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6
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1 #!/usr/bin/env python
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2
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3 import os
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4 import sys
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5 import time
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6 import shutil
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7 from commons.core.checker.RepetException import RepetException
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8 from commons.core.sql.TableJobAdaptator import TableJobAdaptator
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9 from commons.core.sql.DbFactory import DbFactory
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10 from commons.core.sql.Job import Job
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11
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12 try:
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13 newDir = None
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14 print os.uname()
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15 beginTime = time.time()
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16 print 'beginTime=%f' % beginTime
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17 print "work in dir '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch'"
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18 sys.stdout.flush()
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19 if not os.path.exists("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch"):
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20 raise IOError("ERROR: temporary directory '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch' doesn't exist")
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21
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22 fileSize = 0
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23 if not os.path.exists("groupid"):
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24 fileSize = 0.500000
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25 freeGigaNeededInTmpDir = float(1 + fileSize)
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26 freeSpace = os.statvfs("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
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27 if ((freeSpace.f_bavail * freeSpace.f_frsize) / 1073741824.0 < freeGigaNeededInTmpDir):
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28 raise RepetException("ERROR: less than %.2fG of input file in '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch'" % freeGigaNeededInTmpDir)
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29
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30 os.chdir("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
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31 if not os.path.exists("groupid"):
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32 try:
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33 os.mkdir("groupid")
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34 except OSError, e :
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35 if e.args[0] != 17:
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36 raise RepetException("ERROR: can't create 'groupid'")
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37 os.chdir("groupid")
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38 os.system("touch bank.fa")
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39 else:
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40 os.chdir("groupid")
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41
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42 newDir = "groupid_job1_20110505-105353"
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43 if os.path.exists(newDir):
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44 shutil.rmtree(newDir)
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45 os.mkdir(newDir)
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46 os.chdir(newDir)
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47
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48 iJob = Job(jobname = "job1", groupid = "groupid", launcherFile = "ClusterLauncher", node = os.getenv("HOSTNAME"))
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49 iDb = DbFactory.createInstance()
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50 iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
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51 print "current status: %s" % iTJA.getJobStatus(iJob)
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52 iTJA.changeJobStatus(iJob, "running")
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53 print "updated status: %s" % iTJA.getJobStatus(iJob)
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54 sys.stdout.flush()
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55 iDb.close()
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56
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57 log = os.system("touch dummyFile1")
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58 if log != 0:
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59 raise RepetException("ERROR: job returned %i" % log)
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60 else:
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61 print "job finished successfully"
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62 sys.stdout.flush()
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63 shutil.move("dummyFile1", "/home/user/workspace/repet_pipe/commons/core/launcher/test")
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64
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65 os.chdir("..")
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66 shutil.rmtree(newDir)
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67
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68 iDb = DbFactory.createInstance()
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69 iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
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70 print "current status: %s" % iTJA.getJobStatus(iJob)
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71 iTJA.changeJobStatus(iJob, "finished")
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72 print "updated status: %s" % iTJA.getJobStatus(iJob)
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73 sys.stdout.flush()
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74 iDb.close()
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75
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76 endTime = time.time()
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77 print 'endTime=%f' % endTime
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78 print 'executionTime=%f' % (endTime - beginTime)
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79 print os.uname()
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80 sys.stdout.flush()
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81
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82 except IOError, e :
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83 print e
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84 iJob = Job(jobname = "job1", groupid = "groupid", launcherFile = "ClusterLauncher", node = os.getenv("HOSTNAME"))
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85 iDb = DbFactory.createInstance()
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86 iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
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87 print "current status: %s" % iTJA.getJobStatus(iJob)
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88 iTJA.changeJobStatus(iJob, "error")
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89 print "updated status: %s" % iTJA.getJobStatus(iJob)
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90 sys.stdout.flush()
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91 iDb.close()
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92 sys.exit(1)
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93
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94 except Exception, e :
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95 print "tmpDir is : /home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch"
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96 print "cDir is : /home/user/workspace/repet_pipe/commons/core/launcher/test/"
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97 print e
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98 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):
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99 os.chdir("..")
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100 shutil.move(newDir, "/home/user/workspace/repet_pipe/commons/core/launcher/test//%s" % newDir)
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101 iJob = Job(jobname = "job1", groupid = "groupid", launcherFile = "ClusterLauncher", node = os.getenv("HOSTNAME"))
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102 iDb = DbFactory.createInstance()
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103 iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
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104 print "current status: %s" % iTJA.getJobStatus(iJob)
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105 iTJA.changeJobStatus(iJob, "error")
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106 print "updated status: %s" % iTJA.getJobStatus(iJob)
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107 sys.stdout.flush()
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108 iDb.close()
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109 sys.exit(1)
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