def test_dir_option_manager():
conf_dir = mkdtemp()
app = TestApp(ud={"galaxy_conf_dir": conf_dir})
option_manager = galaxy_option_manager(app)
option_manager.setup()
_set_test_property(option_manager)
option_file_path = join(conf_dir, '400_cloudman_override_admin_users.ini')
content = open(option_file_path, 'r').read()
assert content == "[app:main]\[email protected]"
def test_dir_option_manager():
conf_dir = mkdtemp()
app = TestApp(ud={"galaxy_conf_dir": conf_dir})
option_manager = galaxy_option_manager(app)
option_manager.setup()
_set_test_property(option_manager)
option_file_path = join(conf_dir, '400_cloudman_override_admin_users.ini')
content = open(option_file_path, 'r').read()
assert content == "[app:main]\[email protected]"
def test_file_option_manager():
app = TestApp()
option_manager = galaxy_option_manager(app)
option_manager.setup()
_set_test_property(option_manager)
test_galaxy_home = app.path_resolver.galaxy_home
universe_path = join(test_galaxy_home, 'universe_wsgi.ini')
with open(universe_path, 'rt') as f:
parser = SafeConfigParser()
parser.readfp(f)
assert parser.get('app:main', "admin_users") == "*****@*****.**"
def test_file_option_manager():
app = TestApp()
option_manager = galaxy_option_manager(app)
option_manager.setup()
_set_test_property(option_manager)
test_galaxy_home = app.path_resolver.galaxy_home
universe_path = join(test_galaxy_home, 'universe_wsgi.ini')
with open(universe_path, 'rt') as f:
parser = SafeConfigParser()
parser.readfp(f)
assert parser.get('app:main', "admin_users") == "*****@*****.**"
def test_on_universe_missing_uses_sample():
app = TestApp()
option_manager = galaxy_option_manager(app)
option_manager.setup()
# Rename universe_wsgi.ini to universe_wsgi.ini.sample so it is missing.
test_galaxy_home = app.path_resolver.galaxy_home
universe_path = join(test_galaxy_home, 'universe_wsgi.ini')
sample_path = join(test_galaxy_home, 'universe_wsgi.ini.sample')
rename(universe_path, sample_path)
_set_test_property(option_manager)
with open(universe_path, 'rt') as f:
parser = SafeConfigParser()
parser.readfp(f)
assert parser.get('app:main', "admin_users") == "*****@*****.**"
def test_on_universe_missing_uses_sample():
app = TestApp()
option_manager = galaxy_option_manager(app)
option_manager.setup()
# Rename universe_wsgi.ini to universe_wsgi.ini.sample so it is missing.
test_galaxy_home = app.path_resolver.galaxy_home
universe_path = join(test_galaxy_home, 'universe_wsgi.ini')
sample_path = join(test_galaxy_home, 'universe_wsgi.ini.sample')
rename(universe_path, sample_path)
_set_test_property(option_manager)
with open(universe_path, 'rt') as f:
parser = SafeConfigParser()
parser.readfp(f)
assert parser.get('app:main', "admin_users") == "*****@*****.**"
def __init__(self, app):
super(GalaxyService, self).__init__(app)
self.name = ServiceRole.to_string(ServiceRole.GALAXY)
self.svc_roles = [ServiceRole.GALAXY]
self.remaining_start_attempts = NUM_START_ATTEMPTS
self.configured = False # Indicates if the environment for running Galaxy has been configured
self.ssl_is_on = False
# Environment variables to set before executing galaxy's run.sh
self.env_vars = {}
self.dependencies = [
ServiceDependency(self, ServiceRole.JOB_MANAGER),
ServiceDependency(self, ServiceRole.GALAXY_POSTGRES),
ServiceDependency(self, ServiceRole.GALAXY_DATA),
ServiceDependency(self, ServiceRole.GALAXY_INDICES),
ServiceDependency(self, ServiceRole.GALAXY_TOOLS),
ServiceDependency(self, ServiceRole.PROFTPD)
]
self.option_manager = galaxy_option_manager(app)
def __init__(self, app):
super(GalaxyService, self).__init__(app)
self.name = ServiceRole.to_string(ServiceRole.GALAXY)
self.svc_roles = [ServiceRole.GALAXY]
self.remaining_start_attempts = NUM_START_ATTEMPTS
# Indicates if the environment for running Galaxy has been configured
self.configured = False
self.ssl_is_on = False
# Environment variables to set before executing galaxy's run.sh
self.env_vars = {}
self.dependencies = [
ServiceDependency(self, ServiceRole.JOB_MANAGER),
ServiceDependency(self, ServiceRole.GALAXY_POSTGRES),
ServiceDependency(self, ServiceRole.GALAXY_DATA),
ServiceDependency(self, ServiceRole.GALAXY_INDICES),
# ServiceDependency(self, ServiceRole.PROFTPD),
ServiceDependency(self, ServiceRole.GALAXY_TOOLS)
]
self.option_manager = galaxy_option_manager(app)
def __init__(self, app):
super(GalaxyService, self).__init__(app)
self.name = ServiceRole.to_string(ServiceRole.GALAXY)
self.svc_roles = [ServiceRole.GALAXY]
self.remaining_start_attempts = NUM_START_ATTEMPTS
self.configured = False # Indicates if the environment for running Galaxy has been configured
# Environment variables to set before executing galaxy's run.sh
self.env_vars = {
"SGE_ROOT": self.app.path_resolver.sge_root,
"DRMAA_LIBRARY_PATH": self.app.path_resolver.drmaa_library_path
}
self.dependencies = [
ServiceDependency(self, ServiceRole.SGE),
ServiceDependency(self, ServiceRole.GALAXY_POSTGRES),
ServiceDependency(self, ServiceRole.GALAXY_DATA),
ServiceDependency(self, ServiceRole.GALAXY_INDICES),
ServiceDependency(self, ServiceRole.GALAXY_TOOLS),
ServiceDependency(self, ServiceRole.PROFTPD)
]
self.option_manager = galaxy_option_manager(app)
