INSTALL

mobyle2 installation procedure
==============================

Disclaimer: this document is a work in progress, which is currently only aimed
at facilitating setup for development purposes.

Development setup
-----------------

This procedure describes the installation of mobyle2 in a virtualenv sandbox for 
development purposes.

### Install Prerequisites
Prior to setting up mobyle2, you need to:
* install virtualenv: **virtualenv** is a tool to create isolated Python environments. It's safer to
set up your mobyle2 development environment in such a sandbox, to prevent
library conflicts with your default Python environment.
* install mongodb

Distribution-specific notes for the installation of these prerequisites are available at the end of 
this document (currently Ubuntu and CentOS).

### Modify etc/hosts configuration for velruse authentication library to work
For authentication to work properly, the current code of mobyle2/velruse
forces you to connect to Mobyle in HTTP using the **mobyle2** host name.
Just add the following line in your '/etc/hosts' file:
    127.0.0.1 mobyle2

### Install mobyle2 in virtualenv

1. Create a mobyle2 environment
    $virtualenv mobyle2
or if you do not have a virtualenv wrapper
    $python [virtualenv.py full path] mobyle2
This will create the mobyle2 folder, which will contain the Mobyle2 environment.

Note: depending on your virtualenv version, it may be necessary to add the '--no-site-packages' option.
This option has no effect in recent relases, so it won't hurt to use it in any cases.

2. Run the activate script
    $cd mobyle2
    $. bin/activate


3. Install mobyle2
    $pip install -e git+https://github.com/mobyle2/mf-pyramid.git#egg=mf
    $pip install -e git+https://github.com/mobyle2/mobyle2.lib.git@develop#egg=mobyle2.lib
    $pip install -r src/mobyle2.lib/requirements.txt
    $pip install -e git+https://github.com/mobyle2/mobyle2.conf.git@develop#egg=mobyle2.conf
    $pip install -e git+https://github.com/mobyle2/mobyle2.web.git@develop#egg=mobyle2.web
Option '-e' will install mobyle2 in **edit mode** in the 'src/mobyle.web' folder
and create automatically a mobyle.web.pth path configuration file, so that you can
edit and test it directly.

4. Initialize the database

    python src/mobyle2.lib/scripts/db/mob_seed  --config src/mobyle2.conf/mobyle.ini

5. Load EDAM
(EDAM ontology, in OWL format, can be found at http://edamontology.org/EDAM.owl)
    python src/mobyle2.lib/scripts/imports/edam_import.py --config src/mobyle2.web/development.ini --edamfile [path to EDAM ontology owl file] init

6. Load Mobyle services
You can either:
- load existing Mobyle2 services directly. You can have such examples of descriptions in the Mobyle 2 services repository (https://github.com/mobyle2/mobyle2.services)
  you can chekout this repository locally along your other git repositories then load the services with the following command:
    python src/mobyle2.lib/scripts/db/mob_services_loader -public -init --config src/mobyle2.conf/mobyle.ini --load src/mobyle2.services/*.yaml
- import Mobyle1 XML service descriptions.
(XML files for Mobyle 1 can be found at ftp://ftp.pasteur.fr/pub/gensoft/projects/mobyle)
    python src/mobyle2.lib/import/mob_m1_services_import --config src/mobyle2.conf/mobyle.ini [path to Mobyle 1 XML files] -init -public

7. Start and connect to your mobyle2 server

    $pserve --reload src/mobyle2.web/development.ini

You're done! Go to:
http://mobyle2:6543/

10. Unit tests
You first need to install nose in the virtualenv:
$pip install nose
Once this is done, bin/activate needs to be re-sourced to update the path:
    $. bin/activate
**Warning**: to run the tests, please note that you need to start the server.
Otherwise, at least the login tests will fail.
Simply call:
    $python /usr/bin/nosetests src/mobyle2.web
(If nose is not installed on your system: $pip install nose)

### Ubuntu installation notes

1. Virtualenv
    $sudo apt-get install python-virtualenv

2. MongoDB
    $sudo apt-get install mongodb

### CentOS

1. Virtualenv
    $easy_install virtualenv

2. MongoDB
To install mongodb in CentOS:
Create a /etc/yum.repos.d/10gen.repo file to hold information about your repository.
If you are running a 64-bit system (recommended) place the following configuration in
/etc/yum.repos.d/10gen.repo file:

[10gen]
name=10gen Repository
baseurl=http://downloads-distro.mongodb.org/repo/redhat/os/x86_64
gpgcheck=0
enabled=1

    $yum update
    $yum install mongo-10gen mongo-10gen-server
    $mkdir /data
    $cd /data
    $mkdir db

for more information see: 
http://docs.mongodb.org/manual/tutorial/install-mongodb-on-redhat-centos-or-fedora-linux/

3. Git
    $yum install git.x86_64

4. Python on CentOS
You may have to recompile your Python Interpreter with --with-ssl option, if SSL support is not 
available by default in your installation.
    $cd Python-2.7.3
    $./configure --with-ssl 
    $make 
    $su
    $make install