def run_in_config(ctx,
config,
run=run_galaxy_command,
test_data_target_dir=None,
**kwds):
"""Run Galaxy tests with the run_tests.sh command.
The specified `config` object describes the context for tool
execution.
"""
config_directory = config.config_directory
html_report_file = kwds["test_output"]
job_output_files = kwds.get("job_output_files", None)
if job_output_files is None:
job_output_files = os.path.join(config_directory, "jobfiles")
xunit_report_file = _xunit_state(kwds, config)
xunit_report_file_tracker = _FileChangeTracker(xunit_report_file)
structured_report_file = _structured_report_file(kwds, config)
structured_report_file_tracker = _FileChangeTracker(structured_report_file)
info("Testing using galaxy_root %s", config.galaxy_root)
# TODO: Allow running dockerized Galaxy here instead.
server_ini = os.path.join(config_directory, "galaxy.ini")
config.env["GALAXY_CONFIG_FILE"] = server_ini
config.env["GALAXY_TEST_VERBOSE_ERRORS"] = "true"
config.env["GALAXY_TEST_SAVE"] = job_output_files
cd_to_galaxy_command = ['cd', config.galaxy_root]
test_cmd = test_structures.GalaxyTestCommand(
html_report_file,
xunit_report_file,
structured_report_file,
failed=kwds.get("failed", False),
installed=kwds.get("installed", False),
).build()
setup_common_startup_args = ""
if kwds.get("skip_venv", False):
setup_common_startup_args = shell_join(
'COMMON_STARTUP_ARGS=--skip-venv',
'export COMMON_STARTUP_ARGS',
'echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"',
)
setup_venv_command = setup_venv(ctx, kwds)
cmd = shell_join(
cd_to_galaxy_command,
setup_common_startup_args,
setup_venv_command,
test_cmd,
)
action = "Testing tools"
return_code = run(ctx, cmd, config.env, action)
if kwds.get('update_test_data', False):
copy_tree(job_output_files, test_data_target_dir
or config.test_data_dir)
_check_test_outputs(xunit_report_file_tracker,
structured_report_file_tracker)
test_results = test_structures.GalaxyTestResults(
structured_report_file,
xunit_report_file,
html_report_file,
return_code,
)
structured_data = test_results.structured_data
return handle_reports_and_summary(ctx,
structured_data,
exit_code=test_results.exit_code,
kwds=kwds)
def run_in_config(ctx, config, **kwds):
config_directory = config.config_directory
html_report_file = kwds["test_output"]
job_output_files = kwds.get("job_output_files", None)
if job_output_files is None:
job_output_files = os.path.join(config_directory, "jobfiles")
xunit_supported, xunit_report_file = __xunit_state(kwds, config)
structured_report_file = __structured_report_file(kwds, config)
info("Testing using galaxy_root %s", config.galaxy_root)
# TODO: Allow running dockerized Galaxy here instead.
server_ini = os.path.join(config_directory, "galaxy.ini")
config.env["GALAXY_CONFIG_FILE"] = server_ini
config.env["GALAXY_TEST_VERBOSE_ERRORS"] = "true"
config.env["GALAXY_TEST_SAVE"] = job_output_files
cd_to_galaxy_command = "cd %s" % config.galaxy_root
test_cmd = test_structures.GalaxyTestCommand(
html_report_file,
xunit_report_file,
structured_report_file,
failed=kwds.get("failed", False),
installed=kwds.get("installed", False),
).build()
setup_common_startup_args = ""
if kwds.get("skip_venv", False):
setup_common_startup_args = (
'COMMON_STARTUP_ARGS=--skip-venv; '
'export COMMON_STARTUP_ARGS; '
'echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"')
setup_venv_command = setup_venv(ctx, kwds)
cmd = shell_join(
cd_to_galaxy_command,
setup_common_startup_args,
setup_venv_command,
test_cmd,
)
action = "Testing tools"
return_code = run_galaxy_command(ctx, cmd, config.env, action)
if kwds.get('update_test_data', False):
update_cp_args = (job_output_files, config.test_data_dir)
shell('cp -r "%s"/* "%s"' % update_cp_args)
if xunit_report_file and (not os.path.exists(xunit_report_file)):
warn(NO_XUNIT_MESSAGE)
xunit_report_file = None
test_results = test_structures.GalaxyTestResults(
structured_report_file,
xunit_report_file,
html_report_file,
return_code,
)
test_data = test_results.structured_data
handle_reports(ctx, test_data, kwds)
__handle_summary(test_results, **kwds)
return return_code
def run_in_config(ctx, config, run=run_galaxy_command, **kwds):
"""Run Galaxy tests with the run_tests.sh command.
The specified `config` object describes the context for tool
execution.
"""
config_directory = config.config_directory
html_report_file = kwds["test_output"]
job_output_files = kwds.get("job_output_files", None)
if job_output_files is None:
job_output_files = os.path.join(config_directory, "jobfiles")
xunit_report_file = _xunit_state(kwds, config)
xunit_report_file_tracker = _FileChangeTracker(xunit_report_file)
structured_report_file = _structured_report_file(kwds, config)
structured_report_file_tracker = _FileChangeTracker(structured_report_file)
info("Testing using galaxy_root %s", config.galaxy_root)
# TODO: Allow running dockerized Galaxy here instead.
server_ini = os.path.join(config_directory, "galaxy.ini")
config.env["GALAXY_CONFIG_FILE"] = server_ini
config.env["GALAXY_TEST_VERBOSE_ERRORS"] = "true"
config.env["GALAXY_TEST_SAVE"] = job_output_files
cd_to_galaxy_command = "cd %s" % config.galaxy_root
test_cmd = test_structures.GalaxyTestCommand(
html_report_file,
xunit_report_file,
structured_report_file,
failed=kwds.get("failed", False),
installed=kwds.get("installed", False),
).build()
setup_common_startup_args = ""
if kwds.get("skip_venv", False):
setup_common_startup_args = (
'COMMON_STARTUP_ARGS=--skip-venv; '
'export COMMON_STARTUP_ARGS; '
'echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"'
)
setup_venv_command = setup_venv(ctx, kwds)
cmd = shell_join(
cd_to_galaxy_command,
setup_common_startup_args,
setup_venv_command,
test_cmd,
)
action = "Testing tools"
return_code = run(
ctx,
cmd,
config.env,
action
)
if kwds.get('update_test_data', False):
update_cp_args = (job_output_files, config.test_data_dir)
shell('cp -r "%s"/* "%s"' % update_cp_args)
_check_test_outputs(xunit_report_file_tracker, structured_report_file_tracker)
test_results = test_structures.GalaxyTestResults(
structured_report_file,
xunit_report_file,
html_report_file,
return_code,
)
structured_data = test_results.structured_data
return handle_reports_and_summary(
ctx,
structured_data,
exit_code=test_results.exit_code,
kwds=kwds
)
def run_in_config(ctx, config, **kwds):
config_directory = config.config_directory
html_report_file = kwds["test_output"]
job_output_files = kwds.get("job_output_files", None)
if job_output_files is None:
job_output_files = os.path.join(config_directory, "jobfiles")
xunit_supported, xunit_report_file = __xunit_state(kwds, config)
structured_report_file = __structured_report_file(kwds, config)
info("Testing using galaxy_root %s", config.galaxy_root)
# TODO: Allow running dockerized Galaxy here instead.
server_ini = os.path.join(config_directory, "galaxy.ini")
config.env["GALAXY_CONFIG_FILE"] = server_ini
config.env["GALAXY_TEST_VERBOSE_ERRORS"] = "true"
config.env["GALAXY_TEST_SAVE"] = job_output_files
cd_to_galaxy_command = "cd %s" % config.galaxy_root
test_cmd = test_structures.GalaxyTestCommand(
html_report_file,
xunit_report_file,
structured_report_file,
failed=kwds.get("failed", False),
installed=kwds.get("installed", False),
).build()
setup_common_startup_args = ""
if kwds.get("skip_venv", False):
setup_common_startup_args = (
'COMMON_STARTUP_ARGS=--skip-venv; '
'export COMMON_STARTUP_ARGS; '
'echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"'
)
setup_venv_command = setup_venv(ctx, kwds)
cmd = shell_join(
cd_to_galaxy_command,
setup_common_startup_args,
setup_venv_command,
test_cmd,
)
action = "Testing tools"
return_code = run_galaxy_command(
ctx,
cmd,
config.env,
action
)
if kwds.get('update_test_data', False):
update_cp_args = (job_output_files, config.test_data_dir)
shell('cp -r "%s"/* "%s"' % update_cp_args)
if xunit_report_file and (not os.path.exists(xunit_report_file)):
warn(NO_XUNIT_MESSAGE)
xunit_report_file = None
test_results = test_structures.GalaxyTestResults(
structured_report_file,
xunit_report_file,
html_report_file,
return_code,
)
test_data = test_results.structured_data
handle_reports(ctx, test_data, kwds)
__handle_summary(
test_results,
**kwds
)
return return_code