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Option to include parents for phenotype download #6172

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2b60546
pedigree option
titima15 Jun 16, 2026
2da084e
pedigree option on manage trials page and stock details page
titima15 Jun 17, 2026
3579e7c
retrieve parents
titima15 Jun 19, 2026
31ba6ae
modified dialog titles
titima15 Jun 22, 2026
fabfc4a
include parent search in query
titima15 Jun 22, 2026
9f56f9d
clean up
titima15 Jun 22, 2026
dd304cf
fix ordering
titima15 Jun 23, 2026
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11 changes: 6 additions & 5 deletions js/source/modules/wizard-downloads.js
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Original file line number Diff line number Diff line change
Expand Up @@ -196,6 +196,7 @@ export function WizardDownloads(main_id,wizard){
var entry_numbers = d3.selectAll('.wizard-download-phenotypes-entry-numbers').property('checked')?1:0;
var trait_synonyms = d3.selectAll('.wizard-download-phenotypes-trait-synonyms').property('checked')?1:0;
var intercrop = d3.selectAll('.wizard-download-phenotypes-intercrop').property('checked')?1:0;
var pedigree_parents = d3.selectAll('.wizard-download-phenotypes-pedigree_parents').property('checked')?1:0;
var outliers = d3.selectAll('.wizard-download-phenotypes-outliers').property('checked')?1:0;
var names = JSON.stringify(d3.select(".wizard-download-phenotypes-name").node().value.split(","));
var min = d3.select(".wizard-download-phenotypes-min").node().value;
Expand All @@ -206,7 +207,7 @@ export function WizardDownloads(main_id,wizard){

//alert('start date = '+phenotype_start_date);
//alert('repetitive type = '+repetitive_measurements);

var url = document.location.origin+'/breeders/trials/phenotype/download';
openWindowWithPost(url, {
trial_list: trial_ids,
Expand All @@ -229,7 +230,7 @@ export function WizardDownloads(main_id,wizard){
trait_contains: names,
include_row_and_column_numbers: 1,
exclude_phenotype_outlier: outliers,
include_pedigree_parents: 0,
include_pedigree_parents: pedigree_parents,
repetitive_measurements: repetitive_measurements,
phenotype_start_date: phenotype_start_date,
phenotype_end_date: phenotype_end_date
Expand All @@ -244,7 +245,7 @@ export function WizardDownloads(main_id,wizard){
var years = categories.indexOf("years")!=-1 ? selections["years"] : [];
var tissue_samples = categories.indexOf("tissue_sample")!=-1 ? selections["tissue_sample"] : [];
var protocols = categories.indexOf("protocols")!=-1 ? selections["protocols"] : [];
var instances = categories.indexOf("instances")!=-1 ? selections["instances"] : [];
var instances = categories.indexOf("instances")!=-1 ? selections["instances"] : [];

main.selectAll(".wizard-download-high-dim-phenotypes-info")
.attr("value",`${trials.length||"Too few"} trials`);
Expand Down Expand Up @@ -279,7 +280,7 @@ export function WizardDownloads(main_id,wizard){

//alert('start date = '+phenotype_start_date);
//alert('repetitive type = '+repetitive_measurements);

var url = document.location.origin+'/breeders/trials/phenotype/download';
openWindowWithPost(url, {
trial_list: trial_ids,
Expand All @@ -302,7 +303,7 @@ export function WizardDownloads(main_id,wizard){
intercrop: intercrop,
include_row_and_column_numbers: 1,
//exclude_phenotype_outlier: outliers,
include_pedigree_parents: 0,
include_pedigree_parents: pedigree_parents,
//repetitive_measurements: repetitive_measurements,
phenotype_start_date: phenotype_start_date,
phenotype_end_date: phenotype_end_date
Expand Down
12 changes: 10 additions & 2 deletions lib/CXGN/Phenotypes/PhenotypeMatrix.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,6 @@ sub get_phenotype_matrix {
my $include_entry_numbers = $self->include_entry_numbers;
my $include_trait_synonyms = $self->include_trait_synonyms;
my %trial_entry_numbers;

$self->trait_repeat_types( $self->retrieve_trait_repeat_types() );
print STDERR "GET PHENOMATRIX ".$self->search_type."\n";

Expand Down Expand Up @@ -274,6 +273,7 @@ sub get_phenotype_matrix {
end_date => $self->end_date(),
include_dateless_items => $self->include_dateless_items(),
include_intercrop_stocks => $include_intercrop_stocks,
include_pedigree_parents => $include_pedigree_parents,
limit=>$self->limit,
offset=>$self->offset
}
Expand Down Expand Up @@ -435,7 +435,7 @@ sub get_phenotype_matrix {
else { ### NATIVE ??!!

$data = $phenotypes_search->search();
#print STDERR "the download data structure =". Dumper($data)."\n";
# print STDERR "the download data structure =". Dumper($data)."\n";

my %obsunit_data;
my %traits;
Expand All @@ -445,6 +445,10 @@ sub get_phenotype_matrix {
my @unique_obsunit_list = ();
my %seen_obsunits;

if ($include_pedigree_parents){
push @metadata_headers, ('germplasmPedigreeFemaleParentName', 'germplasmPedigreeFemaleParentDbId', 'germplasmPedigreeMaleParentName', 'germplasmPedigreeMaleParentDbId');
}

# Add intercrop stock headers, if requested
if ( $include_intercrop_stocks ) {
push(@metadata_headers, 'intercropGermplasmDbId', 'intercropGermplasmName');
Expand Down Expand Up @@ -535,6 +539,10 @@ sub get_phenotype_matrix {
$d->{plant_number}
];

if ($include_pedigree_parents) {
push(@{$obsunit_data{$obsunit_id}->{metadata}}, ($d->{'female_parent_name'}, $d->{'female_parent_id'}, $d->{'male_parent_name'}, $d->{'male_parent_id'}));
}

# add intercrop stocks, if requested
if ( $include_intercrop_stocks ) {
my @ic_stock_ids;
Expand Down
166 changes: 92 additions & 74 deletions lib/CXGN/Phenotypes/Search/Native.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -227,6 +227,8 @@ sub search {
my $plant_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plant_of', 'stock_relationship')->cvterm_id();
my $subplot_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'subplot_of', 'stock_relationship')->cvterm_id();
my $tissue_sample_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tissue_sample_of', 'stock_relationship')->cvterm_id();
my $female_parent_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'female_parent', 'stock_relationship')->cvterm_id();
my $male_parent_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'male_parent', 'stock_relationship')->cvterm_id();

my $include_timestamp = $self->include_timestamp;
my $numeric_regex = '^-?[0-9]+([,.][0-9]+)?$';
Expand Down Expand Up @@ -274,7 +276,7 @@ sub search {
}
}


#For performace reasons it is faster to include specific stock_ids in the query.
if ($self->data_level eq 'analysis_instance'){
if (!$self->plot_list){
Expand Down Expand Up @@ -346,7 +348,7 @@ sub search {
LEFT JOIN stockprop AS is_a_control ON (observationunit.stock_id=is_a_control.stock_id AND is_a_control.type_id = $is_a_control_type_id) ";
$design_layout_select = " ,rep.value, block_number.value, plot_number.value, is_a_control.value, row_number.value, col_number.value, plant_number.value";
}

if ($self->exclude_phenotype_outlier) {
$phenotypeprop_sql = "JOIN (
SELECT phenotype_id
Expand All @@ -360,13 +362,17 @@ sub search {
ON not_outliers.phenotype_id = nd_experiment_phenotype.phenotype_id"
};

my $from_clause = " FROM stock as observationunit
my $from_clause = " FROM stock as observationunit
LEFT JOIN stock_relationship ON (observationunit.stock_id=stock_relationship.subject_id) AND stock_relationship.type_id IN ($analysis_instance_of_type_id, $plot_of_type_id, $plant_of_type_id, $subplot_of_type_id, $tissue_sample_of_type_id)
LEFT JOIN stock_relationship AS icsr ON (observationunit.stock_id=icsr.subject_id) AND icsr.type_id = $intercrop_plot_rel_type_id
LEFT JOIN stock AS ics ON (icsr.object_id=ics.stock_id)
LEFT JOIN cvterm as observationunit_type ON (observationunit_type.cvterm_id = observationunit.type_id)
JOIN stock as germplasm ON (stock_relationship.object_id=germplasm.stock_id) AND germplasm.type_id IN ($accession_type_id, $analysis_result_type_id, $cross_type_id, $family_name_type_id)
$design_layout_sql
LEFT JOIN stock_relationship AS female_relationship ON (germplasm.stock_id = female_relationship.object_id) AND female_relationship.type_id = $female_parent_type_id
LEFT JOIN stock AS female_parent ON (female_relationship.subject_id = female_parent.stock_id)
LEFT JOIN stock_relationship AS male_relationship ON (germplasm.stock_id = male_relationship.object_id) AND male_relationship.type_id = $male_parent_type_id
LEFT JOIN stock AS male_parent ON (male_relationship.subject_id = male_parent.stock_id)
LEFT JOIN nd_experiment_stock ON(nd_experiment_stock.stock_id=observationunit.stock_id)
LEFT JOIN nd_experiment_phenotype ON (nd_experiment_phenotype.nd_experiment_id=nd_experiment_stock.nd_experiment_id)
LEFT JOIN phenotype USING(phenotype_id)
Expand Down Expand Up @@ -395,88 +401,96 @@ sub search {
LEFT JOIN project_relationship folder_rel ON (project.project_id = folder_rel.subject_project_id AND folder_rel.type_id = $folder_rel_type_id)
LEFT JOIN project folder ON (folder.project_id = folder_rel.object_project_id)";

my $select_clause = "SELECT observationunit.stock_id,
observationunit.uniquename,
observationunit_type.name,
germplasm.uniquename,
germplasm.stock_id,
project.project_id,
project.name,
project.description,
plot_width.value,
plot_length.value,
field_size.value,
field_trial_is_planned_to_be_genotyped.value,
field_trial_is_planned_to_cross.value,
breeding_program.project_id,
breeding_program.name,
breeding_program.description,
year.value,
design.value,
location.value,
planting_date.value,
harvest_date.value,
folder.project_id,
folder.name,
folder.description,
cvterm.cvterm_id,
(((cvterm.name::text || '|'::text) || db.name::text) || ':'::text) || dbxref.accession::text,
my $select_clause = "SELECT observationunit.stock_id,
observationunit.uniquename,
observationunit_type.name,
germplasm.uniquename,
germplasm.stock_id,
project.project_id,
project.name,
project.description,
plot_width.value,
plot_length.value,
field_size.value,
field_trial_is_planned_to_be_genotyped.value,
field_trial_is_planned_to_cross.value,
breeding_program.project_id,
breeding_program.name,
breeding_program.description,
year.value,
design.value,
location.value,
planting_date.value,
harvest_date.value,
folder.project_id,
folder.name,
folder.description,
cvterm.cvterm_id,
(((cvterm.name::text || '|'::text) || db.name::text) || ':'::text) || dbxref.accession::text,
MIN(cvtermsynonym.synonym),
phenotype.value,
phenotype.uniquename,
phenotype.phenotype_id,
phenotype.collect_date,
phenotype.operator,
additional_info.value,
external_references.value,
count(phenotype.phenotype_id) OVER() AS full_count,
phenotype.value,
phenotype.uniquename,
phenotype.phenotype_id,
phenotype.collect_date,
phenotype.operator,
additional_info.value,
female_parent.uniquename,
female_parent.stock_id,
male_parent.uniquename,
male_parent.stock_id,
external_references.value,
count(phenotype.phenotype_id) OVER() AS full_count,
string_agg(distinct(notes.value), ', ') AS notes,
STRING_AGG(DISTINCT(ics.stock_id)::text, '|'),
STRING_AGG(DISTINCT(ics.stock_id)::text, '|'),
STRING_AGG(DISTINCT(ics.uniquename), ',')
".$design_layout_select;

my $order_clause = " ORDER BY 6, 2, 30";

my $group_by = " GROUP BY observationunit.stock_id,
observationunit.uniquename,
observationunit_type.name,
germplasm.uniquename,
germplasm.stock_id,
project.project_id,
project.name,
my $group_by = " GROUP BY observationunit.stock_id,
observationunit.uniquename,
observationunit_type.name,
germplasm.uniquename,
germplasm.stock_id,
project.project_id,
project.name,
project.description,
plot_width.value,
plot_length.value,
field_size.value,
field_trial_is_planned_to_be_genotyped.value,
field_trial_is_planned_to_cross.value,
breeding_program.project_id,
breeding_program.name,
breeding_program.description,
year.value,
design.value,
location.value,
planting_date.value,
harvest_date.value,
folder.project_id,
folder.name,
folder.description,
cvterm.cvterm_id,
(((cvterm.name::text || '|'::text) || db.name::text) || ':'::text) || dbxref.accession::text,
phenotype.value,
phenotype.uniquename,
phenotype.phenotype_id,
phenotype.collect_date,
phenotype.operator,
additional_info.value,
plot_width.value,
plot_length.value,
field_size.value,
field_trial_is_planned_to_be_genotyped.value,
field_trial_is_planned_to_cross.value,
breeding_program.project_id,
breeding_program.name,
breeding_program.description,
year.value,
design.value,
location.value,
planting_date.value,
harvest_date.value,
folder.project_id,
folder.name,
folder.description,
cvterm.cvterm_id,
(((cvterm.name::text || '|'::text) || db.name::text) || ':'::text) || dbxref.accession::text,
phenotype.value,
phenotype.uniquename,
phenotype.phenotype_id,
phenotype.collect_date,
phenotype.operator,
additional_info.value,
female_parent.uniquename,
female_parent.stock_id,
male_parent.uniquename,
male_parent.stock_id,
external_references.value ".$design_layout_select;

my @where_clause;
my $accession_list = $self->accession_list;
print STDERR "Native search Accession list is ".Dumper($accession_list)."\n";

my $analysis_result_stock_list = $self->analysis_result_stock_list;

if ($self->analysis_result_stock_list && scalar(@{$self->analysis_result_stock_list})>0) {
print STDERR "Native search adding analysis result_stock_list to sql\n";
my $accession_sql = _sql_from_arrayref($self->analysis_result_stock_list);
Expand Down Expand Up @@ -607,10 +621,10 @@ sub search {
my $stock_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, $data_level, 'stock_type')->cvterm_id();
push @where_clause, "observationunit.type_id = $stock_type_id"; #ONLY plot or plant or subplot or tissue_sample
} else {
push @where_clause, "(observationunit.type_id = $plot_type_id
push @where_clause, "(observationunit.type_id = $plot_type_id
OR observationunit.type_id = $plant_type_id
OR observationunit.type_id = $analysis_instance_id
OR observationunit.type_id = $subplot_type_id
OR observationunit.type_id = $analysis_instance_id
OR observationunit.type_id = $subplot_type_id
OR observationunit.type_id = $tissue_sample_type_id)"; #plots AND plants AND subplots AND tissue_samples
}

Expand Down Expand Up @@ -638,7 +652,7 @@ sub search {

my $calendar_funcs = CXGN::Calendar->new({});

while (my ($observationunit_stock_id, $observationunit_uniquename, $observationunit_type_name, $germplasm_uniquename, $germplasm_stock_id, $project_project_id, $project_name, $project_description, $plot_width, $plot_length, $field_size, $field_trial_is_planned_to_be_genotyped, $field_trial_is_planned_to_cross, $breeding_program_project_id, $breeding_program_name, $breeding_program_description, $year, $design, $location_id, $planting_date, $harvest_date, $folder_id, $folder_name, $folder_description, $trait_id, $trait_name, $trait_synonym, $phenotype_value, $phenotype_uniquename, $phenotype_id, $phenotype_collect_date, $phenotype_operator, $phenotype_additional_info, $phenotype_external_references, $full_count, $notes, $intercrop_stock_id, $intercrop_stock_name, $rep_select, $block_number_select, $plot_number_select, $is_a_control_select, $row_number_select, $col_number_select, $plant_number) = $h->fetchrow_array()) {
while (my ($observationunit_stock_id, $observationunit_uniquename, $observationunit_type_name, $germplasm_uniquename, $germplasm_stock_id, $project_project_id, $project_name, $project_description, $plot_width, $plot_length, $field_size, $field_trial_is_planned_to_be_genotyped, $field_trial_is_planned_to_cross, $breeding_program_project_id, $breeding_program_name, $breeding_program_description, $year, $design, $location_id, $planting_date, $harvest_date, $folder_id, $folder_name, $folder_description, $trait_id, $trait_name, $trait_synonym, $phenotype_value, $phenotype_uniquename, $phenotype_id, $phenotype_collect_date, $phenotype_operator, $phenotype_additional_info, $female_parent_name, $female_parent_id, $male_parent_name, $male_parent_id, $phenotype_external_references, $full_count, $notes, $intercrop_stock_id, $intercrop_stock_name, $rep_select, $block_number_select, $plot_number_select, $is_a_control_select, $row_number_select, $col_number_select, $plant_number) = $h->fetchrow_array()) {
my $timestamp_value;
my $operator_value;
if ($include_timestamp) {
Expand Down Expand Up @@ -712,6 +726,10 @@ sub search {
obsunit_type_name => $observationunit_type_name,
accession_uniquename => $germplasm_uniquename,
accession_stock_id => $germplasm_stock_id,
female_parent_name => $female_parent_name,
female_parent_id => $female_parent_id,
male_parent_name => $male_parent_name,
male_parent_id => $male_parent_id,
synonyms => $synonyms,
trial_id => $project_project_id,
trial_name => $project_name,
Expand Down
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