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242 lines
7.6 KiB
Perl
242 lines
7.6 KiB
Perl
#!/usr/bin/perl
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# create HTML file in the nullModel directory
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# call the calculation script and run it via the pbs queuing mechanism
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use CGI;
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use CGI qw(:standard);
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use CGI::Carp qw(warningsToBrowser fatalsToBrowser);
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use strict;
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use Storable;
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use lib "/bioseq/bioSequence_scripts_and_constants";
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use GENERAL_CONSTANTS;
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use BIOSEQUENCE_FUNCTIONS;
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my $run_number = param('run_number');
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my $runCalcInput = param('input_file');
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my $Q_log = param('Q_log');
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my $user_mail = param('receipent');
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my %run_data = ();
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my ($WorkingDir, $outHtml, $WWWdir, $walltime);
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&read_input;
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my $selecton_url = GENERAL_CONSTANTS::SELECTON_URL;
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my $user_ip = $ENV{'REMOTE_ADDR'};
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&BIOSEQUENCE_FUNCTIONS::check_if_user_is_allowed("selecton",$user_ip, $user_mail);
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#print header;
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#print start_html("Get Form");
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#print "selecton_url is: $selecton_url";
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#print end_html;
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#exit;
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my $nullDir = $WorkingDir . "nullModel/";
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my $null_html_out = $nullDir . "output.html"; #new OUTPUT to the user regarding the statistical test run
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my $qstat_script = "/bioseq/Selecton/statTest.pl";
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my $qsub_script = $WorkingDir."qsub_statTest.sh";
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my $Qstat_No_file = "QSTAT_NO_NULL_MODEL";
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#------------------------------------------------------------------------------------------------
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#-------------------------------------- S C R I P T ---------------------------------------------
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#------------------------------------------------------------------------------------------------
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my $curr_time = &BIOSEQUENCE_FUNCTIONS::printTime();
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# add this run to the log
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open LIST, ">>".GENERAL_CONSTANTS::SELECTON_LOG;
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flock LIST, 2;
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print LIST $curr_time." null_$run_number $user_ip $user_mail\n";
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flock LIST, 8;
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close LIST;
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# print the user's ip and run name in the running jobs list
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open RUN_LIST, ">>".GENERAL_CONSTANTS::SELECTON_RUNNING_JOBS;
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flock RUN_LIST, 2;
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print RUN_LIST "null_$run_number $user_ip $user_mail\n";
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flock RUN_LIST, 8;
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close RUN_LIST;
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open LOG, ">>".$Q_log;
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print LOG "\n\n-----------------------------------\n\n**** Running statistical Test ****\n\n";
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mkdir $nullDir;
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&start_output_html;
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&store_new_data;
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# Move directly to the output file
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print "Location: ".$WWWdir."output.html\n\n";
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close(STDIN);
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close(STDOUT);
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close(STDERR);
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##----------------------
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#
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##print end_html;
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# create shell file with the perl script command
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# run this on the Q - get the job id
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# if something goes wrong: output a message saying the statistical test has an error
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unless (open QSUB_SH, ">$qsub_script"){
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&exit_on_system_error("cannot open the file $qsub_script for writing $!\n", $user_mail);
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}
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print QSUB_SH '#!/bin/sh';
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print QSUB_SH "\nperl $qstat_script $run_number $runCalcInput > $WorkingDir"."statTest_std.out";
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close QSUB_SH;
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chmod 0755, $qsub_script;
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print LOG "submitting qsub job \"SELECTON_NULL_$run_number\"\n";
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my $qsub_command = "ssh bioseq\@biocluster qsub -q bioseq -e $WorkingDir -o $WorkingDir -N SELECTON_NULL_$run_number $qsub_script";
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if ($walltime ne "none"){
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$qsub_command.=" -l walltime=$walltime";
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}
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else{
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$qsub_command.=" -l walltime=".GENERAL_CONSTANTS::MAX_WALLTIME;
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}
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print LOG "going to run qsub command: ".$qsub_command."\n";
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my $qsub_job_no = `$qsub_command`;
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chomp($qsub_job_no); # the command returns an extra new line character
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# writing the job number to a file.
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open JOB_NO, ">".$WorkingDir.$Qstat_No_file;
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print JOB_NO $qsub_job_no;
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close JOB_NO;
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chmod 0644, $WorkingDir.$Qstat_No_file;
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$qsub_job_no =~ /(\d+)/;
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$qsub_job_no = $1; # extracting only the process (Q) number
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print LOG "\nafter submitting qsub job. JOB NUMBER: $qsub_job_no\n";
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unless (open LIST, ">>".GENERAL_CONSTANTS::QUEUING_JOBS){
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print LOG "Could not open file ".GENERAL_CONSTANTS::QUEUING_JOBS.". Reason: $!\nThe job was not listed in the queuing_jobs list.\n";
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&printTime();
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}
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else{
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flock LIST, 2; # locks the list, so no other process will write to it. On the same time - if the list is currently locked by another process - it waits until the list file is realeased. The "2" and "8" are the operation symbols for "lock" and "unlock".
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print LIST "$qsub_job_no Selecton null_$run_number ".&BIOSEQUENCE_FUNCTIONS::printTime()."\n";
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flock LIST, 8;
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close LIST;
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}
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print LOG "\n\nCGI ended successfully.";
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close LOG;
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exit;
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#######################################################################################
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sub read_input{
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# --- storable on ---
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my $data = retrieve($runCalcInput);
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%run_data = %$data;
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$WorkingDir = $run_data{WorkingDir};
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$outHtml = $run_data{OutHtmlFile};
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$WWWdir = $run_data{WWWdir}."nullModel/";
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$walltime = $run_data{estimated_run_time};
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# --- storable on ---
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# --- storable off ---
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#$WorkingDir = GENERAL_CONSTANTS::SERVERS_RESULTS_DIR."Selecton/".$run_number."/";
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#$outHtml = $WorkingDir."output.html";
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#$WWWdir = GENERAL_CONSTANTS::SELECTON_RESULTS_URL.$run_number."/nullModel/";
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# --- storable off ---
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}
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#######################################################################################
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sub store_new_data{
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unlink $runCalcInput;
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$run_data{nullDir} = $nullDir;
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$run_data{null_html_out} = $null_html_out;
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store \%run_data, $runCalcInput;
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if (!(-e $runCalcInput) or (-z $runCalcInput)){
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&exit_on_system_error("\nstore_new_data : Seems that the store failed. the file $runCalcInput doesn't exists or is of size zero\n", $user_mail);
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}
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}
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#######################################################################################
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# Start writing the output web page of Selecton
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sub start_output_html {
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system 'echo "(touch '.$null_html_out.'; chmod oug+rxw '.$null_html_out.')" | /bin/tcsh';
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unless (open OUTPUT, ">$null_html_out"){
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&exit_on_system_error("start_output_html : cannot open $null_html_out $!\n", "problems in statTest.cgi: cannot open the file $null_html_out for writing $!");
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}
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print OUTPUT <<EndOfHTML;
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<HTML>
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<HEAD> <META HTTP-EQUIV="REFRESH" CONTENT=30> </HEAD>
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<HEAD> <META HTTP-EQUIV="PRAGMA" CONTENT="NO-CACHE"> </HEAD>
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<TITLE>Selecton Statistical Test Results - Run $run_number</TITLE>
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<style type="text/css">
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#menu {
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text-decoration: none;
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color: white;
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font-size: 12px;
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font-weight: 700;
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}
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</style>
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</HEAD>
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<BODY bgcolor="#FFF5EE">
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<table width=100% bgcolor="#400080"> <tr><td>
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<table border=0 cols=6 width=450 bgcolor="#400080" cellpadding=1 cellspacing=0 >
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<tr >
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<td align=center><a href="$selecton_url/index.html" id=menu target=_top>HOME</a></td>
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<td align=center><a href="$selecton_url/overview.html" id=menu target=_top>OVERVIEW</a></td>
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<td align=center><a href="$selecton_url/gallery.html" id=menu target=_top>GALLERY</a></td>
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<td align=center><a href="$selecton_url/credits.html" id=menu target=_top>CREDITS</a></td>
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</tr>
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</table>
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</td><tr></table>
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<H1 align=center>Selecton Job Status Page</H1>
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<H3 align=center>Statistical Test Results</H3>
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<blockquote>
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<p><font face=Verdana size=2>
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Selecton is now calculating the statistical significance of your results.<br>
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<b>Please note that this process will take approximately the same time as the original running time.</b><br>
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An email will be sent to the address you supplied once the calculation is finished.<br>
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This page will be automatically updated every 30 seconds. You can also reload it manually.<br>
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<br><br>
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</font></p>
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EndOfHTML
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close OUTPUT;
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}
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#######################################################################################
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sub exit_on_system_error{
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my $log_err = shift;
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my $err = shift;
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print LOG $log_err;
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&GENERAL_CONSTANTS::send_mail("Selecton", GENERAL_CONSTANTS::ADMIN_EMAIL, $run_number."_nullModel", 'error', $err);
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&BIOSEQUENCE_FUNCTIONS::remove_job_from_running_log("Selecton", "null_$run_number");
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close LOG;
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exit;
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} |