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More fixes for setting tool shed repsoitory metadata.

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This commit is contained in:
Greg Von Kuster
2012-04-20 21:45:30 -04:00
parent c30aae2342
commit 7142248e04
3 changed files with 20 additions and 9 deletions
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lib/galaxy/util/shed_util.py
+9 -4
View File
@@ -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:
lib/galaxy/webapps/community/controllers/common.py
+9 -4
View File
@@ -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
lib/galaxy/webapps/community/controllers/repository.py
+2 -1
View File
@@ -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: