details: http://www.bx.psu.edu/hg/galaxy/rev/6dbe31bbbf02 changeset: 3427:6dbe31bbbf02 user: Nate Coraor nate@bx.psu.edu date: Tue Feb 23 15:14:28 2010 -0500 description: Modify functional_tests.py to allow for testing of an environment nearly identical to Galaxy Test/Main via buildbot

diffstat:

scripts/functional_tests.py | 132 +++++++++++++++++++++++++++++++++----------- 1 files changed, 99 insertions(+), 33 deletions(-)

diffs (206 lines):

diff -r 1f05b0c4071f -r 6dbe31bbbf02 scripts/functional_tests.py --- a/scripts/functional_tests.py Tue Feb 23 10:40:19 2010 -0500 +++ b/scripts/functional_tests.py Tue Feb 23 15:14:28 2010 -0500 @@ -1,6 +1,6 @@ #!/usr/bin/env python

-import os, sys +import os, sys, shutil

# Assume we are run from the galaxy root directory, add lib to the python path cwd = os.getcwd() @@ -52,32 +52,68 @@ if not os.path.isabs( galaxy_test_file_dir ): galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ + tool_path = os.environ.get( 'GALAXY_TEST_TOOL_PATH', 'tools' ) if start_server: - if 'GALAXY_TEST_DBPATH' in os.environ: - db_path = os.environ['GALAXY_TEST_DBPATH'] - else: - tempdir = tempfile.mkdtemp() - db_path = os.path.join( tempdir, 'database' ) - file_path = os.path.join( db_path, 'files' ) - try: - os.makedirs( file_path ) - except OSError: - pass - if 'GALAXY_TEST_DBURI' in os.environ: - database_connection = os.environ['GALAXY_TEST_DBURI'] + psu_production = False + galaxy_test_proxy_port = None + if 'GALAXY_TEST_PSU_PRODUCTION' in os.environ: + if not galaxy_test_port: + raise Exception( 'Please set GALAXY_TEST_PORT to the port to which the proxy server will proxy' ) + galaxy_test_proxy_port = os.environ.get( 'GALAXY_TEST_PROXY_PORT', None ) + if not galaxy_test_proxy_port: + raise Exception( 'Please set GALAXY_TEST_PROXY_PORT to the port on which the proxy server is listening' ) + base_file_path = os.environ.get( 'GALAXY_TEST_BASE_FILE_PATH', None ) + if not base_file_path: + raise Exception( 'Please set GALAXY_TEST_BASE_FILE_PATH to the directory which will contain the dataset files directory' ) + base_new_file_path = os.environ.get( 'GALAXY_TEST_BASE_NEW_FILE_PATH', None ) + if not base_new_file_path: + raise Exception( 'Please set GALAXY_TEST_BASE_NEW_FILE_PATH to the directory which will contain the temporary directory' ) + database_connection = os.environ.get( 'GALAXY_TEST_DBURI', None ) + if not database_connection: + raise Exception( 'Please set GALAXY_TEST_DBURI to the URI of the database to be used for tests' ) + nginx_upload_store = os.environ.get( 'GALAXY_TEST_NGINX_UPLOAD_STORE', None ) + if not nginx_upload_store: + raise Exception( 'Please set GALAXY_TEST_NGINX_UPLOAD_STORE to the path where the nginx upload module places uploaded files' ) + file_path = tempfile.mkdtemp( dir=base_file_path ) + new_file_path = tempfile.mkdtemp( dir=base_new_file_path ) + cluster_files_directory = os.path.join( new_file_path, 'pbs' ) + job_working_directory = os.path.join( new_file_path, 'job_working_directory' ) + os.mkdir( cluster_files_directory ) + os.mkdir( job_working_directory ) + kwargs = dict( database_engine_option_pool_size = '10', + database_engine_option_max_overflow = '20', + database_engine_option_strategy = 'threadlocal', + nginx_x_accel_redirect_base = '/_x_accel_redirect', + nginx_upload_store = nginx_upload_store, + nginx_upload_path = '/_upload', + cluster_files_directory = cluster_files_directory, + job_working_directory = job_working_directory, + outputs_to_working_directory = 'True', + set_metadata_externally = 'True', + static_enabled = 'False', + debug = 'False', + track_jobs_in_database = 'True', + job_scheduler_policy = 'FIFO', + start_job_runners = 'pbs', + default_cluster_job_runner = 'pbs:///', ) + psu_production = True else: - database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' ) - if 'GALAXY_TEST_RUNNERS' in os.environ: - start_job_runners = os.environ['GALAXY_TEST_RUNNERS'] - else: - start_job_runners = None - if 'GALAXY_TEST_DEF_RUNNER' in os.environ: - default_cluster_job_runner = os.environ['GALAXY_TEST_DEF_RUNNER'] - else: - default_cluster_job_runner = 'local:///' - set_metadata_externally = False - if 'GALAXY_SET_METADATA_EXTERNALLY' in os.environ: - set_metadata_externally = True + if 'GALAXY_TEST_DBPATH' in os.environ: + db_path = os.environ['GALAXY_TEST_DBPATH'] + else: + tempdir = tempfile.mkdtemp() + db_path = os.path.join( tempdir, 'database' ) + file_path = os.path.join( db_path, 'files' ) + new_file_path = os.path.join( db_path, 'tmp' ) + if 'GALAXY_TEST_DBURI' in os.environ: + database_connection = os.environ['GALAXY_TEST_DBURI'] + else: + database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' ) + try: + os.makedirs( file_path ) + except OSError: + pass + kwargs = {}

print "Database connection:", database_connection

@@ -91,17 +127,20 @@

if start_server:

+ global_conf = { '__file__' : 'universe_wsgi.ini.sample' } + if psu_production: + global_conf = None + # Build the Universe Application app = UniverseApplication( job_queue_workers = 5, - start_job_runners = start_job_runners, - default_cluster_job_runner = default_cluster_job_runner, id_secret = 'changethisinproductiontoo', template_path = "templates", database_connection = database_connection, file_path = file_path, + new_file_path = new_file_path, + tool_path = tool_path, tool_config_file = "tool_conf.xml.sample", datatype_converters_config_file = "datatype_converters_conf.xml.sample", - tool_path = "tools", tool_parse_help = False, test_conf = "test.conf", log_destination = "stdout", @@ -111,8 +150,8 @@ admin_users = 'test@bx.psu.edu', library_import_dir = galaxy_test_file_dir, user_library_import_dir = os.path.join( galaxy_test_file_dir, 'users' ), - set_metadata_externally = set_metadata_externally, - global_conf = { "__file__": "universe_wsgi.ini.sample" } ) + global_conf = global_conf, + **kwargs )

log.info( "Embedded Universe application started" );

@@ -140,14 +179,17 @@ raise else: 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 ) ) - os.environ['GALAXY_TEST_PORT'] = galaxy_test_port + if galaxy_test_proxy_port: + os.environ['GALAXY_TEST_PORT'] = galaxy_test_proxy_port + else: + os.environ['GALAXY_TEST_PORT'] = galaxy_test_port

t = threading.Thread( target=server.serve_forever ) t.start()

# Test if the server is up for i in range( 10 ): - conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port ) + conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port ) # directly test the app, not the proxy conn.request( "GET", "/" ) if conn.getresponse().status == 200: break @@ -155,6 +197,13 @@ else: raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" )

+ # Test if the proxy server is up + if psu_production: + conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_proxy_port ) # directly test the app, not the proxy + conn.request( "GET", "/" ) + if not conn.getresponse().status == 200: + raise Exception( "Test HTTP proxy server did not return '200 OK'" ) + log.info( "Embedded web server started" )

@@ -179,7 +228,10 @@

# ---- Find tests ---------------------------------------------------------

- log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) + 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

@@ -231,6 +283,20 @@ 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 ) + 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