Updating Debian and MediaWiki

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The neuro.imm.dtu.dk runs Debian and was on oldstable Lenny which is unfortunately running out of security updates so it was pressing to update to stable Squeeze. I edited my /etc/apt/sources.list and pressed the big “aptitude dist-upgrade” button.

I got a “Possible missing firmware /lib/firmware/e100/d102e_ucode.bin” issue which “aptitude install firmware-linux” apparently solved. Phew.

The computer is very old running lilo, and it now has a problem with booting. It wants to look at the floppy drive. F1 and a manual selection in the lilo menu gets it up and running. Maybe this has something to do with the root device ID that needs to be passed as a kernel parameter? I am unsure how to upgrade to grub.

I made the installation overwrite the /etc/mime.types with the distribution version loosing the “image/x-nifti-1 nii” line. With that line setup again I can serve the Nifti neuroimages from the Brede Wiki to client fslview or Chris Rorden’s MRIcron, see Eye muscle proprioception is represented bilaterally in the sensorimotor cortex on the Brede Wiki, where there are volumes linked.

After the upgrade of the system I wanted to go from an old version of MediaWiki installed outside the distribution system to the newer distribution-provided 1.15 MediaWiki. I installed the MediaWiki with “aptitude install mediawiki mediawiki-extensions mediawiki-semediawiki” which went without problems. However the associated database upgrade and reconfiguration are harder.

“php5 maintainance/update.php” almost worked. I ran into a GRANT issue getting an error. With “mysql -p wikidb” and the mysql command “GRANT ALL PRIVILEGES ON wikidb.* TO ‘wikiuser’@’localhost’ IDENTIFIED BY ‘password’ WITH GRANT OPTION ;” might have solved it. At least executing the update.php script the second time completed.

I copied my old LocalSettings.php to /var/lib/mediawiki rather than /etc/mediawiki, not sure why the other thing didn’t work. I enabled ParserFunctions, Cite, Graphviz extensions that where available in the distribution. OpenStreetMap extension SimpleMap seems not to be available in Debian so I copied the old version. I also copied the images to /var/lib/mediawiki/images and made new aliases in /etc/apache2/sites-available/default.

I installed ConfirmEdit extension and perhaps need to look into ReCaptcha as I am struggling with spam and “$wgSorbsURL = ‘http.dnsbl.sorbs.net.’;” not working much. I would also like to enable some Table rendering. At the moment tabulator- and comma-separated material is rendered poorly (as poorly as before the upgrade) in the wiki, see, e.g., an example on the Brede Wiki. There are some extensions that I didn’t get to work well with the old version of MediaWiki. A sortable table would be nice. Now the inclusion template just uses “white-space:pre; font-family: monospace;” style for the entire csv page.

Yet another issue is an update of a small Semantic MediaWiki on the server. hmmm…

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