view smart_toolShed/commons/core/sql/RepetJob.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
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# abiding by the rules of distribution of free software.  You can  use, 
# modify and/ or redistribute the software under the terms of the CeCILL
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# "http://www.cecill.info". 
#
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# modify and redistribute granted by the license, users are provided only
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# economic rights,  and the successive licensors  have only  limited
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# software by the user in light of its specific status of free software,
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# therefore means  that it is reserved for developers  and  experienced
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import os
import time
import sys
from commons.core.sql.DbMySql import DbMySql
from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory

#TODO: to remove... => replace all RepetJob() by TableJobAdaptator()...
## Methods for Job persistence 
#
class RepetJob( DbMySql ):
        
        
    ## Record a job
    #
    # @param job Job instance with the job informations
    #
    def recordJob( self, job ):
        self.removeJob( job )
        sqlCmd = "INSERT INTO %s" % ( job.tablename )
        sqlCmd += " VALUES ("
        sqlCmd += " \"%s\"," % ( job.jobid )
        sqlCmd += " \"%s\"," % ( job.jobname )
        sqlCmd += " \"%s\"," % ( job.groupid )
        sqlCmd += " \"%s\"," % ( job.command.replace("\"","\'") )
        sqlCmd += " \"%s\"," % ( job.launcher )
        sqlCmd += " \"%s\"," % ( job.queue )
        sqlCmd += " \"waiting\","
        sqlCmd += " \"%s\"," % ( time.strftime( "%Y-%m-%d %H:%M:%S" ) )
        sqlCmd += " \"?\" );"
        self.execute( sqlCmd )
        
        
    ## Remove a job from the job table
    #
    #  @param job: job instance to remove
    #
    def removeJob( self, job ):
        qry = "DELETE FROM %s" % ( job.tablename )
        qry += " WHERE groupid='%s'" % ( job.groupid )
        qry += " AND jobname='%s'" % ( job.jobname )
        qry += " AND queue='%s';" % ( job.queue )
        self.execute( qry )
            
            
    ## Set the jobid of a job with the id of SGE
    #
    # @param job job instance
    # @param jobid integer
    #
    def setJobIdFromSge( self, job, jobid ):
        qry = "UPDATE %s" % ( job.tablename )
        qry += " SET jobid='%i'" % ( int(jobid) )
        qry += " WHERE jobname='%s'" % ( job.jobname )
        qry += " AND groupid='%s'" % ( job.groupid )
        qry += " AND queue='%s';" % ( job.queue )
        self.execute( qry )
        
        
    ## Get a job status
    #
    # @param job: a Job instance with the job informations
    #
    def getJobStatus( self, job ):
        if job.jobid != 0 and job.jobname == "":
            job.jobname = job.jobid
            job.jobid = 0
        qry = "SELECT status FROM %s" % ( job.tablename )
        qry += " WHERE groupid='%s'" % ( job.groupid )
        qry += " AND jobname='%s'" % ( job.jobname )
        qry += " AND queue='%s';" % ( job.queue )
        self.execute( qry )
        res = self.fetchall()
        if len(res) > 1:
            msg = "ERROR while getting job status: non-unique jobs"
            sys.stderr.write( "%s\n" % msg )
            sys.stderr.flush()
            sys.exit(1)
        if res == None or len(res) == 0:
            return "unknown"
        return res[0][0]
    
    
    ## Change a job status
    #
    # @param job: a Job instance with the job informations
    # @param status: the new status (waiting,finished,error)
    # @param method: db or file
    #
    def changeJobStatus( self, job, status, method=""):
        sqlCmd = "UPDATE %s" % ( job.tablename )
        sqlCmd += " SET status='%s'" % ( status )
        sqlCmd += ",node='%s'" % ( job.node )
        sqlCmd += " WHERE groupid='%s'" % ( job.groupid )
        sqlCmd += " AND jobname='%s'" % ( job.jobname )
        sqlCmd += " AND queue='%s';" % ( job.queue )
        self.execute( sqlCmd )
        
        
    ## Get the number of jobs belonging to the desired groupid with the desired status.
    #
    # @param tablename string table name to record the jobs   
    # @param groupid string a group identifier to record related job series 
    # @param status string job status (waiting, running, finished, error)
    # @return int
    #
    def getCountStatus( self, tablename, groupid, status ):
        qry = "SELECT count(jobname) FROM %s" % ( tablename )
        qry += " WHERE groupid='%s'" % ( groupid )
        qry += " AND status='%s';" % ( status )
        self.execute( qry )
        res = self.fetchall()
        return int( res[0][0] )
        
        
    ## Clean all job from a job group
    #
    # @param tablename table name to record the jobs
    # @param groupid: a group identifier to record related job series
    #
    def cleanJobGroup( self, tablename, groupid ):
        if self.doesTableExist( tablename ):
            qry = "DELETE FROM %s WHERE groupid='%s';" % ( tablename, groupid )
            self.execute( qry )
            
            
    ## Check if there is unfinished job from a job group.
    #
    # @param tablename string table name to record the jobs
    # @param groupid string a group identifier to record related job series 
    #        
    def hasUnfinishedJob( self, tablename, groupid ):
        if not self.doesTableExist( tablename ):
            return False
        qry = "SELECT * FROM %s" % ( tablename )
        qry += " WHERE groupid='%s'" % ( groupid )
        qry += " and status!='finished';" 
        self.execute( qry )
        res = self.fetchall()
        if len(res) == 0:
            return False
        return True
    
         
    ## Check if a job is still handled by SGE
    #
    # @param jobid string job identifier
    # @param jobname string job name
    #  
    def isJobStillHandledBySge( self, jobid, jobname ):
        isJobInQstat = False
        qstatFile = "qstat_stdout"
        cmd = "qstat > %s" % ( qstatFile )
        returnStatus = os.system( cmd )
        if returnStatus != 0:
            msg = "ERROR while launching 'qstat'"
            sys.stderr.write( "%s\n" % msg )
            sys.exit(1)
        qstatFileHandler = open( qstatFile, "r" )
        lLines = qstatFileHandler.readlines()
        for line in lLines:
            tokens = line.split()
            if len(tokens) > 3 and tokens[0] == str(jobid) and tokens[2] == jobname[0:len(tokens[2])]:
                isJobInQstat = True
                break
        qstatFileHandler.close()
        os.remove( qstatFile )
        return isJobInQstat
    
    
    ## Wait job finished status from a job group.
    #  Job are re-launched if error (max. 3 times)
    #
    # @param tableName string table name to record the jobs
    # @param groupid string a group identifier to record related job series
    # @param checkInterval integer time laps in seconds between two checks (default = 5)
    # @param maxRelaunch integer max nb of times a job in error is relaunch before exiting (default = 3)
    # @param exitIfTooManyErrors boolean exit if a job is still in error above maxRelaunch (default = True)
    # @param timeOutPerJob integer max nb of seconds after which one tests if a job is still in SGE or not (default = 60*60=1h)
    #
    def waitJobGroup(self, tableName, groupid, checkInterval=5, maxRelaunch=3, exitIfTooManyErrors=True, timeOutPerJob=60*60):
        iTJA = TableJobAdaptatorFactory.createInstance(self, tableName)
        iTJA.waitJobGroup(groupid, checkInterval, maxRelaunch, exitIfTooManyErrors, timeOutPerJob)
                        
    ## Submit a job to a queue and record it in job table.
    #
    # @param job a job instance
    # @param maxNbWaitingJobs integer max nb of waiting jobs before submitting a new one (default = 10000)
    # @param checkInterval integer time laps in seconds between two checks (default = 30)
    # @param verbose integer (default = 0)
    #               
    def submitJob( self, job, verbose=0, maxNbWaitingJobs=10000, checkInterval=30 ):
        iTJA = TableJobAdaptatorFactory.createInstance(self, job.tablename)
        return iTJA.submitJob(job, verbose, maxNbWaitingJobs, checkInterval)
                        
        
    ## Get the list of nodes where jobs of one group were executed
    #
    # @param tablename string table name where jobs are recored   
    # @param groupid string a group identifier of job series 
    # @return lNodes list of nodes names
    #
    def getNodesListByGroupId( self, tableName, groupId ):
        qry = "SELECT node FROM %s" % tableName
        qry += " WHERE groupid='%s'" % groupId
        self.execute( qry )
        res = self.fetchall()
        lNodes = []
        for resTuple in res:
            lNodes.append(resTuple[0])
        return lNodes
    
    def getDbName(self):
        return "DbMySql"
    
    def _getJobidAndNbJob(self, jobid) :
        tab = []
        tab = jobid.split(".")
        jobid = tab[0]
        tab = tab[1].split(":")
        nbJob = tab[0]
        return jobid, nbJob