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Initial Server Setup

This usage guide should be followed if setting up this repository on a server from scratch.

Server Dependencies

The following must be available on your server:

  • wheel
  • pymongo
  • docker

Clone the Repository

Clone the reporistory onto the target machine using git clone.

Creating and Starting the Docker Container for the MongoDB

Navigate to the /api subdirectory and run the create_mongodb_container.py script:

cd api 
python create_mongodb_container.py $SER 
docker ps --all

The first command will navigate you into the api directory. The second command will run the script. The $SER argument should be replaced with the server you are running on (dev, tst, beta, prd). The last command lists all docker containers. You should see the docker mongodb docker container that the script created, in the format of running_biomarker-api_mongo_$SER where $SER is the specified server.

Start the MongoDB container using the docker start {container} command or by creating a service file (instructions for this in the Managing the Docker Containers with a Service File) section.

Initialize MongoDB User

Stay in the /api subdirectory and run the init_mongodb.py script:

python init_mongodb.py $SER

Where the $SER argument is the specified server. This should only be run once on initial setup for each server.

Creating and Starting Docker Container for the API

To create the API container, run the create_api_container.py script from the /api directory.

python create_api_container.py $SER
docker ps --all

The first command will run the script. The $SER argument should be replaced with the server you are running on. The last command lists all docker containers. You should see the api container that the script created, in the format of running_biomarker-api_api_$SER where $SER is the specified server. Start the docker container with the docker start command or create a service file (recommended).

Managing the Docker Containers with a Service File

The service files should be located at /usr/lib/systemd/system/ and named something along the lines of docker-biomarker-api-mongo-{SER}.service (using the MongoDB container as an example) where {SER} indicates the server. Place the following content in it:

[Unit]
Description=Biomarker Backend API MongoDB Container
Requires=docker.service
After=docker.service

[Service]
Restart=always
ExecStart=/usr/bin/docker start -a running_biomarker-api_mongo_$SER
ExecStop=/usr/bin/docker stop -t 2 running_biomarker-api_mongo_$SER

[Install]
WantedBy=default.target

This will ensure the container is automatically restarted in case of server reboot. You can start/stop the container with the following commands:

$ sudo systemctl daemon-reload 
$ sudo systemctl enable docker-biomarker-api-mongo-{SER}.service
$ sudo systemctl start docker-biomarker-api-mongo-{SER}.service
$ sudo systemctl stop docker-biomarker-api-mongo-{SER}.service

Loading an Existing Data Version

To load an existing data version, go to https://data.biomarkerkb.org/ftp/ and select the desired data version directory. TODO