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