Installed DirectedGraphWebMapPlugin -- Ian Holmes, 11 November 2005

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

Installed KoalaSkin, added new logo. -- Ian Holmes, 15 October 2005

Implemented a basic form of spam prevention: adding new external links is prohibited to non-authenticated users. -- Ian Holmes, 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... Ian Holmes, 07 Mar 05

We now have a simple blog-like functionality (LabLogPlugin, developed in-house). See Web Critic for a functional example. I've also added SessionPlugin (see Logon link on left bar) and EFetchPlugin (see e.g. PhylogeneticAlignmentReader^? or Paper Archive). - Ian Holmes, 5 March 2005

Put the TWiki code under CVS - Ian Holmes, 28 Feb 05

Ideas for upcoming enhancements:

• Simplest Possible Blog^?: create a Blog Web, with pages like Ian Holmes Current^?, Ian Holmes Recent^? and Ian Holmes Archive^? (auto-updated by "New Entry" button); also e.g. Ian Holmes 2802051218^? (for an entry on 28th Feb 2005 at 12:18 PM); the New Entry button puts INCLUDE directives in Ian Holmes Current^?, 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
• Simplest Possible Genome Browser^?: create a DNA Web, whose entries (when whitespace and other punctuation is stripped out) are DNA sequences. Then, for example, Human Chromosome I^?/1000-2000 auto-creates a link returning the substring from position 1000 to position 2000 of the Human Chromosome I^? page in the DNA Web. Later, add a reverse search feature that gives a graphical display showing all pages that have links to Human Chromosome I^?.
  • update (11/11/05): watch the Generic Genome Browser page and the mighty works of Andrew Uzilov!

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.org/$1
AliasMatch ^/$ /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