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fix javascript errors on trial details page #6107

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f38a01a
fix javascript errors on trial details page
ClayBirkett May 14, 2026
d3066bb
fix upload
ClayBirkett May 18, 2026
50d1840
fix upload
ClayBirkett May 18, 2026
4adb4df
fix some more javascript errors
ClayBirkett May 18, 2026
5117a4a
remove bad css files
ClayBirkett May 18, 2026
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76 changes: 36 additions & 40 deletions js/source/legacy/solGS/loadAcronyms.js
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Original file line number Diff line number Diff line change
Expand Up @@ -4,65 +4,61 @@
*
*/


var solGS = solGS || function solGS () {};

solGS.acronyms = {

loadAcronyms: function() {
var id;
var page = document.URL;
var id = page.match(/breeders\/trial\//)
? jQuery('#trial_id').val()
: jQuery('#training_pop_id').val();

if (page.match(/breeders\/trial\//)) {
id = jQuery('#trial_id').val();
} else {
id = jQuery('#training_pop_id').val();
}

var acros = jQuery.ajax({
return jQuery.ajax({
type : 'POST',
dataType: 'json',
data : {'id': id},
data : { id: id },
url : '/solgs/load/trait/acronyms/',
});

return acros;
},


displayAcronyms: function(data) {

var table = jQuery('#trait_acronyms_table').DataTable({
'searching' : false,
'ordering' : false,
'processing': true,
'paging' : false,
'info' : false,
});
if (!data || !data.length) return;

var table;
if (jQuery.fn.DataTable.isDataTable('#trait_acronyms_table')) {
table = jQuery('#trait_acronyms_table').DataTable();
} else {
table = jQuery('#trait_acronyms_table').DataTable({
searching : false,
ordering : false,
processing : true,
paging : false,
info : false,
});
}

table.rows.add(data).draw();
},

}

/////////////
}
////////////


jQuery(document).ready( function() {
jQuery('#trait_acronyms_div').show();

solGS.acronyms.loadAcronyms().done( function(res) {
solGS.acronyms.displayAcronyms(res.acronyms);
});

solGS.acronyms.loadAcronyms().fail( function(res) {
jQuery('#trait_acronyms_table').hide();
var errorMsg = 'Error occured loading acronyms';
showError: function() {
jQuery('#trait_acronyms_table').hide();
jQuery('#acronyms_message')
.html(errorMsg)
.html('Error occurred loading acronyms')
.show()
.fadeOut(50000);
});
.fadeOut(5000);
},
};

jQuery(document).ready(function() {
jQuery('#trait_acronyms_div').show();

solGS.acronyms.loadAcronyms()
.done(function(res) {
solGS.acronyms.displayAcronyms(res.acronyms);
})
.fail(function() {
solGS.acronyms.showError();
});
});
2 changes: 1 addition & 1 deletion lib/CXGN/Stock/Vector/ParseUpload/Plugin/VectorsGeneric.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ sub _validate_with_plugin {
file => $filename,
required_columns => ['uniquename'],
optional_columns => $editable_vector_stockprops,
unique_only_columns => {'uniquename' => 1},
unique_only_columns => ['uniquename'],
column_aliases => {
'uniquename' => ['Uniquename', 'Name', 'name', 'vector_name', 'vector name'],
'Strain' => ['strain'],
Expand Down
19 changes: 15 additions & 4 deletions lib/SGN/Controller/solGS/Trait.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -242,9 +242,20 @@ sub get_acronym_pairs {
$pop_id = $c->stash->{training_pop_id} if !$pop_id;
#$pop_id = $c->stash->{combo_pops_id} if !$pop_id;

my @acronym_pairs;
my $dir = $c->stash->{solgs_cache_dir};
opendir my $dh, $dir
or die "can't open $dir: $!\n";

if ( !defined $dir || !-d $dir ) {
print STDERR "solgs cache dir does not exists: $dir";
$c->stash->{acronym} = \@acronym_pairs;
return \@acronym_pairs;
}

opendir my $dh, $dir or do {
print STDERR "can not open $dir: $!";
$c->stash->{acronym} = \@acronym_pairs;
return \@acronym_pairs;
};

no warnings 'uninitialized';

Expand All @@ -256,8 +267,8 @@ sub get_acronym_pairs {
my @acronym_pairs;
if (-f $acronyms_file)
{
@acronym_pairs = map { [ split(/\t/) ] } read_file($acronyms_file, {binmode => ':utf8'});
shift(@acronym_pairs); # remove header;
@acronym_pairs = map { [ split(/\t/) ] } read_file($acronyms_file, {binmode => ':utf8'});
shift(@acronym_pairs); # remove header
}

@acronym_pairs = sort {uc $a->[0] cmp uc $b->[0] } @acronym_pairs;
Expand Down
30 changes: 20 additions & 10 deletions mason/breeders_toolbox/trial.mas
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Original file line number Diff line number Diff line change
Expand Up @@ -89,15 +89,25 @@ $project_id => undef
% $barcode_section_title = 'Generate barcode labels for plots or plants or accessions in this trial.';
% }

<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/v/bs4/jszip-2.5.0/dt-1.11.2/b-2.0.1/b-html5-2.0.1/b-print-2.0.1/fc-4.1.2/fh-3.1.9/r-2.2.9/sp-1.4.0/sl-1.3.3/datatables.min.css"/>
<script type="text/javascript" src="https://cdn.datatables.net/v/bs4/jszip-2.5.0/dt-1.11.2/b-2.0.1/b-html5-2.0.1/b-print-2.0.1/fc-4.1.2/fh-3.1.9/r-2.2.9/sp-1.4.0/sl-1.3.3/datatables.min.js"></script>
<script src="https://cdn.datatables.net/buttons/2.3.2/js/dataTables.buttons.min.js"></script>
<script src="https://cdn.datatables.net/buttons/2.3.2/js/buttons.print.min.js"></script>
<script src="https://cdn.datatables.net/select/1.5.0/js/dataTables.select.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.53/pdfmake.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.53/vfs_fonts.js"></script>
<script src="https://cdn.datatables.net/buttons/2.3.2/js/buttons.html5.min.js"></script>
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.11.2/css/dataTables.bootstrap4.min.css"/>

<script src="https://cdn.datatables.net/1.11.2/js/jquery.dataTables.min.js"></script>
<script src="https://cdn.datatables.net/1.11.2/js/dataTables.bootstrap4.min.js"></script>
<!-- JSZip and pdfmake must load before buttons.html5 -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.53/pdfmake.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.53/vfs_fonts.js"></script>
<!-- Buttons -->
<script src="https://cdn.datatables.net/buttons/2.3.2/js/dataTables.buttons.min.js"></script>
<script src="https://cdn.datatables.net/buttons/2.3.2/js/buttons.bootstrap4.min.js"></script>
<script src="https://cdn.datatables.net/buttons/2.3.2/js/buttons.html5.min.js"></script>
<script src="https://cdn.datatables.net/buttons/2.3.2/js/buttons.print.min.js"></script>

<script src="https://cdn.datatables.net/fixedcolumns/4.1.0/js/dataTables.fixedColumns.min.js"></script>
<script src="https://cdn.datatables.net/fixedheader/3.1.9/js/dataTables.fixedHeader.min.js"></script>
<script src="https://cdn.datatables.net/responsive/2.2.9/js/dataTables.responsive.min.js"></script>
<script src="https://cdn.datatables.net/searchpanes/1.4.0/js/dataTables.searchPanes.min.js"></script>
<script src="https://cdn.datatables.net/select/1.5.0/js/dataTables.select.min.js"></script>

<div class="row">
<div class="col-sm-6">
Expand Down Expand Up @@ -201,7 +211,7 @@ icon_class => "glyphicon glyphicon-list-alt", info_section_id => "trial_design_s
<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, info_section_title => "<h4 style='display:inline'>Compute New Phenotypes</h4>", info_section_subtitle => 'Compute derived traits or compute plot phenotypes from plant phenotypes.', icon_class => "glyphicon glyphicon-scale", info_section_id => "compute_derived_traits" &>

<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, info_section_title => "<h4 style='display:inline'>Phenotype Raw Data</h4>", info_section_subtitle => 'View phenotyping raw data.', info_section_id => "trial_raw_data", trial_name => $trial_name, site_project_name => $site_project_name, sgn_session_id => $sgn_session_id, user_name => $user_name, main_production_site_url => $main_production_site_url, trial_stock_type => $trial_stock_type, user_can_modify => $user_can_modify &>
<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, trial_name => $trial_name, site_projct_name => $site_project_name, sgn_session_id => $sgn_session_id, username=> $user_name, main_production_site_url => $main_production_site_url, trial_stock_type => $trial_stock_type, info_section_title => "<h4 style='display:inline'>Repetitive Measurements</h4>", info_section_subtitle => 'View a plot by repetitive measurements level', info_section_id => "repetitive_measurements_data", icon_class => "glyphicon glyphicon-repeat" &>
<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, trial_name => $trial_name, site_project_name => $site_project_name, sgn_session_id => $sgn_session_id, username=> $user_name, main_production_site_url => $main_production_site_url, trial_stock_type => $trial_stock_type, info_section_title => "<h4 style='display:inline'>Repetitive Measurements</h4>", info_section_subtitle => 'View a plot by repetitive measurements level', info_section_id => "repetitive_measurements_data", icon_class => "glyphicon glyphicon-repeat" &>
<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, info_section_title => "<h4 style='display:inline'>Phenotype Summary Statistics</h4>", info_section_subtitle => 'View and download uploaded phenotype data.', buttons_html => "<button class='btn btn-sm btn-primary' style='margin:3px' id='trial_download_phenotypes_button'>Download Trial Data</button>", icon_class => "glyphicon glyphicon-equalizer", info_section_id => "trial_detail_traits_assayed", has_expression_atlas => $has_expression_atlas, trial_name => $trial_name, expression_atlas_url => $expression_atlas_url, site_project_name => $site_project_name, sgn_session_id => $sgn_session_id, user_name => $user_name, main_production_site_url => $main_production_site_url, trial_stock_type => $trial_stock_type &>

<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, info_section_title => "<h4 style='display:inline'>Analysis Tools</h4>", info_section_subtitle => 'Run correlation, anova, population structure (PCA), or clustering. Also access HIDAP, if enabled on this site.', icon_class => "glyphicon glyphicon-signal", info_section_id => "trial_analysis_tools", hidap_enabled => $hidap_enabled, main_production_site_url => $main_production_site_url, breeding_program_name => $breeding_program_name, folder_name => $folder_name, trial_name => $trial_name &>
Expand Down
1 change: 1 addition & 0 deletions mason/breeders_toolbox/trial/repetitive_measurements_data.mas
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Expand Up @@ -5,6 +5,7 @@ $trial_stock_type => undef

<& /util/import_javascript.mas, classes => ['CXGN.BreedersToolbox.HTMLSelect', 'jquery.iframe-post-form', 'jszip-min', 'buttons.bootstrap-min', 'buttons.html5-min', 'jquery', 'jquery.dataTables', 'jquery.dataTables-select-min', 'd3.d3v4Min', 'd3.graphers.lineGraphRepetitiveValues', 'solGS.olsLine'] &>

<script src="https://unpkg.com/d3-regression@1.3.10/dist/d3-regression.min.js"></script>
<script>

const regression = d3.regressionLinear()
Expand Down
5 changes: 2 additions & 3 deletions mason/breeders_toolbox/trial/trial_nirs_data.mas
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,8 @@ $stockref => undef
</%args>

<script src="https://cdn.jsdelivr.net/npm/chart.js"></script>
<script src="/js/source/legacy/d3/graphers/nirsDataLineGraph.js"></script>

<& /util/import_javascript.mas, classes => [ 'jquery', 'thickbox', 'jquery.dataTables', 'd3.graphers.nirsDataLineGraph.js', 'd3.d3v4Min' ] &>
<& /util/import_javascript.mas, classes => [ 'jquery', 'thickbox', 'jquery.dataTables', 'jquery.dataTables-buttons-min', 'd3.graphers.nirsDataLineGraph.js', 'd3.d3v4Min' ] &>

<style>
#nirs_spectra_table tbody tr {
Expand Down Expand Up @@ -346,4 +345,4 @@ jQuery(document).ready(function() {
});


</script>
</script>
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