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Commit 8432454d authored by Keith Jolley's avatar Keith Jolley
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AlleleInfoPage: Source formatting.

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lib/BIGSdb/AlleleInfoPage.pm
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#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).
......@@ -39,24 +39,24 @@ sub print_content {
my $allele_id = $q->param('allele_id');
if ( !$self->{'datastore'}->is_locus($locus) ) {
say "<h1>Allele information</h1>";
say "<div class=\"box\" id=\"statusbad\"><p>Invalid locus selected.</p></div>";
say qq(<div class="box" id="statusbad"><p>Invalid locus selected.</p></div>);
return;
}
my $cleaned_locus = $self->clean_locus($locus);
say "<h1>Allele information" . ( defined $allele_id ? " - $cleaned_locus: $allele_id\n" : '' ) . "</h1>";
if ( $self->{'system'}->{'dbtype'} eq 'isolates' ) {
say "<div class=\"box\" id=\"statusbad\"><p>This function is not available from an isolate database.</p></div>";
say qq(<div class="box" id="statusbad"><p>This function is not available from an isolate database.</p></div>);
return;
}
if ( !defined $allele_id ) {
say "<div class=\"box\" id=\"statusbad\"><p>No allele id selected.</p></div>";
say qq(<div class="box" id="statusbad"><p>No allele id selected.</p></div>);
return;
}
my $seq_ref =
$self->{'datastore'}
->run_query( "SELECT * FROM sequences WHERE locus=? AND allele_id=?", [ $locus, $allele_id ], { fetch => 'row_hashref' } );
if ( !$seq_ref ) {
say "<div class=\"box\" id=\"statusbad\"><p>This sequence does not exist.</p></div>";
say qq(<div class="box" id="statusbad"><p>This sequence does not exist.</p></div>);
return;
}
my $length = length( $seq_ref->{'sequence'} );
......@@ -68,15 +68,16 @@ sub print_content {
? "(E-mail: <a href=\"mailto:$sender_info->{'email'}\">$sender_info->{'email'}</a>)"
: '';
my $curator_info = $self->{'datastore'}->get_user_info( $seq_ref->{'curator'} );
my $desc_exists = $self->{'datastore'}->run_simple_query( "SELECT COUNT(*) FROM locus_descriptions WHERE locus=?", $locus )->[0];
my $desc_exists = $self->{'datastore'}->run_query( "SELECT EXISTS(SELECT * FROM locus_descriptions WHERE locus=?)", $locus );
my $desc_link =
$desc_exists
? "<a href=\"$self->{'system'}->{'script_name'}?db=$self->{'instance'}&amp;page=locusInfo&amp;locus=$locus\" class=\"info_tooltip\">&nbsp;i&nbsp;</a>"
? qq(<a href="$self->{'system'}->{'script_name'}?db=$self->{'instance'}&amp;page=locusInfo&amp;locus=$locus" )
. qq(class="info_tooltip">i</a>)
: '';
say "<div class=\"box\" id=\"resultspanel\">";
say "<div class=\"scrollable\">";
say qq(<div class="box" id="resultspanel">);
say qq(<div class="scrollable">);
say "<h2>Provenance/meta data</h2>";
say "<dl class=\"data\">";
say qq(<dl class="data">);
say "<dt>locus</dt><dd>$cleaned_locus $desc_link</dd>";
say "<dt>allele</dt><dd>$allele_id</dd>";
......@@ -85,13 +86,11 @@ sub print_content {
} elsif ( $allele_id eq 'N' ) {
say "<dt>description</dt><dd>This is an arbitrary allele. When included in a profile it means that this locus is ignored.</dd>";
} else {
print << "HTML";
<dt>sequences</dt><dd style="text-align:left" class="seq">$seq</dd>
<dt>length</dt><dd>$length</dd>
<dt>status</dt><dd>$seq_ref->{'status'}</dd>
<dt>date entered</dt><dd>$seq_ref->{'date_entered'}</dd>
<dt>datestamp</dt><dd>$seq_ref->{'datestamp'}</dd>
HTML
say qq(<dt>sequences</dt><dd style="text-align:left" class="seq">$seq</dd>)
. qq(<dt>length</dt><dd>$length</dd>)
. qq(<dt>status</dt><dd>$seq_ref->{'status'}</dd>)
. qq(<dt>date entered</dt><dd>$seq_ref->{'date_entered'}</dd>)
. qq(<dt>datestamp</dt><dd>$seq_ref->{'datestamp'}</dd>);
if ( $sender_info->{'first_name'} || $sender_info->{'surname'} ) {
print "<dt>sender</dt><dd>$sender_info->{'first_name'} $sender_info->{'surname'}";
print ", $sender_info->{'affiliation'}$sender_email" if $seq_ref->{'sender'} != $seq_ref->{'curator'};
......@@ -127,15 +126,11 @@ HTML
if (@$scheme_list) {
my $profile_buffer;
foreach my $scheme (@$scheme_list) {
my $scheme_info = $self->{'datastore'}->get_scheme_info( $scheme->{'id'}, { set_id => $set_id } );
my $pk_ref =
$self->{'datastore'}
->run_simple_query( "SELECT field FROM scheme_fields WHERE scheme_id=? AND primary_key", $scheme->{'id'} );
next if ref $pk_ref ne 'ARRAY';
my $pk = $pk_ref->[0];
my $scheme_info = $self->{'datastore'}->get_scheme_info( $scheme->{'id'}, { set_id => $set_id, get_pk => 1 } );
next if !$scheme_info->{'primary_key'};
my $profiles =
$self->{'datastore'}->run_simple_query( "SELECT COUNT(*) FROM profile_members WHERE scheme_id=? AND locus=? AND allele_id=?",
$scheme->{'id'}, $locus, $allele_id )->[0];
$self->{'datastore'}->run_query( "SELECT COUNT(*) FROM profile_members WHERE scheme_id=? AND locus=? AND allele_id=?",
[ $scheme->{'id'}, $locus, $allele_id ] );
next if !$profiles;
$profile_buffer .= "<dt>$scheme_info->{'description'}</dt>";
my $plural = $profiles == 1 ? '' : 's';
......@@ -147,15 +142,15 @@ HTML
$q->param( s1 => $locus );
$q->param( y1 => '=' );
$q->param( t1 => $allele_id );
$q->param( 'order', $pk );
$q->param( 'submit', 1 );
$q->param( order => $scheme_info->{'primary_key'} );
$q->param( submit => 1 );
$profile_buffer .= $q->hidden($_) foreach qw (db page scheme_id s1 y1 t1 order submit);
$profile_buffer .= $q->submit( -label => "$profiles profile$plural", -class => 'smallbutton' );
$profile_buffer .= $q->end_form;
$profile_buffer .= "</dd>";
}
if ($profile_buffer) {
say "<h2>Profiles containing this allele</h2>\n<dl class=\"data\">\n$profile_buffer</dl>";
say qq(<h2>Profiles containing this allele</h2>\n<dl class="data">\n$profile_buffer</dl>);
}
}
$self->_print_client_database_data( $locus, $allele_id );
......@@ -209,7 +204,7 @@ sub _print_client_database_data {
$buffer .= "</dd>";
}
if ($buffer) {
say "<h2>Isolate databases</h2>\n<dl class=\"data\">";
say qq(<h2>Isolate databases</h2>\n<dl class="data">);
say $buffer;
say "</dl>";
}
......@@ -222,8 +217,8 @@ sub _process_flags {
if ( ( $self->{'system'}->{'allele_flags'} // '' ) eq 'yes' ) {
my $flags = $self->{'datastore'}->get_allele_flags( $locus, $allele_id );
if (@$flags) {
local $" = "</span> <span class=\"seqflag\">";
say "<dt>flags</dt><dd><span class=\"seqflag\">@$flags</span></dd>";
local $" = qq(</span> <span class="seqflag">);
say qq(<dt>flags</dt><dd><span class="seqflag">@$flags</span></dd>);
}
}
return;
......@@ -247,15 +242,14 @@ sub initiate {
sub _print_accessions {
my ( $self, $locus, $allele_id ) = @_;
my $qry = "SELECT databank, databank_id FROM accession WHERE locus=? and allele_id=? ORDER BY databank,databank_id";
my $accession_list =
$self->{'datastore'}->run_query( $qry, [ $locus, $allele_id ], { fetch => 'all_arrayref', slice => {} } );
my $buffer = '';
my $qry = "SELECT databank, databank_id FROM accession WHERE locus=? and allele_id=? ORDER BY databank,databank_id";
my $accession_list = $self->{'datastore'}->run_query( $qry, [ $locus, $allele_id ], { fetch => 'all_arrayref', slice => {} } );
my $buffer = '';
if (@$accession_list) {
say "<h2>Accession" . ( @$accession_list > 1 ? 's' : '' ) . " (" . @$accession_list . ")";
my $display = @$accession_list > 4 ? 'none' : 'block';
say "<span style=\"margin-left:1em\"><a id=\"show_accessions\" class=\"smallbutton\" style=\"cursor:pointer\">&nbsp;"
. "show/hide&nbsp;</a></span>"
say qq(<span style="margin-left:1em"><a id="show_accessions" class="smallbutton" style="cursor:pointer">&nbsp;)
. qq(show/hide&nbsp;</a></span>)
if $display eq 'none';
say "</h2>\n";
my $id = $display eq 'none' ? 'hidden_accessions' : 'accessions';
......@@ -264,30 +258,31 @@ sub _print_accessions {
foreach my $accession (@$accession_list) {
say "<dt>$accession->{'databank'}</dt>";
if ( $accession->{'databank'} eq 'Genbank' ) {
say "<dd><a href=\"http://www.ncbi.nlm.nih.gov/nuccore/$accession->{'databank_id'}\">"
. "$accession->{'databank_id'}</a></dd>";
say qq(<dd><a href="http://www.ncbi.nlm.nih.gov/nuccore/$accession->{'databank_id'}">)
. qq($accession->{'databank_id'}</a></dd>);
} elsif ( $accession->{'databank'} eq 'ENA' ) {
say "<dd><a href=\"http://www.ebi.ac.uk/ena/data/view/$accession->{'databank_id'}\">"
. "$accession->{'databank_id'}</a></dd>";
say qq(<dd><a href="http://www.ebi.ac.uk/ena/data/view/$accession->{'databank_id'}">)
. qq($accession->{'databank_id'}</a></dd>);
} else {
say "<dd>$accession->{'databank_id'}</dd>";
}
}
say "</dl></div>\n";
say "</dl></div>";
}
return $buffer;
}
sub _print_ref_links {
my ( $self, $locus, $allele_id ) = @_;
my $pmids =
$self->{'datastore'}
->run_list_query( "SELECT pubmed_id FROM sequence_refs WHERE locus=? and allele_id=? ORDER BY pubmed_id", $locus, $allele_id );
my $pmids = $self->{'datastore'}->run_query(
"SELECT pubmed_id FROM sequence_refs WHERE locus=? and allele_id=? ORDER BY pubmed_id",
[ $locus, $allele_id ],
{ fetch => 'col_arrayref' }
);
if (@$pmids) {
say "<h2>Publication" . ( @$pmids > 1 ? 's' : '' ) . " (" . @$pmids . ")";
my $display = @$pmids > 4 ? 'none' : 'block';
say
"<span style=\"margin-left:1em\"><a id=\"show_refs\" class=\"smallbutton\" style=\"cursor:pointer\">&nbsp;show/hide&nbsp;</a></span>"
say qq(<span style="margin-left:1em"><a id="show_refs" class="smallbutton" style="cursor:pointer">&nbsp;show/hide&nbsp;</a></span>)
if $display eq 'none';
say "</h2>\n";
my $id = $display eq 'none' ? 'hidden_references' : 'references';
......@@ -296,7 +291,7 @@ sub _print_ref_links {
$self->{'datastore'}
->get_citation_hash( $pmids, { formatted => 1, all_authors => 1, state_if_unavailable => 1, link_pubmed => 1 } );
foreach my $pmid ( sort { $citations->{$a} cmp $citations->{$b} } @$pmids ) {
say "<li style=\"padding-bottom:1em\">$citations->{$pmid}</li>";
say qq(<li style="padding-bottom:1em">$citations->{$pmid}</li>);
}
say "</ul>";
}
......
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