def cli(ctx, uris, **kwds):
"""Launch Galaxy instance with specified tools.
The Galaxy tool panel will include just the referenced tool or tools (by
default all the tools in the current working directory) and the upload
tool.
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.
``planemo`` will run the Galaxy instance in an existing virtualenv if one
exists in a ``.venv`` directory in the specified ``--galaxy_root``.
Otherwise, the Galaxy instance will run in a clean virtualenv created in
``/tmp``.
``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 be careful and do not try this against a production
Galaxy instance.
"""
paths = uris_to_paths(ctx, uris)
runnables = for_paths(paths)
galaxy_serve(ctx, runnables, **kwds)
def test_serve_daemon(self):
"""Test serving a galaxy tool via a daemon Galaxy process."""
port = network_util.get_free_port()
cat_path = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
config = galaxy_serve(
self.test_context,
[for_path(cat_path)],
install_galaxy=True,
port=port,
daemon=True,
no_dependency_resolution=True,
)
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
config_dict = config.gi.config.get_config()
assert "allow_user_dataset_purge" in config_dict
config.kill()
assert not network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
def test_serve_daemon(self):
"""Test serving a galaxy tool via a daemon Galaxy process."""
port = network_util.get_free_port()
cat_path = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
config = galaxy_serve(
self.test_context,
[for_path(cat_path)],
install_galaxy=True,
port=port,
daemon=True,
no_dependency_resolution=True,
)
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
config_dict = config.gi.config.get_config()
assert "allow_user_dataset_purge" in config_dict
config.kill()
assert not network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
def test_serve_daemon(self):
"""Test serving a galaxy tool via a daemon Galaxy process."""
port = network_util.get_free_port()
cat_path = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
config = galaxy_serve(
self.test_context,
[for_path(cat_path)],
install_galaxy=True,
galaxy_branch=target_galaxy_branch(),
port=port,
daemon=True,
no_dependency_resolution=True,
)
_assert_service_up(config)
config.kill()
_assert_service_down(config)
def test_serve_workflow(self):
"""Test serving a galaxy workflow via a daemon Galaxy process."""
port = network_util.get_free_port()
random_lines = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "randomlines.xml")
cat = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
worklfow = os.path.join(TEST_DATA_DIR, "wf1.gxwf.yml")
extra_tools = [random_lines, cat]
config = galaxy_serve(
self.test_context,
[for_path(worklfow)],
install_galaxy=True,
port=port,
daemon=True,
extra_tools=extra_tools,
)
user_gi = config.user_gi
assert user_gi.tools.get_tools(tool_id="random_lines1")
assert len(user_gi.workflows.get_workflows()) == 1
config.kill()
def test_serve_daemon(self):
port = network_util.get_free_port()
cat_path = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
config = galaxy_serve(
self.test_context,
cat_path,
install_galaxy=True,
port=port,
daemon=True,
)
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
config_dict = config.gi.config.get_config()
assert "allow_user_dataset_purge" in config_dict
config.kill()
assert not network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
