1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/d8009117d5a0/ changeset: d8009117d5a0 user: inithello date: 2013-03-12 16:29:12 summary: Automated script to mark repositories as deprecated if no metadata records are associated with the repository, and the repository is older than the specified cutoff date. affected #: 1 file

diff -r 2c56c1e49f288ed53234f485c0f19606d013dd1b -r d8009117d5a0af02767c27162a2d5bd3befb9b5d lib/tool_shed/scripts/deprecate_repositories_without_metadata.py --- /dev/null +++ b/lib/tool_shed/scripts/deprecate_repositories_without_metadata.py @@ -0,0 +1,169 @@ +#!/usr/bin/env python + +import os, sys, logging, string, textwrap + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +log = logging.getLogger() +log.setLevel( 10 ) +log.addHandler( logging.StreamHandler( sys.stdout ) ) + +from galaxy import eggs +import pkg_resources +pkg_resources.require( "SQLAlchemy >= 0.4" ) + +import time, ConfigParser, shutil +from datetime import datetime, timedelta +from time import strftime +from optparse import OptionParser + +from galaxy.tools import parameters +from tool_shed.util.shed_util_common import url_join +import galaxy.webapps.tool_shed.config as tool_shed_config +import galaxy.webapps.tool_shed.model.mapping +import sqlalchemy as sa +from galaxy.model.orm import and_, not_, distinct +from galaxy.util import send_mail as galaxy_send_mail + +assert sys.version_info[:2] >= ( 2, 4 ) + +def build_citable_url( host, repository ): + return url_join( host, 'view', repository.user.username, repository.name ) + +def main(): + ''' + Script to deprecate any repositories that are older than n days, and have been empty since creation. + ''' + parser = OptionParser() + parser.add_option( "-d", "--days", dest="days", action="store", type="int", help="number of days (14)", default=14 ) + parser.add_option( "-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False ) + parser.add_option( "-v", "--verbose", action="store_true", dest="verbose", help="verbose mode, print the name of each repository", default=False ) + ( options, args ) = parser.parse_args() + ini_file = args[0] + config_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} ) + config_parser.read( ini_file ) + config_dict = {} + for key, value in config_parser.items( "app:main" ): + config_dict[key] = value + config = tool_shed_config.Configuration( **config_dict ) + + app = DeprecateRepositoriesApplication( config ) + cutoff_time = datetime.utcnow() - timedelta( days=options.days ) + now = strftime( "%Y-%m-%d %H:%M:%S" ) + print "\n####################################################################################" + print "# %s - Handling stuff older than %i days" % ( now, options.days ) + + if options.info_only: + print "# Displaying info only ( --info_only )" + + deprecate_repositories( app, cutoff_time, days=options.days, info_only=options.info_only, verbose=options.verbose ) + +def send_mail_to_owner( app, name, owner, email, repositories_deprecated, days=14 ): + ''' + Sends an email to the owner of the provided repository. + ''' + smtp_server = app.config.get( 'smtp_server', None ) + from_address = app.config.get( 'email_from', None ) + # Since there is no way to programmatically determine the URL for the tool shed from the .ini file, this method requires that + # an environment variable named TOOL_SHED_CANONICAL_URL be set, pointing to the tool shed that is being checked. + url = os.environ.get( 'TOOL_SHED_CANONICAL_URL', None ) + if None in [ smtp_server, from_address ]: + print '# Mail not configured, not sending email to repository owner.' + return + elif url is None: + print '# Environment variable TOOL_SHED_CANONICAL_URL not set, not sending email to repository owner.' + return + subject = "Regarding your tool shed repositories at %s" % url + message_body_template = 'The tool shed automated repository checker has discovered that one or more of your repositories hosted ' + \ + 'at this tool shed url ${url} have remained empty for over ${days} days, so they have been marked as deprecated. If you have plans ' + \ + 'for these repositories, you can mark them as un-deprecated at any time.' + message_template = string.Template( message_body_template ) + body = '\n'.join( textwrap.wrap( message_template.safe_substitute( days=days, url=url ), width=95 ) ) + body += '\n\n' + body += 'Repositories that were deprecated:\n' + body += '\n'.join( [ build_citable_url( url, repository ) for repository in repositories_deprecated ] ) + try: + galaxy_send_mail( from_address, repository.user.email, subject, body, app.config ) + print "# An email has been sent to %s, the owner of %s." % ( repository.user.username, ', '.join( [ repository.name for repository in repositories_deprecated ] ) ) + return True + except Exception, e: + print "# An error occurred attempting to send email: %s" % str( e ) + return False + +def deprecate_repositories( app, cutoff_time, days=14, info_only=False, verbose=False ): + # This method will get a list of repositories that were created on or before cutoff_time, but have never + # had any metadata records associated with them. Then it will iterate through that list and deprecate the + # repositories, sending an email to each repository owner. + dataset_count = 0 + disk_space = 0 + start = time.time() + repository_ids_to_not_check = [] + # Get a unique list of repository ids from the repository_metadata table. Any repository ID found in this table is not + # empty, and will not be checked. + metadata_records = sa.select( [ distinct( app.model.RepositoryMetadata.table.c.repository_id ) ], + from_obj=app.model.RepositoryMetadata.table ) \ + .execute() + for metadata_record in metadata_records: + repository_ids_to_not_check.append( metadata_record.repository_id ) + # Get the repositories that are A) not present in the above list, and b) older than the specified time. + # This will yield a list of repositories that have been created more than n days ago, but never populated. + repository_query = sa.select( [ app.model.Repository.table.c.id ], + whereclause = and_( app.model.Repository.table.c.create_time < cutoff_time, + app.model.Repository.table.c.deprecated == False, + app.model.Repository.table.c.deleted == False, + not_( app.model.Repository.table.c.id.in_( repository_ids_to_not_check ) ) ), + from_obj = [ app.model.Repository.table ] ) + query_result = repository_query.execute() + repositories = [] + repositories_by_owner = {} + repository_ids = [ row.id for row in query_result ] + # Iterate through the list of repository ids for empty repositories and deprecate them unless info_only is set. + for repository_id in repository_ids: + repository = app.sa_session.query( app.model.Repository ) \ + .filter( app.model.Repository.table.c.id == repository_id ) \ + .one() + owner = repository.user + if info_only: + print '# Repository %s owned by %s would have been deprecated, but info_only was set.' % ( repository.name, repository.user.username ) + else: + if verbose: + print '# Deprecating repository %s owned by %s.' % ( repository.name, owner.username ) + if owner.username not in repositories_by_owner: + repositories_by_owner[ owner.username ] = dict( owner=owner, repositories=[] ) + repositories_by_owner[ owner.username ][ 'repositories' ].append( repository ) + repositories.append( repository ) + # Send an email to each repository owner, listing the repositories that were deprecated. + for repository_owner in repositories_by_owner: + for repository in repositories_by_owner[ repository_owner ][ 'repositories' ]: + repository.deprecated = True + app.sa_session.add( repository ) + app.sa_session.flush() + owner = repositories_by_owner[ repository_owner ][ 'owner' ] + send_mail_to_owner( app, repository.name, owner.username, owner.email, repositories_by_owner[ repository_owner ][ 'repositories' ], days ) + stop = time.time() + print '# Deprecated %d repositories.' % len( repositories ) + print "# Elapsed time: ", stop - start + print "####################################################################################" + +class DeprecateRepositoriesApplication( object ): + """Encapsulates the state of a Universe application""" + def __init__( self, config ): + if config.database_connection is False: + config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database + # Setup the database engine and ORM + self.model = galaxy.webapps.tool_shed.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False ) + self.config = config + @property + def sa_session( self ): + """ + Returns a SQLAlchemy session -- currently just gets the current + session from the threadlocal session context, but this is provided + to allow migration toward a more SQLAlchemy 0.4 style of use. + """ + return self.model.context.current + def shutdown( self ): + pass + +if __name__ == "__main__": main()

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

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