def test_tool_dependencies():
# Setup directories
with __test_base_path() as base_path:
for name, version, sub in [ ( "dep1", "1.0", "env.sh" ), ( "dep1", "2.0", "bin" ), ( "dep2", "1.0", None ) ]:
if sub == "bin":
p = os.path.join( base_path, name, version, "bin" )
else:
p = os.path.join( base_path, name, version )
try:
makedirs( p )
except:
pass
if sub == "env.sh":
__touch( os.path.join( p, "env.sh" ) )
dm = DependencyManager( default_base_path=base_path )
dependency = dm.find_dep( "dep1", "1.0" )
assert dependency.script == os.path.join( base_path, 'dep1', '1.0', 'env.sh' )
assert dependency.path == os.path.join( base_path, 'dep1', '1.0' )
assert dependency.version == "1.0"
dependency = dm.find_dep( "dep1", "2.0" )
assert dependency.script == None
assert dependency.path == os.path.join( base_path, 'dep1', '2.0' )
assert dependency.version == "2.0"
## Test default versions
symlink( os.path.join( base_path, 'dep1', '2.0'), os.path.join( base_path, 'dep1', 'default' ) )
dependency = dm.find_dep( "dep1", None )
assert dependency.version == "2.0"
## Test default resolve will be fall back on default package dependency
## when using the default resolver.
dependency = dm.find_dep( "dep1", "2.1" )
assert dependency.version == "2.0" # 2.0 is defined as default_version
def test_tool_dependencies():
# Setup directories
with __test_base_path() as base_path:
for name, version, sub in [ ( "dep1", "1.0", "env.sh" ), ( "dep1", "2.0", "bin" ), ( "dep2", "1.0", None ) ]:
if sub == "bin":
p = os.path.join( base_path, name, version, "bin" )
else:
p = os.path.join( base_path, name, version )
try:
makedirs( p )
except:
pass
if sub == "env.sh":
__touch( os.path.join( p, "env.sh" ) )
dm = DependencyManager( default_base_path=base_path )
dependency = dm.find_dep( "dep1", "1.0" )
assert dependency.script == os.path.join( base_path, 'dep1', '1.0', 'env.sh' )
assert dependency.path == os.path.join( base_path, 'dep1', '1.0' )
assert dependency.version == "1.0"
dependency = dm.find_dep( "dep1", "2.0" )
assert dependency.script is None
assert dependency.path == os.path.join( base_path, 'dep1', '2.0' )
assert dependency.version == "2.0"
# Test default versions
symlink( os.path.join( base_path, 'dep1', '2.0'), os.path.join( base_path, 'dep1', 'default' ) )
dependency = dm.find_dep( "dep1", None )
assert dependency.version == "2.0"
# Test default resolve will be fall back on default package dependency
# when using the default resolver.
dependency = dm.find_dep( "dep1", "2.1" )
assert dependency.version == "2.0" # 2.0 is defined as default_version
def test_toolshed_tools_fallback_on_manual_dependencies():
with __test_base_path() as base_path:
dm = DependencyManager( default_base_path=base_path )
test_repo = __build_test_repo('package', version=TEST_VERSION)
env_path = __setup_galaxy_package_dep(base_path, "dep1", "1.0")
dependency = dm.find_dep( "dep1", version="1.0", type='package', installed_tool_dependencies=[test_repo] )
assert dependency.version == "1.0"
assert dependency.script == env_path
def test_toolshed_package_requirements():
with __test_base_path() as base_path:
test_repo = __build_test_repo('package', version=TEST_VERSION)
dm = DependencyManager( default_base_path=base_path )
package_dir = __build_ts_test_package(base_path)
dependency = dm.find_dep( TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo] )
assert dependency.version == TEST_VERSION
assert dependency.script == os.path.join(package_dir, "env.sh")
def test_toolshed_tools_fallback_on_manual_dependencies():
with __test_base_path() as base_path:
dm = DependencyManager( default_base_path=base_path )
test_repo = __build_test_repo('package', version=TEST_VERSION)
env_path = __setup_galaxy_package_dep(base_path, "dep1", "1.0")
dependency = dm.find_dep( "dep1", version="1.0", type='package', installed_tool_dependencies=[test_repo] )
assert dependency.version == "1.0"
assert dependency.script == env_path
def test_toolshed_package_requirements():
with __test_base_path() as base_path:
test_repo = __build_test_repo('package', version=TEST_VERSION)
dm = DependencyManager( default_base_path=base_path )
package_dir = __build_ts_test_package(base_path)
dependency = dm.find_dep( TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo] )
assert dependency.version == TEST_VERSION
assert dependency.script == os.path.join(package_dir, "env.sh")
def test_toolshed_set_enviornment_requiremetns():
with __test_base_path() as base_path:
test_repo = __build_test_repo('set_environment')
dm = DependencyManager( default_base_path=base_path )
env_settings_dir = os.path.join(base_path, "environment_settings", TEST_REPO_NAME, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET)
os.makedirs(env_settings_dir)
dependency = dm.find_dep( TEST_REPO_NAME, version=None, type='set_environment', installed_tool_dependencies=[test_repo] )
assert dependency.version == None
assert dependency.script == os.path.join(env_settings_dir, "env.sh")
def test_toolshed_set_enviornment_requiremetns():
with __test_base_path() as base_path:
test_repo = __build_test_repo('set_environment')
dm = DependencyManager( default_base_path=base_path )
env_settings_dir = os.path.join(base_path, "environment_settings", TEST_REPO_NAME, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET)
os.makedirs(env_settings_dir)
dependency = dm.find_dep( TEST_REPO_NAME, version=None, type='set_environment', installed_tool_dependencies=[test_repo] )
assert dependency.version is None
assert dependency.script == os.path.join(env_settings_dir, "env.sh")
def test_toolshed_greater_precendence():
with __test_base_path() as base_path:
dm = DependencyManager( default_base_path=base_path )
test_repo = __build_test_repo('package', version=TEST_VERSION)
ts_package_dir = __build_ts_test_package(base_path)
gx_env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION)
ts_env_path = os.path.join(ts_package_dir, "env.sh")
dependency = dm.find_dep( TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo] )
assert dependency.script != gx_env_path # Not the galaxy path, it should be the tool shed path used.
assert dependency.script == ts_env_path
def test_toolshed_greater_precendence():
with __test_base_path() as base_path:
dm = DependencyManager( default_base_path=base_path )
test_repo = __build_test_repo('package', version=TEST_VERSION)
ts_package_dir = __build_ts_test_package(base_path)
gx_env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION)
ts_env_path = os.path.join(ts_package_dir, "env.sh")
dependency = dm.find_dep( TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo] )
assert dependency.script != gx_env_path # Not the galaxy path, it should be the tool shed path used.
assert dependency.script == ts_env_path