IGEM:Washington/2009/Notebook/WikiDust/Entry Base

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iGEM Project name 1 Main project page

July 5

Did some more coding.

July 1

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.

June 30

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.

June 29

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:

  • create tinkercell device skeleton from sequence?
  • create imagemap of tinkercell device
  • suggest registry pages to link to
  • create new pages from tinkercell device
  • NOT automate actual submission process
  • create plots for tinkercell device
  • add data to plots

June 26

Realized the Tinkercell blog is a much better starting point than the module index. Read through a lot of it.

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.

June 25

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.

June 23

figured out how to add functions to tinkercell

  • edit the pythonscripts file
  • put symlinks to each .py in the py directory
  • are headers in each .py necessary anymore? no. keeping them for now though, just in case.

learned some stuff about how tinkercell loads python scripts, which forced a reorganization of the program

  • smee will be split into addlink, createmap, and submitpart (and possibly more later)
  • each of those will import tinkercelladapter and wikiadapter rather than having tinkercell actually load them
  • wikiadapter will load wikitools in turn and createmap will load Image
  • do i need to import tinkercell from my functions or is that automatic? automatic.
made a better diagram because i think it'll be useful in keeping the big picture in mind while coding:













June 22

did some more coding on Smee (which I've decided to call it unless I come up with something better after watching Peter Pan):

  • came up with a general structure for the program(bad webcam pic below)
  • defined a few classes and started adding methods
  • worked a lot on getting tinkercell to recognize my methods and visa versa (the method for adding your python code to tinkercell described here didn't work for some reason)
  • learned some basic stuff about how Mercurial works

June 21

worked some more on adding text to jeffwiki

  • can put text in an "added by jeffplugin" section at the top or bottom now
  • should be able to add whatever info from tinkercell is needed rather than just the part names

still need:

  • to figure out how to get info about the screenshot file (will probably just hard-code it for now)
  • to come up with an overall structure for the program

found out how to make templates and install skins, but still need a lot more before anything looks professional

June 20

installed python-wikitools

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:

  • login (only admin, not wikiuser works for some reason)
  • create a page
  • add text
  • delete a page

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

  • take charge of official uw gem wiki
  • http://2009.igem.org/Help:Template/Examples
  • set up an openwetware wiki
    • look at the other pages
    • move stuff from jeffwiki
    • move stuff from buildabetterregistry
    • move stuff from soslabwiki
    • embed stuff from google sites
  • oscillator blog by christina agapakis
  • learn about mediawiki templates
    • look at some of the good ones
    • take a nice photo for our custom one
  • contact bill flanigan about openwetware/iGEM/parts of the registry
  • testing pathway:
    • first jeffwiki
    • then openwetware
    • then sandbox on registry
  • imagemap from w3schools.com
  • string from tc to wiki

June 19

looked for ways to automate accessing mediwiki:

June 18

worked on a couple python methods for getting part information from the registry

so far most of it doesn't work

June 10

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

updated the Project Overview with my purpose and overview sections from the SOSLab wiki

June 9

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

Mediawiki installation

sudo aptitude install apache2 mysql-server php5 php5-mysql mediawiki

We are installing locally in /home/jeff

Pasted from <http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Ubuntu>


sudo vi /etc/php5/apache2/php.ini

Pasted from <http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Ubuntu>


upload_max_filesize = 8M

Pasted from <http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Ubuntu> memory_limit = 32M

Pasted from <http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Ubuntu>

cat /etc/lsb-release

Pasted from <http://blog.websitestyle.com/index.php/2007/01/18/how-to-find-out-your-ubuntu-version-name/>

DISTRIB_ID=Ubuntu DISTRIB_RELEASE=9.04 DISTRIB_CODENAME=jaunty DISTRIB_DESCRIPTION="Ubuntu 9.04"


?sudo vi /etc/mediawiki/apache.conf

Pasted from <http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Ubuntu>


mysql -u root -pwildcat

create database jeffwiki; grant create, select, insert, update, delete, alter, lock tables on jeffwiki.* to 'wikiuser'@'localhost' identified by '32kn2kjh'; flush privileges;

Pasted from <http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Damnsmalllinux>


Alias /jeffwiki /var/www/sbol.bhi.washington.edu/jeff/mediawiki-1.15.3/

June 3

set up editing by FTP:

  • Fetch
  • TextWrangler

added logos

found that /include/DefaultSettings.php has examples of all the customizations you can do installed stubmanager (needed for jmol plugin)

installed Jmol extension

  • created Jmol folder in /extensions
  • added files to it
  • added require_once('extensions/Jmol/Jmol.php'); to LocalSettings.php

customized Jmol

tried to upload a pdb file, but looks like file uploading isn't set up

waiting to meet with Mike for help with that

May 17

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

  • add motivation/background to powerpoint




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