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Refactor toolbox hacks used by installed and migration tool tests out...

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into driver_util. This greatly simplifies the code structure of scripts/functional_tests.py's main method.

Add description of GALAXY_TEST_SHED_TOOL_CONF and some documentation to all of this.
This commit is contained in:
John Chilton
2016-03-29 08:04:24 -04:00
parent d03651f4ef
commit e7b5293534
3 changed files with 53 additions and 38 deletions
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run_tests.sh
+2 -1
View File
@@ -69,7 +69,8 @@ GALAXY_TEST_NO_CLEANUP Do not cleanup main test directory after tests,
GALAXY_TEST_HOST Host to use for Galaxy server setup for testing.
GALAXY_TEST_PORT Port to use for Galaxy server setup for testing.
GALAXY_TEST_TOOL_PATH Defaults to 'tools'
GALAXY_TEST_SHED_TOOL_CONF Shed toolbox conf (defaults to config/shed_tool_conf.xml)
used when testing installed to tools with -installed.
TOOL_SHED_TEST_HOST Host to use for shed server setup for testing.
TOOL_SHED_TEST_PORT Port to use for shed server setup for testing.
TOOL_SHED_TEST_FILE_DIR Defaults to test/tool_shed/test_data.
scripts/functional_tests.py
+13 -37
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@@ -10,7 +10,6 @@ import os.path
import sys
import tempfile
from ConfigParser import SafeConfigParser
from json import dumps
galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir))
sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ]
@@ -21,18 +20,12 @@ log = driver_util.build_logger()
from base.api_util import get_master_api_key, get_user_api_key
from base.test_logging import logging_config_file
from base.tool_shed_util import parse_tool_panel_config
from functional import database_contexts
from galaxy import tools
from galaxy.app import UniverseApplication
from galaxy.util.properties import load_app_properties
from galaxy.web import buildapp
default_galaxy_test_host = "localhost"
migrated_tool_panel_config = 'config/migrated_tools_conf.xml'
installed_tool_panel_configs = [
os.environ.get('GALAXY_TEST_SHED_TOOL_CONF', 'config/shed_tool_conf.xml')
]
# Set up a job_conf.xml that explicitly limits jobs to 10 minutes.
@@ -98,13 +91,14 @@ def main():
testing_installed_tools = _check_arg( '-installed' )
datatypes_conf_override = None
use_test_file_dir = not (testing_migrated_tools or testing_installed_tools)
if not use_test_file_dir:
testing_shed_tools = testing_migrated_tools or testing_installed_tools
if testing_shed_tools:
# Store a jsonified dictionary of tool_id : GALAXY_TEST_FILE_DIR pairs.
galaxy_tool_shed_test_file = 'shed_tools_dict'
# We need the upload tool for functional tests, so we'll create a temporary tool panel config that defines it.
tool_config_file = driver_util.FRAMEWORK_UPLOAD_TOOL_CONF
else:
galaxy_tool_shed_test_file = None
framework_test = _check_arg( '-framework' ) # Run through suite of tests testing framework.
if framework_test:
tool_conf = driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF
@@ -153,7 +147,7 @@ def main():
galaxy_db_path = driver_util.database_files_path(tempdir)
galaxy_config = driver_util.setup_galaxy_config(
galaxy_db_path,
use_test_file_dir=use_test_file_dir
use_test_file_dir=not testing_shed_tools,
)
database_connection, database_auto_migrate = driver_util.database_conf(galaxy_db_path)
@@ -225,7 +219,6 @@ def main():
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?
# Pass in through script setenv, will leave a copy of ALL test validate files
os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host
@@ -263,36 +256,19 @@ def main():
)
return driver_util.nose_config_and_run()
if not use_test_file_dir:
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( 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 )
if testing_shed_tools:
driver_util.setup_shed_tools_for_test(
app,
galaxy_tool_shed_test_file,
testing_migrated_tools,
testing_installed_tools,
)
success = _run_functional_test( testing_shed_tools=True )
if galaxy_tool_shed_test_file is not None:
try:
os.unlink( galaxy_tool_shed_test_file )
except:
log.info( "Unable to remove file: %s" % galaxy_tool_shed_test_file )
else:
success = _run_functional_test( )
except:
log.exception( "Failure running tests" )
test/base/driver_util.py
+38
View File
@@ -1,6 +1,7 @@
"""Scripts for drivers of Galaxy functional tests."""
import httplib
import json
import logging
import os
import random
@@ -20,6 +21,7 @@ import nose.plugins.manager
from paste import httpserver
from .tool_shed_util import parse_tool_panel_config
from .nose_util import run
from .instrument import StructuredTestDataPlugin
@@ -33,6 +35,10 @@ FRAMEWORK_TOOLS_DIR = os.path.join(GALAXY_TEST_DIRECTORY, "functional", "tools")
FRAMEWORK_UPLOAD_TOOL_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "upload_tool_conf.xml")
FRAMEWORK_SAMPLE_TOOLS_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "samples_tool_conf.xml")
FRAMEWORK_DATATYPES_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "sample_datatypes_conf.xml")
MIGRATED_TOOL_PANEL_CONFIG = 'config/migrated_tools_conf.xml'
INSTALLED_TOOL_PANEL_CONFIGS = [
os.environ.get('GALAXY_TEST_SHED_TOOL_CONF', 'config/shed_tool_conf.xml')
]
DEFAULT_LOCALES = "en"
@@ -314,6 +320,37 @@ def cleanup_directory(tempdir):
pass
def setup_shed_tools_for_test(app, galaxy_tool_shed_test_file, testing_migrated_tools, testing_installed_tools):
"""Modify Galaxy app's toolbox for migrated or installed tool tests."""
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.
with open(galaxy_tool_shed_test_file, 'w') as shed_tools_file:
shed_tools_file.write(json.dumps(shed_tools_dict))
if not os.path.isabs(galaxy_tool_shed_test_file):
galaxy_tool_shed_test_file = os.path.join(galaxy_root, galaxy_tool_shed_test_file)
os.environ['GALAXY_TOOL_SHED_TEST_FILE'] = galaxy_tool_shed_test_file
if testing_installed_tools:
# TODO: Do this without modifying app - that is a pretty violation
# of Galaxy's abstraction - we shouldn't require app at all let alone
# be modifying it.
tool_configs = app.config.tool_configs
# 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)
from galaxy import tools # noqa, delay import because this brings in so many modules for small tests
app.toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
__all__ = [
"cleanup_directory",
"configure_environment",
@@ -326,5 +363,6 @@ __all__ = [
"get_webapp_global_conf",
"nose_config_and_run",
"setup_galaxy_config",
"setup_shed_tools_for_test",
"wait_for_http_server",
]