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README
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README
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/*
* README
*
* Copyright 2012 Chaitanya Talnikar <[email protected]>
*
*/
Welcome to the biographer simulator.
The simulator uses a Makefile to manage the project. make by default
executes the directive 'all' which consists of 'lint', 'doc', 'test' and
'pkg'.
The simulator source code does not consist of any external libraries
by default and they have to be fetched and installed.
Build libs:
1. If you are using Ubuntu, install necessary dependences to test and
build the software by typing in the terminal:
make deps
Otherwise please refer below for a list of dependencies:
#required to build bui
nodejs
npm
node-uglify
#required to build libSBGN.js
ant
git-core(git)
#required for creating documentation
jsdoc-toolkit(jsdoc)
#required for the offline app
libqtwebkit4
python-qt4
#required for lint code check
jshint
#required for unit testing
selenium python api
chromedriver(selenium webdriver)
2. Fetch and build the libs by executing the command:
make libs
The above commands adds the following libs:
biographer-ui
d3.js
libSBGN.js
3. To support SBML files in the simulator the biographer server needs to
be setup. First clone it:
hg clone https://code.google.com/p/biographer.server/ server
Now go through the README to install it and then link the server directory
to the web2py applications directory
ln -s $PWD/server /path/to/web2py/applications/biographer
Ensure that the correct server URL is put in main/settings.js(The
default URL is 'http://127.0.0.1:8000/biographer'):
serverURL = 'http://web2py-url:port/application-name'
Also the biographer server web2py app needs to know the location of the
simulator, so create a symlink to the main directory of the simulator to
the static directory of the biographer server application:
rm -rf /path/to/web2py/applications/biographer/static
ln -s $PWD/main /path/to/web2py/applications/biographer/static
or just copy the main directory to the server static folder:
cp -R main/. /path/to/web2py/biographer-server/static
4. For testing purposes if you are using Chrome you need to download the
Chrome WebDriver available at the following url:
http://code.google.com/p/chromedriver/downloads/list
Download the linux zip depending on your architechture and install it using
the commands:
tar -xvf chromedriver*.zip
sudo cp chromedriver /usr/bin
Now once you have the necessary libs you are ready to test the simulator or
create a deployable package.
Offline App(browse):
To test the application offline(no SBML support) using the qt webkit engine. Run:
make browse
Testing(test):
To run all the tests for the simulator, run:
make test
This executes all the tests including the file import/export, SBML server
tests and the Simulate, Analyse and Plot features using the selenium
browser testing framework along with python's unittest.
To run specific tests take a look at the main.py file in the tests directory.
The default browser is Chrome and the default URL is the localhost web2py
server. To change these settings modify the simulator.py file.
Packaging(pkg):
To create a package which can be easily deployed on a server execute:
make pkg
A zip file simulator.zip will be created in the root directory.
The following tasks don't really require the libs.
Code checking(lint):
To perform jshint on the js files execute:
make lint
Documentation(doc):
To generate documentation using jsdoc execute:
make doc
The docs will reside in the jsdoc directory.