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113 lines
6.3 KiB
Python
Executable File
113 lines
6.3 KiB
Python
Executable File
#!/usr/bin/env python
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"""
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Fetch jobs using gops_intersect, gops_merge, gops_subtract, gops_complement, gops_coverage
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wherein the second dataset doesn't have chr, start and end in standard columns 1, 2 and 3.
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"""
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import sys, os, ConfigParser, tempfile
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import galaxy.app
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import galaxy.model.mapping
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import sqlalchemy as sa
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assert sys.version_info[:2] >= ( 2, 4 )
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class TestApplication( object ):
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"""Encapsulates the state of a Universe application"""
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def __init__( self, database_connection=None, file_path=None ):
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print >> sys.stderr, "python path is: " + ", ".join( sys.path )
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if database_connection is None:
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raise Exception( "CleanupDatasetsApplication requires a database_connection value" )
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if file_path is None:
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raise Exception( "CleanupDatasetsApplication requires a file_path value" )
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self.database_connection = database_connection
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self.file_path = file_path
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# Setup the database engine and ORM
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self.model = galaxy.model.mapping.init( self.file_path, self.database_connection, engine_options={}, create_tables=False )
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def main():
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ini_file = sys.argv[1]
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conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} )
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conf_parser.read( ini_file )
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configuration = {}
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for key, value in conf_parser.items( "app:main" ):
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configuration[key] = value
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database_connection = configuration['database_connection']
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file_path = configuration['file_path']
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app = TestApplication( database_connection=database_connection, file_path=file_path )
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jobs = {}
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try:
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for job in app.model.Job.filter( sa.and_( app.model.Job.table.c.create_time.between( '2008-05-23', '2008-11-29' ),
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app.model.Job.table.c.state == 'ok',
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sa.or_(
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sa.and_( sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1',
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app.model.Job.table.c.tool_id == 'gops_subtract_1',
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app.model.Job.table.c.tool_id == 'gops_coverage_1',
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),
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sa.not_( app.model.Job.table.c.command_line.like( '%-2 1,2,3%' ) )
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),
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sa.and_( sa.or_( app.model.Job.table.c.tool_id == 'gops_complement_1',
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app.model.Job.table.c.tool_id == 'gops_merge_1',
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),
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sa.not_( app.model.Job.table.c.command_line.like( '%-1 1,2,3%' ) )
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)
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)
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)
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).all():
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print "# processing job id %s" % str( job.id )
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for jtoda in job.output_datasets:
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print "# --> processing JobToOutputDatasetAssociation id %s" % str( jtoda.id )
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hda = app.model.HistoryDatasetAssociation.get( jtoda.dataset_id )
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print "# ----> processing HistoryDatasetAssociation id %s" % str( hda.id )
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if not hda.deleted:
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# Probably don't need this check, since the job state should suffice, but...
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if hda.dataset.state == 'ok':
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history = app.model.History.get( hda.history_id )
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print "# ------> processing history id %s" % str( history.id )
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if history.user_id:
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cmd_line = str( job.command_line )
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new_output = tempfile.NamedTemporaryFile('w')
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if job.tool_id in ['gops_intersect_1','gops_subtract_1','gops_coverage_1']:
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new_cmd_line = " ".join(map(str,cmd_line.split()[:4])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[5:]))
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job_output = cmd_line.split()[4]
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else:
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new_cmd_line = " ".join(map(str,cmd_line.split()[:3])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[4:]))
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job_output = cmd_line.split()[3]
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try:
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os.system(new_cmd_line)
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except:
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pass
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diff_status = os.system('diff %s %s >> /dev/null' %(new_output.name, job_output))
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if diff_status == 0:
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continue
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print "# --------> Outputs differ"
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user = app.model.User.get( history.user_id )
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jobs[ job.id ] = {}
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jobs[ job.id ][ 'hda_id' ] = hda.id
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jobs[ job.id ][ 'hda_name' ] = hda.name
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jobs[ job.id ][ 'hda_info' ] = hda.info
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jobs[ job.id ][ 'history_id' ] = history.id
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jobs[ job.id ][ 'history_name' ] = history.name
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jobs[ job.id ][ 'history_update_time' ] = history.update_time
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jobs[ job.id ][ 'user_email' ] = user.email
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except Exception, e:
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print "# caught exception: %s" % str( e )
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print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) )
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print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email"
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for jid in jobs:
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print '%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' % \
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( str( jid ),
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str( jobs[ jid ][ 'hda_id' ] ),
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jobs[ jid ][ 'hda_name' ],
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jobs[ jid ][ 'hda_info' ],
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str( jobs[ jid ][ 'history_id' ] ),
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jobs[ jid ][ 'history_name' ],
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jobs[ jid ][ 'history_update_time' ],
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jobs[ jid ][ 'user_email' ]
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)
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sys.exit(0)
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if __name__ == "__main__":
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main()
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