datacube-explorer 2.12.3

Web-based exploration of Open Data Cube collections

Data Cube Explorer

Usage (quick-start)

Assuming you already have an Open Data Cube instance, Explorer will use its existing settings.

Install Explorer:

pip install datacube-explorer

Generate summaries for all of your products:

cubedash-gen --init --all

Run Explorer locally:

cubedash-run

It will now be viewable on http://localhost:8090

Developer Setup

These directions are for running from a local folder in development. But it will run from any typical Python WSGI server.

Firstly, install the Open Data Cube. Use of a Data Cube conda environment is recommended. You may need to also conda install -c conda-forge postgis

Test that you can run datacube system check, and that it's connecting to the correct datacube instance.

Dependencies

Now install the explorer dependencies:

# These two should come from conda if you're using it, not pypi
conda install fiona shapely

pip install -e .

Summary generation

Initialise and create product summaries:

cubedash-gen --init --all

(This can take a long time the first time, depending on your datacube size.)

Other available options can be seen by running cubedash-gen --help.

Run

A cubedash-run command is available to run Explorer locally:

$ cubedash-run
    * Running on http://localhost:8080/ (Press CTRL+C to quit)

(see cubedash-run --help for list of options)

But Explorer can be run using any typical Python WSGI server, for example gunicorn:

pip install gunicorn
gunicorn -b '127.0.0.1:8080' -w 4 cubedash:create_app()

Products will begin appearing one-by-one as the summaries are generated in the background. If impatient, you can manually navigate to a product using /<product_name. (Eg /ls5_nbar_albers)

Code Style

All code is formatted using black, and checked with pyflakes.

They are included when installing the test dependencies:

pip install --upgrade --no-deps --extra-index-url https://packages.dea.ga.gov.au/ 'datacube' 'digitalearthau'

pip install -e .[test]

Run make lint to check your changes, and make format to format your code automatically.

You may want to configure your editor to run black automatically on file save (see the Black page for directions), or install the pre-commit hook within Git:

Pre-commit setup

A pre-commit config is provided to automatically format and check your code changes. This allows you to immediately catch and fix issues before you raise a failing pull request (which run the same checks under Travis).

Install pre-commit from pip, and initialise it in your repo:

pip install pre-commit
pre-commit install

Your code will now be formatted and validated before each commit. You can also invoke it manually by running pre-commit run

Note: If you use Conda, install from conda-forge (This is required because the pip version uses virtualenvs which are incompatible with Conda's environments)

conda install pre_commit

FAQ

Can I use a different datacube environment?

Set ODC's environment variable before running the server:

export DATACUBE_ENVIRONMENT=staging

You can always see which environment/settings will be used by running datacube system check.

See the ODC documentation for config and datacube environments

How can I set different timezone

Datacube-explorer default timezone is configured to: Australia/Darwin.

To configure the instance to a different timezone, the following configuration needs to be applied:

• app.config variable CUBEDASH_DEFAULT_TIMEZONE (via environment variable CUBEDASH_SETTINGS, which points to a .env.py file)

Can I add custom scripts or text to the page (such as analytics)?

Create one of the following *.env.html files:

• Global include: for <script> and other tags at the bottom of every page.

  cubedash/templates/include-global.env.html
  

• Footer text include. For human text such as Copyright statements.

  echo "Server <strong>staging-1.test</strong>" > cubedash/templates/include-footer.env.html
  

(*.env.html is the naming convention used for environment-specific templates: they are ignored by Git)

How can I configure the deployment?

refer to deployment instructions and app-config

How do I modify the CSS/Javascript?

The CSS is compiled from Sass, and the Javascript is compiled from Typescript.

Install npm, and then install them both:

npm install -g sass typescript

You can now run make static to rebuild all the static files, or individually with make style or make js.

Alternatively, if using PyCharm, open a Sass file and you will be prompted to enable a File Watcher to compile automatically.

PyCharm will also compile the Typescript automatically by ticking the "Recompile on changes" option in Languages & Frameworks -> Typescript.

How do I run the integration tests?

The integration tests run against a real PostgreSQL database, which is automatically started and stopped using Docker. This requires Docker to be available, but no further database setup is required.

Install the test dependencies: pip install -e .[test]

The run the tests with: pytest integration_tests

How do I add test data for the automated tests?

Most of the automated tests for Datacube Explorer require sample data to run. This comprises definitions of ODC Metadata Types, Products and Datasets.

These are contained within YAML files in the integration_tests/data directory.

Test data is loaded using a pytest fixture called auto_odc_db, which is activated per test module, and will automatically populate the database using files referenced in module global variables. Activate and use it similar to the following example:

pytestmark = pytest.mark.usefixtures("auto_odc_db")

METADATA_TYPES = ["metadata/qga_eo.yaml"]
PRODUCTS = ["products/ga_s2_ard.odc-product.yaml"]
DATASETS = ["s2a_ard_granule.yaml.gz"]

To add sample datasets required for the test case, create a .yaml file with the product name and place all the sample datasets split by --- in the yaml.

If the sample datasets file is large, compress it with gzip <dataset_file>.yaml and reference that file instead.

Roles for production deployments

The roles directory contains sql files for creating Postgres roles for Explorer. These are suitable for running each Explorer task with minimum needed security permissions.

Three roles are created:

• explorer-viewer: A read-only user of datacube and Explorer. Suitable for the web interface and cli (cubedash-view) commands.
• explorer-generator: Suitable for generating and updating summaries (ie. Running cubedash-gen)
• explorer-owner: For creating and updating the schema. (ie. Running cubedash-gen --init)

Note that these roles extend the built-in datacube role agdc_user. If you created your datacube without permissions, a stand-alone creator of the agdc_user role is available as a prerequisite in the same roles directory.

Docker for Development and running tests

You need to have Docker and Docker Compose installed on your system.

To create your environment, run make up or docker-compose up.

You need an ODC database, so you'll need to refer to the ODC docs for help on indexing, but you can create the database by running make initdb or docker-compose exec explorer datacube system init. (This is not enough, you still need to add a product and index datasets.)

When you have some ODC data indexed, you can run make index to create the Explorer indexes.

Once Explorer indexes have been created, you can browse the running application at http://localhost:5000.

You can run tests by first creating a test database make create-test-db-docker and then running tests with make test-docker.

And you can run a single test in Docker using a command like this: docker-compose --file docker-compose.yml run explorer pytest integration_tests/test_dataset_listing.py

Docker-compose for Development and running tests

Testing with app.config

edit .docker/settings_docker.py and setup application config. Then docker-compose -f docker-compose.yml -f docker-compose.override.yml up to bring up explorer docker with database, explorer with settings

STAC API Extensions

The STAC endpoint implements the filter, fields, and sort extensions, all of which are bound to the STAC API - Item Search (/search) endpoint. All support both GET and POST request syntax.

Fields contained in the item properties must be prefixed with properties., ex properties.dea:dataset_maturity.

The implementation of fields differs somewhat from the suggested include/exclude semantics in that it does not permit for invalid STAC entities, so the id, type, geometry, bbox, links, assets, properties.datetime, collection, and stac_version fields will always be included, regardless of user input.

The sort and filter implementations will recognise any syntactically valid version of a property name, which is the say, the STAC, eo3, and search field (as defined by the metadata type) variants of the name, with or without the item. or properties. prefixes. If a property does not exist for an item, sort will ignore it while filter will treat it as NULL.

The filter extension supports both cql2-text and cql2-json for both GET and POST requesets, and uses pygeofilter to parse the cql and convert it to a sqlalchemy filter expression. filter-crs only accepts http://www.opengis.net/def/crs/OGC/1.3/CRS84 as a valid value.