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test_cmd_workflow_lint.py
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"""Tests for the ``workflow_lint`` command."""
import glob
import os
from .test_utils import (
CliTestCase,
TEST_DATA_DIR,
)
class CmdWorkflowLintTestCase(CliTestCase):
def test_gxformat2_examples_as_repos(self):
repos = glob.glob(_wf_repo("from_format2") + "/*")
for repo in repos:
repo_basename = os.path.basename(repo)
try:
expected_exit_code = int(repo_basename[0])
except ValueError:
# not a repo, just skip.
continue
lint_cmd = ["workflow_lint", "--skip", "tests", repo]
self._check_exit_code(lint_cmd, exit_code=expected_exit_code)
def test_fail_level(self):
# ensure missing tests normally cause it to fail...
repo = _wf_repo("from_format2/0_basic_format2")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
# ... but not if fail_level is error
repo = _wf_repo("from_format2/0_basic_format2")
lint_cmd = ["workflow_lint", "--fail_level", "error", repo]
self._check_exit_code(lint_cmd, exit_code=0)
def test_workflow_test_linting(self):
repo = _wf_repo("basic_format2_ok")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_native_ok")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_input_misspelled")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
repo = _wf_repo("basic_format2_input_missing")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
repo = _wf_repo("basic_format2_output_misnamed")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
repo = _wf_repo("basic_format2_missing_input")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
def test_workflow_test_linting_control(self):
# if we skip the tests linting - the above failures should pass
repo = _wf_repo("basic_format2_input_misspelled")
lint_cmd = ["workflow_lint", "--skip", "tests", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_input_missing")
lint_cmd = ["workflow_lint", "--skip", "tests", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_output_misnamed")
lint_cmd = ["workflow_lint", "--skip", "tests", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_missing_input")
lint_cmd = ["workflow_lint", "--skip", "tests", repo]
self._check_exit_code(lint_cmd, exit_code=0)
def test_workflow_dockstore_linting(self):
repo = _wf_repo("basic_format2_dockstore")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_dockstore_empty")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
repo = _wf_repo("basic_format2_dockstore_invalid_yaml")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
repo = _wf_repo("basic_format2_dockstore_wrong_descriptor")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
repo = _wf_repo("basic_format2_dockstore_wrong_test_file")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
repo = _wf_repo("basic_format2_dockstore_misspelled_primary_key")
lint_cmd = ["workflow_lint", repo]
self._check_exit_code(lint_cmd, exit_code=1)
def test_workflow_dockstore_linting_control(self):
# run same tests as above but make sure if we skip dockstore they
# all pass
repo = _wf_repo("basic_format2_dockstore")
lint_cmd = ["workflow_lint", "--skip", "dockstore", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_dockstore_empty")
lint_cmd = ["workflow_lint", "--skip", "dockstore", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_dockstore_invalid_yaml")
lint_cmd = ["workflow_lint", "--skip", "dockstore", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_dockstore_wrong_descriptor")
lint_cmd = ["workflow_lint", "--skip", "dockstore", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_dockstore_wrong_test_file")
lint_cmd = ["workflow_lint", "--skip", "dockstore", repo]
self._check_exit_code(lint_cmd, exit_code=0)
repo = _wf_repo("basic_format2_dockstore_misspelled_primary_key")
lint_cmd = ["workflow_lint", "--skip", "dockstore", repo]
self._check_exit_code(lint_cmd, exit_code=0)
def test_lint_test_examples(self):
tags_wf = os.path.join(TEST_DATA_DIR, "wf10-tags-and-rules.gxwf.yml")
lint_cmd = ["workflow_lint", tags_wf]
self._check_exit_code(lint_cmd, exit_code=0)
def _wf_repo(rel_path):
return os.path.join(TEST_DATA_DIR, "wf_repos", rel_path)