ClinicalTrialsDataProcessing

This is used to build tools which process and standardize the data.

More data later.

proposed architecture:

AACT Dockerfile #when built on its own, allows for the creation of the AACT database.

• Should create appropriate users.

ClinicalTrialHistory Dockerfile #inherits from AACT (multistage builds?) and adds initialization steps to the database.

• adds schemas, tables, and views for both http requests and parsed history tables.
• adds connection roles
• adds connection users

ClinicalTrialDataProcessing docker-compose.yaml #deploys a ClinicalTrialHistory container, pgadmin4, and eventually the downloading program/environment.

Background on Docker

Docker uses the following flow

1. configuration using docker-compose.yaml or a Dockerfile
2. docker build . to generate an image
3. docker run xxxxxx to take the image and create a container.
   • when the container is created, it starts, running commands as configured in the dockerfile.
   • Consequently, the AACT database image when run must initialize the postgres db, then run the initalization details.
   • Here is where bind mounts come into play.

Multistage builds

https://stackoverflow.com/questions/53659993/docker-multi-stage-how-to-split-up-into-multiple-dockerfiles

https://docs.docker.com/develop/develop-images/multistage-build/

Basically

Dockerfile vs docker-compose.yaml

A Dockerfile is used to create images.

A docker-compose.yaml is used to automate the deployment of containers.

Types of storage

COPY/ADD (Dockerfile)

In a dockerfile, this adds a file permanently to the image.

This adds files one way to or from the container when initialized.

Volumes (docker-compose.yaml && Dockerfile)

Useable in both docker-compose and Dockerfile's, this creates a permanent storage. It can be maintained by docker or stored in a particular location.

Good for longer term storage such as databases.

Bind mounts (docker-compose.yaml)

Bind mounts are used to make a host filesystem resource available