diff smart_toolShed/commons/core/launcher/test/expFiles/expJobScriptTemplate.py @ 0:e0f8dcca02ed

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/launcher/test/expFiles/expJobScriptTemplate.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,95 @@
+#!/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")
+	
+	minFreeGigaInTmpDir = 1
+	freeSpace = os.statvfs("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
+	if ((freeSpace.f_bavail * freeSpace.f_frsize) / 1073741824.0 < minFreeGigaInTmpDir):
+		raise RepetException("ERROR: less than %iG of input file in '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch'" % minFreeGigaInTmpDir)
+	
+	os.chdir("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
+	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)