def serve(ctx, paths, **kwds):
# TODO: Preceate a user.
# TODO: Setup an admin user.
# TODO: Pass through more parameters.
# TODO: Populate test-data directory as FTP directory.
daemon = kwds.get("daemon", False)
if daemon:
kwds["no_cleanup"] = True
with galaxy_config.galaxy_config(ctx, paths, **kwds) as config:
# TODO: Allow running dockerized Galaxy here instead.
run_script = os.path.join(config.galaxy_root, "run.sh")
if daemon:
run_script += " --daemon --wait"
config.env["GALAXY_RUN_ALL"] = "1"
else:
run_script += " --server-name '%s' --reload" % config.server_name
server_ini = os.path.join(config.config_directory, "galaxy.ini")
config.env["GALAXY_CONFIG_FILE"] = server_ini
cmds = [
run_script,
]
cmd = "; ".join(cmds)
action = "Starting galaxy"
galaxy_run.run_galaxy_command(
ctx,
cmd,
config.env,
action,
)
return config
def serve(ctx, path, **kwds):
# TODO: Preceate a user.
# TODO: Setup an admin user.
# TODO: Pass through more parameters.
# TODO: Populate test-data directory as FTP directory.
with galaxy_config.galaxy_config(ctx, path, **kwds) as config:
# TODO: Allow running dockerized Galaxy here instead.
run_script = os.path.join(config.galaxy_root, "run.sh") + " --reload"
server_ini = os.path.join(config.config_directory, "galaxy.ini")
config.env["GALAXY_CONFIG_FILE"] = server_ini
cmds = [
run_script,
]
cmd = "; ".join(cmds)
action = "Starting galaxy"
galaxy_run.run_galaxy_command(ctx, cmd, config.env, action)
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 serve(ctx, paths, **kwds):
# TODO: Preceate a user.
# TODO: Setup an admin user.
# TODO: Pass through more parameters.
# TODO: Populate test-data directory as FTP directory.
daemon = kwds.get("daemon", False)
if daemon:
kwds["no_cleanup"] = True
with galaxy_config.galaxy_config(ctx, paths, **kwds) as config:
# TODO: Allow running dockerized Galaxy here instead.
setup_common_startup_args = galaxy_run.set_variable_if_wheels(
"COMMON_STARTUP_ARGS", "--skip-venv"
)
setup_venv_command = galaxy_run.setup_venv(ctx, kwds)
run_script = os.path.join(config.galaxy_root, "run.sh")
run_script += " $COMMON_STARTUP_ARGS"
if daemon:
run_script += " --daemon --wait"
config.env["GALAXY_RUN_ALL"] = "1"
else:
run_script += " --server-name '%s' --reload" % config.server_name
server_ini = os.path.join(config.config_directory, "galaxy.ini")
config.env["GALAXY_CONFIG_FILE"] = server_ini
cd_to_galaxy_command = "cd %s" % config.galaxy_root
cmd = io.shell_join(
cd_to_galaxy_command,
setup_common_startup_args,
setup_venv_command,
run_script,
)
action = "Starting galaxy"
galaxy_run.run_galaxy_command(
ctx,
cmd,
config.env,
action,
)
return config
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 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)
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 = galaxy_run.set_variable_if_wheels(
"COMMON_STARTUP_ARGS", "--skip-venv --skip-common-startup"
)
setup_venv_command = galaxy_run.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 = 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,
)
test_data = test_results.structured_data
handle_reports(ctx, test_data, kwds)
__handle_summary(
test_results,
**kwds
)
return return_code