Difference between revisions of "Upgrades and Changes"

Revision as of 08:42, 7 January 2013

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.

2012-01-04

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. Gregor Hagedorn 20:07, 4 January 2012 (CET)

2012-01-04

Installed git on species-id. Not entirely sure if that makes as widely available as needed on biowikifarm. --BobMorris 19:12, 11 January 2012 (CET)

2012-01-12

"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. --Gregor Hagedorn 00:35, 13 January 2012 (CET)

2012-01-27

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). Gregor Hagedorn 09:02, 27 January 2012 (CET)

2012-02-15

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! Gregor Hagedorn 23:18, 15 February 2012 (CET)

2012-02-16

Problem: SMW formats values with type URL as http:////www... , 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. Gregor Hagedorn 00:14, 16 February 2012 (CET)

2012-02-16

SMW wikis presently still have https://bugzilla.wikimedia.org/show_bug.cgi?id=34044 to be fixed soon Gregor Hagedorn 09:47, 16 February 2012 (CET)

2012-02-19

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

2012-02-21

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"). Gregor Hagedorn 00:59, 22 February 2012 (CET)

2012-03-01

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. Gregor Hagedorn 09:44, 2 March 2012 (CET)

2012-03-05

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 --Gregor Hagedorn 20:39, 5 March 2012 (CET)

2012-03-15

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:) svn switch http://svn.wikimedia.org/svnroot/mediawiki/tags/extensions/SemanticResultFormats/REL_1_7_1 SemanticResultFormats -- Gregor Hagedorn 09:09, 15 March 2012 (CET)

2012-03-21

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.

2012-03-30

SVG-Handling: changed $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 $wgMaxShellMemory needed to be increased (2×default). Installed strace for debugging of commands. Edit: it is set back again to 'rsvg' because $wgMaxShellMemory did the trick in rendering large SVG files and $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?]). Andreas Plank 09:49, 30 March 2012 (CEST)

2012-04-12

Enabling SMW on Specialmedia as well Gregor Hagedorn 08:41, 12 April 2012 (CEST)

2012-05-04

Added features via phpmyadmin-table support in phpmyadmin. See /etc/phpmyadmin/config-db.php /etc/dbconfig-common/phpmyadmin.conf --Andreas Plank 09:20, 4 May 2012 (CEST)

2012-07-13

Added profiling for http://offene-naturfuehrer.de --Andreas Plank 11:21, 13 July 2012 (CEST)

2012-07-26

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! Gregor Hagedorn 08:46, 26 July 2012 (CEST)

2012-08-17

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? --WikiSysop 01:32, 18 August 2012 (CEST)

2012-08-21

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 :-( --Gregor Hagedorn 10:26, 21 August 2012 (CEST)

2012-08-22

Note: found an incredible configuration help for both apache and nginx, which includes the thumb.php rewrites! See http://shorturls.redwerks.org/ --Gregor Hagedorn 18:49, 22 August 2012 (CEST)

2012-08-22

Added oggvideotools 0.8-1+b1 for http://www.mediawiki.org/wiki/Extension:OggHandler but is still not showing thumbs. --Andreas Plank 20:14, 22 August 2012 (CEST)

2012-08-23

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." --Gregor Hagedorn 01:52, 24 August 2012 (CEST)

2012-08-24

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. --Gregor Hagedorn 05:35, 24 August 2012 (CEST)

(Therefore reverted to the dotdebian php-version on 25.8., nginx/php-fpm do not work with the squeeze version... --Gregor Hagedorn 10:50, 26 August 2012 (CEST)

2012-08-29

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; --Gregor Hagedorn 21:20, 29 August 2012 (CEST)

2012-09-14

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. --Gregor Hagedorn 09:57, 14 September 2012 (CEST)

2012-09-22

1. 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.
2. 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.
3. Disabling MassEditRegex. This extension was useful, but was not compatible with 1.18, and is not available in 1.20 git.
4. 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.
5. Some cleanup in LocalSVNextensions of unused extensions, renamed or removed, see Svn logs for details if error should occur.
6. The preparation for testing 1.20 is yet incomplete; see Mediawiki snv to git migration for further extensions to check.

Gregor Hagedorn 22:56, 22 September 2012 (CEST)

2012-09-24

Added http://www.mediawiki.org/wiki/Extension:ContactPage for Special:Contact --Gregor Hagedorn 17:10, 24 September 2012 (CEST)

2012-10-13

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... --Gregor Hagedorn 12:02, 13 October 2012 (CEST)

2013-01-04

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 …

sudo -u www-data php ./maintenance/update.php  --quick --conf ./LocalSettings.php

… 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`. -- Andreas Plank 10:45, 4 January 2013 (CET)

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 --Gregor Hagedorn 23:44, 4 January 2013 (CET)

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. --Gregor Hagedorn 23:42, 4 January 2013 (CET)

2013-01-07

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!) --Gregor Hagedorn 08:42, 7 January 2013 (CET)