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469 lines
22 KiB
Python
469 lines
22 KiB
Python
#!/usr/bin/env python
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import httplib
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import os
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import os.path
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import random
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import re
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import shutil
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import socket
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import sys
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import tempfile
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import threading
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import time
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from ConfigParser import SafeConfigParser
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from json import dumps
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from paste import httpserver
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galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir))
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sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ]
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from base import driver_util
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driver_util.configure_environment()
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log = driver_util.build_logger()
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from base.api_util import get_master_api_key, get_user_api_key
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from base.test_logging import logging_config_file
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from base.tool_shed_util import parse_tool_panel_config
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from functional import database_contexts
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from galaxy import tools
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from galaxy.app import UniverseApplication
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from galaxy.util.properties import load_app_properties
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from galaxy.web import buildapp
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default_galaxy_test_host = "localhost"
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default_galaxy_test_port_min = 8000
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default_galaxy_test_port_max = 9999
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default_galaxy_locales = 'en'
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default_galaxy_test_file_dir = "test-data,https://github.com/galaxyproject/galaxy-test-data.git"
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migrated_tool_panel_config = 'config/migrated_tools_conf.xml'
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installed_tool_panel_configs = [
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os.environ.get('GALAXY_TEST_SHED_TOOL_CONF', 'config/shed_tool_conf.xml')
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]
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# Set up a job_conf.xml that explicitly limits jobs to 10 minutes.
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job_conf_xml = '''<?xml version="1.0"?>
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<!-- A test job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
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<job_conf>
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<plugins>
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<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
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</plugins>
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<handlers>
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<handler id="main"/>
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</handlers>
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<destinations>
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<destination id="local" runner="local"/>
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</destinations>
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<limits>
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<limit type="walltime">00:10:00</limit>
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</limits>
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</job_conf>
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'''
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def generate_config_file( input_filename, output_filename, config_items ):
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'''
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Generate a config file with the configuration that has been defined for the embedded web application.
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This is mostly relevant when setting metadata externally, since the script for doing that does not
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have access to app.config.
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'''
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cp = SafeConfigParser()
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cp.read( input_filename )
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config_items_by_section = []
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for label, value in config_items:
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found = False
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# Attempt to determine the correct section for this configuration option.
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for section in cp.sections():
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if cp.has_option( section, label ):
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config_tuple = section, label, value
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config_items_by_section.append( config_tuple )
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found = True
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continue
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# Default to app:main if no section was found.
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if not found:
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config_tuple = 'app:main', label, value
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config_items_by_section.append( config_tuple )
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print( config_items_by_section )
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# Replace the default values with the provided configuration.
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for section, label, value in config_items_by_section:
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if cp.has_option( section, label ):
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cp.remove_option( section, label )
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cp.set( section, label, str( value ) )
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fh = open( output_filename, 'w' )
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cp.write( fh )
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fh.close()
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def main():
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# ---- Configuration ------------------------------------------------------
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galaxy_test_host = os.environ.get( 'GALAXY_TEST_HOST', default_galaxy_test_host )
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galaxy_test_port = os.environ.get( 'GALAXY_TEST_PORT', None )
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galaxy_test_save = os.environ.get( 'GALAXY_TEST_SAVE', None)
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tool_path = os.environ.get( 'GALAXY_TEST_TOOL_PATH', 'tools' )
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if 'HTTP_ACCEPT_LANGUAGE' not in os.environ:
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os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales
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testing_migrated_tools = __check_arg( '-migrated' )
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testing_installed_tools = __check_arg( '-installed' )
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datatypes_conf_override = None
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if testing_migrated_tools or testing_installed_tools:
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# Store a jsonified dictionary of tool_id : GALAXY_TEST_FILE_DIR pairs.
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galaxy_tool_shed_test_file = 'shed_tools_dict'
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# We need the upload tool for functional tests, so we'll create a temporary tool panel config that defines it.
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fd, tmp_tool_panel_conf = tempfile.mkstemp()
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os.write( fd, '<?xml version="1.0"?>\n' )
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os.write( fd, '<toolbox>\n' )
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os.write( fd, '<tool file="data_source/upload.xml"/>\n' )
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os.write( fd, '</toolbox>\n' )
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os.close( fd )
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tool_config_file = tmp_tool_panel_conf
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galaxy_test_file_dir = None
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library_import_dir = None
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user_library_import_dir = None
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# Exclude all files except test_toolbox.py.
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ignore_files = ( re.compile( r'^test_[adghlmsu]*' ), re.compile( r'^test_ta*' ) )
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else:
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framework_tool_dir = os.path.join('test', 'functional', 'tools')
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framework_test = __check_arg( '-framework' ) # Run through suite of tests testing framework.
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if framework_test:
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tool_conf = os.path.join( framework_tool_dir, 'samples_tool_conf.xml' )
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datatypes_conf_override = os.path.join( framework_tool_dir, 'sample_datatypes_conf.xml' )
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else:
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# Use tool_conf.xml toolbox.
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tool_conf = None
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if __check_arg( '-with_framework_test_tools' ):
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tool_conf = "%s,%s" % ( 'config/tool_conf.xml.sample', os.path.join( framework_tool_dir, 'samples_tool_conf.xml' ) )
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test_dir = default_galaxy_test_file_dir
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tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', tool_conf )
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galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', test_dir )
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first_test_file_dir = galaxy_test_file_dir.split(",")[0]
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if not os.path.isabs( first_test_file_dir ):
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first_test_file_dir = os.path.join( os.getcwd(), first_test_file_dir )
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library_import_dir = first_test_file_dir
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import_dir = os.path.join( first_test_file_dir, 'users' )
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if os.path.exists(import_dir):
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user_library_import_dir = import_dir
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else:
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user_library_import_dir = None
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ignore_files = ()
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start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ
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tool_data_table_config_path = None
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if os.path.exists( 'tool_data_table_conf.test.xml' ):
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# If explicitly defined tables for test, use those.
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tool_data_table_config_path = 'tool_data_table_conf.test.xml'
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else:
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# ... otherise find whatever Galaxy would use as the default and
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# the sample data for fucntional tests to that.
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default_tool_data_config = 'config/tool_data_table_conf.xml.sample'
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for tool_data_config in ['config/tool_data_table_conf.xml', 'tool_data_table_conf.xml' ]:
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if os.path.exists( tool_data_config ):
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default_tool_data_config = tool_data_config
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tool_data_table_config_path = '%s,test/functional/tool-data/sample_tool_data_tables.xml' % default_tool_data_config
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default_data_manager_config = 'config/data_manager_conf.xml.sample'
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for data_manager_config in ['config/data_manager_conf.xml', 'data_manager_conf.xml' ]:
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if os.path.exists( data_manager_config ):
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default_data_manager_config = data_manager_config
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data_manager_config_file = "%s,test/functional/tools/sample_data_manager_conf.xml" % default_data_manager_config
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shed_tool_data_table_config = 'config/shed_tool_data_table_conf.xml'
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tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None )
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use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False )
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galaxy_test_tmp_dir = os.environ.get( 'GALAXY_TEST_TMP_DIR', None )
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if galaxy_test_tmp_dir is None:
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galaxy_test_tmp_dir = tempfile.mkdtemp()
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galaxy_job_conf_file = os.environ.get( 'GALAXY_TEST_JOB_CONF',
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os.path.join( galaxy_test_tmp_dir, 'test_job_conf.xml' ) )
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# Generate the job_conf.xml file.
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file( galaxy_job_conf_file, 'w' ).write( job_conf_xml )
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database_auto_migrate = False
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galaxy_test_proxy_port = None
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if start_server:
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tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir )
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# Configure the database path.
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if 'GALAXY_TEST_DBPATH' in os.environ:
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galaxy_db_path = os.environ[ 'GALAXY_TEST_DBPATH' ]
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else:
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galaxy_db_path = os.path.join( tempdir, 'database' )
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# Configure the paths Galaxy needs to test tools.
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file_path = os.path.join( galaxy_db_path, 'files' )
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template_cache_path = os.path.join( galaxy_db_path, 'compiled_templates' )
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new_file_path = tempfile.mkdtemp( prefix='new_files_path_', dir=tempdir )
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job_working_directory = tempfile.mkdtemp( prefix='job_working_directory_', dir=tempdir )
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install_database_connection = os.environ.get( 'GALAXY_TEST_INSTALL_DBURI', None )
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if 'GALAXY_TEST_DBURI' in os.environ:
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database_connection = os.environ['GALAXY_TEST_DBURI']
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else:
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db_path = os.path.join( galaxy_db_path, 'universe.sqlite' )
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if 'GALAXY_TEST_DB_TEMPLATE' in os.environ:
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# Middle ground between recreating a completely new
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# database and pointing at existing database with
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# GALAXY_TEST_DBURI. The former requires a lot of setup
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# time, the latter results in test failures in certain
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# cases (namely tool shed tests expecting clean database).
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log.debug( "Copying database template from %s.", os.environ['GALAXY_TEST_DB_TEMPLATE'] )
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driver_util.copy_database_template(os.environ['GALAXY_TEST_DB_TEMPLATE'], db_path)
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database_auto_migrate = True
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database_connection = 'sqlite:///%s' % db_path
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kwargs = {}
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for dir in file_path, new_file_path, template_cache_path:
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try:
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if not os.path.exists( dir ):
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os.makedirs( dir )
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except OSError:
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pass
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# Data Manager testing temp path
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# For storing Data Manager outputs and .loc files so that real ones don't get clobbered
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data_manager_test_tmp_path = tempfile.mkdtemp( prefix='data_manager_test_tmp', dir=galaxy_test_tmp_dir )
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galaxy_data_manager_data_path = tempfile.mkdtemp( prefix='data_manager_tool-data', dir=data_manager_test_tmp_path )
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# ---- Build Application --------------------------------------------------
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master_api_key = get_master_api_key()
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app = None
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if start_server:
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kwargs = dict( admin_users='test@bx.psu.edu',
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api_allow_run_as='test@bx.psu.edu',
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allow_library_path_paste=True,
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allow_user_creation=True,
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allow_user_deletion=True,
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database_connection=database_connection,
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database_auto_migrate=database_auto_migrate,
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datatype_converters_config_file="datatype_converters_conf.xml.sample",
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file_path=file_path,
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id_secret='changethisinproductiontoo',
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job_queue_workers=5,
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job_working_directory=job_working_directory,
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library_import_dir=library_import_dir,
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log_destination="stdout",
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new_file_path=new_file_path,
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template_cache_path=template_cache_path,
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running_functional_tests=True,
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shed_tool_data_table_config=shed_tool_data_table_config,
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template_path="templates",
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test_conf="test.conf",
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tool_config_file=tool_config_file,
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tool_data_table_config_path=tool_data_table_config_path,
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tool_path=tool_path,
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galaxy_data_manager_data_path=galaxy_data_manager_data_path,
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tool_parse_help=False,
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update_integrated_tool_panel=False,
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use_heartbeat=False,
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user_library_import_dir=user_library_import_dir,
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master_api_key=master_api_key,
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use_tasked_jobs=True,
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check_migrate_tools=False,
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cleanup_job='onsuccess',
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enable_beta_tool_formats=True,
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auto_configure_logging=logging_config_file is None,
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data_manager_config_file=data_manager_config_file )
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if install_database_connection is not None:
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kwargs[ 'install_database_connection' ] = install_database_connection
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if not database_connection.startswith( 'sqlite://' ):
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kwargs[ 'database_engine_option_max_overflow' ] = '20'
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kwargs[ 'database_engine_option_pool_size' ] = '10'
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if tool_dependency_dir is not None:
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kwargs[ 'tool_dependency_dir' ] = tool_dependency_dir
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if use_distributed_object_store:
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kwargs[ 'object_store' ] = 'distributed'
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kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample'
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if datatypes_conf_override:
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kwargs[ 'datatypes_config_file' ] = datatypes_conf_override
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# If the user has passed in a path for the .ini file, do not overwrite it.
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galaxy_config_file = os.environ.get( 'GALAXY_TEST_INI_FILE', None )
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if not galaxy_config_file:
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galaxy_config_file = os.path.join( galaxy_test_tmp_dir, 'functional_tests_wsgi.ini' )
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config_items = []
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for label in kwargs:
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config_tuple = label, kwargs[ label ]
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config_items.append( config_tuple )
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# Write a temporary file, based on config/galaxy.ini.sample, using the configuration options defined above.
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generate_config_file( 'config/galaxy.ini.sample', galaxy_config_file, config_items )
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# Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh.
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kwargs[ 'global_conf' ] = driver_util.get_webapp_global_conf()
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kwargs[ 'global_conf' ][ '__file__' ] = galaxy_config_file
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kwargs[ 'config_file' ] = galaxy_config_file
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kwargs = load_app_properties(
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kwds=kwargs
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)
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# Build the Universe Application
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app = UniverseApplication( **kwargs )
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database_contexts.galaxy_context = app.model.context
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log.info( "Embedded Universe application started" )
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# ---- Run webserver ------------------------------------------------------
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server = None
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if start_server:
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webapp = buildapp.app_factory( kwargs[ 'global_conf' ], app=app,
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use_translogger=False, static_enabled=True )
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if galaxy_test_port is not None:
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server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False )
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else:
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random.seed()
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for i in range( 0, 9 ):
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try:
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galaxy_test_port = str( random.randint( default_galaxy_test_port_min, default_galaxy_test_port_max ) )
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log.debug( "Attempting to serve app on randomly chosen port: %s" % galaxy_test_port )
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server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False )
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break
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except socket.error, e:
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if e[0] == 98:
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continue
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raise
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else:
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raise Exception( "Unable to open a port between %s and %s to start Galaxy server" % ( default_galaxy_test_port_min, default_galaxy_test_port_max ) )
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if galaxy_test_proxy_port:
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os.environ['GALAXY_TEST_PORT'] = galaxy_test_proxy_port
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else:
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os.environ['GALAXY_TEST_PORT'] = galaxy_test_port
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t = threading.Thread( target=server.serve_forever )
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t.start()
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# Test if the server is up
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for i in range( 10 ):
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conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port ) # directly test the app, not the proxy
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conn.request( "GET", "/" )
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if conn.getresponse().status == 200:
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break
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time.sleep( 0.1 )
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else:
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raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" )
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log.info( "Embedded web server started" )
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# ---- Find tests ---------------------------------------------------------
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if galaxy_test_proxy_port:
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log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_proxy_port ) )
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else:
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log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) )
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success = False
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try:
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tool_configs = app.config.tool_configs
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# What requires these? Handy for (eg) functional tests to save outputs?
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if galaxy_test_save:
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os.environ[ 'GALAXY_TEST_SAVE' ] = galaxy_test_save
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# Pass in through script setenv, will leave a copy of ALL test validate files
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os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host
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def _run_functional_test( testing_shed_tools=None ):
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workflow_test = __check_arg( '-workflow', param=True )
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if workflow_test:
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import functional.workflow
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functional.workflow.WorkflowTestCase.workflow_test_file = workflow_test
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functional.workflow.WorkflowTestCase.master_api_key = master_api_key
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functional.workflow.WorkflowTestCase.user_api_key = get_user_api_key()
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data_manager_test = __check_arg( '-data_managers', param=False )
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if data_manager_test:
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import functional.test_data_managers
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functional.test_data_managers.data_managers = app.data_managers # seems like a hack...
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functional.test_data_managers.build_tests(
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tmp_dir=data_manager_test_tmp_path,
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testing_shed_tools=testing_shed_tools,
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master_api_key=master_api_key,
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user_api_key=get_user_api_key(),
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)
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else:
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# We must make sure that functional.test_toolbox is always imported after
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# database_contexts.galaxy_content is set (which occurs in this method above).
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# If functional.test_toolbox is imported before database_contexts.galaxy_content
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# is set, sa_session will be None in all methods that use it.
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import functional.test_toolbox
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functional.test_toolbox.toolbox = app.toolbox
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# When testing data managers, do not test toolbox.
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functional.test_toolbox.build_tests(
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app=app,
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testing_shed_tools=testing_shed_tools,
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master_api_key=master_api_key,
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user_api_key=get_user_api_key(),
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)
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return driver_util.nose_config_and_run(
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ignore_files=ignore_files,
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)
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if testing_migrated_tools or testing_installed_tools:
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shed_tools_dict = {}
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if testing_migrated_tools:
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has_test_data, shed_tools_dict = parse_tool_panel_config( migrated_tool_panel_config, shed_tools_dict )
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elif testing_installed_tools:
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for shed_tool_config in installed_tool_panel_configs:
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has_test_data, shed_tools_dict = parse_tool_panel_config( shed_tool_config, shed_tools_dict )
|
|
# Persist the shed_tools_dict to the galaxy_tool_shed_test_file.
|
|
shed_tools_file = open( galaxy_tool_shed_test_file, 'w' )
|
|
shed_tools_file.write( dumps( shed_tools_dict ) )
|
|
shed_tools_file.close()
|
|
if not os.path.isabs( galaxy_tool_shed_test_file ):
|
|
galaxy_tool_shed_test_file = os.path.join( os.getcwd(), galaxy_tool_shed_test_file )
|
|
os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_tool_shed_test_file
|
|
if testing_installed_tools:
|
|
# Eliminate the migrated_tool_panel_config from the app's tool_configs, append the list of installed_tool_panel_configs,
|
|
# and reload the app's toolbox.
|
|
relative_migrated_tool_panel_config = os.path.join( app.config.root, migrated_tool_panel_config )
|
|
if relative_migrated_tool_panel_config in tool_configs:
|
|
tool_configs.remove( relative_migrated_tool_panel_config )
|
|
for installed_tool_panel_config in installed_tool_panel_configs:
|
|
tool_configs.append( installed_tool_panel_config )
|
|
app.toolbox = tools.ToolBox( tool_configs, app.config.tool_path, app )
|
|
success = _run_functional_test( testing_shed_tools=True )
|
|
try:
|
|
os.unlink( tmp_tool_panel_conf )
|
|
except:
|
|
log.info( "Unable to remove temporary file: %s" % tmp_tool_panel_conf )
|
|
try:
|
|
os.unlink( galaxy_tool_shed_test_file )
|
|
except:
|
|
log.info( "Unable to remove file: %s" % galaxy_tool_shed_test_file )
|
|
else:
|
|
if galaxy_test_file_dir:
|
|
os.environ[ 'GALAXY_TEST_FILE_DIR' ] = galaxy_test_file_dir
|
|
success = _run_functional_test( )
|
|
except:
|
|
log.exception( "Failure running tests" )
|
|
|
|
log.info( "Shutting down" )
|
|
# ---- Tear down -----------------------------------------------------------
|
|
if server:
|
|
log.info( "Shutting down embedded web server" )
|
|
server.server_close()
|
|
server = None
|
|
log.info( "Embedded web server stopped" )
|
|
if app:
|
|
log.info( "Shutting down app" )
|
|
app.shutdown()
|
|
app = None
|
|
log.info( "Embedded Universe application stopped" )
|
|
try:
|
|
if os.path.exists( tempdir ) and 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
|
|
log.info( "Cleaning up temporary files in %s" % tempdir )
|
|
shutil.rmtree( tempdir )
|
|
else:
|
|
log.info( "GALAXY_TEST_NO_CLEANUP is on. Temporary files in %s" % tempdir )
|
|
except:
|
|
pass
|
|
if success:
|
|
return 0
|
|
else:
|
|
return 1
|
|
|
|
|
|
def __check_arg( name, param=False ):
|
|
try:
|
|
index = sys.argv.index( name )
|
|
del sys.argv[ index ]
|
|
if param:
|
|
ret_val = sys.argv[ index ]
|
|
del sys.argv[ index ]
|
|
else:
|
|
ret_val = True
|
|
except ValueError:
|
|
ret_val = False
|
|
return ret_val
|
|
|
|
if __name__ == "__main__":
|
|
sys.exit( main() )
|