Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/launcher/test/Test_Launcher.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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children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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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diff changeset
125 f = open(acronym +".o2", "w")
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yufei-luo
parents:
diff changeset
126 f.write("executionTime=1000.000000")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
127 f.close()
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yufei-luo
parents:
diff changeset
128
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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129 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
130 obsStat = iLauncher.getStatsOfExecutionTime(acronym)
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yufei-luo
parents:
diff changeset
131
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yufei-luo
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diff changeset
132 self.assertEqual(expStat, obsStat)
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yufei-luo
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diff changeset
133
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yufei-luo
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diff changeset
134 def test_endRun(self):
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yufei-luo
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diff changeset
135 acronym = "testU_EndRun"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
136 cmd_start = "log = os.system( \"date;sleep 10;date\" )\n"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
137 pyFileName = "%s/launcherFileTest_EndRun.py" % os.getcwd()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
138 if Test_Launcher.SARUMAN_NAME == os.getenv("HOSTNAME"):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
139 iJob = Job(1, acronym, self._groupid, "", cmd_start, pyFileName, lResources=["test=TRUE"])
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
140 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
141 iJob = Job(1, acronym, self._groupid, "", cmd_start, pyFileName)
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diff changeset
142
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
143 iWriteScript = WriteScript(iJob, self._jobdb, self._cDir, self._tmpDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
144 iWriteScript.run(cmd_start, "", pyFileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
145 os.chmod(pyFileName, stat.S_IREAD | stat.S_IWRITE | stat.S_IEXEC)
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yufei-luo
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diff changeset
146 self._jobdb.submitJob(iJob)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
147 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
148 iLauncher.job.groupid = self._groupid
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yufei-luo
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diff changeset
149 iLauncher.endRun()
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yufei-luo
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diff changeset
150
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
151 self.assertTrue(self._jobdb.getCountStatus(self._groupid, "finished") == 0)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
152 self.assertTrue(self._jobdb.getCountStatus(self._groupid, "error") == 0)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
153 self.assertTrue(self._jobdb.getCountStatus(self._groupid, "waiting") == 0)
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yufei-luo
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diff changeset
154
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yufei-luo
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diff changeset
155 os.remove(iJob.launcher)
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yufei-luo
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diff changeset
156
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yufei-luo
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diff changeset
157 def test_clean(self):
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yufei-luo
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diff changeset
158 acronym = "test_clean"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
159 f = open("ClusterLauncher" + acronym + ".py", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
160 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
161 f = open(acronym + ".o1", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
162 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
163 f = open(acronym + ".e1", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
164 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
165 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
166 iLauncher.clean(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
167 self.assertFalse(FileUtils.isRessourceExists("ClusterLauncher" + acronym + ".py"))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
168
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
169 def test_clean_without_acronym(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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170 acronym = ""
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
171 acronym2 = "toto"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
172 f = open("ClusterLauncher" + acronym2 + ".py", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
173 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
174 f = open(acronym2 + ".o1", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
175 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
176 f = open(acronym2 + ".e1", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
177 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
178 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", self._cDir, self._tmpDir, "", self._queue, self._groupid, acronym2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
179 iLauncher.clean(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
180 self.assertFalse(FileUtils.isRessourceExists("ClusterLauncher" + acronym2 + ".py"))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
181
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
182 def test_getQueueNameAndResources_queue_no_resource(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
183 configQueue = "all.q"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
184 expQueueName = "all.q"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
185 expResources = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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186 iLauncher = Launcher(self._jobdb)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
187 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
188 self.assertEquals(expQueueName, obsQueueName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
189 self.assertEquals(expResources, obsResources)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
190
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
191 def test_getQueueNameAndResources_queue_one_resource(self):
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diff changeset
192 configQueue = "test.q 'test=TRUE'"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
193 expQueueName = "test.q"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
194 expResources = ["test=TRUE"]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
195 iLauncher = Launcher(self._jobdb)
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yufei-luo
parents:
diff changeset
196 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
197 self.assertEquals(expQueueName, obsQueueName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
198 self.assertEquals(expResources, obsResources)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
199
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
200 def test_getQueueNameAndResources_queue_two_resources(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
201 configQueue = "big.q 's_data=8G s_cpu=96:00:00'"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
202 expQueueName = "big.q"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
203 expResources = ["s_data=8G", "s_cpu=96:00:00"]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
204 iLauncher = Launcher(self._jobdb)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
205 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
206 self.assertEquals(expQueueName, obsQueueName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
207 self.assertEquals(expResources, obsResources)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
208
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
209 def test_getQueueNameAndResources_no_queue_no_resource(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
210 configQueue = ""
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
211 expQueueName = ""
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
212 expResources = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
213 iLauncher = Launcher(self._jobdb)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
214 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
215 self.assertEquals(expQueueName, obsQueueName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
216 self.assertEquals(expResources, obsResources)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
217
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
218 def test_getQueueNameAndResources_no_queue_one_resource(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
219 configQueue = "s_data=8G"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
220 expQueueName = ""
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
221 expResources = ["s_data=8G"]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
222 iLauncher = Launcher(self._jobdb)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
223 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
224 self.assertEquals(expQueueName, obsQueueName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
225 self.assertEquals(expResources, obsResources)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
226
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
227 def test_getQueueNameAndResources_no_queue_two_resource(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
228 configQueue = "s_data=8G s_cpu=96:00:00"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
229 expQueueName = ""
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
230 expResources = ["s_data=8G", "s_cpu=96:00:00"]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
231 iLauncher = Launcher(self._jobdb)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
232 obsQueueName, obsResources = iLauncher.getQueueNameAndResources(configQueue)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
233 self.assertEquals(expQueueName, obsQueueName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
234 self.assertEquals(expResources, obsResources)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
235
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
236 # #TODO: test with at least 2 lines in cmd
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
237 def test_runSingleJob(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
238 acronym = "Test_runSingleJob"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
239 os.mkdir(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
240 os.chdir(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
241 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", os.getcwd(), self._tmpDir, "", self._queue, self._groupid, acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
242 iLauncher.job.groupid = self._groupid
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
243 iLauncher.job.jobname = acronym
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
244 iLauncher.job.queue = self._queue
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
245 if Test_Launcher.SARUMAN_NAME == os.getenv("HOSTNAME"):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
246 iLauncher.job.lResources = ["test=TRUE"]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
247 cmd = "log = os.system(\"touch 'YuFei'\")\n"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
248 iLauncher.runSingleJob(cmd)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
249 time.sleep(20)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
250 jobStatus = self._jobdb.getJobStatus(iLauncher.job)
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251 os.chdir(self._cDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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252 shutil.rmtree(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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253 self.assertEqual(jobStatus, "finished")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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254
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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255 def test_runSingleJob_catch_error_wrong_tmpDir(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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256 acronym = "Test_runSingleJob_catch_error"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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257 os.mkdir(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
258 os.chdir(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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259 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", os.getcwd(), "%s/toto" % self._tmpDir, "", self._queue, self._groupid, acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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260 iLauncher.job.groupid = self._groupid
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
261 iLauncher.job.jobname = acronym
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
262 iLauncher.job.queue = self._queue
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
263 if Test_Launcher.SARUMAN_NAME == os.getenv("HOSTNAME"):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
264 iLauncher.job.lResources = ["test=TRUE"]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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265 cmd = "log = os.system(\"touch 'YuFei'\")\n"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
266 iLauncher.runSingleJob(cmd)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
267 time.sleep(20)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
268 jobStatus = self._jobdb.getJobStatus(iLauncher.job)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
269 os.chdir(self._cDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
270 shutil.rmtree(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
271 self.assertEqual(jobStatus, "error")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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272
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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273 def test_runSingleJob_catch_error_wrong_cmd(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
274 acronym = "Test_runSingleJob_catch_error"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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275 os.mkdir(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
276 os.chdir(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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277 iLauncher = Launcher(self._jobdb, os.getcwd(), "", "", os.getcwd(), self._tmpDir, "", self._queue, self._groupid, acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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278 iLauncher.job.groupid = self._groupid
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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279 iLauncher.job.jobname = acronym
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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280 iLauncher.job.queue = self._queue
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
281 if Test_Launcher.SARUMAN_NAME == os.getenv("HOSTNAME"):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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282 iLauncher.job.lResources = ["test=TRUE"]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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283 cmd = "log = os.system(\"truc -i toto\")\n"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
284 iLauncher.runSingleJob(cmd)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
285 time.sleep(20)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
286 jobStatus = self._jobdb.getJobStatus(iLauncher.job)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
287 self._jobdb.cleanJobGroup(self._groupid)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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288 os.chdir(self._cDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
289 shutil.rmtree(acronym)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
290 self.assertEqual(jobStatus, "error")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
291
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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294 expCmdFinish = "if os.path.exists(\"yufei.align\"):\n\t\tshutil.move(\"yufei.align\", \"yufeiLuo/.\" )\n\t"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
295 expCmdSize = "fileSize = 3.2\n\t\t"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
296 expCmdCopy = "shutil.copy(\"PY/Yufei_db/Yufei_chunks.fa\", \".\")\n\t\tshutil.copy(\"PY/Yufei_db/Yufei_chunks.fa_cut\", \".\")\n\t\t"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
297
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
298 lCmdStart = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
299 lCmdStart.append("os.symlink(\"../Yufei_chunks.fa\", \"Yufei_chunks.fa\")")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
300 lCmdStart.append("os.symlink(\"../Yufei_chunks.fa_cut\", \"Yufei_chunks.fa_cut\")")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
301 lCmds = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
302 lCmds.append("log = os.system(\"touch file\")")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
303 lCmdFinish = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
304 lCmdFinish.append("if os.path.exists(\"yufei.align\"):")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
305 lCmdFinish.append("\tshutil.move(\"yufei.align\", \"yufeiLuo/.\" )")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
306 lCmdSize = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
307 lCmdSize.append("fileSize = 3.2")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
308 lCmdCopy = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
309 lCmdCopy.append("shutil.copy(\"PY/Yufei_db/Yufei_chunks.fa\", \".\")")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
310 lCmdCopy.append("shutil.copy(\"PY/Yufei_db/Yufei_chunks.fa_cut\", \".\")")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
311
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
312 iLauncher = Launcher(self._jobdb)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
313 obsCmdStart, obsCmdFinish, obsCmdSize, obsCmdCopy = iLauncher.prepareCommands(lCmds, lCmdStart, lCmdFinish, lCmdSize, lCmdCopy)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
314
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
315 self.assertEquals(expCmdStart, obsCmdStart)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
316 self.assertEquals(expCmdFinish, obsCmdFinish)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
317 self.assertEquals(expCmdSize, obsCmdSize)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
318 self.assertEquals(expCmdCopy, obsCmdCopy)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
319
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
320 def test_getSystemCommand(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
321 prg = "touch"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
322 lArgs = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
323 lArgs.append("file")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
324 expCmd = "log = os.system(\"touch file\")"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
325 iLauncher = Launcher(self._jobdb)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
326 obsCmd = iLauncher.getSystemCommand(prg, lArgs)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
327 self.assertEquals(expCmd, obsCmd)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
328
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
329
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
330 test_suite = unittest.TestSuite()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
331 test_suite.addTest( unittest.makeSuite( Test_Launcher ) )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
332 if __name__ == "__main__":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
333 unittest.TextTestRunner(verbosity=2).run( test_suite )