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https://github.com/galaxyproject/galaxy.git
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405 lines
20 KiB
Python
405 lines
20 KiB
Python
#!/usr/bin/env python
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import os, sys, shutil, tempfile, re
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# Assume we are run from the galaxy root directory, add lib to the python path
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cwd = os.getcwd()
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new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, "test" ) ]
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new_path.extend( sys.path[1:] )
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sys.path = new_path
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from base.util import parse_tool_panel_config
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from galaxy import eggs
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eggs.require( "nose" )
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eggs.require( "NoseHTML" )
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eggs.require( "NoseTestDiff" )
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eggs.require( "twill==0.9" )
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eggs.require( "Paste" )
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eggs.require( "PasteDeploy" )
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eggs.require( "Cheetah" )
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# this should not be required, but it is under certain conditions, thanks to this bug:
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# http://code.google.com/p/python-nose/issues/detail?id=284
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eggs.require( "pysqlite" )
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import atexit, logging, os, os.path, sys, tempfile
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import twill, unittest, time
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import subprocess, sys, threading, random
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import httplib, socket
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from paste import httpserver
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import galaxy.app
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from galaxy.app import UniverseApplication
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from galaxy.web import buildapp
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from galaxy import tools
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from galaxy.util import bunch
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from galaxy import util
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from galaxy.util.json import to_json_string
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import nose.core
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import nose.config
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import nose.loader
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import nose.plugins.manager
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log = logging.getLogger( "functional_tests.py" )
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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"
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migrated_tool_panel_config = 'migrated_tools_conf.xml'
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installed_tool_panel_configs = [ 'shed_tool_conf.xml' ]
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# should this serve static resources (scripts, images, styles, etc.)
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STATIC_ENABLED = True
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def get_static_settings():
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"""Returns dictionary of the settings necessary for a galaxy App
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to be wrapped in the static middleware.
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This mainly consists of the filesystem locations of url-mapped
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static resources.
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"""
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cwd = os.getcwd()
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static_dir = os.path.join( cwd, 'static' )
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#TODO: these should be copied from universe_wsgi.ini
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return dict(
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#TODO: static_enabled needed here?
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static_enabled = True,
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static_cache_time = 360,
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static_dir = static_dir,
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static_images_dir = os.path.join( static_dir, 'images', '' ),
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static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ),
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static_scripts_dir = os.path.join( static_dir, 'scripts', '' ),
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static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ),
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static_robots_txt = os.path.join( static_dir, 'robots.txt' ),
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)
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def get_webapp_global_conf():
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"""Get the global_conf dictionary sent as the first argument to app_factory.
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"""
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# (was originally sent 'dict()') - nothing here for now except static settings
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global_conf = dict()
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if STATIC_ENABLED:
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global_conf.update( get_static_settings() )
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return global_conf
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def run_tests( test_config ):
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loader = nose.loader.TestLoader( config=test_config )
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plug_loader = test_config.plugins.prepareTestLoader( loader )
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if plug_loader is not None:
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loader = plug_loader
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tests = loader.loadTestsFromNames( test_config.testNames )
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test_runner = nose.core.TextTestRunner( stream=test_config.stream,
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verbosity=test_config.verbosity,
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config=test_config )
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plug_runner = test_config.plugins.prepareTestRunner( test_runner )
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if plug_runner is not None:
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test_runner = plug_runner
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return test_runner.run( tests )
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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 = '-migrated' in sys.argv
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testing_installed_tools = '-installed' in sys.argv
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if testing_migrated_tools or testing_installed_tools:
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sys.argv.pop()
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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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tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' )
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galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', default_galaxy_test_file_dir )
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if not os.path.isabs( galaxy_test_file_dir ):
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galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir )
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library_import_dir = galaxy_test_file_dir
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user_library_import_dir = os.path.join( galaxy_test_file_dir, 'users' )
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ignore_files = ()
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start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ
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if os.path.exists( 'tool_data_table_conf.test.xml' ):
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tool_data_table_config_path = 'tool_data_table_conf.test.xml'
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else:
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tool_data_table_config_path = 'tool_data_table_conf.xml'
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shed_tool_data_table_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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if start_server:
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psu_production = False
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galaxy_test_proxy_port = None
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if 'GALAXY_TEST_PSU_PRODUCTION' in os.environ:
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if not galaxy_test_port:
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raise Exception( 'Please set GALAXY_TEST_PORT to the port to which the proxy server will proxy' )
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galaxy_test_proxy_port = os.environ.get( 'GALAXY_TEST_PROXY_PORT', None )
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if not galaxy_test_proxy_port:
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raise Exception( 'Please set GALAXY_TEST_PROXY_PORT to the port on which the proxy server is listening' )
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base_file_path = os.environ.get( 'GALAXY_TEST_BASE_FILE_PATH', None )
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if not base_file_path:
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raise Exception( 'Please set GALAXY_TEST_BASE_FILE_PATH to the directory which will contain the dataset files directory' )
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base_new_file_path = os.environ.get( 'GALAXY_TEST_BASE_NEW_FILE_PATH', None )
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if not base_new_file_path:
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raise Exception( 'Please set GALAXY_TEST_BASE_NEW_FILE_PATH to the directory which will contain the temporary directory' )
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database_connection = os.environ.get( 'GALAXY_TEST_DBURI', None )
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if not database_connection:
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raise Exception( 'Please set GALAXY_TEST_DBURI to the URI of the database to be used for tests' )
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nginx_upload_store = os.environ.get( 'GALAXY_TEST_NGINX_UPLOAD_STORE', None )
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if not nginx_upload_store:
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raise Exception( 'Please set GALAXY_TEST_NGINX_UPLOAD_STORE to the path where the nginx upload module places uploaded files' )
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tool_config_file = 'tool_conf.xml.main'
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default_cluster_job_runner = os.environ.get( 'GALAXY_TEST_DEFAULT_CLUSTER_JOB_RUNNER', 'pbs:///' )
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file_path = tempfile.mkdtemp( dir=base_file_path )
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new_file_path = tempfile.mkdtemp( dir=base_new_file_path )
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cluster_files_directory = os.path.join( new_file_path, 'pbs' )
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job_working_directory = os.path.join( new_file_path, 'job_working_directory' )
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os.mkdir( cluster_files_directory )
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os.mkdir( job_working_directory )
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kwargs = dict( database_engine_option_pool_size = '10',
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database_engine_option_max_overflow = '20',
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database_engine_option_strategy = 'threadlocal',
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nginx_x_accel_redirect_base = '/_x_accel_redirect',
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nginx_upload_store = nginx_upload_store,
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nginx_upload_path = '/_upload',
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allow_library_path_paste = 'True',
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cluster_files_directory = cluster_files_directory,
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job_working_directory = job_working_directory,
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outputs_to_working_directory = 'True',
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set_metadata_externally = 'True',
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static_enabled = 'False',
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debug = 'False',
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track_jobs_in_database = 'True',
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job_scheduler_policy = 'FIFO',
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start_job_runners = 'pbs',
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default_cluster_job_runner = default_cluster_job_runner )
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psu_production = True
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else:
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if 'GALAXY_TEST_DBPATH' in os.environ:
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db_path = os.environ['GALAXY_TEST_DBPATH']
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else:
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tempdir = tempfile.mkdtemp()
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db_path = os.path.join( tempdir, 'database' )
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file_path = os.path.join( db_path, 'files' )
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new_file_path = os.path.join( db_path, 'tmp' )
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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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database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' )
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kwargs = {}
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for dir in file_path, new_file_path:
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try:
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os.makedirs( dir )
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except OSError:
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pass
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# ---- Build Application --------------------------------------------------
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app = None
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if start_server:
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global_conf = { '__file__' : 'universe_wsgi.ini.sample' }
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if psu_production:
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global_conf = None
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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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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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# Build the Universe Application
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app = UniverseApplication( job_queue_workers = 5,
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id_secret = 'changethisinproductiontoo',
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template_path = "templates",
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database_connection = database_connection,
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database_engine_option_pool_size = '10',
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file_path = file_path,
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new_file_path = new_file_path,
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tool_path = tool_path,
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update_integrated_tool_panel = False,
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tool_config_file = tool_config_file,
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datatype_converters_config_file = "datatype_converters_conf.xml.sample",
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tool_parse_help = False,
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test_conf = "test.conf",
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tool_data_table_config_path = tool_data_table_config_path,
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shed_tool_data_table_config = shed_tool_data_table_config,
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log_destination = "stdout",
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use_heartbeat = False,
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allow_user_creation = True,
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allow_user_deletion = True,
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admin_users = 'test@bx.psu.edu',
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allow_library_path_paste = True,
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library_import_dir = library_import_dir,
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user_library_import_dir = user_library_import_dir,
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global_conf = global_conf,
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running_functional_tests=True,
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**kwargs )
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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( get_webapp_global_conf(), app=app,
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use_translogger=False, static_enabled=STATIC_ENABLED )
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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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# Test if the proxy server is up
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if psu_production:
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conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_proxy_port ) # directly test the app, not the proxy
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conn.request( "GET", "/" )
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if not conn.getresponse().status == 200:
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raise Exception( "Test HTTP proxy server did not return '200 OK'" )
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log.info( "Embedded web server started" )
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# ---- Load toolbox for generated tests -----------------------------------
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# We don't add the tests to the path until everything is up and running
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new_path = [ os.path.join( cwd, "test" ) ]
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new_path.extend( sys.path[1:] )
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sys.path = new_path
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import functional.test_toolbox
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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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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 )
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# Persist the shed_tools_dict to the galaxy_tool_shed_test_file.
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shed_tools_file = open( galaxy_tool_shed_test_file, 'w' )
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shed_tools_file.write( to_json_string( shed_tools_dict ) )
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shed_tools_file.close()
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if not os.path.isabs( galaxy_tool_shed_test_file ):
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galaxy_tool_shed_test_file = os.path.join( os.getcwd(), galaxy_tool_shed_test_file )
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os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_tool_shed_test_file
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if testing_installed_tools:
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# Eliminate the migrated_tool_panel_config from the app's tool_configs, append the list of installed_tool_panel_configs,
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# and reload the app's toolbox.
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relative_migrated_tool_panel_config = os.path.join( app.config.root, migrated_tool_panel_config )
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if relative_migrated_tool_panel_config in tool_configs:
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tool_configs.remove( relative_migrated_tool_panel_config )
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for installed_tool_panel_config in installed_tool_panel_configs:
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tool_configs.append( installed_tool_panel_config )
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app.toolbox = tools.ToolBox( tool_configs, app.config.tool_path, app )
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functional.test_toolbox.toolbox = app.toolbox
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functional.test_toolbox.build_tests( testing_shed_tools=True )
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test_config = nose.config.Config( env=os.environ, ignoreFiles=ignore_files, plugins=nose.plugins.manager.DefaultPluginManager() )
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test_config.configure( sys.argv )
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result = run_tests( test_config )
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success = result.wasSuccessful()
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try:
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os.unlink( tmp_tool_panel_conf )
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except:
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log.info( "Unable to remove temporary file: %s" % tmp_tool_panel_conf )
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try:
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os.unlink( galaxy_tool_shed_test_file )
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except:
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log.info( "Unable to remove file: %s" % galaxy_tool_shed_test_file )
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else:
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functional.test_toolbox.toolbox = app.toolbox
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functional.test_toolbox.build_tests()
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if galaxy_test_file_dir:
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os.environ[ 'GALAXY_TEST_FILE_DIR' ] = galaxy_test_file_dir
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test_config = nose.config.Config( env=os.environ, ignoreFiles=ignore_files, plugins=nose.plugins.manager.DefaultPluginManager() )
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test_config.configure( sys.argv )
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result = run_tests( test_config )
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success = result.wasSuccessful()
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except:
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log.exception( "Failure running tests" )
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log.info( "Shutting down" )
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# ---- Tear down -----------------------------------------------------------
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if server:
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log.info( "Shutting down embedded web server" )
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server.server_close()
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server = None
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log.info( "Embedded web server stopped" )
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if app:
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log.info( "Shutting down app" )
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app.shutdown()
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app = None
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log.info( "Embedded Universe application stopped" )
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try:
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if os.path.exists( tempdir ) and 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
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log.info( "Cleaning up temporary files in %s" % tempdir )
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shutil.rmtree( tempdir )
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else:
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log.info( "GALAXY_TEST_NO_CLEANUP is on. Temporary files in %s" % tempdir )
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except:
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pass
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if psu_production and 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
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for dir in ( file_path, new_file_path ):
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try:
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if os.path.exists( dir ):
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log.info( 'Cleaning up temporary files in %s' % dir )
|
|
shutil.rmtree( dir )
|
|
except:
|
|
pass
|
|
if success:
|
|
return 0
|
|
else:
|
|
return 1
|
|
|
|
if __name__ == "__main__":
|
|
sys.exit( main() )
|