Wiki

Version 260 (Etienne Pallier, 03/22/2016 11:58 pm)

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h1. Technical Documentation for the PYROS project (FGFT-CC)
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HOWTO Format Redmine Wiki : http://www.redmine.org/projects/redmine/wiki/FrRedmineWikiFormatting
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{{>toc}}
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---
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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}I - TODO%
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 * Intégration dans Eclipse
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 * Séparation des BD Django et Pyros
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 * Intégration des modules Django déjà développés
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---
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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}I - DATABASE SCHEMA (v0.2.1)%
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{{thumbnail(PYROS_PDM_v021.png, size=300, title=Pyros data model)}}
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---
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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}II - Get the project (from gitlab)%
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h3. Project structure
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Once you have fetched the project, you should obtain this structure:
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<pre>
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PYROS/
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├── install/
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│   └── REQUIREMENTS.txt
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│   └── INSTALLATION.txt
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├── public/
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│   └── static/
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├── src/
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│   ├── manage.py
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│   ├── pyros/
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│   │   ├── __init__.py
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│   │   ├── __pycache__
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│   │   ├── settings.py
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│   │   ├── urls.py
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│   │   └── wsgi.py
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│   └── pyrosapp/
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│       ├── __init__.py
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│       ├── admin.py
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│       ├── apps.py
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│       ├── migrations
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│       ├── models.py
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│       ├── tests.py
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│       └── views.py
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</pre>
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h3. Get the project from the terminal
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<pre>
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git clone https://gitlab.irap.omp.eu/epallier/pyros.git PYROS
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(or also : git clone git@gitlab.irap.omp.eu:epallier/pyros.git PYROS)
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</pre>
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This creates a PYROS/ folder containing the project (with a .git/ subfolder for synchronization with the git repository)
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_If you just wanted a static copy of the project (without synchronization), just remove the .git/ folder:_
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<pre>
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$ rm -r .git/
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</pre>
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h3. Get the project from Eclipse
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1) Fetch the project
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File/Import project from git
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Select repository source: Clone URI: https://gitlab.irap.omp.eu/epallier/pyros.git
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Directory: 
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par défaut, il propose : /Users/epallier/git/pyros
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mais on peut le mettre ailleurs (c'est ce que j'ai fait)
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initial branch: master
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remote name: origin
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Import as general project
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Project name: PYROS
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2) Configure the project
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The project is created. Now, you have to set it as a «PyDev » and a « Django » project.
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clic droit sur le projet / PyDev / set as a PyDev project
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clic droit sur le projet / PyDev / set as a Django project
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clic droit sur le projet : on doit maintenant avoir un sous-menu Django
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clic droit sur le dossier src / PyDev / set as source folder (add to PYTHONPATH)
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clic droit sur projet / Properties / Pydev-Django :
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  - Django manage.py : src/manage.py
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  - Django settings module : pyros.settings
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3) Test by running the web server :
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clic droit sur projet, Django/Custom command/runserver
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check http://localhost:8000/
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4) Set Code style
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Window/Preferences : Pydev / Editor
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- Auto Imports : uncheck « Do auto import »
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- Code style:
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	- Locals … : camelCase
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	- Methods : camelCase() with first lower
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- Code style / Code Formatter: activer « use autopep8.py for code formatting »
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- Tabs : Tab length : 4
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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}III - INSTALLATION%
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---
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h3. Install MySql (only if necessary)
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 * Linux Ubuntu
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<pre>
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$ sudo apt-get install mysql-server
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$ sudo apt-get install mysql-client
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</pre>
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 * Linux CentOS
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<pre>
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TODO:
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$ sudo yum install mysql
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...
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</pre>
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 * Mac OS X
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Install XAMPP
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(but you could also use the pre-installed Mac OS MySql)
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<pre>
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TODO:
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</pre>
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 * Windows
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<pre>
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Download and install the newest version on https://dev.mysql.com/downloads/installer/
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Once installed, launch MySQL Installer. Clic on 'Add...' on the right.
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In MySQLServers section, choose the newest, then clic on next.
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Install and configure the server (just follow the installation guide).
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Then launch mysql (via the Windows menu).
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</pre>
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---
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h3. Install Python3.5 (only if necessary)
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 * Mac OS X :
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<pre>
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1) Installer MacPort
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(TODO: doc)
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2) Installer le "port" python35
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$ sudo port install python35
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</pre>
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 * Linux (Ubuntu) :
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<pre>
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$ sudo add-apt-repository ppa:fkrull/deadsnakes
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$ sudo apt-get update
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$ sudo apt-get install python3.5
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$ sudo pip install virtualenv
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</pre>
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 * Windows 7 :
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<pre>
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Go to https://www.python.org/downloads/windows/ , choose the wanted version
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On the wanted version’s page, download Windows x86 executable installer
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Run the executable
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    * On the first page, check "Add python3.5 to PATH"
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    * Choose "Install now" option
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Open cmd (windows + R, cmd) :
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 $ python -m pip install --upgrade pip
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 $ pip install virtualenv
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</pre>
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 * Windows 10 :
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<pre>
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TODO:
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</pre>
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---
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h3. Create a Python3 virtual environment dedicated to the project (inside the project folder)
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<pre>
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$ mkdir private/
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$ cd private/
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$ which python3.5 ("where python" for windows)
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/opt/local/bin/python3.5
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$ virtualenv-3.5 venv_py35_pyros -p /opt/local/bin/python3.5
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=> creates a venv_py35_pyros/ folder inside PYROS/private/
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</pre>
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---
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h3. Activate the python virtual environment (from inside the project)
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<pre>
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$ pwd
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.../PYROS/private
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$ source ./venv_py35_pyros/bin/activate (venv_py35_pyros/Scripts/activate on Windows)
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$ python -V
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Python 3.5.1
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$ which pip
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.../PYROS/venv_py35_pyros/bin/pip
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Upgrade pip to last version available:
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$ pip install --upgrade pip
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Collecting pip
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  Downloading pip-8.1.1-py2.py3-none-any.whl (1.2MB)
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Installing collected packages: pip
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  Found existing installation: pip 7.1.2
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    Uninstalling pip-7.1.2:
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      Successfully uninstalled pip-7.1.2
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Successfully installed pip-8.1.1
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Upgrade wheel to last version available:
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$ pip install --upgrade wheel
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Collecting wheel
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  Downloading wheel-0.29.0-py2.py3-none-any.whl (66kB)
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Installing collected packages: wheel
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  Found existing installation: wheel 0.24.0
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    Uninstalling wheel-0.24.0:
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      Successfully uninstalled wheel-0.24.0
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Successfully installed wheel-0.29.0
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</pre>
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h3. Install the needed Python packages (from within the virtual environment)
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First, be sure that the virtual environment is activated:
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<pre>
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$ python -V
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Python 3.5.1
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</pre>
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 * *Automatic Installation of all packages*
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<pre>
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$ pip install -r REQUIREMENTS.txt
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</pre>
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 * *Or, manual installation of each package*
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  * *Install Django* :
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<pre>
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$ pip install django
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Collecting django
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  Downloading Django-1.9.4-py2.py3-none-any.whl (6.6MB)
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Installing collected packages: django
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Successfully installed django-1.9.4
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$ pip install django-admin-tools
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Collecting django-admin-tools
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  Downloading django_admin_tools-0.7.2-py2.py3-none-any.whl (289kB)
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Installing collected packages: django-admin-tools
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Successfully installed django-admin-tools-0.7.2
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$ pip install django-debug-toolbar
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Collecting django-debug-toolbar
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  Downloading django_debug_toolbar-1.4-py2.py3-none-any.whl (212kB)
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Requirement already satisfied (use --upgrade to upgrade): Django>=1.7 in ./venv_py35_pyros/lib/python3.5/site-packages (from django-debug-toolbar)
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Collecting sqlparse (from django-debug-toolbar)
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  Downloading sqlparse-0.1.19.tar.gz (58kB)
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Building wheels for collected packages: sqlparse
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  Running setup.py bdist_wheel for sqlparse ... done
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  Stored in directory: /Users/epallier/Library/Caches/pip/wheels/7b/d4/72/6011bb100dd5fc213164e4bbee13d4e03261dd54ce6a5de6b8
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Successfully built sqlparse
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Installing collected packages: sqlparse, django-debug-toolbar
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Successfully installed django-debug-toolbar-1.4 sqlparse-0.1.19
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$ pip install django-extensions
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Collecting django-extensions
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  Downloading django_extensions-1.6.1-py2.py3-none-any.whl (202kB)
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Collecting six>=1.2 (from django-extensions)
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  Downloading six-1.10.0-py2.py3-none-any.whl
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Installing collected packages: six, django-extensions
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Successfully installed django-extensions-1.6.1 six-1.10.0
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$ pip install django-suit
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Collecting django-suit
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  Downloading django-suit-0.2.18.tar.gz (587kB)
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Building wheels for collected packages: django-suit
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  Running setup.py bdist_wheel for django-suit ... done
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  Stored in directory: /Users/epallier/Library/Caches/pip/wheels/12/8b/9a/e02ab0ad9229881638aa040d47d77c8f562999533811927d41
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Successfully built django-suit
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Installing collected packages: django-suit
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Successfully installed django-suit-0.2.18
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</pre>
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  * *Install the web application server gunicorn (will be used in production instead of the dev django web server)* :
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<pre>
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$ pip install gunicorn
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Collecting gunicorn
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  Downloading gunicorn-19.4.5-py2.py3-none-any.whl (112kB)
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Installing collected packages: gunicorn
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Successfully installed gunicorn-19.4.5
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</pre>
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  * *Install the python mysql client*:
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<pre>
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$ pip install mysqlclient
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...
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</pre>
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   * => Issue under Mac OS X:
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<pre>
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$ pip install mysqlclient
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Collecting mysqlclient
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  Downloading mysqlclient-1.3.7.tar.gz (79kB)
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Building wheels for collected packages: mysqlclient
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  Running setup.py bdist_wheel for mysqlclient ... error
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  ----------------------------------------
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  Failed building wheel for mysqlclient
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  Running setup.py clean for mysqlclient
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Failed to build mysqlclient
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Installing collected packages: mysqlclient
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  Running setup.py install for mysqlclient ... done
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Successfully installed mysqlclient-1.3.7
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BOUH !!!
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$ pip install --upgrade wheel
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Collecting wheel
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  Downloading wheel-0.29.0-py2.py3-none-any.whl (66kB)
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Installing collected packages: wheel
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  Found existing installation: wheel 0.24.0
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    Uninstalling wheel-0.24.0:
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      Successfully uninstalled wheel-0.24.0
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Successfully installed wheel-0.29.0
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$ pip uninstall mysqlclient
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$ pip install mysqlclient
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Collecting mysqlclient
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  Using cached mysqlclient-1.3.7.tar.gz
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Building wheels for collected packages: mysqlclient
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  Running setup.py bdist_wheel for mysqlclient ... done
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  Stored in directory: /Users/epallier/Library/Caches/pip/wheels/9b/06/50/d11418c26cf8f2156b13d4363b5afde8e7e75ebb8540d0228d
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Successfully built mysqlclient
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Installing collected packages: mysqlclient
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Successfully installed mysqlclient-1.3.7
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YES !!!
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</pre>
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   * => Issues under Ubuntu:
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<pre>
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$ pip install mysqlclient
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Collecting mysqlclient
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  Downloading mysqlclient-1.3.7.tar.gz (79kB)
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    100% |████████████████████████████████| 81kB 1.5MB/s
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    Complete output from command python setup.py egg_info:
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    /bin/sh: 1: mysql_config: not found
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    Traceback (most recent call last):
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      File "<string>", line 1, in <module>
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    [...]
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    ----------------------------------------
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Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-q6j4inuz/mysqlclient/
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BOUH !!!
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$ sudo apt-get install libmysqlclient-dev
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$ pip install mysqlclient
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Collecting mysqlclient
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  Using cached mysqlclient-1.3.7.tar.gz
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Building wheels for collected packages: mysqlclient
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  Running setup.py bdist_wheel for mysqlclient ... error
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    _mysql.c:40:20: fatal error: Python.h: No such file or directory
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     #include "Python.h"
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                        ^
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    compilation terminated.
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    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
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    ----------------------------------------
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Command "/home/carens_p/pyros/venv_py35_pyros/bin/python3.5 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-k3klv92j/mysqlclient/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-gz242xxs-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/carens_p/pyros/venv_py35_pyros/include/site/python3.5/mysqlclient" failed with error code 1 in /tmp/pip-build-k3klv92j/mysqlclient/
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BOUH !!!
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$ sudo apt-get install python3.5-dev
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$ pip install mysqlclient
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YES !!!
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</pre>
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 * => Issue under Windows
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<pre>
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Same message as the issue for Mac.
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Go to http://www.lfd.uci.edu/~gohlke/pythonlibs/#mysqlclient to download the newest mysqlclient wheel
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$ pip install path\to\mysqlclient\wheel
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No need to redo "pip install mysqlclient"
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</pre>
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---
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h3. Eclipse only
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mkdir private
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sudo port install py35-virtualenv
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virtualenv-3.5 venv_py35_pyros -p /opt/local/bin/python3.5
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pip install -r ../PYROS/private/REQUIREMENTS.txt
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clic droit sur projet / Properties / PyDev - Interpreter/Grammar :
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Grammar version : 3
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Interpreter : click on « click here to configure an interpreter not listed »
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click on « New » :
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- Interpreter name : venv_py35_pyros
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- Interpreter executable : click on « Browse »
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	Select your private/venv_py35_pyros/bin/python3.5 executable
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	click OK
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	click OK again
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Interpreter: select now venv_py35_pyros from the list
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h3. Test the project
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<pre>
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$ cd src/
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$ ./manage.py runserver
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(or gunicorn pyros.wsgi)
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==> http://localhost:8000
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...
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...
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Ctrl-c
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</pre>
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---
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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}IV - CONFIGURATION of the Django Back Office (administration interface)%
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---
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h3. Back Office setup
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 * Prerequisites in src/pyros/settings.py :
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    * INSTALLED_APPS must (at least) contain :
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        * django.contrib.admin
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        * django.contrib.auth
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        * django.contrib.contenttypes
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        * django.contrib.sessions
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    * MIDDLEWARES must (at least) contain :
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        * django.contrib.sessions.middleware.SessionMiddleware
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        * django.middleware.common.CommonMiddleware
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        * django.contrib.auth.middleware.AuthenticationMiddleware
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 * At least one 'python manage.py migrate' must have been executed
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 * Create a superuser for the administration :
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<pre>
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$ python manage.py createsuperuser
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</pre>
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* For each app of the project, fill the admin.py file :
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<pre>
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from django.contrib import admin
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from app.models import Model1, Model2
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admin.site.register(Model1)
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admin.site.register(Model2)
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</pre>
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*Reminder* : each application must be registered in the settings.py INSTALLED_APPS variable.
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* For each model in models.py, add a '__str__()' method in order to identify the object on the back office. Example :
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<pre>
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class UserLevel(models.Model):
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    name = models.CharField(max_length=45, blank=True, null=True)
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    desc = models.TextField(blank=True, null=True)
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    priority = models.IntegerField(blank=True, null=True)
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    quota = models.FloatField(blank=True, null=True)
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    class Meta:
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        managed = True
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        db_table = 'userlevel'
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    def __str__(self):
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        return (str(self.name))
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</pre>
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*Naming convention* : Use self.name when possible, the creation time/date otherwise. Example :
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<pre>
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class SiteWatch(models.Model):
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    updated = models.DateTimeField(blank=True, null=True)
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    lights = models.CharField(max_length=45, blank=True, null=True)
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    dome = models.CharField(max_length=45, blank=True, null=True)
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    doors = models.CharField(max_length=45, blank=True, null=True)
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    temperature = models.FloatField(blank=True, null=True)
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    class Meta:
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        managed = True
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        db_table = 'sitewatch'
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    def __str__(self):
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        return (str(self.updated))
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</pre>
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---
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h3. Adaptation of the one-to-many and many-to-many display
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* The one-to-many relationships are the following (One.many format) :
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    * Schedule.sequences
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    * Request.sequences
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    * Sequence.albums
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    * Album.plans
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    * Plan.images
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    * Telescope.detectors
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    * Detector.filters
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    * NrtAnalysis.images
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    * Filter.plans
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    * Detector.albums
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    * UserLevel.users
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    * Country.users
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    * ScientificProgram.requests
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    * User.requests
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    * StrategyObs.alerts
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    * SequenceType.sequences
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* For each "many", create a new class in admin.py just after the imports, following these examples :
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<pre>
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For Schedule.sequences, Request.sequences and Sequentype.sequences, we will need :
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class SequenceInline(admin.TabularInline):
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    model = Sequence
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    fields = ("name",)
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    show_change_link = True
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For Sequence.albums and Detector.albums, we will need :
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class AlbumInline(admin.TabularInline):
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    model = Album
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    fields = ("name",)
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    show_change_link = True
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For StrategyObs.alerts, we will need :
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class AlertInline(admin.TabularInline):
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    model = Alert
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    fields = ("request.name",) # there is no 'name' attribute in the Alert model
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    show_change_link = True
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</pre>
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* For each "One", declare a new class in admin.py, just after the "Inlines" class declaration, as done in the following examples :
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<pre>
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For Request.sequences :
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class RequestAdmin(admin.ModelAdmin):
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    inlines = [
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	SequenceInline,
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    ]
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For Detector.filters and Detector.albums :
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class DetectorAdmin(admin.ModelAdmin):
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    inlines = [
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	FilterInline,
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        AlbumInline,
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    ]
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</pre>
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* The many-to-many relationships are the following :
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    * ScientificProgram - User
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    * ScheduleHistory - Sequence
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* For each many-to-many relationship, declare a new "Inline" class in admin.py just after the imports, like this :
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<pre>
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For ScientificProgram - User :
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class UserAndSPInline(admin.TabularInline):
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    model = ScientificProgram.users.through
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For ScheduleHistory - Sequence
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class SequenceAndSHInline(admin.TabularInline):
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    model = ScheduleHistory.sequences.through
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</pre>
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+Note :+ The order in the line "model = ScientificProgram.users.through" is very important : the first model (ScientificProgram) is the one in which is declared the ManyToManyField relationship.
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* For each many-to-many relationship, declare two new classes in admin.py, just after the inlines, like in the following examples :
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<pre>
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For the ScheduleHistory - Sequence relationship :
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class ScheduleHistoryAdmin(admin.ModelAdmin):
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    inlines = [
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        SequenceAndSHInline,
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    ]
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    exclude = ('sequences',) # ScheduleHistory declares the ManyToManyField, and we want to replace its display in the back office, so we won't display the default field
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class SequenceAdmin(admin.ModelAdmin):
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    inlines = [
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        AlbumInline,        # This is the Inline for the one-to-many relationship Sequence.albums
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        SequenceAndSHInline,                                                                
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    ]
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For the ScientificProgram - User relationship :
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class ScientificProgramAdmin(admin.ModelAdmin):
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    inlines = [
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        RequestInline,
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	UserAndSPInline,                                                                         
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    ]
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    exclude = ('users',) # Same as ScheduleHistory                                                                         
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class UserAdmin(admin.ModelAdmin):
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    inlines = [
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	RequestInline,   # This is the Inline for the one-to-many relationship User.requests
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        UserAndSPInline,                                                                    
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    ]
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</pre>
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* For each ModelAdmin class in the admin.py, change the registering line
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<pre>
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admin.site.register(Album)
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</pre>
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to
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<pre>
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admin.site.register(Album, AlbumAdmin)
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</pre>
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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}V - INSTALLATION FROM THE BEGINNING (for dev only, history of the initial project creation)%
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[[pyros_install_from_start|Pyros installation from the beginning]]