mason/tools/bulk/display/browse_html.mas

   1
   2 <%args>
   3 $data
   4 </%args>
   5
   6 <& /tools/bulk/display/buttons.mas,
   7    page_size=>$data->{page_size} || 50,
   8    page_number => $data->{page_number},
   9    idType => $data->{idType},
  10    dumpfile => $data->{dumpfile} &>
  11
  12 <%perl>
  13 use Data::Dumper;
  14 use File::Slurp qw | read_file |;
  15 use CXGN::Page::FormattingHelpers qw | html_break_string |;
  16 print STDERR "DATA:".Data::Dumper::Dumper($data);
  17
  18 $data->{page_size} || ($data->{page_size} = 50);
  19
  20 if ( !( exists($data->{page_number}) ||  $data->{page_number} ) ) {
  21 $data->{page_number} = 1;
  22 }
  23 if ( !( exists($data->{page_size}) || $data->{page_size} )) { $data->{page_size} = 50; }
  24 my $file = $data->{tempdir} . "/" . $data->{dumpfile};
  25
  26
  27 my $content = "";
  28 my @file_lines = read_file($file);
  29
  30 print STDERR "Line Count in the file: ".scalar(@file_lines)."\n";
  31
  32 if ( @file_lines < 2 ) {
  33               $content .=
  34               "No data was retrieved. Please verify your input parameters. Thanks.<br /><br />\n";
  35               }
  36               else {
  37
  38               # read the column definitions
  39               #
  40               my @output_fields;
  41               my $defs = shift @file_lines;
  42               if ($defs) { chomp($defs); @output_fields = split /\t/, $defs; }
  43               print STDERR  "column definitions: " . ( join " ", @output_fields )."\n";
  44
  45               # define the links
  46         my %links = (
  47             clone_name =>
  48 "/search/est.pl?request_type=10&amp;search=Search&amp;request_id=",
  49             SGN_U        => "/search/unigene.pl?unigene_id=",
  50             converted_id => "/search/unigene.pl?unigene_id=",
  51         );
  52         $data->{links} = \%links;
  53
  54         #
  55         # read in the required page
  56         #
  57         my $line_count = 0;
  58         my @data = ();
  59
  60         $content .= "<table summary=\"\" border=\"1\">\n";
  61
  62         # print table header
  63         $content .=
  64             "<tr><td>line</td><td>"
  65           . ( join "</td><td>", @output_fields )
  66           . "</td></tr>";
  67
  68         foreach my $fl (@file_lines) {
  69             print STDERR "Processing line $fl...\n";
  70             chomp($fl);
  71             $line_count++;
  72
  73             my $show_line = ( $line_count >= ($data->{page_number} - 1 ) * $data->{page_size} + 1 )
  74                 && ($line_count <=  ( $data->{page_number} ) * $data->{page_size} );
  75
  76             if ($show_line) {
  77                 my @fields = split /\t/, $fl;
  78                 my %row;
  79                 for ( my $i = 0 ; $i < @fields ; $i++ ) {
  80                     $row{ $output_fields[$i] } = $fields[$i];
  81                 }
  82
  83                 # format the sequence data for output to browser.
  84                 # number of letters in sequence or qual to wrap on
  85                 my $breakspace_num = 60;
  86
  87                 $row{est_seq} =
  88                   html_break_string( $row{est_seq}, $breakspace_num );
  89
  90                 $row{est_seq} =
  91 "<span class=\"sequence\" style=\"font-size: smaller;\"> $row{est_seq}</span>";
  92
  93                 $row{unigene_seq} =
  94                   html_break_string( $row{unigene_seq}, $breakspace_num );
  95                 $row{unigene_seq} =
  96 "<span class=\"sequence\" style=\"font-size: smaller;\"> $row{unigene_seq}</span>";
  97
  98                 $row{protein_seq} =
  99                   html_break_string( $row{protein_seq}, $breakspace_num );
 100                 $row{protein_seq} =
 101 "<span class=\"sequence\" style=\"font-size: smaller;\"> $row{protein_seq}</span>";
 102                 $row{estscan_seq} =
 103                   html_break_string( $row{estscan_seq}, $breakspace_num );
 104                 $row{estscan_seq} =
 105 "<span class=\"sequence\" style=\"font-size: smaller;\"> $row{estscan_seq}</span>";
 106                 $row{longest6frame_seq} =
 107                   html_break_string( $row{longest6frame_seq}, $breakspace_num );
 108                 $row{longest6frame_seq} =
 109 "<span class=\"sequence\" style=\"font-size: smaller;\"> $row{longest6frame_seq}</span>";
 110                 $row{preferred_protein_seq} =
 111                   html_break_string( $row{preferred_protein_seq},
 112                     $breakspace_num );
 113                 $row{preferred_protein_seq} =
 114 "<span class=\"sequence\" style=\"font-size: smaller;\"> $row{preferred_protein_seq}</span>";
 115
 116                 $row{bac_end_sequence} =
 117                   html_break_string( $row{bac_end_sequence}, $breakspace_num );
 118                 $row{bac_end_sequence} =
 119 "<span class=\"sequence\" style=\"font-size: smaller;\"> $row{bac_end_sequence}</span>";
 120
 121                 my $qual = $row{qual_value_seq};
 122                 my @qual = split /\s+/, $qual;
 123                 $row{qual_value_seq} = "";
 124                 s/^(\d)$/&nbsp;$1/ foreach (@qual);
 125                 while ( my @a = splice( @qual, 0, $breakspace_num ) ) {
 126                     $row{qual_value_seq} .= join( "&nbsp;", @a ) . "<br />";
 127                 }
 128                 $row{qual_value_seq} =
 129 "<span class=\"sequence\" style=\"font-size: smaller;\"> $row{qual_value_seq}</span>";
 130
 131                 my @output;
 132
 133          #
 134          # cycle through @output_fields and find the corresponding hash elements
 135          #
 136                 $content .= "<tr><td>$line_count</td>\n";
 137                 foreach my $f (@output_fields) {
 138
 139                     #$data-> debug("outputting $row{$f}...");
 140                     if ( !exists( $row{$f} ) || $row{$f} eq undef ) {
 141                         $row{$f} = "N.A.";
 142                     }
 143
 144 #
 145 # add links as required. Links for each output field are stored in the %links hash.
 146 #
 147                     if ( exists( $links{$f} ) && $row{$f} ne "N.A." ) {
 148                         $row{$f} =
 149                           "<a href=\"$links{$f}$row{$f}\">$row{$f}</a>";
 150                     }
 151                     if ( $f eq "clone_id" ) {
 152                         $content .= "<td>$row{$f}</td>";
 153                     }
 154                     else {
 155                         $content .= "<td>$row{$f}</td>";
 156                     }
 157
 158                     #push @output, $row{$f};
 159                 }
 160                 $content .= "</tr>\n";
 161
 162      #$content .= "<tr><td>".(join "</td><td>", @output) . "</td></tr>";
 163             }
 164         }
 165         $content .= "</table><!-- dump info -->\n";
 166 #$data->buttons();
 167 }
 168
 169 #
 170 # output to browser
 171 #
 172 print $content;
 173
 174 close(F);
 175
 176
 177 </%perl>
 178
 179 <& /tools/bulk/display/buttons.mas,
 180   line_count => $data->{line_count},
 181   page_size=>$data->{page_size},
 182   page_number => $data->{page_number},
 183   dumpfile => $data->{dumpfile},
 184   idType => $data->{idType}
 185
 186 &>