README

BioLadder is an interactive tree of life viewer and wiki, 
and is open source under the GPL-V3 License. 

It is hosted at:
http://bioladder.kylethayer.com/
https://github.com/kylethayer/bioladder

If you wish to help, go to the project wiki page for more info:
https://github.com/kylethayer/bioladder/wiki/HowToHelp

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    Installing to run the site:
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To run it yourself, you need a web server, PHP and a MySQL Database.
You can get a combo install of all of them at:
http://www.apachefriends.org/en/xampp.html

Once you have those, make sure you have the code checked out in a 
directory that is being hosted.

Next go to the wiki page (localhost/wiki) and run through the setup,
connecting it to your database and such. When you are done, save the
LocalSettings.php file and add the following line to the end of it:
require_once( "$IP/LocalSettingsExtras.php" );
You may need to update the string "localhost" in LocalSettingsExtras.php
Next go to the Semantic MediaWiki setup
wiki/index.php?title=Special:SMWAdmin
and press the "Initialise or upgrade tables" button

Next you need data in your wiki. In order to set up the semantic forms
like they are on BioLadder.Org. Copy the source following pages from
     http://bioladder.kylethayer.com/wiki/index.php?title=
 to  http://localhost/wiki/index.php?title=
For the following pages:
  Property:Has_Simplified_Ancestor
  Property:Has_Wikipedia_Image
  Property:Has_Wikipedia_Page
  Template:Entry
  Form:Entry
  Category:Entry
  Project:Main

Now you can use the forms to fill out data, so Copy the data from, 
for example, http://bioladder.kylethayer.com/wiki/index.php?title=Human
to http://localhost/wiki/index.php?title=Human
"human" (http://localhost/wiki/index.php?title=Human&action=edit) 

Now go to http://localhost/ and the viewer should work.

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    Additional Installation for bots and code editing
***********************************************************

To modify the css, you will need the ruby gem Compass. Install
Ruby from here: http://www.ruby-lang.org/en/downloads/
and then install compass by running: gem install compass
To compile the Sass file run
compass compile viewer/resources/sass
To have compass monitor the Sass files as you edit it, run:
compass watch viewer/resources/sass

In order to compile the viewer for production, you will need
Sencha CMD (requires ruby and compass from above)
Version used in code is 3.1.1:
http://www.sencha.com/products/sencha-cmd/download
Then go to your viewer directory (in the shell or cmd) and type
sencha app build
It will put the compiled code in viewer/build/BioLadderOrg/production

If you want Google Analytics code to be built into your production
versions of the viewer code, just copy the 
googleAnalyticsInclude.html.template file, remove the template and
put in your google analytics ID.

For Google Analytics in the wiki, add to the end of LocalSettings.php:
$wgGoogleAnalyticsAccount = "UA-*********";

The PopularDescendants bot requires Ruby (see above) with the
mediawiki-gateway and rubygems installed.
  gem install rubygems-update
  gem install mediawiki-gateway
    (0.5.2 wouldn't install on it's own, you may need to run:
       gem install mediawiki-gateway -v '0.5.1')

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                The Code:
***********************************************************
The Code
There are two parts of the project:
1) wiki directory, which contains a mediawiki with symantic wiki
2) viewer directory, which contains a Sencha 2.1 app (only works 
   with IE10, Safari and Chrome)