grz-cli 1.7.0__tar.gz → 1.7.2__tar.gz

{grz_cli-1.7.0 → grz_cli-1.7.2}/CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## [1.7.2](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.7.1...grz-cli-v1.7.2) (2026-06-02)
+
+
+### Bug Fixes
+
+* **grzctl,grz-cli:** use correct argument name "mmap" in validate callback function ([#590](https://github.com/BfArM-MVH/grz-tools/issues/590)) ([9f5cc42](https://github.com/BfArM-MVH/grz-tools/commit/9f5cc425bd1626f65dfb197d21c27eccb02f16b1))
+
+## [1.7.1](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.7.0...grz-cli-v1.7.1) (2026-05-29)
+
+
+### Bug Fixes
+
+* **grz-cli:** handle tuple from multi-config in submit ([#588](https://github.com/BfArM-MVH/grz-tools/issues/588)) ([553f4e9](https://github.com/BfArM-MVH/grz-tools/commit/553f4e99ce7146d839d4502c8a9ee07778e50f04))
+
 ## [1.7.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.6.1...grz-cli-v1.7.0) (2026-05-19)
 
 

{grz_cli-1.7.0 → grz_cli-1.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: grz-cli
-Version: 1.7.0
+Version: 1.7.2
 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

grz_cli-1.7.2/src/grz_cli/__init__.py

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

{grz_cli-1.7.0 → grz_cli-1.7.2}/src/grz_cli/commands/submit.py

@@ -1,6 +1,7 @@
 """Command for submitting (validating, encrypting, and uploading) a submission."""
 
 import logging
+from typing import Any
 
 import click
 from grz_cli.utils.version_check import check_version_and_exit_if_needed
@@ -18,11 +19,11 @@ from ..models.config import UploadConfig
 
 @click.command("submit")
 @grzcli.submission_dir
-@grzcli.config_file
+@grzcli.configuration
 @grzcli.threads
 @grzcli.force
 @click.pass_context
-def submit(ctx, submission_dir, config_file, threads, force):
+def submit(ctx, configuration: dict[str, Any], submission_dir, threads, force, **kwargs):
     """
     Validate, encrypt, and then upload.
 
@@ -31,11 +32,11 @@ def submit(ctx, submission_dir, config_file, threads, force):
     2. Encrypt the submission
     3. Upload the encrypted submission
     """
-    config = UploadConfig.from_path(config_file)
+    config = UploadConfig.model_validate(configuration)
     check_version_and_exit_if_needed(config.s3)
 
     click.echo("Starting submission process...")
-    ctx.invoke(validate, submission_dir=submission_dir, config_file=config_file, force=force)
-    ctx.invoke(encrypt, submission_dir=submission_dir, config_file=config_file, force=force, check_validation_logs=True)
-    ctx.invoke(upload, submission_dir=submission_dir, config_file=config_file, threads=threads)
+    ctx.invoke(validate, submission_dir=submission_dir, force=force)
+    ctx.invoke(encrypt, submission_dir=submission_dir, force=force, check_validation_logs=True)
+    ctx.invoke(upload, submission_dir=submission_dir, threads=threads)
     click.echo("Submission finished!")

{grz_cli-1.7.0 → grz_cli-1.7.2}/src/grz_cli/commands/validate.py

@@ -20,7 +20,7 @@ log = logging.getLogger(__name__)
 @click.option(
     "--mmap/--no-mmap",
     "mmap",
-    default=True,
+    default=False,
     hidden=True,
     help="Whether to use mmap.",
 )

grz_cli-1.7.2/tests/conftest.py

@@ -0,0 +1,32 @@
+"""Shared fixtures for grz-cli tests."""
+
+from pathlib import Path
+
+import pytest
+import yaml
+
+MINIMAL_S3_CONFIG: dict[str, dict[str, str]] = {
+    "s3": {
+        "endpoint_url": "https://example.invalid",
+        "bucket": "test-bucket",
+        "access_key": "test-key",
+        "secret": "test-secret",
+    },
+}
+
+
+@pytest.fixture
+def s3_config_path(tmp_path: Path) -> Path:
+    """Write a minimal S3 config file and return its path."""
+    config_path = tmp_path / "config.yaml"
+    config_path.write_text(yaml.dump(MINIMAL_S3_CONFIG))
+    return config_path
+
+
+@pytest.fixture
+def submission_dir(tmp_path: Path) -> Path:
+    """Empty submission directory with the four standard subdirectories."""
+    submission_dir = tmp_path / "submission"
+    for sub in ("metadata", "files", "encrypted_files", "logs"):
+        (submission_dir / sub).mkdir(parents=True)
+    return submission_dir

grz_cli-1.7.2/tests/test_submit.py

@@ -0,0 +1,71 @@
+"""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

grz_cli-1.7.0/src/grz_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.7.0"