Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/test/Tst_F_RepetJob.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 import os |
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2 import time |
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3 import sys |
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4 import stat |
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5 import unittest |
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6 import glob |
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7 from commons.core.sql.DbMySql import DbMySql |
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8 from commons.core.sql.RepetJob import RepetJob |
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9 from commons.core.sql.Job import Job |
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10 |
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11 class Test_F_RepetJob(unittest.TestCase): |
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12 |
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13 def setUp(self): |
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14 self._jobTableName = "dummyJobTable" |
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15 self._db = DbMySql() |
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16 self._iRepetJob = RepetJob() |
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17 self._configFileName = "dummyConfigFile" |
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18 configF = open(self._configFileName, "w" ) |
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19 configF.write( "[repet_env]\n" ) |
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20 configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) ) |
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21 configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) ) |
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22 configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) ) |
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23 configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) ) |
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24 configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) ) |
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25 configF.close() |
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26 |
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27 def tearDown(self): |
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28 self._iRepetJob = None |
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29 self._db.dropTable( self._jobTableName ) |
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30 self._db.close() |
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31 os.remove(self._configFileName) |
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32 |
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33 def test_submitJob_with_multiple_jobs(self): |
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34 job1 = self._createJobInstance("job1") |
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35 self._createLauncherFile(job1) |
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36 |
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37 job2 = self._createJobInstance("job2") |
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38 self._createLauncherFile(job2) |
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39 |
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40 job3 = self._createJobInstance("job3") |
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41 self._createLauncherFile(job3) |
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42 |
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43 self._iRepetJob.submitJob( job1, maxNbWaitingJobs=3, checkInterval=5, verbose=0 ) |
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44 self._iRepetJob.submitJob( job2, maxNbWaitingJobs=3, checkInterval=5, verbose=0 ) |
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45 self._iRepetJob.submitJob( job3, maxNbWaitingJobs=3, checkInterval=5, verbose=0 ) |
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46 |
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47 time.sleep(70) |
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48 |
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49 expJobStatus = "finished" |
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50 obsJobStatus1 = self._iRepetJob.getJobStatus(job1) |
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51 obsJobStatus2 = self._iRepetJob.getJobStatus(job2) |
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52 obsJobStatus3 = self._iRepetJob.getJobStatus(job3) |
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53 |
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54 self.assertEquals(expJobStatus, obsJobStatus1) |
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55 self.assertEquals(expJobStatus, obsJobStatus2) |
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56 self.assertEquals(expJobStatus, obsJobStatus3) |
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57 |
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58 jobName1 = job1.jobname |
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59 jobName2 = job2.jobname |
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60 jobName3 = job3.jobname |
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61 |
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62 expErrorFilePrefix1 = jobName1+ ".e" |
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63 expOutputFilePrefix1 = jobName1 + ".o" |
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64 expErrorFilePrefix2 = jobName2 + ".e" |
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65 expOutputFilePrefix2 = jobName2 + ".o" |
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66 expErrorFilePrefix3 = jobName3 + ".e" |
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67 expOutputFilePrefix3 = jobName3 + ".o" |
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68 |
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69 lErrorFiles1 = glob.glob(expErrorFilePrefix1 + "*") |
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70 lOutputFiles1 = glob.glob(expOutputFilePrefix1 + "*") |
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71 lErrorFiles2 = glob.glob(expErrorFilePrefix2 + "*") |
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72 lOutputFiles2 = glob.glob(expOutputFilePrefix2 + "*") |
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73 lErrorFiles3 = glob.glob(expErrorFilePrefix3 + "*") |
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74 lOutputFiles3 = glob.glob(expOutputFilePrefix3 + "*") |
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75 |
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76 isLErrorFileNotEmpty1 = (len(lErrorFiles1) != 0) |
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77 isLOutputFileNotEmpty1 = (len(lOutputFiles1) != 0) |
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78 isLErrorFileNotEmpty2 = (len(lErrorFiles2) != 0) |
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79 isLOutputFileNotEmpty2 = (len(lOutputFiles2) != 0) |
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80 isLErrorFileNotEmpty3 = (len(lErrorFiles3) != 0) |
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81 isLOutputFileNotEmpty3 = (len(lOutputFiles3) != 0) |
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82 |
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83 os.system("rm launcherFileTest*.py *.e* *.o*") |
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84 self.assertTrue(isLErrorFileNotEmpty1 and isLOutputFileNotEmpty1) |
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85 self.assertTrue(isLErrorFileNotEmpty2 and isLOutputFileNotEmpty2) |
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86 self.assertTrue(isLErrorFileNotEmpty3 and isLOutputFileNotEmpty3) |
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87 |
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88 def test_submitJob_job_already_submitted(self): |
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89 self._iRepetJob.createTable(self._jobTableName, "jobs") |
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90 iJob = self._createJobInstance("job") |
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91 self._iRepetJob.recordJob(iJob) |
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92 |
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93 isSysExitRaised = False |
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94 try: |
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95 self._iRepetJob.submitJob(iJob) |
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96 except SystemExit: |
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97 isSysExitRaised = True |
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98 self.assertTrue(isSysExitRaised) |
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99 |
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100 def test_waitJobGroup_with_several_nbTimeOut_waiting(self): |
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101 self._iRepetJob.createTable(self._jobTableName, "jobs") |
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102 iJob = self._createJobInstance("job") |
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103 self._createLauncherFile(iJob) |
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104 self._iRepetJob.recordJob(iJob) |
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105 self._iRepetJob.changeJobStatus(iJob, "running", "method") |
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106 |
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107 expMsg = "ERROR: job '%s', supposedly still running, is not handled by SGE anymore\n" % ( iJob.jobid ) |
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108 |
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109 obsError = "obsError.txt" |
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110 obsErrorHandler = open(obsError, "w") |
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111 stderrRef = sys.stderr |
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112 sys.stderr = obsErrorHandler |
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113 |
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114 isSysExitRaised = False |
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115 try: |
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116 self._iRepetJob.waitJobGroup(self._jobTableName ,iJob.groupid, timeOutPerJob=3) |
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117 except SystemExit: |
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118 isSysExitRaised = True |
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119 |
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120 obsErrorHandler.close() |
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121 |
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122 obsErrorHandler = open(obsError, "r") |
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123 obsMsg = obsErrorHandler.readline() |
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124 obsErrorHandler.close() |
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125 |
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126 sys.stderr = stderrRef |
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127 os.remove(obsError) |
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128 os.system("rm launcherFileTest*.py") |
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129 self.assertTrue(isSysExitRaised) |
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130 self.assertEquals(expMsg, obsMsg) |
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131 |
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132 def test_waitJobGroup_with_error_job_maxRelaunch_two(self): |
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133 self._iRepetJob.createTable(self._jobTableName, "jobs") |
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134 iJob = self._createJobInstance("job") |
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135 self._createLauncherFile(iJob) |
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136 |
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137 self._iRepetJob.recordJob(iJob) |
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138 self._iRepetJob.changeJobStatus(iJob, "error", "method") |
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139 |
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140 self._iRepetJob.waitJobGroup(self._jobTableName ,iJob.groupid, 0, 2) |
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141 |
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142 time.sleep(10) |
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143 |
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144 expJobStatus = "finished" |
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145 obsJobStatus1 = self._iRepetJob.getJobStatus(iJob) |
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146 |
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147 self.assertEquals(expJobStatus, obsJobStatus1) |
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148 |
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149 jobName = iJob.jobname |
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150 |
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151 expErrorFilePrefix1 = jobName + ".e" |
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152 expOutputFilePrefix1 = jobName + ".o" |
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153 |
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154 lErrorFiles1 = glob.glob(expErrorFilePrefix1 + "*") |
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155 lOutputFiles1 = glob.glob(expOutputFilePrefix1 + "*") |
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156 |
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157 isLErrorFileNotEmpty1 = (len(lErrorFiles1) != 0) |
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158 isLOutputFileNotEmpty1 = (len(lOutputFiles1) != 0) |
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159 |
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160 self._iRepetJob.removeJob(iJob) |
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161 os.system("rm launcherFileTest*.py *.e* *.o*") |
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162 self.assertTrue(isLErrorFileNotEmpty1 and isLOutputFileNotEmpty1) |
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163 |
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164 |
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165 def test_isJobStillHandledBySge_True(self): |
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166 self._iRepetJob.createTable(self._jobTableName, "jobs") |
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167 iJob = self._createJobInstance("job") |
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168 self._createLauncherFile(iJob) |
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169 self._iRepetJob.submitJob(iJob) |
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170 |
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171 isJobHandledBySge = self._iRepetJob.isJobStillHandledBySge(iJob.jobid, iJob.jobname) |
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172 os.system("rm launcherFileTest*.py") |
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173 |
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174 self.assertTrue(isJobHandledBySge) |
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175 |
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176 def test_isJobStillHandledBySge_False(self): |
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177 self._iRepetJob.createTable(self._jobTableName, "jobs") |
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178 iJob = self._createJobInstance("job") |
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179 self._createLauncherFile(iJob) |
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180 self._iRepetJob.recordJob(iJob) |
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181 |
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182 isJobHandledBySge = self._iRepetJob.isJobStillHandledBySge(iJob.jobid, iJob.jobname) |
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183 os.system("rm launcherFileTest*.py") |
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184 |
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185 self.assertFalse(isJobHandledBySge) |
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186 |
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187 def _createJobInstance(self, name): |
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188 return Job(self._jobTableName, 0, name, "test", "", "date;sleep 5;date", "./launcherFileTest_"+ name +".py") |
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189 |
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190 def _createLauncherFile(self, iJob): |
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191 jobFileHandler = open( iJob.launcher , "w" ) |
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192 |
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193 launcher = "#!/usr/bin/python\n" |
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194 launcher += "import os\n" |
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195 launcher += "import sys\n" |
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196 |
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197 launcher += "print \"system:\", os.uname()\n" |
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198 launcher += "sys.stdout.flush()\n" |
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199 newStatus = "running" |
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200 prg = "%s/bin/srptChangeJobStatus.py" % (os.environ["REPET_PATH"]) |
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201 cmd = prg |
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202 cmd += " -t %s" % ( iJob.tablename ) |
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203 cmd += " -n %s" % ( iJob.jobname ) |
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204 cmd += " -g %s" % ( iJob.groupid ) |
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205 if iJob.queue != "": |
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206 cmd += " -q %s" % ( iJob.queue ) |
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207 cmd += " -s %s" % ( newStatus ) |
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208 cmd += " -c %s" %( self._configFileName ) |
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209 cmd += " -v 1" |
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210 launcher +="os.system( \"" + cmd + "\" )\n" |
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211 |
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212 launcher += "print \"LAUNCH: "+ iJob.command + "\"\n" |
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213 launcher += "sys.stdout.flush()\n" |
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214 launcher += "exitStatus = os.system (\"" + iJob.command + "\")\n" |
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215 launcher += "if exitStatus != 0:\n" |
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216 launcher += "\tprint \"ERROR: "+ iJob.command + " returned exit status '%i'\" % ( exitStatus )\n" |
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217 |
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218 newStatus = "finished" |
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219 prg = os.environ["REPET_PATH"] + "/bin/srptChangeJobStatus.py" |
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220 cmd = prg |
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221 cmd += " -t %s" % ( iJob.tablename ) |
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222 cmd += " -n %s" % ( iJob.jobname ) |
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223 cmd += " -g %s" % ( iJob.groupid ) |
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224 if iJob.queue != "": |
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225 cmd += " -q %s" % ( iJob.queue ) |
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226 cmd += " -s %s" % ( newStatus ) |
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227 cmd += " -c %s" %( self._configFileName ) |
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228 cmd += " -v 1" |
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229 launcher +="os.system( \"" + cmd + "\" )\n" |
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230 launcher += "sys.exit(0)\n" |
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231 jobFileHandler.write(launcher) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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232 jobFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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233 os.chmod( iJob.launcher, stat.S_IREAD | stat.S_IWRITE | stat.S_IEXEC ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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234 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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235 if __name__ == "__main__": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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236 unittest.main() |