Install and configure apache2 for python3 on your server.
Install wsgi for python3 on your server, by running the following command
sudo apt-get install python3-pip libapache2-mod-wsgi-py3
If you have an wsgi for python2 installed then: first uninstall it by the following command and then run the above command
sudo apt-get install python3-pip libapache2-mod-wsgi-py3
Install python3-mysqldb.
Install sudo apt-get install libmysqlclient-dev
Install virtualenv using the below command:
sudo pip3 install virtualenv
Run
git clone https://github.com/RedHenLab/RapidAnnotator-2.0 rapidannotator
cd rapidannotator
virtualenv -p python3 venv
source venv/bin/activate
pip3 install -r requirements.txt
Since we need to deploy rapidannotator [flask app] on apache server, we need to link Flask and Apache using wsgi interface. For that you need to add the following lines in /etc/apache2/sites-enabled/000-default.conf
Copy wsgi_template.py to wsgi.py and make the required changes in the new file.
cp wsgi_template.py wsgi.py
<VirtualHost *:8000>
WSGIScriptAlias / /var/www/rapidannotator/wsgi.py
<Directory /var/www/rapidannotator>
Require all granted
</Directory>
</VirtualHost>
Add the following line to listen to port 8000 in /etc/apache2/ports.conf
Listen 8000
In the wsgi.py file in the activate_this replace the current path i.e.
[Path_to_virtual_environment]/bin/activate_this.py to /path/to/venv
Next, in wsgi.py file in the rapidannotator replace the current path i.e.
[Path_to_rapidannotator]/rapidannotator to /path/to/rapidannotator
After that run : sudo service apache2 restart
As the last step we need to link the database[MySQL] to rapidannotator.
Login to MySQL : mysql -u root -p
To enable full utf8 support, check if you mysql already supports full utf8 by running the following command
SHOW VARIABLES WHERE Variable_name LIKE 'character\_set\_%' OR Variable_name LIKE 'collation%';
If it shows utf8 instead of utf8mb4 then add the following lines in /etc/mysql/my.cnf file otherwise move to next step.
[client]
default-character-set = utf8mb4
[mysql]
default-character-set = utf8mb4
[mysqld]
character-set-client-handshake = FALSE
character-set-server = utf8mb4
collation-server = utf8mb4_unicode_ci
For more information check this guide
Now, create a database for rapidannotator and select it :
create database [database_name];
use [database_name];
Create a new user:
CREATE USER username@localhost IDENTIFIED BY <passoword>;
Now grant the privileges to rapidannotator :
grant all privileges on [Database_name].* to username@localhost with grant option;
Tell the server to reload the grant tables
flush privileges;
Copy config_template.py to config.py and make the required changes in the new file.
cp config_template.py config.py
Finally in rapidannotator/config.py update the database uri :
SQLALCHEMY_DATABASE_URI = 'mysql://username:password@localhost/[Database_name]'
# Run the following commands on terminal inside the project folder
# You are supposed to be in the parent directory of the repository and venv is active (the virtual environment is active)
# Run the following commands after setting up the db at config file
# Initialize the flask-migrate files.
flask db init
# Make a migration, it is like commit it and a comment beside.
flask db migrate -m "Initial migration." # OR just add your comment right there
# Then apply your migration to the database, it is like push.
flask db upgrade Run the following in the directory where rapidannotator is kept.
mkdir -p [Path_to_storage_directory]
Change this line accordingly.
After running the above steps you should be able to access the interface at http://localhost:8000/frontpage/ in your browser.
Create a user there and make it admin by running the following command in mysql database.
UPDATE User SET admin=1 WHERE id='X';
Here X is the id of the user you want to make the admin.
Follow the user guide to proceed with the rest of the process. :)