Mercurial > repos > devteam > column_maker

comparison column_maker.py @ 0:08a01b2ce4cd draft

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Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:56:15 -0400
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children 464b9305180e
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-1:000000000000 0:08a01b2ce4cd
1 #!/usr/bin/env python
2 # This tool takes a tab-delimited textfile as input and creates another column in the file which is the result of
3 # a computation performed on every row in the original file. The tool will skip over invalid lines within the file,
4 # informing the user about the number of lines skipped.
5
6 import sys, re
7 # These functions may be used in compute expression:
8 from math import log,exp,sqrt,ceil,floor
9
10
11 assert sys.version_info[:2] >= ( 2, 4 )
12
13 def stop_err( msg ):
14 sys.stderr.write( msg )
15 sys.exit()
16
17 inp_file = sys.argv[1]
18 out_file = sys.argv[2]
19 expr = sys.argv[3]
20 round_result = sys.argv[4]
21 try:
22 in_columns = int( sys.argv[5] )
23 except:
24 stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
25 if in_columns < 2:
26 # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
27 stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
28 try:
29 in_column_types = sys.argv[6].split( ',' )
30 except:
31 stop_err( "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
32 if len( in_column_types ) != in_columns:
33 stop_err( "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
34
35 # Unescape if input has been escaped
36 mapped_str = {
37 '__lt__': '<',
38 '__le__': '<=',
39 '__eq__': '==',
40 '__ne__': '!=',
41 '__gt__': '>',
42 '__ge__': '>=',
43 '__sq__': '\'',
44 '__dq__': '"',
45 }
46 for key, value in mapped_str.items():
47 expr = expr.replace( key, value )
48
49 operators = 'is|not|or|and'
50 builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor'
51 string_and_list_methods = [ name for name in dir('') + dir([]) if not name.startswith('_') ]
52 whitelist = "^([c0-9\+\-\*\/\(\)\.\'\"><=,:! ]|%s|%s|%s)*$" % (operators, builtin_and_math_functions, '|'.join(string_and_list_methods))
53 if not re.compile(whitelist).match(expr):
54 stop_err("Invalid expression")
55
56 # Prepare the column variable names and wrappers for column data types
57 cols, type_casts = [], []
58 for col in range( 1, in_columns + 1 ):
59 col_name = "c%d" % col
60 cols.append( col_name )
61 col_type = in_column_types[ col - 1 ].strip()
62 if round_result == 'no' and col_type == 'int':
63 col_type = 'float'
64 type_cast = "%s(%s)" % ( col_type, col_name )
65 type_casts.append( type_cast )
66
67 col_str = ', '.join( cols ) # 'c1, c2, c3, c4'
68 type_cast_str = ', '.join( type_casts ) # 'str(c1), int(c2), int(c3), str(c4)'
69 assign = "%s = line.split( '\\t' )" % col_str
70 wrap = "%s = %s" % ( col_str, type_cast_str )
71 skipped_lines = 0
72 first_invalid_line = 0
73 invalid_line = None
74 lines_kept = 0
75 total_lines = 0
76 out = open( out_file, 'wt' )
77
78 # Read input file, skipping invalid lines, and perform computation that will result in a new column
79 code = '''
80 for i, line in enumerate( file( inp_file ) ):
81 total_lines += 1
82 line = line.rstrip( '\\r\\n' )
83 if not line or line.startswith( '#' ):
84 skipped_lines += 1
85 if not invalid_line:
86 first_invalid_line = i + 1
87 invalid_line = line
88 continue
89 try:
90 %s
91 %s
92 new_val = %s
93 if round_result == "yes":
94 new_val = int( round( new_val ) )
95 new_line = line + '\\t' + str( new_val )
96 print >> out, new_line
97 lines_kept += 1
98 except:
99 skipped_lines += 1
100 if not invalid_line:
101 first_invalid_line = i + 1
102 invalid_line = line
103 ''' % ( assign, wrap, expr )
104
105 valid_expr = True
106 try:
107 exec code
108 except Exception, e:
109 out.close()
110 if str( e ).startswith( 'invalid syntax' ):
111 valid_expr = False
112 stop_err( 'Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr )
113 else:
114 stop_err( str( e ) )
115
116 if valid_expr:
117 out.close()
118 valid_lines = total_lines - skipped_lines
119 print 'Creating column %d with expression %s' % ( in_columns + 1, expr )
120 if valid_lines > 0:
121 print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines )
122 else:
123 print 'Possible invalid expression "%s" or non-existent column referenced. See tool tips, syntax and examples.' % expr
124 if skipped_lines > 0:
125 print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )