Skip to content

GitLab

Commit c70bf603 authored by Keith Jolley's avatar Keith Jolley
Browse files

Limit number of schemes/loci displayed by AJAX call in isolate info. 

If over limit (set to 1000), a link is provided to display the
information on a separate page.
Closes #219.
parent b03e9da5
Hide whitespace changes
Inline Side-by-side
lib/BIGSdb/IsolateInfoPage.pm
View file @ c70bf603
......@@ -24,10 +24,11 @@ use parent qw(BIGSdb::TreeViewPage);
use BIGSdb::Constants qw(:interface);
use Log::Log4perl qw(get_logger);
use Error qw(:try);
use List::MoreUtils qw(none);
use List::MoreUtils qw(none uniq);
my $logger = get_logger('BIGSdb.Page');
use constant ISOLATE_SUMMARY => 1;
use constant LOCUS_SUMMARY => 2;
use constant MAX_DISPLAY => 1000;
sub set_pref_requirements {
my ($self) = @_;
......@@ -142,24 +143,24 @@ sub _get_child_group_scheme_tables {
my $parent_level = $level - 1;
if ( $self->{'open_divs'} > $parent_level ) {
my $divs_to_close = $self->{'open_divs'} - $parent_level;
for ( 0 .. $divs_to_close ) {
$parent_buffer .= '</div>';
for ( 0 .. $divs_to_close - 1 ) {
$parent_buffer .= qq(</div>\n);
$self->{'open_divs'}--;
}
}
$parent_buffer .= q(<div style="float:left;padding-right:0.5em">)
. qq(<h3 class="group group$parent_level">$parent_group_info->{'name'}</h3>);
$parent_buffer .= qq(<div style="float:left;padding-right:0.5em">\n)
. qq(<h3 class="group group$parent_level">$parent_group_info->{'name'}</h3>\n);
$self->{'open_divs'}++;
}
my $group_buffer = '';
my $group_buffer = q();
if (@$child_groups) {
foreach my $child_group (@$child_groups) {
if ( $self->{'groups_with_data'}->{$child_group} ) {
my $group_info = $self->{'datastore'}->get_scheme_group_info($child_group);
my $new_level = $level;
last if $new_level == 10; #prevent runaway if child is set as the parent of a parental group
if ( $new_level == $self->{'level'} ) {
$group_buffer .= '</div>';
if ( $new_level == $self->{'level'} && $new_level > 1 ) {
$group_buffer .= qq(</div>\n);
$self->{'open_divs'}--;
}
my $buffer = $self->_get_child_group_scheme_tables( $child_group, $isolate_id, ++$new_level );
......@@ -208,29 +209,146 @@ sub _get_group_scheme_tables {
sub _handle_scheme_ajax {
my ( $self, $isolate_id ) = @_;
my $q = $self->{'cgi'};
if ( defined $q->param('group_id') && BIGSdb::Utils::is_int( $q->param('group_id') ) ) {
return if !$q->param('no_header');
my $should_display_items = $self->_should_display_items($isolate_id);
if ( !$should_display_items ) {
my $param;
if ( BIGSdb::Utils::is_int( $q->param('group_id') ) ) {
$param = q(group_id=) . $q->param('group_id');
} elsif ( BIGSdb::Utils::is_int( $q->param('scheme_id') ) ) {
$param = q(scheme_id=) . $q->param('scheme_id');
}
say q(Too many items to display - )
. qq(<a href="$self->{'system'}->{'script_name'}?db=$self->{'instance'}&amp;page=info&amp;)
. qq(id=$isolate_id&amp;function=scheme_display&amp;$param">display selected schemes separately.</a>);
return 1;
}
if ( BIGSdb::Utils::is_int( $q->param('group_id') ) ) {
$self->_print_group_data( $isolate_id, $q->param('group_id') );
return 1;
} elsif ( BIGSdb::Utils::is_int( $q->param('scheme_id') ) ) {
$self->_print_scheme_data( $isolate_id, $q->param('scheme_id') );
return 1;
}
return;
}
sub _print_group_data {
my ( $self, $isolate_id, $group_id ) = @_;
$self->{'groups_with_data'} =
$self->get_tree( $isolate_id, { isolate_display => $self->{'curate'} ? 0 : 1, get_groups => 1 } );
if ( $group_id == 0 ) { #Other schemes (not part of a scheme group)
$self->_print_other_schemes($isolate_id);
} else { #Scheme group
say $self->_get_child_group_scheme_tables( $group_id, $isolate_id, 1 );
say $self->_get_group_scheme_tables( $group_id, $isolate_id );
$self->_close_divs;
}
return;
}
sub _print_scheme_data {
my ( $self, $isolate_id, $scheme_id ) = @_;
if ( $scheme_id == -1 ) { #All schemes/loci
$self->{'groups_with_data'} =
$self->get_tree( $isolate_id, { isolate_display => $self->{'curate'} ? 0 : 1, get_groups => 1 } );
$self->_print_all_loci($isolate_id);
} else {
say $self->_get_scheme( $scheme_id, $isolate_id, $self->{'curate'} );
}
return;
}
sub _should_display_items {
my ( $self, $isolate_id ) = @_;
my $q = $self->{'cgi'};
my $items = 0;
if ( BIGSdb::Utils::is_int( $q->param('group_id') ) ) {
my $group_id = $q->param('group_id');
my $scheme_ids;
if ( $group_id == 0 ) { #Other schemes (not part of a scheme group)
$self->_print_other_schemes($isolate_id);
my $scheme_ids = $self->{'datastore'}->run_query(
'SELECT id FROM schemes WHERE id NOT IN (SELECT scheme_id FROM '
. 'scheme_group_scheme_members) ORDER BY display_order,description',
undef,
{ fetch => 'col_arrayref' }
);
foreach my $scheme_id (@$scheme_ids) {
$items += $self->_get_display_items_in_scheme( $isolate_id, $scheme_id );
return if $items > MAX_DISPLAY;
}
} else { #Scheme group
say $self->_get_child_group_scheme_tables( $group_id, $isolate_id, 1 );
say $self->_get_group_scheme_tables( $group_id, $isolate_id );
$self->_close_divs;
my $schemes = $self->{'datastore'}->get_schemes_in_group($group_id);
foreach my $scheme_id (@$schemes) {
$items += $self->_get_display_items_in_scheme( $isolate_id, $scheme_id );
return if $items > MAX_DISPLAY;
}
}
return 1;
} elsif ( defined $q->param('scheme_id') && BIGSdb::Utils::is_int( $q->param('scheme_id') ) ) {
} elsif ( BIGSdb::Utils::is_int( $q->param('scheme_id') ) ) {
my $scheme_id = $q->param('scheme_id');
if ( $scheme_id == -1 ) { #All schemes/loci
$self->{'groups_with_data'} =
$self->get_tree( $isolate_id, { isolate_display => $self->{'curate'} ? 0 : 1, get_groups => 1 } );
$self->_print_all_loci($isolate_id);
my $set_id = $self->get_set_id;
my $schemes = $self->{'datastore'}->get_scheme_list( { set_id => $set_id } );
foreach my $scheme (@$schemes) {
$items += $self->_get_display_items_in_scheme( $isolate_id, $scheme->{'id'} );
return if $items > MAX_DISPLAY;
}
$items += $self->_get_display_items_in_scheme( $isolate_id, 0 );
} else {
say $self->_get_scheme( $scheme_id, $isolate_id, $self->{'curate'} );
$items = $self->_get_display_items_in_scheme( $isolate_id, $scheme_id );
}
return 1;
}
return if $items > MAX_DISPLAY;
return 1;
}
sub _get_display_items_in_scheme {
my ( $self, $isolate_id, $scheme_id ) = @_;
my $items = 0;
if ($scheme_id) {
return 0 if !$self->{'prefs'}->{'isolate_display_schemes'}->{$scheme_id};
my $should_display = $self->_should_display_scheme( $isolate_id, $scheme_id );
return 0 if !$should_display;
my $scheme_fields = $self->{'datastore'}->get_scheme_fields($scheme_id);
foreach my $field (@$scheme_fields) {
$items++ if $self->{'prefs'}->{'isolate_display_scheme_fields'}->{$scheme_id}->{$field};
}
my $loci = $self->{'datastore'}->get_scheme_loci($scheme_id);
foreach my $locus (@$loci) {
$items++ if $self->{'prefs'}->{'isolate_display_loci'}->{$locus} ne 'hide';
}
} else {
my $loci = $self->{'datastore'}->get_loci_in_no_scheme;
my $list_table = $self->{'datastore'}->create_temp_list_table_from_array( 'text', $loci );
my $loci_with_designations =
$self->{'datastore'}->run_query(
"SELECT locus FROM allele_designations WHERE isolate_id=? AND locus IN (SELECT value FROM $list_table)",
$isolate_id, { fetch => 'col_arrayref' } );
my $loci_with_seqs =
$self->{'datastore'}->run_query(
"SELECT locus FROM allele_sequences WHERE isolate_id=? AND locus IN (SELECT value FROM $list_table)",
$isolate_id, { fetch => 'col_arrayref' } );
foreach my $locus ( uniq( @$loci_with_designations, @$loci_with_seqs ) ) {
$items++ if $self->{'prefs'}->{'isolate_display_loci'}->{$locus} ne 'hide';
}
}
return $items;
}
sub _print_separate_scheme_data {
my ( $self, $isolate_id ) = @_;
my $q = $self->{'cgi'};
if ( BIGSdb::Utils::is_int( $q->param('group_id') ) ) {
say q(<div class="box" id="resultspanel">);
$self->_print_group_data( $isolate_id, $q->param('group_id') );
say q(<div style="clear:both"></div>);
say q(</div>);
} elsif ( BIGSdb::Utils::is_int( $q->param('scheme_id') ) ) {
say q(<div class="box" id="resultspanel">);
$self->_print_scheme_data( $isolate_id, $q->param('scheme_id') );
say q(<div style="clear:both"></div>);
say q(</div>);
} else {
say q(<div class="box" id="statusbad"><p>No scheme or group passed.</p></div>);
}
return;
}
......@@ -269,13 +387,20 @@ sub print_content {
. q(have permission to view this record.</p></div>);
return;
}
if ( defined $data->{ $self->{'system'}->{'labelfield'} } && $data->{ $self->{'system'}->{'labelfield'} } ne '' ) {
my $identifier = $self->{'system'}->{'labelfield'};
$identifier =~ tr/_/ /;
say qq(<h1>Full information on $identifier $data->{lc($self->{'system'}->{'labelfield'})}</h1>);
my $identifier;
if ( ( $data->{ $self->{'system'}->{'labelfield'} } // q() ) ne q() ) {
my $field = $self->{'system'}->{'labelfield'};
$field =~ tr/_/ /;
$identifier = qq($field $data->{lc($self->{'system'}->{'labelfield'})} (id:$data->{'id'}));
} else {
say qq(<h1>Full information on id $data->{'id'}</h1>);
$identifier = qq(id $data->{'id'});
}
if ( ( $q->param('function') // q() ) eq 'scheme_display' ) {
say qq(<h1>Selected scheme/locus breakdown for $identifier</h1>);
$self->_print_separate_scheme_data($isolate_id);
return;
}
say qq(<h1>Full information on $identifier</h1>);
if ( $self->{'cgi'}->param('history') ) {
say q(<div class="box" id="resultstable">);
say q(<h2>Update history</h2>);
......@@ -334,7 +459,7 @@ sub print_content {
sub _close_divs {
my ($self) = @_;
if ( $self->{'open_divs'} ) {
for ( 0 .. $self->{'open_divs'} ) {
for ( 0 .. $self->{'open_divs'} - 1 ) {
say q(</div>);
}
$self->{'open_divs'} = 0;
......@@ -818,25 +943,24 @@ sub _get_loci_not_in_schemes {
sub _should_display_scheme {
my ( $self, $isolate_id, $scheme_id, $summary_view ) = @_;
my $set_id = $self->get_set_id;
my $scheme_data = $self->{'datastore'}->get_scheme_list( { set_id => $set_id } );
my ( $scheme_ids_ref, $desc_ref ) = $self->extract_scheme_desc($scheme_data);
return 0 if none { $scheme_id eq $_ } @$scheme_ids_ref;
my $scheme_fields = $self->{'datastore'}->get_scheme_fields($scheme_id);
my $loci = $self->{'datastore'}->get_scheme_loci($scheme_id);
if ($set_id) {
return if !$self->{'datastore'}->is_scheme_in_set( $scheme_id, $set_id );
}
my $designations_exist = $self->{'datastore'}->run_query(
'SELECT EXISTS(SELECT isolate_id FROM allele_designations LEFT JOIN scheme_members ON '
. 'scheme_members.locus=allele_designations.locus WHERE (isolate_id,scheme_id)=(?,?))',
[ $isolate_id, $scheme_id ],
{ cache => 'IsolateInfoPage::should_display_scheme::designations' }
);
return 1 if $designations_exist;
my $sequences_exist = $self->{'datastore'}->run_query(
'SELECT EXISTS(SELECT isolate_id FROM allele_sequences LEFT JOIN scheme_members ON '
. 'allele_sequences.locus=scheme_members.locus WHERE (isolate_id,scheme_id)=(?,?))',
[ $isolate_id, $scheme_id ],
{ cache => 'IsolateInfoPage::should_display_scheme::sequences' }
);
my $should_display = ( $designations_exist || $sequences_exist ) ? 1 : 0;
return $should_display;
return 1 if $sequences_exist;
return;
}
sub _get_scheme_field_values {
......@@ -910,8 +1034,9 @@ sub _get_scheme {
$scheme_info->{'description'} = 'Loci not in schemes';
}
}
return '' if !( $locus_display_count + $scheme_fields_count );
$buffer .= qq(<div style="float:left;padding-right:0.5em"><h3 class="scheme">$scheme_info->{'description'}</h3>);
return q() if !( $locus_display_count + $scheme_fields_count );
$buffer .= qq(<div style="float:left;padding-right:0.5em">\n);
$buffer .= qq(<h3 class="scheme">$scheme_info->{'description'}</h3>\n);
my @args = (
{
loci => $loci,
......@@ -922,7 +1047,7 @@ sub _get_scheme {
}
);
$buffer .= $self->_get_scheme_values(@args);
$buffer .= q(</div>);
$buffer .= qq(</div>\n);
return $buffer;
}
......@@ -1064,7 +1189,7 @@ sub get_title {
my ($self) = @_;
my $q = $self->{'cgi'};
my $isolate_id = $q->param('id');
return '' if defined $q->param('scheme_id') || defined $q->param('group_id');
return q() if $q->param('no_header');
return q(Invalid isolate id) if !BIGSdb::Utils::is_int($isolate_id);
my $name = $self->get_name($isolate_id);
my $title = qq(Isolate information: id-$isolate_id);
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment