$title - Running

package SetupPipeline; use FileManager; use POSIX; use Digest::MD5 qw/md5_base64/; use IPC::Open3; use XML::LibXML; use Site; use strict; use FindBin; use lib "$FindBin::Bin/../../../lib/perl"; use SBEAMS::Connection::Settings; our @ISA = qw/Exporter/; our @EXPORT = qw/rand_token jobsummary create_files start_job parse_sample_groups_file first_key_val add_upload_expression_button log_job parse_exprSet parse_aafTable create_directory/; #### Subroutine: rand_token # Generate a random token 8 characters long #### sub rand_token { my $token = md5_base64(time * $$); $token =~ s/[+\/=]//g; return substr($token, 0, 8); } #### Subroutine: jobsummary # Creates the job summary table using pairs of arguments #### sub jobsummary { my @args = @_; my $jobsummary = <Job Summary: END for (my $i = 0; $i < @args; $i += 3) { $jobsummary .= '\n"; } $jobsummary .= < END } #### Subroutine: create_directory ######################################## # Creates a directory # ######################################################## sub create_directory { my ($dir,$jobname) = @_; # Create job directory print STDERR "JOB DIR1 '$dir/$jobname'\n"; umask(0000); #delete for production my $umask = umask(); #delete for production mkdir("$dir/$jobname", 0775) || return("Couldn't create result directory. '$dir/$jobname' "); #chown(-1, 1052, "$dir/$jobname"); return undef; } #### Subroutine: create_files # Creates the directory and files for running the job #### sub create_files { my %args = @_; my $dir = $args{dir}; my $job_dir = $args{job_dir}; my $jobname = $args{jobname}; my $title = $args{title}; my $jobsummary = $args{jobsummary}; my $output = $args{output}; my $refresh = $args{refresh}; my $perl_script = $args{script}; my $email = $args{email}; # Create job directory #print STDERR "JOB DIR2 '$dir/$jobname'\n"; unless (-d "$job_dir/$jobname"){ # umask(0000); #delete for production # my $umask = umask(); #delete for production mkdir("$job_dir/$jobname", 0775) || return("Couldn't create result directory. '$job_dir/$jobname' "); chmod(0777,"$job_dir/$jobname"); #delete for production } # Create perl script that runs pipeline my $perl_script_name = $job_dir.'/'.$jobname.'/'.$jobname.'.pl'; open(SCRIPT, ">$perl_script_name") || return("Couldn't create perl script file. '$job_dir/$jobname/$jobname.pl' "); print SCRIPT $perl_script; close SCRIPT; chmod(0777,$perl_script_name) || return("Couldn't change the mode of perl script. '$perl_script_name' "); # Generate Shell script my $sh = generate_sh( output_dir => $dir, job_dir => $job_dir, jobname => $jobname, email => $email, perl_script => $perl_script_name ); open (SH, ">$job_dir/$jobname/$jobname.sh") || return("Couldn't create shell script. '$job_dir/$jobname/$jobname.sh' "); print SH $sh; close (SH); chmod(0777,"$job_dir/$jobname/$jobname.sh") || return("Couldnt change the mode of shell script. '$job_dir/$jobname/$jobname.sh' "); # Create processing index file open(INDEX, ">$job_dir/$jobname/index.html") || return("Couldn't create HTML file."); print INDEX < $title - Running

Running...

Click here to manually refresh.

Click here to cancel the job.

$jobsummary END close(INDEX); chmod(0666, "$job_dir/$jobname/index.html"); # Create results index file open(INDEXRESULT, ">$job_dir/$jobname/indexresult.html") || return("Couldn't create HTML file."); print INDEXRESULT < $title $output

Output Archive:

$jobname.tar.gz
$jobsummary END close(INDEXRESULT); chmod(0666, "$job_dir/$jobname/indexresult.html"); # Create error index file open(INDEXERROR, ">$job_dir/$jobname/indexerror.html") || return("Couldn't create HTML file."); print INDEXERROR < $title - Error

Error:

An error occured while processing the job. Please check the input and try again. If the problem persists, please contact the site administrator.

Click here to see the error.

To re-run or delete this job, go the the Status Page.

$jobsummary END close(INDEXERROR); chmod(0666, "$job_dir/$jobname/indexerror.html"); return undef; } #### Subroutine: generate_sh # Generate the shell script to run the perl script and move files #### sub generate_sh { my (%argHash)=@_; my @required_opts=qw(output_dir job_dir email jobname perl_script); my @missing=grep {!defined $argHash{$_}} @required_opts; die "missing opts: ",join(', ',@missing)." from supplied ",join(', ',%argHash) if @missing; my ($output_dir,$job_dir,$email,$jobname,$perl_script)= @argHash{qw(output_dir job_dir email jobname perl_script)}; my $sh=<<"SH"; #!/bin/sh #PBS -N $jobname #PBS -M $email #PBS -M solxabot\@systemsbiology.org #PBS -m ea #PBS -o $jobname.out #PBS -e $job_dir/$jobname/$jobname.err touch $job_dir/$jobname/timestamp SH my $cmd="/tools64/bin/perl $perl_script"; die "$perl_script not found and/or not executable: $!" unless -x $perl_script; # $qsub.="perl $base_dir/echo.pl $opts\n"; # leave this around for debugging $sh.= "$cmd\n"; $sh .= < Subject: Job Completed: $jobname To: $email Your job has finished processing. See the results here: $SERVER_BASE_DIR$RESULT_URL?action=view_file&jobname=$jobname&analysis_file=index&file_ext=html END_EMAIL END $sh .= < Subject: Job Error: $jobname To: $email There was a problem while processing your job. See the error here: $SERVER_BASE_DIR$RESULT_URL?action=view_file&jobname=$jobname&analysis_file=index&file_ext=html END_EMAIL END $sh .= <path; my $time = time(); return undef if (! $fm || ! $fm->path); #open(LOG, ">>$path/.log") || # return("Couldn't write to log file"); #print LOG "$jobname\t$title\t$time\n"; #close(LOG); return undef; } #### Subroutine: parse_sample_groups_file # Parse the XML file containing the sample group information #Return a hash of values #### sub parse_sample_groups_file{ my %args = @_; my $folder_name = $args{folder}; my $data_type = $args{data_type}; my $file = "$BC_UPLOAD_DIR/$folder_name/$SAMPLE_GROUP_XML"; my $parse_setup = XML::LibXML->new(); #Object for parsing the file my $doc = $parse_setup->parse_file("$file"); my $root = $doc->getDocumentElement; my $xpath = 'file_sample_group_info/sample_groups/file_name'; my $file_names_ns = $doc->findnodes($xpath); my %sample_groups = (); #print STDERR "IN PARSE SAMPLE"; if ($data_type eq 'get_reference_sample'){ my $reference_sample_group_node = $root->findnodes('//reference_sample_group'); my $reference_sample_group = $reference_sample_group_node->to_literal; return $reference_sample_group } #return just the sample group names and the class number if ($data_type eq 'sample_group_ids'){ #print STDERR "IN SAMPLE GROUP IDS SUB "; foreach my $file_name_node ($file_names_ns->get_nodelist) { my $sample_group = $file_name_node->findnodes('./@sample_group_name')->string_value(); my $class_number = $file_name_node->findnodes('./@class_number')->string_value(); $sample_groups{$class_number} = $sample_group; #print STDERR "SAMPLE GROUP $sample_group => $class_number"; } return ( \%sample_groups); } # return reference to hash with defined keys, each of which points to an arrayref # of some particular data associated with a file if ($data_type eq 'file_info'){ my %info; foreach my $file_name_node ($file_names_ns->get_nodelist) { push @{$info{file_names}}, $file_name_node->to_literal(); push @{$info{sample_groups}}, $file_name_node->findnodes('./@sample_group_name')->string_value(); push @{$info{sample_names}}, $file_name_node->findnodes('./@sample_name')->string_value(); push @{$info{class_numbers}}, $file_name_node->findnodes('./@class_number')->string_value(); } return ( \%info ); } my $order_count = 1; foreach my $file_name_node ($file_names_ns->get_nodelist) { my $sample_group = $file_name_node->findnodes('./@sample_group_name')->string_value(); my $sample_name = $file_name_node->findnodes('./@sample_name')->string_value(); my $class_number = $file_name_node->findnodes('./@class_number')->string_value(); my $file_name = $file_name_node->to_literal; $sample_groups{$sample_group}{$file_name} = $order_count; $order_count++; $sample_groups{SAMPLE_NAMES}{$sample_name} = $class_number; #print "FILE NAME '$file_name' SMAPLE GROUP '$sample_group'\n"; } return ( \%sample_groups); } #### Subroutine: first_key_val # return the first key of a href #### sub first_key_val{ my $href = shift; foreach my $k (keys %$href){ return $href->{$k}; } }

'; $jobsummary .= $args[$i]; $jobsummary .= '

'; $jobsummary .= defined($args[$i+1]) ? $args[$i+1] : ""; $jobsummary .= "