cgi-bin/search/trace_download.pl

   1 #!/usr/bin/perl -w
   2 use strict;
   3 use warnings;
   4 use CXGN::Page;
   5 use CXGN::Genomic::Chromat;
   6 use CXGN::DB::Connection;
   7 use CatalystX::GlobalContext '$c';
   8
   9 # KONI 2003 August 4
  10 #
  11 # New download script for chromatogram access.
  12 our $trace_basepath;
  13 our $page = CXGN::Page->new( "Trace Download", "Koni");
  14
  15 my $dbh = CXGN::DB::Connection->new();
  16
  17 #read_id is for a chromat from sgn.seqread
  18 #chromat_id is for a chromat from genomic.chromat
  19 my ($read_id,$chromat_id) = $page->get_arguments(qw/read_id chrid/);
  20
  21 unless ((defined($read_id) && $read_id =~ m/^[0-9]+$/)
  22         || (defined($chromat_id) && $chromat_id =~ m/^[0-9]+$/)) {
  23   $page->message_page("Invalid: '$chromat_id', '$read_id'.\n");
  24 #  invalid_search($page);
  25 }
  26
  27 my ($tablename,$idcol);
  28 my ($path, $name);
  29 if($read_id) {
  30   my $schema = $dbh->qualify_schema('sgn');
  31   $tablename = "$schema.seqread";
  32   $idcol = 'read_id';
  33   ($path, $name) = $dbh->selectrow_array("SELECT trace_location,trace_name FROM $tablename WHERE $idcol=?",undef,$read_id||$chromat_id);
  34 } elsif($chromat_id) {
  35     my $chromat = CXGN::Genomic::Chromat->retrieve($chromat_id);
  36     $path = $chromat->subpath;
  37     $name = $chromat->filename;
  38 } else {
  39   $page->error_page('Invalid GET parameters');
  40 }
  41
  42 ($path && $name) || not_found($page, $read_id);
  43
  44 my $basename = $c->config->{'trace_path'}."/$path/$name";
  45 my $full_pathname = '';
  46
  47 # The actual extension used should have been stored in the database, but it
  48 # was not. This is because most chromatograms we had at the start did not have
  49 # an extension. Overtime, it became clear that preserving the facility's
  50 # specified filename is necessary, thus conventions for file extenstions are
  51 # not standardized. This nested loop below wastes some time, but is arguably
  52 # robust and easily extended to new types.
  53 #
  54 # Add the extenstion used to seqread in the database to solve the problem
  55 # cleanly, do NOT standardize the extensions used on the file system.
  56 my $type_ext;
  57 my $comp_ext;
  58 foreach $type_ext ( '',qw/.ab1 .abi .scf .esd .SCF/) {
  59   foreach $comp_ext ( '',qw/.gz .Z .bz2/) {
  60     if ( -f "$basename$type_ext$comp_ext" ) {
  61       $full_pathname = $basename . $type_ext . $comp_ext;
  62       $name .= $type_ext . $comp_ext;
  63       last;
  64     }
  65   }
  66 }
  67
  68 if (!$full_pathname) {
  69     print STDERR "Can't find chromatogram file at $basename";
  70   $page->message_page("This sequence does not seem to have an associated chromatogram.");
  71 }
  72
  73 open F, "<$full_pathname"
  74  or $page->error_page("Failed to open chromatogram file for SGN-T$read_id ($!)");
  75
  76 print "Pragma: \"no-cache\"\nContent-Disposition: filename=$name\n";
  77 print "Content-type: application/data\n\n";
  78
  79
  80 while(read(F,$_,4096)) {
  81     print;
  82 }
  83
  84 close F;
  85
  86 sub invalid_search {
  87   my ($page) = @_;
  88
  89   $page->header();
  90
  91   print <<EOF;
  92
  93 Requested search is invalid.
  94 EOF
  95
  96   $page->footer();
  97   exit 0;
  98 }
  99
 100 sub not_found {
 101   my ($page, $id) = @_;
 102
 103   $page->header();
 104
 105   print <<EOF;
 106
 107 No chromatogram was found for SGN-T$id.
 108
 109 EOF
 110
 111   $page->footer();
 112   exit 0;
 113 }
 114
 115