Data Access Service

Run the app with Docker

Simply run ./startServer.sh to run the app, this will create a docker image and run the image for you.

Host will be http://localhost:8000.

Run the app for development

Requirements

• Conda (recommended for creating a virtual environment)

1. Install Conda (if not already installed):

   Follow the instructions at Conda Installation.

2. Create Conda virtual environment:

   $ conda env create -f environment.yml

Dependency management

Poetry is used for dependency management, the pyproject.toml file is what is the most important, it will orchestrate the project and its dependencies.

You can update the file pyproject.toml for adding/removing dependencies by using

$ poetry add <pypi-dependency-name> # e.g poetry add numpy
$ poetry remove <pypi-dependency-name> # e.g. poetry remove numpy

You might want to update the poetry.lock file after manually modifying pyproject.toml with poetry lock command. To update all dependencies, use poetry update command.

There is a library aodn_cloud_optimised, which referencing direct AODN's GitHub repository as source instead of PyPi. It is written by PO to access cloud optimized data. Please do not access S3 directly and should via this library.

Right now the version is always main branch which is not idea, we should be able to use tag version

aodn_cloud_optimised = { git = "https://github.com/aodn/aodn_cloud_optimised.git", tag = "v0.1.44" }

Error in dependencies

You may try to clean the cache by using the following command

poetry cache clear --all PyPI
poetry env remove --all
poetry lock
poetry install

Installation and Usage

1. Activate Conda virtual environment:

   $ conda activate data-access-service

2. Install dependencies using Poetry:

   # after cloning the repo with git clone command
   $ cd data-access-service
   $ poetry install

   # You should not need to install lib locally, if your python version is correct.
   # https://arrow.apache.org/install/
   sudo apt update
   sudo apt install -y -V ca-certificates lsb-release wget
   wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
   sudo apt install -y -V ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
   sudo apt update
   sudo apt install -y -V libarrow-dev # For C++
   sudo apt install -y -V libarrow-glib-dev # For GLib (C)
   sudo apt install -y -V libarrow-dataset-dev # For Apache Arrow Dataset C++
   sudo apt install -y -V libarrow-dataset-glib-dev # For Apache Arrow Dataset GLib (C)
   sudo apt install -y -V libarrow-acero-dev # For Apache Arrow Acero
   sudo apt install -y -V libarrow-flight-dev # For Apache Arrow Flight C++
   sudo apt install -y -V libarrow-flight-glib-dev # For Apache Arrow Flight GLib (C)
   sudo apt install -y -V libarrow-flight-sql-dev # For Apache Arrow Flight SQL C++
   sudo apt install -y -V libarrow-flight-sql-glib-dev # For Apache Arrow Flight SQL GLib (C)
   sudo apt install -y -V libgandiva-dev # For Gandiva C++
   sudo apt install -y -V libgandiva-glib-dev # For Gandiva GLib (C)
   sudo apt install -y -V libparquet-dev # For Apache Parquet C++
   sudo apt install -y -V libparquet-glib-dev # For Apache Parquet GLib (C)
   sudo apt install -y ninja-build

3. Run the app: In project root folder, create a '.env' file, which contains your API key, e.g.:

   API_KEY="your_actual_api_key_here"
   

   Host will be http://localhost:5000 and default profile is DEV

   $ python -m data_access_service.server

Code formatting

The command below is for manual checks; checks are also executed when you run git commit.

The configurations for pre-commit hooks are defined in .pre-commit-config.yaml.

pre-commit run --all-files

Environment variables

In the root directory of the project, create a .env file.

Profiles

You can use one of the following profiles, set an environment variable call PROFILE in .env

1. dev (default)
2. edge
3. staging
4. prod

E.g

PROFILE=edge

Endpoints

Description	Endpoints	Param	Environment
Health check	/api/v1/das/health	none	ALL
Formatted metadata list	/api/v1/das/metadata	none	ALL
Formatted metadata	/api/v1/das/metadata/{uuid}	none	ALL
Raw metadata	/api/v1/das/metadata/{uuid}/raw	none	ALL
Get Python notebook url	/api/v1/das/data/{uuid}/notebook_url	none	ALL
Subsetting	/api/v1/das/data/{uuid}	start_date=2023-12-25T14:30:00, end_date=2024-02-25T14:30:00, start_depth=-0.06, f=netcdf or json, columns=TIME&columns=DEPTH&columns=LONGITUDE&columns=LATITUDE (array of column return)	ALL
Check has data or not within a timeframe	/api/v1/das/data/{uuid}/has_data	start_date=2023-12-25T14:30:00, end_date=2024-02-25T14:30:00	ALL
Get temporal extent	/api/v1/das/data/{uuid}/temporal_extent	none	ALL

Running Tests

To run the tests for the project:

poetry run python -m unittest discover

This will discover and run all the test cases in your project.

If you have "ModuleNotFoundError" or similar issues, you may need to install dependencies before running the tests:

poetry install

Batch jobs

Another part of this project is to run batch jobs for dataset subsetting.

Local running testing

• If you want to test the batch job codes locally, (running in your local machine) Please export aws environment variables first (or use profile etc..) (for example, if use edge, please go to aws access portal, and pick AODN-Edge -> AodnAdminAccess) and also export AWS_BATCH_JOB_ID (please go to batch console to copy an existing job id). After several exporting, make sure your terminal is at the root folder of this project. Then please run:

./entry_point.py

• If you have error like: "mount/efs permission denied" or other errors about the mount/efs folder, please go to generate_csv_file.py, at the top of the file, make sure efs_mount_point ="" is in use and efs_mount_point = "/mount/efs/" is commented out. This is just a temp solution. We will then use source file to manage these different values in different environments.

aws running testing

• If you want to test the batch job codes in AWS, (running in AWS Batch), please change the efs_mount_point ="" back to efs_mount_point = "/mount/efs/" (if you did the change before), and then:
  1. Build the docker image and push it to ECR (havier-test-ecr). Please do it by following the instructions in the havier-test-ecr repo by clicking button "View push commands" at the top right corner.
  2. Open the ogc-api project locally
  3. In class DatasetDownloadEnums of the ogc-api project, go to JobDefinition enum and change the value of GENERATE_CSV_DATA_FILE from "generate-csv-data-file" into "generate-csv-data-file-dev" (add "-dev" at the end of the string).
  4. run the ogc-api project locally and run the portal project locally (make sure your local portal is pointing to the local ogc-api project).
  5. Go to localhost:5173, and navigate to an IMOS hosted dataset. On the detail page, select any date range and / or spatial area, and click "Download" button. This will trigger the batch job.
  6. For dev stage, if you cannot receive the email, please make sure the email address you provided has added into the AWS SES verified email list.