Upgrades and Changes

This page documents changes in the installed software on the biowikifarm (new software, new version, new configuration, etc.), including notes on known problems.

2010-10-12

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). --Andreas Plank 15:43, 12 October 2010 (CEST)

2010-10-14

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 Adding a new directory link. --Andreas Plank 15:28, 14 October 2010 (CEST)

2010-10-15

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
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
Removed sudo apt-get remove html2text ntfsprogs gparted gnome-mime-data --Gregor Hagedorn 12:06, 15 October 2010 (CEST)

2010-10-17

Updated VariablesExtension to v 1.3 (July 2010), from http://www.mediawiki.org/wiki/Extension:VariablesExtension --Gregor Hagedorn 23:58, 17 October 2010 (CEST)

2011-01-04

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. --Gregor Hagedorn 21:36, 4 January 2011 (CET)

2011-01-11

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. --Andreas Plank 00:14, 12 January 2011 (CET)

2011-01-15

Enabling MultiUpload extension again Gregor Hagedorn 11:36, 15 January 2011 (CET)

2011-01-22

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!

Fixed later by putting a cludge into the common.js files of assigning jquery/$. Only necessary for IE, annotated such.

2011-02-12

1. 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.
2. 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...
3. 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.
4. Hoping the thumb problem can be solved with this! Gregor Hagedorn 17:34, 12 February 2011 (CET)

2011-02-22

• Upgrade of testwiki to r82580, but still errors that need to be solved. See Error pages on testwiki. Upgrade of the semantic bundle in production wikis to r82579. --Andreas Plank 01:06, 22 February 2011 (CET)

2011-03-31

Activated apache module mod_deflate to compress files for client-server traffic. Settings see apache2.conf.--Andreas Plank 14:41, 31 March 2011 (CEST)

2011-05-27

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

 svn checkout https://biowikifarm.net/svn/NonSvnExtensions /path/to/local/NonSvnExtensions 
 # or a specific extension
 svn checkout https://biowikifarm.net/svn/NonSvnExtensions/myextension /path/to/local/myextension

If you check out the entire repository (svn co https://biowikifarm.net/svn/) you will get:

./svn
  ./artenquiz
  ./NonSvnExtensions

--Andreas Plank 10:52, 27 May 2011 (CEST)

2011-05-30

Upgrade of SMW (r88777) only on testwiki required additional extension Validator installed. Version 82579 of SMW shows no auto completion due to wrong 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. --Andreas Plank 11:40, 30 May 2011 (CEST)

2011-06-01

Upgrade testwiki’s semantic extension bundle to r89282 removed previous errors occurring using forms. Still some errors on Special:Types page. --Andreas Plank 00:02, 2 June 2011 (CEST)

2011-08-09

Upgrade to revision 93922 on all wikis. SMW causes some problems but can be solved as follows: (1) include_once("$IP/extensions/SemanticForms/SemanticForms.php"); is correct instead of old inclusion include_once("$IP/extensions/SemanticForms/includes/SF_Settings.php"); (2): on the wiki page Special: SMWAdmin all SMW-tables on all enabled wikis must be upgraded by «Initialise or upgrade tables» --Andreas Plank 00:27, 10 August 2011 (CEST)

2011-08-25

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.

2011-08-25

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!

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? Gregor Hagedorn 00:54, 27 August 2011 (CEST)

2011-09-05

Installing of ffmpeg for thumbs of OggHandler videos, but somehow it didn't help yet. --Andreas Plank 22:12, 6 September 2011 (CEST)

2011-09-08

A script rsvgWrapper.sh was written to get non-ASCII SVG-files working too (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/ --Andreas Plank 02:10, 9 September 2011 (CEST)

2011-09-16

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. Gregor Hagedorn 00:18, 17 September 2011 (CEST)

2011-09-26

As a fix to 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.

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.

2011-10-05

Under todays version of MediaWiki 1.18alpha (r98164) ISPI reports errors when running runJobs: cd /var/www/v-ispi/w; php ./maintenance/runJobs.php -v --conf ./LocalSettings.php 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.

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.

Gregor Hagedorn 18:24, 5 October 2011 (CEST)

2011-10-19

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. -- Gregor Hagedorn 00:08, 20 October 2011 (CEST)

2011-11-09

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! -- Gregor Hagedorn 20:31, 9 November 2011 (CET)