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https://github.com/MillironX/nf-core_modules.git
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f3a405e4f2
* hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Ignores version file checking if testing for error * Added comment Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com> Co-authored-by: Tamara Hodgetts <hodgett@crick.ac.uk>
60 lines
2.3 KiB
Python
60 lines
2.3 KiB
Python
from pathlib import Path
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import pytest
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import yaml
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import re
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from textwrap import dedent
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def _get_workflow_names():
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"""Get all names of all workflows which have a test.yml in the tests directory.
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To do so, recursively finds all test.yml files and parses their content.
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"""
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here = Path(__file__).parent.resolve()
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pytest_workflow_files = here.glob("modules/**/test.yml")
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for f in pytest_workflow_files:
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# test_config = yaml.safe_load(f.read_text())
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test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
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for workflow in test_config:
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# https://github.com/nf-core/modules/pull/1242 - added to cover tests
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# that expect an error and therefore will not generate a versions.yml
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if 'exit_code' not in workflow:
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yield workflow["name"]
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@pytest.mark.workflow(*_get_workflow_names())
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def test_ensure_valid_version_yml(workflow_dir):
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workflow_dir = Path(workflow_dir)
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software_name = workflow_dir.name.split("_")[0].lower()
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try:
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versions_yml_file = workflow_dir / f"output/{software_name}/versions.yml"
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versions_yml = versions_yml_file.read_text()
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except FileNotFoundError:
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raise AssertionError(
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dedent(
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f"""\
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`versions.yml` not found in the output directory.
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Expected path: `{versions_yml_file}`
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This can have multiple reasons:
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* The test-workflow failed before a `versions.yml` could be generated.
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* The workflow name in `test.yml` does not start with the tool name.
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"""
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)
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)
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assert (
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"END_VERSIONS" not in versions_yml
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), "END_VERSIONS detected in versions.yml. This is a sign of an ill-formatted HEREDOC"
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# Raises an exception if yaml is not valid
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versions = yaml.safe_load(versions_yml)
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assert (
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len(versions) == 1
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), "The top-level of versions.yml must contain exactly one entry: the process name as dict key"
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software_versions = next(iter(versions.values()))
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assert len(software_versions), "There must be at least one version emitted."
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for tool, version in software_versions.items():
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assert re.match(
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r"^\d+.*", str(version)
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), f"Version number for {tool} must start with a number. "
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