Installed DirectedGraphWebMapPlugin -- IanHolmes, 11 November 2005

Installed MathModePlugin for excellent latex2html-style math graphics in pages. See KaKsRatios for an example. -- IanHolmes, 11 November 2005

Installed KoalaSkin, added new logo. -- IanHolmes, 15 October 2005

Implemented a basic form of spam prevention: adding new external links is prohibited to non-authenticated users. -- IanHolmes, 7 July 2005

Hmmmm, added InterSeqs and edited InterWikis, but link to YaleCGI:TestingCGIApplications failed when I omitted trailing $page. Think I messed up the code for that... IanHolmes, 07 Mar 05

We now have a simple blog-like functionality (LabLogPlugin, developed in-house). See WebCritic for a functional example. I've also added SessionPlugin (see %MAKETEXT{"Log In"}% link on left bar) and EFetchPlugin (see e.g. PhylogeneticAlignmentReader or PaperArchive). - IanHolmes, 5 March 2005

Put the TWiki code under CVS - IanHolmes, 28 Feb 05

Ideas for upcoming enhancements:

• SimplestPossibleBlog: create a Blog Web, with pages like IanHolmesCurrent, IanHolmesRecent and IanHolmesArchive (auto-updated by "New Entry" button); also e.g. IanHolmes2802051218 (for an entry on 28th Feb 2005 at 12:18 PM); the New Entry button puts INCLUDE directives in IanHolmesCurrent, etc, pointing to the newly-created entry. Should be just a few lines of perl
  • update (11/11/05): the LabLogPlugin does this (sort of). See e.g. WebCritic
• SimplestPossibleGenomeBrowser: create a DNA Web, whose entries (when whitespace and other punctuation is stripped out) are DNA sequences. Then, for example, HumanChromosomeI/1000-2000 auto-creates a link returning the substring from position 1000 to position 2000 of the HumanChromosomeI page in the DNA Web. Later, add a reverse search feature that gives a graphical display showing all pages that have links to HumanChromosomeI.
  • update (11/11/05): watch the GenericGenomeBrowser page and the mighty works of AndrewUzilov!

Chris, I'll probably do this quite soon but just to keep a journal & let you know what's up (feel free to dive into the Perl and do it yourself if the mood strikes you; I've been ordered to do chores this morning): RCS seems to be working except that if you edit a file while the lock is active, then it treats all your edits as part of the same revision.

There is a checkbox on the save page that says "release lock file". This does delete the RCS lockfile. However, currently the TWiki's concept of whether the "lock" is active actually doesn't depend on the lockfile, but only on whether the file was recently edited.

Quick fix (done): Temporarily changed line 399 of file /var/www/twiki/lib/TWiki.cfg from $doKeepRevIfEditLock = "1"; ...to... $doKeepRevIfEditLock = "0"; so that RCS is used even if the "lock" is active

Proper long-term fix (not yet done): Check for RCS lockfile on line 840 of /var/www/twiki/lib/TWiki/Store.pm (see "TODO" comment)

Will probably want to put a lockfile detection method in one of these files /var/www/twiki/lib/TWiki/Store/RcsFile.pm /var/www/twiki/lib/TWiki/Store/RcsWrap.pm

NB the line numbers might be slightly different from the ones in TWiki20040902.tar.gz because I uncommented a few debug/logging statements and may have inserted some lines here & there. Have not substantially edited the code yet though.

For reference:

• TWiki logfile for Feb 2005 is /var/www/twiki/data/log200502.txt
• TWiki debug file is /var/www/twiki/data/debug.txt
• Apache error logfile is /var/log/apache/error.log
• Apache access logfile is /var/log/apache/access.log

-- IanHolmes - 25 Feb 2005

Redirects and aliases in httpd.conf:

RedirectMatch ^/twiki/bin/view/Main/WebHome/?$ http://biowiki.org/
RedirectMatch ^/twiki/bin/view/Main/([A-Z][A-Za-z_]+[A-Z][A-Za-z_]+)/?$ http://biowiki.o\
rg/$1
AliasMatch ^/$ /var/www/twiki/bin/view
AliasMatch ^/([A-Z][A-Za-z_]+[A-Z][A-Za-z_]+)/?$ /var/www/twiki/bin/view/Main/$1
ScriptAlias /twiki/bin/ /var/www/twiki/bin/
... (rest of usual TWiki stuff)

-- IanHolmes - 25 Feb 2005