annotate smart_toolShed/commons/core/launcher/test/expFiles/expJobScriptWithFilesCopyTemplate.py @ 0:e0f8dcca02ed

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

#!/usr/bin/env python

import os
import sys
import time
import shutil
from commons.core.checker.RepetException import RepetException
from commons.core.sql.TableJobAdaptator import TableJobAdaptator
from commons.core.sql.DbFactory import DbFactory
from commons.core.sql.Job import Job

try:
	newDir = None
	print os.uname()
	beginTime = time.time()
	print 'beginTime=%f' % beginTime
	print "work in dir '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch'"
	sys.stdout.flush()
	if not os.path.exists("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch"):
		raise IOError("ERROR: temporary directory '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch' doesn't exist")
	
	fileSize = 0
	if not os.path.exists("groupid"):
		fileSize = 0.500000
	freeGigaNeededInTmpDir = float(1 + fileSize)
	freeSpace = os.statvfs("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
	if ((freeSpace.f_bavail * freeSpace.f_frsize) / 1073741824.0 < freeGigaNeededInTmpDir):
		raise RepetException("ERROR: less than %.2fG of input file in '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch'" % freeGigaNeededInTmpDir)
	
	os.chdir("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
	if not os.path.exists("groupid"):
		try:
			os.mkdir("groupid")
		except OSError, e :
			if e.args[0] != 17:
				raise RepetException("ERROR: can't create 'groupid'")
		os.chdir("groupid")
		os.system("touch bank.fa")
	else:
		os.chdir("groupid")
	
	newDir = "groupid_job1_20110505-105353"
	if os.path.exists(newDir):
		shutil.rmtree(newDir)
	os.mkdir(newDir)
	os.chdir(newDir)
	
	iJob = Job(jobname = "job1", groupid = "groupid", launcherFile = "ClusterLauncher", node = os.getenv("HOSTNAME"))
	iDb = DbFactory.createInstance()
	iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
	print "current status: %s" % iTJA.getJobStatus(iJob)
	iTJA.changeJobStatus(iJob, "running")
	print "updated status: %s" % iTJA.getJobStatus(iJob)
	sys.stdout.flush()
	iDb.close()
	
	log = os.system("touch dummyFile1")
	if log != 0:
		raise RepetException("ERROR: job returned %i" % log)
	else:
		print "job finished successfully"
	sys.stdout.flush()
	shutil.move("dummyFile1", "/home/user/workspace/repet_pipe/commons/core/launcher/test")
	
	os.chdir("..")
	shutil.rmtree(newDir)
	
	iDb = DbFactory.createInstance()
	iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
	print "current status: %s" % iTJA.getJobStatus(iJob)
	iTJA.changeJobStatus(iJob, "finished")
	print "updated status: %s" % iTJA.getJobStatus(iJob)
	sys.stdout.flush()
	iDb.close()
	
	endTime = time.time()
	print 'endTime=%f' % endTime
	print 'executionTime=%f' % (endTime - beginTime)
	print os.uname()
	sys.stdout.flush()

except IOError, e :
	print e
	iJob = Job(jobname = "job1", groupid = "groupid", launcherFile = "ClusterLauncher", node = os.getenv("HOSTNAME"))
	iDb = DbFactory.createInstance()
	iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
	print "current status: %s" % iTJA.getJobStatus(iJob)
	iTJA.changeJobStatus(iJob, "error")
	print "updated status: %s" % iTJA.getJobStatus(iJob)
	sys.stdout.flush()
	iDb.close()
	sys.exit(1)

except Exception, e :
	print "tmpDir is : /home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch"
	print "cDir is : /home/user/workspace/repet_pipe/commons/core/launcher/test/"
	print e
	if newDir != None and os.path.exists("../%s" % newDir) and not os.path.exists("/home/user/workspace/repet_pipe/commons/core/launcher/test//%s" % newDir):
		os.chdir("..")
		shutil.move(newDir, "/home/user/workspace/repet_pipe/commons/core/launcher/test//%s" % newDir)
	iJob = Job(jobname = "job1", groupid = "groupid", launcherFile = "ClusterLauncher", node = os.getenv("HOSTNAME"))
	iDb = DbFactory.createInstance()
	iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
	print "current status: %s" % iTJA.getJobStatus(iJob)
	iTJA.changeJobStatus(iJob, "error")
	print "updated status: %s" % iTJA.getJobStatus(iJob)
	sys.stdout.flush()
	iDb.close()
	sys.exit(1)