Skip to content

Add synonym and parent UI to cvterm detail page #6165

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ryan-preble wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Add synonym and parent UI to cvterm detail page #6165

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
b7ef5dc
Enable multiple parents for trait and treatment terms
ryan-preble Jun 15, 2026
51c616e
Add synonym UI and parent term UI to cvterm detail page
ryan-preble Jun 16, 2026
8f88506
Fix unit fixture tests
ryan-preble Jun 17, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
37 changes: 37 additions & 0 deletions lib/CXGN/Cvterm.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -415,6 +415,43 @@ sub _store_cvtermprop {



sub add_parent_terms {
my $self = shift;
my $parent_ids = shift;

my $schema = $self->schema();
my $cvterm_id = $self->cvterm_id();

my $relationship_cv = $schema->resultset("Cv::Cv")->find({ name => 'relationship' });
die "No 'relationship' CV found in the database.\n" unless $relationship_cv;
my $rel_cv_id = $relationship_cv->cv_id();

my $variable_of = $schema->resultset("Cv::Cvterm")->find({ name => 'VARIABLE_OF', cv_id => $rel_cv_id });
my $isa = $schema->resultset("Cv::Cvterm")->find({ name => 'is_a', cv_id => $rel_cv_id });
die "No 'is_a' relationship type found.\n" unless $isa;

my $type_id = $isa->cvterm_id();
if ($variable_of) {
my $has_variable_of = $schema->resultset("Cv::CvtermRelationship")->search({
subject_id => $cvterm_id,
type_id => $variable_of->cvterm_id(),
})->count();
if ($has_variable_of > 0) {
$type_id = $variable_of->cvterm_id();
}
}

$schema->txn_do(sub {
for my $parent_id (@$parent_ids) {
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
subject_id => $cvterm_id,
object_id => $parent_id,
type_id => $type_id,
});
}
});
}

__PACKAGE__->meta->make_immutable;

##########
Expand Down
49 changes: 27 additions & 22 deletions lib/CXGN/Trait.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -795,11 +795,11 @@ sub delete_existing_synonyms {

sub interactive_store {
my $self = shift;
my $parent_term = shift;
my $parent_terms_json = shift;

my $schema = $self->bcs_schema();

my $parent_id;
my @parent_ids;

my $name = $self->name() || die "No name found.\n";
my $definition = $self->definition() || die "No definition found.\n";
Expand Down Expand Up @@ -878,17 +878,20 @@ sub interactive_store {

my $db_name = $h->fetchrow_array();

if ($parent_term) {
my $parent_terms = [];
if ($parent_terms_json) {
$parent_terms = decode_json($parent_terms_json);
}

if (@$parent_terms) {
my $lt = CXGN::List::Transform->new();

my $transform = $lt->transform($schema, "traits_2_trait_ids", [$parent_term]);
my $transform = $lt->transform($schema, "traits_2_trait_ids", $parent_terms);

if (@{$transform->{missing}}>0) {
die "Parent term $parent_term could not be found in the database.\n";
if (@{$transform->{missing}} > 0) {
die "Parent term(s) " . join(", ", @{$transform->{missing}}) . " could not be found in the database.\n";
}

my @parent_id_list = @{$transform->{transform}};
$parent_id = $parent_id_list[0];
@parent_ids = @{$transform->{transform}};
} else {
my $ontology_obj = CXGN::Onto->new({
schema => $schema
Expand All @@ -897,7 +900,7 @@ sub interactive_store {

my $root_term_name = $root_nodes[0]->[1] =~ s/\w+:\d+ //r;

$parent_id = $schema->resultset("Cv::Cvterm")->find({
push @parent_ids, $schema->resultset("Cv::Cvterm")->find({
name => $root_term_name,
cv_id => $root_nodes[0]->[0]
})->cvterm_id();
Expand Down Expand Up @@ -947,18 +950,20 @@ sub interactive_store {
dbxref => "$zeroes"."$accession_num"
})->cvterm_id();

if ($format eq "ontology") {
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
object_id => $parent_id,
subject_id => $new_trait_id,
type_id => $isa_id
});
} else {
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
object_id => $parent_id,
subject_id => $new_trait_id,
type_id => $variable_of_id
});
foreach my $pid (@parent_ids) {
if ($format eq "ontology") {
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
object_id => $pid,
subject_id => $new_trait_id,
type_id => $isa_id
});
} else {
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
object_id => $pid,
subject_id => $new_trait_id,
type_id => $variable_of_id
});
}
}

$new_trait = $schema->resultset("Cv::Cvterm")->find({
Expand Down
48 changes: 28 additions & 20 deletions lib/CXGN/Trait/Treatment.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,20 +42,26 @@ sub BUILD {

sub store {
my $self = shift;
my $parent_term = shift;
my $parent_terms_json = shift;

my $schema = $self->bcs_schema();


my $parent_terms = [];
if ($parent_terms_json) {
$parent_terms = decode_json($parent_terms_json);
}
if (!@$parent_terms) {
$parent_terms = ['Experimental treatment ontology|EXPERIMENT_TREATMENT:0000000'];
}

my $lt = CXGN::List::Transform->new();

my $transform = $lt->transform($schema, "traits_2_trait_ids", [$parent_term]);
my $transform = $lt->transform($schema, "traits_2_trait_ids", $parent_terms);

if (@{$transform->{missing}}>0) {
die "Parent term $parent_term could not be found in the database.\n";
if (@{$transform->{missing}} > 0) {
die "Parent term(s) " . join(", ", @{$transform->{missing}}) . " could not be found in the database.\n";
}

my @parent_id_list = @{$transform->{transform}};
my $parent_id = $parent_id_list[0];
my @parent_ids = @{$transform->{transform}};

my $name = $self->name() || die "No name found.\n";
my $definition = $self->definition() || die "No definition found.\n";
Expand Down Expand Up @@ -166,18 +172,20 @@ sub store {
dbxref => "$zeroes"."$accession_num"
})->cvterm_id();

if ($format eq "ontology") {
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
object_id => $parent_id,
subject_id => $new_treatment_id,
type_id => $isa_id
});
} else {
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
object_id => $parent_id,
subject_id => $new_treatment_id,
type_id => $variable_of_id
});
foreach my $pid (@parent_ids) {
if ($format eq "ontology") {
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
object_id => $pid,
subject_id => $new_treatment_id,
type_id => $isa_id
});
} else {
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
object_id => $pid,
subject_id => $new_treatment_id,
type_id => $variable_of_id
});
}
}

$new_treatment = $schema->resultset("Cv::Cvterm")->find({
Expand Down
Loading
Loading