Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/test/Test_F_TableJobAdaptator.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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() |