Work started on auto-refreshing job viewer.

bigsdb.pl

@@ -76,6 +76,7 @@ use BIGSdb::ExtractedSequencePage;
 use BIGSdb::AlleleQueryPage;
 use BIGSdb::LocusInfoPage;
 use BIGSdb::OfflineJobManager;
+use BIGSdb::JobViewerPage;
 
 my $r = shift;    #Apache request object (used for mod_perl)
 Log::Log4perl->init_once( CONFIG_DIR . '/logging.conf' );

lib/BIGSdb/Application.pm

@@ -54,7 +54,9 @@ sub new {
 			$self->_setup_prefstore();
 			$self->_initiate_authdb if $self->{'system'}->{'authentication'} eq 'builtin';
 			$self->_initiate_jobmanager( $config_dir, $plugin_dir, $dbase_config_dir )
-			  if $self->{'cgi'}->param('page') eq 'plugin' && $self->{'config'}->{'jobs_db'};
+			  if ( $self->{'cgi'}->param('page') eq 'plugin'
+				|| $self->{'cgi'}->param('page') eq 'job' )
+			  && $self->{'config'}->{'jobs_db'};
 			$self->_initiate_plugins($plugin_dir);
 		}
 	}
@@ -334,7 +336,8 @@ sub print_page {
 		'fieldValues'        => 'FieldHelpPage',
 		'extractedSequence'  => 'ExtractedSequencePage',
 		'alleleQuery'        => 'AlleleQueryPage',
-		'locusInfo'          => 'LocusInfoPage'
+		'locusInfo'          => 'LocusInfoPage',
+		'job'				 => 'JobViewerPage'
 	);
 	my $page;
 	my %page_attributes = (
@@ -351,6 +354,7 @@ sub print_page {
 		'dataConnector'    => $self->{'dataConnector'},
 		'pluginManager'    => $self->{'pluginManager'},
 		'mod_perl_request' => $self->{'mod_perl_request'},
+		'jobManager'       => $self->{'jobManager'},
 	);
 	my $continue = 1;
 	my $auth_cookies_ref;

lib/BIGSdb/JobViewerPage.pm

+#Written by Keith Jolley
+#Copyright (c) 2010, University of Oxford
+#E-mail: keith.jolley@zoo.ox.ac.uk
+#
+#This file is part of Bacterial Isolate Genome Sequence Database (BIGSdb).
+#
+#BIGSdb is free software: you can redistribute it and/or modify
+#it under the terms of the GNU General Public License as published by
+#the Free Software Foundation, either version 3 of the License, or
+#(at your option) any later version.
+#
+#BIGSdb is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#GNU General Public License for more details.
+#
+#You should have received a copy of the GNU General Public License
+#along with BIGSdb.  If not, see <http://www.gnu.org/licenses/>.
+
+package BIGSdb::JobViewerPage;
+use strict;
+use base qw(BIGSdb::Page);
+use Log::Log4perl qw(get_logger);
+my $logger = get_logger('BIGSdb.Page');
+
+sub initiate {
+	my ($self) = @_;
+	$self->{'jQuery'}  = 1;
+	$self->{'noCache'} = 1;
+	$self->{'refresh'} = 30;
+}
+
+sub print_content {
+	my ($self) = @_;
+	my $q = $self->{'cgi'};
+	print "<h1>Job status viewer</h1>";
+	my $id = $q->param('id');
+	if ($id !~ /BIGSdb_\d+/){
+		print "<div class=\"box\" id=\"statusbad\">\n";
+		print "<p>The submitted job id is invalid.</p>\n";
+		print "</div>";
+		return;
+	}
+	my ($job,$params,$output) = $self->{'jobManager'}->get_job($id);
+	if (ref $job ne 'HASH' || !$job->{'id'}){
+		print "<div class=\"box\" id=\"statusbad\">\n";
+		print "<p>The submitted job does not exist.</p>\n";
+		print "</div>\n";
+		return;
+	}
+	(my $submit_time = $job->{'submit_time'}) =~ s/\.\d+$//; #remove fractions of second 
+	(my $start_time = $job->{'start_time'}) =~ s/\.\d+$//;
+	(my $stop_time = $job->{'stop_time'}) =~ s/\.\d+$//;
+	print << "HTML";
+<div class="box" id="resultstable">
+<h2>Status</h2>
+<table class="resultstable">
+<tr class="td1"><th style="text-align:right">Job id: </th><td style="text-align:left">$id</td></tr>
+<tr class="td2"><th style="text-align:right">Submit time: </th><td style="text-align:left">$submit_time</td></tr>
+<tr class="td1"><th style="text-align:right">Status: </th><td style="text-align:left">$job->{'status'}</td></tr>
+<tr class="td2"><th style="text-align:right">Start time: </th><td style="text-align:left">$start_time</td></tr>
+<tr class="td1"><th style="text-align:right">% complete: </th><td style="text-align:left">$job->{'percent_complete'}</td></tr>
+<tr class="td2"><th style="text-align:right">Stop time: </th><td style="text-align:left">$stop_time</td></tr>
+</table>
+<h2>Output</h2>
+HTML
+	if (!($job->{'message_html'} || ref $output eq 'HASH')){
+		print "<p>No output yet.</p>\n";
+	} else {
+		print "$job->{'message_html'}";
+	}
+	print "<p>This page will reload in $self->{'refresh'} seconds.  You can refresh it any time, or bookmark it and close your browser if you wish.</p>\n";
+	print "</div>\n";
+}
+
+sub get_title {
+	my ($self) = @_;
+	my $desc = $self->{'system'}->{'description'} || 'BIGSdb';
+	return "Job status viewer - $desc";
+}
+1;
\ No newline at end of file

lib/BIGSdb/OfflineJobManager.pm

@@ -21,10 +21,10 @@ use strict;
 use base qw(BIGSdb::Application);
 use Error qw(:try);
 use Log::Log4perl qw(get_logger);
-
 my $logger = get_logger('BIGSdb.Job');
 
 sub new {
+
 	#The job manager uses its own Dataconnector since it may be called by a stand-alone script.
 	my ( $class, $config_dir, $plugin_dir, $dbase_config_dir, $host, $port, $user, $password ) = @_;
 	my $self = {};
@@ -75,6 +75,7 @@ sub _db_connect {
 }
 
 sub add_job {
+
 	#Required params:
 	#dbase_config: name of db configuration direction in /etc/dbases
 	#ip_address: connecting address
@@ -93,17 +94,17 @@ sub add_job {
 		}
 	}
 	$params->{'priority'} = 5 if !$params->{'priority'};
-	my $id = BIGSdb::Utils::get_random();
+	my $id         = BIGSdb::Utils::get_random();
 	my $cgi_params = $params->{'parameters'};
-	if (ref $cgi_params ne 'HASH'){
+	if ( ref $cgi_params ne 'HASH' ) {
 		$logger->error("CGI parameters not passed as a ref");
 		throw BIGSdb::DataException("CGI parameters not passed as a ref");
 	}
 	eval {
 		$self->{'db'}->do(
 "INSERT INTO jobs (id,dbase_config,username,email,ip_address,submit_time,module,status,percent_complete,priority) VALUES (?,?,?,?,?,?,?,?,?,?)",
-			undef, 
-			$id, 
+			undef,
+			$id,
 			$params->{'dbase_config'},
 			$params->{'username'},
 			$params->{'email'},
@@ -115,13 +116,36 @@ sub add_job {
 			$params->{'priority'}
 		);
 		my $param_sql = $self->{'db'}->prepare("INSERT INTO params (job_id,key,value) VALUES (?,?,?)");
-		$"='||';
-		foreach (keys %$cgi_params){
-			my @values = split("\0",$cgi_params->{$_});
-			$param_sql->execute($id,$_,"@values");
+		$" = '||';
+		foreach ( keys %$cgi_params ) {
+			my @values = split( "\0", $cgi_params->{$_} );
+			$param_sql->execute( $id, $_, "@values" );
 		}
 	};
-	if ($@){
+	if ($@) {
+		$logger->error($@);
+		$self->{'db'}->rollback;
+	} else {
+		$self->{'db'}->commit;
+	}
+	return $id;
+}
+
+sub update_job_output {
+	my ( $self, $job_id, $output_hash ) = @_;
+	if ( ref $output_hash ne 'HASH' ) {
+		$logger->error("status hash not passed as a ref");
+		throw BIGSdb::DataException("status hash not passed as a ref");
+	}
+	eval {
+		$self->{'db'}->do(
+			"UPDATE output SET filename=?, description=? WHERE job_id=?",
+			undef,
+			$output_hash->{'filename'},
+			$output_hash->{'description'}, $job_id
+		);
+	};
+	if ($@) {
 		$logger->error($@);
 		$self->{'db'}->rollback;
 	} else {
@@ -130,18 +154,19 @@ sub add_job {
 }
 
 sub update_job_status {
-	my ($self,$job_id,$status_hash) = @_;
-	if (ref $status_hash ne 'HASH'){
+	my ( $self, $job_id, $status_hash ) = @_;
+	if ( ref $status_hash ne 'HASH' ) {
 		$logger->error("status hash not passed as a ref");
 		throw BIGSdb::DataException("status hash not passed as a ref");
 	}
 	eval {
-		foreach (keys %$status_hash){
-			$self->{'db'}->do("UPDATE jobs SET $_=? WHERE id=?",undef,$status_hash->{$_},$job_id);
-			$logger->debug("$job_id $_: $status_hash->{$_}")
+		foreach ( keys %$status_hash )
+		{
+			$self->{'db'}->do( "UPDATE jobs SET $_=? WHERE id=?", undef, $status_hash->{$_}, $job_id );
+			$logger->debug("$job_id $_: $status_hash->{$_}");
 		}
 	};
-	if ($@){
+	if ($@) {
 		$logger->error($@);
 		$self->{'db'}->rollback;
 	} else {
@@ -150,54 +175,56 @@ sub update_job_status {
 }
 
 sub get_job {
-	my ($self, $job_id) = @_;
+	my ( $self, $job_id ) = @_;
 	my $sql = $self->{'db'}->prepare("SELECT * FROM jobs WHERE id=?");
-	eval {
-		$sql->execute($job_id);		
-	};
-	if ($@){
+	eval { $sql->execute($job_id); };
+	if ($@) {
 		$logger->error($@);
 		return;
 	}
 	my $job = $sql->fetchrow_hashref;
 	$sql = $self->{'db'}->prepare("SELECT key,value FROM params WHERE job_id=?");
-	my $params;
-	eval {
-		$sql->execute($job->{'id'});		
-	};
-	if ($@){
+	my ($params,$output);
+	eval { $sql->execute( $job->{'id'} ); };
+	if ($@) {
 		$logger->error($@);
 		return;
 	}
-	while (my ($key,$value) = $sql->fetchrow_array){
+	while ( my ( $key, $value ) = $sql->fetchrow_array ) {
 		$params->{$key} = $value;
 	}
-	return ($job, $params);	
+	$sql = $self->{'db'}->prepare("SELECT filename,description FROM output WHERE job_id=?");
+	eval { $sql->execute( $job->{'id'} ); };
+	if ($@) {
+		$logger->error($@);
+		return;
+	}
+	while ( my ( $filename, $desc ) = $sql->fetchrow_array ) {
+		$output->{$desc} = $filename;
+	}
+	return ( $job, $params, $output );
 }
 
 sub get_next_job_id {
 	my ($self) = @_;
 	my $sql = $self->{'db'}->prepare("SELECT id FROM jobs WHERE status='submitted' ORDER BY priority asc,submit_time asc LIMIT 1");
-	eval {
-		$sql->execute;		
-	};
-	if ($@){
+	eval { $sql->execute; };
+	if ($@) {
 		$logger->error($@);
 		return;
 	}
 	my ($job) = $sql->fetchrow_array;
-	return $job;	
+	return $job;
 }
 
 sub get_load_average {
 	my $uptime = `uptime`;
 	my $load;
-	if ($uptime =~ /load average:\s+([\d\.]+)/){
+	if ( $uptime =~ /load average:\s+([\d\.]+)/ ) {
 		$load = $1;
 	} else {
 		throw BIGSdb::DataException("Can't determine load average");
 	}
 	return $load;
 }
-
 1;

lib/BIGSdb/Page.pm

@@ -190,16 +190,21 @@ sub print {
 				close $fh;
 			}
 		}
+		my $http_equiv;
+		if ($self->{'refresh'}){
+			$http_equiv = "<meta http-equiv=\"refresh\" content=\"$self->{'refresh'}\" />";
+		} 
+		
 		if (%shortcut_icon) {
 			print $q->start_html(
 				-title  => $title,
 				-meta   => {%meta_content},
 				-style  => { -src => $stylesheet },
-				-head   => CGI->Link( {%shortcut_icon} ),
+				-head   => [CGI->Link( {%shortcut_icon} ), $http_equiv],
 				-script => \@javascript
 			);
 		} else {
-			print $q->start_html( -title => $title, -meta => {%meta_content}, -style => { -src => $stylesheet }, -script => \@javascript );
+			print $q->start_html( -title => $title, -meta => {%meta_content}, -style => { -src => $stylesheet }, -script => \@javascript, -head => $http_equiv );
 		}
 		$self->_print_header();
 		$self->_print_login_details if $self->{'system'}->{'read_access'} ne 'public' || $self->{'curate'};

lib/BIGSdb/Plugins/XmfaExport.pm

@@ -111,19 +111,11 @@ sub run {
 		if ( !@fields_selected ) {
 			print "<div class=\"box\" id=\"statusbad\"><p>No fields have been selected!</p></div>\n";
 		} else {
-			print <<"HTML";
-<div class="box" id="resultstable">
-<p>The output file has been submitted to the job queue.</p>
-<p>Please be aware that this job may take a long time depending on the number of sequences to align.</p>	
-</div>		
-HTML
-#			my $filename  = ( BIGSdb::Utils::get_random() ) . '.txt';
-#			my $full_path = "$self->{'config'}->{'tmp_dir'}/$filename";
 			my $params    = $q->Vars;
 			$params->{'pk'} = $pk;
 			(my $list = $q->param('list')) =~ s/[\r\n]+/\|\|/g;
 			$params->{'list'} = $list;
-			$self->{'jobManager'}->add_job(
+			my $job_id = $self->{'jobManager'}->add_job(
 				{
 					'dbase_config' => $self->{'instance'},
 					'ip_address'   => $q->remote_host,
@@ -132,6 +124,16 @@ HTML
 					'parameters'   => $params
 				}
 			);
+			print <<"HTML";
+<div class="box" id="resultstable">
+<p>This analysis has been submitted to the job queue.</p>
+<p>Please be aware that this job may take a long time depending on the number of sequences to align
+and how busy the server is.  Alignment of hundreds of sequences can take many hours!</p>
+<p><a href="$self->{'script_name'}?db=$self->{'instance'}&amp;page=job&amp;id=$job_id">
+Follow the progress of this job and view the output.</a></p> 	
+</div>	
+HTML
+
 
 		 #			$| = 1;
 		 #			my ( $problem_ids, $no_output ) = $self->_write_xmfa( $list, \@fields_selected, $full_path, $pk );

sql/jobs.sql

@@ -10,7 +10,7 @@ stop_time timestamp,
 module text NOT NULL,
 status text NOT NULL,
 percent_complete int,
-message text,
+message_html text,
 priority int NOT NULL,
 PRIMARY KEY(id)
 );
@@ -29,3 +29,14 @@ ON UPDATE CASCADE
 
 GRANT SELECT,UPDATE,INSERT,DELETE ON params TO apache,bigsdb;
 
+CREATE TABLE output (
+job_id text NOT NULL,
+filename text NOT NULL,
+description text NOT NULL,
+PRIMARY KEY (job_id),
+CONSTRAINT o_job_id FOREIGN KEY (job_id) REFERENCES jobs
+ON DELETE CASCADE
+ON UPDATE CASCADE
+);
+
+GRANT SELECT,UPDATE,INSERT,DELETE ON output TO apache,bigsdb;