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#! /usr/bin/env python
#############################################################
# #
# Author: Bertrand Neron #
# Organization:'Biological Software and Databases' Group, #
# Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the #
# COPYING.LIB document. #
# #
#############################################################
import os , sys
MOBYLEHOME = None
if os.environ.has_key('MOBYLEHOME'):
MOBYLEHOME = os.environ['MOBYLEHOME']
if not MOBYLEHOME:
sys.exit( 'MOBYLEHOME must be defined in your environment' )
if ( os.path.join( MOBYLEHOME , 'Src' ) ) not in sys.path:
sys.path.append( os.path.join( MOBYLEHOME , 'Src' ) )
import shutil
import re
from lxml import etree
from Mobyle.ConfigManager import Config
from Mobyle.JobState import JobState
from Mobyle.Registry import registry
from Mobyle.MobyleError import MobyleError
class JobUpdater(object):
def __init__(self , config , logger ):
self.cfg = config
self.log = logger
self.skipped_jobs = []
self.skipped_services = []
self.jobs_url = self.cfg.results_url()
def _on_error(self , err ):
self.log.warning( "%s : %s" ( err.filename , err ))
def update( self , repository , force = False , dry_run = False , status_only = False ):
skipped_jobs = []
jobs_paths = os.walk( repository , onerror = self._on_error )
current_service = ''
for path in jobs_paths:
job_path = path[0]
if 'index.xml' in path[2]:
if not '.admin' in path[2]:
self.log.warning( "the directory %s have an index.xlm but not .admin may be not a job : skip" %path[2] )
skipped_jobs.append( job_path )
continue
service_name , job_key = os.path.split( path[0] )
service_name = os.path.basename( service_name )
if service_name != current_service:
current_service = service_name
self.log.info( "-------- enter service %s --------" % service_name)
self.log.info( "====================" )
self.log.info( "updating job %s" %job_key )
job_dir_mtime = os.path.getmtime( job_path )
job_dir_atime = os.path.getatime( job_path )
index_mtime = os.path.getmtime( os.path.join( job_path , 'index.xml') )
index_atime = os.path.getatime( os.path.join( job_path , 'index.xml') )
index_path = os.path.join( job_path , 'index.xml')
try:
os.utime( job_path , ( job_dir_atime , job_dir_mtime ) )
except Exception , err :
self.log.warning( "cannot modify the mtime of %s : %s : fix this problem before rerun updater" %(job_path , err ) )
continue
bckp_path = self.back_up(job_path, index_path, dry_run)
try:
if not status_only:
try:
self.fix_definition( job_path , service_name , job_key , index_path , bckp_path , force = force , dry_run = dry_run )
except Exception, err:
self.roll_back(bckp_path, index_path)
try:
self.fix_status( job_path , index_path , force = force , dry_run = dry_run )
except Exception, err:
self.log.warning( "Error occured during status fixing : %s" % err, exc_info = True )
self.roll_back(bckp_path, index_path)
finally:
self.set_time(index_path, index_atime, index_mtime, job_path, job_dir_atime, job_dir_mtime)
def fix_definition( self , job_path , service_name , job_key ,index_path , bckp_path ,force = False ,dry_run = False):
self.log.info( "fixing %s job definition" % job_path )
try:
js = JobState( uri = job_path )
except Exception , err:
self.log.warning( "cannot load job %s : %s : skipped" %( job_path , err ) )
return
if js.getDefinition() is not None and not force:
self.log.warning("the job %s has already a definition: skipped " % job_path )
return
new_program_def_url = registry.getProgramUrl( service_name , 'local' )
self.log.info( "registry.getProgramUrl( %s , 'local' ) = %s "% (service_name , new_program_def_url ) )
new_host = self.cfg.root_url()
self.log.info( "new host = %s "% new_host )
job_id = js.getID()
new_job_id = "%s/%s" %(self.jobs_url , re.search( '.*/(.*/.*)$' , job_id ).group(1) )
self.log.info( "new job id = %s "% new_job_id )
if not dry_run:
js.setName( new_program_def_url )
try:
js.setDefinition( new_program_def_url)
except MobyleError:
self.log.warning( "the service : local.%s is not deployed to update job %s, deploy %s before" %(service_name ,
job_path,
service_name) )
return
js.setHost( new_host )
js.setID( new_job_id )
try:
js.commit()
except Exception ,err :
self.log.warning( "cannot commit updated job %s : %s " %( job_path , err ) )
self.roll_back(bckp_path, index_path)
else:
pass
def fix_status(self , job_path , index_path , force = False , dry_run = False ):
self.log.info( "fixing %s job status" % job_path )
status_path = os.path.join( job_path , 'mobyle_status.xml')
if os.path.exists( status_path ) and not force:
self.log.info("%s already exist : skip" % status_path )
return
else:
doc = etree.parse( os.path.join( job_path , 'index.xml') )
root = doc.getroot()
status_node = root.find( 'status' )
status = status_node.find( 'value' ).text
if status in ( "submitted", "pending", "running", "hold"):
return
try:
status_file = open( status_path , 'w' )
status_file.write( etree.tostring( status_node , pretty_print = True , encoding='UTF-8' ))
except Exception , err :
self.log.error( 'cannot make mobyle_status.xml : %s' % err )
finally:
try:
status_file.close()
except:
pass
root.remove( status_node )
try:
tmp_file = open( os.path.join( job_path ,'tmp_index.xml' ) , 'w' )
tmp_file.write( etree.tostring( doc , pretty_print = True , encoding='UTF-8' ))
tmp_file.close()
os.rename( tmp_file.name , index_path )
except Exception , err :
self.log.error( 'cannot make index.xml : %s' % err )
def back_up(self , job_path , index_path , dry_run = False ):
bckp_path = os.path.join( job_path , '.index.xml.bckp')
if not os.path.exists( bckp_path ):
self.log.debug( "make %s back up" % job_path )
if not dry_run:
try:
shutil.copy( index_path , bckp_path )
except Exception , err:
self.log.warning( "cannot make %s back up " % index_path)
return bckp_path
def roll_back(self , bckp_path , index_path ):
try:
shutil.copy( bckp_path , index_path )
except Exception:
self.log.warning( "cannot roll back ")
return
try:
os.unlink( bckp_path )
except Exception:
self.log.warning( "cannot remove back up index % " % bckp_path )
return
self.log.warning( "job %s has been rolled back " %( os.path.dirname( index_path ) ) )
return
def set_time(self , index_path , index_atime , index_mtime , job_path , job_dir_atime , job_dir_mtime ):
os.utime( index_path , ( index_atime , index_mtime ) )
os.utime( job_path , ( job_dir_atime , job_dir_mtime ) )
if __name__ == "__main__":
from optparse import OptionParser
parser = OptionParser( )
parser.add_option( "-s" , "--services",
action="store",
type = 'string',
dest="services",
help="comma separated list of SERVICES to update."
)
parser.add_option( "-l" , "--log",
action="store",
type = 'string',
dest = "log_file",
help= "Path to the Logfile where put the logs.")
parser.add_option( "-n" , "--dry-run",
action="store_true",
dest = "dry_run",
default = False ,
help= "don't actually do anything.")
parser.add_option( "-f" , "--force",
action="store_true",
dest = "force",
default = False ,
help= "force to update job even if it was already updated.")
parser.add_option("-v", "--verbose",
action="count",
dest="verbosity",
default= 0,
help="increase the verbosity level. There is 4 levels: Error messages (default), Warning (-v), Info (-vv) and Debug.(-vvv)")
parser.add_option("--status-only",
action="store_true",
dest="status_only",
default= False,
help="fix the job status only")
options, args = parser.parse_args()
import logging
logger = logging.getLogger( 'jobUpdater' )
if options.log_file is None:
handler = logging.StreamHandler( sys.stderr )
else:
try:
handler = logging.FileHandler( options.log_file , 'w' )
except(IOError , OSError) , err:
print >> sys.stderr , "cannot log messages in %s: %s"%( options.log_file , err )
sys.exit(1)
if options.verbosity < 2:
formatter = logging.Formatter( '%(filename)-10s : %(levelname)-8s : %(asctime)s : %(message)s' , '%a, %d %b %Y %H:%M:%S' )
else:
formatter = logging.Formatter( '%(filename)-10s : %(levelname)-8s : L %(lineno)d : %(asctime)s : %(message)s' , '%a, %d %b %Y %H:%M:%S' )
handler.setFormatter( formatter )
logger.addHandler( handler)
if options.verbosity == 0:
logger.setLevel( logging.WARNING )
elif options.verbosity == 1:
logger.setLevel( logging.INFO )
else:
logger.setLevel( logging.DEBUG )
config = Config()
job_updater = JobUpdater( config , logger )
jobs_repository = config.results_path()
if options.services is None:
job_updater.update( jobs_repository , force = options.force , dry_run = options.dry_run , status_only = options.status_only )
else:
services = options.services.split( ',' )
for service in services:
service_path = os.path.join( jobs_repository , service )
job_updater.update( service_path , force = options.force , dry_run = options.dry_run , status_only = options.status_only )
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