1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/d0ac928b3c1d/ Changeset: d0ac928b3c1d User: Dave Bouvier Date: 2013-11-19 22:37:11 Summary: Script to check the contents of an S3 bucket for tool dependency installation paths that have no contents, or that contain only the installation log. Optionally delete any found paths. Affected #: 1 file

diff -r 5b91b8e9e71b037478dd76b105f34a775b7279dc -r d0ac928b3c1d529e32793a0fc27710e4a1585346 lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py --- /dev/null +++ b/lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py @@ -0,0 +1,155 @@ +import argparse +import os +import sys + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +from galaxy.util import asbool +from galaxy import eggs +eggs.require( 'boto' ) + +import boto + +from tool_shed.galaxy_install.tool_dependencies.fabric_util import INSTALLATION_LOG + + +class BucketList( object ): + + def __init__( self, amazon_id, amazon_secret, bucket ): + # Connect to S3 using the provided Amazon access key and secret identifier. + self.s3 = boto.connect_s3( amazon_id, amazon_secret ) + self.bucket_name = bucket + # Connect to S3 using the received bucket name. + self.bucket = boto.s3.bucket.Bucket( self.s3, bucket ) + self.install_dirs = self.get_tool_dependency_install_paths() + self.empty_installation_paths = self.check_for_empty_tool_dependency_installation_paths() + + def display_empty_installation_paths( self ): + for empty_installation_path in self.empty_installation_paths: + print empty_installation_path + + def delete_empty_installation_paths( self ): + print 'Deleting empty installation paths.' + for empty_installation_path in self.empty_installation_paths: + # Get all keys in the S3 bucket that start with the installation path, and delete each one. + for path_to_delete in self.bucket.list( prefix=empty_installation_path ): + self.bucket.delete_key( path_to_delete.key ) + print 'Deleted empty path %s' % str( empty_installation_path ) + + def get_tool_dependency_install_paths( self ): + found_paths = [] + for item in self.bucket.list(): + name = str( item.name ) + # Skip environment_settings and __virtualenv_src, since these directories do not contain package tool dependencies. + if name.startswith( 'environment_settings' ) or name.startswith( '__virtualenv_src' ): + continue + paths = name.rstrip('/').split( '/' ) + # Paths are in the format name/version/owner/repository/changeset_revision. If the changeset revision is + # present, we need to check the contents of that path. If not, then the tool dependency was completely + # uninstalled. + if len( paths ) >= 5: + td_install_dir = '/'.join( paths[ :5 ] ) + '/' + if td_install_dir not in found_paths: + found_paths.append( name ) + return found_paths + + def check_for_empty_tool_dependency_installation_paths( self ): + empty_directories = [] + for item in self.install_dirs: + # Get all entries under the path for this tool dependency. + contents = self.bucket.list( prefix=item ) + tool_dependency_path_contents = [] + # Find out if there are two or less items in the path. The first entry will be the installation path itself. + # If only one other item exists, and the full path ends with the installation log, this is an incorrectly installed + # tool dependency. + for item in contents: + tool_dependency_path_contents.append( item ) + # If there are more than two items in the path, we cannot safely assume that the dependency failed to + # install correctly. + if len( tool_dependency_path_contents ) > 2: + break + # If the root directory is the only entry in the path, we have an empty tool dependency installation path. + if len( tool_dependency_path_contents ) == 1: + empty_directories.append( tool_dependency_path_contents[ 0 ] ) + # Otherwise, if the only other entry is the installation log, we have an installation path that should be deleted. + # This would not be the case in a Galaxy instance, since the Galaxy admin will need to verify the contents of + # the installation path in order to determine which action should be taken. + elif len( tool_dependency_path_contents ) == 2 and tool_dependency_path_contents[1].name.endswith( INSTALLATION_LOG ): + empty_directories.append( tool_dependency_path_contents[ 0 ] ) + return [ item.name for item in empty_directories ] + +def main( args ): + ''' + Amazon credentials can be provided in one of three ways: + 1. By specifying them on the command line with the --id and --secret arguments. + 2. By specifying a path to a file that contains the credentials in the form ACCESS_KEY:SECRET_KEY + using the --s3passwd argument. + 3. By specifying the above path in the 's3passwd' environment variable. + Each listed option will override the ones below it, if present. + ''' + if None in [ args.id, args.secret ]: + if args.s3passwd is None: + args.s3passwd = os.environ.get( 's3passwd', None ) + if args.s3passwd is not None and os.path.exists( args.s3passwd ): + awsid, secret = file( args.s3passwd, 'r' ).read().rstrip( '\n' ).split( ':' ) + else: + print 'Amazon ID and secret not provided, and no s3passwd file found.' + return 1 + else: + awsid = args.id + secret = args.secret + dependency_cleaner = BucketList( awsid, secret, args.bucket ) + if len( dependency_cleaner.empty_installation_paths ) == 0: + print 'No empty installation paths found, exiting.' + return 0 + print 'The following %d tool dependency installation paths were found to be empty or contain only the file %s.' % \ + ( len( dependency_cleaner.empty_installation_paths ), INSTALLATION_LOG ) + if asbool( args.delete ): + dependency_cleaner.delete_empty_installation_paths() + else: + for empty_installation_path in dependency_cleaner.empty_installation_paths: + print empty_installation_path + return 0 + +if __name__ == '__main__': + description = 'Determine if there are any tool dependency installation paths that should be removed. Remove them if ' + description += 'the --delete command line argument is provided with a true value.' + parser = argparse.ArgumentParser( description=description ) + parser.add_argument( '--delete', + dest='delete', + required=True, + action='store', + default=False, + type=asbool, + help='Whether to delete empty folders or list them on exit.' ) + parser.add_argument( '--bucket', + dest='bucket', + required=True, + action='store', + metavar='name', + help='The S3 bucket where tool dependencies are installed.' ) + parser.add_argument( '--id', + dest='id', + required=False, + action='store', + default=None, + metavar='ACCESS_KEY', + help='The identifier for an amazon account that has read access to the bucket.' ) + parser.add_argument( '--secret', + dest='secret', + required=False, + action='store', + default=None, + metavar='SECRET_KEY', + help='The secret key for an amazon account that has upload/delete access to the bucket.' ) + parser.add_argument( '--s3passwd', + dest='s3passwd', + required=False, + action='store', + default=None, + metavar='path/file', + help='The path to a file containing Amazon access credentials, in the format KEY:SECRET.' ) + args = parser.parse_args() + sys.exit( main( args ) )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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