def build_tool_tests(self,
testing_shed_tools=None,
return_test_classes=False):
if self.app is None:
return
if testing_shed_tools is None:
testing_shed_tools = getattr(self, "testing_shed_tools", False)
# We must make sure that functional.test_toolbox is always imported after
# database_contexts.galaxy_content is set (which occurs in this method above).
# If functional.test_toolbox is imported before database_contexts.galaxy_content
# is set, sa_session will be None in all methods that use it.
import functional.test_toolbox
functional.test_toolbox.toolbox = self.app.toolbox
# When testing data managers, do not test toolbox.
test_classes = functional.test_toolbox.build_tests(
app=self.app,
testing_shed_tools=testing_shed_tools,
master_api_key=get_master_api_key(),
user_api_key=get_user_api_key(),
)
if return_test_classes:
return test_classes
return functional.test_toolbox
def build_tests(self):
"""Build data manager test methods."""
import functional.test_data_managers
functional.test_data_managers.data_managers = self.app.data_managers
functional.test_data_managers.build_tests(
tmp_dir=self.galaxy_test_tmp_dir,
testing_shed_tools=self.testing_shed_tools,
master_api_key=get_master_api_key(),
user_api_key=get_user_api_key(),
user_email=self.app.config.admin_users_list[0],
create_admin=True,
)
def run_tool_test(self, tool_id, index=0, resource_parameters={}):
host, port, url = target_url_parts()
galaxy_interactor_kwds = {
"galaxy_url": url,
"master_api_key": get_master_api_key(),
"api_key": get_user_api_key(),
"keep_outputs_dir": None,
}
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
verify_tool(tool_id=tool_id,
test_index=index,
galaxy_interactor=galaxy_interactor,
resource_parameters=resource_parameters)
def setup_galaxy_config(
tmpdir,
use_test_file_dir=False,
default_install_db_merged=True,
default_tool_data_table_config_path=None,
default_shed_tool_data_table_config=None,
default_job_config_file=None,
enable_tool_shed_check=False,
default_tool_conf=None,
shed_tool_conf=None,
datatypes_conf=None,
update_integrated_tool_panel=False,
prefer_template_database=False,
log_format=None,
conda_auto_init=False,
conda_auto_install=False,
use_shared_connection_for_amqp=False,
):
"""Setup environment and build config for test Galaxy instance."""
# For certain docker operations this needs to be evaluated out - e.g. for cwltool.
tmpdir = os.path.realpath(tmpdir)
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
template_cache_path = tempfile.mkdtemp(prefix='compiled_templates_',
dir=tmpdir)
new_file_path = tempfile.mkdtemp(prefix='new_files_path_', dir=tmpdir)
job_working_directory = tempfile.mkdtemp(prefix='job_working_directory_',
dir=tmpdir)
if use_test_file_dir:
first_test_file_dir = ensure_test_file_dir_set()
if not os.path.isabs(first_test_file_dir):
first_test_file_dir = os.path.join(galaxy_root,
first_test_file_dir)
library_import_dir = first_test_file_dir
import_dir = os.path.join(first_test_file_dir, 'users')
if os.path.exists(import_dir):
user_library_import_dir = import_dir
else:
user_library_import_dir = None
else:
user_library_import_dir = None
library_import_dir = None
job_config_file = os.environ.get('GALAXY_TEST_JOB_CONFIG_FILE',
default_job_config_file)
tool_path = os.environ.get('GALAXY_TEST_TOOL_PATH', 'tools')
tool_data_table_config_path = _tool_data_table_config_path(
default_tool_data_table_config_path)
default_data_manager_config = None
for data_manager_config in [
'config/data_manager_conf.xml', 'data_manager_conf.xml'
]:
if os.path.exists(data_manager_config):
default_data_manager_config = data_manager_config
data_manager_config_file = "test/functional/tools/sample_data_manager_conf.xml"
if default_data_manager_config is not None:
data_manager_config_file = "%s,%s" % (default_data_manager_config,
data_manager_config_file)
master_api_key = get_master_api_key()
cleanup_job = 'never' if (
"GALAXY_TEST_NO_CLEANUP" in os.environ
or "TOOL_SHED_TEST_NO_CLEANUP" in os.environ) else 'onsuccess'
# Data Manager testing temp path
# For storing Data Manager outputs and .loc files so that real ones don't get clobbered
galaxy_data_manager_data_path = tempfile.mkdtemp(
prefix='data_manager_tool-data', dir=tmpdir)
tool_conf = os.environ.get('GALAXY_TEST_TOOL_CONF', default_tool_conf)
conda_auto_install = os.environ.get('GALAXY_TEST_CONDA_AUTO_INSTALL',
conda_auto_install)
conda_auto_init = os.environ.get('GALAXY_TEST_CONDA_AUTO_INIT',
conda_auto_init)
conda_prefix = os.environ.get('GALAXY_TEST_CONDA_PREFIX')
if tool_conf is None:
# As a fallback always at least allow upload.
tool_conf = FRAMEWORK_UPLOAD_TOOL_CONF
if shed_tool_conf is not None:
tool_conf = "%s,%s" % (tool_conf, shed_tool_conf)
shed_tool_data_table_config = default_shed_tool_data_table_config
config = dict(
admin_users='*****@*****.**',
allow_library_path_paste=True,
allow_user_creation=True,
allow_user_deletion=True,
api_allow_run_as='*****@*****.**',
auto_configure_logging=logging_config_file is None,
check_migrate_tools=False,
chunk_upload_size=100,
conda_prefix=conda_prefix,
conda_auto_init=conda_auto_init,
conda_auto_install=conda_auto_install,
cleanup_job=cleanup_job,
retry_metadata_internally=False,
data_dir=tmpdir,
data_manager_config_file=data_manager_config_file,
enable_beta_tool_formats=True,
expose_dataset_path=True,
ftp_upload_purge=False,
galaxy_data_manager_data_path=galaxy_data_manager_data_path,
id_secret='changethisinproductiontoo',
job_config_file=job_config_file,
job_working_directory=job_working_directory,
library_import_dir=library_import_dir,
log_destination="stdout",
new_file_path=new_file_path,
override_tempdir=False,
master_api_key=master_api_key,
running_functional_tests=True,
shed_tool_data_table_config=shed_tool_data_table_config,
template_cache_path=template_cache_path,
template_path='templates',
tool_config_file=tool_conf,
tool_data_table_config_path=tool_data_table_config_path,
tool_parse_help=False,
tool_path=tool_path,
update_integrated_tool_panel=update_integrated_tool_panel,
use_tasked_jobs=True,
use_heartbeat=False,
user_library_import_dir=user_library_import_dir,
webhooks_dir=TEST_WEBHOOKS_DIR,
logging=LOGGING_CONFIG_DEFAULT,
monitor_thread_join_timeout=5,
object_store_store_by="uuid",
)
if not use_shared_connection_for_amqp:
config[
"amqp_internal_connection"] = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % os.path.join(
tmpdir, "control.sqlite")
config.update(
database_conf(tmpdir,
prefer_template_database=prefer_template_database))
config.update(
install_database_conf(tmpdir,
default_merged=default_install_db_merged))
if asbool(os.environ.get("GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE")):
object_store_config = os.path.join(tmpdir, "object_store_conf.yml")
with open(object_store_config, "w") as f:
contents = """
type: hierarchical
backends:
- id: files1
type: disk
weight: 1
files_dir: "${temp_directory}/files1"
extra_dirs:
- type: temp
path: "${temp_directory}/tmp1"
- type: job_work
path: "${temp_directory}/job_working_directory1"
- id: files2
type: disk
weight: 1
files_dir: "${temp_directory}/files2"
extra_dirs:
- type: temp
path: "${temp_directory}/tmp2"
- type: job_work
path: "${temp_directory}/job_working_directory2"
"""
contents_template = string.Template(contents)
expanded_contents = contents_template.safe_substitute(
temp_directory=tmpdir)
f.write(expanded_contents)
config["object_store_config_file"] = object_store_config
if datatypes_conf is not None:
config['datatypes_config_file'] = datatypes_conf
if enable_tool_shed_check:
config["enable_tool_shed_check"] = enable_tool_shed_check
config["hours_between_check"] = 0.001
tool_dependency_dir = os.environ.get('GALAXY_TOOL_DEPENDENCY_DIR')
if tool_dependency_dir:
config["tool_dependency_dir"] = tool_dependency_dir
# Used by shed's twill dependency stuff
# TODO: read from Galaxy's config API.
os.environ[
"GALAXY_TEST_TOOL_DEPENDENCY_DIR"] = tool_dependency_dir or os.path.join(
tmpdir, 'dependencies')
return config
def _setup_interactor(self):
self.user_api_key = get_user_api_key()
self.master_api_key = get_master_api_key()
self.galaxy_interactor = ApiTestInteractor(self)
