Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/sql/test/Test_F_TableJobAdaptator.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
1 from commons.core.launcher.WriteScript import WriteScript
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2 from commons.core.sql.Job import Job
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3 from commons.core.sql.DbFactory import DbFactory
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4 from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
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5 import sys
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6 import stat
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7 import os
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8 import time
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9 import unittest
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10 import glob
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11
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12 class Test_F_TableJobAdaptator(unittest.TestCase):
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13
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14 def setUp(self):
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15 self._jobTableName = "dummyJobTable"
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16 self._db = DbFactory.createInstance()
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17 self._iTJA = TableJobAdaptatorFactory.createInstance(self._db, self._jobTableName)
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18
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19 def tearDown(self):
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20 self._db.dropTable(self._jobTableName)
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21 self._db.close()
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22
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23 def test_submitJob_with_multiple_jobs(self):
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24 self._db.createTable(self._jobTableName, "jobs", overwrite = True)
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25 job1 = _createJobInstance("job1")
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26 _createLauncherFile(job1, self._iTJA)
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27 job2 = _createJobInstance("job2")
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28 _createLauncherFile(job2, self._iTJA)
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29 job3 = _createJobInstance("job3")
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30 _createLauncherFile(job3, self._iTJA)
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31
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32 self._iTJA.submitJob( job1, maxNbWaitingJobs=3, checkInterval=5, verbose=0 )
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33 self._iTJA.submitJob( job2, maxNbWaitingJobs=3, checkInterval=5, verbose=0 )
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34 self._iTJA.submitJob( job3, maxNbWaitingJobs=3, checkInterval=5, verbose=0 )
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35
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36 time.sleep(120)
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37
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38 expJobStatus = "finished"
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39 obsJobStatus1 = self._iTJA.getJobStatus(job1)
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40 obsJobStatus2 = self._iTJA.getJobStatus(job2)
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41 obsJobStatus3 = self._iTJA.getJobStatus(job3)
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42
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43 self.assertEquals(expJobStatus, obsJobStatus1)
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44 self.assertEquals(expJobStatus, obsJobStatus2)
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45 self.assertEquals(expJobStatus, obsJobStatus3)
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46
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47 expErrorFilePrefix1 = job1.jobname + ".e"
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48 expOutputFilePrefix1 = job1.jobname + ".o"
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49 expErrorFilePrefix2 = job2.jobname + ".e"
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50 expOutputFilePrefix2 = job2.jobname + ".o"
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51 expErrorFilePrefix3 = job3.jobname + ".e"
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52 expOutputFilePrefix3 = job3.jobname + ".o"
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53
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54 lErrorFiles1 = glob.glob(expErrorFilePrefix1 + "*")
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55 lOutputFiles1 = glob.glob(expOutputFilePrefix1 + "*")
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56 lErrorFiles2 = glob.glob(expErrorFilePrefix2 + "*")
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57 lOutputFiles2 = glob.glob(expOutputFilePrefix2 + "*")
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58 lErrorFiles3 = glob.glob(expErrorFilePrefix3 + "*")
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59 lOutputFiles3 = glob.glob(expOutputFilePrefix3 + "*")
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60
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61 isLErrorFileNotEmpty1 = (len(lErrorFiles1) != 0)
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62 isLOutputFileNotEmpty1 = (len(lOutputFiles1) != 0)
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63 isLErrorFileNotEmpty2 = (len(lErrorFiles2) != 0)
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64 isLOutputFileNotEmpty2 = (len(lOutputFiles2) != 0)
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65 isLErrorFileNotEmpty3 = (len(lErrorFiles3) != 0)
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66 isLOutputFileNotEmpty3 = (len(lOutputFiles3) != 0)
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67
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68 os.system("rm launcherFileTest*.py *.e* *.o*")
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69 self.assertTrue(isLErrorFileNotEmpty1 and isLOutputFileNotEmpty1)
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70 self.assertTrue(isLErrorFileNotEmpty2 and isLOutputFileNotEmpty2)
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71 self.assertTrue(isLErrorFileNotEmpty3 and isLOutputFileNotEmpty3)
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72
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73 def test_submitJob_job_already_submitted(self):
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74 self._db.createTable(self._jobTableName, "jobs", overwrite = True)
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75 iJob = _createJobInstance("job")
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76 self._iTJA.recordJob(iJob)
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77
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78 isSysExitRaised = False
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79 try:
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80 self._iTJA.submitJob(iJob)
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81 except SystemExit:
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82 isSysExitRaised = True
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83 self.assertTrue(isSysExitRaised)
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84
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85 def test_waitJobGroup_with_error_job_maxRelaunch_two(self):
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86 self._db.createTable(self._jobTableName, "jobs", overwrite = True)
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87 iJob = _createJobInstance("job")
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88 _createLauncherFile(iJob, self._iTJA)
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89
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90 self._iTJA.recordJob(iJob)
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91 self._iTJA.changeJobStatus(iJob, "error")
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92
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93 self._iTJA.waitJobGroup(iJob.groupid, 0, 2)
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94
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95 time.sleep(120)
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96
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97 expJobStatus = "finished"
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98 obsJobStatus1 = self._iTJA.getJobStatus(iJob)
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99
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100 self.assertEquals(expJobStatus, obsJobStatus1)
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101
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102 expErrorFilePrefix1 = iJob.jobname + ".e"
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103 expOutputFilePrefix1 = iJob.jobname + ".o"
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104
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105 lErrorFiles1 = glob.glob(expErrorFilePrefix1 + "*")
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106 lOutputFiles1 = glob.glob(expOutputFilePrefix1 + "*")
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107
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108 isLErrorFileNotEmpty1 = (len(lErrorFiles1) != 0)
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109 isLOutputFileNotEmpty1 = (len(lOutputFiles1) != 0)
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110
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111 self._iTJA.removeJob(iJob)
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112 os.system("rm launcherFileTest*.py *.e* *.o*")
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113 self.assertTrue(isLErrorFileNotEmpty1 and isLOutputFileNotEmpty1)
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114
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115 class Test_F_TableJobAdaptator_SGE(unittest.TestCase):
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116
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117 def setUp(self):
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118 if os.environ["REPET_JOB_MANAGER"].lower() != "sge":
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119 print "ERROR: jobs manager is not SGE: REPET_JOB_MANAGER = %s." % os.environ["REPET_JOB_MANAGER"]
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120 sys.exit(0)
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121 self._jobTableName = "dummyJobTable"
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122 self._db = DbFactory.createInstance()
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123 self._db.createTable(self._jobTableName, "jobs", overwrite = True)
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124 self._iTJA = TableJobAdaptatorFactory.createInstance(self._db, self._jobTableName)
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125 self._iJob = _createJobInstance("job")
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126 _createLauncherFile(self._iJob, self._iTJA)
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127
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128 def tearDown(self):
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129 self._db.dropTable(self._jobTableName)
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130 self._db.close()
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131
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132 def test_waitJobGroup_with_several_nbTimeOut_waiting(self):
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133 self._iTJA.recordJob(self._iJob)
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134 self._iTJA.changeJobStatus(self._iJob, "running")
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135
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136 expMsg = "ERROR: job '%s', supposedly still running, is not handled by SGE anymore\n" % self._iJob.jobid
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137
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138 obsError = "obsError.txt"
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139 obsErrorHandler = open(obsError, "w")
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140 stderrRef = sys.stderr
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141 sys.stderr = obsErrorHandler
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142
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143 isSysExitRaised = False
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144 try:
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145 self._iTJA.waitJobGroup(self._iJob.groupid, timeOutPerJob = 3)
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146 except SystemExit:
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147 isSysExitRaised = True
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148
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149 obsErrorHandler.close()
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150
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151 obsErrorHandler = open(obsError, "r")
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152 obsMsg = obsErrorHandler.readline()
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153 obsErrorHandler.close()
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154
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155 sys.stderr = stderrRef
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156 os.remove(obsError)
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157 os.system("rm launcherFileTest*.py")
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158 self.assertTrue(isSysExitRaised)
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159 self.assertEquals(expMsg, obsMsg)
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160
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161 def test_isJobStillHandledBySge_True(self):
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162 self._iTJA.submitJob(self._iJob)
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163 isJobHandledBySge = self._iTJA.isJobStillHandledBySge(self._iJob.jobid, self._iJob.jobname)
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164 os.system("rm launcherFileTest*.py")
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165 self.assertTrue(isJobHandledBySge)
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166
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167 def test_isJobStillHandledBySge_False(self):
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168 self._iTJA.recordJob(self._iJob)
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169 isJobHandledBySge = self._iTJA.isJobStillHandledBySge(self._iJob.jobid, self._iJob.jobname)
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170 os.system("rm launcherFileTest*.py")
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171 self.assertFalse(isJobHandledBySge)
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172
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173 def _createJobInstance(name):
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174 lResources = []
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175 if os.environ.get("HOSTNAME") == "compute-2-46.local":
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176 lResources.append("test=TRUE")
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177 return Job(0, name, "test", "", "log = os.system(\"date;sleep 5;date\")", "%s/launcherFileTest_%s.py" % (os.getcwd(), name), lResources=lResources)
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178
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179 def _createLauncherFile(iJob, iTJA):
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180 iWriteScript = WriteScript(iJob, iTJA, os.getcwd(), os.getcwd())
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181 iWriteScript.run(iJob.command, "", iJob.launcher)
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182 os.chmod(iJob.launcher, stat.S_IRWXU+stat.S_IRWXG+stat.S_IRWXO)
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183
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184 if __name__ == "__main__":
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185 unittest.main()