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Replace outbox pub with persistent publisher (GSI-1500) (#104)
* DCS: Publish file staging request events via normal publisher * IFRS: Use normal consumer and persistent publisher * FIS: Use persistent publisher and add v2 migration The migration is to move previously published outbox events to the persistent event collection * PCS: Replace outbox pub with persistent pub * UCS: replace outbox pub with persistent pub * FIS: Add migration test and make migration forward only * IFRS: Remove migration * DCS: Remove migration * IFRS: Add republish capability * IRS: Consume FileUploadReceived via normal consumer * IRS: replace outbox DAO with persistent publisher and add a test for it * Update license header year only * DCS: Publish 'file deleted' via persistent publisher * DCS: Consume FileDeletionRequest via normal consumer * Update dependencies and misc items * Do some misc cleanup * Disable a warning * Update missed license headers * DCS: Fix persistent publisher topic setup * Remove duplicate license header * FIS: Simplify migration test * IFRS: Raise an error for invalid topic/type combo
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.devcontainer/license_header.txt

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Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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for the German Human Genome-Phenome Archive (GHGA)
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Licensed under the Apache License, Version 2.0 (the "License");

.github/workflows/push_to_docker/action.yaml

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# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# for the German Human Genome-Phenome Archive (GHGA)
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#
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# Licensed under the Apache License, Version 2.0 (the "License");

.pre-commit-config.yaml

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- id: no-commit-to-branch
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args: [--branch, dev, --branch, int, --branch, main]
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.9.9
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rev: v0.11.2
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hooks:
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix]

.pyproject_generation/pyproject_custom.toml

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dependencies = [
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"typer >= 0.12",
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"ghga-service-commons[api, auth, crypt] >= 3.4",
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"ghga-event-schemas >= 4.1",
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"hexkit[akafka, s3, mongodb] >= 4.1.1",
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"ghga-event-schemas >= 5.0",
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"hexkit[akafka, s3, mongodb] >= 4.2.0",
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"crypt4gh>=1.6",
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"hvac>=2",
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"httpx>=0.27",

Dockerfile

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# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# for the German Human Genome-Phenome Archive (GHGA)
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#
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# Licensed under the Apache License, Version 2.0 (the "License");

LICENSE

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same "printed page" as the copyright notice for easier
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identification within third-party archives.
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Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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for the German Human Genome-Phenome Archive (GHGA)
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Licensed under the Apache License, Version 2.0 (the "License");

lock/requirements-dev.txt

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lock/requirements.txt

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pyproject.toml

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dependencies = [
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"ghga-service-commons[api, auth, crypt] >= 3.4",
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"ghga-event-schemas >= 4.1",
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"hexkit[akafka, s3, mongodb] >= 4.1.1",
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"ghga-event-schemas >= 5.0",
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"hexkit[akafka, s3, mongodb] >= 4.2.0",
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"crypt4gh>=1.6",
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"hvac>=2",
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"httpx>=0.27",

scripts/__init__.py

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# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# for the German Human Genome-Phenome Archive (GHGA)
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#
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# Licensed under the Apache License, Version 2.0 (the "License");

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