submissions-tracking-interface

An interface for browsing the ArrayExpress submissions tracking database

Installation

Create envirnonment file, e.g. ".env", containing the DB connection details:

AUTOSUBS_DB=*** <br>
AUTOSUBS_CUR_USERNAME=*** <br>
AUTOSUBS_CUR_PASSWORD=***

Run locally with Docker

Commands:
docker build -t node-subs-interface-test .
docker run --name node-subs-interface-test -p 3004:3004 --env-file .env node-subs-interface-test

Then runs on localhost:3004

To update page names and colouring at run time use the following command:
docker run -d --name node-subs-interface-test -p 3004:3004 --env-file .env --entrypoint '/bin/sh' node-subs-interface-test -c 'cd /home/node/app; sed -i "s/ENVIRONMENT/TEST/g" ui/*.html && sed -i "s/ENV_COLOUR/#28B463/g" ui/*.html && node sbRestApiServer.js'

Run with Singularity

Due to the read-only default nature of Singularity we need a workaround to pass the variables and modify the code at run time, e.g. to change the text and colour of the headers.

Then environment file should contain the following variables:

AUTOSUBS_DB=***
AUTOSUBS_CUR_USERNAME=***
AUTOSUBS_CUR_PASSWORD=***

SUBS_TRACKING_API_PORT=3004

ENV_COLOUR=#28B463
ENV_NAME=TEST

RUN_DIR=/path/to/writable/directory/tmp_software_test

Create a run script to start the server which will be passed to the singularity exec command.

#!/bin/sh

cd ${RUN_DIR}
cp -r /home/node/app/* ${RUN_DIR}
sed -i "s/ENVIRONMENT/${ENV_NAME}/g" ui/*.html
sed -i "s/ENV_COLOUR/${ENV_COLOUR}/g" ui/*.html
node sbRestApiServer.js

We will also need a directory outside the container that is writable. Create a directory there, one per instance, e.g. tmp_software_test.

Then the server can be started like this in the directory which has the env file and the run script: singularity exec --bind /path/to/writable/directory/ --contain --env-file /path/to/<env_file_name> docker://quay.io/ebigxa/submissions-tracking-interface /path/to/<run_script_name> &

Tested with singularity version 3.5.3