Mercurial > repos > yufei-luo > s_mart

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

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed 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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12 class Test_F_TableJobAdaptator(unittest.TestCase):
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14 def setUp(self):
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15 self._jobTableName = "dummyJobTable"
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16 self._iJA = TableJobAdaptatorFactory.createJobInstance()
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18 def tearDown(self):
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19 pass
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21 def test_submitJob(self):
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22 job1 = self._createJobInstance("job1")
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23 self._createLauncherFile(job1, self._iJA)
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24 job2 = self._createJobInstance("job2")
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25 self._createLauncherFile(job2, self._iJA)
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26 job3 = self._createJobInstance("job3")
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27 self._createLauncherFile(job3, self._iJA)
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29 self._iJA.submitJob( job1, maxNbWaitingJobs=3, checkInterval=5, verbose=0 )
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30 self._iJA.submitJob( job2, maxNbWaitingJobs=3, checkInterval=5, verbose=0 )
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31 self._iJA.submitJob( job3, maxNbWaitingJobs=3, checkInterval=5, verbose=0 )
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33 time.sleep(120)
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34
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35 expErrorFilePrefix1 = job1.jobname + ".e"
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36 expOutputFilePrefix1 = job1.jobname + ".o"
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37 expErrorFilePrefix2 = job2.jobname + ".e"
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38 expOutputFilePrefix2 = job2.jobname + ".o"
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39 expErrorFilePrefix3 = job3.jobname + ".e"
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40 expOutputFilePrefix3 = job3.jobname + ".o"
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41
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42 lErrorFiles1 = glob.glob(expErrorFilePrefix1 + "*")
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43 lOutputFiles1 = glob.glob(expOutputFilePrefix1 + "*")
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44 lErrorFiles2 = glob.glob(expErrorFilePrefix2 + "*")
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45 lOutputFiles2 = glob.glob(expOutputFilePrefix2 + "*")
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46 lErrorFiles3 = glob.glob(expErrorFilePrefix3 + "*")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 lOutputFiles3 = glob.glob(expOutputFilePrefix3 + "*")
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48
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49 isLErrorFileNotEmpty1 = (len(lErrorFiles1) != 0)
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50 isLOutputFileNotEmpty1 = (len(lOutputFiles1) != 0)
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51 isLErrorFileNotEmpty2 = (len(lErrorFiles2) != 0)
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52 isLOutputFileNotEmpty2 = (len(lOutputFiles2) != 0)
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53 isLErrorFileNotEmpty3 = (len(lErrorFiles3) != 0)
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54 isLOutputFileNotEmpty3 = (len(lOutputFiles3) != 0)
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55
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56 os.system("rm launcherFileTest*.py *.e* *.o*")
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57 self.assertTrue(isLErrorFileNotEmpty1 and isLOutputFileNotEmpty1)
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58 self.assertTrue(isLErrorFileNotEmpty2 and isLOutputFileNotEmpty2)
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59 self.assertTrue(isLErrorFileNotEmpty3 and isLOutputFileNotEmpty3)
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61 def test_submit_and_waitJobGroup(self):
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62 iJob = self._createJobInstance("test")
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63 self._createLauncherFile(iJob, self._iJA)
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65 self._iJA.submitJob( iJob, maxNbWaitingJobs=3, checkInterval=5, verbose=0 )
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66 self._iJA.waitJobGroup(iJob.groupid, 0, 2)
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67
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68 expErrorFilePrefix1 = iJob.jobname + ".e"
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69 expOutputFilePrefix1 = iJob.jobname + ".o"
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70
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71 lErrorFiles1 = glob.glob(expErrorFilePrefix1 + "*")
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72 lOutputFiles1 = glob.glob(expOutputFilePrefix1 + "*")
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73
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74 isLErrorFileExist = (len(lErrorFiles1) != 0)
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75 isLOutputFileExist = (len(lOutputFiles1) != 0)
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76 os.system("rm launcherFileTest*.py *.e* *.o*")
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77 self.assertTrue(isLErrorFileExist and isLOutputFileExist)
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78
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79 def _createJobInstance(self, name):
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80 lResources = []
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81 if os.environ.get("HOSTNAME") == "compute-2-46.local":
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82 lResources.append("test=TRUE")
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83 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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84
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85 def _createLauncherFile(self, iJob, iJA):
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86 iWriteScript = WriteScript(iJob, iJA, os.getcwd(), os.getcwd(), False, True)
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87 iWriteScript.run(iJob.command, "", iJob.launcher)
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88 os.chmod(iJob.launcher, stat.S_IRWXU+stat.S_IRWXG+stat.S_IRWXO)
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89
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90 if __name__ == "__main__":
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91 unittest.main()