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Did some more coding.
tried to get the "upload imagemap" script fully working, but there's an issue with wikitools.wikifile.File.upload() freezing tinkercell. other than that it works. it's also pretty barebones and could use some polishing, but i guess that's for later.
installed poster-0.6.0 in the windows pythonpath because it's required for uploading with wikitools. i think it's the only dependency.
planning to separate the methods used from the actual "create imagemap" script. that way they can be loaded when tinkercell starts (somehow) and people can use them separately.
signed up for an OpenWetWare account
wrote a method to open all the edited pages after the rest of the script is done
put all my iGEM stuff into a somewhat organized directory structure
renamed Smee to WikiDust. i like the new name better, plus it implies that this project is a subset of tinkercell and that its purpose is to enhance things.
also did away with tinkercelladapter and wikiadapter (so much for that pretty diagram). they were getting in the way rather than helping. now that i've been coding with tinkercell for a while its C API is starting to seem more natural and i think i can just use it directly.
duplicated the imagemap method for wiki-formatted imagemaps. with a little more work the whole process of creating and uploading one should be working—at least on jeffwiki. the only problem is that Tinkercell thinks every part has width and height 1 pixel... so clicking on the links is an issue.
Tried to get the Create Imagemap function running. It generates a valid HTML imagemap (i think), but mediawiki doesn't support maps without an extension! I guess only some HTML tags are allowed on the Registry. I don't think there's any way to get it working on the Registry as it now stands.
And if we're going to be using an extension anyway, might as well convert my tools to use the wiki format imagemap.
installed the imagemap extension on jeffwiki.
brainstormed about what functions i'm really trying to implement:
Also looked around the Registry for different ways to get part information. You can do a BLAST search, which I didn't expect. A database made from downloaded part info and automatically updated somehow still seems like the best bet.
I've had the stomach flu for the last 2 days, so not much has been getting done.
I did watch Peter Pan, and I think I'll go with Smee.
There have been some issues getting a good setup in which to work with Tinkercell because the mac version is old and has different method names, and I haven't been able to sucessfully compile the new one. I've been running Tinkercell inside windows, which sort of works but is slow and cumbersome.
figured out how to add functions to tinkercell
learned some stuff about how tinkercell loads python scripts, which forced a reorganization of the program
did some more coding on Smee (which I've decided to call it unless I come up with something better after watching Peter Pan):
worked some more on adding text to jeffwiki
found out how to make templates and install skins, but still need a lot more before anything looks professional
installed VirtualBox and Windows XP to run the windows version of TinkerCell
skimmed the wikitools files and figured out how to do things with jeffwiki:
wrote a script to get a node name from tinkercell and create a page based on it
wrote some random bit of various methods... will need to come up with a good overall structure at some point
wrote part of a method to generate the imagemap
notes from 6/19 meeting
looked for ways to automate accessing mediwiki:
worked on a couple python methods for getting part information from the registry
so far most of it doesn't work
put most of my notes on this page (but not the parts that might be a security issue)
made an example part page to test things out in
read the mol plugin instructions again and realized you need to put the require_once() stuff at the bottom of LocalSettings.php, not just anywhere.
moved it and the plugin works!
learned some basic usage of the plugin like placing buttons and adjusting the features displayed
sudo aptitude install apache2 mysql-server php5 php5-mysql mediawiki
We are installing locally in /home/jeff
sudo vi /etc/php5/apache2/php.ini
Pasted from <http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Ubuntu> memory_limit = 32M
DISTRIB_ID=Ubuntu DISTRIB_RELEASE=9.04 DISTRIB_CODENAME=jaunty DISTRIB_DESCRIPTION="Ubuntu 9.04"
?sudo vi /etc/mediawiki/apache.conf
create database jeffwiki; grant create, select, insert, update, delete, alter, lock tables on jeffwiki.* to 'wikiuser'@'localhost' identified by '32kn2kjh'; flush privileges;
set up editing by FTP:
found that /include/DefaultSettings.php has examples of all the customizations you can do installed stubmanager (needed for jmol plugin)
installed Jmol extension
tried to upload a pdb file, but looks like file uploading isn't set up
waiting to meet with Mike for help with that
put in modify and delete options
sudo apt-get install apache2; sudo apt-get install php5; sudo apt-get install libapache2-mod-php5; sudo /etc/init.d/apache2 restart
creative commons license
jeffdevwiki just redirects to jeffwiki right now
so does the original mediawiki folder
also they both use the same database
meet with sean, deepak friday