def cli(ctx, path):
"""Create files to use GitHub/TravisCI testing.
Setup files in a github tool repository to enable continuous
integration testing.::
% planemo travis_init .
% # setup Ubuntu 12.04 w/ dependencies in
% vim .travis/setup_custom_dependencies.bash
% git add .travis.yml .travis
% git commit -m "Add Travis CI testing infrastructure for tools."
% git push # and register repository @ http://travis-ci.org/
These tests were inspired by work original done and documented by Peter
C**k here http://bit.ly/gxtravisci.
"""
# TODO: Option --verbose_travis_yaml to unroll travis_test.sh line by line
# and place all but last in 'install' section and last in 'script'. Would
# require a yaml dependency though.
shell("mkdir -p '%s/.travis'" % path)
travis_yml = os.path.join(path, ".travis.yml")
setup_sh = os.path.join(path, ".travis", "setup_custom_dependencies.bash")
if not os.path.exists(travis_yml):
open(travis_yml, "w").write(TRAVIS_YML)
else:
warn(".travis.yml file already exists, not overwriting.")
if not os.path.exists(setup_sh):
open(setup_sh, "w").write(TRAVIS_SETUP)
else:
warn(
".travis/setup_custom_dependencies.bash already exists, not overwriting."
)
info(PREPARE_MESSAGE)
def cli(ctx, path):
"""Create files to use GitHub/TravisCI testing.
Setup files in a github tool repository to enable continuous
integration testing.::
% planemo travis_init .
% # setup Ubuntu 12.04 w/ dependencies in
% vim .travis/setup_custom_dependencies.bash
% git add .travis.yml .travis
% git commit -m "Add Travis CI testing infrastructure for tools."
% git push # and register repository @ http://travis-ci.org/
These tests were inspired by work original done and documented by Peter
C**k here http://bit.ly/gxtravisci.
"""
# TODO: Option --verbose_travis_yaml to unroll travis_test.sh line by line
# and place all but last in 'install' section and last in 'script'. Would
# require a yaml dependency though.
shell("mkdir -p '%s/.travis'" % path)
travis_yml = os.path.join(path, ".travis.yml")
setup_sh = os.path.join(path, ".travis", "setup_custom_dependencies.bash")
if not os.path.exists(travis_yml):
open(travis_yml, "w").write(TRAVIS_YML)
else:
warn(".travis.yml file already exists, not overwriting.")
if not os.path.exists(setup_sh):
open(setup_sh, "w").write(TRAVIS_SETUP)
else:
warn(".travis/setup_custom_dependencies.bash already exists, not overwriting.")
info(PREPARE_MESSAGE)
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()
cmd = "; ".join([
cd_to_galaxy_command,
galaxy_run.ACTIVATE_COMMAND, # TODO: this should be moved to
# run_tests.sh to match run.sh.
test_cmd,
])
action = "Testing tools"
return_code = galaxy_run.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,
)
try:
test_data = test_results.structured_data
new_report = build_report.build_report(test_data)
open(test_results.output_html_path, "w").write(new_report)
except Exception:
pass
__handle_summary(test_results, **kwds)
return return_code
def shell(cmds, **kwds):
if isinstance(cmds, list):
cmd_string = commands.argv_to_str(cmds)
else:
cmd_string = cmds
info(cmd_string)
return commands.shell(cmds, **kwds)
def run_galaxy_command(ctx, command, env, action, daemon=False):
message = "%s with command [%s]" % (action, command)
info(message)
ctx.vlog("With environment variables:")
ctx.vlog("============================")
for key, value in env.items():
ctx.vlog('%s="%s"' % (key, value))
ctx.vlog("============================")
return shell(command, env=env)
def run_galaxy_command(ctx, command, env, action, daemon=False):
message = "%s with command [%s]" % (action, command)
info(message)
ctx.vlog("With environment variables:")
ctx.vlog("============================")
for key, value in env.items():
ctx.vlog('%s="%s"' % (key, value))
ctx.vlog("============================")
return shell(command, env=env)
def run_galaxy_command(ctx, command, env, action):
"""Run Galaxy command with informative verbose logging."""
message = "%s with command [%s]" % (action, command)
info(message)
ctx.vlog("With environment variables:")
ctx.vlog("============================")
for key, value in env.items():
ctx.vlog('%s="%s"' % (key, value))
ctx.vlog("============================")
exit_code = shell(command, env=env)
ctx.vlog("run command exited with return code %s" % exit_code)
return exit_code
def run_galaxy_command(ctx, command, env, action):
"""Run Galaxy command with informative verbose logging."""
message = "%s with command [%s]" % (action, command)
info(message)
ctx.vlog("With environment variables:")
ctx.vlog("============================")
for key, value in env.items():
ctx.vlog('%s="%s"' % (key, value))
ctx.vlog("============================")
exit_code = shell(command, env=env)
ctx.vlog("run command exited with return code %s" % exit_code)
return exit_code
def __xunit_state(kwds, config):
xunit_supported = True
if shell("grep -q xunit '%s'/run_tests.sh" % config.galaxy_root):
xunit_supported = False
xunit_report_file = kwds.get("test_output_xunit", None)
if xunit_report_file is None and xunit_supported:
xunit_report_file = os.path.join(config.config_directory, "xunit.xml")
elif xunit_report_file is not None and not xunit_supported:
warn(XUNIT_UPGRADE_MESSAGE)
xunit_report_file = None
return xunit_supported, xunit_report_file
def __xunit_state(kwds, config):
xunit_supported = True
if shell("grep -q xunit '%s'/run_tests.sh" % config.galaxy_root):
xunit_supported = False
xunit_report_file = kwds.get("test_output_xunit", None)
if xunit_report_file is None and xunit_supported:
xunit_report_file = os.path.join(config.config_directory, "xunit.xml")
elif xunit_report_file is not None and not xunit_supported:
warn(XUNIT_UPGRADE_MESSAGE)
xunit_report_file = None
return xunit_supported, xunit_report_file
def __structured_report_file(kwds, config):
structured_data_supported = True
if shell("grep -q structured_data '%s'/run_tests.sh" % config.galaxy_root):
structured_data_supported = False
structured_report_file = None
structured_report_file = kwds.get("test_output_json", None)
if structured_report_file is None and structured_data_supported:
conf_dir = config.config_directory
structured_report_file = os.path.join(conf_dir, "structured_data.json")
elif structured_report_file is not None and not structured_data_supported:
warn(NO_JSON_MESSAGE)
structured_report_file = None
return structured_report_file
def __structured_report_file(kwds, config):
structured_data_supported = True
if shell("grep -q structured_data '%s'/run_tests.sh" % config.galaxy_root):
structured_data_supported = False
structured_report_file = None
structured_report_file = kwds.get("test_output_json", None)
if structured_report_file is None and structured_data_supported:
conf_dir = config.config_directory
structured_report_file = os.path.join(conf_dir, "structured_data.json")
elif structured_report_file is not None and not structured_data_supported:
warn(NO_JSON_MESSAGE)
structured_report_file = None
return structured_report_file
def shell(cmds, **kwds):
info(cmds)
return commands.shell(cmds, **kwds)
def shell(cmds, **kwds):
info(cmds)
return commands.shell(cmds, **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, **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 shell(cmds, **kwds):
cmd_string = args_to_str(cmds)
info(cmd_string)
return commands.shell(cmds, **kwds)
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()
cmd = "; ".join([
cd_to_galaxy_command,
galaxy_run.ACTIVATE_COMMAND, # TODO: this should be moved to
# run_tests.sh to match run.sh.
test_cmd,
])
action = "Testing tools"
return_code = galaxy_run.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,
)
try:
test_data = test_results.structured_data
if 'test_output' in kwds:
output_path = kwds['test_output']
if output_path is not None:
with open(output_path, 'w') as handle:
handle.write(build_report.build_report(test_data))
for kw_name in ('markdown', 'text'):
if 'test_output_%s' % kw_name in kwds:
output_path = kwds['test_output_%s' % kw_name]
if output_path is None:
continue
with open(output_path, 'w') as handle:
handle.write(build_report.build_report(test_data, report_type=kw_name))
except Exception:
ctx.vlog("Problem producing test output.", exception=True)
__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 shell(cmds, **kwds):
cmd_string = args_to_str(cmds)
info(cmd_string)
return commands.shell(cmds, **kwds)
def cli(ctx, path, **kwds):
"""Run the tests in the specified tool tests in a Galaxy instance.
All referenced tools (by default all the tools in the current working
directory) will be tested and the results quickly summarized.
To run these tests planemo needs a Galaxy instance to utilize, planemo
will search parent directories to see if any is a Galaxy instance
- but one can pick the Galaxy instance to use with the --galaxy_root
option or force planemo to download a disposable instance with the
``--install_galaxy`` flag.
In additon to to quick summary printed to the console - various detailed
output summaries can be configured. ``tool_test_output.html`` (settable
via ``--test_output``) will contain a human consumable HTML report
describing the test run. A JSON file (settable via ``--test_output_json``
and defaulting to ``tool_test_output.json``) will also be created. These
files can can be disabled by passing in empty arguments or globally by
setting the values ``default_test_output`` and/or
``default_test_output_json`` in ``~/.planemo.yml`` to ``null``. For
continuous integration testing a xUnit-style report can be confiured using
the ``--test_output_xunit``.
planemo uses temporarily generated config files and environment variables
to attempt to shield this execution of Galaxy from manually launched runs
against that same Galaxy root - but this may not be bullet proof yet so
please careful and do not try this against production Galaxy instances.
"""
for name, default in OUTPUT_DFEAULTS.items():
__populate_default_output(ctx, name, kwds, default)
kwds["for_tests"] = True
with galaxy_config.galaxy_config(ctx, path, **kwds) as config:
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
cmd = "; ".join([
cd_to_galaxy_command,
galaxy_run.ACTIVATE_COMMAND, # TODO: this should be moved to
# run_tests.sh to match run.sh.
__run_tests_cmd(
html_report_file,
xunit_report_file,
structured_report_file,
),
])
action = "Testing tools"
return_code = galaxy_run.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 = galaxy_test.GalaxyTestResults(
structured_report_file,
xunit_report_file,
html_report_file,
return_code,
)
try:
test_data = test_results.structured_data
new_report = build_report.build_report(test_data)
open(test_results.output_html_path, "w").write(new_report)
except Exception:
pass
__handle_summary(
test_results,
**kwds
)
if return_code:
sys.exit(1)
def cli(ctx, path, **kwds):
"""Run the tests in the specified tool tests in a Galaxy instance.
All referenced tools (by default all the tools in the current working
directory) will be tested and the results quickly summarized.
To run these tests planemo needs a Galaxy instance to utilize, planemo
will search parent directories to see if any is a Galaxy instance
- but one can pick the Galaxy instance to use with the --galaxy_root
option or force planemo to download a disposable instance with the
``--install_galaxy`` flag.
In additon to to quick summary printed to the console - various detailed
output summaries can be configured. ``tool_test_output.html`` (settable
via ``--test_output``) will contain a human consumable HTML report
describing the test run. A JSON file (settable via ``--test_output_json``
and defaulting to ``tool_test_output.json``) will also be created. These
files can can be disabled by passing in empty arguments or globally by
setting the values ``default_test_output`` and/or
``default_test_output_json`` in ``~/.planemo.yml`` to ``null``. For
continuous integration testing a xUnit-style report can be confiured using
the ``--test_output_xunit``.
planemo uses temporarily generated config files and environment variables
to attempt to shield this execution of Galaxy from manually launched runs
against that same Galaxy root - but this may not be bullet proof yet so
please careful and do not try this against production Galaxy instances.
"""
for name, default in OUTPUT_DFEAULTS.items():
__populate_default_output(ctx, name, kwds, default)
kwds["for_tests"] = True
with galaxy_config.galaxy_config(ctx, path, **kwds) as config:
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
cmd = "; ".join([
cd_to_galaxy_command,
galaxy_run.ACTIVATE_COMMAND, # TODO: this should be moved to
# run_tests.sh to match run.sh.
__run_tests_cmd(
html_report_file,
xunit_report_file,
structured_report_file,
),
])
action = "Testing tools"
return_code = galaxy_run.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 = galaxy_test.GalaxyTestResults(
structured_report_file,
xunit_report_file,
html_report_file,
return_code,
)
try:
test_data = test_results.structured_data
new_report = build_report.build_report(test_data)
open(test_results.output_html_path, "w").write(new_report)
except Exception:
pass
__handle_summary(test_results, **kwds)
if return_code:
sys.exit(1)
