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1 <html>
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3 <title>MayaChemTools:Code:ModifySDFilesDataFields.pl</title>
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13 <pre>
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14 1 #!/usr/bin/perl -w
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: ModifySDFilesDataFields.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
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18 5 <span class="c"># $Revision: 1.27 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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51 38
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52 39 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
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53 40
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54 41 <span class="c"># Autoflush STDOUT</span>
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55 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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56 43
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57 44 <span class="c"># Starting message...</span>
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58 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
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59 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
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60 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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61 48
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62 49 <span class="c"># Get the options and setup script...</span>
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63 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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64 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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65 52 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span>
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66 53 <span class="s">}</span>
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67 54
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68 55 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
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69 56 <span class="i">@SDFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="sc">;</span>
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70 57
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71 58 <span class="c"># Process options...</span>
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72 59 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
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73 60 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
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74 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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75 62
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76 63 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span>
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77 64 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
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78 65 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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79 66
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80 67 <span class="c"># Generate output files...</span>
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81 68 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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82 69 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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83 70 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span>
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84 71 <span class="s">}</span>
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85 72 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
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86 73 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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87 74 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
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88 75 <span class="i">ModifySDFile</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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89 76 <span class="s">}</span>
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90 77 <span class="s">}</span>
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91 78 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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92 79
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93 80 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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94 81 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span>
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95 82 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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96 83
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97 84 <span class="c">###############################################################################</span>
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98 85
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99 86 <span class="c"># Modify SD file data fields....</span>
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100 <a name="ModifySDFile-"></a> 87 <span class="k">sub </span><span class="m">ModifySDFile</span> <span class="s">{</span>
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101 88 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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102 89 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$NewSDFile</span><span class="s">)</span><span class="sc">;</span>
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103 90
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104 91 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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105 92 <span class="i">$NewSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
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106 93
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107 94 <span class="k">print</span> <span class="q">"Generating new SD file $NewSDFile...\n"</span><span class="sc">;</span>
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108 95 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">">$NewSDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewSDFile: $! \n"</span><span class="sc">;</span>
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109 96 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $SDFile: $! \n"</span><span class="sc">;</span>
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110 97
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111 98 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$CmpdData</span><span class="cm">,</span> <span class="i">$MolName</span><span class="cm">,</span> <span class="i">$OldSDField</span><span class="cm">,</span> <span class="i">$NewSDField</span><span class="cm">,</span> <span class="i">$CommonSDField</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$FieldValues</span><span class="cm">,</span> <span class="i">$MolNameDataField</span><span class="cm">,</span> <span class="i">$URLCmpdIdFieldName</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldAndValues</span><span class="cm">,</span> <span class="i">@DataFieldLabels</span><span class="s">)</span><span class="sc">;</span>
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112 99 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
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113 100
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114 101 <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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115 102 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
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116 103 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
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117 104 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseDataFieldForMolName</span>} || <span class="i">$OptionsInfo</span>{<span class="w">ModifyDataFields</span>}<span class="s">)</span> <span class="s">{</span>
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118 105 <span class="i">%DataFieldAndValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
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119 106 <span class="s">}</span>
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120 107 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ModifyMolName</span>}<span class="s">)</span> <span class="s">{</span>
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121 108 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AlwaysReplaceMolName</span>} || !<span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$CmpdLines</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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122 109 <span class="i">$MolNameDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">MolNameDataField</span>}<span class="sc">;</span>
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123 110 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseDataFieldForMolName</span>} && <span class="k">exists</span><span class="s">(</span><span class="i">$DataFieldAndValues</span>{<span class="i">$MolNameDataField</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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124 111 <span class="i">$MolName</span> = <span class="i">$DataFieldAndValues</span>{<span class="i">$MolNameDataField</span>}<span class="sc">;</span>
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125 112 <span class="k">if</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span> > <span class="n">80</span><span class="s">)</span> <span class="s">{</span>
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126 113 <span class="i">$MolName</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$MolName</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="n">80</span><span class="s">)</span><span class="sc">;</span>
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127 114 <span class="s">}</span>
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128 115 <span class="s">}</span>
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129 116 <span class="k">else</span> <span class="s">{</span>
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130 117 <span class="i">$MolName</span> = <span class="q">"$OptionsInfo{MolNamePrefix}${CmpdCount}"</span><span class="sc">;</span>
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131 118 <span class="s">}</span>
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132 119 <span class="i">$CmpdLines</span>[<span class="n">0</span>] = <span class="i">$MolName</span><span class="sc">;</span>
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133 120 <span class="i">$CmpdString</span> = <span class="k">join</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="sc">;</span>
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134 121 <span class="s">}</span>
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135 122 <span class="s">}</span>
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136 123 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">ModifyDataFields</span>}<span class="s">)</span> <span class="s">{</span>
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137 124 <span class="c"># Just write the data and get the next compound...</span>
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138 125 <span class="k">print</span> <span class="i">NEWSDFILE</span> <span class="q">"$CmpdString\n"</span><span class="sc">;</span>
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139 126 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
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140 127 <span class="s">}</span>
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141 128 <span class="c"># Write out the structure data now and handle the old data fields later...</span>
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142 129 <span class="s">(</span><span class="i">$CmpdData</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\n>/</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
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143 130 <span class="k">print</span> <span class="i">NEWSDFILE</span> <span class="q">"$CmpdData\n"</span><span class="sc">;</span>
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144 131
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145 132 <span class="c"># Modify specified data fields...</span>
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146 133 <span class="k">for</span> <span class="i">$NewSDField</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNewToOldSDFieldMap</span>}}<span class="s">)</span> <span class="s">{</span>
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147 134 <span class="i">$FieldValues</span> = <span class="q">""</span><span class="sc">;</span>
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148 135 <span class="k">for</span> <span class="i">$OldSDField</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNewToOldSDFieldMap</span>}{<span class="i">$NewSDField</span>}}<span class="s">)</span> <span class="s">{</span>
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149 136 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$DataFieldAndValues</span>{<span class="i">$OldSDField</span>}<span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$DataFieldAndValues</span>{<span class="i">$OldSDField</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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150 137 <span class="i">$Value</span> = <span class="i">$DataFieldAndValues</span>{<span class="i">$OldSDField</span>}<span class="sc">;</span>
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151 138 <span class="i">$FieldValues</span> .= <span class="s">(</span><span class="i">$FieldValues</span><span class="s">)</span> ? <span class="q">"\n$Value"</span> <span class="co">:</span> <span class="i">$Value</span><span class="sc">;</span>
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152 139 <span class="s">}</span>
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153 140 <span class="s">}</span>
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154 141 <span class="k">print</span> <span class="i">NEWSDFILE</span> <span class="q">"> <$NewSDField>\n$FieldValues\n\n"</span><span class="sc">;</span>
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155 142 <span class="s">}</span>
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156 143 <span class="c"># Add specified common fields...</span>
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157 144 <span class="k">for</span> <span class="i">$CommonSDField</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCommonFieldMap</span>}}<span class="s">)</span> <span class="s">{</span>
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158 145 <span class="i">$Value</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCommonFieldMap</span>}{<span class="i">$CommonSDField</span>}<span class="sc">;</span>
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159 146 <span class="k">print</span> <span class="i">NEWSDFILE</span> <span class="q">"> <$CommonSDField>\n$Value\n\n"</span><span class="sc">;</span>
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160 147 <span class="s">}</span>
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161 148 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CreateDataFieldURL</span>}<span class="s">)</span> <span class="s">{</span>
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162 149 <span class="i">$Value</span> = <span class="q">""</span><span class="sc">;</span>
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163 150 <span class="i">$URLCmpdIdFieldName</span> = <span class="i">$OptionsInfo</span>{<span class="w">URLCmpdIdFieldName</span>}<span class="sc">;</span>
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164 151 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$DataFieldAndValues</span>{<span class="i">$URLCmpdIdFieldName</span>}<span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$DataFieldAndValues</span>{<span class="i">$URLCmpdIdFieldName</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
165 152 <span class="i">$Value</span> = <span class="i">$DataFieldAndValues</span>{<span class="i">$URLCmpdIdFieldName</span>}<span class="sc">;</span>
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|
|
166 153 <span class="i">$Value</span> = <span class="q">"$OptionsInfo{URLCGIScriptName}?$OptionsInfo{URLParamName}=${Value}"</span><span class="sc">;</span>
|
|
|
167 154 <span class="s">}</span>
|
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|
168 155 <span class="k">print</span> <span class="i">NEWSDFILE</span> <span class="q">"> <$OptionsInfo{URLDataFieldLabel}>\n$Value\n\n"</span><span class="sc">;</span>
|
|
|
169 156 <span class="s">}</span>
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170 157
|
|
|
171 158 <span class="c"># Handle old data fields and write 'em in the same order as they appear in the input</span>
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|
|
172 159 <span class="c"># files...</span>
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|
173 160 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepAllOldDataFields</span>} || <span class="i">$OptionsInfo</span>{<span class="w">KeepUnMappedOldDataFields</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
174 161 <span class="k">my</span><span class="s">(</span><span class="i">$KeepLabel</span><span class="s">)</span><span class="sc">;</span>
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|
175 162 <span class="i">@DataFieldLabels</span> = <span class="i">GetCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
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|
176 163 <span class="j">LABEL:</span> <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@DataFieldLabels</span><span class="s">)</span> <span class="s">{</span>
|
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|
177 164 <span class="i">$KeepLabel</span> = <span class="i">$OptionsInfo</span>{<span class="w">KeepAllOldDataFields</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="s">(</span> <span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedOldToNewSDFieldMap</span>}{<span class="i">$Label</span>}<span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span> <span class="s">)</span><span class="sc">;</span>
|
|
|
178 165 <span class="k">if</span> <span class="s">(</span>!<span class="i">$KeepLabel</span><span class="s">)</span> <span class="s">{</span>
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|
179 166 <span class="k">next</span> <span class="j">LABEL</span><span class="sc">;</span>
|
|
|
180 167 <span class="s">}</span>
|
|
|
181 168 <span class="i">$Value</span> = <span class="i">$DataFieldAndValues</span>{<span class="i">$Label</span>}<span class="sc">;</span>
|
|
|
182 169 <span class="k">print</span> <span class="i">NEWSDFILE</span> <span class="q">"> <$Label>\n$Value\n\n"</span><span class="sc">;</span>
|
|
|
183 170 <span class="s">}</span>
|
|
|
184 171 <span class="s">}</span>
|
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|
185 172
|
|
|
186 173 <span class="k">print</span> <span class="i">NEWSDFILE</span> <span class="q">"\$\$\$\$\n"</span><span class="sc">;</span>
|
|
|
187 174 <span class="s">}</span>
|
|
|
188 175 <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span>
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|
189 176 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
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|
190 177 <span class="s">}</span>
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191 178
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|
|
192 179 <span class="c"># Process option values...</span>
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|
193 <a name="ProcessOptions-"></a> 180 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
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|
194 181 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
195 182
|
|
|
196 183 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
|
|
|
197 184
|
|
|
198 185 <span class="i">$OptionsInfo</span>{<span class="w">ModifyMolName</span>} = <span class="n">1</span><span class="sc">;</span> <span class="i">$OptionsInfo</span>{<span class="w">ModifyDataFields</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
199 186 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^both$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
200 187 <span class="i">$OptionsInfo</span>{<span class="w">ModifyMolName</span>} = <span class="n">1</span><span class="sc">;</span> <span class="i">$OptionsInfo</span>{<span class="w">ModifyDataFields</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
201 188 <span class="s">}</span>
|
|
|
202 189 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^datafields$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
203 190 <span class="i">$OptionsInfo</span>{<span class="w">ModifyMolName</span>} = <span class="n">0</span><span class="sc">;</span> <span class="i">$OptionsInfo</span>{<span class="w">ModifyDataFields</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
204 191 <span class="s">}</span>
|
|
|
205 192
|
|
|
206 193 <span class="i">$OptionsInfo</span>{<span class="w">KeepOldDataFields</span>} = <span class="i">$Options</span>{<span class="w">keepolddatafields</span>}<span class="sc">;</span>
|
|
|
207 194 <span class="i">$OptionsInfo</span>{<span class="w">KeepAllOldDataFields</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepolddatafields</span>} =~ <span class="q">/^all$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
208 195 <span class="i">$OptionsInfo</span>{<span class="w">KeepUnMappedOldDataFields</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepolddatafields</span>} =~ <span class="q">/^unmappedonly$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
209 196
|
|
|
210 197 <span class="i">$OptionsInfo</span>{<span class="w">MolNameMode</span>} = <span class="i">$Options</span>{<span class="w">molnamemode</span>}<span class="sc">;</span>
|
|
|
211 198 <span class="i">$OptionsInfo</span>{<span class="w">UseDataFieldForMolName</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">molnamemode</span>} =~ <span class="q">/^datafield$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
212 199
|
|
|
213 200 <span class="i">$OptionsInfo</span>{<span class="w">MolName</span>} = <span class="i">$Options</span>{<span class="w">molname</span>}<span class="sc">;</span>
|
|
|
214 201 <span class="i">$OptionsInfo</span>{<span class="w">MolNameDataField</span>} = <span class="q">""</span><span class="sc">;</span> <span class="i">$OptionsInfo</span>{<span class="w">MolNamePrefix</span>} = <span class="q">"Cmpd"</span><span class="sc">;</span>
|
|
|
215 202 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">molname</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
216 203 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseDataFieldForMolName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
217 204 <span class="i">$OptionsInfo</span>{<span class="w">MolNameDataField</span>} = <span class="i">$Options</span>{<span class="w">molname</span>}<span class="sc">;</span>
|
|
|
218 205 <span class="s">}</span>
|
|
|
219 206 <span class="k">else</span> <span class="s">{</span>
|
|
|
220 207 <span class="i">$OptionsInfo</span>{<span class="w">MolNamePrefix</span>} = <span class="i">$Options</span>{<span class="w">molname</span>}<span class="sc">;</span>
|
|
|
221 208 <span class="s">}</span>
|
|
|
222 209 <span class="s">}</span>
|
|
|
223 210
|
|
|
224 211 <span class="i">$OptionsInfo</span>{<span class="w">MolNameReplace</span>} = <span class="i">$Options</span>{<span class="w">molnamereplace</span>}<span class="sc">;</span>
|
|
|
225 212 <span class="i">$OptionsInfo</span>{<span class="w">AlwaysReplaceMolName</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">molnamereplace</span>} =~ <span class="q">/^always$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
226 213
|
|
|
227 214 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmap</span>} && <span class="i">$Options</span>{<span class="w">datafieldsmapfile</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
228 215 <span class="k">die</span> <span class="q">"Error: Both \"--datafieldsmap\" and \"--datafieldsmapfile\" options specified: only one is allowed at a time\n"</span><span class="sc">;</span>
|
|
|
229 216 <span class="s">}</span>
|
|
|
230 217
|
|
|
231 218 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMap</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmap</span>} ? <span class="i">$Options</span>{<span class="w">datafieldsmap</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
232 219 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMapFile</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmapfile</span>} ? <span class="i">$Options</span>{<span class="w">datafieldsmapfile</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
233 220
|
|
|
234 221 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataFieldMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
235 222
|
|
|
236 223 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNewToOldSDFieldMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
237 224 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedOldToNewSDFieldMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
238 225
|
|
|
239 226 <span class="i">$SpecifiedDataFieldMap</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmap</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
241 228 <span class="i">$SpecifiedDataFieldMap</span> = <span class="i">$Options</span>{<span class="w">datafieldsmap</span>}<span class="sc">;</span>
|
|
|
242 229 <span class="s">}</span>
|
|
|
243 230 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmapfile</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
244 231 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
|
|
|
245 232 <span class="k">open</span> <span class="w">DATAFIELDSFILE</span><span class="cm">,</span> <span class="q">"$Options{datafieldsmapfile}"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $Options{datafieldsmapfile}: $! \n"</span><span class="sc">;</span>
|
|
|
246 233 <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFIELDSFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
247 234 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="q">";"</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
248 235 <span class="i">$SpecifiedDataFieldMap</span> .= <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="q">";"</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
249 236 <span class="s">}</span>
|
|
|
250 237 <span class="k">close</span> <span class="w">DATAFIELDSFILE</span><span class="sc">;</span>
|
|
|
251 238 <span class="s">}</span>
|
|
|
252 239
|
|
|
253 240 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedDataFieldMap</span><span class="s">)</span> <span class="s">{</span>
|
|
|
254 241 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldMap</span><span class="cm">,</span> <span class="i">$DataField</span><span class="cm">,</span> <span class="i">$NewSDField</span><span class="cm">,</span> <span class="i">@OldSDFields</span><span class="cm">,</span> <span class="i">@DataFieldMapSplit</span><span class="cm">,</span> <span class="i">@DataFieldsSplit</span><span class="cm">,</span> <span class="i">$FirstField</span><span class="s">)</span><span class="sc">;</span>
|
|
|
255 242 <span class="i">@DataFieldMapSplit</span> = <span class="k">split</span> <span class="q">";"</span><span class="cm">,</span> <span class="i">$SpecifiedDataFieldMap</span><span class="sc">;</span>
|
|
|
256 243 <span class="k">for</span> <span class="i">$DataFieldMap</span> <span class="s">(</span><span class="i">@DataFieldMapSplit</span><span class="s">)</span> <span class="s">{</span>
|
|
|
257 244 <span class="i">@DataFieldsSplit</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$DataFieldMap</span><span class="sc">;</span>
|
|
|
258 245 <span class="k">if</span> <span class="s">(</span><span class="i">@DataFieldsSplit</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
259 246 <span class="k">die</span> <span class="q">"Error: Invalid number of comma delimited values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@DataFieldsSplit</span><span class="s">)</span><span class="cm">,</span> <span class="q">", specified, @DataFieldsSplit, using \"--datafieldsmap or --datafieldsmapfile\" option: it must contain more than one value.\n"</span><span class="sc">;</span>
|
|
|
260 247 <span class="s">}</span>
|
|
|
261 248 <span class="i">$FirstField</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
262 249 <span class="i">@OldSDFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
263 250 <span class="k">for</span> <span class="i">$DataField</span> <span class="s">(</span><span class="i">@DataFieldsSplit</span><span class="s">)</span> <span class="s">{</span>
|
|
|
264 251 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$DataField</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$DataField</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
265 252 <span class="k">die</span> <span class="q">"Error: One of the comma delimited values, \""</span><span class="cm">,</span> <span class="k">join</span><span class="s">(</span><span class="q">","</span><span class="cm">,</span> <span class="i">@DataFieldsSplit</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\", specified using \"--datafieldsmap or --datafieldsmapfile\" option is empty.\n"</span><span class="sc">;</span>
|
|
|
266 253 <span class="s">}</span>
|
|
|
267 254 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstField</span><span class="s">)</span> <span class="s">{</span>
|
|
|
268 255 <span class="i">$FirstField</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
269 256 <span class="i">$NewSDField</span> = <span class="i">$DataField</span><span class="sc">;</span>
|
|
|
270 257 <span class="s">}</span>
|
|
|
271 258 <span class="k">else</span> <span class="s">{</span>
|
|
|
272 259 <span class="k">push</span> <span class="i">@OldSDFields</span><span class="cm">,</span> <span class="i">$DataField</span><span class="sc">;</span>
|
|
|
273 260 <span class="s">}</span>
|
|
|
274 261 <span class="s">}</span>
|
|
|
275 262 <span class="c"># Make sure a datafield is only specified once...</span>
|
|
|
276 263 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNewToOldSDFieldMap</span>}{<span class="i">$NewSDField</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
277 264 <span class="k">die</span> <span class="q">"Error: New data field, $NewSDField, specified more than once using \"--datafieldsmap or --datafieldsmapfile\" option.\n"</span><span class="sc">;</span>
|
|
|
278 265 <span class="s">}</span>
|
|
|
279 266 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNewToOldSDFieldMap</span>}{<span class="i">$NewSDField</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
280 267 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNewToOldSDFieldMap</span>}{<span class="i">$NewSDField</span>}}<span class="cm">,</span> <span class="i">@OldSDFields</span><span class="sc">;</span>
|
|
|
281 268 <span class="k">for</span> <span class="i">$DataField</span> <span class="s">(</span><span class="i">@OldSDFields</span><span class="s">)</span> <span class="s">{</span>
|
|
|
282 269 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedOldToNewSDFieldMap</span>}{<span class="i">$DataField</span>} <span class="s">)</span> <span class="s">{</span>
|
|
|
283 270 <span class="k">die</span> <span class="q">"Error: SD field, $DataField, specified more than once using \"--datafieldsmap or --datafieldsmapfile\" option.\n"</span><span class="sc">;</span>
|
|
|
284 271 <span class="s">}</span>
|
|
|
285 272 <span class="k">else</span> <span class="s">{</span>
|
|
|
286 273 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedOldToNewSDFieldMap</span>}{<span class="i">$DataField</span>} = <span class="i">$NewSDField</span><span class="sc">;</span>
|
|
|
287 274 <span class="s">}</span>
|
|
|
288 275 <span class="s">}</span>
|
|
|
289 276
|
|
|
290 277 <span class="s">}</span>
|
|
|
291 278 <span class="s">}</span>
|
|
|
292 279
|
|
|
293 280 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsCommon</span>} = <span class="i">$Options</span>{<span class="w">datafieldscommon</span>} ? <span class="i">$Options</span>{<span class="w">datafieldscommon</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
294 281 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCommonFieldMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
295 282
|
|
|
296 283 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldscommon</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
297 284 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldName</span><span class="cm">,</span> <span class="i">$DataFieldValue</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">@CommonDataFieldsSplit</span><span class="s">)</span><span class="sc">;</span>
|
|
|
298 285 <span class="i">@CommonDataFieldsSplit</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafieldscommon</span>}<span class="sc">;</span>
|
|
|
299 286 <span class="k">if</span> <span class="s">(</span><span class="i">@CommonDataFieldsSplit</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
300 287 <span class="k">die</span> <span class="q">"Error: Invalid number of comma delimited values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@CommonDataFieldsSplit</span><span class="s">)</span><span class="cm">,</span> <span class="q">", specified \""</span><span class="cm">,</span> <span class="k">join</span><span class="s">(</span><span class="q">","</span><span class="cm">,</span> <span class="i">@CommonDataFieldsSplit</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\" using \"--datafieldscommon\" option: it must contain even number of values.\n"</span><span class="sc">;</span>
|
|
|
301 288 <span class="s">}</span>
|
|
|
302 289 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">@CommonDataFieldsSplit</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
303 290 <span class="i">$DataFieldName</span> = <span class="i">$CommonDataFieldsSplit</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
304 291 <span class="i">$DataFieldValue</span> = <span class="i">$CommonDataFieldsSplit</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
305 292 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCommonFieldMap</span>}{<span class="i">$DataFieldName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
306 293 <span class="k">die</span> <span class="q">"Error: Common data field, $DataFieldName, specified more than once using \"--datafieldscommon\" option.\n"</span><span class="sc">;</span>
|
|
|
307 294 <span class="s">}</span>
|
|
|
308 295 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNewToOldSDFieldMap</span>}{<span class="i">$DataFieldName</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedOldToNewSDFieldMap</span>}{<span class="i">$DataFieldName</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
309 296 <span class="k">die</span> <span class="q">"Error: Common data field, $DataFieldName, specified using \"--datafieldscommon\" option cannot be specified in \"--datafieldsmap or --datafieldsmapfile\" option.\n"</span><span class="sc">;</span>
|
|
|
310 297 <span class="s">}</span>
|
|
|
311 298 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCommonFieldMap</span>}{<span class="i">$DataFieldName</span>} = <span class="i">$DataFieldValue</span><span class="sc">;</span>
|
|
|
312 299 <span class="s">}</span>
|
|
|
313 300 <span class="s">}</span>
|
|
|
314 301
|
|
|
315 302 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldURL</span>} = <span class="i">$Options</span>{<span class="w">datafieldurl</span>} ? <span class="i">$Options</span>{<span class="w">datafieldurl</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
316 303 <span class="i">$OptionsInfo</span>{<span class="w">CreateDataFieldURL</span>} = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldurl</span>}<span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldurl</span>}<span class="s">)</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
317 304
|
|
|
318 305 <span class="i">$OptionsInfo</span>{<span class="w">URLDataFieldLabel</span>} = <span class="q">""</span><span class="sc">;</span> <span class="i">$OptionsInfo</span>{<span class="w">URLCGIScriptName</span>} = <span class="q">""</span><span class="sc">;</span>
|
|
|
319 306 <span class="i">$OptionsInfo</span>{<span class="w">URLParamName</span>} = <span class="q">""</span><span class="sc">;</span> <span class="i">$OptionsInfo</span>{<span class="w">URLCmpdIdFieldName</span>} = <span class="q">""</span><span class="sc">;</span>
|
|
|
320 307
|
|
|
321 308 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CreateDataFieldURL</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
322 309 <span class="k">my</span><span class="s">(</span><span class="i">@DataFieldURLSplit</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
323 310 <span class="i">@DataFieldURLSplit</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafieldurl</span>}<span class="sc">;</span>
|
|
|
324 311 <span class="k">if</span> <span class="s">(</span><span class="i">@DataFieldURLSplit</span> != <span class="n">4</span><span class="s">)</span> <span class="s">{</span>
|
|
|
325 312 <span class="k">die</span> <span class="q">"Error: Invalid number of values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@DataFieldURLSplit</span><span class="s">)</span><span class="cm">,</span> <span class="q">", specified using \"--datafieldURL\" option: it must contain 4 values.\n"</span><span class="sc">;</span>
|
|
|
326 313 <span class="s">}</span>
|
|
|
327 314 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@DataFieldURLSplit</span><span class="s">)</span> <span class="s">{</span>
|
|
|
328 315 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
329 316 <span class="k">die</span> <span class="q">"Error: One of the values, $Options{datafieldurl}, specified using \"--datafieldURL\" option is empty.\n"</span><span class="sc">;</span>
|
|
|
330 317 <span class="s">}</span>
|
|
|
331 318 <span class="s">}</span>
|
|
|
332 319 <span class="i">$OptionsInfo</span>{<span class="w">URLDataFieldLabel</span>} = <span class="i">$DataFieldURLSplit</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
333 320 <span class="i">$OptionsInfo</span>{<span class="w">URLCGIScriptName</span>} = <span class="i">$DataFieldURLSplit</span>[<span class="n">1</span>]<span class="sc">;</span>
|
|
|
334 321 <span class="i">$OptionsInfo</span>{<span class="w">URLParamName</span>} = <span class="i">$DataFieldURLSplit</span>[<span class="n">2</span>]<span class="sc">;</span>
|
|
|
335 322 <span class="i">$OptionsInfo</span>{<span class="w">URLCmpdIdFieldName</span>} = <span class="i">$DataFieldURLSplit</span>[<span class="n">3</span>]<span class="sc">;</span>
|
|
|
336 323 <span class="s">}</span>
|
|
|
337 324
|
|
|
338 325 <span class="s">}</span>
|
|
|
339 326
|
|
|
340 327 <span class="c"># Retrieve information about input SD files...</span>
|
|
|
341 <a name="RetrieveSDFilesInfo-"></a> 328 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
|
|
|
342 329 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFile</span><span class="cm">,</span> <span class="i">$DataFieldName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
343 330
|
|
|
344 331 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
345 332 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
346 333 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
347 334
|
|
|
348 335 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
|
|
|
349 336 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
350 337
|
|
|
351 338 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
352 339 <span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
353 340
|
|
|
354 341 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
355 342 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span>
|
|
|
356 343 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
357 344 <span class="s">}</span>
|
|
|
358 345 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
359 346 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span>
|
|
|
360 347 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
361 348 <span class="s">}</span>
|
|
|
362 349 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
363 350 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
364 351 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
365 352 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
|
|
|
367 354 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
|
|
|
368 355 <span class="s">}</span>
|
|
|
369 356 <span class="k">else</span> <span class="s">{</span>
|
|
|
370 357 <span class="i">$FileName</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span>
|
|
|
371 358 <span class="s">}</span>
|
|
|
372 359 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
|
|
|
373 360 <span class="s">}</span>
|
|
|
374 361 <span class="k">else</span> <span class="s">{</span>
|
|
|
375 362 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span> . <span class="q">"ModifiedDataFields"</span><span class="sc">;</span>
|
|
|
376 363 <span class="s">}</span>
|
|
|
377 364
|
|
|
378 365 <span class="i">$OutFile</span> = <span class="i">$OutFileRoot</span> . <span class="q">".$FileExt"</span><span class="sc">;</span>
|
|
|
379 366 <span class="k">if</span> <span class="s">(</span><span class="k">lc</span><span class="s">(</span><span class="i">$OutFile</span><span class="s">)</span> <span class="k">eq</span> <span class="k">lc</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
380 367 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n"</span><span class="sc">;</span>
|
|
|
381 368 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
382 369 <span class="s">}</span>
|
|
|
383 370 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
384 371 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFile</span><span class="s">)</span> <span class="s">{</span>
|
|
|
385 372 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $OutFile already exists\n"</span><span class="sc">;</span>
|
|
|
386 373 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
387 374 <span class="s">}</span>
|
|
|
388 375 <span class="s">}</span>
|
|
|
389 376
|
|
|
390 377 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
|
|
|
391 378 <span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="i">$OutFile</span><span class="sc">;</span>
|
|
|
392 379 <span class="s">}</span>
|
|
|
393 380 <span class="s">}</span>
|
|
|
394 381
|
|
|
395 382 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
|
|
|
396 <a name="SetupScriptUsage-"></a> 383 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
|
|
|
397 384
|
|
|
398 385 <span class="c"># Retrieve all the options...</span>
|
|
|
399 386 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
400 387 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
401 388 <span class="i">$Options</span>{<span class="w">keepolddatafields</span>} = <span class="q">"none"</span><span class="sc">;</span>
|
|
|
402 389 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">"molname"</span><span class="sc">;</span>
|
|
|
403 390 <span class="i">$Options</span>{<span class="w">molnamemode</span>} = <span class="q">"labelprefix"</span><span class="sc">;</span>
|
|
|
404 391 <span class="i">$Options</span>{<span class="w">molnamereplace</span>} = <span class="q">"empty"</span><span class="sc">;</span>
|
|
|
405 392
|
|
|
406 393 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"detail|d=i"</span><span class="cm">,</span> <span class="q">"datafieldscommon=s"</span><span class="cm">,</span> <span class="q">"datafieldsmap=s"</span><span class="cm">,</span> <span class="q">"datafieldsmapfile=s"</span><span class="cm">,</span> <span class="q">"datafieldurl=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"keepolddatafields|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"molname=s"</span><span class="cm">,</span> <span class="q">"molnamemode=s"</span><span class="cm">,</span> <span class="q">"molnamereplace=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
407 394 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
|
|
|
408 395 <span class="s">}</span>
|
|
|
409 396 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
410 397 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
411 398 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
|
|
|
412 399 <span class="s">}</span>
|
|
|
413 400 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span>
|
|
|
414 401 <span class="s">}</span>
|
|
|
415 402 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepolddatafields</span>} !~ <span class="q">/^(all|unmappedonly|none)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
416 403 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keepolddatafields}, for option \"-k --keepolddatafields\" is not valid. Allowed values: all, unmappedonly, or none\n"</span><span class="sc">;</span>
|
|
|
417 404 <span class="s">}</span>
|
|
|
418 405 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(molname|datafields|both)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
419 406 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: molname, datafields, or both\n"</span><span class="sc">;</span>
|
|
|
420 407 <span class="s">}</span>
|
|
|
421 408 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">molnamemode</span>} !~ <span class="q">/^(datafield|labelprefix)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
422 409 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{molnamemode}, for option \"--molnamemode\" is not valid. Allowed values: datafield or labelprefix\n"</span><span class="sc">;</span>
|
|
|
423 410 <span class="s">}</span>
|
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424 411 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">molnamereplace</span>} !~ <span class="q">/^(always|empty)$/i</span><span class="s">)</span> <span class="s">{</span>
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425 412 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{molnamereplace}, for option \"--molnamereplace\" is not valid. Allowed values: always or empty\n"</span><span class="sc">;</span>
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426 413 <span class="s">}</span>
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427 414 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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428 415 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n"</span><span class="sc">;</span>
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429 416 <span class="s">}</span>
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430 417 <span class="s">}</span>
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431 418
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432 <a name="EOF-"></a></pre>
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433 <p> </p>
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434 <br />
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435 <center>
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436 <img src="../../../images/h2o2.png">
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437 </center>
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438 </body>
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439 </html>
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