PYROS

h1. Technical Documentation for the PYROS project (FGFT-CC)

HOWTO Format Redmine Wiki : http://www.redmine.org/projects/redmine/wiki/FrRedmineWikiFormatting

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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}I - TODO%

 * installation sur windows

 * gitlab

 * séparation des BD Django et Pyros

 * intégration dans Eclipse

 * récupération des modules existants

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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}I - DATABASE SCHEMA (v0.2.1)%

{{thumbnail(PYROS_PDM_v021.png, size=300, title=Pyros data model)}}

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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}II - Get the project (from gitlab)%

https://gitlab.irap.omp.eu/epallier/pyros

h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}III - INSTALLATION%

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h3. If necessary, install MySql

 * Linux Ubuntu

<pre>

$ sudo apt-get install mysql-server

$ sudo apt-get install mysql-client

</pre>

 * Linux CentOS

<pre>

TODO:

$ sudo yum install mysql

...

</pre>

 * Mac OS X

<pre>

TODO:

Install XAMPP

(but you could also use the pre-installed Mac OS MySql)

</pre>

 * Windows

<pre>

TODO:

</pre>

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h3. Create database

 * Linux and Mac OS X:

<pre>

One liner:

$ mysql -u root < pyros_create.sql

Or :

$ mysql -u root

mysql> create database pyros;

mysql> use pyros;

mysql> source pyros_create.sql;

(

TODO:

mysql> grant all on pyros.* to pyros@localhost identified by ‘pyros’;)

mysql> flush privileges;

)

</pre>

 * Windows:

<pre>

TODO: Use phpmyadmin ?

</pre>

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h3. Install python3.5

 * Mac OS X :

<pre>

1) Installer MacPort

(TODO: doc)

2) Installer le "port" python35

$ sudo port install python35

</pre>

 * Linux (Ubuntu) :

<pre>

sudo add-apt-repository ppa:fkrull/deadsnakes

sudo apt-get update

sudo apt-get install python3.5

sudo pip install virtualenv

</pre>

---

h3. Get the project (from git)

<pre>

TODO:

$ git http://pyros... PYROS

</pre>

This creates a PYROS folder containing the project

---

h3. Create project structure

<pre>

$ mkdir PYROS

</pre>

Example of a good organization :

1 project = N applis

(but 1 appli can be part of many projects)

1 appli = 1 Python module, organized for Django, by default = appli web (but not mandatory)

(then 1 appli = N models)

<pre>

MYPROJECT/

	src/

		myproject/

		appli1/

		appli2/

		…

		appliN/

	public/

		static/

	private/

		REQUIREMENTS.txt

		venv_py35_pyros/

</pre>

Set needed folders:

<pre>

$ cd PYROS/

$ mkdir private public

$ mkdir public/static

</pre>

---

h3. Create virtualenv with python3.5 dedicated to pyros project (inside the project folder)

<pre>

$ cd private/

$ which python3.5

/opt/local/bin/python3.5

$ virtualenv-3.5 venv_py35_pyros -p /opt/local/bin/python3.5

=> creates a venv_py35_pyros/ folder inside PYROS/private/

</pre>

---

h3. Activate the python virtual environment (from inside the project)

<pre>

$ pwd

.../PYROS/private

$ source ./venv_py35_pyros/bin/activate

$ python -V

Python 3.5.1

$ which pip

.../PYROS/venv_py35_pyros/bin/pip

Upgrade pip to last version available :

$ pip install --upgrade pip

Collecting pip

  Downloading pip-8.1.1-py2.py3-none-any.whl (1.2MB)

Installing collected packages: pip

  Found existing installation: pip 7.1.2

    Uninstalling pip-7.1.2:

      Successfully uninstalled pip-7.1.2

Successfully installed pip-8.1.1

</pre>

h3. Install needed python packages (from within the virtual environment)

First, be sure that the virtual environment is activated:

<pre>

$ python -V

Python 3.5.1

</pre>

 * *Automatic Installation of all packages*

<pre>

$ pip install -r REQUIREMENTS.txt

</pre>

 * *Or, manual installation of each package*

  * *Install Django* :

<pre>

$ pip install django

Collecting django

  Downloading Django-1.9.4-py2.py3-none-any.whl (6.6MB)

Installing collected packages: django

Successfully installed django-1.9.4

$ pip install django-admin-tools

Collecting django-admin-tools

  Downloading django_admin_tools-0.7.2-py2.py3-none-any.whl (289kB)

Installing collected packages: django-admin-tools

Successfully installed django-admin-tools-0.7.2

$ pip install django-debug-toolbar

Collecting django-debug-toolbar

  Downloading django_debug_toolbar-1.4-py2.py3-none-any.whl (212kB)

Requirement already satisfied (use --upgrade to upgrade): Django>=1.7 in ./venv_py35_pyros/lib/python3.5/site-packages (from django-debug-toolbar)

Collecting sqlparse (from django-debug-toolbar)

  Downloading sqlparse-0.1.19.tar.gz (58kB)

Building wheels for collected packages: sqlparse

  Running setup.py bdist_wheel for sqlparse ... done

  Stored in directory: /Users/epallier/Library/Caches/pip/wheels/7b/d4/72/6011bb100dd5fc213164e4bbee13d4e03261dd54ce6a5de6b8

Successfully built sqlparse

Installing collected packages: sqlparse, django-debug-toolbar

Successfully installed django-debug-toolbar-1.4 sqlparse-0.1.19

$ pip install django-extensions

Collecting django-extensions

  Downloading django_extensions-1.6.1-py2.py3-none-any.whl (202kB)

Collecting six>=1.2 (from django-extensions)

  Downloading six-1.10.0-py2.py3-none-any.whl

Installing collected packages: six, django-extensions

Successfully installed django-extensions-1.6.1 six-1.10.0

$ pip install django-suit

Collecting django-suit

  Downloading django-suit-0.2.18.tar.gz (587kB)

Building wheels for collected packages: django-suit

  Running setup.py bdist_wheel for django-suit ... done

  Stored in directory: /Users/epallier/Library/Caches/pip/wheels/12/8b/9a/e02ab0ad9229881638aa040d47d77c8f562999533811927d41

Successfully built django-suit

Installing collected packages: django-suit

Successfully installed django-suit-0.2.18

</pre>

  * *Install the web application server gunicorn (will be used in production instead of the dev django web server)* :

<pre>

$ pip install gunicorn

Collecting gunicorn

  Downloading gunicorn-19.4.5-py2.py3-none-any.whl (112kB)

Installing collected packages: gunicorn

Successfully installed gunicorn-19.4.5

</pre>

  * *Install the python mysql client*:

<pre>

$ pip install mysqlclient

...

</pre>

   * => Issue under Mac OS X:

<pre>

$ pip install mysqlclient

Collecting mysqlclient

  Downloading mysqlclient-1.3.7.tar.gz (79kB)

Building wheels for collected packages: mysqlclient

  Running setup.py bdist_wheel for mysqlclient ... error

…

  ----------------------------------------

  Failed building wheel for mysqlclient

  Running setup.py clean for mysqlclient

Failed to build mysqlclient

Installing collected packages: mysqlclient

  Running setup.py install for mysqlclient ... done

Successfully installed mysqlclient-1.3.7

BOUH !!!

$ pip install --upgrade wheel

Collecting wheel

  Downloading wheel-0.29.0-py2.py3-none-any.whl (66kB)

Installing collected packages: wheel

  Found existing installation: wheel 0.24.0

    Uninstalling wheel-0.24.0:

      Successfully uninstalled wheel-0.24.0

Successfully installed wheel-0.29.0

$ pip uninstall mysqlclient

$ pip install mysqlclient

Collecting mysqlclient

  Using cached mysqlclient-1.3.7.tar.gz

Building wheels for collected packages: mysqlclient

  Running setup.py bdist_wheel for mysqlclient ... done

  Stored in directory: /Users/epallier/Library/Caches/pip/wheels/9b/06/50/d11418c26cf8f2156b13d4363b5afde8e7e75ebb8540d0228d

Successfully built mysqlclient

Installing collected packages: mysqlclient

Successfully installed mysqlclient-1.3.7

YES !!!

</pre>

   * => Issues under Ubuntu:

<pre>

$ pip install mysqlclient

Collecting mysqlclient

  Downloading mysqlclient-1.3.7.tar.gz (79kB)

    100% |████████████████████████████████| 81kB 1.5MB/s

    Complete output from command python setup.py egg_info:

    /bin/sh: 1: mysql_config: not found

    Traceback (most recent call last):

      File "<string>", line 1, in <module>

    [...]

    ----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-q6j4inuz/mysqlclient/

BOUH !!!

$ sudo apt-get install libmysqlclient-dev

$ pip install mysqlclient

Collecting mysqlclient

  Using cached mysqlclient-1.3.7.tar.gz

Building wheels for collected packages: mysqlclient

  Running setup.py bdist_wheel for mysqlclient ... error

…

    _mysql.c:40:20: fatal error: Python.h: No such file or directory

     #include "Python.h"

                        ^

    compilation terminated.

    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

    ----------------------------------------

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/

BOUH !!!

$ sudo apt-get install python3.5-dev

$ pip install mysqlclient

YES !!!

</pre>

 * *Set Requirements*

<pre>

$ pip freeze > REQUIREMENTS.txt

$ mv REQUIREMENTS.txt .../PYROS/private/

</pre>

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h3. Create Django project pyros

<pre>

From inside the project:

$ pwd

.../PYROS/

$ django-admin startproject pyros

$ mv pyros src

We have then this architecture:

PYROS

├── private

│   └── REQUIREMENTS.txt

│   └── venv_py35_pyros

├── public

│   └── static

├── src

│   ├── manage.py

│   ├── pyros

│   │   ├── __init__.py

│   │   ├── settings.py

│   │   ├── urls.py

│   │   └── wsgi.py

</pre>

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h3. Test the project

<pre>

$ ./manage.py runserver

(or gunicorn pyros.wsgi)

==> http://localhost:8000

...

...

Ctrl-c

</pre>

---

h3. The Web server

Apache : gère tous les fichiers statiques (images, html…), et délègue les fichiers python au serveur django (par défaut)

Le fichier pyros/urls.py prend le relai pour tout ce qui est django

Le moteur web django sera soit du wsgi soit du unicorn

Par défaut, 1 seul worker, mais on peut en configurer plusieurs, l’idéal étant de faire "nb coeurs + 1" 

(le worker maître qui fait le dispatching aux autres)

Frontend : Apache ou Ngininx

Backend : gunicorn (gère facilement des workers) ou uwsgi

==> gunicorn pyros.wsgi

(à la place de manage runserver ==> A EVITER EN PROD)

Ou encore:

gunicorn - - workers 5 library.wsgi

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h3. Set Database engine as MySql

Edit src/pyros/settings.py

<pre>

DATABASES = {

    'default': {

        'ENGINE': 'django.db.backends.mysql',

        'NAME': 'pyros',

        'USER': 'root',

        'PASSWORD': ''

    }

}

</pre>

---

h3. Import database into Django (with inspectdb)

From src/ :

<pre>

$ ./manage.py inspectdb > models.py

</pre>

Issue on Mac OS X:

<pre>

Traceback (most recent call last):

  File "/Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/django/db/backends/mysql/base.py", line 25, in <module>

    import MySQLdb as Database

  File "/Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/MySQLdb/__init__.py", line 19, in <module>

    import _mysql

ImportError: dlopen(/Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/_mysql.cpython-35m-darwin.so, 2): Library not loaded: libmysqlclient.18.dylib

  Referenced from: /Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/_mysql.cpython-35m-darwin.so

  Reason: image not found

=> BOUH !!!

LA SOLUTION EST ICI : http://stackoverflow.com/questions/6383310/python-mysqldb-library-not-loaded-libmysqlclient-18-dylib

Il suffit de faire ceci:

$ sudo mkdir -p /usr/local/lib   

$ sudo ln -s /Applications/XAMPP/xamppfiles/lib/libmysql* /usr/local/lib/

Mais on peut aussi faire ceci:

Okay, so the offending file is /Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/_mysql.cpython-35m-darwin.so

Next, figure out where _mysql.so thinks it should find libmysqlclient.18.dylib:

$ otool -L /Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/_mysql.cpython-35m-darwin.so

/Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/_mysql.cpython-35m-darwin.so:

	libmysqlclient.18.dylib (compatibility version 18.0.0, current version 18.0.0)

...

So, it's looking for libmysqlclient.18.dylib with no path information, let's fix that:

$ locate libmysqlclient.18.dylib

/Applications/XAMPP/xamppfiles/lib/libmysqlclient.18.dylib

/Library/SystemMigration/History/Migration-68137DFB-CB6A-4FBB-81E2-11BDB5D01E48/QuarantineRoot/usr/lib/libmysqlclient.18.dylib

$ sudo install_name_tool -change libmysqlclient.18.dylib /Applications/XAMPP/xamppfiles/lib/libmysqlclient.18.dylib /Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/_mysql.cpython-35m-darwin.so

Now _mysql.so knows the full path to the library and everything works, regardless of environment variables.

$ otool -L /Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/_mysql.cpython-35m-darwin.so

/Users/epallier/Documents/_W_more/PROJECTS/GFT/SOFT/PYROS/pyros/venv_py35_pyros/lib/python3.5/site-packages/_mysql.cpython-35m-darwin.so:

	/Applications/XAMPP/xamppfiles/lib/libmysqlclient.18.dylib (compatibility version 18.0.0, current version 18.0.0)

...

$ ./manage.py inspectdb > models.py

=> YES !!!

</pre>

---

h3. Create a Django application pyrosapp

From src/ :

<pre>

$ ./manage.py startapp pyrosapp

</pre>

We obtain this structure:

<pre>

PYROS/

├── private

│   └── REQUIREMENTS.txt

├── public

│   └── static

├── src

│   ├── db.sqlite3

│   ├── manage.py

│   ├── pyros

│   │   ├── __init__.py

│   │   ├── __pycache__

│   │   ├── settings.py

│   │   ├── urls.py

│   │   └── wsgi.py

│   └── pyrosapp

│       ├── __init__.py

│       ├── admin.py

│       ├── apps.py

│       ├── migrations

│       ├── models.py

│       ├── tests.py

│       └── views.py

└── venv_py35_pyros

</pre>

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h3. Replace the default pyrosapp models.py with the inspectdb generated one

From src/ :

<pre>

$ mv models.py pyrosapp/

</pre>

Add pyrosapp to the project's applications :

Edit src/pyros/settings.py

<pre>

INSTALLED_APPS = [

    'django.contrib.admin',

    'django.contrib.auth',

    'django.contrib.contenttypes',

    'django.contrib.sessions',

    'django.contrib.messages',

    'django.contrib.staticfiles',

    'pyrosapp',

]

</pre>

---

h3. Fix and improve the pyrosapp models.py file (generated by inspectdb)

Once models.py file generated, we need to delete the database and create an empty one :

<pre>

$ mysql -u root [-p (if password needed)]

mysql> DROP DATABSE pyros

mysql> CREATE SCHEMA IF NOT EXISTS 'pyros' DEFAULT CHARACTER SET utf8;

</pre>

Then edit pyrosapp/models.py :

 * Change 'managed = False' to 'managed = True' for every model

 * Change classes names to CamelCase (do not change the 'db_table = ...' lines). *Be careful* : it is needed to change all occurences :

    * NrtAlanysis

    * ScheduleHistory

    * ScientificProgram

    * SequenceType

    * SiteWatch

    * SiteWatchHistory

    * StrategyObs

    * WeatherWatch

    * WeatherWatchHistory

 * Change the deleting mode from 'models.DO_NOTHING' to 'models.CASCADE' for the following foreign keys :

    * Image.plan

    * Plan.album

    * Album.sequence

    * Sequence.request

 * Change the 'ForeignKey' liaisons to 'OneToOneField' liaisons (just replace ForeignKey by OneToOneField), and change deleting mode to 'models.CASCADE' for the following foreign keys :

    * Alert.request

    * Detector.device

    * Filter.device

    * Telescope.device

 * We need to redefine many to many relationships for the following classes :

    * User - ScientificProgram :

        * add 'users = models.ManyToManyField('User')' in ScientificProgram class

        * delete UserHasScientificProgram class

    * Sequence - ScheduleHistory

        * add 'sequences = models.ManyToManyField('Sequence')' in ScheduleHistory class

        * delete ScheduleHasSequences class

 * Finally apply modifications to the database :

<pre>

$ pwd

.../PYROS/src

$ python manage.py makemigrations pyrosapp

$ python manage.py migrate

</pre>

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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}II - CONFIGURATION of the Django Back Office (administration interface)%