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subworkflow_tests.py
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subworkflow_tests.py
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"""
Lint the tests of a subworkflow in nf-core/modules
"""
import json
import logging
from pathlib import Path
import yaml
from nf_core.components.nfcore_component import NFCoreComponent
log = logging.getLogger(__name__)
def subworkflow_tests(_, subworkflow: NFCoreComponent):
"""
Lint the tests of a subworkflow in ``nf-core/modules``
It verifies that the test directory exists
and contains a ``main.nf.test`` a ``main.nf.test.snap`` and ``tags.yml``.
Additionally, checks that all included components in test ``main.nf`` are specified in ``test.yml``
"""
repo_dir = subworkflow.component_dir.parts[
: subworkflow.component_dir.parts.index(subworkflow.component_name.split("/")[0])
][-1]
test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", repo_dir, subworkflow.component_name)
pytest_main_nf = Path(test_dir, "main.nf")
is_pytest = pytest_main_nf.is_file()
log.debug(f"{pytest_main_nf} is pytest: {is_pytest}")
if subworkflow.nftest_testdir.is_dir():
subworkflow.passed.append(("test_dir_exists", "nf-test test directory exists", subworkflow.nftest_testdir))
else:
if is_pytest:
subworkflow.warned.append(("test_dir_exists", "nf-test directory is missing", subworkflow.nftest_testdir))
else:
subworkflow.failed.append(("test_dir_exists", "nf-test directory is missing", subworkflow.nftest_testdir))
return
# Lint the test main.nf file
if subworkflow.nftest_main_nf.is_file():
subworkflow.passed.append(("test_main_nf_exists", "test `main.nf.test` exists", subworkflow.nftest_main_nf))
else:
if is_pytest:
subworkflow.warned.append(
("test_main_nf_exists", "test `main.nf.test` does not exist", subworkflow.nftest_main_nf)
)
else:
subworkflow.failed.append(
("test_main_nf_exists", "test `main.nf.test` does not exist", subworkflow.nftest_main_nf)
)
if subworkflow.nftest_main_nf.is_file():
with open(subworkflow.nftest_main_nf) as fh:
# Check if main.nf.test.snap file exists, if 'snap(' is inside main.nf.test
if "snapshot(" in fh.read():
snap_file = subworkflow.nftest_testdir / "main.nf.test.snap"
if snap_file.is_file():
subworkflow.passed.append(("test_snapshot_exists", "test `main.nf.test.snap` exists", snap_file))
# Validate no empty files
with open(snap_file) as snap_fh:
try:
snap_content = json.load(snap_fh)
for test_name in snap_content.keys():
if "d41d8cd98f00b204e9800998ecf8427e" in str(snap_content[test_name]):
if "stub" not in test_name:
subworkflow.failed.append(
(
"test_snap_md5sum",
"md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
snap_file,
)
)
else:
subworkflow.passed.append(
(
"test_snap_md5sum",
"md5sum for empty file found, but it is a stub test",
snap_file,
)
)
else:
subworkflow.passed.append(
(
"test_snap_md5sum",
"no md5sum for empty file found",
snap_file,
)
)
if "7029066c27ac6f5ef18d660d5741979a" in str(snap_content[test_name]):
if "stub" not in test_name:
subworkflow.failed.append(
(
"test_snap_md5sum",
"md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
snap_file,
)
)
else:
subworkflow.failed.append(
(
"test_snap_md5sum",
"md5sum for compressed empty file found, but it is a stub test",
snap_file,
)
)
else:
subworkflow.passed.append(
(
"test_snap_md5sum",
"no md5sum for compressed empty file found",
snap_file,
)
)
if "versions" in str(snap_content[test_name]) or "versions" in str(snap_content.keys()):
subworkflow.passed.append(
(
"test_snap_versions",
"versions found in snapshot file",
snap_file,
)
)
else:
subworkflow.warned.append(
(
"test_snap_versions",
"versions not found in snapshot file",
snap_file,
)
)
except json.decoder.JSONDecodeError as e:
subworkflow.failed.append(
(
"test_snapshot_exists",
f"snapshot file `main.nf.test.snap` can't be read: {e}",
snap_file,
)
)
else:
subworkflow.failed.append(
("test_snapshot_exists", "test `main.nf.test.snap` does not exist", snap_file)
)
# Verify that tags are correct.
main_nf_tags = subworkflow._get_main_nf_tags(subworkflow.nftest_main_nf)
required_tags = [
"subworkflows",
f"subworkflows/{subworkflow.component_name}",
"subworkflows_nfcore",
]
included_components = []
if subworkflow.main_nf.is_file():
included_components = subworkflow._get_included_components(subworkflow.main_nf)
chained_components_tags = subworkflow._get_included_components_in_chained_tests(subworkflow.nftest_main_nf)
log.debug(f"Included components: {included_components}")
log.debug(f"Required tags: {required_tags}")
log.debug(f"Included components for chained nf-tests: {chained_components_tags}")
missing_tags = []
for tag in set(required_tags + included_components + chained_components_tags):
if tag not in main_nf_tags:
missing_tags.append(tag)
if len(missing_tags) == 0:
subworkflow.passed.append(("test_main_tags", "Tags adhere to guidelines", subworkflow.nftest_main_nf))
else:
subworkflow.failed.append(
(
"test_main_tags",
f"Tags do not adhere to guidelines. Tags missing in `main.nf.test`: {missing_tags}",
subworkflow.nftest_main_nf,
)
)
# Check pytest_modules.yml does not contain entries for subworkflows with nf-test
pytest_yml_path = subworkflow.base_dir / "tests" / "config" / "pytest_modules.yml"
if pytest_yml_path.is_file() and not is_pytest:
try:
with open(pytest_yml_path) as fh:
pytest_yml = yaml.safe_load(fh)
if "subworkflows/" + subworkflow.component_name in pytest_yml.keys():
subworkflow.failed.append(
(
"test_pytest_yml",
"subworkflow with nf-test should not be listed in pytest_modules.yml",
pytest_yml_path,
)
)
else:
subworkflow.passed.append(
("test_pytest_yml", "subworkflow with nf-test not in pytest_modules.yml", pytest_yml_path)
)
except FileNotFoundError:
subworkflow.warned.append(("test_pytest_yml", "Could not open pytest_modules.yml file", pytest_yml_path))
if subworkflow.tags_yml.is_file():
# Check tags.yml exists and it has the correct entry
subworkflow.passed.append(("test_tags_yml_exists", "file `tags.yml` exists", subworkflow.tags_yml))
with open(subworkflow.tags_yml) as fh:
tags_yml = yaml.safe_load(fh)
if "subworkflows/" + subworkflow.component_name in tags_yml.keys():
subworkflow.passed.append(("test_tags_yml", "correct entry in tags.yml", subworkflow.tags_yml))
if (
f"subworkflows/{subworkflow.org}/{subworkflow.component_name}/**"
in tags_yml["subworkflows/" + subworkflow.component_name]
):
subworkflow.passed.append(("test_tags_yml", "correct path in tags.yml", subworkflow.tags_yml))
else:
subworkflow.failed.append(("test_tags_yml", "incorrect path in tags.yml", subworkflow.tags_yml))
else:
subworkflow.failed.append(
(
"test_tags_yml",
"incorrect entry in tags.yml, should be 'subworkflows/<SUBWORKFLOW_NAME>'",
subworkflow.tags_yml,
)
)
else:
if is_pytest:
subworkflow.warned.append(("test_tags_yml_exists", "file `tags.yml` does not exist", subworkflow.tags_yml))
else:
subworkflow.failed.append(("test_tags_yml_exists", "file `tags.yml` does not exist", subworkflow.tags_yml))
# Check that the old test directory does not exist
if not is_pytest:
old_test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", subworkflow.component_name)
if old_test_dir.is_dir():
subworkflow.failed.append(("test_old_test_dir", "old test directory exists", old_test_dir))
else:
subworkflow.passed.append(("test_old_test_dir", "old test directory does not exist", old_test_dir))