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Merge pull request #34 from SandhraSokhal/PLFM-7962
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documentation improvement
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SandhraSokhal authored Sep 29, 2023
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# Synapse-ETL-Jobs
The Synapse ETL jobs project maintains all the Python-based Glue job scripts respoonsible for moving
Synapse Warehouse data to S3 where it can be queried by Athena.
The scripts are deployed to S3, from where the Synapse Stack Builder can include them in a Glue
CloudFormation stack it creates.
For more information please see the [design documentation](https://sagebionetworks.jira.com/wiki/spaces/DW/pages/2732916846/Processing+Access+Records+using+AWS+High+Level+Design).
[AWS Glue](https://docs.aws.amazon.com/glue/latest/dg/what-is-glue.html) is a cloud service that prepares data for analysis
through automated extract, transform and load (ETL) processes. The Glue job uses the scripts for the ETL process.
The Synapse-ETL-Jobs project maintains all the Python-based Glue job scripts. The Glue jobs are responsible for moving
Synapse warehouse json data to S3 in parquet format, which can be queried by Athena. The [Synapse-Stack-Builder](https://github.com/Sage-Bionetworks/Synapse-Stack-Builder)
project deploys these Python scripts to s3 and creates the Glue jobs. For more information please see
the [design documentation](https://sagebionetworks.jira.com/wiki/spaces/DW/pages/2732916846/Processing+Access+Records+using+AWS+High+Level+Design).

# Repository structure
This repository only contains the Python scripts which are used by Glue jobs.
This repository contains the Python scripts, which are only used by Glue jobs.

### `src/`
This directory contains job scripts.
This directory contains the Glue job scripts.

### `tests/`
This directory contains unit tests.
This directory contains the unit tests for Glue job scripts.

### `.github/`
This directory contains the scripts for our GitHub Actions.
This directory contains the scripts for GitHub Actions.

# Local environment setup
The project uses AWS Glue libraries and Python, and requires Docker.

To install Python on MacOS use the command below, which requires Python version 3 to be installed.
PIP (PIP is a package manager for Python packages, or modules ) is included in python version 3.4 or later.
# Local Python setup
The project's scripts are Python-based. In order to make use of Python libraries and address syntax errors,
it's essential to have Python 3 installed, as Glue employs Python 3.

```
brew install python
brew install python@3.8
```

The following steps build and run a Docker container.
# Local test environment setup
In order to execute the tests, the presence of Glue libraries is necessary. To address the dependencies related to Glue,
build a Docker container using the AWS Glue image to ensure the provisioning of essential prerequisites.

Build image
1. Install and start Docker. If you’re on Mac, you can download and install Docker Desktop (https://www.docker.com/products/docker-desktop).
Note that you’ll need to create a Docker account.
2. Create a Docker project directory for your AWS Glue container. Name could be like ~/docker/AWSGlue
3. In that directory, create a file called docker-compose.yml. Its contents should contain
```
version: '3.3'
services:
aws-glue:
image: aws-glue
container_name: 'aws-glue'
ports:
- 8888:8888
- 4040:4040
```
4. In the same directory, run docker-compose up -d. This will launch a Docker container with the image.

If you already have a docker container, run the following command to build the image.
```
docker build -t aws-glue .
```

To run tests use the following command. It will execute the test files, whose names start with test.
To initiate tests, run the following command, which will execute the test files prefixed with 'test'.

```
docker run -v ~/.aws:/home/glue_user/.aws -v ${GITHUB_WORKSPACE}:/home/glue_user/workspace/ -e DISABLE_SSL=true --rm -p 4040:4040 -p 18080:18080 aws-glue -c "python3 -m pytest"
docker run -v ~/.aws:/home/glue_user/.aws -v ${LOCAL_WORKSPACE ../SageBionetworks/Synapse-ETL-Service}:/home/glue_user/workspace/ -e DISABLE_SSL=true --rm -p 4040:4040 -p 8888:8888 aws-glue -c "python3 -m pytest"
```

# GitHub Actions

1. python-package.yml : This action sets up python, installs dependencies and checks syntax errors or undefined names.
Also, it builds the docker image and run the tests.
1. python-package.yml : This action sets up the Python environment, installs dependencies and checks syntax errors
or undefined references. Furthermore, it builds the docker image and executes the tests.

2. tag_release.yml : A GitHub action to automatically bump and tag develop, on merge, with the latest
2. tag_release.yml : A GitHub action to automatically `bump` and `tag` develop branch, on merge, with the latest
SemVer formatted (Major.Minor.Patch) version. If no version is provided, the `Minor` field is bumped.
The desired bump can be specified in the commit message, e.g. with `#major`, `#minor`, or `#patch`. For more information,
please see the [documentation](https://github.com/anothrNick/github-tag-action).

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