details: http://www.bx.psu.edu/hg/galaxy/rev/bffe6becd372 changeset: 1624:bffe6becd372 user: guru date: Tue Nov 11 15:20:36 2008 -0500 description: Script to fetch gops jobs that might have produced incorrect/empty oUtput due to the bug in BitsetSafeReaderWrapper. 2 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py scripts/others/incorrect_gops_jobs.sh diffs (92 lines): diff -r 41a4d178466d -r bffe6becd372 scripts/others/incorrect_gops_jobs.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/others/incorrect_gops_jobs.py Tue Nov 11 15:20:36 2008 -0500 @@ -0,0 +1,80 @@ +#!/usr/bin/env python +""" +Fetch jobs using gops_intersect, gops_merge, gops_subtract, gops_complement, gops_coverage wherein the second dataset doesn't have chr, start and end in standard columns 1,2 and 3. +""" + +from galaxy import eggs +import sys, os, ConfigParser +import galaxy.app +#from galaxy.util.bunch import Bunch + +import galaxy.model.mapping +import pkg_resources + +pkg_resources.require( "SQLAlchemy >= 0.4" ) +import sqlalchemy as sa +#from sqlalchemy.orm import * + +assert sys.version_info[:2] >= ( 2, 4 ) + +class TestApplication( object ): + """Encapsulates the state of a Universe application""" + def __init__( self, database_connection=None, file_path=None ): + print >> sys.stderr, "python path is: " + ", ".join( sys.path ) + if database_connection is None: + raise Exception( "CleanupDatasetsApplication requires a database_connection value" ) + if file_path is None: + raise Exception( "CleanupDatasetsApplication requires a file_path value" ) + self.database_connection = database_connection + self.file_path = file_path + # Setup the database engine and ORM + self.model = galaxy.model.mapping.init( self.file_path, self.database_connection, engine_options={}, create_tables=False ) + +def main(): + ini_file = sys.argv[1] + conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} ) + conf_parser.read( ini_file ) + configuration = {} + for key, value in conf_parser.items( "app:main" ): + configuration[key] = value + database_connection = configuration['database_connection'] + file_path = configuration['file_path'] + app = TestApplication( database_connection=database_connection, file_path=file_path ) + jobs = {} + for job in app.model.Job.filter( + sa.and_( + app.model.Job.table.c.create_time.between('2008-05-23','2008-11-29'), + app.model.Job.table.c.state == 'ok', + sa.or_(app.model.Job.table.c.tool_id == 'gops_intersect_1', + app.model.Job.table.c.tool_id == 'gops_subtract_1', + app.model.Job.table.c.tool_id == 'gops_merge_1', + app.model.Job.table.c.tool_id == 'gops_coverage_1', + app.model.Job.table.c.tool_id == 'gops_complement_1', + ), + sa.not_(app.model.Job.table.c.command_line.like('%-2 1,2,3%')) + )).all(): + for od in job.output_datasets: + ds = app.model.Dataset.get(od.dataset_id) + if not ds.deleted: + hda = app.model.HistoryDatasetAssociation.filter(app.model.HistoryDatasetAssociation.table.c.dataset_id == ds.id)[0] + hist = app.model.History.get(hda.history_id) + if hist.user_id: + user = app.model.User.get(hist.user_id) + jobs[job.id] = {} + jobs[job.id]['dataset_id'] = ds.id + jobs[job.id]['dataset_create_time'] = ds.create_time + jobs[job.id]['dataset_name'] = hda.name + jobs[job.id]['hda_id'] = hda.id + jobs[job.id]['hist_id'] = hist.id + jobs[job.id]['hist_name'] = hist.name + jobs[job.id]['hist_modified_time'] = hist.update_time + jobs[job.id]['user_email'] = user.email + + print "Number of Incorrect Jobs: %d\n"%(len(jobs)) + print "#job_id\tdataset_id\tdataset_create_time\thda_id\thistory_id\thistory_name\thistory_modified_time\tuser_email" + for jid in jobs: + print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" %(jid,jobs[jid]['dataset_id'],jobs[jid]['dataset_create_time'],jobs[jid]['dataset_name'],jobs[jid]['hda_id'],jobs[jid]['hist_id'],jobs[jid]['hist_name'],jobs[jid]['hist_modified_time'],jobs[jid]['user_email'] ) + sys.exit(0) + +if __name__ == "__main__": + main() diff -r 41a4d178466d -r bffe6becd372 scripts/others/incorrect_gops_jobs.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/others/incorrect_gops_jobs.sh Tue Nov 11 15:20:36 2008 -0500 @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/others/incorrect_gops_jobs.py ./universe_wsgi.ini