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Add synonym and ID to trait search #5977

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Merged
lukasmueller merged 3 commits into from
Mar 30, 2026
Merged

Add synonym and ID to trait search #5977

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67dda40
Add synonym to trait search, and add field for searching by accession…
bm743 Mar 19, 2026
7b47748
Fix query for matching synonyms
bm743 Mar 23, 2026
b96c19f
Add id and synonym to treatment search
bm743 Mar 26, 2026
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31 changes: 29 additions & 2 deletions lib/CXGN/Trait/Search.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,11 @@ has 'trait_name_list' => (
is => 'rw',
);

has 'trait_synonym_list' => (
isa => 'ArrayRef[Str]|Undef',
is =>'rw',
);

has 'trait_name_is_exact' => (
isa => 'Bool|Undef',
is => 'rw',
Expand Down Expand Up @@ -129,7 +134,9 @@ sub search {
}

if ($self->accession_list && scalar(@{$self->accession_list}) > 0){
$and_conditions{'dbxref.accession'} = { -in => $self->accession_list };
foreach my $term (@{$self->accession_list}) {
push @{$and_conditions{'dbxref.accession'}}, {'ilike' => '%' . $term . '%'};
}
}

if ($self->trait_definition_list && scalar(@{$self->trait_definition_list}) > 0){
Expand All @@ -140,6 +147,20 @@ sub search {
}
}

if ($self->trait_synonym_list && scalar(@{$self->trait_synonym_list}) > 0){
my @synonym_conditions;

foreach (@{$self->trait_synonym_list}){
my @words = split "\s+", $_;
my $match_string = join '%', @words;

push @synonym_conditions, {
'cvtermsynonyms.synonym' => { 'ilike' => '%' . $match_string . '%' }
};
}
$and_conditions{'-or'} = \@synonym_conditions;
}

if ($self->trait_name_list && scalar(@{$self->trait_name_list}) > 0){
my $trait_name_is_exact = $self->trait_name_is_exact;
if ($trait_name_is_exact){
Expand Down Expand Up @@ -173,10 +194,16 @@ sub search {
$where_join{'type.name'} = 'VARIABLE_OF';
}

my @joins = ({'cvterm_relationship_subjects' => 'type'}, {'dbxref' => 'db'});

if ($self->trait_synonym_list && @{$self->trait_synonym_list}) {
push @joins, 'cvtermsynonyms';
}

my $trait_rs = $schema->resultset("Cv::Cvterm")->search(
\%and_conditions,
{
join => [{'cvterm_relationship_subjects' => 'type'}, {'dbxref' => 'db'} ],
join => [{'cvterm_relationship_subjects' => 'type'}, {'dbxref' => 'db'}, 'cvtermsynonyms' ],
where => \%where_join,
order_by => { '-asc' => $order_by },
'+select' => ['db.name', 'dbxref.accession', 'type.name'],
Expand Down
12 changes: 12 additions & 0 deletions lib/SGN/Controller/AJAX/Search/Trait.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,16 @@ sub search : Path('/ajax/search/traits') Args(0) {
push @$subset_traits, $params->{trait_any_name};
}

my $trait_ids;
if ($params->{trait_id}){
push @$trait_ids, $params->{trait_id};
}

my $trait_synonyms;
if ($params->{trait_synonym}){
push @$trait_synonyms, $params->{trait_synonym};
}

my $definitions;
if ($params->{trait_definition}){
push @$definitions, $params->{trait_definition};
Expand All @@ -62,6 +72,8 @@ sub search : Path('/ajax/search/traits') Args(0) {
limit => $limit,
offset => $offset,
trait_name_list => $subset_traits,
accession_list => $trait_ids,
trait_synonym_list => $trait_synonyms,
trait_definition_list => $definitions
});
my ($data, $records_total) = $trait_search->search();
Expand Down
12 changes: 12 additions & 0 deletions lib/SGN/Controller/AJAX/Search/Treatment.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,16 @@ sub search : Path('/ajax/search/treatments') Args(0) {
push @$subset_treatments, $params->{treatment_any_name};
}

my $treatment_ids;
if ($params->{treatment_id}){
push @$treatment_ids, $params->{treatment_id};
}

my $treatment_synonyms;
if ($params->{treatment_synonym}){
push @$treatment_synonyms, $params->{treatment_synonym};
}

my $definitions;
if ($params->{treatment_definition}){
push @$definitions, $params->{treatment_definition};
Expand All @@ -82,6 +92,8 @@ sub search : Path('/ajax/search/treatments') Args(0) {
limit => $limit,
offset => $offset,
trait_name_list => $subset_treatments,
accession_list => $treatment_ids,
trait_synonym_list => $treatment_synonyms,
trait_definition_list => $definitions
});
my ($data, $records_total) = $trait_search->search();
Expand Down
14 changes: 14 additions & 0 deletions mason/search/traits.mas
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,18 @@
<input type="text" class="form-control" id="trait_search_name" placeholder="Search any trait name or piece of name"/>
</div>
</div>
<div class="form-group form-group-sm">
<label class="col-sm-3 control-label">Search Trait ID: </label>
<div class="col-sm-9" >
<input type="text" class="form-control" id="trait_search_id" placeholder="Search any trait ID or part of an ID"/>
</div>
</div>
<div class="form-group form-group-sm">
<label class="col-sm-3 control-label">Search Trait Synonym: </label>
<div class="col-sm-9" >
<input type="text" class="form-control" id="trait_search_synonym" placeholder="Search any trait synonym or part of a synonym"/>
</div>
</div>
<div class="form-group form-group-sm">
<label class="col-sm-3 control-label">Search Definition: </label>
<div class="col-sm-9" >
Expand Down Expand Up @@ -161,6 +173,8 @@ jQuery(document).ready(function () {
'data': function(d) {
d.trait_search_list_id = jQuery('#trait_search_list_select_list_select').val();
d.trait_any_name = jQuery('#trait_search_name').val();
d.trait_id = jQuery('#trait_search_id').val();
d.trait_synonym = jQuery('#trait_search_synonym').val();
d.trait_definition = jQuery('#trait_search_definition').val();
d.ontology_db_id = selectedontologies;
}
Expand Down
14 changes: 14 additions & 0 deletions mason/search/treatments.mas
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,18 @@
<input type="text" class="form-control" id="treatment_search_name" placeholder="Search any treatment name or piece of name"/>
</div>
</div>
<div class="form-group form-group-sm">
<label class="col-sm-3 control-label">Search Treatment ID: </label>
<div class="col-sm-9" >
<input type="text" class="form-control" id="treatment_search_id" placeholder="Search any trait ID or part of an ID"/>
</div>
</div>
<div class="form-group form-group-sm">
<label class="col-sm-3 control-label">Search Treatment Synonym: </label>
<div class="col-sm-9" >
<input type="text" class="form-control" id="treatment_search_synonym" placeholder="Search any trait synonym or part of a synonym"/>
</div>
</div>
<div class="form-group form-group-sm">
<label class="col-sm-3 control-label">Search Definition: </label>
<div class="col-sm-9" >
Expand Down Expand Up @@ -142,6 +154,8 @@ jQuery(document).ready(function () {
'data': function(d) {
d.treatment_search_list_id = jQuery('#treatment_search_list_select_list_select').val();
d.treatment_any_name = jQuery('#treatment_search_name').val();
d.treatment_id = jQuery('#treatment_search_id').val();
d.treatment_synonym = jQuery('#treatment_search_synonym').val();
d.treatment_definition = jQuery('#treatment_search_definition').val();
d.ontology_db_id = selectedontologies;
}
Expand Down
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