def update_galaxy_config(self):
"""
Update Galaxy application configuration.
Optionally set Galaxy to use multiple processes, then populate dynamic
options (i.e., arbitrary options coming from user data), adjust system
paths and set admin users.
"""
if self.multiple_processes():
populate_process_options(self.option_manager)
populate_dynamic_options(self.option_manager)
populate_galaxy_paths(self.option_manager)
populate_admin_users(self.option_manager)
def update_galaxy_config(self):
"""
Update Galaxy application configuration.
Optionally set Galaxy to use multiple processes, then populate dynamic
options (i.e., arbitrary options coming from user data), adjust system
paths and set admin users.
"""
if self.multiple_processes():
populate_process_options(self.option_manager)
populate_dynamic_options(self.option_manager)
populate_galaxy_paths(self.option_manager)
populate_admin_users(self.option_manager)
def test_populate_galaxy_paths():
app = TestApp()
option_manager = TestOptionManager(app)
populate_galaxy_paths(option_manager)
main_options = option_manager.options["app:main"]
assert main_options["genome_data_path"] == \
join(TEST_INDICES_DIR, "genomes")
assert main_options["len_file_path"] == \
join(TEST_DATA_DIR, "configuration_data", "len")
assert main_options["tool_dependency_dir"] == \
join(TEST_TOOLS_DIR, "tools")
assert main_options["file_path"] == \
join(TEST_DATA_DIR, "files")
assert main_options["new_file_path"] == \
join(TEST_DATA_DIR, "tmp")
assert main_options["job_working_directory"] == \
join(TEST_DATA_DIR, "tmp", "job_working_directory")
assert main_options["cluster_files_directory"] == \
join(TEST_DATA_DIR, "tmp", "pbs")
assert main_options["ftp_upload_dir"] == \
join(TEST_DATA_DIR, "tmp", "ftp")
assert main_options["nginx_upload_store"] == \
join(TEST_DATA_DIR, "upload_store")
def test_populate_galaxy_paths():
app = TestApp()
option_manager = TestOptionManager(app)
populate_galaxy_paths(option_manager)
main_options = option_manager.options["app:main"]
assert main_options["genome_data_path"] == \
join(TEST_INDICES_DIR, "genomes")
assert main_options["len_file_path"] == \
join(TEST_DATA_DIR, "configuration_data", "len")
assert main_options["tool_dependency_dir"] == \
join(TEST_TOOLS_DIR, "tools")
assert main_options["file_path"] == \
join(TEST_DATA_DIR, "files")
assert main_options["new_file_path"] == \
join(TEST_DATA_DIR, "tmp")
assert main_options["job_working_directory"] == \
join(TEST_DATA_DIR, "tmp", "job_working_directory")
assert main_options["cluster_files_directory"] == \
join(TEST_DATA_DIR, "tmp", "pbs")
assert main_options["ftp_upload_dir"] == \
join(TEST_DATA_DIR, "tmp", "ftp")
assert main_options["nginx_upload_store"] == \
join(TEST_DATA_DIR, "upload_store")
def update_galaxy_config(self):
if self._multiple_processes():
populate_process_options(self.option_manager)
populate_dynamic_options(self.option_manager)
populate_galaxy_paths(self.option_manager)
populate_admin_users(self.option_manager)
