Partially lint scripts/ .

This commit is contained in:
Nicola Soranzo
2015-07-13 20:13:28 +01:00
parent 29c4f1ae85
commit 6569c2dcc3
40 changed files with 514 additions and 498 deletions
+11 -23
View File
@@ -1,14 +1,10 @@
#!/usr/bin/env python
# Import system subprocess now before twill so we don't get its
# variant that breaks things.
import subprocess
import os
import sys
import shutil
import tempfile
import re
import shutil
import sys
import tempfile
from ConfigParser import SafeConfigParser
# Assume we are run from the galaxy root directory, add lib to the python path
@@ -25,7 +21,6 @@ from galaxy.util.properties import load_app_properties
eggs.require( "nose" )
eggs.require( "NoseHTML" )
eggs.require( "NoseTestDiff" )
eggs.require( "twill==0.9" )
eggs.require( "Paste" )
eggs.require( "PasteDeploy" )
eggs.require( "Cheetah" )
@@ -34,25 +29,18 @@ eggs.require( "Cheetah" )
# http://code.google.com/p/python-nose/issues/detail?id=284
eggs.require( "pysqlite" )
import atexit
import logging
import os.path
import twill
import unittest
import time
import subprocess
import threading
import random
import httplib
import socket
import urllib
from paste import httpserver
import galaxy.app
from galaxy.app import UniverseApplication
from galaxy.web import buildapp
from galaxy import tools
from galaxy.util import bunch
from galaxy import util
from galaxy.util.json import dumps
from functional import database_contexts
@@ -101,6 +89,7 @@ job_conf_xml = '''<?xml version="1.0"?>
</job_conf>
'''
def get_static_settings():
"""Returns dictionary of the settings necessary for a galaxy App
to be wrapped in the static middleware.
@@ -110,9 +99,9 @@ def get_static_settings():
"""
cwd = os.getcwd()
static_dir = os.path.join( cwd, 'static' )
#TODO: these should be copied from config/galaxy.ini
# TODO: these should be copied from config/galaxy.ini
return dict(
#TODO: static_enabled needed here?
# TODO: static_enabled needed here?
static_enabled=True,
static_cache_time=360,
static_dir=static_dir,
@@ -308,11 +297,11 @@ def main():
except OSError:
pass
#Data Manager testing temp path
#For storing Data Manager outputs and .loc files so that real ones don't get clobbered
# Data Manager testing temp path
# For storing Data Manager outputs and .loc files so that real ones don't get clobbered
data_manager_test_tmp_path = tempfile.mkdtemp( prefix='data_manager_test_tmp', dir=galaxy_test_tmp_dir )
galaxy_data_manager_data_path = tempfile.mkdtemp( prefix='data_manager_tool-data', dir=data_manager_test_tmp_path )
# ---- Build Application --------------------------------------------------
master_api_key = get_master_api_key()
app = None
@@ -348,8 +337,7 @@ def main():
use_tasked_jobs=True,
cleanup_job='onsuccess',
enable_beta_tool_formats=True,
data_manager_config_file=data_manager_config_file,
)
data_manager_config_file=data_manager_config_file )
if install_database_connection is not None:
kwargs[ 'install_database_connection' ] = install_database_connection
if not database_connection.startswith( 'sqlite://' ):
@@ -448,7 +436,7 @@ def main():
data_manager_test = __check_arg( '-data_managers', param=False )
if data_manager_test:
import functional.test_data_managers
functional.test_data_managers.data_managers = app.data_managers #seems like a hack...
functional.test_data_managers.data_managers = app.data_managers # seems like a hack...
functional.test_data_managers.build_tests(
tmp_dir=data_manager_test_tmp_path,
testing_shed_tools=testing_shed_tools,