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Merged in dannon/galaxy-central/stable (pull request #668)

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[STABLE] Egg-fetching related bugfixes grafted from default.
This commit is contained in:
Nate Coraor
2015-02-12 13:20:29 -05:00
parent 082ff4d493 3961d4834f
commit 212b1f9cb9
26 changed files with 26 additions and 26 deletions
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lib/galaxy/eggs/__init__.py
+1 -1
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@@ -421,7 +421,7 @@ def unpack_zipfile( filename, extract_dir, ignores=[] ):
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
scripts/check_eggs.py
+1 -1
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@@ -37,7 +37,7 @@ if config_set:
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
scripts/check_galaxy.py
+1 -1
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@@ -90,7 +90,7 @@ except:
# 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" )
scripts/dist-scramble.py
+1 -1
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@@ -44,7 +44,7 @@ root.setLevel( 10 )
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
scripts/fetch_eggs.py
+1 -1
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@@ -32,7 +32,7 @@ root.setLevel( 10 )
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
scripts/get_platforms.py
+1 -1
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@@ -5,7 +5,7 @@ import os, sys
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
scripts/helper.py
+1 -1
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@@ -26,7 +26,7 @@ except:
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
scripts/make_egg_packager.py
+1 -1
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@@ -17,7 +17,7 @@ root.setLevel( 10 )
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
scripts/scramble.py
+1 -1
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@@ -15,7 +15,7 @@ root.setLevel( 10 )
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
scripts/scramble/scripts/DRMAA_python-macosx.py
+1 -1
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@@ -10,7 +10,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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
scripts/scramble/scripts/DRMAA_python-solaris.py
+1 -1
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@@ -10,7 +10,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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
scripts/scramble/scripts/DRMAA_python.py
+1 -1
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@@ -10,7 +10,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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
scripts/scramble/scripts/MySQL_python-solaris.py
+1 -1
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@@ -50,7 +50,7 @@ if __name__ == '__main__':
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()
scripts/scramble/scripts/MySQL_python.py
+1 -1
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@@ -47,7 +47,7 @@ if __name__ == '__main__':
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()
scripts/scramble/scripts/PyRods.py
+1 -1
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@@ -6,7 +6,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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
scripts/scramble/scripts/bx_python-solaris.py
+1 -1
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@@ -5,7 +5,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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
scripts/scramble/scripts/generic.py
+1 -1
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@@ -5,7 +5,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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
scripts/scramble/scripts/pbs_python.py
+1 -1
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@@ -10,7 +10,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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
scripts/scramble/scripts/psycopg2-linux.py
+1 -1
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@@ -44,7 +44,7 @@ if __name__ == '__main__':
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()
scripts/scramble/scripts/psycopg2-macosx.py
+1 -1
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@@ -50,7 +50,7 @@ if __name__ == '__main__':
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()
scripts/scramble/scripts/psycopg2-solaris.py
+1 -1
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@@ -47,7 +47,7 @@ if __name__ == '__main__':
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()
scripts/scramble/scripts/psycopg2.py
+1 -1
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@@ -44,7 +44,7 @@ if __name__ == '__main__':
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()
scripts/scramble/scripts/pysam-solaris.py
+1 -1
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@@ -5,7 +5,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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
scripts/scramble/scripts/pysqlite.py
+1 -1
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@@ -10,7 +10,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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
scripts/set_dataset_sizes.py
+1 -1
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@@ -13,7 +13,7 @@ parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config
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
scripts/set_user_disk_usage.py
+1 -1
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@@ -21,7 +21,7 @@ def init():
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