Difference between revisions of "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.
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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 [[Upgrade and Change Archive|archived]]
  
 
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== 2010-10-12 ==
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== 2017-10-26 ==
  
Tried updating semantic forms (because of problems with rendering of partial forms) with svn checkout to 2.0.1 but this is r74654 and the current version r69050 is still 1.9.1. Currently no update done but altered includes/SF_LinkUtils.php according to r74654 (empty title handling). --[[User:Andreas Plank|Andreas Plank]] 15:43, 12 October 2010 (CEST)
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Entire Biowikfarm now runs on at least MW 1.26.2 [[User:Andreas Plank|Andreas Plank]] ([[User talk:Andreas Plank|talk]]) 22:32, 26 October 2017 (CEST)
  
== 2010-10-14 ==
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== 2017-11-12 ==
  
Upgrade of testwiki to r72972 caused odd webpages because new directories and files have been introduced by mediawiki.org: ./resources/ ./config/ ./load.php and the files ./load.php5 and ./trackback.php5. New symblic links were created also for the wikis following [[Mediawiki_installation#Adding a new directory link|Adding a new directory link]]. --[[User:Andreas Plank|Andreas Plank]] 15:28, 14 October 2010 (CEST)
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New Wiki https://biowikifarm.net/wikibase/ for experimenting with properties covering multiple Wikis at once --[[User:Andreas Plank|Andreas Plank]] ([[User talk:Andreas Plank|talk]]) 17:01, 16 November 2017 (CET)
  
== 2010-10-15 ==
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== 2017-12-30 ==
  
Removed obsolete packages:  sudo apt-get remove libldap2 liblzo1 libpq4 libsnmp9 libdb4.3 libdb4.4 libmyspell3c2 libnss3-0d libparted1.7-1 gcj-4.1-base libc-client2002edebian libdevmapper1.02 libjasper-1.701-1 libmagick9 libntfs9 libopencdk8 libbonobo2-0 libbonobo2-common<br/>
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Between 14. and 29.12 the biowikifarm experienced a serious outage. No data were lost, but a sequence of suddenly increased usage (perhaps through bots), resulting in a necessity to optimize and update software. However, in turn, this lead to software compatibility problems which proved hard to solve for all current administrators. We are working on improving our procedures and available resources to avoid such problems in the future. Among other changes, php was updated to 5.6 and the database to MariaDB 10.2 in this period. -[[User:Gregor Hagedorn|Gregor Hagedorn]] ([[User talk:Gregor Hagedorn|talk]]) 01:06, 30 December 2017 (CET)
Removed perl-libs, no dependencies violated, unclear whether needed or not: sudo apt-get remove libparse-debianchangelog-perl libclass-accessor-perl libxml-sax-perl  libxml-namespacesupport-perl libhtml-format-perl libfont-afm-perl libxml-simple-perl libxml-sax-expat-perl libxml-parser-perl libwww-perl libhtml-tree-perl libhtml-parser-perl libhtml-tagset-perl libio-string-perl libmailtools-perl liburi-perl<br/>
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Removed sudo apt-get remove html2text ntfsprogs gparted gnome-mime-data --[[User:Gregor Hagedorn|Gregor Hagedorn]] 12:06, 15 October 2010 (CEST)
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== 2010-10-17 ==
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== 2018-02-14 ==
  
Updated VariablesExtension to v 1.3 (July 2010), from http://www.mediawiki.org/wiki/Extension:VariablesExtension --[[User:Gregor Hagedorn|Gregor Hagedorn]] 23:58, 17 October 2010 (CEST)
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Installed and activated https://www.mediawiki.org/wiki/Extension:CookieWarning . The extension was not yet installed for version 1.26, and manually added (this may be relevant on next upgrade!) Folders .../mediawiki26/extensions-rich-features/CookieWarning and .../mediawiki26/extensions-simple-features/CookieWarning were manually created and filled with separately downloaded code (version 1.30). --[[User:Gregor Hagedorn|Gregor Hagedorn]] ([[User talk:Gregor Hagedorn|talk]]) 01:37, 14 February 2018 (CET)
  
== 2011-01-04 ==
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== 2018-12-19 ==
  
Mediawiki: Both main and staging upgraded to SVN revision 79596, this fixes the Semantic Forms bug as well as the bug with the new DB-Repo access problem. However, we tested only a slightly earlier version, so we may experience some new problems - please test and report everyone. --[[User:Gregor Hagedorn|Gregor Hagedorn]] 21:36, 4 January 2011 (CET)
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A new version of nodejs and parsoid have been installed, which makes it now possible to active the VisualEditor. The steps required to install nodejs and parsoid have been documented at [[Parsoid installation]] and here is [[Visual Editor|the guide to activate the Visual Editor in the individual wikis with different possible settings]]. This should make editing the wikis for regular users a lot easier.  
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--[[User:David Fichtmueller|David Fichtmueller]] ([[User talk:David Fichtmueller|talk]]) 16:08, 19 December 2018 (CET)
  
== 2011-01-11 ==
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== 2019-04-10 ==
  
Linked SemanticResultFormats, SemanticMediaWiki, SemanticForms, SemanticInternalObjects, SemanticDrilldown to the /usr/share/mediawiki/phase3/extension2 folder with higher svn version (r79970) to update them later separately. It was due to a bug in MySQL LIMIT calculations triggert by large offset and limit values in #ask queries. --[[User:Andreas Plank|Andreas Plank]] 00:14, 12 January 2011 (CET)
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Fix [[mediawikiwiki:Extension:UploadWizard|Extension:UploadWizard]] globally to have also soft dependency of [[mediawikiwiki:Extension:EventLogging|Extension:EventLogging]] for creating Campaigns it is necessary --[[User:Andreas Plank|Andreas Plank]] ([[User talk:Andreas Plank|talk]]) 12:58, 11 April 2019 (CEST)
  
== 2011-01-15 ==
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== 2019-07-10 ==
  
Enabling MultiUpload extension again [[User:Gregor Hagedorn|Gregor Hagedorn]] 11:36, 15 January 2011 (CET)
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Added extension Arrays to https://offene-naturfuehrer.de for the use to get large data unique --[[User:Andreas Plank|Andreas Plank]] ([[User talk:Andreas Plank|talk]]) 15:32, 10 July 2019 (CEST)
  
== 2011-01-22 ==
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== 2019-11-13 ==
  
Upgrading mediawiki to 1.18alpha (r80728) results in jKey and other Javascript failing in IE 8, while still working in Chrome and Firefox. Also r79970: same situation. Reverted to 79596 - no improvement. Javascript on IE fails, probably failed already before updating!
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Added cron job for <code>runJobs.php</code> of wikis with the simple extensions setup and added <code>/etc/logrotate.d/wiki-runJobs</code> for those logfiles generated by the cronjob triggered script of <code>extensions/CommonsMediaCaching/runJobs_simple-extensions.sh</code>. (Hope it works) --[[User:Andreas Plank|Andreas Plank]] ([[User talk:Andreas Plank|talk]]) 13:36, 13 November 2019 (CET)
  
Fixed later by putting a cludge into the common.js files of assigning jquery/$. Only necessary for IE, annotated such.
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== 2019-12-16 ==
  
== 2011-02-12 ==
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Fix RDF export for [[Extension:XMLTransformation]] (eg. used on https://terms.tdwg.org): <code>xsltproc</code> does not parse external URLs (?any more?), so local temporary files are created to process and transform the XML. --[[User:Andreas Plank|Andreas Plank]] ([[User talk:Andreas Plank|talk]]) 14:10, 16 December 2019 (CET)
  
# Tried to upgrade to Debian 6 Squeeze. Does not work with current xen kernel 2.6.18xen, squeeze requires at least 2.26 or udev (all user mode devices) will not work. Fail. Back to backup of virtual machine.
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== 2020-11-12 ==
# Checking whether to update the kernel. XenServer 5.5 (and present 5.6) support a lenny kernel with 2.6.xx (check). However, we run XenServer 5.0 with service packs. Installing current XenServer 5.6.xx requires ISO-to-CD, direct updating at physical server. -> not enough time, 1 day wasted...
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# However, [[Upgrading Imagemagick to a current version‎]] allowed to selectively compile only ImageMagick. This is now at '''6.6.0-4''' - identical to the current Lenny release.
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# Hoping the thumb problem can be solved with this! [[User:Gregor Hagedorn|Gregor Hagedorn]] 17:34, 12 February 2011 (CET)
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== 2011-02-22 ==
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Currently there are issues with the email notifications, which also means that it is not easy for new users to register: (1) the emails to confirm the email address are not send out,(2) the notifications to the admins to confirm the accounts are not send and even if they know that people registered and approved the accounts manually, (3) the email with the temporary passwords are not send out as well, so the users can't log in. Issues 1 and 2 can be avoided by regularly checking Special:ConfirmAccounts of your wiki, but the third issue can be solved by logging into the server via SSH and then running:
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cd /var/www/metawiki/
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php maintenance/changePassword.php --user=User\ Name --password=<insert temporary yet secure password here> --conf LocalSettings.php
  
* Upgrade of testwiki to r82580, but still errors that need to be solved. See [http://biowikifarm.net/testwiki/index.php?title=Error_pages&oldid=12012 Error pages on testwiki]. Upgrade of the semantic bundle in production wikis to r82579. --[[User:Andreas Plank|Andreas Plank]] 01:06, 22 February 2011 (CET)
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You can then send the temporary password to the users manually and ask them to change it once they have logged in (not sure if this happens automatically)
 
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Maybe this helps some of you. [[User:David Fichtmueller|David Fichtmueller]] ([[User talk:David Fichtmueller|talk]]) 15:16, 12 November 2020 (CET)
== 2011-03-31 ==
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Activated apache module mod_deflate to compress files for client-server traffic. Settings see apache2.conf.--[[User:Andreas Plank|Andreas Plank]] 14:41, 31 March 2011 (CEST)
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== 2011-05-27 ==
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Subversion control now of /usr/share/mediawiki/NonSvnExtensions '''and''' /usr/share/mediawikistaging/NonSvnExtensions. Currently mediawikistaging and mediawiki are synchronised when committing (somehow a compromise). In general, use svn (TortoiseSVN, kdesvn etc.) to manage those extensions. Use
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<source lang="bash">
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svn checkout https://biowikifarm.net/svn/NonSvnExtensions /path/to/local/NonSvnExtensions
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# or a specific extension
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svn checkout https://biowikifarm.net/svn/NonSvnExtensions/myextension /path/to/local/myextension
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</source>
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If you check out the entire repository (svn co https://biowikifarm.net/svn/) you will get:
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./svn
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  ./artenquiz
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  ./NonSvnExtensions
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--[[User:Andreas Plank|Andreas Plank]] 10:52, 27 May 2011 (CEST)
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== 2011-05-30 ==
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Upgrade of {{abbr|SMW}} (r88777) only on testwiki required additional extension Validator installed. Version 82579 of {{abbr|SMW}} shows no auto completion due to wrong {{abbr|JSON}} generation. But version r88777 has a bug when creating forms https://bugzilla.wikimedia.org/show_bug.cgi?id=29093. So an upgrade on productive wikis hasn't been done yet. --[[User:Andreas Plank|Andreas Plank]] 11:40, 30 May 2011 (CEST)
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== 2011-06-01 ==
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Upgrade testwiki’s semantic extension bundle to r89282 removed previous errors occurring using forms. Still some errors on Special:Types page. --[[User:Andreas Plank|Andreas Plank]] 00:02, 2 June 2011 (CEST)
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== 2011-08-09 ==
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Upgrade to revision 93922 on all wikis. {{Abbr|SMW}} causes some problems but can be solved as follows: (1) <code>include_once("$IP/extensions/SemanticForms/SemanticForms.php");</code> is correct instead of old inclusion <code>include_once("$IP/extensions/SemanticForms/includes/SF_Settings.php");</code> (2): on the wiki page [[Special: SMWAdmin]] all {{Abbr|SMW}}-tables on all enabled wikis must be upgraded by «Initialise or upgrade tables» --[[User:Andreas Plank|Andreas Plank]] 00:27, 10 August 2011 (CEST)
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== 2011-08-25 ==
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Changed the stable version fundamentally, abandoning the concept of extensions2, introducing extension for stable (currently 1.18), ext-trunk for newest, ext-tagged-release for extensions that have separate release cycles (especially the SMW extensions are annoyingly '''UNSTABLE''' in the "stable" mediawiki checkouts. Furthermore, changed the NonSVNExtensions folder, which no longer is NonSVN, but rather a checkout of the local biowikifarm svn!, to "ext-LOCAL-svn". Basically working, but several problems still known.
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== 2011-08-25 ==
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Fixed runJobs and media-caching-bot. Both run again on a 10 minute cron job. Actually, we could improve on it, so the metadata is better now. Reloading all previously cached images again to fix up the metadata! Thanks again to Manol, the original author of the caching bot, and to all who helped with testing the biowikifarm update!
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Open issues are the problems with sending emails, and a spurious error that rotates and distort a small number of images. Any more open issues for which neither a workaround nor a bug report exists yet? [[User:Gregor Hagedorn|Gregor Hagedorn]] 00:54, 27 August 2011 (CEST)
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== 2011-09-05 ==
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Installing of ffmpeg for thumbs of OggHandler videos, but somehow it didn't help yet. --[[User:Andreas Plank|Andreas Plank]] 22:12, 6 September 2011 (CEST)
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== 2011-09-08 ==
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A script rsvgWrapper.sh was written to get non-{{Abbr|ASCII}} {{Abbr|SVG}}-files working too ([https://bugzilla.wikimedia.org/show_bug.cgi?id=17678 bug] in rsvg-convert v2.22.2). You'll find it linked in MediaWikiCommonSettings.php. It translates in- and output files to a md5 hash and does the scaling in the openmedia cache folder. After it's done, it moves them back. when an update of rsvg is made, the script won't be necessary. Add: it was moved to /usr/share/mediawiki/ext-LOCAL-svn/SVGHandling/ --[[User:Andreas Plank|Andreas Plank]] 02:10, 9 September 2011 (CEST)
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== 2011-09-16 ==
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Test update of production version: https://bugzilla.wikimedia.org/show_bug.cgi?id=30844 is still prevent semantic forms to work with the newest version. However, since the RequestAccount bug (https://bugzilla.wikimedia.org/show_bug.cgi?id=30851 ) had been fixed, updated  "cd /usr/share/mediawiki; sudo svn update ext-trunk" to 97326 and switched /usr/share/mediawiki/phase3/extensions/ConfirmAccount symlink from 1.18 (../../extensions/ConfirmAccount) to trunk (../../ext-trunk/ConfirmAccount). -- Plus in stable (1.18): Maps and SemanticMaps von 1.0.2 auf 1.0.3 updated. [[User:Gregor Hagedorn|Gregor Hagedorn]] 00:18, 17 September 2011 (CEST)
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== 2011-09-26 ==
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As a fix to [https://bugzilla.wikimedia.org/show_bug.cgi?id=30844 bug 30844] today 1.18 was updated to newest SVN version ( 1.18alpha r98122), and SemanticForms was re-linked from a tagged version to 1.19 trunk (r98122). For long term stability, SemanticForms should later be linked back either to tagged or to 1.18, depending on which is being updated.
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[http://www.mediawiki.org/wiki/Extension:AccessControl Extension:AccessControl] is newly installed in the LocalSVN branch, i.e. /usr/share/mediawiki/ext-LOCAL-svn/AccessControl. It will next be tested on testwiki.
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== 2011-10-05 ==
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Under todays version of MediaWiki 1.18alpha (r98164) ISPI reports errors when running runJobs:
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cd /var/www/v-ispi/w; php ./maintenance/runJobs.php -v --conf ./LocalSettings.php
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resulting in "Failed opening required '/usr/share/mediawiki/phase3/StartProfiler.php' in /usr/share/mediawiki/phase3/maintenance/commandLine.inc on line 42". Today we upgraded to r99011 and the runJobs error seems to have been fixed.
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Documentation note: trunk, including Semantic Forms and Confirm Account, is on r98122. It may be problematic to change these, esp. Confirm Account is being strongly restructured. The tagged versions (most SMW extensions) are mostly at r95551, but should be unproblematic, because tagged to a release.
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[[User:Gregor Hagedorn|Gregor Hagedorn]] 18:24, 5 October 2011 (CEST)
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== 2011-10-19 ==
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Fixed problems with a botched installation of extensions into phase3/extensions (where only links should be in order to increase our ability to mix and match extension versions). In this process the stable version was updated to -r100281 and the following tagged extensions updated to newest tag: REL_1_3_2 ExternalData - REL_1_0_4 Maps - REL_1_0_4 SemanticMaps - REL_0_3 SemanticCompoundQueries - REL_1_6_2 SemanticMediaWiki - REL_1_6_2 SemanticResultFormats - REL_0_3 SemanticSignup. Within mediawiki (i.e. stable) ext-trunk was NOT updated (ConfirmEdit and Semantic Forms linking there). The MassEditRegex extension was newly linked (through stable). It is test-enabled on test (see http://biowikifarm.net/test/Special:Version) but not yet on the stable wikis. -- [[User:Gregor Hagedorn|Gregor Hagedorn]] 00:08, 20 October 2011 (CEST)
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== 2011-11-09 ==
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Updating mediawiki 1.18alpha (r100281) to 1.18.0beta1 (r102635). Updating AdminLinks to tagged 0.1.5, SemanticDrilldown to tagged 1.0, SemanticInternalObjects to tagged 0.6.7. UPDATE: ext-trunk (on which Semantic Forms and ConfirmAccount depend) was also accidentially updated to r102570, later reverted to r98122! -- [[User:Gregor Hagedorn|Gregor Hagedorn]] 20:31, 9 November 2011 (CET)
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== 2011-11-12 ==
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Problem with confirm account, bug reported, but no compatible version found. Reverting did not help. It turns out that running update.php on the testwiki in version 1.19 will destroy the 1.18 installations (because of the linked user authorization system, 1.19 modifies the 1.18 installation). Fixed by manually updating the user table, but: '''DO NOT RUN update.php on testwiki again''' -- Also, created a new extensions folder for Semantic Forms and ConfirmAccount in trunk-r98122, called ext-98122. Semantic Forms and ConfirmAccount now come from there, allowing to experiment with other extensions in newer trunk versions. Updating all of phase3, extensions, and ext-trunk to r102874 -- [[User:Gregor Hagedorn|Gregor Hagedorn]] 12 and 13. November 2011 (CET)
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Latest revision as of 15:16, 12 November 2020

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

2017-10-26

Entire Biowikfarm now runs on at least MW 1.26.2 Andreas Plank (talk) 22:32, 26 October 2017 (CEST)

2017-11-12

New Wiki https://biowikifarm.net/wikibase/ for experimenting with properties covering multiple Wikis at once --Andreas Plank (talk) 17:01, 16 November 2017 (CET)

2017-12-30

Between 14. and 29.12 the biowikifarm experienced a serious outage. No data were lost, but a sequence of suddenly increased usage (perhaps through bots), resulting in a necessity to optimize and update software. However, in turn, this lead to software compatibility problems which proved hard to solve for all current administrators. We are working on improving our procedures and available resources to avoid such problems in the future. Among other changes, php was updated to 5.6 and the database to MariaDB 10.2 in this period. -Gregor Hagedorn (talk) 01:06, 30 December 2017 (CET)

2018-02-14

Installed and activated https://www.mediawiki.org/wiki/Extension:CookieWarning . The extension was not yet installed for version 1.26, and manually added (this may be relevant on next upgrade!) Folders .../mediawiki26/extensions-rich-features/CookieWarning and .../mediawiki26/extensions-simple-features/CookieWarning were manually created and filled with separately downloaded code (version 1.30). --Gregor Hagedorn (talk) 01:37, 14 February 2018 (CET)

2018-12-19

A new version of nodejs and parsoid have been installed, which makes it now possible to active the VisualEditor. The steps required to install nodejs and parsoid have been documented at Parsoid installation and here is the guide to activate the Visual Editor in the individual wikis with different possible settings. This should make editing the wikis for regular users a lot easier. --David Fichtmueller (talk) 16:08, 19 December 2018 (CET)

2019-04-10

Fix Extension:UploadWizard globally to have also soft dependency of Extension:EventLogging for creating Campaigns it is necessary --Andreas Plank (talk) 12:58, 11 April 2019 (CEST)

2019-07-10

Added extension Arrays to https://offene-naturfuehrer.de for the use to get large data unique --Andreas Plank (talk) 15:32, 10 July 2019 (CEST)

2019-11-13

Added cron job for runJobs.php of wikis with the simple extensions setup and added /etc/logrotate.d/wiki-runJobs for those logfiles generated by the cronjob triggered script of extensions/CommonsMediaCaching/runJobs_simple-extensions.sh. (Hope it works) --Andreas Plank (talk) 13:36, 13 November 2019 (CET)

2019-12-16

Fix RDF export for Extension:XMLTransformation (eg. used on https://terms.tdwg.org): xsltproc does not parse external URLs (?any more?), so local temporary files are created to process and transform the XML. --Andreas Plank (talk) 14:10, 16 December 2019 (CET)

2020-11-12

Currently there are issues with the email notifications, which also means that it is not easy for new users to register: (1) the emails to confirm the email address are not send out,(2) the notifications to the admins to confirm the accounts are not send and even if they know that people registered and approved the accounts manually, (3) the email with the temporary passwords are not send out as well, so the users can't log in. Issues 1 and 2 can be avoided by regularly checking Special:ConfirmAccounts of your wiki, but the third issue can be solved by logging into the server via SSH and then running:

cd /var/www/metawiki/
php maintenance/changePassword.php --user=User\ Name --password=<insert temporary yet secure password here> --conf LocalSettings.php

You can then send the temporary password to the users manually and ask them to change it once they have logged in (not sure if this happens automatically) Maybe this helps some of you. David Fichtmueller (talk) 15:16, 12 November 2020 (CET)