def cli(ctx, paths, **kwds):
""" Run tests of published shed artifacts.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and run the tool tests for these commands.
This command requires the target to be version 15.07 or newer.
"""
galaxy_test.process_defaults(ctx, kwds)
install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
port = get_free_port()
kwds["port"] = port
return_code = 1
with galaxy_serve.shed_serve(ctx, install_args_list, **kwds) as config:
config.kill()
return_code = galaxy_test.run_in_config(
ctx,
config,
installed=True,
**kwds
)
if return_code:
sys.exit(return_code)
def cli(ctx, paths, **kwds):
""" Serve a transient Galaxy with published repositories installed.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and serve a Galaxy instances that can be
logged into and explored interactively.
"""
install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
with shed_serve(ctx, install_args_list, **kwds) as config:
gx_url = "http://localhost:%d/" % config.port
io.info("Galaxy running with tools installed at %s" % gx_url)
time.sleep(1000000)
def cli(ctx, paths, **kwds):
"""Launch Galaxy with Tool Shed dependencies.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and serve a Galaxy instances that can be
logged into and explored interactively.
"""
kwds['galaxy_skip_client_build'] = False
install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
with shed_serve(ctx, install_args_list, **kwds) as config:
io.info("Galaxy running with tools installed at %s" % config.galaxy_url)
sleep_for_serve()
def cli(ctx, paths, **kwds):
"""Launch Galaxy with Tool Shed dependencies.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and serve a Galaxy instances that can be
logged into and explored interactively.
"""
kwds['galaxy_skip_client_build'] = False
install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
with shed_serve(ctx, install_args_list, **kwds) as config:
io.info("Galaxy running with tools installed at %s" %
config.galaxy_url)
sleep_for_serve()
def cli(ctx, paths, **kwds):
""" Run tests of published shed artifacts.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and run the tool tests for these commands.
This command requires the target to be version 15.07 or newer.
"""
install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
port = get_free_port()
kwds["port"] = port
return_code = 1
with shed_serve(ctx, install_args_list, **kwds) as config:
config.kill()
return_code = run_in_config(ctx, config, installed=True, **kwds)
if return_code:
sys.exit(return_code)
def test_shed_serve_daemon(self):
port = network_util.get_free_port()
fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc")
ctx = self.test_context
install_args_list = shed.install_arg_lists(
ctx, [fastqc_path],
shed_target="toolshed",
)
with galaxy_serve.shed_serve(
ctx, install_args_list,
port=port,
skip_dependencies=True,
install_galaxy=True,
) as config:
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
def test_shed_serve_daemon(self):
"""Test serving FASTQC from the tool shed via a daemon Galaxy process."""
port = network_util.get_free_port()
fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc")
ctx = self.test_context
install_args_list = shed.install_arg_lists(
ctx,
[fastqc_path],
shed_target="toolshed",
)
with shed_serve(
ctx,
install_args_list,
port=port,
skip_dependencies=True,
install_galaxy=True,
galaxy_branch=target_galaxy_branch(),
) as config:
_assert_service_up(config)
def test_shed_serve_daemon(self):
port = network_util.get_free_port()
fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc")
ctx = self.test_context
install_args_list = shed.install_arg_lists(
ctx, [fastqc_path],
shed_target="toolshed",
)
with shed_serve(
ctx, install_args_list,
port=port,
skip_dependencies=True,
install_galaxy=True,
) as config:
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)