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"""
Test functions in bioblend.galaxy.container_resolution
"""
from . import (
GalaxyTestBase,
test_util,
)
class TestGalaxyContainerResolution(GalaxyTestBase.GalaxyTestBase):
@test_util.skip_unless_galaxy("release_22.05")
def test_get_container_resolvers(self):
container_resolvers = self.gi.container_resolution.get_container_resolvers()
assert isinstance(container_resolvers, list)
assert len(container_resolvers) > 0
assert isinstance(container_resolvers[0], dict)
assert container_resolvers[0]["model_class"] == "ExplicitContainerResolver"
assert container_resolvers[0]["resolver_type"] == "explicit"
assert container_resolvers[0]["can_uninstall_dependencies"] is False
assert container_resolvers[0]["builds_on_resolution"] is False
@test_util.skip_unless_galaxy("release_22.05")
def test_show_container_resolver(self):
container_resolver = self.gi.container_resolution.show_container_resolver(0)
print(container_resolver)
assert isinstance(container_resolver, dict)
assert container_resolver["model_class"] == "ExplicitContainerResolver"
assert container_resolver["resolver_type"] == "explicit"
assert container_resolver["can_uninstall_dependencies"] is False
assert container_resolver["builds_on_resolution"] is False
@test_util.skip_unless_galaxy("release_22.05")
def test_resolve(self):
tool = self.gi.container_resolution.resolve(tool_id="CONVERTER_parquet_to_csv")
print(tool)
assert isinstance(tool, dict)
tool_requirements_only = self.gi.container_resolution.resolve(
tool_id="CONVERTER_parquet_to_csv", requirements_only=True
)
assert isinstance(tool_requirements_only, dict)
@test_util.skip_unless_galaxy("release_22.05")
def test_resolve_toolbox(self):
toolbox = self.gi.container_resolution.resolve_toolbox()
assert isinstance(toolbox, list)
assert len(toolbox) > 0
assert isinstance(toolbox[0], dict)
toolbox_by_tool_ids = self.gi.container_resolution.resolve_toolbox(tool_ids=[toolbox[0]["tool_id"]])
assert isinstance(toolbox_by_tool_ids, list)
assert len(toolbox_by_tool_ids) == 1
assert isinstance(toolbox_by_tool_ids[0], dict)
toolbox_by_resolver_type = self.gi.container_resolution.resolve_toolbox(resolver_type="mulled")
assert isinstance(toolbox_by_resolver_type, list)
assert len(toolbox_by_resolver_type) > 0
assert isinstance(toolbox_by_resolver_type[0], dict)
assert len(toolbox) == len(toolbox_by_resolver_type)
for tool in toolbox_by_resolver_type:
print(tool)
assert (
tool["status"]["dependency_type"] is None
or tool["status"]["container_resolver"]["resolver_type"] == "mulled"
)
toolbox_by_container_type = self.gi.container_resolution.resolve_toolbox(container_type="docker")
assert isinstance(toolbox_by_container_type, list)
assert len(toolbox_by_container_type) > 0
assert isinstance(toolbox_by_container_type[0], dict)
assert len(toolbox) == len(toolbox_by_container_type)
for tool in toolbox_by_container_type:
assert tool["status"]["dependency_type"] is None or tool["status"]["dependency_type"] == "docker"
assert (
tool["status"]["dependency_type"] is None or tool["status"]["container_description"]["type"] == "docker"
)
toolbox_requirements_only = self.gi.container_resolution.resolve_toolbox(requirements_only=True)
assert isinstance(toolbox_requirements_only, list)
assert len(toolbox_requirements_only) > 0
assert isinstance(toolbox_requirements_only[0], dict)
assert len(toolbox) == len(toolbox_requirements_only)
# TODO unless containers are available this may fallback to conda by default?
# depending on Galaxy's config
# toolbox_by_index = self.gi.container_resolution.resolve_toolbox(tool_ids=[toolbox[0]['tool_id']], index=0, install=True)
# assert isinstance(toolbox_by_index, list)
# assert len(toolbox_by_index) > 0
# assert isinstance(toolbox_by_index[0], dict)
# TODO unless containers are available this may fallback to conda by default?
# depending on Galaxy's config
# def test_resolve_toolbox_with_install(self):
# toolbox = self.gi.container_resolution.resolve_toolbox_with_install(tool_ids=[])
# assert isinstance(toolbox, list)
# assert len(toolbox) == 0
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