Gunicorn and Application Image¶

Required files and folders¶

In “local_enterobase/Singularity_Images/Gunicorn_App” sub-folder

Recipe file for the base image: local_enterobase_reci_base.def
Recipe file for the application image : local_enterobase_reci.def

Content of the recipe files¶

This image is built in two stages:
- The first stage is building the base image which contains the dependency packages
- The second one is based on the image which is generated from the first stage and adding local EnteroBase application and the container entry points.
The reason for using two stages is to reduce the total buld time
- Building of the first image takes long time and it is not changed often.
- While building of the second one takes much less time, and we need to re-build this iamge when changing the Local EnteroBase code which happens frequently.

The first image is built using “local_enterobase_reci_base.def” recipe file.

The first two lines in the recipe files pull the a singularity image which is based on ubintu 18.04

Bootstrap:library
From: ubuntu:18.04

Then, at the post section, it downloads and installs the different dependency packages.

The second image is built using “local_enterobase_reci.def” recipe file

The first two lines instruct that the image is built based on a local image, then sets the local image name.

Bootstrap:localimage
From : local_base_image.sif

Then, at the files section, it copies the local enterobase project code to the image.

%files
      $HOME/local_enterobase/ /var/www/

Then it creates an entry point to create a password for the local adminstrator

%apprun set_password "@"
  python3 /var/www/local_enterobase/manage.py set_local_password "$@"

This entry point takes one argument which is the password
Another entry point is created to run Gunicorn as a singularity instance

%startscript
   cd /var/www/local_enterobase/
   APP_PATH="/var/www/local_enterobase/"
   PYTHONPATH=$APP_PATH:$PYTHONPATH
   echo $PYTHONPATH
   gunicorn -b 0.0.0.0:8000  "local_entero:create_app('production')" --timeout 300 --name "local_entero" --log-file=$HOME/logs/gunilog.log --bind=unix:$HOME/sock

This instructs that Gunicorn runs Local Enterobase, listens to port 8000 and sets time out to be 300 seconds.

Building the images¶

Assuming that the local_enterobase repository is saved in the sub-folder “local_enterobase” from the current working folder, run the following command to build a singularity image named as “local_base_image.sif”, the local_base_image is built using the following command:

sudo singularity build local_base_image.sif local_enterobase/Singularity_Images/Gunicorn_App/local_enterobase_reci_base.def

The following command is used to build the second image:

sudo singularity build local_enterobase.sif local_enterobase/Singularity_Images/Gunicorn_App/local_enterobase_reci.def

Running the container¶

The user needs to set up a system password so they can use the web interface to configure the application, registers local EnteroBase instance with Warwick EnteroBase and tests upload files to Warwick EnteroBase.
- The local admin should use the following command to set up the password after replacing “mypassword” to their own passwords:
```
singularity run --app set_password local_enterobase.sif -p mypassword
```
- Please note that the user may get error messages regarding database configuration when running the previous command, but these messages can be ignored at this stage
Then the user needs to use the following command to the run the gunicron and the application as a singularity instance which is called “local_enterobase” (the user may choose to use any other name).

singularity instance start local_enterobase.sif local_enterobase

To be sure that the local_enterobase instance is running, the local admin can use the following command to list all the running Singularity instances:

singularity instance list

The output will include the running instance name “i.e. local_enterobase”, it will look something like this:

INSTANCE NAME	PID	IP	IMAGE
local_enterobase	23456		/home/khaled/local_enterobase.sif

If the user wants to restart the system, they should stop the instance first, then run it again using the following two commands:

singularity instance  stop local_enterobase
singularity instance start local_enterobase.sif local_enterobase