useful.txt with the text editor of you choice [edit-useful uses nano]). Maybe this is of help for some of you, which is why I documented it here. --David Fichtmueller (talk) 12:49, 30 July 2015 (CEST)


Move of backups to external partition failed. Here's the log: User:Alvaro Ortiz-Troncoso/Moved_backups_to_/mnt/backup.


I made some minor updates to the backup scripts. The section for v-practicalplants (which is done separately from other wikis and media files) is now located in its separate script (daily_bak_special.sh) and is saved in <back_up_dir>/DAILY/special and the tar and 7zip commands are also executed there (the commands being executed in /var/www was partially responsible for the hard drive filling up). Additionally there is now another archive, also being saved in DAILY/special, which contains everything from /var/www, except the various cache/ and media/ directories and v-practicalplants. For details see Server backup and restore. --David Fichtmueller (talk) 16:31, 14 October 2015 (CEST)


I blocked and (bing bot) in the server .conf since they were misbehaving and didn't care about robots.txt Alvaro Ortiz-Troncoso (talk) 11:42, 10 November 2015 (CET)


Moved backups to external partition. Here's the log: User:Alvaro Ortiz-Troncoso/Moved_backups_to_/mnt/backup.


Activated Extension:Semantic Maps, Extension:Maps on OpenMedia to enable usage of coordinates of taken images. --Andreas Plank (talk) 23:47, 22 January 2016 (CET)


Activated Extension:Mp3Handler on all Wikis globally. Modified version is in biowikifarm subversion. --Andreas Plank (talk) 23:39, 27 January 2016 (CET)


Upgrade http://nnvm.eu/web/ from 1.20.7 to 1.26.2. Works. Yet TODO Modified icons in maps do not appear. --Andreas Plank (talk) 01:08, 20 February 2016 (CET)

2016-04-22 Installing Varnish

Added a test installation of Varnish on 8080. See http://biowikifarm.net/meta/Varnish . For MobileFrontend the Filecache which we still use HAS to be turned off. --WikiSysop (talk) 18:07, 22 April 2016 (CEST)


Generated new SSL certificates for all domains related to the biowikifarm, using Let's Encrypt. All wikis now fully support https, without the warnings many browsers has shown before. The list of all domains and subdomains supported is in the file /root/generate_certificates.sh. It was based on the list of Member wikis. If there are new wikis/domains in use, please update the list.

See HTTPS Support via Let’s Encrypt for more information. If there are mixed content warnings in your browser, when you try to access your wiki via https, check if there are no files connected via regular http-links, e.g. the wiki logo file.

The only domain I was not able to cover was http://wiki.infoflora.ch because it uses a proxy server. --David Fichtmueller (talk) 18:03, 22 June 2016 (CEST)


Both dump and storage partitions were recreated with considerably larger size. --Gregor Hagedorn (talk) 17:32, 12 December 2016 (CET)


Root partition is close to full, mainly because many different versions of mediawiki take up too much space. As a first relief, the local git checkout was moved to /mnt/storage/usr-share-mw-wmf-clone storage partition, linking back to /usr/share/. --Gregor Hagedorn (talk) 11:12, 12 August 2017 (CEST)

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