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1 from commons.core.utils.FileUtils import FileUtils
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2 import shutil
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3 import unittest
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4 import os
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5 from commons.tools.LaunchMatcherInParallel import LaunchMatcherInParallel
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6
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7 class Test_F_LaunchMatcherInParallel(unittest.TestCase):
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8
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9 CLUSTER_HOST = "compute-2-46.local"
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10
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11 def setUp(self):
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12 self._configFileName = "TE.cfg"
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13 self._writeConfig()
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14
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15 def tearDown(self):
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16 FileUtils.removeFilesByPattern("DmelChr4*")
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17 os.remove(self._configFileName)
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18
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19 def test_run_as_class_1_seq(self):
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20 inFileName = "DmelChr4.align"
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21 fastaFileName = "DmelChr4.fa"
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22 inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], inFileName)
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23 inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], fastaFileName)
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24 os.symlink(inFilePath, inFileName)
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25 os.symlink(inFastaPath, fastaFileName)
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26 expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"]
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27 expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"]
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28
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29 obsPathFileName = "%s.match.path" % inFileName
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30 obsTabFileName = "%s.match.tab" % inFileName
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31
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32 iLaunchMatcherInParallel = LaunchMatcherInParallel(align=inFileName, queryFileName=fastaFileName, subjectFileName=fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True, config=self._configFileName)
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33 iLaunchMatcherInParallel.run()
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34
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35 self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
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36 self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
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37
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38 def test_run_as_class_n_seq_less_jobs_than_n(self):
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39 inFileName = "DmelChr4_dummy.align"
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40 fastaFileName = "DmelChr4.fa"
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41 inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], inFileName)
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42 inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], fastaFileName)
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43 os.symlink(inFilePath, inFileName)
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44 os.symlink(inFastaPath, fastaFileName)
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45 expPathFileName = "%s/Tools/DmelChr4_dummy.align.match.path" % os.environ["REPET_DATA"]
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46 expTabFileName = "%s/Tools/DmelChr4_dummy.align.match.tab" % os.environ["REPET_DATA"]
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47
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48 obsPathFileName = "%s.match.path" % inFileName
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49 obsTabFileName = "%s.match.tab" % inFileName
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50
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51 iLaunchMatcherInParallel = LaunchMatcherInParallel(align=inFileName, queryFileName=fastaFileName, subjectFileName=fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True, config=self._configFileName, doClean=True)
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52 iLaunchMatcherInParallel.run()
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53
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54 self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
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55 self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
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56
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57 def test_run_as_class_n_seq_less_jobs_than_n_not_merged_results(self):
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58 inFileName = "DmelChr4_dummy.align"
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59 fastaFileName = "DmelChr4.fa"
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60 inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], inFileName)
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61 inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], fastaFileName)
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62 os.symlink(inFilePath, inFileName)
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63 os.symlink(inFastaPath, fastaFileName)
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64
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65 iLaunchMatcherInParallel = LaunchMatcherInParallel(align=inFileName, queryFileName=fastaFileName, subjectFileName=fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True, config=self._configFileName, maxFileSize=100, mergeResults=False)
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66 iLaunchMatcherInParallel.run()
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67
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68 baseFileName = os.path.splitext(inFileName)[0]
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69 lExpMatchFileNames = ["%s_1.align.match.path" % baseFileName, "%s_2.align.match.path" % baseFileName, "%s_3.align.match.path" % baseFileName]
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70 lExpTabFileNames = ["%s_1.align.match.tab" % baseFileName, "%s_2.align.match.tab" % baseFileName, "%s_3.align.match.tab" % baseFileName]
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71 for i in range(0,3):
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72 self.assertTrue(FileUtils.isRessourceExists("tmpMatcher/%s" % lExpMatchFileNames[i]))
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73 self.assertTrue(FileUtils.isRessourceExists("tmpMatcher/%s" % lExpTabFileNames[i]))
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74 shutil.rmtree("tmpMatcher")
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75
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76 def _writeConfig(self):
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77 with open(self._configFileName, "w") as fh:
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78 fh.write("[jobs]\n")
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79 if os.getenv("HOSTNAME") == self.CLUSTER_HOST:
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80 fh.write("resources: test\n")
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81 else:
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82 fh.write("resources:\n")
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83 fh.write("tmpDir:\n")
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84 fh.write("copy: no\n")
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85 fh.write("clean: yes\n")
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86
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87 if __name__ == "__main__":
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88 unittest.main() |
