[1337] | 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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[1340] | 6 | # Contact: Sebastien.Denvil__at__ipsl.jussieu.fr |
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[1337] | 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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[1339] | 15 | import os, pwd, sys, traceback, argparse |
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[1337] | 16 | import xml.etree.ElementTree as ET |
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[1339] | 17 | #import readline, rlcompleter |
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| 18 | #readline.parse_and_bind("tab: complete") |
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[1337] | 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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[1346] | 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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[1337] | 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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[1349] | 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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[1337] | 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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[1349] | 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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[1413] | 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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[1349] | 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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[1337] | 81 | def findField(root): |
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[1339] | 82 | """Recursively find and list field tag with "id" or "field_ref" attribute.""" |
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[1337] | 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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[1346] | 112 | exitCode=0 |
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[1337] | 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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[1346] | 115 | try: |
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| 116 | tree = ET.parse(args.field[0]) |
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| 117 | except: |
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[1352] | 118 | print 'Parse error with %s. Please fix so that it can be parsed.' % (args.field[0]) |
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[1346] | 119 | traceback.print_exc(file=sys.stdout) |
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| 120 | return |
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[1337] | 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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[1346] | 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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[1337] | 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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[1339] | 146 | if args.verbosity >= 1: print '\nALL GOOD with %s' % (inputFile) |
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[1337] | 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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[1339] | 150 | if args.verbosity >= 1: print '\nTROUBLE AHEAD with %s' % (inputFile) |
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[1337] | 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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[1420] | 177 | |
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[1535] | 178 | def modifydr2xmlIPSL(args): |
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[1420] | 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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[1425] | 196 | if not elem.attrib.get('mode') == 'read': |
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| 197 | name=elem.attrib.get('name') |
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[1535] | 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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[1537] | 204 | if args.splitLastDate is not None: elem.set('split_last_date', args.splitLastDate[0] + '-01-01 00:00:00') |
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[1535] | 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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[1467] | 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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[1425] | 250 | if args.verbosity >= 2: print elem.tag, elem.attrib |
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[1535] | 251 | |
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[1420] | 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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[1434] | 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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[1443] | 263 | # Need to fine tune their freq_op and freq_offset |
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[1435] | 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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[1443] | 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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[1435] | 267 | |
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[1434] | 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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[1436] | 282 | # Change some elements to overrule dr2xml |
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[1434] | 283 | for elem in tree.iter(tag='field'): |
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[1435] | 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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[1443] | 295 | # Change elements related to CFsubhr files |
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[1442] | 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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[1443] | 301 | elem.set('split_start_offset', '2ts') |
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[1442] | 302 | if args.verbosity >= 2: print elem.tag, elem.attrib |
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[1443] | 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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[1445] | 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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[1442] | 319 | # Ready |
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[1434] | 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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[1337] | 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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[1349] | 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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[1337] | 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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[1535] | 353 | |
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[1337] | 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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[1535] | 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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[1337] | 369 | |
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[1420] | 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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[1467] | 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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[1420] | 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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[1434] | 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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[1420] | 381 | |
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| 382 | # create the parser for the "showtime" command |
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[1337] | 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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[1346] | 396 | except Exception: |
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| 397 | traceback.print_exc(file=sys.stdout) |
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[1337] | 398 | sys.exit(0) |
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