PYROS

h1. Project Installation

Project Development page : [[Project Development]]

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

{{>toc}}

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

Pyros needs 1 or 2 prerequisites : 

* Python 3

* (optional) a Mysql Database server (but you can use Sqlite instead, with no installation)

---

h3. Install a database server (only if necessary)

_If the MySql database server is already installed on your computer, skip this section_

By default, Pyros uses Mysql, but this implies that you have to install the Mysql database server...

Thus, to make things easier, avoid Mysql installation by using Sqlite instead as the database server (which will need no installation at all) :

=> *For this, just edit the file PYROS/src/pyros/settings.py and set MYSQL variable to False, and that's it. You can go to next section*

Now, if you really want to use Mysql (which is the default), you will need to install it (only if not already installed), so keep reading.

_(Skip this if you are using Sqlite instead of MySql)_

 * Linux Ubuntu

<pre>

First, update your system:

$ sudo apt-get update

$ sudo apt-get install mysql-server

$ sudo apt-get install mysql-client

$ sudo apt-get install libmysqlclient-dev

(needed for python package mysqlclient)

</pre>

 * Linux CentOS : cf https://www.howtoforge.com/apache_php_mysql_on_centos_7_lamp#-installing-mysql-

<pre>

First, update your system:

$ sudo yum update yum

$ sudo yum update kernel

$ sudo yum update

$ sudo yum install mariadb-server 

$ sudo yum install mariadb

$ sudo yum install mariadb-devel

(needed for python package mysqlclient)

$ sudo systemctl start mariadb.service

$ sudo systemctl enable mariadb.service

=> Created symlink from /etc/systemd/system/multi-user.target.wants/mariadb.service to /usr/lib/systemd/system/mariadb.service.

$ sudo mysql_secure_installation

</pre>

 * Mac OS X

Install XAMPP

(but you could also use the pre-installed Mac OS MySql, or install MySql from macport)

<pre>

TODO:

</pre>

 * Windows (tested with Windows 7)

<pre>

Download and install the newest version on https://dev.mysql.com/downloads/installer/

Once installed, launch MySQL Installer. Clic on 'Add...' on the right.

In MySQLServers section, choose the newest, then clic on next.

Install and configure the server (just follow the installation guide).

Then launch mysql (via the Windows menu).

</pre>

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h3. Install Python3 + pip + virtualenv (only if necessary)

_If Python 3 is already installed on your computer, skip this section_

 * Linux (CentOS 7.1, main target): (python35 not yet available as rpm)

<pre>

$ sudo yum update yum

$ sudo yum update kernel

$ sudo yum update

$ sudo yum install python34

$ python3.4 -V

Python 3.4.3

$ sudo yum install python34-devel

(needed for python package mysqlclient)

$ sudo yum update python-setuptools

$ easy_install --version

setuptools 0.9.8

$ sudo easy_install pip

$ pip --version

pip 8.1.1 from /usr/lib/python2.7/site-packages/pip-8.1.1-py2.7.egg (python 2.7)

$ sudo pip install virtualenv

$ virtualenv --version

15.0.1

</pre>

 * Linux (Ubuntu) :

<pre>

$ sudo add-apt-repository ppa:fkrull/deadsnakes

$ sudo apt-get update

$ sudo apt-get install python3.5

$ sudo apt-get install python3.5-dev

(needed for python package mysqlclient)

$ sudo pip install virtualenv

</pre>

 * Mac OS X :

  * From binary (Mac OS native application)

(TODO:)

  * From MacPort

   * a) install macport

(TODO:)

   * b) install the "port" python35

<pre>

$ sudo port install python35

</pre>

 * Windows (tested with Windows 7) :

(TODO: test with Windows 10)

<pre>

Go to https://www.python.org/downloads/windows/ , choose the wanted version

On the wanted version’s page, download Windows x86 executable installer

Run the executable

    * On the first page, check "Add python3.5 to PATH"

    * Choose "Install now" option

Open cmd (windows + R, cmd) :

 $ python -m pip install --upgrade pip

 $ pip install virtualenv

</pre>

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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}II - GET THE PYROS SOFTWARE%

h3. Authenticate to https://gitlab.irap.omp.eu/epallier/pyros

In order to get this software, you must first authenticate on the IRAP gitlab.

For this, just go to https://gitlab.irap.omp.eu/epallier/pyros

and either sign in with your LDAP account (if you are from IRAP),

or register via the "Sign up" form.

h3. Software structure

Once you have fetched the project, you should obtain AT LEAST this structure:

<pre>

PYROS/

├── install/

│   └── REQUIREMENTS.txt

│   └── INSTALLATION.txt

├── public/

│   └── static/

├── src/

│   ├── 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

</pre>

h3. Browse the code (from gitlab)

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

h3. Download it (static version, not synchronized)

You can download the current version of the software.

Go to https://gitlab.irap.omp.eu/epallier/pyros/tree/master

Click on "Download zip" on the up right hand corner.

Double-click on it to unzip it.

You should get a "pyros.git" folder.

In this documentation, this software folder will be referenced as "PYROS".

(you can rename "pyros.git" as "PYROS" if you want : "mv pyros.git PYROS")

h3. Get it from GIT (dynamic version, synchronized)

(If you are using Windows, you must first get the git software, see below "Get git for Windows")

By getting the software from git, you will get a dynamically synchronized version,

which means that you will be able to update your version as soon as a new version is available

(with the command : "git pull").

* From Eclipse : See below, section "NOTES FOR ECLIPSE USERS"

* From the terminal

<pre>

git clone https://gitlab.irap.omp.eu/epallier/pyros.git PYROS

</pre>

_(or also : git clone git@gitlab.irap.omp.eu:epallier/pyros.git PYROS)_

If you ever get this error message :

<pre>

fatal: unable to access 'https://gitlab.irap.omp.eu/epallier/pyros.git/': Peer's certificate issuer has been marked as not trusted by the user.

</pre>

Then, type this command (and then run again the git clone command):

<pre>

$ git config --global http.sslVerify false

</pre>

(Also, the first time you get the project, it will ask you for a login and password)

This creates a PYROS/ folder containing the project (with a .git/ subfolder for synchronization with the git repository)

h4. (Windows only) : Get git for Windows

 * Download git at https://git-scm.com/download/win

 * Run setup (keep default configurations)

 * Once installed, open cmd

<pre>

$ git config --global http.sslVerify false

</pre>

You can now use your git from the cmd or the graphic client !

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

Install the needed Python dependencies and the database (within a Python virtual environment)

Go into the PYROS/install/ folder and Run the install_requirements.sh script.

(You will be prompted to enter a username, an email, and a password for the superuser)

* Mac and Linux:

<pre>

./install_requirements.sh

</pre>

* Windows:

<pre>

install_requirements_windows.bat

</pre>

_If something goes wrong, install manually each package (see section "MANUAL INSTALLATION OF PYTHON PACKAGES, ONE BY ONE")_

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h3. (Eclipse only) Set the Python3 virtual environment as the project interpreter

See below, in section "NOTES FOR ECLIPSE USERS"

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

(Tests are classes declared in all apps' test.py file. The test classes inherit from django.test.TestCase)

You can run the tests suite, just to be sure that the software is well installed.

h3. From Terminal

<pre>

$ cd PYROS/

$ ./pyrosrun test

Ran 5 tests in 0.093s

OK

</pre>

h3. From Eclipse

See below, in section "NOTES FOR ECLIPSE USERS"

h3. Custom commands

$ [./manage.py] test app.tests                           # Run tests for the application 'app'

$ [./manage.py] test app.tests.ModelTests                # Run test methods declared in the class app.tests.ModelTests

$ [./manage.py] test app.tests.ModelTests.test_method    # Only run the method test_method declared in app.tests.ModelTests

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

* From the terminal

<pre>

$ cd PYROS/

$ ./pyrosrun server

</pre>

Now, go to "http://localhost:8000/admin" in your browser

(and login as "pyros" with the password 'DjangoPyros')

(Ctrl-c to stop)

* From Eclipse : see below, in section "NOTES FOR ECLIPSE USERS"

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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}NOTES FOR ECLIPSE USERS%

0) Install Eclipse (if necessary)

Get the Eclipse version for Php

Install the plug-in pydev (via install new software, add http://pydev.org/updates)

Install the django template editor (via install new software, add http://eclipse.kacprzak.org/updates)

1) Deactivate CA certificate verification

Window -> Preferences -> Team -> git -> configuration -> Add entry

Key = http.sslVerify

Value = false

2) Fetch the project

File/Import project from git

Select repository source: Clone URI: https://gitlab.irap.omp.eu/epallier/pyros.git

Directory: 

par défaut, il propose : /Users/epallier/git/pyros

mais on peut le mettre ailleurs (c'est ce que j'ai fait)

initial branch: master

remote name: origin

Import as general project

Project name: PYROS

3) Configure the project

The project is created. Now, you have to set it as a «PyDev » and a « Django » project.

clic droit sur le projet / PyDev / set as a PyDev project

clic droit sur le projet / PyDev / set as a Django project

clic droit sur le projet : on doit maintenant avoir un sous-menu Django

clic droit sur le dossier src / PyDev / set as source folder (add to PYTHONPATH)

clic droit sur projet / Properties / Pydev-Django :

  - Django manage.py : src/manage.py

  - Django settings module : pyros.settings

4) Set Code style

Window/Preferences : Pydev / Editor

- Auto Imports : uncheck « Do auto import »

- Code style:

	- Locals … : camelCase

	- Methods : camelCase() with first lower

- Code style / Code Formatter: activer « use autopep8.py for code formatting »

- Tabs : Tab length : 4

5) Now, once the Python3 virtual environment is installed (see above),

set it in Eclipse as the project interpreter:

Right clic on the project / Properties / PyDev - Interpreter/Grammar :

Grammar version : 3

Interpreter : click on « click here to configure an interpreter not listed »

click on « New... » :

- Interpreter name : venv_py35_pyros

- Interpreter executable : click on « Browse »

	Select your virtualenv python35 executable (private/venv_py35_pyros/bin/python3.5)

	click OK

*Now, a last thing to do so that Pydev finds Django:*

In the Python interpreters list, select your virtual env (venv_py35_pyros)

Click on the tab "Libraries"

clic on 'New folder', then select your virtualenv's lib/python3.5/site-packages folder

OK

Interpreter: select now venv_py35_pyros from the list

OK

6) Test

* Right-clic on the project / Django / Run Django tests

* Right-clic on the project / Django / Custom command / ...

7) Run

Right clic on project -> Django/Custom command/runserver

Error on Ubuntu :

<pre>

Traceback (most recent call last):

  File "/home/carens_p/git/pyros/src/manage.py", line 8, in <module>

    from django.core.management import execute_from_command_line

ImportError: No module named 'django'

</pre>

Project -> Properties -> Pydev interpreter -> Clic here to configure an interpreter not listed

select venv_py35_pyros

In Libraries, clic on 'New folder', then select your virtualenv's lib/python3.5/site-packages folder.

OK -> re-select venv_py35_pyros in 'Interpreter' dropdown menu

Then right clic on project -> Django/Custom command/runserver

check http://localhost:8000/

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h2. %{margin-left:0px; font-weight:bold; font-size:25px;  display:block; color:red;}MANUAL INSTALLATION OF PYTHON PACKAGES ONE BY ONE%

*Follow these steps only if the previous guided and nearly automatic installation did not work for you*

h3. (Only if using Mysql) Create the database "pyros" and the pyros user

Only if you are using Mysql, you need to create an empty database "pyros"

(which will be filled automatically by django)

<pre>

$ mysql -u root -p

(enter your root password)

$ mysql> create database if not exists pyros;

</pre>

The user creation depends on your MySQL version :

 * 5.7 and above :

<pre>

$ mysql> DROP USER IF EXISTS pyros;

$ mysql> CREATE USER 'pyros' IDENTIFIED BY 'DjangoPyros';

$ mysql> GRANT ALL PRIVILEGES ON pyros.* TO pyros;

</pre>

 * under 5.7 :

<pre>

$ mysql> GRANT USAGE ON *.* TO 'pyros';

$ mysql> DROP USER 'pyros';

$ mysql> CREATE USER 'pyros' IDENTIFIED BY 'DjangoPyros';

$ mysql> GRANT ALL PRIVILEGES ON pyros.* TO pyros;

</pre>

If none of these solution work, check on the internet to create a user named pyros with the password DjangoPyros.

h3. Create a Python3 virtual environment dedicated to the project (inside the project folder)

<pre>

$ mkdir private/

$ cd private/

$ which python3.5 ("where python" for windows)

/opt/local/bin/python3.5

$ virtualenv 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 (venv_py35_pyros/Scripts/activate on Windows)

</pre>

---

h3. Install needed python packages

Check that the virtual environment is activated

<pre>

$ python -V

Python 3...

$ which pip

.../PYROS/venv_py35_pyros/bin/pip

</pre>

Upgrade pip to last version available:

<pre>

$ 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

Upgrade wheel to last version available:

$ 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

</pre>

Go into the install/ folder:

<pre>

$ cd .../PYROS/install/

</pre>

Install all the needed python packages at once:

<pre>

$ pip install -r REQUIREMENTS.txt

</pre>

If something goes wrong, install them one by one:

  * *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 django boostrap css package* :

<pre>

$ pip install django-bootstrap3

</pre>

(==> 'bootstrap3' is then to be added as an application in settings.py -> INSTALLED_APPS)

  * *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* (not needed if you want to use sqlite):

<pre>

$ pip install mysqlclient

...

</pre>

   * => If 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 !!!

=> Need to upgrade wheel:

$ 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

YES !!!

Only if necessary, you can reinstall mysqlclient:

$ 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

</pre>

   * => If issue under Windows

<pre>

Same message as the issue for Mac.

=> Need to upgrade wheel:

Go to http://www.lfd.uci.edu/~gohlke/pythonlibs/#mysqlclient to download the newest mysqlclient wheel

$ pip install path\to\mysqlclient\wheel

(No need to redo "pip install mysqlclient")

</pre>

  * *Install the julian day converter* :

<pre>

$ pip install jdcal

</pre>