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