[galaxy-commits] commit/galaxy-central: natefoo: Merged in dannon/galaxy-central/stable (pull request #668)

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a6e9a1d72674/ Changeset: a6e9a1d72674 Branch: stable User: natefoo Date: 2015-02-12 18:20:29+00:00 Summary: Merged in dannon/galaxy-central/stable (pull request #668) [STABLE] Egg-fetching related bugfixes grafted from default. Affected #: 26 files diff -r 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -421,7 +421,7 @@ try: for info in z.infolist(): name = info.filename - perm = (info.external_attr >> 16L) & 0777 + mode = (info.external_attr >> 16L) & 0777 # don't extract absolute paths or ones with .. in them if name.startswith('/') or '..' in name: continue diff -r 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 scripts/fetch_eggs.py --- a/scripts/fetch_eggs.py +++ b/scripts/fetch_eggs.py @@ -32,7 +32,7 @@ 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 import pkg_resources diff -r 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 71054665755b0b6c6348aedb56222b954fea3e7b -r a6e9a1d7267410f697f30102ed78317b08274026 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 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.