feat(grzctl): Introduce "backfill" command to re-read metadata from the archive#559
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…he archive (#559) Co-authored-by: Till Hartmann <till.hartmann@bih-charite.de>
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## grz-tools release (2026-05-11) This release updates multiple packages in the `grz-tools` monorepo. See the full changelog and per-package details linked below. ### Versions - `grzctl` `2.0.0` (from `1.4.0`) - `grz-db` `2.0.0` (from `1.2.0`) - `grz-common` `2.0.0` (from `1.6.1`) - `grz-cli` `1.6.0` (from `1.5.1`) - `grz-pydantic-models` `2.6.0` (from `2.5.0`) - `grz-check` `0.3.0` (from `0.2.1`) --- ##⚠️ Breaking / behavior changes - `grzctl` now automatically updates submission state in the DB on subcommand invocation (default `--update-db`; use `--no-update-db` to disable). The DB state enum adds `REPORTING`. (#501) - `grzctl pruefbericht submit` now requires `--submission-id` so the submission can be updated consistently in the DB. (#525) - `grz-cli` enforces a version policy via S3 `version.json` for `upload` / `submit` operations. (#477) - Added `selected_for_qc` column and QC workflow version recording; tools now require/record QC workflow version and log `grzctl` runtime version. (#531, #561) - `grzctl db submission populate-qc` now requires `--qc-workflow-version` (or `GRZCTL_QC_WORKFLOW_VERSION`) to be provided so the QC workflow version can be recorded in the DB. (#561) - `grzctl` introduces `backfill` to re-read metadata from archives and other state/reporting improvements (impacting automation that reads/writes the submission DB). (#559) - Dropped the Python dependency `pysam` from `grz-cli`, `grzctl`, and `grz-common` (installs are lighter; environments that relied on it being installed transitively must install it explicitly). (#565) --- ## Highlights ### grz-cli (`1.6.0`) - Version policy checks for `upload` and `submit` via S3 `version.json` (#477) - Multiple config files are merged into one effective configuration (#490) - `upload` now prints the generated submission ID to stdout (can affect scripts that parse command output). (#556) ### grzctl (`2.0.0`) - `db list`: state-based filtering, with “latest” view by default (#523) - `db submission show`: `--json` output (#510) - Prüfbericht generation using submission ID from database (#525) - `report`: makes `identifiers.le` optional (#488) - `report` supports `--with-submission-ids`. (#539) - Improved redaction during archival. (#517) - Add `selected_for_qc` column to the submission database (#531) - `populate-qc`: accept `THRESHOLD NOT MET` as valid QC status (#529) - Fix displayed QC stats (#508) - Introduce `backfill` to re-read metadata from the archive (#559) - Require and record QC workflow version; log `grzctl` runtime versions (#561) - `db tui`: add `--quarter`/`--year` selection for the “Detailed QC by LE” overview. (#541) ### grz-pydantic-models (`2.6.0`) - Enforce differing checksums for sequencing data (#496) - Fix MII consent period to use datetime instead of date (#491) - Change `minReadLength` default from `0` to `-1` (#506) ### grz-check (`0.3.0`) - Python bindings now power checksum validation across the stack (#554) - Checksum calculation is now exposed correctly in the Python API (#5dce167) - `grz-check` is now built and published as a Python package via `pyproject.toml`/maturin. (#543) ### Maintenance - Dependency updates (#498) - Python crypto dependency updates: `pynacl` and `crypt4gh` --- ## Rollout notes (ops) - Apply the submission DB migrations before using this release. The schema changes include `selected_for_qc`, QC workflow version logging, `grzctl` runtime version logging, and the new `REPORTING` state. - Submission DB migrations in this release also include the `qc_queue` table and additional `submissions` fields (`submission_size`, `submission_metadata`)—make sure your DB is migrated to `head` before running the updated tools. - Update any automation that calls `grzctl pruefbericht submit` to pass `--submission-id`. - If you enforce LE uploads via S3, deploy the `version.json` policy for `grz-cli`. - Deploy the matching `grz-check` Python bindings where Python-based checksum validation is used. --- ## Full details - Full changelog: [changes.md](changes.md) - Per-package changelogs: - [packages/grz-cli/CHANGELOG.md](packages/grz-cli/CHANGELOG.md) - [packages/grzctl/CHANGELOG.md](packages/grzctl/CHANGELOG.md) - [packages/grz-common/CHANGELOG.md](packages/grz-common/CHANGELOG.md) - [packages/grz-db/CHANGELOG.md](packages/grz-db/CHANGELOG.md) - [packages/grz-pydantic-models/CHANGELOG.md](packages/grz-pydantic-models/CHANGELOG.md) - [packages/grz-check/CHANGELOG.md](packages/grz-check/CHANGELOG.md)
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