Mercurial > repos > yufei-luo > s_mart

comparison commons/core/launcher/test/expFiles/expJobScriptSQLiteWithFilesCopyTemplate.py @ 6:769e306b7933

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Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 #!/usr/bin/env python
2
3 import os
4 import sys
5 import time
6 import shutil
7 from commons.core.checker.RepetException import RepetException
8 from commons.core.sql.TableJobAdaptator import TableJobAdaptator
9 from commons.core.sql.DbMySql import DbMySql
10 from commons.core.sql.DbSQLite import DbSQLite
11 from commons.core.sql.Job import Job
12
13 try:
14 newDir = None
15 print os.uname()
16 beginTime = time.time()
17 print 'beginTime=%f' % beginTime
18 print "work in dir '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch'"
19 sys.stdout.flush()
20 if not os.path.exists("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch"):
21 raise IOError("ERROR: temporary directory '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch' doesn't exist")
22
23 fileSize = 0
24 if not os.path.exists("groupid"):
25 fileSize = 0.500000
26 freeGigaNeededInTmpDir = float(1 + fileSize)
27 freeSpace = os.statvfs("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
28 if ((freeSpace.f_bavail * freeSpace.f_frsize) / 1073741824.0 < freeGigaNeededInTmpDir):
29 raise RepetException("ERROR: less than %.2fG of input file in '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch'" % freeGigaNeededInTmpDir)
30
31 os.chdir("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
32 if not os.path.exists("groupid"):
33 try:
34 os.mkdir("groupid")
35 except OSError, e :
36 if e.args[0] != 17:
37 raise RepetException("ERROR: can't create 'groupid'")
38 os.chdir("groupid")
39 os.system("touch bank.fa")
40 else:
41 os.chdir("groupid")
42
43 newDir = "groupid_job1_20110505-105353"
44 if os.path.exists(newDir):
45 shutil.rmtree(newDir)
46 os.mkdir(newDir)
47 os.chdir(newDir)
48
49 queue = "main.q"
50 iJob = Job("jobs", jobname = "job1", groupid = "groupid", queue = queue, node = os.getenv("HOSTNAME"))
51 iDb = DbSQLite("/home/user/workspace/repet_pipe/commons/core/launcher/test/jobs")
52 iTJA = TableJobAdaptator(iDb, "jobs")
53 print "current status: %s" % iTJA.getJobStatus(iJob)
54 iTJA.changeJobStatus(iJob, "running")
55 print "updated status: %s" % iTJA.getJobStatus(iJob)
56 iDb.close()
57
58 log = os.system("touch dummyFile1")
59 if log != 0:
60 raise RepetException("ERROR: job returned %i" % log)
61 else:
62 print "job finished successfully"
63 shutil.move("dummyFile1", "/home/user/workspace/repet_pipe/commons/core/launcher/test")
64
65 os.chdir("..")
66 shutil.rmtree(newDir)
67
68 iDb = DbSQLite("/home/user/workspace/repet_pipe/commons/core/launcher/test/jobs")
69 iTJA = TableJobAdaptator(iDb, "jobs")
70 print "current status: %s" % iTJA.getJobStatus(iJob)
71 iTJA.changeJobStatus(iJob, "finished")
72 print "updated status: %s" % iTJA.getJobStatus(iJob)
73 iDb.close()
74
75 endTime = time.time()
76 print 'endTime=%f' % endTime
77 print 'executionTime=%f' % (endTime - beginTime)
78 print os.uname()
79
80 except IOError, e :
81 print e
82 queue = "main.q"
83 iJob = Job("jobs", jobname = "job1", groupid = "groupid", queue = queue, node = os.getenv("HOSTNAME"))
84 iDb = DbSQLite("/home/user/workspace/repet_pipe/commons/core/launcher/test/jobs")
85 iTJA = TableJobAdaptator(iDb, "jobs")
86 print "current status: %s" % iTJA.getJobStatus(iJob)
87 iTJA.changeJobStatus(iJob, "error")
88 print "updated status: %s" % iTJA.getJobStatus(iJob)
89 iDb.close()
90 sys.exit(1)
91
92 except Exception, e :
93 print "tmpDir is : /home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch"
94 print "cDir is : /home/user/workspace/repet_pipe/commons/core/launcher/test/"
95 print e
96 if newDir != None and os.path.exists("../%s" % newDir) and not os.path.exists("/home/user/workspace/repet_pipe/commons/core/launcher/test//%s" % newDir):
97 os.chdir("..")
98 shutil.move(newDir, "/home/user/workspace/repet_pipe/commons/core/launcher/test//%s" % newDir)
99 queue = "main.q"
100 iJob = Job("jobs", jobname = "job1", groupid = "groupid", queue = queue, node = os.getenv("HOSTNAME"))
101 iDb = DbSQLite("/home/user/workspace/repet_pipe/commons/core/launcher/test/jobs")
102 iTJA = TableJobAdaptator(iDb, "jobs")
103 print "current status: %s" % iTJA.getJobStatus(iJob)
104 iTJA.changeJobStatus(iJob, "error")
105 print "updated status: %s" % iTJA.getJobStatus(iJob)
106 iDb.close()
107 sys.exit(1)