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Fix the install and test framework's handling of external metadata.

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This commit is contained in:
Dave Bouvier
2013-08-02 10:53:41 -04:00
parent 80cfe1c1de
commit f016d2cfef
1 changed files with 114 additions and 33 deletions
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test/install_and_test_tool_shed_repositories/functional_tests.py
+114 -33
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@@ -6,6 +6,7 @@
import os, sys, shutil, tempfile, re, string, urllib, platform
from time import strftime
from ConfigParser import SafeConfigParser
# Assume we are run from the galaxy root directory, add lib to the python path
cwd = os.getcwd()
@@ -73,6 +74,40 @@ default_galaxy_test_port_min = 10000
default_galaxy_test_port_max = 10999
default_galaxy_test_host = '127.0.0.1'
# should this serve static resources (scripts, images, styles, etc.)
STATIC_ENABLED = True
def get_static_settings():
"""Returns dictionary of the settings necessary for a galaxy App
to be wrapped in the static middleware.
This mainly consists of the filesystem locations of url-mapped
static resources.
"""
cwd = os.getcwd()
static_dir = os.path.join( cwd, 'static' )
#TODO: these should be copied from universe_wsgi.ini
return dict(
#TODO: static_enabled needed here?
static_enabled = True,
static_cache_time = 360,
static_dir = static_dir,
static_images_dir = os.path.join( static_dir, 'images', '' ),
static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ),
static_scripts_dir = os.path.join( static_dir, 'scripts', '' ),
static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ),
static_robots_txt = os.path.join( static_dir, 'robots.txt' ),
)
def get_webapp_global_conf():
"""Get the global_conf dictionary sent as the first argument to app_factory.
"""
# (was originally sent 'dict()') - nothing here for now except static settings
global_conf = dict()
if STATIC_ENABLED:
global_conf.update( get_static_settings() )
return global_conf
# Optionally, set the environment variable GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF
# to the location of a tool sheds configuration file that includes the tool shed
# that repositories will be installed from.
@@ -219,6 +254,36 @@ def execute_uninstall_method( app ):
success = result.wasSuccessful()
return success
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 )
# Replace the default values with the provided configuration.
for section, label, value in config_items_by_section:
cp.remove_option( section, label )
cp.set( section, label, str( value ) )
fh = open( output_filename, 'w' )
cp.write( fh )
fh.close()
def get_api_url( base, parts=[], params=None, key=None ):
if 'api' in parts and parts.index( 'api' ) != 0:
parts.pop( parts.index( 'api' ) )
@@ -554,48 +619,64 @@ def main():
# Generate the migrated_tool_conf.xml file.
migrated_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path )
file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml )
# Write the embedded web application's specific configuration to a temporary file. This is necessary in order for
# the external metadata script to find the right datasets.
kwargs = dict( admin_users = 'test@bx.psu.edu',
allow_user_creation = True,
allow_user_deletion = True,
allow_library_path_paste = True,
database_connection = database_connection,
datatype_converters_config_file = "datatype_converters_conf.xml.sample",
file_path = galaxy_file_path,
id_secret = galaxy_encode_secret,
job_queue_workers = 5,
log_destination = "stdout",
migrated_tools_config = galaxy_migrated_tool_conf_file,
new_file_path = galaxy_tempfiles,
running_functional_tests = True,
shed_tool_data_table_config = shed_tool_data_table_conf_file,
shed_tool_path = galaxy_shed_tool_path,
template_path = "templates",
tool_config_file = ','.join( [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] ),
tool_data_path = tool_data_path,
tool_data_table_config_path = galaxy_tool_data_table_conf_file,
tool_dependency_dir = tool_dependency_dir,
tool_path = tool_path,
tool_parse_help = False,
tool_sheds_config_file = galaxy_tool_sheds_conf_file,
update_integrated_tool_panel = False,
use_heartbeat = False )
galaxy_config_file = os.environ.get( 'GALAXY_INSTALL_TEST_INI_FILE', None )
# If the user has passed in a path for the .ini file, do not overwrite it.
if not galaxy_config_file:
galaxy_config_file = os.path.join( galaxy_test_tmp_dir, 'install_test_tool_shed_repositories_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 )
kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ]
# 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
# ---- Build Galaxy Application --------------------------------------------------
global_conf = { '__file__' : 'universe_wsgi.ini.sample' }
if not database_connection.startswith( 'sqlite://' ):
kwargs[ 'database_engine_option_max_overflow' ] = '20'
kwargs[ 'database_engine_option_pool_size' ] = '10'
app = UniverseApplication( admin_users = 'test@bx.psu.edu',
allow_user_creation = True,
allow_user_deletion = True,
allow_library_path_paste = True,
database_connection = database_connection,
datatype_converters_config_file = "datatype_converters_conf.xml.sample",
file_path = galaxy_file_path,
global_conf = global_conf,
id_secret = galaxy_encode_secret,
job_queue_workers = 5,
log_destination = "stdout",
migrated_tools_config = galaxy_migrated_tool_conf_file,
new_file_path = galaxy_tempfiles,
running_functional_tests=True,
shed_tool_data_table_config = shed_tool_data_table_conf_file,
shed_tool_path = galaxy_shed_tool_path,
template_path = "templates",
tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ],
tool_data_path = tool_data_path,
tool_data_table_config_path = galaxy_tool_data_table_conf_file,
tool_dependency_dir = tool_dependency_dir,
tool_path = tool_path,
tool_parse_help = False,
tool_sheds_config_file = galaxy_tool_sheds_conf_file,
update_integrated_tool_panel = False,
use_heartbeat = False,
**kwargs )
kwargs[ 'config_file' ] = galaxy_config_file
app = UniverseApplication( **kwargs )
log.info( "Embedded Galaxy application started" )
# ---- Run galaxy webserver ------------------------------------------------------
server = None
webapp = buildapp.app_factory( dict( database_file=database_connection ),
use_translogger=False,
static_enabled=False,
app=app )
global_conf = get_webapp_global_conf()
global_conf[ 'database_file' ] = database_connection
webapp = buildapp.app_factory( global_conf,
use_translogger=False,
static_enabled=STATIC_ENABLED,
app=app )
# Serve the app on a specified or random port.
if galaxy_test_port is not None: