aiida-s3 0.2.0

AiiDA plugin that provides a storage backend using an S3 object store as the file repository.

aiida-s3

AiiDA plugin that provides various storage backends that allow using cloud data storage services, such as AWS S3 and Azure Blob Storage.

Currently, the following storage backends are available:

• s3.psql_s3: Database provided by PostgreSQL and file repository provided by any service implementing the S3 protocol, for example minIO.
• s3.psql_aws_s3: Database provided by PostgreSQL and file repository provided by AWS S3.
• s3.psql_azure_blob: Database provided by PostgreSQL and file repository provided by Azure Blob Storage.

Installation

The recommended method of installation is through the pip package installer for Python:

pip install aiida-s3

Setup

To use one of the storage backends provided by aiida-s3 with AiiDA, you need to create a profile for it:

1. List the available storage backends:

   aiida-s3 profile setup --help
   

2. Create a profile using one of the available storage backends by passing it as an argument to aiida-s3 profile setup, for example:

   aiida-s3 profile setup s3.psql_s3
   

   The command will prompt for the information required to setup the storage backend. After all information is entered, the storage backend is initialized, such as creating the database schema and creating file containers.

3. Create a default user for the profile:

   verdi -p profile-name user configure --set-default
   

4. The profile is now ready to be used with AiiDA. Optionally, you can set it as the new default profile:

   verdi profile setdefault profile-name
   

5. Optionally, to test that everything is working as intended, launch a test calculation:

   verdi -p profile-name devel launch-add
   

Testing

The unit tests are implemented and run with pytest. To run them, install the package with the tests extra dependencies:

pip install aiida-s3[tests]

The plugin provides interfaces to various services that require credentials, such as AWS S3 and Azure Blob Storage. To run the test suite, one has to provide these credentials or the services have to be mocked. Instructions for each service that is supported are provided below.

S3

The base S3 implementation is interfaced with through the boto3 Python SDK. The moto library allows to mock this interface. This makes it possible to run the test suite without any credentials. To run the tests, simply execute pytest:

pytest

By default, the interactions with S3 are mocked through moto and no actual credentials are required. To run the tests against an actual S3 server, the endpoint URL and credentials need to be specified through environment variables:

export AIIDA_S3_MOCK_S3=False
export AIIDA_S3_ENDPOINT_URL='http://localhost:9000'
export AIIDA_S3_BUCKET_NAME='some-bucket'
export AIIDA_S3_ACCESS_KEY_ID='access-key'
export AIIDA_S3_SECRET_ACCESS_KEY='secret-access-key'
pytest

One example of an open source implementation of a S3-compatible object store is minIO. An instance can easily be created locally using Docker and docker-compose. Simply write the following to docker-compose.yml:

version: '2'

services:
  minio:
    container_name: Minio
    command: server /data --console-address ":9001"
    environment:
      - MINIO_ROOT_USER=admin
      - MINIO_ROOT_PASSWORD=supersecret
    image: quay.io/minio/minio:latest
    ports:
      - '9000:9000'
      - '9001:9001'
    volumes:
      - /tmp/minio:/data
    restart: unless-stopped

and then launch the container with:

docker-compose up -d

The tests can then be run against the server using environment variables as described above.

AWS S3

The AWS S3 service is interfaced with through the boto3 Python SDK. The moto library allows to mock this interface. This makes it possible to run the test suite without any credentials. To run the tests, simply execute pytest:

pytest

By default, the interactions with AWS S3 are mocked through moto and no actual credentials are required. To run the tests against an actual AWS S3 container, the credentials need to be specified through environment variables:

export AIIDA_S3_MOCK_AWS_S3=False
export AIIDA_S3_AWS_BUCKET_NAME='some-bucket'
export AIIDA_S3_AWS_ACCESS_KEY_ID='access-key'
export AIIDA_S3_AWS_SECRET_ACCESS_KEY='secret-access-key'
pytest

Azure Blob Storage

The Azure Blob Storage is communicated with through the azure-blob-storage Python SDK. Currently, there is no good way to mock the clients of this library. Therefore, when the tests are run without credentials, and so the Azure Blob Storage client needs to be mocked, the tests are skipped. To run the tests against an actual AWS S3 container, the credentials need to be specified through environment variables:

export AIIDA_S3_MOCK_AZURE_BLOB=False
export AIIDA_S3_AZURE_BLOB_CONTAINER_NAME='some-container'
export AIIDA_S3_AZURE_BLOB_CONNECTION_STRING='DefaultEndpointsProtocol=https;AccountName=...;AccountKey=...;EndpointSuffix=core.windows.net'
pytest

The specified container does not have to exist yet, it will be created automatically. The connection string can be obtained through the Azure portal.