grz-cli 1.7.2__tar.gz → 2.0.0__tar.gz

{grz_cli-1.7.2 → grz_cli-2.0.0}/CHANGELOG.md

@@ -1,5 +1,26 @@
 # Changelog
 
+## [2.0.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.8.0...grz-cli-v2.0.0) (2026-08-13)
+
+
+### ⚠ BREAKING CHANGES
+
+* **grzctl:** grzctl requires grz-db 3 and grz-cli 2, and so applies the same consent rules when it reads or backfills submission metadata.
+* **grz-cli:** grz-cli requires grz-common 3. Metadata naming a consent dateTime outside the FHIR grammar, or leaving a 2025 researchConsent provision period open-ended, is now rejected rather than accepted.
+
+### Bug Fixes
+
+* **grz-cli:** require grz-common 3 ([#649](https://github.com/BfArM-MVH/grz-tools/issues/649)) ([69b9c17](https://github.com/BfArM-MVH/grz-tools/commit/69b9c171dd1e248bb38bbc6822dc4e7f3857accc))
+* **grzctl:** require grz-db 3 and grz-cli 2 ([69b9c17](https://github.com/BfArM-MVH/grz-tools/commit/69b9c171dd1e248bb38bbc6822dc4e7f3857accc))
+
+## [1.8.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.7.2...grz-cli-v1.8.0) (2026-08-13)
+
+
+### Features
+
+* **grz-db:** ship reusable database fixtures for downstream tests ([#647](https://github.com/BfArM-MVH/grz-tools/issues/647)) ([a72caba](https://github.com/BfArM-MVH/grz-tools/commit/a72caba963512876be92ac4a8469b931fd1c3767))
+* **grzctl, grz-db, grz-common:** Metadata schema version check via version.json ([#624](https://github.com/BfArM-MVH/grz-tools/issues/624)) ([c6f1e7c](https://github.com/BfArM-MVH/grz-tools/commit/c6f1e7ce07cd5772beee5551e0b95b02a9f83914))
+
 ## [1.7.2](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.7.1...grz-cli-v1.7.2) (2026-06-02)
 
 

{grz_cli-1.7.2 → grz_cli-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: grz-cli
-Version: 1.7.2
+Version: 2.0.0
 Summary: Tool for validation, encryption and upload of MV submissions to GDCs.
 Project-URL: Homepage, https://github.com/BfArM-MVH/grz-tools
 Project-URL: Repository, https://github.com/BfArM-MVH/grz-tools
@@ -13,7 +13,7 @@ Keywords: GDC,GRZ,S3
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.12
-Requires-Dist: grz-common<3,>=2.1
+Requires-Dist: grz-common<4,>=3
 Requires-Dist: packaging<27,>=23
 Description-Content-Type: text/markdown
 

{grz_cli-1.7.2 → grz_cli-2.0.0}/pyproject.toml

@@ -14,7 +14,7 @@ authors = [
 dynamic = ["version"]
 dependencies = [
     "packaging >=23,<27",
-    "grz-common >=2.1,<3",
+    "grz-common >=3,<4",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",

grz_cli-2.0.0/src/grz_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "2.0.0"

{grz_cli-1.7.2 → grz_cli-2.0.0}/src/grz_cli/commands/validate.py

@@ -51,6 +51,7 @@ def validate(
         encrypted_files_dir=submission_dir / "encrypted_files",
         threads=threads,
     )
+
     worker_inst.validate(identifiers=config.identifiers, force=force, no_mmap=not mmap)
 
     log.info("Validation finished!")

{grz_cli-1.7.2 → grz_cli-2.0.0}/src/grz_cli/utils/version_check.py

@@ -43,10 +43,30 @@ def check_version_and_exit_if_needed(
     version_file = VersionFile.from_s3(s3_options, version_file_key)
 
     current_version = pkg_version.Version(version("grz-cli"))
-    now = datetime.now(UTC)
+    _check_policy_and_exit_if_needed("grz-cli", current_version, version_file.grzcli_version)
+
+
+def check_metadata_version_and_exit_if_needed(
+    s3_options: S3Options,
+    metadata_schema_version: str,
+    version_file_key: str = "version.json",
+) -> None:
+    """Validate the metadata schema version against the policy defined in version.json."""
+    version_file = VersionFile.from_s3(s3_options, version_file_key)
 
-    policy = _select_active_policy(version_file.grzcli_version, now)
+    current_version = pkg_version.Version(metadata_schema_version)
+    _check_policy_and_exit_if_needed("metadata", current_version, version_file.metadata_version)
 
+
+def _check_policy_and_exit_if_needed(
+    subject: str,
+    current_version: pkg_version.Version,
+    policies: list[VersionInfo],
+) -> None:
+    """Validate a version against the active policy for a subject."""
+    now = datetime.now(UTC)
+
+    policy = _select_active_policy(policies, now)
     if policy is None:
         logger.debug("No active version policy found — skipping version check.")
         return
@@ -56,7 +76,7 @@ def check_version_and_exit_if_needed(
     max_version = policy.max_version
     enforced_from = policy.enforced_from
 
-    logger.debug(f"Current grz-cli version: {current_version}")
+    logger.debug(f"Current {subject} version: {current_version}")
     logger.debug(
         f"Active policy: "
         f"minimal={minimal_version}, "
@@ -68,22 +88,24 @@ def check_version_and_exit_if_needed(
     # old version
     if current_version < minimal_version:
         logger.error(
-            f"Your grz-cli version ({current_version}) is not supported. Minimum required version is {minimal_version}."
+            f"Your {subject} version ({current_version}) is not supported. Minimum required version is {minimal_version}."
         )
         sys.exit(1)
 
     # supported but behind recommended — skip if recommended_version not set
     if recommended_version is not None and minimal_version <= current_version < recommended_version:
         logger.warning(
-            f"You are using grz-cli {current_version}, but the recommended version is "
+            f"You are using {subject} {current_version}, but the recommended version is "
             f"{recommended_version}. Upgrading is strongly recommended."
         )
         return
 
     # too new — skip if max_version not set
     if max_version is not None and current_version > max_version:
-        logger.error(f"grz-cli version {current_version} is newer than the maximum supported version ({max_version}).")
+        logger.error(
+            f"{subject} version {current_version} is newer than the maximum supported version ({max_version})."
+        )
         sys.exit(1)
 
     # best case
-    logger.info(f"grz-cli {current_version} is within the supported and tested range.")
+    logger.info(f"{subject} {current_version} is within the supported and tested range.")

grz_cli-2.0.0/tests/test_submit.py

@@ -0,0 +1,105 @@
+"""Integration tests for the ``grz-cli submit`` command."""
+
+from pathlib import Path
+
+import click.testing
+import pytest
+import yaml
+from grz_cli.cli import build_cli
+from pytest_mock import MockerFixture
+
+
+@pytest.fixture
+def stub_subcommands(mocker: MockerFixture):
+    """Replace the subcommands ``submit`` invokes with no-op mocks.
+
+    ``ctx.invoke`` accepts any callable when the target is not a click
+    ``Command``, so swapping the module-level imports lets the real submit
+    callback run end-to-end without executing real validation, encryption,
+    or upload.
+
+    :returns: A parent mock recording every subcommand call, so their relative order is
+        observable. ``mock_calls`` names them, for example ``call.validate(...)``.
+    """
+    mocker.patch("grz_cli.commands.submit.check_version_and_exit_if_needed")
+    recorder = mocker.MagicMock()
+    for name in ("validate", "encrypt", "upload"):
+        recorder.attach_mock(mocker.patch(f"grz_cli.commands.submit.{name}"), name)
+    return recorder
+
+
+def _called_subcommands(recorder) -> list[str]:
+    """Names of the subcommands ``recorder`` saw, in call order."""
+    return [call[0] for call in recorder.mock_calls]
+
+
+def _subcommand_kwargs(recorder) -> dict[str, dict]:
+    """The keyword arguments each subcommand was called with, keyed by subcommand name."""
+    return {call[0]: call[2] for call in recorder.mock_calls}
+
+
+def _invoke_submit(*extra_args: str) -> click.testing.Result:
+    runner = click.testing.CliRunner()
+    return runner.invoke(build_cli(), ["submit", *extra_args], catch_exceptions=False)
+
+
+def test_submit_runs_subcommands_in_order(
+    s3_config_path: Path,
+    submission_dir: Path,
+    stub_subcommands,
+) -> None:
+    """Encrypting before validating, or uploading before encrypting, would ship bad data."""
+    result = _invoke_submit(
+        "--submission-dir",
+        str(submission_dir),
+        "--config-file",
+        str(s3_config_path),
+    )
+
+    assert result.exit_code == 0, result.output
+    assert _called_subcommands(stub_subcommands) == ["validate", "encrypt", "upload"]
+
+
+def test_submit_hands_each_subcommand_the_submission_it_was_given(
+    s3_config_path: Path,
+    submission_dir: Path,
+    stub_subcommands,
+) -> None:
+    """All three must act on the same directory, and encrypt must refuse to skip the validation logs."""
+    result = _invoke_submit(
+        "--submission-dir",
+        str(submission_dir),
+        "--config-file",
+        str(s3_config_path),
+    )
+    assert result.exit_code == 0, result.output
+
+    kwargs = _subcommand_kwargs(stub_subcommands)
+    assert {name: call["submission_dir"] for name, call in kwargs.items()} == {
+        "validate": submission_dir,
+        "encrypt": submission_dir,
+        "upload": submission_dir,
+    }
+    assert kwargs["encrypt"]["check_validation_logs"] is True, "submit must not encrypt unvalidated data"
+
+
+def test_submit_accepts_multiple_config_files(
+    tmp_path: Path,
+    s3_config_path: Path,
+    submission_dir: Path,
+    stub_subcommands,
+) -> None:
+    """Regression: repeated ``--config-file`` once produced a tuple that crashed config parsing."""
+    override_path = tmp_path / "override.yaml"
+    override_path.write_text(yaml.dump({"s3": {"access_key": "override-key"}}))
+
+    result = _invoke_submit(
+        "--submission-dir",
+        str(submission_dir),
+        "--config-file",
+        str(s3_config_path),
+        "--config-file",
+        str(override_path),
+    )
+
+    assert result.exit_code == 0, result.output

grz_cli-1.7.2/src/grz_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.7.2"

grz_cli-1.7.2/tests/test_submit.py

@@ -1,71 +0,0 @@
-"""Integration tests for the ``grz-cli submit`` command."""
-
-from pathlib import Path
-
-import click.testing
-import pytest
-import yaml
-from grz_cli.cli import build_cli
-from pytest_mock import MockerFixture
-
-
-@pytest.fixture
-def stub_subcommands(mocker: MockerFixture) -> dict[str, object]:
-    """Replace the subcommands ``submit`` invokes with no-op mocks.
-
-    ``ctx.invoke`` accepts any callable when the target is not a click
-    ``Command``, so swapping the module-level imports lets the real submit
-    callback run end-to-end without executing real validation, encryption,
-    or upload.
-    """
-    mocker.patch("grz_cli.commands.submit.check_version_and_exit_if_needed")
-    return {
-        "validate": mocker.patch("grz_cli.commands.submit.validate"),
-        "encrypt": mocker.patch("grz_cli.commands.submit.encrypt"),
-        "upload": mocker.patch("grz_cli.commands.submit.upload"),
-    }
-
-
-def _invoke_submit(*extra_args: str) -> click.testing.Result:
-    runner = click.testing.CliRunner()
-    return runner.invoke(build_cli(), ["submit", *extra_args], catch_exceptions=False)
-
-
-def test_submit_runs_subcommands_in_order(
-    s3_config_path: Path,
-    submission_dir: Path,
-    stub_subcommands: dict[str, object],
-) -> None:
-    result = _invoke_submit(
-        "--submission-dir",
-        str(submission_dir),
-        "--config-file",
-        str(s3_config_path),
-    )
-
-    assert result.exit_code == 0, result.output
-    stub_subcommands["validate"].assert_called_once()
-    stub_subcommands["encrypt"].assert_called_once()
-    stub_subcommands["upload"].assert_called_once()
-
-
-def test_submit_accepts_multiple_config_files(
-    tmp_path: Path,
-    s3_config_path: Path,
-    submission_dir: Path,
-    stub_subcommands: dict[str, object],
-) -> None:
-    """Regression: repeated ``--config-file`` once produced a tuple that crashed config parsing."""
-    override_path = tmp_path / "override.yaml"
-    override_path.write_text(yaml.dump({"s3": {"access_key": "override-key"}}))
-
-    result = _invoke_submit(
-        "--submission-dir",
-        str(submission_dir),
-        "--config-file",
-        str(s3_config_path),
-        "--config-file",
-        str(override_path),
-    )
-
-    assert result.exit_code == 0, result.output