cgi-bin/tools/trace_view.pl

   1 use strict;
   2 use warnings;
   3
   4 use CXGN::Page;
   5 use CXGN::Chromatogram;
   6 use URI::Escape;
   7 use CatalystX::GlobalContext '$c';
   8
   9 my $page = CXGN::Page->new( "Chromatogram viewer", "john" );
  10 my ( $file, $temp ) = $page->get_encoded_arguments( 'file', 'temp' );
  11 if ($file) {
  12
  13 #do not accept files specified with /. because that might be an attempt to view some other file that they
  14 #are not allowed to view
  15     if ( $file =~ /\/\./ ) {
  16         $page->message_page( 'Invalid file location.',
  17             '', '', "Invalid file location: $file" );
  18     }
  19
  20     #if it's a tempfile, look in the tempfile location
  21     if ($temp) {
  22         $file =~ /^[\w\-]+\.mct$/
  23           or $page->message_page( 'Invalid file location.',
  24             '', '', "Invalid file location: $file" )
  25           ; #i made up the extension 'mct' for 'mystery chromatogram type' since we have various kinds of chromatograms and nothing recorded about their file types. --john
  26         $file =
  27             $c->config->{'basepath'}
  28           . $c->config->{'tempfiles_subdir'}
  29           . '/traceimages/'
  30           . $file;
  31     }
  32
  33     #otherwise it will be in data shared
  34     else {
  35         my $data_shared_url = $c->config->{'static_datasets_url'};
  36         my $data_shared_website_path =
  37           $c->config->{'static_datasets_path'};
  38
  39         #find cosii chromatogram
  40         if ( $file =~ /^$data_shared_url\/cosii2?\/[\w\-\/]+\.ab1$/ ) {
  41             $file =~ s/$data_shared_url/$data_shared_website_path/;
  42         }
  43
  44         #or find pgn chromatogram
  45         elsif ( $file =~ /trace_files/ ) {
  46             $file =~
  47 s/trace_files/data\/prod\/public\/pgn_data_processing\/processed_traces\//;
  48         }
  49
  50         #or give up
  51         else {
  52             $page->message_page( 'Invalid file location.',
  53                 '', '', "Invalid file location: $file" );
  54         }
  55     }
  56
  57     my $temp_image_filename;
  58     if ( $file =~ /([\w\-\.]+)\.\w+$/ ) {
  59         $temp_image_filename = $1;
  60     }
  61     else {
  62         $page->message_page( 'Invalid file location.',
  63             '', '', "Invalid file location: $file" );
  64         print STDERR
  65           "/cgi-bin/tools/trace_view.pl: invalid file location: $file\n";
  66     }
  67
  68     my $display_pngfile;
  69     if ( -f ($file) ) {
  70         if ( CXGN::Chromatogram::is_abi_file($file) ) {
  71             $display_pngfile = CXGN::Chromatogram::create_image_file( $file,
  72                 "$temp_image_filename.png" );
  73         }
  74         else {
  75             my $uncompressed_file =
  76                 $c->config->{'basepath'}
  77               . $c->config->{'tempfiles_subdir'}
  78               . "/traceimages/$temp_image_filename"
  79               . "_uncompressed";
  80             CXGN::Chromatogram::uncompress_if_necessary( $file,
  81                 $uncompressed_file );
  82             if ( CXGN::Chromatogram::is_abi_file($uncompressed_file) ) {
  83                 $display_pngfile =
  84                   CXGN::Chromatogram::create_image_file( $uncompressed_file,
  85                     "$temp_image_filename.png" );
  86             }
  87             else {
  88                 $page->message_page(
  89 'Sorry, but the viewer does not support this type of chromatogram file.'
  90                 );
  91             }
  92         }
  93     }
  94     else {
  95         $page->message_page( 'Invalid file location.',
  96             '', '', "Chromatogram file not found at $file" );
  97         print STDERR
  98           "/cgi-bin/tools/trace_view.pl: invalid file location: $file\n";
  99     }
 100
 101     #create the page
 102     $page->header("Chromatogram viewer: $temp_image_filename");
 103     print
 104 "<center><h4>$temp_image_filename</h4></center><img src=\"$display_pngfile\" border=\"0\">";
 105     $page->footer();
 106 }
 107 else {
 108     $page->message_page('Invalid arguments.');
 109 }