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

13 Feb 2015

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