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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. | + | 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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| | + | == 2017-10-26 == |
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| − | == 2012-01-04 ==
| + | 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) |
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| − | SemanticMaps and Maps returned from 1.0.5 to 1.0.4, after Problem with displaying the regional maps in http://nnvm.eu/web was detected. [[User:Gregor Hagedorn|Gregor Hagedorn]] 20:07, 4 January 2012 (CET)
| + | == 2017-11-12 == |
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| − | == 2012-01-04 ==
| + | 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) |
| − | Installed git on species-id. Not entirely sure if that makes as widely available as needed on biowikifarm. --[[User:BobMorris|BobMorris]] 19:12, 11 January 2012 (CET)
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| − | == 2012-01-12 == | + | == 2017-12-30 == |
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| − | "2012-01-11: 1.18.1 released". Updating mediawiki minor version update to svn r108779, including some minor fixes from 1.18.0 to 1.18.). Wikis tested, seem to be ok. Updating Debian with apt-get. --[[User:Gregor Hagedorn|Gregor Hagedorn]] 00:35, 13 January 2012 (CET)
| + | 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) |
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| − | == 2012-01-27 == | + | == 2018-02-14 == |
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| − | Changing collection extension from 1.18 (/usr/share/mediawiki/phase3/extensions/Collection pointing to ../../extensions/Collection) to 1.19 trunk svn (/usr/share/mediawiki/phase3/extensions/Collection pointing to ../../ext-trunk/Collection). [[User:Gregor Hagedorn|Gregor Hagedorn]] 09:02, 27 January 2012 (CET)
| + | 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) |
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| − | == 2012-02-15 == | + | == 2018-12-19 == |
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| − | A full system update has been completed, new and faster hardware is now running Xen 6 virtualization host and the biowikifarm virtual machine is a Debian 6. Previously we had an old kernel specially compiled for Xen, which could no longer be upgrade, so that a complete reinstall was necessary. Some long-standing problems could be improved on the way, but it also took longer than expected. All Wikis, subversion repository, system tools, and Django apps are running again, job and backup completely newly set up, and many more. The Fedora/Tomcat system will follow soon. This is a big achievement of a team consisting of three organisations (JKI, BGBM, SNSB) as well as biowikifarm contributors. This was a true collaborative effort for which I want to thank all! [[User:Gregor Hagedorn|Gregor Hagedorn]] 23:18, 15 February 2012 (CET) | + | 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. |
| | + | --[[User:David Fichtmueller|David Fichtmueller]] ([[User talk:David Fichtmueller|talk]]) 16:08, 19 December 2018 (CET) |
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| − | == 2012-02-16 == | + | == 2019-04-10 == |
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| − | Problem: SMW formats values with type URL as <nowiki>http:////www...</nowiki> , i.e. with four slashes! Firefox/Chrome ignore this, but older browsers don't. Attemt to fix this with minor Mediawiki software updates: Old version: MediaWiki 1.18.1 (r108898), Semantic MediaWiki (Version 1.6.2) (r102570), Semantic Result Formats (Version 1.6.2) (r102570). New version: MediaWiki 1.18.1 (r111595), Semantic MediaWiki (Version 1.7.0.2) (r111595), Semantic Result Formats (Version 1.7) (r111595). The update required an update of the SMW tables. [[User:Gregor Hagedorn|Gregor Hagedorn]] 00:14, 16 February 2012 (CET)
| + | 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) |
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| − | == 2012-02-16 == | + | == 2019-07-10 == |
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| − | SMW wikis presently still have https://bugzilla.wikimedia.org/show_bug.cgi?id=34044 to be fixed soon [[User:Gregor Hagedorn|Gregor Hagedorn]] 09:47, 16 February 2012 (CET)
| + | 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) |
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| − | == 2012-02-19 == | + | == 2019-11-13 == |
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| − | Problems with SMW 1.7. In a few weeks 1.7.1 shall be released - temporarily returning to 1.6: cd /usr/share/mediawiki/ext-tagged-release; sudo svn switch http://svn.wikimedia.org/svnroot/mediawiki/tags/extensions/SemanticMediaWiki/REL_1_6_2 SemanticMediaWiki; sudo svn switch http://svn.wikimedia.org/svnroot/mediawiki/tags/extensions/SemanticResultFormats/REL_1_6_2 SemanticResultFormats
| + | 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) |
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| − | == 2012-02-21 == | + | == 2019-12-16 == |
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| − | Change of configuration: The namespace NS_INTERNAL has been secured so that only logged in users may see it. This may need testing (Create a page that starts with the Namespace prefix in your language; English: "Internal:"; German: ""Intern"). [[User:Gregor Hagedorn|Gregor Hagedorn]] 00:59, 22 February 2012 (CET)
| + | 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) |
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| − | == 2012-03-01 == | + | == 2020-11-12 == |
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| − | Configuration change: ssh-login to the server (not the wikis etc.) is no longer possible with a password. Only login is the ssh public key that has been provided. [[User:Gregor Hagedorn|Gregor Hagedorn]] 09:44, 2 March 2012 (CET)
| + | 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 |
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| − | == 2012-03-05 ==
| + | 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. [[User:David Fichtmueller|David Fichtmueller]] ([[User talk:David Fichtmueller|talk]]) 15:16, 12 November 2020 (CET) |
| − | Upgrading to Semantic Mediawiki 1.7.1 (newly released). This should fix the bug that semantic URL properties are malformed and cannot be opened with older browsers (see above). Executed: cd /usr/share/mediawiki/ext-tagged-release; sudo svn switch http://svn.wikimedia.org/svnroot/mediawiki/tags/extensions/SemanticMediaWiki/REL_1_7_1 SemanticMediaWiki; sudo svn switch http://svn.wikimedia.org/svnroot/mediawiki/tags/extensions/SemanticResultFormats/REL_1_7 SemanticResultFormats --[[User:Gregor Hagedorn|Gregor Hagedorn]] 20:39, 5 March 2012 (CET)
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| − | == 2012-03-15 ==
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| − | Minor update of 1.18.1 to current (r113897) SVN rev. Adding http://www.mediawiki.org/wiki/Extension:JQueryMsg to enable http://www.mediawiki.org/wiki/Extension:UploadWizard. Both are used from trunk (ie. mediawiki version 1.20, not from 18.1 (Upload wizard broken there). Also upgrading SemanticResultFormats (1.7.1, was not yet available when SMW 1.7.1 was recently installed:) <code>svn switch http://svn.wikimedia.org/svnroot/mediawiki/tags/extensions/SemanticResultFormats/REL_1_7_1 SemanticResultFormats</code> -- [[User:Gregor Hagedorn|Gregor Hagedorn]] 09:09, 15 March 2012 (CET)
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| − | == 2012-03-21 ==
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| − | Replacing our locally modified (NonSvn) Version of Extension Loops with the official /mediawiki/ext-trunk/Loops version, the symlink was changed accordingly. Loops by default is limited to 100 loops, LocalSettings.php therefore changed to "ExtLoops::$maxLoops = 500;" -- transferred here from email by B. Zelazny.
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| − | == 2012-03-30 ==
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| − | SVG-Handling: changed [http://www.mediawiki.org/wiki/Manual:$wgSVGConverter $wgSVGConverter] from 'rsvg' to 'ImageMagick' because [[:File:Location Singapore ASEAN.svg]] and some others got not processed with rsvg-convert. Note that 'ImageMagick' uses also rsvg-convert internally, but does not fail to process such file. Additionally [http://www.mediawiki.org/wiki/Manual:$wgMaxShellMemory $wgMaxShellMemory] needed to be increased (2×default). Installed [http://en.wikipedia.org/wiki/Strace strace] for debugging of commands. '''Edit:''' it is set back again to 'rsvg' because [http://www.mediawiki.org/wiki/Manual:$wgMaxShellMemory $wgMaxShellMemory] did the trick in rendering large SVG files and [http://www.mediawiki.org/wiki/Manual:$wgSVGConverter $wgSVGConverter] 'ImageMagick' does not render correctly (it adds a white background [OK] and some parts of the image disappear [not OK: may be related to the white background?]). [[User:Andreas Plank|Andreas Plank]] 09:49, 30 March 2012 (CEST)
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| − | == 2012-04-12 ==
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| − | Enabling SMW on [http://species-id.net/specialmedia/ Specialmedia] as well [[User:Gregor Hagedorn|Gregor Hagedorn]] 08:41, 12 April 2012 (CEST)
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| − | == 2012-05-04 ==
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| − | Added features via phpmyadmin-table support in phpmyadmin. See /etc/phpmyadmin/config-db.php /etc/dbconfig-common/phpmyadmin.conf --[[User:Andreas Plank|Andreas Plank]] 09:20, 4 May 2012 (CEST)
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| − | == 2012-07-13 ==
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| − | Added profiling for http://offene-naturfuehrer.de --[[User:Andreas Plank|Andreas Plank]] 11:21, 13 July 2012 (CEST)
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| − | == 2012-07-26 ==
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| − | MobileFrontend was enabled since 2011-12-06, now temporarily disabled again, because it causes too many problems. For one, sometimes desktops are misidentified as mobile devices. Further, many things go missing, including vital footer information like Terms of use, Disclaimer or copyright icons. Waiting for UPGRADE to 1.20! [[User:Gregor Hagedorn|Gregor Hagedorn]] 08:46, 26 July 2012 (CEST)
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| − | == 2012-08-17 ==
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| − | updated mysql (squeeze), possible only after temporarily disabling dotdebian source, since dotdebian already provides mysql 5.5. Updated dotdebian php5. Left dotdebian source commented out for the moment. Tried downgrading php5 from dotdebian 5.3.15 to squeeze 5.3.3 -- (apt-cache showpkg php5 to show the version number, here 5.3.3-7+squeeze14, then sudo apt-get install php5=5.3.3-7+squeeze14). Result was "warning: downgrading php5 from 5.3.15-1~dotdeb.0 to 5.3.3-7+squeeze14. / (Reading database ... 83709 files and directories currently installed.) / Preparing to replace php5 5.3.15-1~dotdeb.0 (using .../php5_5.3.3-7+squeeze14_all.deb) ... / Unpacking replacement php5 ... / Setting up php5 (5.3.3-7+squeeze14) ...". But then the system still seems to be running the dotdebian version? --[[User:WikiSysop|WikiSysop]] 01:32, 18 August 2012 (CEST)
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| − | == 2012-08-21 ==
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| − | Added apt-get install ffmpeg ffmpeg2theora which was missing in our install. Symptom: thumb-images for videos are not generated. Install is necessary, but does not seem to be sufficient, thumbs still are not generated :-( --[[User:Gregor Hagedorn|Gregor Hagedorn]] 10:26, 21 August 2012 (CEST)
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| − | == 2012-08-22 ==
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| − | Note: found an incredible configuration help for both apache and nginx, which includes the thumb.php rewrites! See http://shorturls.redwerks.org/ --[[User:Gregor Hagedorn|Gregor Hagedorn]] 18:49, 22 August 2012 (CEST)
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| − | == 2012-08-22 ==
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| − | Added oggvideotools 0.8-1+b1 for http://www.mediawiki.org/wiki/Extension:OggHandler but is still not showing thumbs. --[[User:Andreas Plank|Andreas Plank]] 20:14, 22 August 2012 (CEST)
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| − | == 2012-08-23 ==
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| − | Trying new large-png scaler, see updated [[Mediawiki installation]], added $wgCustomConvertCommandsByExtension['png'] = "/usr/bin/pngscale %s %d %w %h"; to MediaWikiCommonSettings.php. BUT: Fail, wgCustomConvertCommandsByExtension does not exist in standard mediawiki, pngscaler's author dc writes: "That's something I added in a patch, that I attached to the bug, but patch was rejected. It's not necessary as you can perform conversions using a script which identifies the extension and invokes the correct tool." --[[User:Gregor Hagedorn|Gregor Hagedorn]] 01:52, 24 August 2012 (CEST)
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| − | == 2012-08-24 ==
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| − | Resetting php from the dotdebian 5.3.15 to the debian 6 squeeze version (5.3.3-7+squeeze14 apache2handler). deinstalled all php5 parts, reinstalled afterwards. But: memory requirements have not dropped significantly. --[[User:Gregor Hagedorn|Gregor Hagedorn]] 05:35, 24 August 2012 (CEST)
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| − | (Therefore reverted to the dotdebian php-version on 25.8., nginx/php-fpm do not work with the squeeze version... --[[User:Gregor Hagedorn|Gregor Hagedorn]] 10:50, 26 August 2012 (CEST)
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| − | == 2012-08-29 ==
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| − | Where a semantic form is available, the semantic form tab will be renamed to "edit" and normal edit to "edit source". Setting for all Wikis: $sfgRenameEditTabs = true; --[[User:Gregor Hagedorn|Gregor Hagedorn]] 21:20, 29 August 2012 (CEST)
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| − | == 2012-09-14 ==
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| − | In recent months we had some performance problems on the biowikifarm in response to increasing traffic. Some php-scripts require significant memory and as apache grows to a maximum memory footprint, we had to decrease the number of concurrently serving apache processes. We had been testing nginx configurations for a number of weeks and have switched them to active today. While all php is permanently switched, svn-dav, django (artenquiz) and fedora/java interaction remain presently reverse proxied to a few remaining apache processes. Traffic on these installations is presently low and we can address the reconfiguration separately. --[[User:Gregor Hagedorn|Gregor Hagedorn]] 09:57, 14 September 2012 (CEST)
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| − | == 2012-09-22 ==
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| − | # Changing timeout settings and the path to phymyadmin (to further reduce risk script bots which are constantly trying to break it). Contact me to learn the new location.
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| − | # Working towards installing mediawiki 1.20 from git, all checkouts have been made, but integrating old and new extensions still major work. Disabling MathStatFunctions (probably was never used, will become redundant with arrival of Lua). No wiki uses AddMediaWizard any longer, removed.
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| − | # Disabling MassEditRegex. This extension was useful, but was not compatible with 1.18, and is not available in 1.20 git.
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| − | # Disabling DPL=DynamicPageList=DynamicPageList2 which was used only on http://www.keytonature.eu/ + http://www.keytonature.eu/handbook/ + http://wiki.pms-lj.si/wiki/ + testwiki. This extension was deprecated already a long time; we would be using semantic mediawiki today. All remaining pages using DPL were searched and deleted or replaced.
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| − | # Some cleanup in LocalSVNextensions of unused extensions, renamed or removed, see Svn logs for details if error should occur.
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| − | # The preparation for testing 1.20 is yet incomplete; see [[Mediawiki snv to git migration]] for further extensions to check.
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| − | [[User:Gregor Hagedorn|Gregor Hagedorn]] 22:56, 22 September 2012 (CEST)
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| − | == 2012-09-24 ==
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| − | Added http://www.mediawiki.org/wiki/Extension:ContactPage for [[Special:Contact]] --[[User:Gregor Hagedorn|Gregor Hagedorn]] 17:10, 24 September 2012 (CEST)
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| − | == 2012-10-13 ==
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| − | Apache-behind-nginx minimized (most services, including php and jsp run without by now, only python/django not yet reconfigured): StartServers 1, MinSpareServers 1, MaxSpareServers 1, MaxClients 6, MaxRequestsPerChild 100. KeepAlive remains ON, the primary client is nginx... --[[User:Gregor Hagedorn|Gregor Hagedorn]] 12:02, 13 October 2012 (CEST)
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| − | == 2013-01-04 ==
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| − | Added http://www.mediawiki.org/wiki/Extension:OpenID to http://terms.gbif.org. There were problems with authentication with google: “Fehler:invalid_request. Error in parsing the OpenID auth request.”. Changing $wgTrustRoot = "http://terms.gbif.org/"; solved the problem. Update …
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| − | <syntaxhighlight lang="bash" style="margin-left:1.5em;">
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| − | sudo -u www-data php ./maintenance/update.php --quick --conf ./LocalSettings.php
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| − | </syntaxhighlight>
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| − | … caused an error while upgrading table `metawiki`.`account_requests`. Could be solved by manually adding the last 2 (new) columns acr_xff + acr_agent in `metawiki`.`account_requests`. -- [[User:Andreas Plank|Andreas Plank]] 10:45, 4 January 2013 (CET)
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| − | Due to the update above, the user database was broken until the evening (only some special operations failed, like new user confirmation and changing user settings). The update.php above affected the shared tables and user database and confirm accounts became version 1.20, which is incompatible with the 1.18 version that most mediawikis still use. The problem has been fixed by a restore of the failed tables from backup. User creation was identical, the only potential losses are user preference settings in the early morning hours --[[User:Gregor Hagedorn|Gregor Hagedorn]] 23:44, 4 January 2013 (CET)
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| − | Manually patched /usr/share/mediawiki20/extensions/Vector/modules/ext.vector.collapsibleNav.js to https://gerrit.wikimedia.org/r/#/c/40084/2/modules/ext.vector.collapsibleNav.js (see https://bugzilla.wikimedia.org/show_bug.cgi?id=43227). Vector menus are now working. --[[User:Gregor Hagedorn|Gregor Hagedorn]] 23:42, 4 January 2013 (CET)
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| − | == 2013-01-07 ==
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| − | Disabling EditOnlyOwnUserpage by David Fichtmüller, presumably due to changes in new mediawiki version it no longer allows non-admin users to edit their own user page. (Test with normal user, admin users are not affected!) --[[User:Gregor Hagedorn|Gregor Hagedorn]] 08:42, 7 January 2013 (CET)
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| − | == 2013-01-08 ==
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| − | Update of http://offene-naturfuehrer.de to MW 1.20.2.
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| − | * SMWAskAPI manually
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| − | * <code>$wgSharedTables = array("interwiki");</code> before running update, after update use MediaWikiCommonSettings again
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| − | * unclear error while SMW update process:<br/><code>Warning: mb_substr() expects parameter 2 to be long, string given in /usr/share/mediawiki20/extensions/ParserFunctions/ParserFunctions_body.php on line 670</code>
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| − | ON seem to work so far in MW 1.20.2.
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| − | --[[User:Andreas Plank|Andreas Plank]] 10:34, 8 January 2013 (CET)
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| − | == 2013-01-11 ==
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| − | mysql upgrade to 5.1.66-0+squeeze1. Note: php5-fpm is at 5.4.10. To improve catching the php error messages changed catch_workers_output = yes in /etc/php5/fpm/pool.d/www.conf --[[User:Gregor Hagedorn|Gregor Hagedorn]] 15:43, 11 January 2013 (CET)
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| − | == 2013-02-22 ==
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| − | Created full copy of VM. Upgrading debian, php now 5.4.11, mysql now 5.5.30, nginx now 1.2.7. Minor bugfix upgrade of mediawiki and extensions, without major version changes. HEAD of Vector and Widgets are now incompatible with mediawiki 1.20.x! --[[User:Gregor Hagedorn|Gregor Hagedorn]] ([[User talk:Gregor Hagedorn|talk]]) 08:03, 22 February 2013 (CET)
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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
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)
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:
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)
