Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/srptExportTable.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #!/usr/bin/env python
2
3 import user, os, sys, getopt, exceptions, ConfigParser
4
5 #-----------------------------------------------------------------------------
6
7 def help():
8
9 """
10 Give the list of the command-line options.
11 """
12
13 print
14 print "usage:",sys.argv[0]," [ options ]"
15 print "options:"
16 print " -h: this help"
17 print " -i: name of the table to export"
18 print " -o: name of the output file (default=inTable)"
19 print " -p: extra parameters to add to the SQL query (e.g. 'ORDER BY path')"
20 print " -k: keep the first line"
21 print " -C: configuration file from TEdenovo or TEannot pipeline"
22 print " -H: MySQL host (if no configuration file)"
23 print " -U: MySQL user (if no configuration file)"
24 print " -P: MySQL password (if no configuration file)"
25 print " -D: MySQL database (if no configuration file)"
26 print " -v: verbose (default=0/1)"
27 print
28
29 #-----------------------------------------------------------------------------
30
31 def main():
32
33 """
34 This program exports all the data contained in a MySQL table into a flat file in the current directory.
35 """
36
37 inTable = ""
38 outFileName = ""
39 param = ""
40 keepFirstLine = False
41 configFileName = ""
42 host = ""
43 user = ""
44 passwd = ""
45 dbname = ""
46 verbose = 0
47
48 try:
49 opts, args = getopt.getopt(sys.argv[1:],"hi:o:p:kC:H:U:P:D:v:")
50 except getopt.GetoptError, err:
51 print str(err)
52 help()
53 sys.exit(1)
54 for o,a in opts:
55 if o == "-h":
56 help()
57 sys.exit(0)
58 elif o == "-i":
59 inTable = a
60 elif o == "-o":
61 outFileName = a
62 elif o == "-p":
63 param = a
64 elif o == "-k":
65 keepFirstLine = True
66 elif o == "-C":
67 configFileName = a
68 elif o == "-H":
69 host = a
70 elif o == "-U":
71 user = a
72 elif o == "-P":
73 passwd = a
74 elif o == "-D":
75 dbname = a
76 elif o == "-v":
77 verbose = int(a)
78
79 if inTable == "":
80 print "*** Error: missing input table name"
81 help()
82 sys.exit(1)
83
84 if configFileName != "":
85 config = ConfigParser.ConfigParser()
86 config.readfp( open(configFileName) )
87 host = config.get("repet_env","repet_host")
88 user = config.get("repet_env","repet_user")
89 passwd = config.get("repet_env","repet_pw")
90 dbname = config.get("repet_env","repet_db")
91 if host == "" or user == "" or passwd == "" or dbname == "":
92 if os.environ.get( "REPET_HOST" ) not in [ "", None ]:
93 host = os.environ.get( "REPET_HOST" )
94 if os.environ.get( "REPET_USER" ) not in [ "", None ]:
95 user = os.environ.get( "REPET_USER" )
96 if os.environ.get( "REPET_PW" ) not in [ "", None ]:
97 passwd = os.environ.get( "REPET_PW" )
98 if os.environ.get( "REPET_DB" ) not in [ "", None ]:
99 dbname = os.environ.get( "REPET_DB" )
100 if host == "" or user == "" or passwd == "" or dbname == "":
101 print "*** Error: missing information about MySQL connection"
102 sys.exit(1)
103
104 if outFileName == "":
105 outFileName = inTable
106
107 prg = "mysql"
108 cmd = prg
109 cmd += " -h %s" % ( host )
110 cmd += " -u %s" % ( user )
111 cmd += " -p\"%s\"" % ( passwd )
112 cmd += " --database=%s" % ( dbname )
113 cmd += " -e\"SELECT * FROM %s" % ( inTable )
114 if param != "":
115 cmd += " %s" % ( param )
116 cmd += ";\""
117 cmd += " > "
118 if keepFirstLine == False:
119 cmd += "%s.tmp" % ( outFileName )
120 else:
121 cmd += "%s" % ( outFileName )
122 if verbose > 0: print cmd; sys.stdout.flush()
123 log = os.system( cmd )
124 if log != 0:
125 print "*** Error: %s returned %i" % ( prg, log )
126 sys.exit(1)
127
128 if keepFirstLine == False:
129 tmpFileName = "%s.tmp" % ( outFileName )
130 tmpFile = open( tmpFileName, "r" )
131 outFile = open( outFileName, "w" )
132 i = 0
133 for line in tmpFile:
134 if i > 0:
135 outFile.write( line )
136 i += 1
137 tmpFile.close()
138 outFile.close()
139 os.remove( tmpFileName )
140
141 return 0
142
143 #----------------------------------------------------------------------------
144
145 if __name__ == '__main__':
146 main()