This is the API backend for ConnecTF. The instructions for the for the react server should be followed after these instructions.

​

Following instructions are using conda

# On linux
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
​
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
​
conda create -n connectf
conda activate connectf
conda install python
conda install nodejs
sudo apt-get install build-essential
​

​

​ A MySQL database instance is required. ​ ​

sudo apt install mariadb-server
sudo apt install mariadb-client
sudo apt-get install libmariadbclient-dev
​
#TODO: confirm the following are required
#sudo apt-get install gcc
#pip install mysql-connector-python
​
sudo system mysql start
sudo mysql_secure_installation
# set a password for user root on mysql

​ Now create database with username and password that will be accessed for connectf. Details of the database should be configured in the config.yaml file in the ./connectf/ folder, alongside settings.py. You can edit settings.py directly if you are more comfortable in configuring a Django project. ​ ​

• db_name=connectf
• db_username=connectfuser
• db_passwd=connectfpwd ​

sudo mysqladmin create connectf
sudo mysql -u root
grant all privileges on connectf.* to 'connectfuser'@'localhost' identified by 'connectfpwd';
flush privileges;
​

pip install -r requirements.txt

Create a config.yaml in the ./connectf folder, alongside the ./connectf/settings.py file.

To set up data files for the server to read from, it is recommended you create a ./data folder at the top level of the project. Put required data files within the ./data folder and edit config.yaml to reflect the changes.

A MySQL database instance is required. Details of the database should be configured in the config.yaml file. You can edit settings.py directly if you are more comfortable in configuring a Django project.

python manage.py migrate

Import data before starting the server.

python manage.py import_annotation -i annotation.csv  # import gene annotations
python manage.py import_data data.csv metadata.txt  # import data/metadata
python manage.py import_edges additional_edges.txt  # import additional edges

Sample files can be found at:

A sample config.yaml file:

N.B. If the file does not exist, create a new config.yaml in the same folder as connectf/settings.py, with the contents similar to the one seen in the sample.

SECRET_KEY: 'django_secret_key'  # see https://docs.djangoproject.com/en/2.2/ref/settings/#secret-key
DEBUG: True
DATABASE:
  NAME: 'db_name'
  USER: 'db_username'
  PASSWORD: 'db_password'
  HOST: 'localhost'
MOTIF_ANNOTATION: '/path/to/file'  # path to cluster motif file motifs.csv.gz
MOTIF_TF_ANNOTATION: '/path/to/file'  # path to tf motif file motifs_indv.csv.gz
MOTIF_CLUSTER_INFO: '/path/to/file'  # path to cluster_info.csv.gz
GENE_LISTS: '/path/to/folder'  # optional gene list folder
TARGET_NETWORKS: '/path/to/folder' # optional target network folder

python manage.py runserver 8000

Deploy using Gunicorn

pip install gunicorn
gunicorn --workers 5 --timeout 200 --bind unix:connectf_backend.sock -m 007 connectf.wsgi
# use "nohup gunicorn [OPTIONS] &" to run in background

This binds the server to a unix socket, which can then be connected to from a reverse proxy such as nginx.

This listens to an HTTPS connection. Remember to include certificates and private keys in the configuration, or use an HTTP configuration instead.

server {
        listen [::]:443 ssl http2;
        listen 443 ssl http2;
        server_name example.com;
        ssl_certificate /path/to/cert.cer;
        ssl_certificate_key /path/to/private_key.pem;
        ssl_protocols TLSv1.2;
        ssl_ciphers HIGH:!aNULL:!MD5;

        add_header Strict-Transport-Security "max-age=86400; includeSubDomains" always;

        client_max_body_size 100M; # ensure file size is big enough for user upload

        root /var/www/html; # path to html files

        index index.html;

        location / {
                # First attempt to serve request as file, then
                # as directory, then fall back to displaying a 404.
                try_files $uri /index.html;
        }

        location ~* ^/(api|queryapp)/ {
            # include proxy_params;
            proxy_set_header Host $http_host;
            proxy_set_header X-Real-IP $remote_addr;
            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
            proxy_set_header X-Forwarded-Proto $scheme;
            proxy_connect_timeout       3600;
            proxy_send_timeout          3600;
            proxy_read_timeout          3600;
            send_timeout                3600;
            proxy_pass http://unix:/path/to/connectf_backend.sock;
        }
}

The front end of this project is built with ReactJS. You can find it at connectf_react.

All data for this project can be found at https://connectf.s3.amazonaws.com/connectf_data_release_v1.tar.gz