[galaxy-commits] commit/galaxy-central: 3 new changesets

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d09ea0b99ac8/ Changeset: d09ea0b99ac8 User: dannon Date: 2015-02-12 15:34:51+00:00 Summary: Fix path insertion vs appending of <galaxy>/lib for all scripts. Affected #: 24 files diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/check_eggs.py --- a/scripts/check_eggs.py +++ b/scripts/check_eggs.py @@ -37,7 +37,7 @@ config_arg = '-c %s' % config lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) -sys.path.append( lib ) +sys.path.insert( 1, lib ) from galaxy.eggs import Crate diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/check_galaxy.py --- a/scripts/check_galaxy.py +++ b/scripts/check_galaxy.py @@ -90,7 +90,7 @@ # find/import twill lib_dir = os.path.join( scripts_dir, "..", "lib" ) -sys.path.append( lib_dir ) +sys.path.insert( 1, lib_dir ) from galaxy import eggs import pkg_resources pkg_resources.require( "twill" ) diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/dist-scramble.py --- a/scripts/dist-scramble.py +++ b/scripts/dist-scramble.py @@ -44,7 +44,7 @@ root.addHandler( logging.StreamHandler( sys.stdout ) ) lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) -sys.path.append( lib ) +sys.path.insert( 1, lib ) from galaxy.eggs.dist import DistScrambleCrate, ScrambleFailure from galaxy.eggs import EggNotFetchable diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/get_platforms.py --- a/scripts/get_platforms.py +++ b/scripts/get_platforms.py @@ -5,7 +5,7 @@ assert sys.version_info[:2] >= ( 2, 4 ) lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) -sys.path.append( lib ) +sys.path.insert( 1, lib ) import galaxy import pkg_resources diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/helper.py --- a/scripts/helper.py +++ b/scripts/helper.py @@ -26,7 +26,7 @@ sys.exit( 1 ) options.config = os.path.abspath( options.config ) -sys.path.append( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) from galaxy import eggs import pkg_resources diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/make_egg_packager.py --- a/scripts/make_egg_packager.py +++ b/scripts/make_egg_packager.py @@ -17,7 +17,7 @@ root.addHandler( logging.StreamHandler( sys.stdout ) ) lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) -sys.path.append( lib ) +sys.path.insert( 1, lib ) from galaxy.eggs import Crate, EggNotFetchable, py import pkg_resources diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble.py --- a/scripts/scramble.py +++ b/scripts/scramble.py @@ -15,7 +15,7 @@ root.addHandler( logging.StreamHandler( sys.stdout ) ) lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) -sys.path.append( lib ) +sys.path.insert( 1, lib ) from galaxy.eggs.scramble import ScrambleCrate, ScrambleFailure, EggNotFetchable diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/DRMAA_python-macosx.py --- a/scripts/scramble/scripts/DRMAA_python-macosx.py +++ b/scripts/scramble/scripts/DRMAA_python-macosx.py @@ -10,7 +10,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * tag = get_tag() # get the tag diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/DRMAA_python-solaris.py --- a/scripts/scramble/scripts/DRMAA_python-solaris.py +++ b/scripts/scramble/scripts/DRMAA_python-solaris.py @@ -10,7 +10,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * tag = get_tag() # get the tag diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/DRMAA_python.py --- a/scripts/scramble/scripts/DRMAA_python.py +++ b/scripts/scramble/scripts/DRMAA_python.py @@ -10,7 +10,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * tag = get_tag() # get the tag diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/MySQL_python-solaris.py --- a/scripts/scramble/scripts/MySQL_python-solaris.py +++ b/scripts/scramble/scripts/MySQL_python-solaris.py @@ -50,7 +50,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools - sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) + sys.path.insert( 1, os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) from scramble_lib import * tag = get_tag() diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/MySQL_python.py --- a/scripts/scramble/scripts/MySQL_python.py +++ b/scripts/scramble/scripts/MySQL_python.py @@ -47,7 +47,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools - sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) + sys.path.insert( 1, os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) from scramble_lib import * tag = get_tag() diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/PyRods.py --- a/scripts/scramble/scripts/PyRods.py +++ b/scripts/scramble/scripts/PyRods.py @@ -6,7 +6,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * tag = get_tag() # get the tag diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/bx_python-solaris.py --- a/scripts/scramble/scripts/bx_python-solaris.py +++ b/scripts/scramble/scripts/bx_python-solaris.py @@ -5,7 +5,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * tag = get_tag() # get the tag diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/generic.py --- a/scripts/scramble/scripts/generic.py +++ b/scripts/scramble/scripts/generic.py @@ -5,7 +5,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * tag = get_tag() # get the tag diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/pbs_python.py --- a/scripts/scramble/scripts/pbs_python.py +++ b/scripts/scramble/scripts/pbs_python.py @@ -10,7 +10,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * tag = get_tag() # get the tag diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/psycopg2-linux.py --- a/scripts/scramble/scripts/psycopg2-linux.py +++ b/scripts/scramble/scripts/psycopg2-linux.py @@ -44,7 +44,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools - sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) + sys.path.insert( 1, os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) from scramble_lib import * tag = get_tag() diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/psycopg2-macosx.py --- a/scripts/scramble/scripts/psycopg2-macosx.py +++ b/scripts/scramble/scripts/psycopg2-macosx.py @@ -50,7 +50,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools - sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) + sys.path.insert( 1, os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) from scramble_lib import * tag = get_tag() diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/psycopg2-solaris.py --- a/scripts/scramble/scripts/psycopg2-solaris.py +++ b/scripts/scramble/scripts/psycopg2-solaris.py @@ -47,7 +47,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools - sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) + sys.path.insert( 1, os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) from scramble_lib import * tag = get_tag() diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/psycopg2.py --- a/scripts/scramble/scripts/psycopg2.py +++ b/scripts/scramble/scripts/psycopg2.py @@ -44,7 +44,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools - sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) + sys.path.insert( 1, os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) from scramble_lib import * tag = get_tag() diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/pysam-solaris.py --- a/scripts/scramble/scripts/pysam-solaris.py +++ b/scripts/scramble/scripts/pysam-solaris.py @@ -5,7 +5,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * tag = get_tag() # get the tag diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/scramble/scripts/pysqlite.py --- a/scripts/scramble/scripts/pysqlite.py +++ b/scripts/scramble/scripts/pysqlite.py @@ -10,7 +10,7 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +sys.path.insert( 1, os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * tag = get_tag() # get the tag diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/set_dataset_sizes.py --- a/scripts/set_dataset_sizes.py +++ b/scripts/set_dataset_sizes.py @@ -13,7 +13,7 @@ def init(): options.config = os.path.abspath( options.config ) - sys.path.append( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) + sys.path.insert( 1, os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) from galaxy import eggs import pkg_resources diff -r a99aafec2a89d95795cf1296ddf43c9fd6a38c8e -r d09ea0b99ac884c7d452b007db91339a4864f606 scripts/set_user_disk_usage.py --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -21,7 +21,7 @@ if options.email == 'all': options.email = None - sys.path.append( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) + sys.path.insert( 1, os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) from galaxy import eggs import pkg_resources https://bitbucket.org/galaxy/galaxy-central/commits/a1a089bdd773/ Changeset: a1a089bdd773 User: dannon Date: 2015-02-12 15:36:10+00:00 Summary: Fix path insertion vs appending of <galaxy>/lib for galaxy/main.py. Affected #: 1 file diff -r d09ea0b99ac884c7d452b007db91339a4864f606 -r a1a089bdd77348340f6ba2c97c1a6e113cc18377 lib/galaxy/main.py --- a/lib/galaxy/main.py +++ b/lib/galaxy/main.py @@ -87,7 +87,7 @@ log.exception("Failed to chdir") raise try: - sys.path.append(GALAXY_LIB_DIR) + sys.path.insert(1, GALAXY_LIB_DIR) except Exception: log.exception("Failed to add Galaxy to sys.path") raise https://bitbucket.org/galaxy/galaxy-central/commits/2c6690a2faea/ Changeset: 2c6690a2faea User: dannon Date: 2015-02-12 15:37:44+00:00 Summary: Fix path insertion vs appending of <galaxy>/lib for unit tests. Affected #: 8 files diff -r a1a089bdd77348340f6ba2c97c1a6e113cc18377 -r 2c6690a2faea4882a688044ec269de5b15569f58 test/unit/managers/mock.py --- a/test/unit/managers/mock.py +++ b/test/unit/managers/mock.py @@ -5,7 +5,7 @@ import os __GALAXY_ROOT__ = os.getcwd() + '/../../../' -sys.path.append( __GALAXY_ROOT__ + 'lib' ) +sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' ) from galaxy import eggs eggs.require( 'SQLAlchemy >= 0.4' ) diff -r a1a089bdd77348340f6ba2c97c1a6e113cc18377 -r 2c6690a2faea4882a688044ec269de5b15569f58 test/unit/managers/test_CollectionManager.py --- a/test/unit/managers/test_CollectionManager.py +++ b/test/unit/managers/test_CollectionManager.py @@ -7,7 +7,7 @@ import unittest __GALAXY_ROOT__ = os.getcwd() + '/../../../' -sys.path.append( __GALAXY_ROOT__ + 'lib' ) +sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' ) from galaxy import eggs eggs.require( 'SQLAlchemy >= 0.4' ) diff -r a1a089bdd77348340f6ba2c97c1a6e113cc18377 -r 2c6690a2faea4882a688044ec269de5b15569f58 test/unit/managers/test_DatasetManager.py --- a/test/unit/managers/test_DatasetManager.py +++ b/test/unit/managers/test_DatasetManager.py @@ -7,7 +7,7 @@ import unittest __GALAXY_ROOT__ = os.getcwd() + '/../../../' -sys.path.append( __GALAXY_ROOT__ + 'lib' ) +sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' ) from galaxy import eggs eggs.require( 'SQLAlchemy >= 0.4' ) diff -r a1a089bdd77348340f6ba2c97c1a6e113cc18377 -r 2c6690a2faea4882a688044ec269de5b15569f58 test/unit/managers/test_HDAManager.py --- a/test/unit/managers/test_HDAManager.py +++ b/test/unit/managers/test_HDAManager.py @@ -4,7 +4,7 @@ import unittest __GALAXY_ROOT__ = os.getcwd() + '/../../../' -sys.path.append( __GALAXY_ROOT__ + 'lib' ) +sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' ) from galaxy import eggs eggs.require( 'SQLAlchemy >= 0.4' ) diff -r a1a089bdd77348340f6ba2c97c1a6e113cc18377 -r 2c6690a2faea4882a688044ec269de5b15569f58 test/unit/managers/test_HistoryManager.py --- a/test/unit/managers/test_HistoryManager.py +++ b/test/unit/managers/test_HistoryManager.py @@ -7,7 +7,7 @@ import unittest __GALAXY_ROOT__ = os.getcwd() + '/../../../' -sys.path.append( __GALAXY_ROOT__ + 'lib' ) +sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' ) from galaxy import eggs eggs.require( 'SQLAlchemy >= 0.4' ) diff -r a1a089bdd77348340f6ba2c97c1a6e113cc18377 -r 2c6690a2faea4882a688044ec269de5b15569f58 test/unit/managers/test_ModelManager.py --- a/test/unit/managers/test_ModelManager.py +++ b/test/unit/managers/test_ModelManager.py @@ -9,7 +9,7 @@ import unittest __GALAXY_ROOT__ = os.getcwd() + '/../../../' -sys.path.append( __GALAXY_ROOT__ + 'lib' ) +sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' ) from galaxy import eggs eggs.require( 'SQLAlchemy >= 0.4' ) diff -r a1a089bdd77348340f6ba2c97c1a6e113cc18377 -r 2c6690a2faea4882a688044ec269de5b15569f58 test/unit/managers/test_UserManager.py --- a/test/unit/managers/test_UserManager.py +++ b/test/unit/managers/test_UserManager.py @@ -7,7 +7,7 @@ import unittest __GALAXY_ROOT__ = os.getcwd() + '/../../../' -sys.path.append( __GALAXY_ROOT__ + 'lib' ) +sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' ) from galaxy import eggs eggs.require( 'SQLAlchemy >= 0.4' ) diff -r a1a089bdd77348340f6ba2c97c1a6e113cc18377 -r 2c6690a2faea4882a688044ec269de5b15569f58 test/unit/util/utility.py --- a/test/unit/util/utility.py +++ b/test/unit/util/utility.py @@ -29,7 +29,7 @@ utility.add_galaxy_lib_to_path( '/test/unit/datatypes/dataproviders' ) """ glx_lib = os.path.join( os.getcwd().replace( this_dir_relative_to_root, '' ), 'lib' ) - sys.path.append( glx_lib ) + sys.path.insert( 1, glx_lib ) def clean_multiline_string( multiline_string, sep='\n' ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.