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Find and add tool help images to the tarball. Delete any temporary files that were generated.

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This commit is contained in:
Dave Bouvier
2014-08-29 15:21:30 -04:00
parent e14fad2db7
commit ffbf0c3963
1 changed files with 32 additions and 1 deletions
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lib/galaxy/tools/__init__.py
+32 -1
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@@ -738,7 +738,34 @@ class ToolBox( object, Dictifiable ):
else:
tool = self.tools_by_id[ tool_id ]
tarball_files = []
tool_tup = ( os.path.abspath( tool.config_file ), os.path.split( tool.config_file )[-1] )
temp_files = []
tool_xml = file( os.path.abspath( tool.config_file ), 'r' ).read()
# Retrieve tool help images and rewrite the tool's xml into a temporary file with the path
# modified to be relative to the repository root.
tool_help = tool.help._source
image_found = False
# Check each line of the rendered tool help for an image tag that points to a location under static/
for help_line in tool_help.split( '\n' ):
image_regex = re.compile( 'img alt="[^"]+" src="\${static_path}/([^"]+)"' )
matches = re.search( image_regex, help_line )
if matches is not None:
tool_help_image = matches.group(1)
tarball_path = tool_help_image
filesystem_path = os.path.abspath( os.path.join( trans.app.config.root, 'static', tool_help_image ) )
if os.path.exists( filesystem_path ):
tarball_files.append( ( filesystem_path, tarball_path ) )
image_found = True
tool_xml = tool_xml.replace( '${static_path}/%s' % tarball_path, tarball_path )
log.debug( tarball_files )
# If one or more tool help images were found, add the modified tool XML to the tarball instead of the original.
if image_found:
fd, new_tool_config = tempfile.mkstemp( suffix='.xml' )
os.close( fd )
file( new_tool_config, 'w' ).write( tool_xml )
tool_tup = ( os.path.abspath( new_tool_config ), os.path.split( tool.config_file )[-1] )
temp_files.append( os.path.abspath( new_tool_config ) )
else:
tool_tup = ( os.path.abspath( tool.config_file ), os.path.split( tool.config_file )[-1] )
tarball_files.append( tool_tup )
# TODO: This feels hacky.
tool_command = tool.command.split( ' ' )[0]
@@ -796,6 +823,7 @@ class ToolBox( object, Dictifiable ):
os.close( fd )
file( table_conf, 'w' ).write( table_definition )
tarball_files.append( ( table_conf, os.path.join( 'tool-data', 'tool_data_table_conf.xml.sample' ) ) )
temp_files.append( table_conf )
# Create the tarball.
fd, tarball_archive = tempfile.mkstemp( suffix='.tgz' )
os.close( fd )
@@ -804,6 +832,9 @@ class ToolBox( object, Dictifiable ):
for fspath, tarpath in tarball_files:
tarball.add( fspath, arcname=tarpath )
tarball.close()
# Delete any temporary files that were generated.
for temp_file in temp_files:
os.remove( temp_file )
return tarball_archive, True, None
return None, False, "An unknown error occurred."