Use __file__ when adding paths to sys.path instead of os.getcwd() .

Also insert additional paths in position 1 unless strictly necessary.

doc/source/conf.py

@@ -11,12 +11,14 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os, datetime
+import datetime
+import os
+import sys
 
 
 ####### REQUIRED GALAXY INCLUDES
 
-sys.path.append(os.path.join(os.getcwd(), '../../lib'))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
 
 #######
 

lib/galaxy/main.py

@@ -58,7 +58,7 @@ REQUIRES_DAEMONIZE_MESSAGE = "Attempted to use Galaxy in daemon mode, but daemon
 
 log = logging.getLogger(__name__)
 
-GALAXY_ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
+GALAXY_ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
 GALAXY_LIB_DIR = os.path.join(GALAXY_ROOT_DIR, "lib")
 DEFAULT_INI_APP = "main"
 DEFAULT_INIS = ["config/galaxy.ini", "universe_wsgi.ini", "config/galaxy.ini.sample"]

lib/galaxy_ext/metadata/set_metadata.py

@@ -11,28 +11,30 @@ set to the path of the dataset on which metadata is being set
 constructed automatically).
 """
 
-import logging
-logging.basicConfig()
-log = logging.getLogger( __name__ )
-
 import cPickle
 import json
+import logging
 import os
 import sys
 
+# insert *this* galaxy before all others on sys.path
+sys.path.insert( 1, os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) ) )
+
+from galaxy import eggs
+eggs.require('SQLAlchemy')
+from sqlalchemy.orm import clear_mappers
+
+import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
+from galaxy.model.custom_types import total_size
+from galaxy.util import stringify_dictionary_keys
+
 # ensure supported version
 assert sys.version_info[:2] >= ( 2, 6 ) and sys.version_info[:2] <= ( 2, 7 ), 'Python version must be 2.6 or 2.7, this is: %s' % sys.version
 
-# insert *this* galaxy before all others on sys.path
-new_path = os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) )
-sys.path.insert( 0, new_path )
-
-import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
-from galaxy.model.custom_types import total_size
+logging.basicConfig()
+log = logging.getLogger( __name__ )
 
 galaxy.model.Job()  # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
-from galaxy.util import stringify_dictionary_keys
-from sqlalchemy.orm import clear_mappers
 
 
 def set_meta_with_tool_provided( dataset_instance, file_dict, set_meta_kwds, datatypes_registry ):

test/base/tool_shed_util.py

@@ -2,14 +2,8 @@ import logging
 import os
 import sys
 
-cwd = os.getcwd()
-if cwd not in sys.path:
-    sys.path.append( cwd )
-
-new_path = [ os.path.join( cwd, "lib" ) ]
-if new_path not in sys.path:
-    new_path.extend( sys.path )
-    sys.path = new_path
+galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir))
+sys.path.insert(1, os.path.join(galaxy_root, 'lib'))
 
 from galaxy.util import parse_xml
 
@@ -70,7 +64,7 @@ def parse_tool_panel_config( config, shed_tools_dict ):
                     has_test_data = True
                 if galaxy_test_file_dir != last_galaxy_test_file_dir:
                     if not os.path.isabs( galaxy_test_file_dir ):
-                        galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir )
+                        galaxy_test_file_dir = os.path.join( galaxy_root, galaxy_test_file_dir )
                 guid = elem.get( 'guid' )
                 shed_tools_dict[ guid ] = galaxy_test_file_dir
                 last_galaxy_test_file_dir = galaxy_test_file_dir
@@ -89,7 +83,7 @@ def parse_tool_panel_config( config, shed_tools_dict ):
                             has_test_data = True
                         if galaxy_test_file_dir != last_galaxy_test_file_dir:
                             if not os.path.isabs( galaxy_test_file_dir ):
-                                galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir )
+                                galaxy_test_file_dir = os.path.join( galaxy_root, galaxy_test_file_dir )
                         guid = section_elem.get( 'guid' )
                         shed_tools_dict[ guid ] = galaxy_test_file_dir
                         last_galaxy_test_file_dir = galaxy_test_file_dir

test/install_and_test_tool_shed_repositories/base/util.py

@@ -8,13 +8,10 @@ import sys
 import time
 from datetime import datetime, timedelta
 
-cwd = os.getcwd()
-sys.path.append( cwd )
-new_path = [ os.path.join( cwd, "lib" ),
-             os.path.join( cwd, 'test' ),
-             os.path.join( cwd, 'lib', 'tool_shed', 'scripts', 'api' ) ]
-new_path.extend( sys.path )
-sys.path = new_path
+galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir, os.path.pardir))
+sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ),
+                  os.path.join( galaxy_root, 'test' ),
+                  os.path.join( galaxy_root, 'lib', 'tool_shed', 'scripts', 'api' ) ]
 
 from galaxy import eggs
 eggs.require( 'mercurial' )
@@ -455,8 +452,7 @@ def get_static_settings():
     Return a dictionary of the settings necessary for a Galaxy application to be wrapped in the static
     middleware.  This mainly consists of the file system locations of url-mapped static resources.
     """
-    cwd = os.getcwd()
-    static_dir = os.path.join( cwd, 'static' )
+    static_dir = os.path.join( galaxy_root, 'static' )
     # TODO: these should be copied from galaxy.ini
     # TODO: static_enabled needed here?
     return dict( static_enabled=True,

test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py

@@ -16,15 +16,11 @@ import tempfile
 import threading
 import time
 
-# Assume we are run from the galaxy root directory, add lib to the python path
-cwd = os.getcwd()
-sys.path.append( cwd )
-new_path = [ os.path.join( cwd, "scripts" ),
-             os.path.join( cwd, "lib" ),
-             os.path.join( cwd, 'test' ),
-             os.path.join( cwd, 'scripts', 'api' ) ]
-new_path.extend( sys.path )
-sys.path = new_path
+galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir, os.path.pardir))
+sys.path[1:1] = [ os.path.join( galaxy_root, "scripts" ),
+                  os.path.join( galaxy_root, "lib" ),
+                  os.path.join( galaxy_root, 'test' ),
+                  os.path.join( galaxy_root, 'scripts', 'api' ) ]
 
 from galaxy import eggs
 eggs.require( "nose" )
@@ -48,7 +44,7 @@ from galaxy.web import buildapp
 log = logging.getLogger( 'install_and_test_repositories_with_tools' )
 
 assert sys.version_info[ :2 ] >= ( 2, 6 )
-test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories', 'repositories_with_tools' )
+test_home_directory = os.path.join( galaxy_root, 'test', 'install_and_test_tool_shed_repositories', 'repositories_with_tools' )
 
 # Here's the directory where everything happens.  Temporary directories are created within this directory to contain
 # the database, new repositories, etc.

test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py

@@ -15,15 +15,11 @@ import tempfile
 import threading
 import time
 
-# Assume we are run from the galaxy root directory, add lib to the python path
-cwd = os.getcwd()
-sys.path.append( cwd )
-new_path = [ os.path.join( cwd, "scripts" ),
-             os.path.join( cwd, "lib" ),
-             os.path.join( cwd, 'test' ),
-             os.path.join( cwd, 'scripts', 'api' ) ]
-new_path.extend( sys.path )
-sys.path = new_path
+galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir, os.path.pardir))
+sys.path[1:1] = [ os.path.join( galaxy_root, "scripts" ),
+                  os.path.join( galaxy_root, "lib" ),
+                  os.path.join( galaxy_root, 'test' ),
+                  os.path.join( galaxy_root, 'scripts', 'api' ) ]
 
 from galaxy import eggs
 eggs.require( "Paste" )
@@ -43,7 +39,7 @@ from galaxy.web import buildapp
 log = logging.getLogger( 'install_and_test_tool_dependency_definitions' )
 
 assert sys.version_info[ :2 ] >= ( 2, 6 )
-test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories', 'tool_dependency_definitions' )
+test_home_directory = os.path.join( galaxy_root, 'test', 'install_and_test_tool_shed_repositories', 'tool_dependency_definitions' )
 
 # Here's the directory where everything happens.  Temporary directories are created within this directory to contain
 # the database, new repositories, etc.

test/manual/workflows_scaling.py

@@ -6,20 +6,14 @@ import sys
 from threading import Thread
 from uuid import uuid4
 
-script_dir = os.path.dirname(__file__)
-galaxy_root = os.path.join(script_dir, os.path.pardir, os.path.pardir)
-new_path = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ]
-new_path.extend( sys.path[1:] )
-sys.path = new_path
+galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir))
+sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ]
 
 try:
     from argparse import ArgumentParser
 except ImportError:
     ArgumentParser = None
 
-from api import yaml_to_workflow
-from api import helpers
-
 try:
     from galaxy import eggs
     eggs.require("requests")
@@ -29,6 +23,8 @@ except ImportError:
 import requests
 from bioblend import galaxy
 
+from api import helpers, yaml_to_workflow
+
 LONG_TIMEOUT = 1000000000
 DESCRIPTION = "Script to exercise the workflow engine."
 

test/tool_shed/functional_tests.py

@@ -14,21 +14,18 @@ import threading
 import time
 import urllib
 
-# Assume we are run from the galaxy root directory, add lib to the python path
-cwd = os.getcwd()
-tool_shed_home_directory = os.path.join( cwd, 'test', 'tool_shed' )
+galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir))
+tool_shed_home_directory = os.path.join( galaxy_root, 'test', 'tool_shed' )
 default_tool_shed_test_file_dir = os.path.join( tool_shed_home_directory, 'test_data' )
 # Here's the directory where everything happens.  Temporary directories are created within this directory to contain
 # the hgweb.config file, the database, new repositories, etc.  Since the tool shed browses repository contents via HTTP,
 # the full path to the temporary directroy wher eht repositories are located cannot contain invalid url characters.
 tool_shed_test_tmp_dir = os.path.join( tool_shed_home_directory, 'tmp' )
 os.environ[ 'TOOL_SHED_TEST_TMP_DIR' ] = tool_shed_test_tmp_dir
-new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, "test" ) ]
-new_path.extend( sys.path[1:] )
-sys.path = new_path
+# Need to remove this directory from sys.path
+sys.path[0:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ]
 
 from galaxy import eggs
-
 eggs.require( "nose" )
 eggs.require( "NoseHTML" )
 eggs.require( "NoseTestDiff" )
@@ -53,8 +50,8 @@ from galaxy.app import UniverseApplication as GalaxyUniverseApplication
 from galaxy.util import asbool
 from galaxy.web import buildapp as galaxybuildapp
 
-from functional import database_contexts
 from base import nose_util
+from functional import database_contexts
 
 log = logging.getLogger( "tool_shed_functional_tests.py" )
 
@@ -82,8 +79,7 @@ def get_static_settings():
     This mainly consists of the filesystem locations of url-mapped
     static resources.
     """
-    cwd = os.getcwd()
-    static_dir = os.path.join( cwd, 'static' )
+    static_dir = os.path.join( galaxy_root, 'static' )
     # TODO: these should be copied from galaxy.ini
     return dict(
         # TODO: static_enabled needed here?
@@ -426,10 +422,6 @@ def main():
         else:
             raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" )
         log.info( "Embedded galaxy web server started" )
-    # We don't add the tests to the path until everything is up and running
-    new_path = [ os.path.join( cwd, 'test' ) ]
-    new_path.extend( sys.path[1:] )
-    sys.path = new_path
     # ---- Find tests ---------------------------------------------------------
     if tool_shed_test_proxy_port:
         log.info( "Functional tests will be run against %s:%s" % ( tool_shed_test_host, tool_shed_test_proxy_port ) )

test/unit/unittest_utils/utility.py

@@ -14,12 +14,12 @@ else:
 
 # =============================================================================
 def get_unittest_utils_path():
-    return os.path.normpath( os.path.join( os.getcwd(), os.path.dirname( __file__ ) ) )
+    return os.path.abspath( os.path.dirname( __file__ ) )
 
 
 def get_galaxy_root():
     # precondition: this file must be at <GALAXY_ROOT>/test/unit/unittest_utils/utility.py
-    return os.path.normpath( os.path.join( get_unittest_utils_path(), '../../../' ) )
+    return os.path.normpath( os.path.join( get_unittest_utils_path(), os.pardir, os.pardir, os.pardir ) )
 
 
 def get_galaxy_libpath():
@@ -42,8 +42,7 @@ def clean_multiline_string( multiline_string, sep='\n' ):
 
 
 # =============================================================================
-sys.path.insert( 0, get_galaxy_libpath() )
-sys.path.insert( 1, get_unittest_utils_path() )
+sys.path[1:1] = [ get_galaxy_libpath(), get_unittest_utils_path() ]
 
 
 __all__ = [