cgi-bin/tools/wait.pl

   1
   2 use strict;
   3 use Storable qw / retrieve /;
   4 use File::Temp qw / tempfile /;
   5 use File::Copy;
   6 use File::Basename qw / basename /;
   7
   8 use Cwd qw/ realpath /;
   9 use File::Spec::Functions;
  10 use File::NFSLock qw/uncache/;
  11
  12 use CXGN::Page;
  13 use CXGN::Page::FormattingHelpers qw/ page_title_html blue_section_html /;
  14 use CXGN::Tools::Run;
  15
  16 use CatalystX::GlobalContext qw( $c );
  17
  18 my $page = CXGN::Page->new("Generic SGN Cluster Job Waiting Page", "Lukas");
  19
  20 #extra_params added since I couldn't prevent encoding/decoding merges
  21 # format: param1:value1::param2:value2::etc3:v3
  22 # this adds parameters to the redirect page
  23
  24 my ($tmp_app_dir, $job_file, $redirect, $out_file_override, $extra_params)
  25         = $page->get_arguments("tmp_app_dir", "job_file", "redirect", "out_file_override", "extra_params");
  26
  27 if( $out_file_override ) {
  28     $out_file_override = realpath( $out_file_override );
  29
  30     print STDERR "OUTFILE: $out_file_override\n";
  31     $out_file_override =~ m!/(data|export)/(prod|shared)|(/tmp)! && $out_file_override !~ /\.\./
  32         or die "is someone trying to do something nasty? illegal out_file_override '$out_file_override'";
  33 }
  34
  35 my ($message) = $page->get_arguments("message");
  36
  37
  38 my $d = CXGN::Debug->new;
  39
  40 $tmp_app_dir =~ s!/!!g;
  41 my $tmpdir = $page->path_to( $page->tempfiles_subdir($tmp_app_dir) );
  42
  43 $job_file = catfile($tmpdir,$job_file);
  44
  45 $d->d("Arguments: job_file = $job_file redirect = $redirect");
  46
  47 unless( -f $job_file ) {
  48   $c->throw( message => "Job not found.  Has it already been executed and the results retrieved?",
  49              is_error => 0,
  50              developer_message => "Job file was '$job_file'\n",
  51             );
  52 }
  53
  54
  55 my $job = retrieve($job_file)
  56   or die "Could not retrieve job_file $job_file";
  57
  58 if ( $job->alive ){
  59     display_not_finished($message);
  60     return;
  61 }
  62 else {
  63     # the job has finished
  64     # copy the cluster temp file back into "apache space"
  65     #
  66     my (undef, $apache_temp) = tempfile( DIR=>$tmpdir,
  67                                          TEMPLATE=>"alignXXXXXX",
  68                                        );
  69
  70     $d->debug("COPY --> OUTFILE: ".$job->out_file()." Apache temp: $apache_temp");
  71
  72     my $job_out_file = $job->out_file();
  73     for( 1..10 ) {
  74       uncache($job_out_file);
  75       last if -f $job_out_file;
  76       sleep 1;
  77     }
  78
  79     -f $job_out_file or die "job output file ($job_out_file) doesn't exist";
  80     -r $job_out_file or die "job output file ($job_out_file) not readable";
  81     -w $apache_temp  or die "apache temp directory doesn't exist or not writable - won't copy";
  82
  83     # You may wish to provide a different output file to send back
  84     # rather than STDOUT from the job.  Use the out_file_override
  85     # parameter if this is the case.
  86     my $out_file = $out_file_override || $job->out_file();
  87     system("ls /data/prod/tmp 2>&1 >/dev/null");
  88     copy($out_file, $apache_temp)
  89         or die "Can't copy result file '$out_file' to temp dir $!";
  90
  91     #clean up the job tempfiles
  92     $job->cleanup();
  93
  94     #also delete the job file
  95     unlink $job_file;
  96
  97
  98     my $redirect_string = $redirect . basename( $apache_temp );
  99
 100     $page->client_redirect($redirect_string);
 101 }
 102
 103
 104 sub display_not_finished {
 105
 106         my $message = shift;
 107         $message ||= "Job running, please wait.";
 108
 109     print <<HTML;
 110 Content-type: text/html
 111
 112 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 113 <html>
 114 <head>
 115 <title>Job running</title>
 116 <meta http-equiv="Refresh" content="3" />
 117 <link rel="stylesheet" href="/css/sgn.css" type="text/css" />
 118 </head>
 119 <body>
 120     <style>
 121       body { padding-top: 80px }
 122       img, div, h2 {
 123         display: block;
 124         margin: 1em auto;
 125         text-align: center;
 126       }
 127     </style>
 128     <img src="/img/sgn_logo_animated.gif" alt="SGN logo"/>
 129     <h2>$message</h2>
 130     <div>Please note: jobs are limited to 1 hour of run time.</div>
 131     <img src="/img/progressbar1.gif" alt="In Progress..."/>
 132 </body>
 133 </html>
 134 HTML
 135
 136 }
 137
 138 sub display_finished {
 139     my $link = shift;
 140
 141     my $title = page_title_html("Job completed.");
 142
 143     $page->header();
 144
 145     print <<HTML;
 146     <br /><br />
 147     $title
 148 <center>
 149
 150 <br />
 151 <a href="$link"><b>View Result</b></a>
 152 <br /><br /><br />
 153 </center>
 154
 155 <!--    Debug info: -->
 156 <!--  -->
 157
 158 <br /><br /><br /><br />
 159 HTML
 160
 161 $page->footer();
 162 }