Merge branch 'develop' into submitter_accounts

lib/BIGSdb/CurateIsolateUpdatePage.pm

@@ -306,8 +306,8 @@ sub _print_interface {
 sub _print_allele_designations {
 	my ( $self, $data ) = @_;
 	my $q = $self->{'cgi'};
-	say "<div class=\"box\" id=\"alleles\" style=\"overflow:auto\">";
-	say "<fieldset style=\"float:left\"><legend>Loci</legend>";
+	say q(<div class="box" id="alleles" style="overflow:auto">);
+	say q(<fieldset style="float:left"><legend>Loci</legend>);
 	my $isolate_record = BIGSdb::IsolateInfoPage->new(
 		(
 			system        => $self->{'system'},
@@ -328,11 +328,11 @@ sub _print_allele_designations {
 	say $q->start_form;
 	my $set_id = $self->get_set_id;
 	my ( $loci, $labels ) = $self->{'datastore'}->get_locus_list( { set_id => $set_id } );
-	say "<label for=\"locus\">Locus: </label>";
+	say q(<label for="locus">Locus: </label>);
 	say $q->popup_menu( -name => 'locus', -id => 'locus', -values => $loci, -labels => $labels );
 	say $q->submit( -label => 'Add/update', -class => 'submit' );
-	$q->param( 'page',       'alleleUpdate' );
-	$q->param( 'isolate_id', $q->param('id') );
+	$q->param( page       => 'alleleUpdate' );
+	$q->param( isolate_id => $q->param('id') );
 	say $q->hidden($_) foreach qw(db page isolate_id);
 	say $q->end_form;
 	say "</fieldset></div>";

lib/BIGSdb/CuratePage.pm

@@ -308,7 +308,7 @@ sub _get_form_fields {
 						-name    => $name,
 						-id      => $name,
 						-values  => [@optlist],
-						-default => $newdata{ $att->{'name'} },
+						-default => $options->{'update'} ? $newdata{ $att->{'name'} } : $att->{'default'},
 						-labels  => $labels,
 						%html5_args
 					);

lib/BIGSdb/CurateTableHeaderPage.pm

@@ -138,9 +138,11 @@ sub get_isolate_loci {
 			}
 		}
 	} else {    #Just list MLST loci
-		my $scheme_id_ref = $self->{'datastore'}->run_simple_query("SELECT id FROM schemes WHERE description = 'MLST'");
-		if ( ref $scheme_id_ref eq 'ARRAY' ) {
-			my $scheme_loci = $self->{'datastore'}->get_scheme_loci( $scheme_id_ref->[0] );
+		my $scheme_ids =
+		  $self->{'datastore'}
+		  ->run_query( "SELECT id FROM schemes WHERE description LIKE 'MLST%' ORDER BY display_order", undef, { fetch => 'col_arrayref' } );
+		foreach my $scheme_id (@$scheme_ids) {
+			my $scheme_loci = $self->{'datastore'}->get_scheme_loci($scheme_id);
 			foreach my $locus (@$scheme_loci) {
 				my $cleaned_name = $self->clean_locus( $locus, { no_common_name => 1, text_output => 1 } );
 				push @headers, $cleaned_name;

lib/BIGSdb/IsolateInfoPage.pm

@@ -519,7 +519,7 @@ sub _get_provenance_fields {
 						&& !$self->{'system'}->{'privacy'} )
 				  )
 				{
-					if ( $value > 0 && $userdata->{'email'} ne '' && $userdata->{'email'} ne '-' ) {
+					if ( $value > 0 && $userdata->{'email'} =~ /@/ ) {
 						$person .= " (E-mail: <a href=\"mailto:$userdata->{'email'}\">$userdata->{'email'}</a>)";
 					}
 				}
@@ -576,27 +576,26 @@ sub _get_provenance_fields {
 			my %attributes = map { $_->{'attribute'} => $_->{'value'} } @$attribute_list;
 			if ( keys %attributes ) {
 				my $rows = keys %attributes || 1;
-				foreach ( sort { $order{$a} <=> $order{$b} } keys(%attributes) ) {
-					my $url_ref =
-					  $self->{'datastore'}
-					  ->run_simple_query( "SELECT url FROM isolate_field_extended_attributes WHERE isolate_field=? AND attribute=?",
-						$field, $_ );
+				foreach my $attribute ( sort { $order{$a} <=> $order{$b} } keys(%attributes) ) {
+					my $url = $self->{'datastore'}->run_query(
+						"SELECT url FROM isolate_field_extended_attributes WHERE isolate_field=? AND attribute=?",
+						[ $field, $attribute ]
+					);
 					my $att_web;
-					if ( ref $url_ref eq 'ARRAY' ) {
-						my $url = $url_ref->[0] || '';
-						$url =~ s/\[\?\]/$attributes{$_}/;
+					if ($url) {
+						$url =~ s/\[\?\]/$attributes{$attribute}/;
 						$url =~ s/\&/\&amp;/g;
 						my $domain;
 						if ( ( lc($url) =~ /http:\/\/(.*?)\/+/ ) ) {
 							$domain = $1;
 						}
-						$att_web = "<a href=\"$url\">$attributes{$_}</a>" if $url;
+						$att_web = qq(<a href="$url">$attributes{$attribute}</a>) if $url;
 						if ( $domain && $domain ne $q->virtual_host ) {
-							$att_web .= " <span class=\"link\"><span style=\"font-size:1.2em\">&rarr;</span> $domain</span>";
+							$att_web .= qq( <span class="link"><span style="font-size:1.2em">&rarr;</span> $domain</span>);
 						}
 					}
-					$buffer .= "<dt class=\"dontend\">$_</dt>\n";
-					$buffer .= "<dd>" . ( $att_web || $attributes{$_} ) . "</dd>\n";
+					$buffer .= "<dt class=\"dontend\">$attribute</dt>\n";
+					$buffer .= "<dd>" . ( $att_web || $attributes{$attribute} ) . "</dd>\n";
 				}
 			}
 		}

lib/BIGSdb/Offline/Script.pm

@@ -93,9 +93,19 @@ sub initiate {
 		}
 	}
 	$self->set_system_overrides;
+
 	$self->{'dataConnector'}->initiate( $self->{'system'}, $self->{'config'} );
 	$self->db_connect;
-	$self->setup_datastore if $self->{'db'};
+	if ($self->{'db'}){
+		$self->setup_datastore ;
+		if ( defined $self->{'options'}->{'v'} ) {
+			my $view_exists =
+			  $self->{'datastore'}
+			  ->run_query( "SELECT EXISTS(SELECT * FROM information_schema.tables WHERE table_name=?)", $self->{'options'}->{'v'} );
+			die "Invalid view selected.\n" if !$view_exists;
+			$self->{'system'}->{'view'} = $self->{'options'}->{'v'};
+		}
+	}
 	return;
 }
 

lib/BIGSdb/Plugins/DatabaseFields.pm

 #DatabaseFields.pm - Database field description plugin for BIGSdb
 #Written by Keith Jolley
-#Copyright (c) 2010-2013, University of Oxford
+#Copyright (c) 2010-2014, University of Oxford
 #E-mail: keith.jolley@zoo.ox.ac.uk
 #
 #This file is part of Bacterial Isolate Genome Sequence Database (BIGSdb).
@@ -34,7 +34,7 @@ sub get_attributes {
 		description => 'Display description of fields defined for the current database',
 		menutext    => 'Description of database fields',
 		module      => 'DatabaseFields',
-		version     => '1.0.2',
+		version     => '1.0.3',
 		section     => 'miscellaneous',
 		order       => 10,
 		dbtype      => 'isolates'
@@ -50,15 +50,15 @@ sub set_pref_requirements {
 
 sub run {
 	my ($self) = @_;
-	say "<h1>Description of database fields</h1>";
-	say "<div class=\"box\" id=\"resultstable\">";
-	say "<p>Order columns by clicking their headings. <a href=\"$self->{'system'}->{'script_name'}?"
-	  . "db=$self->{'instance'}&amp;page=plugin&amp;name=DatabaseFields\">Reset default order</a>.</p>";
-	say "<table class=\"tablesorter\" id=\"sortTable\">\n<thead>";
-	say "<tr><th>field name</th><th>comments</th><th>data type</th><th class=\"{sorter: false}\">allowed values</th>"
-	  . "<th>required</th></tr></thead>\n<tbody>";
+	say q(<h1>Description of database fields</h1>);
+	say q(<div class="box" id="resultstable"><div class="scrollable">);
+	say qq(<p>Order columns by clicking their headings. <a href="$self->{'system'}->{'script_name'}?db=$self->{'instance'}&amp;)
+	  . qq(page=plugin&amp;name=DatabaseFields">Reset default order</a>.</p>);
+	say qq(<table class="tablesorter" id="sortTable">\n<thead>);
+	say qq(<tr><th>field name</th><th>comments</th><th>data type</th><th class="{sorter: false}">allowed values</th><th>required</th></tr>)
+	  . qq(</thead>\n<tbody>);
 	$self->_print_fields;
-	say "</tbody></table>\n</div>";
+	say qq(</tbody></table>\n</div></div>);
 	return;
 }
 
@@ -78,11 +78,15 @@ sub _print_fields {
 		  . "</td><td>$thisfield->{'comments'}</td><td>$thisfield->{'type'}</td><td>";
 		if ( $thisfield->{'optlist'} ) {
 			my $option_list = $self->{'xmlHandler'}->get_field_option_list($field);
-			say "$_<br />" foreach @$option_list;
-		} elsif ( defined $thisfield->{'min'} || defined $thisfield->{'max'} ){
+			foreach my $option (@$option_list) {
+				$option =~ s/</&lt;/g;
+				$option =~ s/>/&gt;/g;
+				say "$option<br />";
+			}
+		} elsif ( defined $thisfield->{'min'} || defined $thisfield->{'max'} ) {
 			print "min: $thisfield->{'min'}" if defined $thisfield->{'min'};
-			print "; " if defined $thisfield->{'min'} && defined $thisfield->{'max'};
-			say "max: $thisfield->{'max'}" if defined $thisfield->{'max'};
+			print "; "                       if defined $thisfield->{'min'} && defined $thisfield->{'max'};
+			say "max: $thisfield->{'max'}"   if defined $thisfield->{'max'};
 		} elsif ( $field eq 'sender' || $field eq 'sequenced_by' || ( $thisfield->{'userfield'} // '' ) eq 'yes' ) {
 			say "<a href=\"$self->{'system'}->{'script_name'}?db=$self->{'instance'}&amp;page=fieldValues&amp;field=f_sender\" "
 			  . "target=\"_blank\">Click for list of sender ids</a>";

scripts/automation/autotag.pl

@@ -62,7 +62,8 @@ GetOptions(
 	'o|order'              => \$opts{'o'},
 	'q|quiet'              => \$opts{'q'},
 	'r|random'             => \$opts{'r'},
-	'T|already_tagged'     => \$opts{'T'}
+	'T|already_tagged'     => \$opts{'T'},
+	'v|view=s'             => \$opts{'v'}
 ) or die("Error in command line arguments\n");
 
 if ( $opts{'h'} ) {
@@ -235,6 +236,9 @@ ${bold}--threads$norm ${under}THREADS$norm
 
 ${bold}-T, --already_tagged$norm
     Scan even when sequence tagged (no designation).
+    
+${bold}-v, --view$norm ${under}VIEW$norm
+    Isolate database view (overrides value set in config.xml).
 
 ${bold}-w, --word_size$norm ${under}SIZE$norm
     BLASTN word size.

scripts/automation/scannew.pl

@@ -63,7 +63,8 @@ GetOptions(
 	'n|new_only'           => \$opts{'n'},
 	'o|order'              => \$opts{'o'},
 	'r|random'             => \$opts{'r'},
-	'T|already_tagged'     => \$opts{'T'}
+	'T|already_tagged'     => \$opts{'T'},
+	'v|view=s'             => \$opts{'v'}
 ) or die("Error in command line arguments\n");
 
 if ( $opts{'h'} ) {
@@ -235,6 +236,9 @@ ${bold}--threads$norm ${under}THREADS$norm
 
 ${bold}-T, --already_tagged$norm
     Scan even when sequence tagged (no designation).
+    
+${bold}-v, --view$norm ${under}VIEW$norm
+    Isolate database view (overrides value set in config.xml).
 
 ${bold}-w, --word_size$norm ${under}SIZE$norm
     BLASTN word size.