ghga-datasteward-kit 2.0.0

GHGA Data Steward Kit - A utils package for GHGA data stewards.

GHGA Data Steward Kit

Utilities for data stewards interacting with GHGA infrastructure.

Installation:

This package can be installed using pip:

pip install ghga-datasteward-kit

Step by Step Guide

It is important to outline that some commands can only be used by Central Data Stewards while other commands address Local Data Stewards.

The workflow for both the Local and Central Data Stewards is outlined in the following paragraphs:

Local Data Steward

In v1.1 of the Archive, Local Data Stewards are responsible for (A) preparing the metadata of a submission and (B) for encrypting and uploading the corresponding files to the Data Hub's S3-compatible Object Storage.

A. Metadata Preparation

The data steward kit has no functionality to help with metadata preparation, however, it is still described here for completeness of the workflow.

To define metadata for a submission, you have two options:

Option 1: Use an excel spreadsheet (please do not use Google Spreadsheets because of data protection). Templates can be found here. You may validate the metadata by:

1. Running the GHGA Metadata Transpiler to generate JSON (as in Option 2).
2. Run the GHGA Metadata Validator on the produced JSON.

Option 2: Directly specify the metadata using JSON compliant with our LinkML schema. Validation of the metadata can be achieved using the GHGA Metadata Validator.

Once your spreadsheet or JSON file have passed validation, you may send the metadata to the Central Data Steward.

B. File Encryption and Upload:

This is achieved using the data steward kit, using the following steps:

1. Generate credentials: The kit interacts with services at GHGA central. To authenticate yourself against these services you need to create a set of credentials using the ghga-datasteward-kit generate-credentials command. Please see this section for further details.

2. Encrypt and Upload: File encryption and upload to the S3-compatible object storage is done in one go. This is achieved using either the ghga-datasteward-kit files upload for uploading a single file or the ghga-datasteward-kit files batch-upload for uploading multiple files at once. Please see this section for further details. This will output one summary JSON per uploaded file. The encryption secret is automatically transferred to GHGA central.

Once the upload of all files of a submission has completed, please notify the GHGA Central Data Steward and provide the summary JSONs obtained in step 2.

Central Data Steward

The Central Data Steward is responsible for ingesting the metadata and the upload summary files into the running system. This is performed with the following steps:

1. Generate credentials: As for the local data stewards, central data stewards need to have credentials for authentication with GHGA Central Services. To create these credentials the ghga-datasteward-kit generate-credentials command is used. Please see this section for further details.
2. Transpile Metadata Spreadsheet: If the Local Data Steward provided a metadata spreadsheet, this spreadsheet has to be first transpiled to the JSON format using the ghga-datasteward-kit metadata transpile command. Please see this section for further details.
3. Include in Submission Registry: The submission JSON is included in a submission registry on the local file system using the ghga-datasteward-kit metadata submit command. Please see this section for further details.
4. Produce Metadata Artifacts: A transformation workflow is run on all submissions in the submission registry to produce multiple query-specific metadata artifacts using the ghga-datasteward-kit metadata transform command. Please see this section for further details.
5. Publish Metadata: To publish all metadata artifacts of all submissions to the running system so that they are available on the GHGA website, the ghga-datasteward-kit load command can be used.
6. Make Files Downloadable: To make files downloadable, the file summary JSONs provided by the Local Data Steward (see here) need to be ingested into the running system using the ghga-datasteward-kit files ingest-upload-metadata command. Please see this section for further details.

Details per Command

An overview of all commands is provided using:

ghga-datasteward-kit --help

The following paragraphs provide additional help for using the different commands.

files (batch-)upload

To be performed by Local Data Stewards.

This command facilitates encrypting files using Crypt4GH and uploading the encrypted content to a (remote) S3-compatible object storage. This process consists of multiple steps:

1. Generate a unique file id
2. Create unencrypted file checksum
3. Encrypt file
4. Extract file secret and remove Crypt4GH envelope
5. Upload encrypted file content
6. Download encrypted file content, decrypt and verify checksum
7. Write file/upload information to output file

The user needs to provide a config yaml containing information as described here.

An overview of important information about each the upload is written to a file called <alias>.json in the output directory.

It contains the following information:

1. The file alias
2. A unique identifier for the file
3. The local file path
4. A SHA256 checksum over the unencrypted content
5. MD5 checksums over all encrypted file parts
6. SHA256 checksums over all encrypted file parts
7. The file encryption/decryption secret

Attention: Keep this output file in a safe, private location. If this file is lost, the uploaded file content becomes inaccessible.

files ingest-upload-metadata

To be performed by Central Data Stewards only.

Upload all file summary JSONs (produced using the files (batch-)upload command) from the given directory to the running system and make the corresponding files available for download.

This command requires a configuration file as described here.

metadata

To be performed by Central Data Stewards only.

The metadata label groups metadata related commands.

Some of them require a configuration file as described here.

load

To be performed by Central Data Stewards only.

The load command makes files and metadata available to user in the running system.

It needs a configuration parameters as described here.

generate-credentials

A command to generate a token/hash pair for interacting with GHGA Central services.

The generated token file should not be moved to a different system and never be shared with another user. The token hash (*not the token) must be shared with the GHGA Central Operation Team. This process has to be done only once per data steward and system (if a data steward is working with multiple compute environments, one set of credentials per environment should be created).

Development

For setting up the development environment, we rely on the devcontainer feature of vscode in combination with Docker Compose.

To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers" extension (ms-vscode-remote.remote-containers) installed. Then open this repository in vscode and run the command Remote-Containers: Reopen in Container from the vscode "Command Palette".

This will give you a full-fledged, pre-configured development environment including:

• infrastructural dependencies (databases, etc.)
• all relevant vscode extensions pre-installed
• pre-configured linting and auto-formating
• a pre-configured debugger
• automatic license-header insertion

If you prefer not to use vscode, you could get a similar setup (without the editor specific features) by running the following commands:

# Execute in the repo's root dir:
cd ./.devcontainer

# build and run the environment with docker-compose
docker-compose up

# attach to the main container:
# (you can open multiple shell sessions like this)
docker exec -it devcontainer_app_1 /bin/bash

License

This repository is free to use and modify according to the Apache 2.0 License.