WebODV Setup

WebODV needs the following items in the installation folder:

• data (ask Sebastian)
• odv_software (ask Sebastian)
• settings (from Github)
• settings/PKTenv (ask Sebastian, secret environment variables)
• docker-compose.yml (from https://raw.githubusercontent.com/SeaDataCloud/vre-config/master/services/odv/docker-compose.yml)
• .env (should be available from Github)

There are some prerequisites in the folder structure above:

• Healthcheck folder (located at /opt/healthchecks for STFC installation)
• Security folder (located at /opt/security for STFC installation)

Instructions

The below instructions are that were used to setup ODV in STFC (Oxford installation)

Create folder structure

The folder structure is open to individual setups, however, recommendation is to follow the below for consistency.

mkdir /opt/odv #Root folder for the entire setup
mkdir /opt/odv/data #Folder holding all ODV_DATA.tgz files including background data and public data for SDN

Create docker network(s)

Each service module has it's own docker network.

docker create network vre_odv_p_extractor_network
docker create network vre_proxy

Healthcheck script

Drop in the healthcheck script in the HEALTH folder.

cd /opt/healthcheck
wget https://raw.githubusercontent.com/SeaDataCloud/vre-config/master/common/healthcheck_nginx.sh

Download the ODV Data folder

This tarball is pretty big - so, it will take a while to download and extract.

cd /opt/odv/data
wget <Data download location, contact Sebastian>
tar -xf ODV_data.tgz
mv data/ODV_data/ data/ODV_background

Set permissions on the data folder

cd /opt/odv
chown 1000:1000 -R data/*

Download the ODV Software

cd /opt/odv/
wget <download link for ODV software from Sebastian>
tar -xf odv_software.tgz

Set permissions for the odv_installation folder

cd /opt/odv/
chown 1000:1000 -R odv_software

Download and drop the necessary docker-compose files for installation

The docker-compose files and the settings for ODV service modules are located in the Github repository. There is no easy way of cloning/downloading just the necessary files. So, we will have to download the whole repository (quite small), move/locate the folders as needed and then, clean up. The below steps will do all of it - so, please follow.

Get the zip downloaded

cd /opt/odv/
wget https://github.com/SeaDataCloud/vre-config/archive/master.zip
unzip master.zip

Move things around

cp -R vre-config-master/services/odv/settings/* settings/
cp vre-config-master/services/odv/docker-compose.yml .

Clean up

rm -rf vre-config-master
rm -f master.zip

Enviroment variables

You need to set the environment variables now. Get the list of variables from Sebastian and paste into the local environment file.

cd /opt/odv
vi .env
<paste the variables from Sebastian>

The .env file should look something like this (from STFC installation):

DATA_PATH=

ODV_PATH=/opt/odv/

MYSQL_ROOT_PASSWORD=
MYSQL_DATABASE=
MYSQL_USER=
MYSQL_PASSWORD=

FDQM=whaleshark.rl.ac.uk

Change settings for WebODV

cd /opt/odv/settings
rm -rf settings/JSON/*
rm -rf settings/TreeviewsVar/*
wget <link for PKTenv file from Sebastian>

Change the client URLs (Line 2) in settings files from "client_url": "sdc-test.argo.grnet.gr" to "client_url": "<your URL for the service>"

Now you should be in a position to start up ODV

Start up ODV

docker-composer down && docker-compose up -d && docker-compose logs --tail=100 -f

If the above doesn't work, try splitting out to each command.

docker-compose down, docker-compose up -d, docker-compose logs --tail=100 -f

Test from the interface the dashboard interface. Be patient - things might take a while to get going. If it doesn't start up the first time, repeat the above step again and see if that helps it (possible bug).