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Move tool_conf logic for drivers into driver_util.

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- Don't generate a tool_conf for upload in tool shed tests - just use the fixed one setup for framework tools.
- Move every mention of that directory and files into constants in driver_util.
This commit is contained in:
John Chilton
2016-03-29 08:04:22 -04:00
parent 97070b4b53
commit fd46a1f987
3 changed files with 14 additions and 17 deletions
Download Patch File Download Diff File Expand all files Collapse all files
scripts/functional_tests.py
+4 -5
View File
@@ -95,25 +95,24 @@ def main():
testing_installed_tools = __check_arg( '-installed' )
datatypes_conf_override = None
framework_tool_dir = os.path.join('test', 'functional', 'tools')
if testing_migrated_tools or testing_installed_tools:
# Store a jsonified dictionary of tool_id : GALAXY_TEST_FILE_DIR pairs.
galaxy_tool_shed_test_file = 'shed_tools_dict'
# We need the upload tool for functional tests, so we'll create a temporary tool panel config that defines it.
tool_config_file = os.path.join( framework_tool_dir, 'upload_tool_conf.xml' )
tool_config_file = driver_util.FRAMEWORK_UPLOAD_TOOL_CONF
galaxy_test_file_dir = None
library_import_dir = None
user_library_import_dir = None
else:
framework_test = __check_arg( '-framework' ) # Run through suite of tests testing framework.
if framework_test:
tool_conf = os.path.join( framework_tool_dir, 'samples_tool_conf.xml' )
datatypes_conf_override = os.path.join( framework_tool_dir, 'sample_datatypes_conf.xml' )
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', os.path.join( framework_tool_dir, 'samples_tool_conf.xml' ) )
tool_conf = "%s,%s" % ( 'config/tool_conf.xml.sample', driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF )
test_dir = default_galaxy_test_file_dir
tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', tool_conf )
galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', test_dir )
test/base/driver_util.py
+9 -1
View File
@@ -24,7 +24,12 @@ from .nose_util import run
from .instrument import StructuredTestDataPlugin
galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir))
TOOL_SHED_TEST_DATA = os.path.join(galaxy_root, "test", "tool_shed", "test_data")
GALAXY_TEST_DIRECTORY = os.path.join(galaxy_root, "test")
TOOL_SHED_TEST_DATA = os.path.join(GALAXY_TEST_DIRECTORY, "tool_shed", "test_data")
FRAMEWORK_TOOLS_DIR = os.path.join(GALAXY_TEST_DIRECTORY, "functional", "tools")
FRAMEWORK_UPLOAD_TOOL_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "upload_tool_conf.xml")
FRAMEWORK_SAMPLE_TOOLS_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "samples_tool_conf.xml")
FRAMEWORK_DATATYPES_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "sample_datatypes_conf.xml")
DEFAULT_LOCALES = "en"
@@ -219,6 +224,9 @@ __all__ = [
"configure_environment",
"copy_database_template",
"build_logger",
"FRAMEWORK_UPLOAD_TOOL_CONF",
"FRAMEWORK_SAMPLE_TOOLS_CONF",
"FRAMEWORK_DATATYPES_CONF",
"galaxy_database_conf",
"get_webapp_global_conf",
"nose_config_and_run",
test/tool_shed/functional_tests.py
+1 -11
View File
@@ -47,14 +47,6 @@ shed_tool_conf_xml_template = '''<?xml version="1.0"?>
</toolbox>
'''
tool_conf_xml = '''<?xml version="1.0"?>
<toolbox>
<section name="Get Data" id="getext">
<tool file="data_source/upload.xml"/>
</section>
</toolbox>
'''
tool_data_table_conf_xml_template = '''<?xml version="1.0"?>
<tables>
</tables>
@@ -84,7 +76,7 @@ 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' ) )
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_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' ) )
@@ -191,8 +183,6 @@ def main():
# ---- Optionally start up a Galaxy instance ------------------------------------------------------
if 'TOOL_SHED_TEST_OMIT_GALAXY' not in os.environ:
# Generate the tool_conf.xml file.
file( galaxy_tool_conf_file, 'w' ).write( tool_conf_xml )
# Generate the shed_tool_conf.xml file.
tool_sheds_conf_template_parser = string.Template( tool_sheds_conf_xml_template )
tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute( shed_url=tool_shed_test_host, shed_port=tool_shed_test_port )