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Commit 1c8a3177 authored by Keith Jolley's avatar Keith Jolley
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DownloadAllelesPage: Remove use of deprecated SQL methods. 

Don't set up own statement handles but use Datastore::run_query instead.
Fix product output in tab-delimited text and Excel files when line
feed/new line characters included.
parent 4e75e59c
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lib/BIGSdb/DownloadAllelesPage.pm
View file @ 1c8a3177
#Written by Keith Jolley
#Copyright (c) 2010-2014, University of Oxford
#Copyright (c) 2010-2015, University of Oxford
#E-mail: keith.jolley@zoo.ox.ac.uk
#
#This file is part of Bacterial Isolate Genome Sequence Database (BIGSdb).
......@@ -56,25 +56,22 @@ sub get_javascript {
sub _print_tree {
my ($self) = @_;
print << "HTML";
<p>Click within the tree to display details of loci belonging to schemes or groups of schemes -
clicking a group folder will display the loci for all schemes within the group and any subgroups.
Click the nodes to expand/collapse.</p>
<noscript>
<p class="highlight">Enable Javascript to enhance your viewing experience.</p>
</noscript>
<div id="tree" class="tree">
HTML
say qq(<p>Click within the tree to display details of loci belonging to schemes or groups of schemes - clicking a group folder will )
. qq(display the loci for all schemes within the group and any subgroups. Click the nodes to expand/collapse.</p>\n)
. qq(<noscript><p class="highlight">Enable Javascript to enhance your viewing experience.</p></noscript>)
. qq(<div id="tree" class="tree">);
say $self->get_tree(undef);
say "</div>\n<div id=\"scheme_table\"></div>";
say qq(</div>\n<div id="scheme_table"></div>);
return;
}
sub _print_child_group_scheme_tables {
my ( $self, $id, $level, $scheme_shown ) = @_;
my $child_groups = $self->{'datastore'}->run_list_query(
"SELECT id FROM scheme_groups LEFT JOIN scheme_group_group_members ON scheme_groups.id=group_id WHERE parent_group_id=? ORDER BY display_order",
$id
my $child_groups = $self->{'datastore'}->run_query(
"SELECT id FROM scheme_groups LEFT JOIN scheme_group_group_members ON "
. "scheme_groups.id=group_id WHERE parent_group_id=? ORDER BY display_order",
$id,
{ fetch => 'col_arrayref', cache => 'DownloadAllelesPage::print_child_group_scheme_tables' }
);
if (@$child_groups) {
foreach (@$child_groups) {
......@@ -90,11 +87,14 @@ sub _print_child_group_scheme_tables {
sub _print_group_scheme_tables {
my ( $self, $id, $scheme_shown ) = @_;
my $set_id = $self->get_set_id;
my $set_id = $self->get_set_id;
my $set_clause = $set_id ? " AND scheme_id IN (SELECT scheme_id FROM set_schemes WHERE set_id=$set_id)" : '';
my $qry =
"SELECT scheme_id FROM scheme_group_scheme_members LEFT JOIN schemes ON schemes.id=scheme_id WHERE group_id=? $set_clause ORDER BY display_order";
my $schemes = $self->{'datastore'}->run_list_query( $qry, $id );
my $schemes = $self->{'datastore'}->run_query(
"SELECT scheme_id FROM scheme_group_scheme_members LEFT JOIN schemes ON "
. "schemes.id=scheme_id WHERE group_id=? $set_clause ORDER BY display_order",
$id,
{ fetch => 'col_arrayref', cache => 'DownloadAllelesPage::print_group_scheme_tables' }
);
if (@$schemes) {
foreach my $scheme_id (@$schemes) {
my $scheme_info = $self->{'datastore'}->get_scheme_info( $scheme_id, { set_id => $set_id } );
......@@ -174,7 +174,7 @@ sub print_content {
my $set_clause = $set_id ? " AND id IN (SELECT scheme_id FROM set_schemes WHERE set_id=$set_id)" : '';
my $qry = "SELECT id FROM schemes WHERE id NOT IN (SELECT scheme_id FROM scheme_group_scheme_members) "
. "$set_clause ORDER BY display_order";
$scheme_ids = $self->{'datastore'}->run_list_query($qry);
$scheme_ids = $self->{'datastore'}->run_query( $qry, undef, { fetch => 'col_arrayref' } );
foreach my $scheme_id (@$scheme_ids) {
my $scheme_info = $self->{'datastore'}->get_scheme_info( $scheme_id, { set_id => $set_id } );
$self->_print_scheme_table( $scheme_id, $scheme_info->{'description'} );
......@@ -267,32 +267,34 @@ sub _print_scheme_table {
my $td = 1;
my ( $scheme_descs_exist, $scheme_aliases_exist, $scheme_curators_exist );
if ($scheme_id) {
$scheme_descs_exist = $self->{'datastore'}->run_simple_query(
"SELECT COUNT(*) FROM locus_descriptions LEFT JOIN scheme_members ON locus_descriptions.locus=scheme_members.locus WHERE scheme_id=?",
$scheme_descs_exist = $self->{'datastore'}->run_query(
"SELECT EXISTS(SELECT * FROM locus_descriptions LEFT JOIN scheme_members ON locus_descriptions.locus=scheme_members.locus "
. "WHERE scheme_id=?)",
$scheme_id
)->[0];
$scheme_aliases_exist =
$self->{'datastore'}->run_simple_query(
"SELECT COUNT(*) FROM locus_aliases LEFT JOIN scheme_members ON locus_aliases.locus=scheme_members.locus WHERE scheme_id=?",
$scheme_id )->[0];
$scheme_curators_exist = $self->{'datastore'}->run_simple_query(
"SELECT COUNT(*) FROM locus_curators LEFT JOIN scheme_members ON locus_curators.locus=scheme_members.locus "
. "WHERE scheme_id=? AND (hide_public IS NULL OR NOT hide_public)",
);
$scheme_aliases_exist = $self->{'datastore'}->run_query(
"SELECT EXISTS(SELECT * FROM locus_aliases LEFT JOIN scheme_members ON locus_aliases.locus=scheme_members.locus WHERE "
. "scheme_id=?)",
$scheme_id
);
$scheme_curators_exist = $self->{'datastore'}->run_query(
"SELECT EXISTS(SELECT * FROM locus_curators LEFT JOIN scheme_members ON locus_curators.locus=scheme_members.locus "
. "WHERE scheme_id=? AND (hide_public IS NULL OR NOT hide_public))",
$scheme_id
)->[0];
);
} else {
$scheme_descs_exist =
$self->{'datastore'}->run_simple_query(
"SELECT COUNT(*) FROM locus_descriptions LEFT JOIN scheme_members ON locus_descriptions.locus=scheme_members.locus "
. "WHERE scheme_id IS NULL" )->[0];
$self->{'datastore'}->run_query(
"SELECT EXISTS(SELECT * FROM locus_descriptions LEFT JOIN scheme_members ON locus_descriptions.locus=scheme_members.locus "
. "WHERE scheme_id IS NULL)" );
$scheme_aliases_exist =
$self->{'datastore'}
->run_simple_query( "SELECT COUNT(*) FROM locus_aliases LEFT JOIN scheme_members ON locus_aliases.locus=scheme_members.locus "
. "WHERE scheme_id IS NULL" )->[0];
$self->{'datastore'}->run_query(
"SELECT EXISTS(SELECT * FROM locus_aliases LEFT JOIN scheme_members ON locus_aliases.locus=scheme_members.locus WHERE "
. "scheme_id IS NULL)" );
$scheme_curators_exist =
$self->{'datastore'}
->run_simple_query( "SELECT COUNT(*) FROM locus_curators LEFT JOIN scheme_members ON locus_curators.locus=scheme_members.locus "
. "WHERE scheme_id IS NULL AND (hide_public IS NULL OR NOT hide_public)" )->[0];
$self->{'datastore'}->run_query(
"SELECT EXISTS(SELECT * FROM locus_curators LEFT JOIN scheme_members ON locus_curators.locus=scheme_members.locus "
. "WHERE scheme_id IS NULL AND (hide_public IS NULL OR NOT hide_public))" );
}
if (@$loci) {
$desc =~ s/\&/\&amp;/g;
......@@ -364,37 +366,18 @@ sub _print_table_header_row {
sub _print_locus_row {
my ( $self, $locus, $display_name, $options ) = @_;
my $locus_info = $self->{'datastore'}->get_locus_info($locus);
if ( !$self->{'sql'}->{'count'} ) {
$self->{'sql'}->{'count'} = $self->{'db'}->prepare("SELECT allele_count, last_updated FROM allele_count WHERE locus=?");
}
if ( !$self->{'sql'}->{'desc'} ) {
$self->{'sql'}->{'desc'} = $self->{'db'}->prepare("SELECT full_name,product FROM locus_descriptions WHERE locus=?");
}
if ( !$self->{'sql'}->{'alias'} ) {
$self->{'sql'}->{'alias'} = $self->{'db'}->prepare("SELECT alias FROM locus_aliases WHERE locus=? ORDER BY alias");
}
if ( !$self->{'sql'}->{'curator'} ) {
$self->{'sql'}->{'curator'} =
$self->{'db'}->prepare("SELECT curator_id FROM locus_curators WHERE locus=? AND (hide_public IS NULL OR NOT hide_public)");
}
eval { $self->{'sql'}->{'count'}->execute($locus) };
$logger->($@) if $@;
my ( $count, $last_updated ) = $self->{'sql'}->{'count'}->fetchrow_array;
my ( $count, $last_updated ) = $self->{'datastore'}->run_query( "SELECT allele_count, last_updated FROM allele_count WHERE locus=?",
$locus, { cache => 'DownloadAllelesPage::print_locus_row::count' } );
$count //= 0;
print "<tr class=\"td$options->{'td'}\"><td>$display_name ";
eval { $self->{'sql'}->{'desc'}->execute($locus) };
$logger->($@) if $@;
my $desc = $self->{'sql'}->{'desc'}->fetchrow_hashref;
if ($desc) {
print " <a href=\"$self->{'system'}->{'script_name'}?db=$self->{'instance'}&amp;page=locusInfo&amp;locus=$locus\" "
. "class=\"info_tooltip\">&nbsp;i&nbsp;</a>";
}
print qq(<tr class="td$options->{'td'}"><td>$display_name );
print qq(<a href="$self->{'system'}->{'script_name'}?db=$self->{'instance'}&amp;page=locusInfo&amp;locus=$locus" )
. qq(class="info_tooltip">&nbsp;i&nbsp;</a>);
print "</td><td>";
print "<a href=\"$self->{'system'}->{'script_name'}?db=$self->{'instance'}&amp;page=downloadAlleles&amp;locus=$locus\" "
. "class=\"downloadbutton\">&darr;</a>"
print qq(<a href="$self->{'system'}->{'script_name'}?db=$self->{'instance'}&amp;page=downloadAlleles&amp;locus=$locus" )
. qq(class="downloadbutton">&darr;</a>)
if $count;
print "</td><td>$locus_info->{'data_type'}</td><td>$count</td>";
if ( $locus_info->{'length_varies'} ) {
print "<td>Variable: ";
if ( $locus_info->{'min_length'} || $locus_info->{'max_length'} ) {
......@@ -412,46 +395,42 @@ sub _print_locus_row {
}
my $products;
if ( $options->{'descs_exist'} ) {
my $desc = $self->{'datastore'}->run_query( "SELECT full_name,product FROM locus_descriptions WHERE locus=?",
$locus, { fetch => 'row_hashref', cache => 'DownloadAllelesPage::print_locus_row::desc' } );
my @names_product;
push @names_product, $desc->{'full_name'} if $desc->{'full_name'};
push @names_product, $desc->{'product'} if $desc->{'product'};
push @names_product, ( $desc->{'full_name'} =~ s/[\r\n]/ /g ) if $desc->{'full_name'};
push @names_product, ( $desc->{'product'} =~ s/[\r\n]/ /g ) if $desc->{'product'};
local $" = ' / ';
$products = "@names_product";
print "<td>$products</td>";
}
my $aliases;
my $aliases = [];
if ( $options->{'aliases_exist'} ) {
eval { $self->{'sql'}->{'alias'}->execute($locus) };
$logger->($@) if $@;
my @aliases;
while ( my ($alias) = $self->{'sql'}->{'alias'}->fetchrow_array ) {
push @aliases, $alias if $display_name !~ /$alias/;
}
$aliases = $self->{'datastore'}->run_query( "SELECT alias FROM locus_aliases WHERE locus=? ORDER BY alias",
$locus, { fetch => 'col_arrayref', cache => 'DownloadAllelesPage::print_locus_row::aliases' } );
local $" = '; ';
$aliases = "@aliases";
print "<td>$aliases</td>\n";
print "<td>@$aliases</td>\n";
}
my $curators;
my $curator_list;
if ( $options->{'curators_exist'} ) {
eval { $self->{'sql'}->{'curator'}->execute($locus) };
$logger->($@) if $@;
my @curators;
my $curator_ids =
$self->{'datastore'}
->run_query( "SELECT curator_id FROM locus_curators WHERE locus=? AND (hide_public IS NULL OR NOT hide_public)",
$locus, { fetch => 'col_arrayref', cache => 'DownloadAllelesPage::print_locus_row::curators' } );
my $info;
while ( my ($curator) = $self->{'sql'}->{'curator'}->fetchrow_array ) {
push @curators, $curator;
$info->{$curator} = $self->{'datastore'}->get_user_info($curator);
foreach my $curator_id (@$curator_ids) {
$info->{$curator_id} = $self->{'datastore'}->get_user_info($curator_id);
}
@curators = sort { $info->{$a}->{'surname'} cmp $info->{$b}->{'surname'} } @curators;
my $first = 1;
print "<td>";
foreach my $curator (@curators) {
foreach my $curator_id ( sort { $info->{$a}->{'surname'} cmp $info->{$b}->{'surname'} } @$curator_ids ) {
print ', ' if !$first;
$curators .= '; ' if !$first;
my $first_initial = $info->{$curator}->{'first_name'} ? substr( $info->{$curator}->{'first_name'}, 0, 1 ) . '. ' : '';
print "<a href=\"mailto:$info->{$curator}->{'email'}\">" if $info->{$curator}->{'email'};
print "$first_initial$info->{$curator}->{'surname'}";
$curators .= "$first_initial$info->{$curator}->{'surname'}";
print "</a>" if $info->{$curator}->{'email'};
$curator_list .= '; ' if !$first;
my $first_initial = $info->{$curator_id}->{'first_name'} ? substr( $info->{$curator_id}->{'first_name'}, 0, 1 ) . '. ' : '';
print qq(<a href="mailto:$info->{$curator_id}->{'email'}">) if $info->{$curator_id}->{'email'};
print "$first_initial$info->{$curator_id}->{'surname'}";
$curator_list .= "$first_initial$info->{$curator_id}->{'surname'}";
print "</a>" if $info->{$curator_id}->{'email'};
$first = 0;
}
print "</td>";
......@@ -461,9 +440,9 @@ sub _print_locus_row {
open( my $fh, '>>', $self->{'outfile'} ) || $logger->error("Can't open $self->{'outfile'} for appending");
if ( !-s $self->{'outfile'} ) {
say $fh ( $options->{'scheme'} ? "scheme\t" : '' )
. "locus\tdata type\talleles\tlength varies\tstandard length\tmin length\t"
. "max length\tfull name/product\taliases\tcurators";
. "locus\tdata type\talleles\tlength varies\tstandard length\tmin length\tmax length\tfull name/product\taliases\tcurators";
}
local $" = '; ';
say $fh ( $options->{'scheme'} ? "$options->{'scheme'}\t" : '' )
. "$locus\t$locus_info->{'data_type'}\t$count\t"
. ( $locus_info->{'length_varies'} ? 'true' : 'false' ) . "\t"
......@@ -471,8 +450,8 @@ sub _print_locus_row {
. ( $locus_info->{'min_length'} // '' ) . "\t"
. ( $locus_info->{'max_length'} // '' ) . "\t"
. ( $products // '' ) . "\t"
. ( $aliases // '' ) . "\t"
. ( $curators // '' );
. ( "@$aliases" // '' ) . "\t"
. ( $curator_list // '' );
close $fh;
return;
}
......@@ -492,19 +471,20 @@ sub _print_alphabetical_list {
$names{"l_$_"} = $self->clean_locus($_) foreach @$main;
$names{"cn_$_->{'id'}"} = "$_->{'common_name'} [$_->{'id'}]" foreach @$common;
$names{"la_$_->{'locus'}||$_->{'alias'}"} = "$_->{'alias'} [$_->{'locus'}]" foreach @$aliases;
my $descs_exist = $self->{'datastore'}->run_simple_query(
"SELECT 1 WHERE EXISTS(SELECT locus FROM locus_descriptions WHERE locus IN (SELECT id FROM loci WHERE UPPER(id) LIKE ? OR "
my $descs_exist = $self->{'datastore'}->run_query(
"SELECT EXISTS(SELECT * FROM locus_descriptions WHERE locus IN (SELECT id FROM loci WHERE UPPER(id) LIKE ? OR "
. "upper(common_name) LIKE ?) OR locus IN (SELECT locus FROM locus_aliases WHERE UPPER(alias) LIKE ?))",
("$qry_letter%") x 3
[ ("$qry_letter%") x 3 ],
{ cache => 'DownloadAllelesPage::print_alphabetical_list::descs_exists' }
);
my $aliases_exist =
$self->{'datastore'}
->run_simple_query( "SELECT 1 WHERE EXISTS(SELECT locus FROM locus_aliases WHERE alias LIKE ?)", "$qry_letter%" );
my $curators_exist = $self->{'datastore'}->run_simple_query(
"SELECT 1 WHERE EXISTS(SELECT locus FROM locus_curators WHERE (locus IN (SELECT id FROM loci WHERE UPPER(id) LIKE ? OR "
my $aliases_exist = $self->{'datastore'}->run_query( "SELECT EXISTS(SELECT * FROM locus_aliases WHERE alias LIKE ?)",
"$qry_letter%", { cache => 'DownloadAllelesPage::print_alphabetical_list::aliases_exists' } );
my $curators_exist = $self->{'datastore'}->run_query(
"SELECT EXISTS(SELECT * FROM locus_curators WHERE (locus IN (SELECT id FROM loci WHERE UPPER(id) LIKE ? OR "
. "upper(common_name) LIKE ?) OR locus IN (SELECT locus FROM locus_aliases WHERE UPPER(alias) LIKE ?)) AND NOT "
. "hide_public)",
("$qry_letter%") x 3
[ ("$qry_letter%") x 3 ],
{ cache => 'DownloadAllelesPage::print_alphabetical_list::curators_exists' }
);
print "<h2>$letter</h2>\n";
print "<table class=\"resultstable\">";
......@@ -535,12 +515,13 @@ sub _get_loci_by_letter {
? "AND ( id IN (SELECT locus FROM scheme_members WHERE scheme_id IN (SELECT scheme_id FROM set_schemes WHERE "
. "set_id=$set_id)) OR id IN (SELECT locus FROM set_loci WHERE set_id=$set_id))"
: '';
my $main = $self->{'datastore'}->run_list_query( "SELECT id FROM loci WHERE UPPER(id) LIKE ? $set_clause", "$letter%" );
my $main = $self->{'datastore'}->run_query( "SELECT id FROM loci WHERE UPPER(id) LIKE ? $set_clause",
"$letter%", { fetch => 'col_arrayref', cache => 'DownloadAllelePage::get_loci_by_letter::main' } );
my $common = $self->{'datastore'}->run_query( "SELECT id,common_name FROM loci WHERE UPPER(common_name) LIKE ? $set_clause",
"$letter%", { fetch => 'all_arrayref', slice => {} } );
"$letter%", { fetch => 'all_arrayref', slice => {}, cache => 'DownloadAllelePage::get_loci_by_letter::common' } );
$set_clause =~ s/ id IN/ locus IN/g;
my $aliases = $self->{'datastore'}->run_query( "SELECT locus,alias FROM locus_aliases WHERE alias ILIKE ? $set_clause",
"$letter%", { fetch => 'all_arrayref', slice => {} } );
"$letter%", { fetch => 'all_arrayref', slice => {}, cache => 'DownloadAllelePage::get_loci_by_letter::aliases' } );
return ( $main, $common, $aliases );
}
......
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