Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/launcher/test/Test_Launcher.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.utils.FileUtils import FileUtils |
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2 from commons.core.launcher.Launcher import Launcher |
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3 from commons.core.launcher.WriteScript import WriteScript |
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4 from commons.core.stat.Stat import Stat |
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5 from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory |
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6 from commons.core.sql.DbFactory import DbFactory |
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7 from commons.core.sql.Job import Job |
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8 import unittest |
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9 import os |
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10 import shutil |
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11 import time |
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12 import stat |
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13 |
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14 #TODO: Test_F_Launcher.py : to execute prepareCommands() and runSingleJob() |
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15 # to test runLauncherForMultipleJobs() |
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16 #TODO: check clean of "Test_runSingleJob" |
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17 #TODO: refactoring => choose between "self._queue" or "lResources" to set resources |
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18 class Test_Launcher(unittest.TestCase): |
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19 |
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20 SARUMAN_NAME = "compute-2-46.local" |
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21 |
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22 def setUp(self): |
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23 self._cDir = os.getcwd() |
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24 self._tmpDir = self._cDir |
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25 self._groupid = "test" |
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26 self._jobTable = "dummyJobTable" |
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27 self._iDb = DbFactory.createInstance() |
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28 self._iDb.createTable(self._jobTable, "jobs", overwrite = True) |
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29 self._jobdb = TableJobAdaptatorFactory.createInstance(self._iDb, self._jobTable) |
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30 self._queue = "" |
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31 self._configFileName = "dummyConfigFile" |
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32 |
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33 def tearDown(self): |
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34 self._iDb.dropTable(self._jobTable) |
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35 self._iDb.close() |
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36 FileUtils.removeFilesByPattern('*.e*') |
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37 FileUtils.removeFilesByPattern('*.o*') |
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38 FileUtils.removeFilesByPattern('launcherFileTest_BeginRun.py') |
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39 FileUtils.removeFilesByPattern(self._configFileName) |
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40 FileUtils.removeFilesByPattern('ClusterLauncher_*') |
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41 |
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42 def test__init__wrong_fields_for_job_table(self): |
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43 self._iDb.dropTable(self._jobTable) |
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44 sqlCmd = "CREATE TABLE " + self._jobTable |
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45 sqlCmd += " ( jobid INT UNSIGNED" |
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46 sqlCmd += ", jobname VARCHAR(255)" |
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47 sqlCmd += ", groupid VARCHAR(255)" |
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48 sqlCmd += ", command TEXT" |
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49 sqlCmd += ", launcher VARCHAR(1024)" |
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50 sqlCmd += ", queue VARCHAR(255)" |
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51 sqlCmd += ", status VARCHAR(255)" |
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52 sqlCmd += ", time DATETIME" |
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53 sqlCmd += ", node VARCHAR(255) )" |
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54 self._iDb.execute(sqlCmd) |
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55 acronym = "Test__init__" |
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56 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym) |
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57 lExpFields = sorted(["jobid", "jobname", "groupid", "launcher", "queue", "resources", "status", "time", "node"]) |
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58 lObsFields = sorted(self._iDb.getFieldList(self._jobTable)) |
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59 self.assertEquals(lExpFields, lObsFields) |
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60 expJob = Job(queue = self._queue) |
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61 obsJob = iLauncher.job |
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62 self.assertEquals(expJob, obsJob) |
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63 |
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64 def test__init__withResources(self): |
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65 queue = "main.q mem_free=3G" |
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66 acronym = "Test__init__" |
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67 expQueue = "main.q" |
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68 explResources = ['mem_free=3G'] |
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69 expJob = Job(queue = expQueue, lResources = explResources) |
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70 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", queue, self._groupid, acronym) |
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71 obsJob = iLauncher.job |
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72 self.assertEquals(expJob, obsJob) |
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73 |
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74 def test_createGroupidIfItNotExist(self): |
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75 acronym = "checkGroupID" |
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76 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym) |
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77 iLauncher.createGroupidIfItNotExist() |
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78 obsGroupid = iLauncher.job.groupid |
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79 self.assertEquals(self._groupid, obsGroupid) |
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80 |
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81 def test_createGroupidIfItNotExist_without_groupid(self): |
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82 groupid = "" |
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83 acronym = "checkGroupID" |
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84 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, groupid, acronym) |
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85 iLauncher.createGroupidIfItNotExist() |
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86 obsGroupid = iLauncher.job.groupid |
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87 self.assertTrue(obsGroupid != "") |
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88 |
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89 def test_beginRun_with_Job_finished_in_Table(self): |
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90 acronym = "BeginRun" |
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91 iJob = Job(queue = self._queue) |
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92 self._jobdb.recordJob(iJob) |
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93 self._jobdb.changeJobStatus(iJob, "finished") |
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94 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym) |
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95 iLauncher.beginRun() |
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96 self.assertTrue(self._jobdb.getCountStatus(self._groupid, "finished") == 0) |
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97 |
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98 def test_beginRun_with_Job_unfinished_in_Table(self): |
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99 acronym = "testU_BeginRun" |
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100 cmd_start = "log = os.system( \"date;sleep 10;date\" )\n" |
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101 pyFileName = "%s/launcherFileTest_BeginRun.py" % os.getcwd() |
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102 if Test_Launcher.SARUMAN_NAME == os.getenv("HOSTNAME"): |
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103 iJob = Job(1, acronym, self._groupid, "", cmd_start, pyFileName, lResources=["test=TRUE"]) |
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104 else: |
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105 iJob = Job(1, acronym, self._groupid, "", cmd_start, pyFileName) |
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106 iWriteScript = WriteScript(iJob, self._jobdb, self._cDir, self._tmpDir) |
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107 iWriteScript.run(cmd_start, "", pyFileName) |
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108 os.chmod(pyFileName, stat.S_IREAD | stat.S_IWRITE | stat.S_IEXEC) |
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109 self._jobdb.submitJob(iJob) |
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110 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym) |
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111 |
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112 iLauncher.beginRun() |
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113 |
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114 self.assertTrue(self._jobdb.getCountStatus(self._groupid, "finished") == 1) |
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115 |
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116 def test_getStatsOfExecutionTime(self): |
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117 acronym = "test_statTime" |
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118 |
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119 expLValues = [1000.00000, 1000.00000] |
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120 expStat = Stat(expLValues) |
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121 |
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122 f = open(acronym +".o1", "w") |
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123 f.write("executionTime=1000.000000") |
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124 f.close() |
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125 f = open(acronym +".o2", "w") |
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126 f.write("executionTime=1000.000000") |
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127 f.close() |
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128 |
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129 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym) |
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130 obsStat = iLauncher.getStatsOfExecutionTime(acronym) |
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131 |
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132 self.assertEqual(expStat, obsStat) |
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133 |
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134 def test_endRun(self): |
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135 acronym = "testU_EndRun" |
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136 cmd_start = "log = os.system( \"date;sleep 10;date\" )\n" |
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137 pyFileName = "%s/launcherFileTest_EndRun.py" % os.getcwd() |
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138 if Test_Launcher.SARUMAN_NAME == os.getenv("HOSTNAME"): |
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139 iJob = Job(1, acronym, self._groupid, "", cmd_start, pyFileName, lResources=["test=TRUE"]) |
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140 else: |
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141 iJob = Job(1, acronym, self._groupid, "", cmd_start, pyFileName) |
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142 |
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143 iWriteScript = WriteScript(iJob, self._jobdb, self._cDir, self._tmpDir) |
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144 iWriteScript.run(cmd_start, "", pyFileName) |
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145 os.chmod(pyFileName, stat.S_IREAD | stat.S_IWRITE | stat.S_IEXEC) |
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146 self._jobdb.submitJob(iJob) |
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147 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym) |
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148 iLauncher.job.groupid = self._groupid |
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149 iLauncher.endRun() |
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150 |
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151 self.assertTrue(self._jobdb.getCountStatus(self._groupid, "finished") == 0) |
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152 self.assertTrue(self._jobdb.getCountStatus(self._groupid, "error") == 0) |
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153 self.assertTrue(self._jobdb.getCountStatus(self._groupid, "waiting") == 0) |
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154 |
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155 os.remove(iJob.launcher) |
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156 |
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157 def test_clean(self): |
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158 acronym = "test_clean" |
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159 f = open("ClusterLauncher" + acronym + ".py", "w") |
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160 f.close() |
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161 f = open(acronym + ".o1", "w") |
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162 f.close() |
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163 f = open(acronym + ".e1", "w") |
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164 f.close() |
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165 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym) |
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166 iLauncher.clean(acronym) |
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167 self.assertFalse(FileUtils.isRessourceExists("ClusterLauncher" + acronym + ".py")) |
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168 |
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169 def test_clean_without_acronym(self): |
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170 acronym = "" |
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171 acronym2 = "toto" |
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172 f = open("ClusterLauncher" + acronym2 + ".py", "w") |
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173 f.close() |
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174 f = open(acronym2 + ".o1", "w") |
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175 f.close() |
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176 f = open(acronym2 + ".e1", "w") |
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177 f.close() |
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178 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym2) |
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179 iLauncher.clean(acronym) |
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180 self.assertFalse(FileUtils.isRessourceExists("ClusterLauncher" + acronym2 + ".py")) |
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181 |
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182 def test_getQueueNameAndResources_queue_no_resource(self): |
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183 configQueue = "all.q" |
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184 expQueueName = "all.q" |
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185 expResources = [] |
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186 iLauncher = Launcher(self._jobdb) |
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187 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue) |
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188 self.assertEquals(expQueueName, obsQueueName) |
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189 self.assertEquals(expResources, obsResources) |
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190 |
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191 def test_getQueueNameAndResources_queue_one_resource(self): |
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192 configQueue = "test.q 'test=TRUE'" |
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193 expQueueName = "test.q" |
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194 expResources = ["test=TRUE"] |
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195 iLauncher = Launcher(self._jobdb) |
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196 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue) |
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197 self.assertEquals(expQueueName, obsQueueName) |
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198 self.assertEquals(expResources, obsResources) |
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199 |
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200 def test_getQueueNameAndResources_queue_two_resources(self): |
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201 configQueue = "big.q 's_data=8G s_cpu=96:00:00'" |
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202 expQueueName = "big.q" |
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203 expResources = ["s_data=8G", "s_cpu=96:00:00"] |
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204 iLauncher = Launcher(self._jobdb) |
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205 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue) |
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206 self.assertEquals(expQueueName, obsQueueName) |
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207 self.assertEquals(expResources, obsResources) |
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208 |
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209 def test_getQueueNameAndResources_no_queue_no_resource(self): |
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210 configQueue = "" |
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211 expQueueName = "" |
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212 expResources = [] |
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213 iLauncher = Launcher(self._jobdb) |
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214 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue) |
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215 self.assertEquals(expQueueName, obsQueueName) |
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216 self.assertEquals(expResources, obsResources) |
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217 |
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218 def test_getQueueNameAndResources_no_queue_one_resource(self): |
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219 configQueue = "s_data=8G" |
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220 expQueueName = "" |
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221 expResources = ["s_data=8G"] |
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222 iLauncher = Launcher(self._jobdb) |
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223 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue) |
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224 self.assertEquals(expQueueName, obsQueueName) |
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225 self.assertEquals(expResources, obsResources) |
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226 |
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227 def test_getQueueNameAndResources_no_queue_two_resource(self): |
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228 configQueue = "s_data=8G s_cpu=96:00:00" |
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229 expQueueName = "" |
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230 expResources = ["s_data=8G", "s_cpu=96:00:00"] |
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231 iLauncher = Launcher(self._jobdb) |
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232 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue) |
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233 self.assertEquals(expQueueName, obsQueueName) |
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234 self.assertEquals(expResources, obsResources) |
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235 |
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236 # #TODO: test with at least 2 lines in cmd |
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237 def test_runSingleJob(self): |
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238 acronym = "Test_runSingleJob" |
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239 os.mkdir(acronym) |
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240 os.chdir(acronym) |
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241 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", os.getcwd(), self._tmpDir, "", self._queue, self._groupid, acronym) |
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242 iLauncher.job.groupid = self._groupid |
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243 iLauncher.job.jobname = acronym |
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244 iLauncher.job.queue = self._queue |
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245 if Test_Launcher.SARUMAN_NAME == os.getenv("HOSTNAME"): |
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246 iLauncher.job.lResources = ["test=TRUE"] |
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247 cmd = "log = os.system(\"touch 'YuFei'\")\n" |
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248 iLauncher.runSingleJob(cmd) |
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249 time.sleep(20) |
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250 jobStatus = self._jobdb.getJobStatus(iLauncher.job) |
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251 os.chdir(self._cDir) |
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252 shutil.rmtree(acronym) |
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253 self.assertEqual(jobStatus, "finished") |
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254 |
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255 def test_runSingleJob_catch_error_wrong_tmpDir(self): |
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256 acronym = "Test_runSingleJob_catch_error" |
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257 os.mkdir(acronym) |
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258 os.chdir(acronym) |
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259 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", os.getcwd(), "%s/toto" % self._tmpDir, "", self._queue, self._groupid, acronym) |
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260 iLauncher.job.groupid = self._groupid |
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261 iLauncher.job.jobname = acronym |
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262 iLauncher.job.queue = self._queue |
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263 if Test_Launcher.SARUMAN_NAME == os.getenv("HOSTNAME"): |
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264 iLauncher.job.lResources = ["test=TRUE"] |
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265 cmd = "log = os.system(\"touch 'YuFei'\")\n" |
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266 iLauncher.runSingleJob(cmd) |
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267 time.sleep(20) |
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268 jobStatus = self._jobdb.getJobStatus(iLauncher.job) |
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269 os.chdir(self._cDir) |
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270 shutil.rmtree(acronym) |
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271 self.assertEqual(jobStatus, "error") |
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272 |
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273 def test_runSingleJob_catch_error_wrong_cmd(self): |
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274 acronym = "Test_runSingleJob_catch_error" |
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275 os.mkdir(acronym) |
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276 os.chdir(acronym) |
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277 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", os.getcwd(), self._tmpDir, "", self._queue, self._groupid, acronym) |
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278 iLauncher.job.groupid = self._groupid |
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279 iLauncher.job.jobname = acronym |
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280 iLauncher.job.queue = self._queue |
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281 if Test_Launcher.SARUMAN_NAME == os.getenv("HOSTNAME"): |
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282 iLauncher.job.lResources = ["test=TRUE"] |
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283 cmd = "log = os.system(\"truc -i toto\")\n" |
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284 iLauncher.runSingleJob(cmd) |
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285 time.sleep(20) |
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286 jobStatus = self._jobdb.getJobStatus(iLauncher.job) |
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287 self._jobdb.cleanJobGroup(self._groupid) |
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288 os.chdir(self._cDir) |
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289 shutil.rmtree(acronym) |
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290 self.assertEqual(jobStatus, "error") |
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291 |
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292 def test_prepareCommands(self): |
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293 expCmdStart = "os.symlink(\"../Yufei_chunks.fa\", \"Yufei_chunks.fa\")\n\tos.symlink(\"../Yufei_chunks.fa_cut\", \"Yufei_chunks.fa_cut\")\n\tlog = os.system(\"touch file\")\n\t" |
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294 expCmdFinish = "if os.path.exists(\"yufei.align\"):\n\t\tshutil.move(\"yufei.align\", \"yufeiLuo/.\" )\n\t" |
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295 expCmdSize = "fileSize = 3.2\n\t\t" |
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296 expCmdCopy = "shutil.copy(\"PY/Yufei_db/Yufei_chunks.fa\", \".\")\n\t\tshutil.copy(\"PY/Yufei_db/Yufei_chunks.fa_cut\", \".\")\n\t\t" |
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297 |
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298 lCmdStart = [] |
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299 lCmdStart.append("os.symlink(\"../Yufei_chunks.fa\", \"Yufei_chunks.fa\")") |
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300 lCmdStart.append("os.symlink(\"../Yufei_chunks.fa_cut\", \"Yufei_chunks.fa_cut\")") |
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301 lCmds = [] |
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302 lCmds.append("log = os.system(\"touch file\")") |
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303 lCmdFinish = [] |
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304 lCmdFinish.append("if os.path.exists(\"yufei.align\"):") |
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305 lCmdFinish.append("\tshutil.move(\"yufei.align\", \"yufeiLuo/.\" )") |
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306 lCmdSize = [] |
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307 lCmdSize.append("fileSize = 3.2") |
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308 lCmdCopy = [] |
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309 lCmdCopy.append("shutil.copy(\"PY/Yufei_db/Yufei_chunks.fa\", \".\")") |
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310 lCmdCopy.append("shutil.copy(\"PY/Yufei_db/Yufei_chunks.fa_cut\", \".\")") |
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311 |
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312 iLauncher = Launcher(self._jobdb) |
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313 obsCmdStart, obsCmdFinish, obsCmdSize, obsCmdCopy = iLauncher.prepareCommands(lCmds, lCmdStart, lCmdFinish, lCmdSize, lCmdCopy) |
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314 |
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315 self.assertEquals(expCmdStart, obsCmdStart) |
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316 self.assertEquals(expCmdFinish, obsCmdFinish) |
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317 self.assertEquals(expCmdSize, obsCmdSize) |
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318 self.assertEquals(expCmdCopy, obsCmdCopy) |
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319 |
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320 def test_getSystemCommand(self): |
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321 prg = "touch" |
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322 lArgs = [] |
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323 lArgs.append("file") |
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324 expCmd = "log = os.system(\"touch file\")" |
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325 iLauncher = Launcher(self._jobdb) |
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326 obsCmd = iLauncher.getSystemCommand(prg, lArgs) |
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327 self.assertEquals(expCmd, obsCmd) |
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328 |
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329 |
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330 test_suite = unittest.TestSuite() |
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331 test_suite.addTest( unittest.makeSuite( Test_Launcher ) ) |
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332 if __name__ == "__main__": |
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333 unittest.TextTestRunner(verbosity=2).run( test_suite ) |