deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi

   1 #!/usr/bin/perl -w
   2
   3 # Deob_detail.cgi
   4 # part of the Deobfuscator package
   5 # by Laura Kavanaugh and Dave Messina
   6 #
   7 # cared for by Dave Messina <dave-pause@davemessina.net>
   8 #
   9 # POD documentation - main docs before the code
  10
  11 =head1 NAME
  12
  13 deob_detail.cgi - displays a web page of detailed information about a BioPerl method
  14
  15 =head1 VERSION
  16
  17 This document describes deob_detail.cgi version 0.0.3
  18
  19
  20 =head1 SYNOPSIS
  21
  22 This program is designed to be called by deob_interface.cgi. See
  23 L</"DESCRIPTION"> for details.
  24
  25 To install deob_detail.cgi and the rest of the Deobfuscator package, see the
  26 README.
  27
  28
  29 =head1 DESCRIPTION
  30
  31 Deob_detail.cgi is called by deob_interface.cgi when a user clicks on a
  32 method name. This program extracts the documentation about that method from
  33 the Deobfuscator Berkeley DBs and returns it in some simple HTML formatting.
  34
  35
  36 =head1 DIAGNOSTICS
  37
  38 None.
  39
  40
  41 =head1 CONFIGURATION AND ENVIRONMENT
  42
  43 This program expects to have the 'methods.db' and 'packages.db' files in the
  44 same directory as itself. These two files are automatically generated when
  45 L<deob_index.pl> is run. If your installation requires that they be in a
  46 different location, change the $BerkeleyDB_packages and $BerkeleyDB_methods
  47 variables below to be fully qualified paths to the db files.
  48
  49
  50 =head1 DEPENDENCIES
  51
  52 L<version>, L<CGI>, L<Deobfuscator>
  53
  54
  55 =head1 INCOMPATIBILITIES
  56
  57 None reported.
  58
  59
  60 =head1 BUGS AND LIMITATIONS
  61
  62 No bugs have been reported.
  63
  64
  65 =head1 FEEDBACK
  66
  67 =head2 Mailing Lists
  68
  69 User feedback is an integral part of the evolution of this and other
  70 Bioperl modules. Send your comments and suggestions preferably to one
  71 of the Bioperl mailing lists.  Your participation is much appreciated.
  72
  73   bioperl-l@bioperl.org                       - General discussion
  74   http://www.bioperl.org/wiki/Mailing_lists   - About the mailing lists
  75
  76 =head2 Reporting Bugs
  77
  78 Report bugs to the Bioperl bug tracking system to help us keep track
  79 the bugs and their resolution.  Bug reports can be submitted via the
  80 web:
  81
  82   http://bugzilla.bioperl.org/
  83
  84
  85 =head1 SEE ALSO
  86
  87 L<Deobfuscator>, L<deob_interface.cgi>, L<deob_index.pl>
  88
  89
  90 =head1 AUTHOR
  91
  92 Laura Kavanaugh
  93
  94
  95 =head1 CONTRIBUTORS
  96
  97 =over
  98
  99 =item Dave Messina C<< <dave-pause@davemessina.net> >>
 100
 101 =item David Curiel
 102
 103 =back
 104
 105
 106 =head1 ACKNOWLEDGMENTS
 107
 108 This software was developed originally at the Cold Spring Harbor Laboratory's
 109 Advanced Bioinformatics Course between Oct 12-25, 2005. Many thanks to David
 110 Curiel, who provided much-needed guidance and assistance on this project.
 111
 112
 113 =head1 LICENSE AND COPYRIGHT
 114
 115 Copyright (C) 2005-6 Laura Kavanaugh and Dave Messina. All Rights Reserved.
 116
 117 This module is free software; you may redistribute it and/or modify it under the same terms as Perl itself. See L<perlartistic>.
 118
 119
 120 =head1 DISCLAIMER
 121
 122 This software is provided "as is" without warranty of any kind.
 123
 124 =cut
 125
 126
 127 # Let the code begin...
 128
 129 ## HARDCODED VALUES ##
 130 # Change these to fit your installation.
 131 use lib './lib';
 132 my $BerkeleyDB_packages = './packages.db';
 133 my $BerkeleyDB_methods  = './methods.db';
 134
 135 ## You shouldn't need to change anything below here ##
 136
 137 use version; $VERSION = qv('0.0.2');
 138 use warnings;
 139 use strict;
 140 use CGI ':standard';
 141 use Deobfuscator;
 142
 143 # Open BerkeleyDBs
 144 my $packages_ref = Deobfuscator::open_db($BerkeleyDB_packages);
 145 my $methods_ref  = Deobfuscator::open_db($BerkeleyDB_methods);
 146
 147 # 'method' is the name of the method passed in from deob_interface.cgi
 148 my $class_method = param('method');
 149
 150 # Get all of the documentation fields out of the db
 151 my $title
 152     = Deobfuscator::get_method_docs( $methods_ref, $class_method, "title" );
 153 if ( $title eq "0" ) { $title = "not documented"; }
 154
 155 my $usage
 156     = Deobfuscator::get_method_docs( $methods_ref, $class_method, "usage" );
 157 if ( $usage eq "0" ) { $usage = "not documented"; }
 158
 159 my $function = Deobfuscator::get_method_docs( $methods_ref, $class_method,
 160     "function" );
 161 if ( $function eq "0" ) { $function = "not documented"; }
 162
 163 my $returns
 164     = Deobfuscator::get_method_docs( $methods_ref, $class_method, "returns" );
 165 if ( $returns eq "0" ) { $returns = "not documented"; }
 166
 167 my $args
 168     = Deobfuscator::get_method_docs( $methods_ref, $class_method, "args" );
 169 if ( $args eq "0" ) { $args = "not documented"; }
 170
 171 ### Make the output page
 172
 173 # Start the page
 174 print header;
 175 print start_html($class_method);
 176
 177 # Define some styles
 178 my $style1
 179     = qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:10px;background-color:lightgrey"};
 180 my $style2
 181     = qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:10px"};
 182 my $style3
 183     = qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:14px"};
 184
 185 # open the table
 186 print '<div style="border:solid black 1px; width:100%; height:200; overflow:auto">';
 187 print '<table width="100%" $style3>';
 188 print "<tr><td colspan=4><center>$class_method</center></td></tr>";
 189
 190 my @sections = ('Usage', 'Function', 'Returns', 'Args');
 191 my $sec_ndx = 0;
 192
 193 foreach my $section ($usage, $function, $returns, $args) {
 194
 195         my $section_html = Deobfuscator::htmlify($section);
 196         print "<tr><td $style1>$sections[$sec_ndx++]</td><td $style2>$section_html</td></tr>\n";
 197 }
 198
 199 # close the table
 200 print "</table></div>";
 201
 202 # finish the page
 203 print end_html;
 204
 205 # close BerkeleyDB
 206 Deobfuscator::close_db($BerkeleyDB_packages);
 207 Deobfuscator::close_db($BerkeleyDB_methods);
 208
 209 __END__