From 7142248e04ee5046e34ced0fbb8333bf1da191fd Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 20 Apr 2012 21:45:30 -0400
Subject: [PATCH] More fixes for setting tool shed repsoitory metadata.

---
 lib/galaxy/util/shed_util.py                        | 13 +++++++++----
 lib/galaxy/webapps/community/controllers/common.py  | 13 +++++++++----
 .../webapps/community/controllers/repository.py     |  3 ++-
 3 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/util/shed_util.py b/lib/galaxy/util/shed_util.py
index 4d736fa606a..17e87876e3c 100644
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -411,10 +411,15 @@ def generate_metadata( toolbox, relative_install_dir, repository_clone_url ):
                     full_path = os.path.abspath( os.path.join( root, name ) )
                     if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ]
                              or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ):
-                        # Make sure we're looking at a tool config and not a display application config or something else.
-                        element_tree = util.parse_xml( full_path )
-                        element_tree_root = element_tree.getroot()
-                        if element_tree_root.tag == 'tool':
+                        try:
+                            # Make sure we're looking at a tool config and not a display application config or something else.
+                            element_tree = util.parse_xml( full_path )
+                            element_tree_root = element_tree.getroot()
+                            is_tool = element_tree_root.tag == 'tool'
+                        except Exception, e:
+                            log.debug( "Error parsing %s, exception: %s" % ( full_path, str( e ) ) )
+                            is_tool = False
+                        if is_tool:
                             try:
                                 tool = toolbox.load_tool( full_path )
                             except Exception, e:
diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index af936e4afc3..299a4adefcb 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -323,10 +323,15 @@ def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, re
                     full_path = os.path.abspath( os.path.join( root, name ) )
                     if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ]
                              or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ):
-                        # Make sure we're looking at a tool config and not a display application config or something else.
-                        element_tree = util.parse_xml( full_path )
-                        element_tree_root = element_tree.getroot()
-                        if element_tree_root.tag == 'tool':
+                        try:
+                            # Make sure we're looking at a tool config and not a display application config or something else.
+                            element_tree = util.parse_xml( full_path )
+                            element_tree_root = element_tree.getroot()
+                            is_tool = element_tree_root.tag == 'tool'
+                        except Exception, e:
+                            log.debug( "Error parsing %s, exception: %s" % ( full_path, str( e ) ) )
+                            is_tool = False
+                        if is_tool:
                             try:
                                 tool = load_tool( trans, full_path )
                                 valid = True
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 650b311dbd7..d4960bfbce9 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -924,7 +924,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                     element_tree = util.parse_xml( tmp_filename )
                                     element_tree_root = element_tree.getroot()
                                     is_tool = element_tree_root.tag == 'tool'
-                                except:
+                                except Exception, e:
+                                    log.debug( "Error parsing %s, exception: %s" % ( tmp_filename, str( e ) ) )
                                     is_tool = False
                                 if is_tool:
                                     try: