1#!/usr/bin/env python 

2# -*- coding: utf-8 -*- 

3# 

4# Copyright (c) 2017, the cclib development team 

5# 

6# This file is part of cclib (http://cclib.github.io) and is distributed under 

7# the terms of the BSD 3-Clause License. 

8 

9"""Script for loading data from computational chemistry files.""" 

10 

11 

12import glob 

13import logging 

14import os.path 

15import difflib 

16from functools import partial 

17from pprint import pprint 

18 

19# This is needed for testing purposes only. 

20import sys 

21 

22import numpy 

23 

24from cclib.parser import ccData 

25from cclib.io import ccread, URL_PATTERN 

26 

27 

28# Set up options for pretty-printing output. 

29pprint = partial(pprint, width=120, compact=True) 

30numpy.set_printoptions(linewidth=120) 

31 

32 

33def ccget(): 

34 """Parse files with cclib based on command line arguments.""" 

35 

36 import argparse 

37 

38 parser = argparse.ArgumentParser() 

39 

40 parser.add_argument( 

41 "attribute_or_compchemlogfile", nargs="+", 

42 help="one or more attributes to be parsed from one ore more logfiles", 

43 ) 

44 

45 group = parser.add_mutually_exclusive_group() 

46 

47 group.add_argument( 

48 "--list", "-l", 

49 action="store_true", 

50 help="print a list of attributes available in each file", 

51 ) 

52 group.add_argument( 

53 "--json", "-j", 

54 action="store_true", 

55 help="the given logfile is in CJSON format", 

56 ) 

57 group.add_argument( 

58 "--multi", "-m", 

59 action="store_true", 

60 help="parse multiple input files as one input stream", 

61 ) 

62 

63 parser.add_argument( 

64 "--verbose", "-v", 

65 action="store_true", 

66 help="more verbose parsing output (only errors by default)", 

67 ) 

68 parser.add_argument( 

69 "--future", "-u", 

70 action="store_true", 

71 help="use experimental features (currently optdone_as_list)", 

72 ) 

73 parser.add_argument( 

74 "--full", "-f", 

75 action="store_true", 

76 help="toggle full print behaviour for attributes", 

77 ) 

78 

79 args = parser.parse_args() 

80 

81 arglist = args.attribute_or_compchemlogfile 

82 showattr = args.list 

83 cjsonfile = args.json 

84 multifile = args.multi 

85 verbose = args.verbose 

86 future = args.future 

87 full = args.full 

88 

89 # Toggle full print behaviour for numpy arrays. 

90 if full: 

91 numpy.set_printoptions(threshold=numpy.inf) 

92 

93 # We need at least one attribute and the filename, so two arguments, or 

94 # just one filename if we want to list attributes that can be extracted. 

95 # In multifile mode, we generally want at least two filenames, so the 

96 # expected number of arguments is a bit different. 

97 if not multifile: 

98 correct_number = (not showattr and len(arglist) > 1) or (showattr and len(arglist) > 0) 

99 else: 

100 correct_number = (not showattr and len(arglist) > 2) or (showattr and len(arglist) > 1) 

101 if not correct_number: 

102 print("The number of arguments does not seem to be correct.") 

103 parser.print_usage() 

104 parser.exit(1) 

105 

106 # Figure out which are the attribute names and which are the filenames or links. 

107 # Note that in Linux, the shell expands wild cards, but not so in Windows, 

108 # so try to do that here using glob. 

109 attrnames = [] 

110 filenames = [] 

111 for arg in arglist: 

112 if arg not in ccData._attrlist: 

113 fuzzy_attr = difflib.get_close_matches(arg, ccData._attrlist, n=1, cutoff=0.85) 

114 if len(fuzzy_attr) > 0: 

115 fuzzy_attr = fuzzy_attr[0] 

116 logging.warning("Attribute '{0}' not found, but attribute '{1}' is close. " 

117 "Using '{1}' instead.".format(arg, fuzzy_attr)) 

118 arg = fuzzy_attr 

119 if arg in ccData._attrlist: 

120 attrnames.append(arg) 

121 elif URL_PATTERN.match(arg) or os.path.isfile(arg): 

122 filenames.append(arg) 

123 else: 

124 wildcardmatches = glob.glob(arg) 

125 if wildcardmatches: 

126 filenames.extend(wildcardmatches) 

127 else: 

128 print("%s is neither a filename nor an attribute name." % arg) 

129 parser.print_usage() 

130 parser.exit(1) 

131 

132 # Since there is some ambiguity to the correct number of arguments, check 

133 # that there is at least one filename (or two in multifile mode), and also 

134 # at least one attribute to parse if the -l option was not passed. 

135 if len(filenames) == 0: 

136 print("No logfiles given") 

137 parser.exit(1) 

138 if multifile and len(filenames) == 1: 

139 print("Expecting at least two logfiles in multifile mode") 

140 parser.exit(1) 

141 if not showattr and len(attrnames) == 0: 

142 print("No attributes given") 

143 parser.exit(1) 

144 

145 # This should be sufficient to correctly handle multiple files, that is to 

146 # run the loop below only once with all logfiles in the variable `filename`. 

147 # Although, perhaps it would be clearer to abstract the contents of the loop 

148 # into another function. 

149 if multifile: 

150 filenames = [filenames] 

151 

152 # Now parse each file and print out the requested attributes. 

153 for filename in filenames: 

154 

155 if multifile: 

156 name = ", ".join(filename[:-1]) + " and " + filename[-1] 

157 else: 

158 name = filename 

159 

160 # The keyword dictionary are not used so much. but could be useful for 

161 # passing options downstream. For example, we might use --future for 

162 # triggering experimental or alternative behavior (as with optdone). 

163 kwargs = {} 

164 if verbose: 

165 kwargs['verbose'] = True 

166 kwargs['loglevel'] = logging.INFO 

167 else: 

168 kwargs['verbose'] = False 

169 kwargs['loglevel'] = logging.ERROR 

170 if future: 

171 kwargs['future'] = True 

172 if cjsonfile: 

173 kwargs['cjson'] = True 

174 

175 print("Attempting to read %s" % name) 

176 data = ccread(filename, **kwargs) 

177 

178 if data is None: 

179 print("Cannot figure out the format of '%s'" % name) 

180 print("Report this to the cclib development team if you think it is an error.") 

181 print("\n" + parser.format_usage()) 

182 parser.exit(1) 

183 

184 if showattr: 

185 print("cclib can parse the following attributes from %s:" % name) 

186 if cjsonfile: 

187 for key in data: 

188 print(key) 

189 break 

190 for attr in data._attrlist: 

191 if hasattr(data, attr): 

192 print(" %s" % attr) 

193 else: 

194 invalid = False 

195 for attr in attrnames: 

196 if cjsonfile: 

197 if attr in data: 

198 print("%s:\n%s" % (attr, data[attr])) 

199 continue 

200 else: 

201 if hasattr(data, attr): 

202 print(attr) 

203 attr_val = getattr(data, attr) 

204 # List of attributes to be printed with new lines 

205 if attr in data._listsofarrays and full: 

206 for val in attr_val: 

207 pprint(val) 

208 else: 

209 pprint(attr_val) 

210 continue 

211 

212 print("Could not parse %s from this file." % attr) 

213 invalid = True 

214 if invalid: 

215 parser.print_help() 

216 

217 

218if __name__ == "__main__": 

219 

220 ccget()