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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). | ||
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# 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. | ||
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### `src/` | ||
This directory contains job scripts. | ||
This directory contains the Glue job scripts. | ||
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### `tests/` | ||
This directory contains unit tests. | ||
This directory contains the unit tests for Glue job scripts. | ||
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### `.github/` | ||
This directory contains the scripts for our GitHub Actions. | ||
This directory contains the scripts for GitHub Actions. | ||
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# Local environment setup | ||
The project uses AWS Glue libraries and Python, and requires Docker. | ||
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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. | ||
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``` | ||
brew install python | ||
brew install python@3.8 | ||
``` | ||
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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. | ||
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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. | ||
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If you already have a docker container, run the following command to build the image. | ||
``` | ||
docker build -t aws-glue . | ||
``` | ||
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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'. | ||
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``` | ||
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" | ||
``` | ||
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# GitHub Actions | ||
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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. | ||
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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). |