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1 from commons.core.utils.FileUtils import FileUtils
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2 from commons.core.launcher.WriteScript import WriteScript
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3 from commons.core.sql.Job import Job
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4 from commons.core.sql.DbFactory import DbFactory
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5 from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
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6 import unittest
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7 import os
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8 import shutil
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9 import time
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10 import threading
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11
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12 class Test_WriteScript(unittest.TestCase):
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13
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14 def setUp(self):
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15 self._testDir = os.getcwd()
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16 self._acronym = "dummyAcronym"
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17 self._jobTable = "dummyJobsTable"
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18 self._iDb = DbFactory.createInstance()
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19 self._iDb.createTable(self._jobTable, "jobs", overwrite = True)
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20 self._jobdb = TableJobAdaptatorFactory.createInstance(self._iDb, self._jobTable)
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21 self._job = Job()
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22 self._job.groupid = "groupid"
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23 self._job.jobname = self._acronym
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24 self._job.launcher = "ClusterLauncher"
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25 self._jobdb.recordJob(self._job)
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26 self._dummyScratch = "dummyScratch"
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27 os.mkdir(self._dummyScratch)
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28 os.chdir(self._dummyScratch)
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29 self._tmpDir = os.getcwd()
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30 self._iScriptWriter = WriteScript(self._job, self._jobdb, self._testDir, self._tmpDir)
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31
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32 def tearDown(self):
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33 self._iDb.dropTable(self._jobTable)
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34 self._iDb.close()
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35 if FileUtils.isRessourceExists(self._dummyScratch):
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36 shutil.rmtree(self._dummyScratch)
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37
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38 def test_run(self):
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39 isScriptAsRun = False
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40 fileToCreate = 'dummyFile'
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41 cmdStart = "log = os.system( \"touch %s\" )\n" % fileToCreate
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42 cmdFinish = "os.system(\"mv %s %s\" )\n" % (fileToCreate, self._testDir)
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43 pyFileName = "%s/ClusterLauncher_%s.py" % (os.getcwd(), self._acronym)
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44
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45 self._iScriptWriter.run(cmdStart, cmdFinish, pyFileName)
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46 os.system("python %s" % pyFileName)
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47
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48 os.chdir(self._testDir)
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49 if FileUtils.isRessourceExists(fileToCreate):
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50 os.remove(fileToCreate)
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51 isScriptAsRun = True
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52 expJobStatus = "finished"
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53 obsJobStatus = self._jobdb.getJobStatus(self._job)
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54
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55 self.assertTrue(isScriptAsRun)
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56 self.assertEquals(expJobStatus, obsJobStatus)
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57
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58 def test_run_with_cmdSize_and_cmdCopy(self):
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59 isScriptAsRun = False
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60 fileToCreate = 'dummyFile'
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61 fileSize = 0.5
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62 cmdSize = "fileSize = %f\n" % fileSize
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63 cmdCopy = "os.system(\"touch bank.fa\")\n"
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64 cmdStart = "log = os.system(\"touch %s\")\n" % fileToCreate
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65 cmdFinish = "shutil.move(\"%s\", \"%s\")" % (fileToCreate, self._testDir)
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66 pyFileName = "%s/ClusterLauncher_%s.py" % (os.getcwd(), self._acronym)
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67
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68 iWriteScript = WriteScript(self._job, self._jobdb, self._testDir, self._tmpDir, True)
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69 iWriteScript.run(cmdStart, cmdFinish, pyFileName, cmdSize, cmdCopy)
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70 os.system("python %s" % pyFileName)
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71
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72 os.chdir(self._testDir)
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73 if FileUtils.isRessourceExists(fileToCreate):
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74 os.remove(fileToCreate)
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75 isScriptAsRun = True
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76 expJobStatus = "finished"
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77 obsJobStatus = self._jobdb.getJobStatus(self._job)
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78
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79 self.assertTrue(isScriptAsRun)
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80 self.assertEquals(expJobStatus, obsJobStatus)
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81
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82 #TODO: how to test ?
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83 # def test_run_2_jobs_trying_to_create_same_groupIdDir(self):
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84 # fileToCreate1 = 'dummyFile1'
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85 # fileToCreate2 = 'dummyFile2'
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86 # flagFileOSError = "osErrorRaised"
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87 #
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88 # fileSize = 0.5
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89 # cmd_checkSize = ""
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90 # cmd_checkSize += "if not os.path.exists( \"%s\" ):\n" % self._job.groupid
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91 # cmd_checkSize += "\tfileSize = %f\n" % fileSize
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92 #
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93 # cmd_checkGroupidDir1 = ""
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94 # cmd_checkGroupidDir1 += "if not os.path.exists(\"%s\"):\n" % self._job.groupid
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95 # cmd_checkGroupidDir1 += "\ttry:\n"
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96 # cmd_checkGroupidDir1 += "\t\ttime.sleep(10)\n"
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97 # cmd_checkGroupidDir1 += "\t\tos.mkdir(\"%s\")\n" % self._job.groupid
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98 # cmd_checkGroupidDir1 += "\texcept OSError, e :\n"
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99 # cmd_checkGroupidDir1 += "\t\tos.system(\"touch %s\")\n" % flagFileOSError
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100 # cmd_checkGroupidDir1 += "\t\tif e.args[0] != 17:\n"
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101 # cmd_checkGroupidDir1 += "\t\t\traise RepetException(\"ERROR: can't create '%s'\")\n" % self._job.groupid
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102 # cmd_checkGroupidDir1 += "\tos.chdir(\"%s\")\n" % self._job.groupid
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103 # cmd_checkGroupidDir1 += "\tos.system(\"touch bank.fa\")\n" #cp
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104 # cmd_checkGroupidDir1 += "else:\n"
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105 # cmd_checkGroupidDir1 += "\tos.chdir(\"%s\")\n" % self._job.groupid
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106 #
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107 # cmdStart1 = "log = os.system(\"touch %s\")\n" % fileToCreate1
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108 # cmdFinish1 = "shutil.move(\"%s\", \"%s\")\n" % (fileToCreate1, self._testDir)
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109 # pyFileName1 = "%s/ClusterLauncher1_job1.py" % os.getcwd()
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110 #
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111 # cmd_checkGroupidDir2 = ""
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112 # cmd_checkGroupidDir2 += "if not os.path.exists(\"%s\"):\n" % self._job.groupid
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113 # cmd_checkGroupidDir2 += "\ttry:\n"
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114 # cmd_checkGroupidDir2 += "\t\tos.mkdir(\"%s\")\n" % self._job.groupid
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115 # cmd_checkGroupidDir2 += "\texcept OSError, e :\n"
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116 # cmd_checkGroupidDir2 += "\t\tif e.args[0] != 17:\n"
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117 # cmd_checkGroupidDir2 += "\t\t\traise RepetException(\"ERROR: can't create '%s'\")\n" % self._job.groupid
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118 # cmd_checkGroupidDir2 += "\tos.chdir(\"%s\")\n" % self._job.groupid
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119 # cmd_checkGroupidDir2 += "\tos.system(\"touch bank.fa\")\n" #cp
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120 # cmd_checkGroupidDir2 += "else:\n"
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121 # cmd_checkGroupidDir2 += "\tos.chdir(\"%s\")\n" % self._job.groupid
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122 #
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123 # cmdStart2 = "log = os.system(\"touch %s\")\n" % fileToCreate2
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124 # cmdFinish2 = "shutil.move(\"%s\", \"%s\")\n" % (fileToCreate2, self._testDir)
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125 # pyFileName2 = "%s/ClusterLauncher2_job2.py" % os.getcwd()
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126 #
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127 # job1 = Job(self._jobTable, jobname = "job1", groupid = self._job.groupid)
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128 # self._jobdb.recordJob(job1)
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129 # job2 = Job(self._jobTable, jobname = "job2", groupid = self._job.groupid)
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130 # self._jobdb.recordJob(job2)
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131 # iScriptWriter1 = WriteScript(job1, self._jobdb, self._testDir, self._tmpDir)
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132 # iScriptWriter1.run(cmdStart1, cmdFinish1, pyFileName1, cmd_checkSize, cmd_checkGroupidDir1)
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133 # iScriptWriter2 = WriteScript(job2, self._jobdb, self._testDir, self._tmpDir)
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134 # iScriptWriter2.run(cmdStart2, cmdFinish2, pyFileName2, cmd_checkSize, cmd_checkGroupidDir2)
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135 #
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136 # iCFT1 = CreateFileThread(pyFileName1)
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137 # iCFT2 = CreateFileThread(pyFileName2)
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138 # iCFT1.start()
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139 # iCFT2.start()
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140 # while iCFT1.isAlive() or iCFT2.isAlive():
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141 # time.sleep(5)
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142 # self.assertTrue(FileUtils.isRessourceExists(flagFileOSError))
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143 # os.chdir(self._testDir)
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144 #
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145 # if FileUtils.isRessourceExists(fileToCreate1):
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146 # os.remove(fileToCreate1)
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147 #
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148 # if FileUtils.isRessourceExists(fileToCreate2):
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149 # os.remove(fileToCreate2)
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150
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151 def test_run_2_lines_in_cmd_start(self):
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152 isScriptAsRun = False
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153 fileToCreate = 'dummyFile'
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154
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155 cmdStart = "log = 0\n\t"
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156 cmdStart += "if True:\n\t"
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157 cmdStart += "\tos.system( \"touch dummyFile\" )\n"
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158 cmdFinish = "os.system(\"mv %s %s\" )\n" % (fileToCreate, self._testDir)
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159 pyFileName = "%s/ClusterLauncher_%s.py" % (os.getcwd(), self._acronym)
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160
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161 self._iScriptWriter.run(cmdStart, cmdFinish, pyFileName)
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162 os.system("python %s" % pyFileName)
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163
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164 os.chdir(self._testDir)
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165 if FileUtils.isRessourceExists(fileToCreate):
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166 os.remove(fileToCreate)
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167 isScriptAsRun = True
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168 self.assertTrue(isScriptAsRun)
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169
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170 def test_run_2_lines_in_cmd_finish(self):
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171 isScriptAsRun = False
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172 fileToCreate = 'dummyFile'
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173
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174 cmdStart = "log = 0\n\t"
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175 cmdStart += "if True:\n\t"
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176 cmdStart += "\tos.system( \"touch dummyFile\" )\n"
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177 cmdFinish = "if True:\n\t"
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178 cmdFinish += "\tos.system(\"mv %s %s\" )\n" % (fileToCreate, self._testDir)
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179 pyFileName = "%s/ClusterLauncher_%s.py" % (os.getcwd(), self._acronym)
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180
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181 self._iScriptWriter.run(cmdStart, cmdFinish, pyFileName)
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182 os.system("python %s" % pyFileName)
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183
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184 os.chdir(self._testDir)
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185 if FileUtils.isRessourceExists(fileToCreate):
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186 os.remove(fileToCreate)
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187 isScriptAsRun = True
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188 self.assertTrue(isScriptAsRun)
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189
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190 def test_fillTemplate_with_JobScriptTemplate(self):
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191 os.chdir("..")
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192 d = {
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193 "tmpDir" : "/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch",
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194 "jobTableName" : "dummyJobsTable",
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195 "groupId" : "groupid",
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196 "jobName" : "job1",
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197 "launcher" : "ClusterLauncher",
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198 "time" : "20110505-105353",
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199 "repet_path" : "/home/user/workspace/repet_pipe",
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200 "repet_host" : "pisano",
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201 "repet_user" : "user",
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202 "repet_pw" : "user",
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203 "repet_db" : "repet_user",
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204 "repet_port" : "3306",
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205 "cmdStart" : "log = os.system(\"touch dummyFile1\")",
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206 "cmdFinish" : "shutil.move(\"dummyFile1\", \"/home/user/workspace/repet_pipe/commons/core/launcher/test\")",
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207 "cDir" : "/home/user/workspace/repet_pipe/commons/core/launcher/test/"
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208 }
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209 expFileName = "expFiles/expJobScriptTemplate.py"
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210 obsFileName = "obsFile.py"
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211
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212 iWS = WriteScript()
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213 iWS.fillTemplate(obsFileName, d)
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214 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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215 os.remove(obsFileName)
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216
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217 def test_fillTemplate_with_JobScriptTemplate_2_lines_in_cmd_start(self):
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218 os.chdir("..")
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219 d = {
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220 "tmpDir" : "/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch",
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221 "jobTableName" : "dummyJobsTable",
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222 "groupId" : "groupid",
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223 "jobName" : "job1",
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224 "launcher" : "ClusterLauncher",
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225 "time" : "20110505-105353",
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226 "repet_path" : "/home/user/workspace/repet_pipe",
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227 "repet_host" : "pisano",
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228 "repet_user" : "user",
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229 "repet_pw" : "user",
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230 "repet_db" : "repet_user",
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231 "repet_port" : "3306",
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232 "cmdStart" : "print \"Hello Yufei\"\n\tlog = os.system(\"touch dummyFile1\")",
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233 "cmdFinish" : "shutil.move(\"dummyFile1\", \"/home/user/workspace/repet_pipe/commons/core/launcher/test\")",
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234 "cDir" : "/home/user/workspace/repet_pipe/commons/core/launcher/test/"
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235 }
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236 expFileName = "expFiles/expJobScriptTemplate_cmdWith2Lines.py"
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237 obsFileName = "obsFile.py"
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238
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239 iWS = WriteScript()
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240 iWS.fillTemplate(obsFileName, d)
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241 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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242 os.remove(obsFileName)
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243
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244 def test_fillTemplate_with_JobScriptWithFilesCopyTemplate(self):
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245 os.chdir("..")
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246 d = {
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247 "tmpDir" : "/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch",
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248 "jobTableName" : "dummyJobsTable",
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249 "groupId" : "groupid",
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250 "jobName" : "job1",
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251 "launcher" : "ClusterLauncher",
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252 "time" : "20110505-105353",
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253 "repet_path" : "/home/user/workspace/repet_pipe",
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254 "repet_host" : "pisano",
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255 "repet_user" : "user",
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256 "repet_pw" : "user",
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257 "repet_db" : "repet_user",
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258 "repet_port" : "3306",
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259 "cmdStart" : "log = os.system(\"touch dummyFile1\")",
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260 "cmdFinish" : "shutil.move(\"dummyFile1\", \"/home/user/workspace/repet_pipe/commons/core/launcher/test\")",
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261 "cDir" : "/home/user/workspace/repet_pipe/commons/core/launcher/test/",
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262 "cmdSize" : "fileSize = 0.500000",
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263 "cmdCopy" : "os.system(\"touch bank.fa\")"
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264 }
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265 expFileName = "expFiles/expJobScriptWithFilesCopyTemplate.py"
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266 obsFileName = "obsFile.py"
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267
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268 iWS = WriteScript(chooseTemplateWithCopy = True)
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269 iWS.fillTemplate(obsFileName, d)
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270 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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271 os.remove(obsFileName)
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272
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273 def test_fillTemplate_with_JobScriptTemplateLight(self):
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274 os.chdir("..")
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275 d = {
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276 "tmpDir" : "/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch",
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277 "jobTableName" : "dummyJobsTable",
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278 "groupId" : "groupid",
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279 "jobName" : "job1",
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280 "launcher" : "ClusterLauncher",
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281 "time" : "20110505-105353",
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282 "repet_path" : "/home/user/workspace/repet_pipe",
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283 "cmdStart" : "log = os.system(\"touch dummyFile1\")",
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284 "cmdFinish" : "shutil.move(\"dummyFile1\", \"/home/user/workspace/repet_pipe/commons/core/launcher/test\")",
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285 "cDir" : "/home/user/workspace/repet_pipe/commons/core/launcher/test/",
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286 "cmdSize" : "fileSize = 0.500000",
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287 "cmdCopy" : "os.system(\"touch bank.fa\")"
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288 }
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289 expFileName = "expFiles/expJobScriptTemplateLight.py"
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290 obsFileName = "obs.py"
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291
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292 iWS = WriteScript(chooseTemplateLight = True)
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293 iWS.fillTemplate(obsFileName, d)
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294 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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295 os.remove(obsFileName)
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296
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297 def test_createJobScriptDict(self):
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298 os.chdir("..")
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299 cmd_start = "log = os.system(\"touch dummyFile1\")"
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300 cmd_finish = "shutil.move(\"dummyFile1\", \"/home/user/workspace/repet_pipe/commons/core/launcher/test\")"
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301 cmd_size = ""
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302 cmd_copy = ""
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303 expDict = {
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304 "tmpDir" : self._tmpDir,
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305 "jobTableName" : self._jobTable,
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306 "groupId" : self._job.groupid,
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307 "jobName" : self._acronym,
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308 "launcher" : self._job.launcher,
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309 "time" : time.strftime("%Y%m%d-%H%M%S"),
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310 "repet_path" : os.environ["REPET_PATH"],
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311 "repet_host" : os.environ["REPET_HOST"],
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312 "repet_user" : os.environ["REPET_USER"],
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313 "repet_pw" : os.environ["REPET_PW"],
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314 "repet_db" : os.environ["REPET_DB"],
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315 "repet_port" : os.environ["REPET_PORT"],
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316 "cmdStart" : cmd_start,
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317 "cmdFinish" : cmd_finish,
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318 "cDir" : self._testDir,
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319 "cmdSize" : cmd_size,
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320 "cmdCopy" : cmd_copy
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321 }
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322 obsDict = self._iScriptWriter.createJobScriptDict(cmd_start, cmd_finish, cmd_size, cmd_copy)
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323 self.assertEquals(expDict, obsDict)
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324
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325 def test_createJobScriptDict_with_cmdSize_and_cmdCopy(self):
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326 os.chdir("..")
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327 cmd_start = "log = os.system(\"touch dummyFile1\")"
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328 cmd_finish = "shutil.move(\"dummyFile1\", \"/home/user/workspace/repet_pipe/commons/core/launcher/test\")"
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329 cmd_size = "fileSize = 0.500000"
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330 cmd_copy = "os.system(\"touch bank.fa\")"
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331 expDict = {
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332 "tmpDir" : self._tmpDir,
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333 "jobTableName" : self._jobTable,
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334 "groupId" : self._job.groupid,
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335 "jobName" : self._acronym,
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336 "launcher" : self._job.launcher,
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337 "time" : time.strftime("%Y%m%d-%H%M%S"),
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338 "repet_path" : os.environ["REPET_PATH"],
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339 "repet_host" : os.environ["REPET_HOST"],
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340 "repet_user" : os.environ["REPET_USER"],
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341 "repet_pw" : os.environ["REPET_PW"],
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342 "repet_db" : os.environ["REPET_DB"],
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343 "repet_port" : os.environ["REPET_PORT"],
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344 "cmdStart" : cmd_start,
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345 "cmdFinish" : cmd_finish,
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346 "cDir" : self._testDir,
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347 "cmdSize" : cmd_size,
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348 "cmdCopy" : cmd_copy
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349 }
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350 obsDict = self._iScriptWriter.createJobScriptDict(cmd_start, cmd_finish, cmd_size, cmd_copy)
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351 self.assertEquals(expDict, obsDict)
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352
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353 class CreateFileThread(threading.Thread):
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354
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355 def __init__(self, pyFileName):
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356 threading.Thread.__init__(self)
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357 self._pyFileName = pyFileName
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358
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359 def run(self):
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360 os.system("python %s" % self._pyFileName)
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361
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362 test_suite = unittest.TestSuite()
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363 test_suite.addTest( unittest.makeSuite( Test_WriteScript ) )
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364 if __name__ == "__main__":
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365 unittest.TextTestRunner(verbosity=2).run( test_suite )
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