1 | #! /usr/bin/env python |
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2 | # coding: utf-8 |
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3 | |
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4 | #************************************************************** |
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5 | # Author: Sebastien Denvil |
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6 | # Contact: Sebastien.Denvil__at__ipsl.jussieu.fr |
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7 | # $Revision:: $ Revision of last commit |
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8 | # $Author:: $ Author of last commit |
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9 | # $Date:: $ Date of last commit |
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10 | # IPSL (2006) |
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11 | # This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC |
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12 | # |
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13 | #************************************************************** |
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14 | |
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15 | import os, pwd, sys, traceback, argparse |
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16 | import xml.etree.ElementTree as ET |
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17 | #import readline, rlcompleter |
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18 | #readline.parse_and_bind("tab: complete") |
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19 | |
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20 | indent = 0 |
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21 | currentDepth = 0 |
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22 | ignoreElems = [] |
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23 | fromField=[] |
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24 | fromFile=[] |
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25 | |
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26 | def dump(args): |
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27 | """Dump XIOS xmls files.""" |
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28 | # Read and dump xios_def_xml |
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29 | for inputFile in args.file: |
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30 | # Read the file_def_xml |
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31 | print '\nReading %s \n|' % (inputFile) |
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32 | try: |
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33 | tree = ET.parse(inputFile) |
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34 | except: |
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35 | print "Parse error. Please fix so that it can be parsed." |
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36 | traceback.print_exc(file=sys.stdout) |
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37 | return |
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38 | root=tree.getroot() |
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39 | # Call the recursive print |
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40 | printRecur(root) |
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41 | |
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42 | def tsquery(args): |
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43 | """query timeseries related parameters from an XIOS xml file.""" |
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44 | if args.verbosity >= 1: print 'Reading timeseries_def_xml=',args.file[0] |
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45 | try: |
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46 | tree = ET.parse(args.file[0]) |
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47 | except: |
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48 | print "Parse error. Please fix so that it can be parsed." |
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49 | traceback.print_exc(file=sys.stdout) |
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50 | return |
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51 | root=tree.getroot() |
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52 | if args.verbosity >= 3: print root.tag, root.attrib |
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53 | findTimeSeries(root) |
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54 | |
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55 | def printRecur(root): |
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56 | """Recursively prints the tree.""" |
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57 | global indent |
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58 | global currentDepth |
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59 | if root.tag in ignoreElems: |
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60 | return |
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61 | print ' '*indent + '|--> %s: %s' % (root.tag, root.attrib) |
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62 | currentDepth += 1 |
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63 | indent += 4 |
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64 | if currentDepth <= args.depth or args.depth == None: |
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65 | for elem in list(root): |
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66 | printRecur(elem) |
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67 | currentDepth -= 1 |
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68 | indent -= 4 |
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69 | |
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70 | def findTimeSeries(root): |
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71 | """Recursively find and list field tag with "timeseries", "id", "output_freq" and enable=.TRUE. attribute.""" |
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72 | if root.tag == 'file' and root.attrib.get('timeseries'): |
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73 | if root.attrib.get('enabled') == '.TRUE.': |
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74 | print 'output_freq=%-5s,id=%s' % (root.attrib.get('output_freq'), root.attrib.get('id')) |
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75 | elif root.tag == 'file' and root.attrib.get('uuid_name'): |
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76 | print 'output_freq=%-5s,name=%85s' % (root.attrib.get('output_freq'), root.attrib.get('name')) |
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77 | else: |
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78 | for elem in list(root): |
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79 | findTimeSeries(elem) |
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80 | |
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81 | def findField(root): |
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82 | """Recursively find and list field tag with "id" or "field_ref" attribute.""" |
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83 | global fromField |
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84 | global fromFile |
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85 | if root.tag in ignoreElems: |
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86 | return |
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87 | if root.tag == 'field' and root.attrib.get('id'): |
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88 | fromField.append(root.attrib.get('id')) |
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89 | elif root.tag == 'field' and root.attrib.get('field_ref'): |
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90 | fromFile.append(root.attrib.get('field_ref')) |
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91 | else: |
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92 | for elem in list(root): |
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93 | findField(elem) |
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94 | |
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95 | def findFieldToRemove(root, fieldToRemove): |
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96 | """Recursively find tag having a field_ref in fieldToRemove.""" |
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97 | if args.verbosity >= 3 and root.tag == 'file' and root.attrib.get('id'): |
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98 | print '\nFIELDS FROM FILE_DEF with id', root.attrib.get('id') |
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99 | for field in root.findall('field'): |
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100 | if args.verbosity >= 3: print 'field_ref=', field.attrib.get('field_ref') |
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101 | if field.attrib.get('field_ref') in fieldToRemove: |
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102 | if args.correction: |
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103 | if args.verbosity >= 2: print 'removing ', field.attrib.get('field_ref') |
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104 | root.remove(field) |
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105 | else: |
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106 | if args.verbosity >= 2: print 'To be removed ', field.attrib.get('field_ref') |
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107 | for elem in list(root): |
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108 | findFieldToRemove(elem, fieldToRemove) |
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109 | |
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110 | def check(args): |
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111 | global fromFile |
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112 | exitCode=0 |
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113 | # Read the field_def_xml |
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114 | if args.verbosity >= 1: print '\nReading field_def_xml=',args.field[0] |
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115 | try: |
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116 | tree = ET.parse(args.field[0]) |
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117 | except: |
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118 | print 'Parse error with %s. Please fix so that it can be parsed.' % (args.field[0]) |
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119 | traceback.print_exc(file=sys.stdout) |
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120 | return |
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121 | root=tree.getroot() |
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122 | if args.verbosity >= 3: print root.tag, root.attrib, '\n' |
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123 | # Build a list of field.id from field_def |
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124 | findField(root) |
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125 | |
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126 | # Loop over file_def files |
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127 | for inputFile in args.file: |
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128 | # Read the file_def_xml |
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129 | if args.verbosity >= 1: print '\nReading file_def_xml=',inputFile |
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130 | try: |
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131 | tree = ET.parse(inputFile) |
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132 | except: |
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133 | print "Parse error. Please fix so that it can be parsed." |
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134 | traceback.print_exc(file=sys.stdout) |
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135 | return |
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136 | root=tree.getroot() |
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137 | fromFile=[] |
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138 | if args.verbosity >= 3: print root.tag, root.attrib, '\n' |
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139 | |
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140 | # Build a list of field_ref from file_def |
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141 | findField(root) |
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142 | #print '4. fromFile=', fromFile |
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143 | |
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144 | # Compare the two lists. fromField must be a superset of fromFile. |
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145 | if set(fromField).issuperset(set(fromFile)): |
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146 | if args.verbosity >= 1: print '\nALL GOOD with %s' % (inputFile) |
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147 | if args.verbosity >= 3: print 'fromField=', fromField |
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148 | if args.verbosity >= 3: print 'fromFile=', fromFile |
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149 | else: |
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150 | if args.verbosity >= 1: print '\nTROUBLE AHEAD with %s' % (inputFile) |
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151 | if args.verbosity >= 3: print ', '.join(sorted(list(set(fromFile)-set(fromField)))) |
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152 | # Identify fields in fromFile but not in fromField |
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153 | fieldToRemove=list(set(fromFile)-set(fromField)) |
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154 | if args.verbosity >= 3: print 'fieldToRemove=', fieldToRemove |
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155 | # |
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156 | # And now locate and remove them if the modify command has been called |
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157 | findFieldToRemove(root, fieldToRemove) |
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158 | # Final steps |
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159 | if args.correction: tree.write('modified.'+inputFile) |
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160 | if not len(fieldToRemove) == 0 and not args.correction: |
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161 | exitCode=1 |
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162 | # The end |
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163 | sys.exit(exitCode) |
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164 | |
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165 | def showtime(args): |
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166 | """ |
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167 | prints table of formatted text format options |
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168 | """ |
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169 | for style in xrange(6): |
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170 | for fg in xrange(30,36): |
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171 | s1 = '' |
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172 | for bg in xrange(40,46): |
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173 | format = ';'.join([str(style), str(fg), str(bg)]) |
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174 | s1 += '\x1b[%sm %s \x1b[0m' % (format, pwd.getpwuid(os.getuid())[4]+' is on fire') |
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175 | print s1 |
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176 | print '\n' |
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177 | |
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178 | def modifydr2xmlIPSL(args): |
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179 | """Recursively find tree element with file tag and change the path prefix of the name attribute.""" |
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180 | |
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181 | # Loop over file_def files |
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182 | for inputFile in args.file: |
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183 | # Read the file_def_xml |
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184 | if args.verbosity >= 1: print '\nReading dr2xml_def_xml=',inputFile |
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185 | try: |
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186 | tree = ET.parse(inputFile) |
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187 | except: |
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188 | print "Parse error. Please fix so that it can be parsed." |
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189 | traceback.print_exc(file=sys.stdout) |
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190 | return |
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191 | root=tree.getroot() |
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192 | if args.verbosity >= 3: print root.tag, root.attrib, '\n' |
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193 | |
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194 | # Change file name prefix to point where we want |
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195 | for elem in tree.iter(tag='file'): |
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196 | if not elem.attrib.get('mode') == 'read': |
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197 | name=elem.attrib.get('name') |
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198 | if args.JobName is not None: |
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199 | name = name.replace('JobName', args.JobName[0]).replace('ModelName', args.ModelName[0]) |
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200 | elem.set('name', os.path.normpath(args.newPath[0]) + '/' + os.path.normpath(name)) |
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201 | else: |
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202 | elem.set('name', os.path.normpath(args.newPath[0]) + '/' + os.path.normpath(name)) |
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203 | if args.verbosity >= 2: print elem.tag, elem.attrib |
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204 | if args.splitLastDate is not None: elem.set('split_last_date', args.splitLastDate[0] + '-01-01 00:00:00') |
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205 | if args.ModelVersion is not None: |
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206 | for childElem in elem.iter(tag='variable'): |
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207 | if args.verbosity >= 2: print childElem.tag, childElem.attrib |
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208 | if childElem.attrib.get('name') is not None: |
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209 | if childElem.attrib.get('name') == 'model_version': |
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210 | childElem.text = args.ModelVersion[0] |
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211 | if args.ModelName is not None: |
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212 | for childElem in elem.iter(tag='variable'): |
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213 | if args.verbosity >= 2: print childElem.tag, childElem.attrib |
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214 | if childElem.attrib.get('name') is not None: |
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215 | if childElem.attrib.get('name') == 'source_id': |
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216 | childElem.text = args.ModelName[0] |
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217 | |
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218 | |
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219 | # Write out the results |
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220 | if args.verbosity >= 1: print '\nWriting dr2xml_def_xml=','modified.' + inputFile |
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221 | try: |
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222 | tree.write ('modified.' + inputFile) |
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223 | except: |
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224 | print "Write error. Please fix so that it can be parsed." |
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225 | traceback.print_exc(file=sys.stdout) |
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226 | return |
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227 | |
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228 | def modifyPath(args): |
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229 | """Recursively find tree element with file tag and change the path prefix of the name attribute.""" |
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230 | # Loop over file_def files |
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231 | for inputFile in args.file: |
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232 | # Read the file_def_xml |
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233 | if args.verbosity >= 1: print '\nReading dr2xml_def_xml=',inputFile |
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234 | try: |
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235 | tree = ET.parse(inputFile) |
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236 | except: |
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237 | print "Parse error. Please fix so that it can be parsed." |
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238 | traceback.print_exc(file=sys.stdout) |
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239 | return |
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240 | root=tree.getroot() |
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241 | if args.verbosity >= 3: print root.tag, root.attrib, '\n' |
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242 | # Change file name prefix to point where we want |
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243 | for elem in tree.iter(tag='file'): |
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244 | if not elem.attrib.get('mode') == 'read': |
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245 | name=elem.attrib.get('name') |
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246 | if args.filePrefix is not None: |
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247 | elem.set('name', os.path.normpath(args.newPath[0]) + '/' + args.filePrefix[0] + '_' + os.path.normpath(name)) |
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248 | else: |
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249 | elem.set('name', os.path.normpath(args.newPath[0]) + '/' + os.path.normpath(name)) |
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250 | if args.verbosity >= 2: print elem.tag, elem.attrib |
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251 | |
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252 | # Write out the results |
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253 | if args.verbosity >= 1: print '\nWriting dr2xml_def_xml=','modified.' + inputFile |
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254 | try: |
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255 | tree.write ('modified.' + inputFile) |
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256 | except: |
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257 | print "Write error. Please fix so that it can be parsed." |
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258 | traceback.print_exc(file=sys.stdout) |
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259 | return |
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260 | |
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261 | def modifyDR2XML(args): |
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262 | """Recursively find tree element with file tag and change the path prefix of the name attribute.""" |
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263 | # Need to fine tune their freq_op and freq_offset |
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264 | cospTuple=('CMIP6_albisccp', 'CMIP6_cfadDbze94', 'CMIP6_cfadLidarsr532', 'CMIP6_clcalipso2', 'CMIP6_clcalipsoice', 'CMIP6_climodis', 'CMIP6_clisccp', 'CMIP6_clmisr', 'CMIP6_cltmodis', 'CMIP6_clwmodis', 'CMIP6_jpdftaureicemodis', 'CMIP6_jpdftaureliqmodis', 'CMIP6_pctisccp', 'CMIP6_parasolRefl', 'CMIP6_clcalipso', 'CMIP6_clhcalipso', 'CMIP6_cllcalipso', 'CMIP6_clmcalipso', 'CMIP6_cltcalipso', 'CMIP6_cltisccp') |
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265 | # Dont touch those when fine tuning cfsites field freq_op |
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266 | excluded_field=('CMIP6_ap', 'CMIP6_b', 'CMIP6_b_bnds', 'CMIP6_ap_bnds') |
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267 | |
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268 | # Loop over file_def files |
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269 | for inputFile in args.file: |
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270 | write=False |
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271 | # Read the file_def_xml |
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272 | if args.verbosity >= 1: print '\nReading dr2xml_def_xml=',inputFile |
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273 | try: |
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274 | tree = ET.parse(inputFile) |
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275 | except: |
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276 | print "Parse error. Please fix so that it can be parsed." |
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277 | traceback.print_exc(file=sys.stdout) |
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278 | return |
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279 | root=tree.getroot() |
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280 | if args.verbosity >= 3: print root.tag, root.attrib, '\n' |
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281 | |
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282 | # Change some elements to overrule dr2xml |
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283 | for elem in tree.iter(tag='field'): |
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284 | if elem.attrib.get('id') is not None: |
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285 | if elem.attrib.get('id') == 'CMIP6_siconc_Scaltypesi': |
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286 | write=True |
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287 | elem.set('freq_op', '2ts') |
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288 | elem.set('freq_offset', '0ts') |
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289 | if args.verbosity >= 2: print elem.tag, elem.attrib |
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290 | elif (elem.attrib.get('id').startswith(cospTuple)): |
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291 | write=True |
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292 | elem.set('freq_op', '3h') |
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293 | elem.set('freq_offset', '0ts') |
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294 | if args.verbosity >= 2: print elem.tag, elem.attrib |
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295 | # Change elements related to CFsubhr files |
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296 | for elem in tree.iter(tag='file'): |
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297 | if elem.attrib.get('id') is not None: |
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298 | if ("_CFsubhr_" in elem.attrib.get('id')): |
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299 | write=True |
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300 | elem.set('output_freq', '2ts') |
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301 | elem.set('split_start_offset', '2ts') |
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302 | if args.verbosity >= 2: print elem.tag, elem.attrib |
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303 | for childElem in elem.iter(tag='field'): |
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304 | if childElem.attrib.get('field_ref') is not None: |
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305 | if childElem.attrib.get('field_ref') not in excluded_field: |
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306 | childElem.set('freq_op', '2ts') |
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307 | if args.verbosity >= 2: print childElem.tag, childElem.attrib |
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308 | # Changes related to cth16 |
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309 | for elem in tree.iter(tag='grid'): |
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310 | if elem.attrib.get('id') is not None: |
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311 | if elem.attrib.get('id') == 'grid4Dmisr_greordered': |
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312 | write=True |
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313 | if args.verbosity >= 2: print elem.tag, elem.attrib |
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314 | for childElem in elem.iter(tag='axis'): |
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315 | if args.verbosity >= 2: print childElem.tag, childElem.attrib |
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316 | if childElem.attrib.get('axis_ref') is not None: |
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317 | if childElem.attrib.get('axis_ref') == 'cth16': |
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318 | childElem.set('axis_ref', 'cth') |
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319 | # Ready |
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320 | if write: |
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321 | # Write out the results |
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322 | if args.verbosity >= 1: print '\nWriting dr2xml_def_xml=','modified.' + inputFile |
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323 | try: |
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324 | tree.write ('modified.' + inputFile) |
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325 | except: |
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326 | print "Write error. Please fix so that it can be parsed." |
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327 | traceback.print_exc(file=sys.stdout) |
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328 | return |
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329 | |
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330 | if __name__ == '__main__': |
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331 | |
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332 | try: |
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333 | # Create the top-level parser |
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334 | parser = argparse.ArgumentParser(description='XIOS2 xml files tooling and ironsmith') |
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335 | subparsers = parser.add_subparsers(description='Dump, check or modify xios xml files') |
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336 | |
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337 | # create the parser for the "dump" command |
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338 | parser_dump = subparsers.add_parser('dump',help='Dump the xml content without all the xml\'s ironsmith') |
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339 | parser_dump.add_argument('-d', '--depth', type=int, default=None, help='How deep do we go. Full tree by default') |
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340 | parser_dump.add_argument('file', nargs='+', help='XIOS xml file(s) to dump') |
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341 | parser_dump.set_defaults(func=dump) |
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342 | |
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343 | # create the parser for the "tsquery" command |
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344 | parser_check = subparsers.add_parser('tsquery', help='query timeseries related parameters from an xml file') |
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345 | parser_check.add_argument('--file', nargs=1, required=True, help='XIOS xml timeseries_def type') |
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346 | parser_check.set_defaults(func=tsquery) |
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347 | |
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348 | # create the parser for the "check" command |
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349 | parser_check = subparsers.add_parser('check', help='Check consistency between field_def and file_def files') |
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350 | parser_check.add_argument('--field', nargs=1, required=True, help='XIOS xml field_def type') |
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351 | parser_check.add_argument('--file', nargs='+', required=True, help='XIOS xml file_def type') |
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352 | parser_check.set_defaults(func=check, correction=False) |
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353 | |
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354 | # create the parser for the "modify" command |
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355 | parser_check = subparsers.add_parser('modify', help='Will make sure field_def is a superset of file_def') |
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356 | parser_check.add_argument('--field', nargs=1, required=True, help='XIOS xml field_def type') |
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357 | parser_check.add_argument('--file', nargs='+', required=True, help='XIOS xml file_def type') |
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358 | parser_check.set_defaults(func=check, correction=True) |
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359 | |
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360 | # create the parser for the "modifydr2xmlIPSL" command |
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361 | parser_check = subparsers.add_parser('modifydr2xmlIPSL', help='Adapt dr2xml_file to produce output files according to IPSL requirements') |
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362 | parser_check.add_argument('--newPath', nargs=1, required=True, help='Directory output for file produced from dr2xml_file type') |
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363 | parser_check.add_argument('--JobName', nargs=1, required=False, help='Name of the simulation to be added in the name of file produced from dr2xml_file type') |
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364 | parser_check.add_argument('--ModelName', nargs=1, required=False, help='Name of the model to be added in the name of file produced from dr2xml_file type') |
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365 | parser_check.add_argument('--ModelVersion', nargs=1, required=False, help='Model version to be added in global attributes of files produced from dr2xml_file type') |
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366 | parser_check.add_argument('--file', nargs='+', required=True, help='XIOS xml dr2xml_file type') |
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367 | parser_check.add_argument('--splitLastDate', nargs=1, required=False, help='Date to be used as split_last_date') |
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368 | parser_check.set_defaults(func=modifydr2xmlIPSL) |
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369 | |
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370 | # create the parser for the "modifyPath" command |
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371 | parser_check = subparsers.add_parser('modifyPath', help='Will make sure dr2xml write files where it should be') |
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372 | parser_check.add_argument('--newPath', nargs=1, required=True, help='Directory output for file produced from dr2xml_file type') |
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373 | parser_check.add_argument('--filePrefix', nargs=1, required=False, help='Prefix to be added to file produced from dr2xml_file type') |
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374 | parser_check.add_argument('--file', nargs='+', required=True, help='XIOS xml dr2xml_file type') |
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375 | parser_check.set_defaults(func=modifyPath) |
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376 | |
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377 | # create the parser for the "modifyDR2XML" command |
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378 | parser_check = subparsers.add_parser('modifyDR2XML', help='Fine tune dr2xml files for CMIP6 production') |
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379 | parser_check.add_argument('--file', nargs='+', required=True, help='XIOS xml dr2xml_file type') |
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380 | parser_check.set_defaults(func=modifyDR2XML) |
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381 | |
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382 | # create the parser for the "showtime" command |
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383 | parser_check = subparsers.add_parser('showtime', help='Just want to make sure you feel good today') |
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384 | parser_check.set_defaults(func=showtime) |
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385 | |
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386 | # Each possible option |
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387 | parser.add_argument('-v', '--verbosity', action='count', default=0) |
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388 | |
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389 | # Parse the args. |
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390 | args = parser.parse_args() |
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391 | |
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392 | # And call whatever function was selected |
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393 | args.func(args) |
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394 | except KeyboardInterrupt: |
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395 | print "Shutdown requested...exiting" |
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396 | except Exception: |
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397 | traceback.print_exc(file=sys.stdout) |
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398 | sys.exit(0) |
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