def build_shed_app(simple_kwargs):
"""Build a Galaxy app object from a simple keyword arguments.
Construct paste style complex dictionary. Also setup "global" reference
to sqlalchemy database context for tool shed database.
"""
log.info("Tool shed database connection: %s", simple_kwargs["database_connection"])
# TODO: Simplify global_conf to match Galaxy above...
simple_kwargs['__file__'] = 'tool_shed_wsgi.ini.sample'
simple_kwargs['global_conf'] = get_webapp_global_conf()
app = ToolshedUniverseApplication( **simple_kwargs )
database_contexts.tool_shed_context = app.model.context
log.info( "Embedded Toolshed application started" )
return app
def main():
# ---- Configuration ------------------------------------------------------
tool_shed_test_host = os.environ.get('TOOL_SHED_TEST_HOST',
default_tool_shed_test_host)
tool_shed_test_port = os.environ.get('TOOL_SHED_TEST_PORT', None)
galaxy_test_host = os.environ.get('GALAXY_TEST_HOST',
default_galaxy_test_host)
galaxy_test_port = os.environ.get('GALAXY_TEST_PORT', None)
tool_path = os.environ.get('TOOL_SHED_TEST_TOOL_PATH', 'tools')
if 'HTTP_ACCEPT_LANGUAGE' not in os.environ:
os.environ['HTTP_ACCEPT_LANGUAGE'] = default_tool_shed_locales
tool_shed_test_file_dir = os.environ.get('TOOL_SHED_TEST_FILE_DIR',
default_tool_shed_test_file_dir)
if not os.path.isabs(tool_shed_test_file_dir):
tool_shed_test_file_dir = tool_shed_test_file_dir
ignore_files = ()
tool_dependency_dir = os.environ.get('TOOL_SHED_TOOL_DEPENDENCY_DIR', None)
use_distributed_object_store = os.environ.get(
'TOOL_SHED_USE_DISTRIBUTED_OBJECT_STORE', False)
if not os.path.isdir(tool_shed_test_tmp_dir):
os.mkdir(tool_shed_test_tmp_dir)
tool_shed_test_proxy_port = None
galaxy_test_proxy_port = None
if 'TOOL_SHED_TEST_DBPATH' in os.environ:
shed_db_path = os.environ['TOOL_SHED_TEST_DBPATH']
else:
tempdir = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
shed_db_path = os.path.join(tempdir, 'database')
shed_tool_data_table_conf_file = os.environ.get(
'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF',
os.path.join(tool_shed_test_tmp_dir, 'shed_tool_data_table_conf.xml'))
galaxy_shed_data_manager_conf_file = os.environ.get(
'GALAXY_SHED_DATA_MANAGER_CONF',
os.path.join(tool_shed_test_tmp_dir,
'test_shed_data_manager_conf.xml'))
galaxy_tool_data_table_conf_file = os.environ.get(
'GALAXY_TEST_TOOL_DATA_TABLE_CONF',
os.path.join(tool_shed_test_tmp_dir, 'tool_data_table_conf.xml'))
galaxy_tool_conf_file = os.environ.get(
'GALAXY_TEST_TOOL_CONF',
os.path.join(tool_shed_test_tmp_dir, 'test_tool_conf.xml'))
galaxy_shed_tool_conf_file = os.environ.get(
'GALAXY_TEST_SHED_TOOL_CONF',
os.path.join(tool_shed_test_tmp_dir, 'test_shed_tool_conf.xml'))
galaxy_migrated_tool_conf_file = os.environ.get(
'GALAXY_TEST_MIGRATED_TOOL_CONF',
os.path.join(tool_shed_test_tmp_dir, 'test_migrated_tool_conf.xml'))
galaxy_tool_sheds_conf_file = os.environ.get(
'GALAXY_TEST_TOOL_SHEDS_CONF',
os.path.join(tool_shed_test_tmp_dir, 'test_sheds_conf.xml'))
if 'GALAXY_TEST_TOOL_DATA_PATH' in os.environ:
tool_data_path = os.environ.get('GALAXY_TEST_TOOL_DATA_PATH')
else:
tool_data_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
os.environ['GALAXY_TEST_TOOL_DATA_PATH'] = tool_data_path
if 'GALAXY_TEST_DBPATH' in os.environ:
galaxy_db_path = os.environ['GALAXY_TEST_DBPATH']
else:
tempdir = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
galaxy_db_path = os.path.join(tempdir, 'database')
shed_file_path = os.path.join(shed_db_path, 'files')
galaxy_file_path = os.path.join(galaxy_db_path, 'files')
hgweb_config_file_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
new_repos_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
galaxy_tempfiles = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
galaxy_shed_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
galaxy_migrated_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
galaxy_tool_dependency_dir = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
os.environ['GALAXY_TEST_TOOL_DEPENDENCY_DIR'] = galaxy_tool_dependency_dir
hgweb_config_dir = hgweb_config_file_path
os.environ['TEST_HG_WEB_CONFIG_DIR'] = hgweb_config_dir
print "Directory location for hgweb.config:", hgweb_config_dir
if 'TOOL_SHED_TEST_DBURI' in os.environ:
toolshed_database_connection = os.environ['TOOL_SHED_TEST_DBURI']
else:
toolshed_database_connection = 'sqlite:///' + os.path.join(
shed_db_path, 'community_test.sqlite')
galaxy_database_auto_migrate = False
if 'GALAXY_TEST_DBURI' in os.environ:
galaxy_database_connection = os.environ['GALAXY_TEST_DBURI']
else:
db_path = os.path.join(galaxy_db_path, 'universe.sqlite')
if 'GALAXY_TEST_DB_TEMPLATE' in os.environ:
# Middle ground between recreating a completely new
# database and pointing at existing database with
# GALAXY_TEST_DBURI. The former requires a lot of setup
# time, the latter results in test failures in certain
# cases (namely tool shed tests expecting clean database).
__copy_database_template(os.environ['GALAXY_TEST_DB_TEMPLATE'],
db_path)
galaxy_database_auto_migrate = True
if not os.path.exists(galaxy_db_path):
os.makedirs(galaxy_db_path)
galaxy_database_connection = 'sqlite:///%s' % db_path
if 'GALAXY_TEST_INSTALL_DBURI' in os.environ:
install_galaxy_database_connection = os.environ[
'GALAXY_TEST_INSTALL_DBURI']
elif asbool(
os.environ.get('GALAXY_TEST_INSTALL_DB_MERGED',
default_install_db_merged)):
install_galaxy_database_connection = galaxy_database_connection
else:
install_galaxy_db_path = os.path.join(galaxy_db_path, 'install.sqlite')
install_galaxy_database_connection = 'sqlite:///%s' % install_galaxy_db_path
tool_shed_global_conf = get_webapp_global_conf()
tool_shed_global_conf['__file__'] = 'tool_shed_wsgi.ini.sample'
kwargs = dict(
admin_users='*****@*****.**',
allow_user_creation=True,
allow_user_deletion=True,
database_connection=toolshed_database_connection,
datatype_converters_config_file='datatype_converters_conf.xml.sample',
file_path=shed_file_path,
global_conf=tool_shed_global_conf,
hgweb_config_dir=hgweb_config_dir,
job_queue_workers=5,
id_secret='changethisinproductiontoo',
log_destination="stdout",
new_file_path=new_repos_path,
running_functional_tests=True,
shed_tool_data_table_config=shed_tool_data_table_conf_file,
smtp_server='smtp.dummy.string.tld',
email_from='functional@localhost',
template_path='templates',
tool_path=tool_path,
tool_parse_help=False,
tool_data_table_config_path=galaxy_tool_data_table_conf_file,
use_heartbeat=False)
for dir in [tool_shed_test_tmp_dir]:
try:
os.makedirs(dir)
except OSError:
pass
print "Tool shed database connection:", toolshed_database_connection
print "Galaxy database connection:", galaxy_database_connection
# Generate the tool_data_table_conf.xml file.
file(galaxy_tool_data_table_conf_file,
'w').write(tool_data_table_conf_xml_template)
# Generate the shed_tool_data_table_conf.xml file.
file(shed_tool_data_table_conf_file,
'w').write(tool_data_table_conf_xml_template)
os.environ[
'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF'] = shed_tool_data_table_conf_file
# ---- Build Tool Shed Application --------------------------------------------------
toolshedapp = None
# if not toolshed_database_connection.startswith( 'sqlite://' ):
# kwargs[ 'database_engine_option_max_overflow' ] = '20'
if tool_dependency_dir is not None:
kwargs['tool_dependency_dir'] = tool_dependency_dir
if use_distributed_object_store:
kwargs['object_store'] = 'distributed'
kwargs[
'distributed_object_store_config_file'] = 'distributed_object_store_conf.xml.sample'
kwargs['global_conf'] = tool_shed_global_conf
if not toolshed_database_connection.startswith('sqlite://'):
kwargs['database_engine_option_pool_size'] = '10'
toolshedapp = ToolshedUniverseApplication(**kwargs)
database_contexts.tool_shed_context = toolshedapp.model.context
log.info("Embedded Toolshed application started")
# ---- Run tool shed webserver ------------------------------------------------------
tool_shed_server = None
tool_shed_global_conf['database_connection'] = toolshed_database_connection
toolshedwebapp = toolshedbuildapp.app_factory(tool_shed_global_conf,
use_translogger=False,
static_enabled=True,
app=toolshedapp)
if tool_shed_test_port is not None:
tool_shed_server = httpserver.serve(toolshedwebapp,
host=tool_shed_test_host,
port=tool_shed_test_port,
start_loop=False)
else:
random.seed()
for i in range(0, 9):
try:
tool_shed_test_port = str(
random.randint(default_tool_shed_test_port_min,
default_tool_shed_test_port_max))
log.debug(
"Attempting to serve app on randomly chosen port: %s" %
tool_shed_test_port)
tool_shed_server = httpserver.serve(toolshedwebapp,
host=tool_shed_test_host,
port=tool_shed_test_port,
start_loop=False)
break
except socket.error, e:
if e[0] == 98:
continue
raise
else: