mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
100 lines
4.7 KiB
Python
100 lines
4.7 KiB
Python
#!/usr/bin/env python
|
|
"""
|
|
Fetch gops_join wherein the use specified minimum coverage is not 1.
|
|
"""
|
|
import ConfigParser
|
|
import os
|
|
import sys
|
|
import tempfile
|
|
|
|
import sqlalchemy as sa
|
|
|
|
import galaxy.app
|
|
import galaxy.model.mapping
|
|
|
|
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 = {}
|
|
try:
|
|
for job in app.model.Job.filter( sa.and_( app.model.Job.table.c.create_time < '2008-12-16',
|
|
app.model.Job.table.c.state == 'ok',
|
|
app.model.Job.table.c.tool_id == 'gops_join_1',
|
|
sa.not_( app.model.Job.table.c.command_line.like( '%-m 1 %' ) ) ) ).all():
|
|
print "# processing job id %s" % str( job.id )
|
|
for jtoda in job.output_datasets:
|
|
print "# --> processing JobToOutputDatasetAssociation id %s" % str( jtoda.id )
|
|
hda = app.model.HistoryDatasetAssociation.get( jtoda.dataset_id )
|
|
print "# ----> processing HistoryDatasetAssociation id %s" % str( hda.id )
|
|
if not hda.deleted:
|
|
# Probably don't need this check, since the job state should suffice, but...
|
|
if hda.dataset.state == 'ok':
|
|
history = app.model.History.get( hda.history_id )
|
|
print "# ------> processing history id %s" % str( history.id )
|
|
if history.user_id:
|
|
cmd_line = str( job.command_line )
|
|
new_output = tempfile.NamedTemporaryFile('w')
|
|
new_cmd_line = " ".join(map(str, cmd_line.split()[:4])) + " " + new_output.name + " " + " ".join(map(str, cmd_line.split()[5:]))
|
|
job_output = cmd_line.split()[4]
|
|
try:
|
|
os.system(new_cmd_line)
|
|
except:
|
|
pass
|
|
diff_status = os.system('diff %s %s >> /dev/null' % (new_output.name, job_output))
|
|
if diff_status == 0:
|
|
continue
|
|
print "# --------> Outputs differ"
|
|
user = app.model.User.get( history.user_id )
|
|
jobs[ job.id ] = {}
|
|
jobs[ job.id ][ 'hda_id' ] = hda.id
|
|
jobs[ job.id ][ 'hda_name' ] = hda.name
|
|
jobs[ job.id ][ 'hda_info' ] = hda.info
|
|
jobs[ job.id ][ 'history_id' ] = history.id
|
|
jobs[ job.id ][ 'history_name' ] = history.name
|
|
jobs[ job.id ][ 'history_update_time' ] = history.update_time
|
|
jobs[ job.id ][ 'user_email' ] = user.email
|
|
except Exception as e:
|
|
print "# caught exception: %s" % str( e )
|
|
|
|
print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) )
|
|
print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email"
|
|
for jid in jobs:
|
|
print '%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' % \
|
|
( str( jid ),
|
|
str( jobs[ jid ][ 'hda_id' ] ),
|
|
jobs[ jid ][ 'hda_name' ],
|
|
jobs[ jid ][ 'hda_info' ],
|
|
str( jobs[ jid ][ 'history_id' ] ),
|
|
jobs[ jid ][ 'history_name' ],
|
|
jobs[ jid ][ 'history_update_time' ],
|
|
jobs[ jid ][ 'user_email' ] )
|
|
sys.exit(0)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|