From 58e9b20965e0f4d88c216f56866a2048071713bb Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 12 Feb 2015 07:57:51 -0500
Subject: [PATCH 1/3] Fix at least one error with zipfile downloads and file
 permissions not being set correctly.

---
 lib/galaxy/eggs/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/eggs/__init__.py b/lib/galaxy/eggs/__init__.py
index 1938009bf99..d4ed05cbb21 100644
--- a/lib/galaxy/eggs/__init__.py
+++ b/lib/galaxy/eggs/__init__.py
@@ -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

From dce9c1a5218fc3deb1a54b4521206bbf977af4ab Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 12 Feb 2015 08:28:37 -0500
Subject: [PATCH 2/3] Fix path manipulation during fetch_eggs.  This getting an
 external version of pkg_resources (and not ours in lib/) is what is causing
 the weird egg fetching errors.  Newer versions of pkg_resources create a
 mangled distribution string for some eggs with nonstandard version
 identifiers.

---
 scripts/fetch_eggs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/fetch_eggs.py b/scripts/fetch_eggs.py
index f96596f6ee7..20f9c8dfcd2 100755
--- a/scripts/fetch_eggs.py
+++ b/scripts/fetch_eggs.py
@@ -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

From 3961d4834fe5c83fd27be176f94dbc6ec95dda9c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 12 Feb 2015 10:34:51 -0500
Subject: [PATCH 3/3] Fix path insertion vs appending of <galaxy>/lib for all
 scripts.

---
 scripts/check_eggs.py                            | 2 +-
 scripts/check_galaxy.py                          | 2 +-
 scripts/dist-scramble.py                         | 2 +-
 scripts/get_platforms.py                         | 2 +-
 scripts/helper.py                                | 2 +-
 scripts/make_egg_packager.py                     | 2 +-
 scripts/scramble.py                              | 2 +-
 scripts/scramble/scripts/DRMAA_python-macosx.py  | 2 +-
 scripts/scramble/scripts/DRMAA_python-solaris.py | 2 +-
 scripts/scramble/scripts/DRMAA_python.py         | 2 +-
 scripts/scramble/scripts/MySQL_python-solaris.py | 2 +-
 scripts/scramble/scripts/MySQL_python.py         | 2 +-
 scripts/scramble/scripts/PyRods.py               | 2 +-
 scripts/scramble/scripts/bx_python-solaris.py    | 2 +-
 scripts/scramble/scripts/generic.py              | 2 +-
 scripts/scramble/scripts/pbs_python.py           | 2 +-
 scripts/scramble/scripts/psycopg2-linux.py       | 2 +-
 scripts/scramble/scripts/psycopg2-macosx.py      | 2 +-
 scripts/scramble/scripts/psycopg2-solaris.py     | 2 +-
 scripts/scramble/scripts/psycopg2.py             | 2 +-
 scripts/scramble/scripts/pysam-solaris.py        | 2 +-
 scripts/scramble/scripts/pysqlite.py             | 2 +-
 scripts/set_dataset_sizes.py                     | 2 +-
 scripts/set_user_disk_usage.py                   | 2 +-
 24 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/scripts/check_eggs.py b/scripts/check_eggs.py
index e3717069cd4..7655eb964cb 100644
--- a/scripts/check_eggs.py
+++ b/scripts/check_eggs.py
@@ -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
 
diff --git a/scripts/check_galaxy.py b/scripts/check_galaxy.py
index e2ce1001aa3..81f50fcf1fd 100755
--- a/scripts/check_galaxy.py
+++ b/scripts/check_galaxy.py
@@ -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" )
diff --git a/scripts/dist-scramble.py b/scripts/dist-scramble.py
index b34301c0f08..04f396be393 100644
--- a/scripts/dist-scramble.py
+++ b/scripts/dist-scramble.py
@@ -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
diff --git a/scripts/get_platforms.py b/scripts/get_platforms.py
index 0035b01542f..b0d11d3c832 100755
--- a/scripts/get_platforms.py
+++ b/scripts/get_platforms.py
@@ -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
diff --git a/scripts/helper.py b/scripts/helper.py
index 13a66a332a9..dad65d6d63c 100644
--- a/scripts/helper.py
+++ b/scripts/helper.py
@@ -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
diff --git a/scripts/make_egg_packager.py b/scripts/make_egg_packager.py
index 9cafe9dc40e..e9d2352b7c7 100644
--- a/scripts/make_egg_packager.py
+++ b/scripts/make_egg_packager.py
@@ -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
diff --git a/scripts/scramble.py b/scripts/scramble.py
index c464b4fa381..ed97a5fe527 100644
--- a/scripts/scramble.py
+++ b/scripts/scramble.py
@@ -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
 
diff --git a/scripts/scramble/scripts/DRMAA_python-macosx.py b/scripts/scramble/scripts/DRMAA_python-macosx.py
index d48a2671a4a..18cc332aeaa 100644
--- a/scripts/scramble/scripts/DRMAA_python-macosx.py
+++ b/scripts/scramble/scripts/DRMAA_python-macosx.py
@@ -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
diff --git a/scripts/scramble/scripts/DRMAA_python-solaris.py b/scripts/scramble/scripts/DRMAA_python-solaris.py
index 2300e04c579..2eb3fbdad01 100644
--- a/scripts/scramble/scripts/DRMAA_python-solaris.py
+++ b/scripts/scramble/scripts/DRMAA_python-solaris.py
@@ -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
diff --git a/scripts/scramble/scripts/DRMAA_python.py b/scripts/scramble/scripts/DRMAA_python.py
index 09e7551ca96..4f2062e1451 100644
--- a/scripts/scramble/scripts/DRMAA_python.py
+++ b/scripts/scramble/scripts/DRMAA_python.py
@@ -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
diff --git a/scripts/scramble/scripts/MySQL_python-solaris.py b/scripts/scramble/scripts/MySQL_python-solaris.py
index 6f8eea8537d..8ef903e90ce 100644
--- a/scripts/scramble/scripts/MySQL_python-solaris.py
+++ b/scripts/scramble/scripts/MySQL_python-solaris.py
@@ -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()
diff --git a/scripts/scramble/scripts/MySQL_python.py b/scripts/scramble/scripts/MySQL_python.py
index bd8ba23852c..496689b3ba8 100644
--- a/scripts/scramble/scripts/MySQL_python.py
+++ b/scripts/scramble/scripts/MySQL_python.py
@@ -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()
diff --git a/scripts/scramble/scripts/PyRods.py b/scripts/scramble/scripts/PyRods.py
index 7553d8e6ea1..3314ad9542c 100644
--- a/scripts/scramble/scripts/PyRods.py
+++ b/scripts/scramble/scripts/PyRods.py
@@ -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
diff --git a/scripts/scramble/scripts/bx_python-solaris.py b/scripts/scramble/scripts/bx_python-solaris.py
index bdeea7976c7..35adfe4b32a 100644
--- a/scripts/scramble/scripts/bx_python-solaris.py
+++ b/scripts/scramble/scripts/bx_python-solaris.py
@@ -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
diff --git a/scripts/scramble/scripts/generic.py b/scripts/scramble/scripts/generic.py
index e40a8261a4f..ba929d636ad 100644
--- a/scripts/scramble/scripts/generic.py
+++ b/scripts/scramble/scripts/generic.py
@@ -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
diff --git a/scripts/scramble/scripts/pbs_python.py b/scripts/scramble/scripts/pbs_python.py
index 5d0d7f69de7..2264530a975 100644
--- a/scripts/scramble/scripts/pbs_python.py
+++ b/scripts/scramble/scripts/pbs_python.py
@@ -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
diff --git a/scripts/scramble/scripts/psycopg2-linux.py b/scripts/scramble/scripts/psycopg2-linux.py
index 9b798fe9c9a..7c91b1da99d 100644
--- a/scripts/scramble/scripts/psycopg2-linux.py
+++ b/scripts/scramble/scripts/psycopg2-linux.py
@@ -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()
diff --git a/scripts/scramble/scripts/psycopg2-macosx.py b/scripts/scramble/scripts/psycopg2-macosx.py
index c82466f1240..77dc699ddcb 100644
--- a/scripts/scramble/scripts/psycopg2-macosx.py
+++ b/scripts/scramble/scripts/psycopg2-macosx.py
@@ -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()
diff --git a/scripts/scramble/scripts/psycopg2-solaris.py b/scripts/scramble/scripts/psycopg2-solaris.py
index 7ef58971164..ff0050558eb 100644
--- a/scripts/scramble/scripts/psycopg2-solaris.py
+++ b/scripts/scramble/scripts/psycopg2-solaris.py
@@ -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()
diff --git a/scripts/scramble/scripts/psycopg2.py b/scripts/scramble/scripts/psycopg2.py
index f895d6bce19..bcaa2081f2c 100644
--- a/scripts/scramble/scripts/psycopg2.py
+++ b/scripts/scramble/scripts/psycopg2.py
@@ -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()
diff --git a/scripts/scramble/scripts/pysam-solaris.py b/scripts/scramble/scripts/pysam-solaris.py
index 25499f2b522..6b4d62c5470 100644
--- a/scripts/scramble/scripts/pysam-solaris.py
+++ b/scripts/scramble/scripts/pysam-solaris.py
@@ -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
diff --git a/scripts/scramble/scripts/pysqlite.py b/scripts/scramble/scripts/pysqlite.py
index c324e928913..4a6e277327d 100644
--- a/scripts/scramble/scripts/pysqlite.py
+++ b/scripts/scramble/scripts/pysqlite.py
@@ -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
diff --git a/scripts/set_dataset_sizes.py b/scripts/set_dataset_sizes.py
index d2d8390c576..8fc5cf18703 100644
--- a/scripts/set_dataset_sizes.py
+++ b/scripts/set_dataset_sizes.py
@@ -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
diff --git a/scripts/set_user_disk_usage.py b/scripts/set_user_disk_usage.py
index 97bd6858ac7..282ad589aa4 100755
--- a/scripts/set_user_disk_usage.py
+++ b/scripts/set_user_disk_usage.py
@@ -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