mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
43a17b3d9b
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). GALAXY_TEST_DB_TEMPLATE can be either a file path (absolute) or URL. In order to facilitate this, a new Galaxy config option (database_auto_migrate) has been added. If this option is enabled, when Galaxy starts up and points at an existing database, if that database is not at the newest version it will be automatically migrated. This option defaults to False, but is enabled in testing if GALAXY_TEST_DB_TEMPLATE is set. I think we should go a step further and make this (database_auto_migrate) default to True if database_connection references an sqlite database - unless we believe there are Galaxy instances out there based on sqlite that are REALLY old or that are production enough to warrent requiring admins to do that database migration in a separate step (presumably encouraging them to make a backup pre-migration). Thoughts?
502 lines
23 KiB
Python
502 lines
23 KiB
Python
#!/usr/bin/env python
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import os
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import sys
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import shutil
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import tempfile
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import re
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from ConfigParser import SafeConfigParser
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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
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import logging
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import os.path
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import twill
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import unittest
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import time
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import subprocess
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import threading
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import random
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import httplib
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import socket
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import urllib
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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 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 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 __copy_database_template( source, db_path ):
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"""
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Copy a 'clean' sqlite template database (from file or URL) to specified
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database path.
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"""
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os.makedirs( os.path.dirname( db_path ) )
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if os.path.exists( source ):
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shutil.copy( source, db_path )
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assert os.path.exists( db_path )
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elif source.startswith("http"):
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urllib.urlretrieve( source, db_path )
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else:
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raise Exception( "Failed to copy database template from source %s" % source )
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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' )
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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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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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database_auto_migrate = 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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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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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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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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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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__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:
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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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# ---- Build Application --------------------------------------------------
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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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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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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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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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if psu_production:
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kwargs[ '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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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 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 universe_wsgi.ini.sample, using the configuration options defined above.
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generate_config_file( 'universe_wsgi.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' ] = 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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# Build the Universe Application
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app = UniverseApplication( **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( kwargs[ '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" ) ]
|
|
new_path.extend( sys.path[1:] )
|
|
sys.path = new_path
|
|
import functional.test_toolbox
|
|
# ---- Find tests ---------------------------------------------------------
|
|
if galaxy_test_proxy_port:
|
|
log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_proxy_port ) )
|
|
else:
|
|
log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) )
|
|
success = False
|
|
try:
|
|
tool_configs = app.config.tool_configs
|
|
# What requires these? Handy for (eg) functional tests to save outputs?
|
|
if galaxy_test_save:
|
|
os.environ[ 'GALAXY_TEST_SAVE' ] = galaxy_test_save
|
|
# Pass in through script setenv, will leave a copy of ALL test validate files
|
|
os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host
|
|
if testing_migrated_tools or testing_installed_tools:
|
|
shed_tools_dict = {}
|
|
if testing_migrated_tools:
|
|
has_test_data, shed_tools_dict = parse_tool_panel_config( migrated_tool_panel_config, shed_tools_dict )
|
|
elif testing_installed_tools:
|
|
for shed_tool_config in installed_tool_panel_configs:
|
|
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( to_json_string( 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 )
|
|
functional.test_toolbox.toolbox = app.toolbox
|
|
functional.test_toolbox.build_tests( testing_shed_tools=True )
|
|
test_config = nose.config.Config( env=os.environ, ignoreFiles=ignore_files, plugins=nose.plugins.manager.DefaultPluginManager() )
|
|
test_config.configure( sys.argv )
|
|
result = run_tests( test_config )
|
|
success = result.wasSuccessful()
|
|
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:
|
|
functional.test_toolbox.toolbox = app.toolbox
|
|
functional.test_toolbox.build_tests()
|
|
if galaxy_test_file_dir:
|
|
os.environ[ 'GALAXY_TEST_FILE_DIR' ] = galaxy_test_file_dir
|
|
test_config = nose.config.Config( env=os.environ, ignoreFiles=ignore_files, plugins=nose.plugins.manager.DefaultPluginManager() )
|
|
test_config.configure( sys.argv )
|
|
result = run_tests( test_config )
|
|
success = result.wasSuccessful()
|
|
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 psu_production and 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
|
|
for dir in ( file_path, new_file_path ):
|
|
try:
|
|
if os.path.exists( dir ):
|
|
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() )
|