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QuickSearch improve error checking #6059

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38aed25
improve error checking
ClayBirkett Apr 22, 2026
b1b2982
add error checks
ClayBirkett Apr 23, 2026
72a7a45
code clean up
ClayBirkett Apr 27, 2026
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156 changes: 65 additions & 91 deletions lib/SGN/Controller/QuickSearch.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ use CXGN::Tools::Text qw/to_tsquery_string trim/;
use SGN::Model::Cvterm;
use Bio::Chado::Schema;
use CXGN::Marker::SearchMatView;
use Try::Tiny;
use Data::Dumper;

=head1 NAME
Expand Down Expand Up @@ -191,20 +192,20 @@ sub execute_predefined_searches: Private {
my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
# execute all the searches and stash the results
for my $search_name ( sort keys %searches ) {
print STDERR "performing quick search for $search_name (". Dumper($searches{$search_name}).")...\n";
my $search = $searches{$search_name};
my $b = time;
my $searchresults = $self->do_quick_search(
#print STDERR "performing quick search for $search_name (". Dumper($searches{$search_name}).")...\n";
my $search = $searches{$search_name};
my $b = time;
my $searchresults = $self->do_quick_search(
$c->dbc->dbh,
%$search,
term => $c->stash->{term},
schema => $c->dbic_schema("Bio::Chado::Schema", undef, $sp_person_id),
);
$c->stash->{results}{$search_name} = {
);
$c->stash->{results}{$search_name} = {
result => $searchresults,
time => time - $b,
exact => $search->{exact}
};
};
print STDERR "SEARCH RESULTS: ".Dumper($searchresults);
}
}
Expand All @@ -224,11 +225,17 @@ sub do_quick_search {
my ( $self, $db, %args ) = @_;

if ($args{function}) { #just run legacy functions and return their results
print STDERR "INVOKING $args{function} with $args{term}\n";
return $args{function}->( $self, $db,$args{term}, $args{schema});
my $result;
try {
$result = $args{function}->($self, $db, $args{term}, $args{schema})
} catch {
warn "Search failed for term '$args{term}': $_";
$result = [undef, "0 results"];
};
return $result;
} else {
my $classname = $args{sf_class}
or die 'Must provide a class name';
my $classname = $args{sf_class} or die 'Must provide a class name';
my $result_desc = $args{result_desc} or die "Must provide result_desc";

Class::Load::load_class( $classname );
$classname->isa( 'CXGN::Search::SearchI' )
Expand All @@ -248,22 +255,17 @@ sub do_quick_search {

if ($count > 0) {
my $qstr = encode_entities($query->to_query_string());
return [ "$args{search_path}?$qstr", "$count $args{result_desc}" ];
return [ "$args{search_path}?$qstr", "$count $result_desc" ];
}
}
return [undef, "0 $args{result_desc}"];
return [undef, "0 $result_desc"];
}

die 'this point should not be reached';
}

###################### LEGACY QUICK SEARCH FUNCTIONS ##########################

sub quick_est_search {
my $self = shift;
my $db = shift;
my $term = shift;

my ( $self, $db, $term ) = @_;
my $est_link = [ undef, "0 EST identifiers" ];

# the est quick search should support identifiers of the form SGN-E999999, SGN_E999999, SGNE999999
Expand All @@ -284,9 +286,7 @@ sub quick_est_search {
}

sub quick_clone_search {
my $self = shift;
my $db = shift;
my $term = shift;
my ( $self, $db, $term ) = @_;

# adjust if EST
unless ($term =~ m|^ccc|) { # coffee clone name.
Expand Down Expand Up @@ -324,10 +324,7 @@ sub quick_clone_search {
# For quick_search queries without the Version#-Release#- prefix, the version and release are
# assumed to both be one. This is hardcoded below in two variables $version and $release.
sub quick_array_search {
my $self = shift;
my $db = shift;
my $term = shift;

my ( $self, $db, $term ) = @_;
my $version = 1; # default version is 1
my $release = 1; # default release is 1
my $spot = "";
Expand Down Expand Up @@ -375,9 +372,7 @@ sub quick_phenotype_search {
}

sub quick_marker_search {
my $self = shift;
my $db = shift;
my $term = shift;
my ( $self, $db, $term ) = @_;

# adjust if EST
$term =~ s/([a-z]{4})(\d{1,2})([a-z]\d{1,2})/$1-$2-$3/i;
Expand All @@ -394,10 +389,7 @@ sub quick_marker_search {
}

sub quick_mapped_geno_marker_search {
my $self = shift;
my $db = shift;
my $term = shift;
my $schema = shift;
my ( $self, $db, $term, $schema ) = @_;

my $count = 0;
my $marker_link = [undef, "0 marker identifiers"];
Expand All @@ -423,9 +415,7 @@ sub quick_mapped_geno_marker_search {
}

sub quick_manual_annotation_search {
my $self = shift;
my $db = shift;
my $term = shift;
my ( $self, $db, $term ) = @_;

# It's a syntax error for whitespace to occur in tsquery query strings. Replace with ampersands.
my $cleaned_term = to_tsquery_string($term);
Expand Down Expand Up @@ -459,9 +449,7 @@ EOSQL
}

sub quick_automatic_annotation_search {
my $self = shift;
my $db = shift;
my $term = shift;
my ( $self, $db, $term ) = @_;
my $cleaned_term = to_tsquery_string($term);
my $count = sql_query_count($db, "select count(*) from blast_defline where defline_fulltext @@ to_tsquery(?)",$cleaned_term);

Expand All @@ -488,11 +476,18 @@ EOSQL
}

sub sql_query_count {
my $db = shift;
my $query = shift;
my $qh = $db -> prepare_cached($query);
$qh -> execute(@_);
my ($count) = $qh -> fetchrow_array();
my ($db, $query, @bind) = @_;
my $count = try {
my $qh = $db -> prepare_cached($query);
$qh -> execute(@bind);
my ($result) = $qh -> fetchrow_array();
$qh->finish;
$result // 0;
} catch {
print STDERR "Query failed: $_";
return 0;
};

return $count;
}

Expand Down Expand Up @@ -536,10 +531,7 @@ sub google_search {
}

sub stock_search {
my $self = shift;
my $schema = shift;
my $type = shift;
my $term = shift;
my ( $self, $schema, $type, $term ) = @_;

my $accession_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, $type, 'stock_type')->cvterm_id();
my $rs = $schema->resultset("Stock::Stock")->search( { uniquename => { ilike => $term} , type_id => $accession_type_id });
Expand All @@ -555,10 +547,7 @@ sub stock_search {
}

sub quick_accession_search {
my $self = shift;
my $db = shift;
my $term = shift;
my $schema = shift;
my ( $self, $db, $term, $schema ) = @_;

my ($id, $name) = $self->stock_search($schema, 'accession', $term);
if ($id) {
Expand All @@ -572,10 +561,7 @@ sub quick_accession_search {
}

sub quick_vector_search {
my $self = shift;
my $db = shift;
my $term = shift;
my $schema = shift;
my ( $self, $db, $term, $schema ) = @_;

my ($id, $name) = $self->stock_search($schema, 'vector_construct', $term);
if ($id) {
Expand All @@ -590,11 +576,7 @@ sub quick_vector_search {


sub quick_plot_search {
my $self = shift;
my $db = shift;
my $term = shift;
my $schema = shift;

my ( $self, $db, $term, $schema ) = @_;
my ($id, $name) = $self->stock_search($schema, 'plot', $term);

if ($id) {
Expand All @@ -606,11 +588,7 @@ sub quick_plot_search {
}

sub quick_populations_search {
my $self = shift;
my $db = shift;
my $term = shift;
my $schema = shift;

my ( $self, $db, $term, $schema ) = @_;
my ($id, $name) = $self->stock_search($schema, 'population', $term);

if ($id) {
Expand All @@ -622,10 +600,7 @@ sub quick_populations_search {
}

sub quick_trials_search {
my $self = shift;
my $db = shift;
my $term = shift;
my $schema = shift;
my ( $self, $db, $term, $schema ) = @_;

my $cv_rs = $schema->resultset("Cv::Cv")->search( { 'me.name' => 'project_type' }, { join => 'cvterms', '+select' => [ 'cvterms.name', 'cvterms.cvterm_id' ], '+as' => [ 'cvterm_name', 'cvterm_id' ] });

Expand Down Expand Up @@ -653,10 +628,7 @@ sub quick_trials_search {
}

sub quick_locations_search {
my $self = shift;
my $db = shift;
my $term = shift;
my $schema = shift;
my ( $self, $db, $term, $schema ) = @_;

print STDERR "LOCATION SEARCH!\n";
my $rs = $schema->resultset("NaturalDiversity::NdGeolocation")->search( { description => { ilike => $term } });
Expand All @@ -666,11 +638,10 @@ sub quick_locations_search {
my $row = $rs->next();
$id = $row->nd_geolocation_id();
$name = $row->description();
}
else {
print STDERR "RETURNED: $id, $name\n";
} else {
print STDERR "LOCATION HAS ".$rs->count()." MATCHES!!!!\n";
}
print STDERR "RETURNED: $id, $name\n";
if ($id) {
return [ '/breeders/locations/', '1 location: '.$name ]; # just link to generic locations page
}
Expand All @@ -680,10 +651,7 @@ sub quick_locations_search {
}

sub quick_traits_search {
my $self = shift;
my $db = shift;
my $term = shift;
my $schema = shift;
my ( $self, $db, $term, $schema ) = @_;

my $trait_search = CXGN::Trait::Search->new({
bcs_schema=>$schema,
Expand All @@ -707,13 +675,19 @@ sub quick_traits_search {
}

sub quick_bp_search {
my $self = shift;
my $db = shift;
my $term = shift;
my $schema = shift;
my ( $self, $db, $term, $schema ) = @_;

print STDERR "breeding program search... \n";
my $rs = $schema->resultset("Project::Project")->search( { 'me.name' => { ilike => $term } } , { cvterm_name => 'breeding_program', join => 'projectprops' => { 'cvterms', '+select' => [ 'cvterm.name'], '+as' => ['cvterm_name'] } } );
my $rs = $schema->resultset("Project::Project")->search(
{
'me.name' => { ilike => $term },
'type.name' => 'breeding_program',
},
{
join => { projectprops => 'type' },
distinct => 1,
}
);

my ($id, $name);

Expand All @@ -722,30 +696,30 @@ sub quick_bp_search {
while (my $row = $rs->next()) {
print STDERR join("\t", $row->name(), $row->project_id())."\n";
}
return [ '', 'too many hits' ];
return [ undef, 'too many hits' ];
}

elsif ($rs->count() == 1) {
my $row = $rs->next();
$id = $row->project_id();
$name = $row->name();
print STDERR "FOUND: $id\n";
}
else {
print STDERR "Sorry, no match!\n";
}

print STDERR "FOUND: $id\n";
if ($id) {
return [ '/breeders/program/'.$id, "1 breeding program: ".$name ];
return [ '/breeders/program/'.$id, "1 breeding program: $name" ];
}
else {
return [ '', '0 breeding programs' ];
return [ undef, '0 breeding programs' ];
}

}

sub quick_web_search {
my ($self, undef,$term) = @_;
my ($self, undef, $term) = @_;
# works the same way as quick_page_search, except that the domain contraint is removed from the
# search.
print STDERR "Performing web search... ";
Expand Down
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