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Containerized app modules for HIVE Lab

All application modules that should be integrated to the main HIVE Lab website needs to be set up following this example application module for BioMuta.

Cloning this example module repositiory

First clone this repo to any direcotry in your server

$ git clone https://github.com/GW-HIVE/biomuta

Getting code for global header and footer

The global header and footer for your module needs to be the same as that of the main HIVE Lab website. To do this, you need to also clone the repo for the main HIVE Lab website and copy relevant code to your module code directory following these cmmands.

$ git clone https://github.com/GW-HIVE/hivelab
$ cp -r ./hivelab/app/src/components/global/ ./biomuta/app/src/components/

Editing menu for your module

Ths config JSON file contains menu information for the module. Please use vi or any editor to edit it.

{
  "module":"biomuta",
  "title":"BioMuta - single-nucleotide variations (SNVs) in cancer",
  "menu":[
    {
      "pageid":"home",
      "label":"BioMuta Home",
      "url":"/biomuta/home",
      "children":[],
      "nav":[
         {"pageid":"tools", "url":"/tools", "label":"TOOLS"}
      ]
    },
    {
      "pageid":"readme",
      "label":"BioMuta README",
      "url":"/biomuta/readme",
      "children":[],
      "nav":[
        {"pageid":"tools", "url":"/tools", "label":"TOOLS"},
	{"pageid":"home", "url":"/biomuta/home", "label":"BioMuta Home"}
      ]
    }
  ]
}

Content of static html pages

For each "pageid" in the config JSON file for the menu, you need to maintain an html files named as page.$PAGE_ID.html.

$ ls -ltr biomuta/app/public/html/
	-rw-r--r--. 1 rykahsay developers 502 Apr 10 11:12 biomuta/app/public/html/page.home.html
	-rw-rw-r--. 1 rykahsay developers 839 Apr 10 11:12 biomuta/app/public/html/page.readme.html

Deploying the module application

Requirements: the following must be available on your server:

  • Node.js and npm
  • docker

Setting config parameters

After cloning this repo, you will need to set the paramters given in app/conf/config.json. The "server" paramater can be "tst" or "prd" for test or production server respectively. The "app_port" is the port in the host that should map to docker container for the app.

$ cd biomuta/app/conf
$ vi config.json

Creating and starting docker container for the APP

From the "app" subdirectory, run the python script given to build and start container:

$ cd biomuta/app/
$ python3 create_app_container.py -s {DEP}
$ docker ps --all

The last command should list docker all containers and you should see the container you created "running_hivelab_app_{DEP}". To start this container, the best way is to create a service file (/usr/lib/systemd/system/docker-hivelab-app-{DEP}.service), and place the following content in it.

[Unit]
Description=Glyds APP Container
Requires=docker.service
After=docker.service

[Service]
Restart=always
ExecStart=/usr/bin/docker start -a running_biomuta_app_{DEP}
ExecStop=/usr/bin/docker stop -t 2 running_biomuta_app_{DEP}

[Install]
WantedBy=default.target

This will allow you to start/stop the container with the following commands, and ensure that the container will start on server reboot.

$ sudo systemctl daemon-reload 
$ sudo systemctl enable docker-hivelab-app-{DEP}.service
$ sudo systemctl start docker-hivelab-app-{DEP}.service
$ sudo systemctl stop docker-hivelab-app-{DEP}.service

Mapping APP and API containers to public domains

To map the APP and API containers to public domains (e.g. www.hivelab.org and api.hivelab.org), add apache VirtualHost directives. This VirtualHost directive can be in a new f ile (e.g. /etc/httpd/conf.d/hivelab.conf).

<VirtualHost *:443>
  ServerName www.hivelab.org

  ProxyPass /biomuta http://127.0.0.1:{APP_PORT}/
  ProxyPassReverse /biomuta http://127.0.0.1:{APP_PORT}/
</VirtualHost>

where {APP_PORT} and {API_PORT} are your port for the APP and API ports in conf/config.json file. You need to restart apache after this changes using the following command:

$ sudo apachectl restart