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Fix for case where running functional tests might overwrite certain files in database/files.

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This commit is contained in:
Dave Bouvier
2013-08-19 13:06:17 -04:00
parent 338517b3c8
commit 7adc736e16
1 changed files with 84 additions and 34 deletions
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scripts/functional_tests.py
+84 -34
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@@ -1,6 +1,7 @@
#!/usr/bin/env python
import os, sys, shutil, tempfile, re
from ConfigParser import SafeConfigParser
# Assume we are run from the galaxy root directory, add lib to the python path
cwd = os.getcwd()
@@ -86,6 +87,39 @@ def get_webapp_global_conf():
global_conf.update( get_static_settings() )
return global_conf
def generate_config_file( input_filename, output_filename, config_items ):
'''
Generate a config file with the configuration that has been defined for the embedded web application.
This is mostly relevant when setting metadata externally, since the script for doing that does not
have access to app.config.
'''
cp = SafeConfigParser()
cp.read( input_filename )
config_items_by_section = []
for label, value in config_items:
found = False
# Attempt to determine the correct section for this configuration option.
for section in cp.sections():
if cp.has_option( section, label ):
config_tuple = section, label, value
config_items_by_section.append( config_tuple )
found = True
continue
# Default to app:main if no section was found.
if not found:
config_tuple = 'app:main', label, value
config_items_by_section.append( config_tuple )
print( config_items_by_section )
# Replace the default values with the provided configuration.
for section, label, value in config_items_by_section:
if cp.has_option( section, label ):
cp.remove_option( section, label )
cp.set( section, label, str( value ) )
fh = open( output_filename, 'w' )
cp.write( fh )
fh.close()
def run_tests( test_config ):
loader = nose.loader.TestLoader( config=test_config )
plug_loader = test_config.plugins.prepareTestLoader( loader )
@@ -145,6 +179,9 @@ def main():
shed_tool_data_table_config = 'shed_tool_data_table_conf.xml'
tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None )
use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False )
galaxy_test_tmp_dir = os.environ.get( 'GALAXY_TEST_TMP_DIR', None )
if galaxy_test_tmp_dir is None:
galaxy_test_tmp_dir = tempfile.mkdtemp()
if start_server:
psu_production = False
@@ -193,13 +230,14 @@ def main():
default_cluster_job_runner = default_cluster_job_runner )
psu_production = True
else:
# Configure the database path.
if 'GALAXY_TEST_DBPATH' in os.environ:
db_path = os.environ['GALAXY_TEST_DBPATH']
galaxy_db_path = os.environ[ 'GALAXY_TEST_DBPATH' ]
else:
tempdir = tempfile.mkdtemp()
db_path = tempfile.mkdtemp( prefix='database_', dir=tempdir )
# FIXME: This is a workaround for cases where metadata is being set externally.
file_path = os.path.join( 'database', 'files' )
tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir )
galaxy_db_path = os.path.join( tempdir, 'database' )
# Configure the paths Galaxy needs to test tools.
file_path = os.path.join( galaxy_db_path, 'files' )
new_file_path = tempfile.mkdtemp( prefix='new_files_path_', dir=tempdir )
job_working_directory = tempfile.mkdtemp( prefix='job_working_directory_', dir=tempdir )
if 'GALAXY_TEST_DBURI' in os.environ:
@@ -217,9 +255,32 @@ def main():
# ---- Build Application --------------------------------------------------
app = None
if start_server:
global_conf = { '__file__' : 'universe_wsgi.ini.sample' }
kwargs = dict( admin_users = 'test@bx.psu.edu',
allow_library_path_paste = True,
allow_user_creation = True,
allow_user_deletion = True,
database_connection = database_connection,
datatype_converters_config_file = "datatype_converters_conf.xml.sample",
file_path = file_path,
id_secret = 'changethisinproductiontoo',
job_queue_workers = 5,
job_working_directory = job_working_directory,
library_import_dir = library_import_dir,
log_destination = "stdout",
new_file_path = new_file_path,
running_functional_tests = True,
shed_tool_data_table_config = shed_tool_data_table_config,
template_path = "templates",
test_conf = "test.conf",
tool_config_file = tool_config_file,
tool_data_table_config_path = tool_data_table_config_path,
tool_path = tool_path,
tool_parse_help = False,
update_integrated_tool_panel = False,
use_heartbeat = False,
user_library_import_dir = user_library_import_dir )
if psu_production:
global_conf = None
kwargs[ 'global_conf' ] = None
if not database_connection.startswith( 'sqlite://' ):
kwargs[ 'database_engine_option_max_overflow' ] = '20'
kwargs[ 'database_engine_option_pool_size' ] = '10'
@@ -228,40 +289,29 @@ def main():
if use_distributed_object_store:
kwargs[ 'object_store' ] = 'distributed'
kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample'
# If the user has passed in a path for the .ini file, do not overwrite it.
galaxy_config_file = os.environ.get( 'GALAXY_TEST_INI_FILE', None )
if not galaxy_config_file:
galaxy_config_file = os.path.join( galaxy_test_tmp_dir, 'functional_tests_wsgi.ini' )
config_items = []
for label in kwargs:
config_tuple = label, kwargs[ label ]
config_items.append( config_tuple )
# Write a temporary file, based on universe_wsgi.ini.sample, using the configuration options defined above.
generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items )
# Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh.
kwargs[ 'global_conf' ] = get_webapp_global_conf()
kwargs[ 'global_conf' ][ '__file__' ] = galaxy_config_file
kwargs[ 'config_file' ] = galaxy_config_file
# Build the Universe Application
app = UniverseApplication( admin_users = 'test@bx.psu.edu',
allow_library_path_paste = True,
allow_user_creation = True,
allow_user_deletion = True,
database_connection = database_connection,
datatype_converters_config_file = "datatype_converters_conf.xml.sample",
file_path = file_path,
global_conf = global_conf,
id_secret = 'changethisinproductiontoo',
job_queue_workers = 5,
job_working_directory = job_working_directory,
library_import_dir = library_import_dir,
log_destination = "stdout",
new_file_path = new_file_path,
running_functional_tests = True,
shed_tool_data_table_config = shed_tool_data_table_config,
template_path = "templates",
test_conf = "test.conf",
tool_config_file = tool_config_file,
tool_data_table_config_path = tool_data_table_config_path,
tool_path = tool_path,
tool_parse_help = False,
update_integrated_tool_panel = False,
use_heartbeat = False,
user_library_import_dir = user_library_import_dir,
**kwargs )
app = UniverseApplication( **kwargs )
log.info( "Embedded Universe application started" )
# ---- Run webserver ------------------------------------------------------
server = None
if start_server:
webapp = buildapp.app_factory( get_webapp_global_conf(), app=app,
webapp = buildapp.app_factory( kwargs[ 'global_conf' ], app=app,
use_translogger=False, static_enabled=STATIC_ENABLED )
if galaxy_test_port is not None:
server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False )