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Simplify/unify tool conf handling logic across two driver util...

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This commit is contained in:
John Chilton
2016-03-29 08:04:27 -04:00
parent f3c757ff1c
commit e1aa0b3acc
3 changed files with 18 additions and 11 deletions
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scripts/functional_tests.py
+5 -9
View File
@@ -28,21 +28,17 @@ def main():
testing_installed_tools = _check_arg( '-installed' )
datatypes_conf_override = None
default_tool_conf = None
testing_shed_tools = testing_migrated_tools or testing_installed_tools
if testing_shed_tools:
# We need the upload tool for functional tests, so we'll create a temporary tool panel config that defines it.
tool_config_file = driver_util.FRAMEWORK_UPLOAD_TOOL_CONF
else:
if not testing_shed_tools:
framework_test = _check_arg( '-framework' ) # Run through suite of tests testing framework.
if framework_test:
tool_conf = driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF
default_tool_conf = driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF
datatypes_conf_override = driver_util.FRAMEWORK_DATATYPES_CONF
else:
# Use tool_conf.xml toolbox.
tool_conf = None
if _check_arg( '-with_framework_test_tools' ):
tool_conf = "%s,%s" % ( 'config/tool_conf.xml.sample', driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF )
tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', tool_conf )
default_tool_conf = "%s,%s" % ( 'config/tool_conf.xml.sample', driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF )
start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ
@@ -57,6 +53,7 @@ def main():
galaxy_db_path,
use_test_file_dir=not testing_shed_tools,
default_install_db_merged=True,
default_tool_conf=default_tool_conf,
)
app = None
@@ -65,7 +62,6 @@ def main():
if start_server:
# ---- Build Application --------------------------------------------------
kwargs = dict( shed_tool_data_table_config=shed_tool_data_table_config,
tool_config_file=tool_config_file,
update_integrated_tool_panel=False, )
kwargs.update(galaxy_config)
if datatypes_conf_override:
test/base/driver_util.py
+11
View File
@@ -96,6 +96,8 @@ def setup_galaxy_config(
default_install_db_merged=True,
default_tool_data_table_config_path=None,
enable_tool_shed_check=False,
default_tool_conf=None,
shed_tool_conf=None,
):
"""Setup environment and build config for test Galaxy instance."""
if not os.path.exists(tmpdir):
@@ -136,6 +138,14 @@ def setup_galaxy_config(
# 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)
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)
config = dict(
admin_users='test@bx.psu.edu',
allow_library_path_paste=True,
@@ -159,6 +169,7 @@ def setup_galaxy_config(
running_functional_tests=True,
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,
test/tool_shed/functional_tests.py
+2 -2
View File
@@ -57,7 +57,6 @@ def main():
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' ) )
default_tool_data_table_config_path = os.path.join( tool_shed_test_tmp_dir, 'tool_data_table_conf.xml' )
galaxy_tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', driver_util.FRAMEWORK_UPLOAD_TOOL_CONF )
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' ) )
@@ -137,7 +136,7 @@ def main():
shed_tool_data_table_config=shed_tool_data_table_conf_file,
shed_tool_path=galaxy_shed_tool_path,
tool_data_path=tool_data_path,
tool_config_file=[ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ],
tool_sheds_config_file=galaxy_tool_sheds_conf_file )
kwargs.update(
driver_util.setup_galaxy_config(
@@ -146,6 +145,7 @@ def main():
default_install_db_merged=False,
default_tool_data_table_config_path=default_tool_data_table_config_path,
enable_tool_shed_check=True,
shed_tool_conf=galaxy_shed_tool_conf_file,
)
)
print "Galaxy database connection:", kwargs["database_connection"]