From 9c3477aa5af29cdaddef8b78668b125a449182cf Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Wed, 4 Feb 2026 12:18:09 -0500
Subject: [PATCH 01/18] Allow spatial layout uploads even after layout already
 uploaded. Cleanup deletion dialog

---
 js/source/legacy/CXGN/Trial.js                     | 12 ++++++++----
 mason/breeders_toolbox/trial.mas                   |  4 ++--
 mason/breeders_toolbox/trial/phenotype_heatmap.mas |  7 -------
 mason/breeders_toolbox/trial/trial_coords.mas      |  6 ------
 4 files changed, 10 insertions(+), 19 deletions(-)

diff --git a/js/source/legacy/CXGN/Trial.js b/js/source/legacy/CXGN/Trial.js
index 2980c91a4b..61ae077d71 100644
--- a/js/source/legacy/CXGN/Trial.js
+++ b/js/source/legacy/CXGN/Trial.js
@@ -221,10 +221,10 @@ function delete_field_map() {
 	     jQuery('#working_modal').modal("hide");
 
       if (response.error) {
-		      alert("Error Deleting Field Map: "+response.error);
+		      alert("Error deleting field map: "+response.error);
       } else {
-          //alert("Field map deletion Successful...");
-		      jQuery('#delete_field_map_dialog_message').dialog("open");
+              alert("Field map deletion successful.");
+		      location.reload();
           }
 	 },
 	 error: function () {
@@ -493,7 +493,11 @@ delete_field_map();
 
 
 jQuery('#delete_field_map_hm_link').click(function () {
-    jQuery('#delete_field_map_dialog').dialog("open");
+    if (confirm("Are you sure you want to delete the spatial layout of this trial?")) {
+        delete_field_map();
+    } else {
+        return;
+    }
 });
 
 jQuery("#delete_field_map_dialog_message").dialog({
diff --git a/mason/breeders_toolbox/trial.mas b/mason/breeders_toolbox/trial.mas
index c73c5c75e0..f19869e230 100644
--- a/mason/breeders_toolbox/trial.mas
+++ b/mason/breeders_toolbox/trial.mas
@@ -171,9 +171,9 @@ $project_id => undef
 % my $subtitle = 'View and edit the spatial layout of the experiment. Also view a heatmap for phenotyped traits.';
 % my $layout_buttons = '';
 % if ($has_col_and_row_numbers){
-%     $layout_buttons = '<h3><span class="glyphicon glyphicon-ok-sign text-success"></span>&nbsp;&nbsp;&nbsp;This experiment has spatial layout info uploaded!</h3><button class="btn btn-primary" style="margin:3px" id="edit_field_map_link">Edit Field Layout</button><button class="btn btn-primary" style="margin:3px" id="trial_fieldmap_download_layout_button">Download Spatial Layout</button> <button class="btn btn-primary" style="margin:3px" id="gps_field_map_link">Edit Geo Field Layout</button><button class="btn btn-primary" style="margin:3px" id="calculate_spatial_correction">Calculate Spatial Correction</button><button class="btn btn-danger" id="delete_field_map_hm_link" style="margin:3px">Delete Spatial Layout</button> <button class="btn btn-default" style="margin:3px" data-toggle="modal" data-target="#fieldmap_usage_modal">Usage Help <span class="glyphicon glyphicon-question-sign"></span></button>';
+%     $layout_buttons = '<h3><span class="glyphicon glyphicon-ok-sign text-success"></span>&nbsp;&nbsp;&nbsp;This experiment has spatial layout info uploaded!</h3><button class="btn btn-primary" style="margin:3px" id="heatmap_upload_trial_coords_link">Upload Spatial Layout</button><button class="btn btn-primary" style="margin:3px" id="edit_field_map_link">Edit Field Layout</button><button class="btn btn-primary" style="margin:3px" id="trial_fieldmap_download_layout_button">Download Spatial Layout</button> <button class="btn btn-primary" style="margin:3px" id="gps_field_map_link">Edit Geo Field Layout</button><button class="btn btn-primary" style="margin:3px" id="calculate_spatial_correction">Calculate Spatial Correction</button><button class="btn btn-danger" id="delete_field_map_hm_link" style="margin:3px">Delete Spatial Layout</button> <button class="btn btn-default" style="margin:3px" data-toggle="modal" data-target="#fieldmap_usage_modal">Usage Help <span class="glyphicon glyphicon-question-sign"></span></button>';
 % } else {
-%    $layout_buttons = '<h3><span class="glyphicon glyphicon-remove-sign text-danger"></span>&nbsp;&nbsp;&nbsp;This experiment does not have spatial layout info!</h3><button class="btn btn-primary" style="margin:3px" id="heatmap_upload_trial_coords_link">Upload Spatial Layout</button> <button class="btn btn-primary" style="margin:3px" id="edit_field_map_link">Edit Field Layout</button> <button class="btn btn-default" style="margin:3px" data-toggle="modal" data-target="#fieldmap_usage_modal">Usage Help <span class="glyphicon glyphicon-question-sign"></span></button>';
+%    $layout_buttons = '<h3><span class="glyphicon glyphicon-remove-sign text-danger"></span>&nbsp;&nbsp;&nbsp;This experiment does not have spatial layout info!</h3><button class="btn btn-primary" style="margin:3px" id="heatmap_upload_trial_coords_link">Upload Spatial Layout</button><button class="btn btn-primary" style="margin:3px" id="edit_field_map_link">Edit Field Layout</button> <button class="btn btn-default" style="margin:3px" data-toggle="modal" data-target="#fieldmap_usage_modal">Usage Help <span class="glyphicon glyphicon-question-sign"></span></button>';
 % }
 
 % my $design_section_buttons = '';
diff --git a/mason/breeders_toolbox/trial/phenotype_heatmap.mas b/mason/breeders_toolbox/trial/phenotype_heatmap.mas
index 04dc9140bb..0f0b34f5f5 100644
--- a/mason/breeders_toolbox/trial/phenotype_heatmap.mas
+++ b/mason/breeders_toolbox/trial/phenotype_heatmap.mas
@@ -341,13 +341,6 @@ $trial_stock_type => undef
 </div> -->
 
 
-<div id="delete_field_map_dialog_message" title="Physical Field Map Deletion" style="display:none;">
-   <p>
-       <span class="ui-icon ui-icon-circle-check" style="float: left; margin: 0 7px 50px 0;"></span>
-       The field coordinates were deleted successfully...
-   </p>
-</div>
-
 <div id="delete_field_map_dialog" title="Physical Field Map Deletion" style="display:none;">
    <div id="trait_list_dc" name="trait_list">
        <label id="trait_list_label_dc" for="trait_list_list_select" style="display: inline-block; width: 300px;">Please, confirm field map deletion... <br />
diff --git a/mason/breeders_toolbox/trial/trial_coords.mas b/mason/breeders_toolbox/trial/trial_coords.mas
index fe23f184b1..19fbeac6dc 100644
--- a/mason/breeders_toolbox/trial/trial_coords.mas
+++ b/mason/breeders_toolbox/trial/trial_coords.mas
@@ -308,12 +308,6 @@ var trial_id = <% $trial_id %>;
 
 </script>
 
-<div id="delete_field_map_dialog_message" title="Physical Field Map Deletion" style="display:none;">
-   <p>
-       <span class="ui-icon ui-icon-circle-check" style="float: left; margin: 0 7px 50px 0;"></span>
-       The field coordinates were deleted successfully...
-   </p>
-</div>
 
 <div id="delete_field_map_dialog" title="Physical Field Map Deletion" style="display:none;">
    <div id="trait_list_dc" name="trait_list">

From 4da8fa859c08eda8d1eeab50edbf020e5e7e0489 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Fri, 13 Feb 2026 08:08:20 -0500
Subject: [PATCH 02/18] Add generic file parser for spatial layout

---
 js/source/legacy/CXGN/Trial.js                |  71 ++++---
 .../Plugin/TrialSpatialLayoutGeneric.pm       | 197 ++++++++++++++++++
 lib/SGN/Controller/AJAX/TrialMetadata.pm      |  77 +++++--
 3 files changed, 296 insertions(+), 49 deletions(-)
 create mode 100644 lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm

diff --git a/js/source/legacy/CXGN/Trial.js b/js/source/legacy/CXGN/Trial.js
index 61ae077d71..24c0c9463d 100644
--- a/js/source/legacy/CXGN/Trial.js
+++ b/js/source/legacy/CXGN/Trial.js
@@ -639,34 +639,53 @@ jQuery(document).ready(function ($) {
          $("#trial_coord_upload_spreadsheet_info_dialog" ).modal("show");
     });
 
-     $('#upload_trial_coordinates_form').iframePostForm({
-	json: true,
-	post: function () {
-            var uploadedtrialcoordFile = $("#trial_coordinates_uploaded_file").val();
-	    $('#working_modal').modal("show");
-            if (uploadedtrialcoordFile === '') {
-		$('#working_modal').modal("hide");
-		alert("No file selected");
-            }
-	},
-	complete: function (response) {
-	    $('#working_modal').modal("hide");
-            if (response.error_string) {
-		$("#upload_trial_coord_error_display tbody").html('');
-		$("#upload_trial_coord_error_display tbody").append(response.error_string);
-        jQuery('#upload_trial_coord_error_display').modal('show');
+    $('#upload_trial_coordinates_form').iframePostForm({
+        json: true,
+        post: function () {
+                var uploadedtrialcoordFile = $("#trial_coordinates_uploaded_file").val();
+            $('#working_modal').modal("show");
+                if (uploadedtrialcoordFile === '') {
+            $('#working_modal').modal("hide");
+            alert("No file selected");
+                }
+        },
+        complete: function (response) {
+            $('#working_modal').modal("hide");
+
+            try {
+                // Check if response exists and is valid
+                if (!response) {
+                    alert("Error: No response received from server. Please try again.");
+                    return;
+                }
 
-		return;
-            }
-            if (response.error) {
-		alert(response.error);
-		return;
-            }
-            if (response.success) {
-		$('#trial_coord_upload_success_dialog_message').modal("show");
-		//alert("File uploaded successfully");
+                if (response.error_string) {
+                    $("#upload_trial_coord_error_display tbody").html('');
+                    $("#upload_trial_coord_error_display tbody").append(response.error_string);
+                    jQuery('#upload_trial_coord_error_display').modal('show');
+                    return;
+                }
+
+                if (response.error) {
+                    alert(response.error);
+                    return;
+                }
+
+                if (response.success) {
+                    $('#trial_coord_upload_success_dialog_message').modal("show");
+                    //alert("File uploaded successfully");
+                    return;
+                }
+
+                // Catch-all for unexpected responses
+                console.error("Unexpected server response:", response);
+                alert("An unexpected error occurred. The server response was not in the expected format. Please check the console for details or contact support.");
+
+            } catch (e) {
+                console.error("Error processing server response:", e);
+                alert("An error occurred while processing the server response: " + e.message);
             }
-	}
+        }
     });
 
 	function upload_trial_coord_file() {
diff --git a/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm b/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm
new file mode 100644
index 0000000000..84ea09255b
--- /dev/null
+++ b/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm
@@ -0,0 +1,197 @@
+package CXGN::Trial::ParseUpload::Plugin::TrialSpatialLayoutGeneric;
+
+use Moose::Role;
+use List::MoreUtils qw(uniq);
+use CXGN::File::Parse;
+use SGN::Model::Cvterm;
+use CXGN::List::Validate;
+use CXGN::Stock;
+
+my @REQUIRED_COLUMNS = qw|plot_name row_number col_number|;
+my @OPTIONAL_COLUMNS = qw||;
+# Any additional columns are unsupported and will return an error
+
+sub _validate_with_plugin {
+    my $self = shift;
+    my $filename = $self->get_filename();
+    my $schema = $self->get_chado_schema();
+
+    # List validator
+    my $validator = CXGN::List::Validate->new();
+
+    # Encountered Error and Warning Messages
+    my %errors;
+    my @error_messages;
+    my %warnings;
+    my @warning_messages;
+
+    # Read and parse the upload file
+    my $parser = CXGN::File::Parse->new(
+        file => $filename,
+        required_columns => \@REQUIRED_COLUMNS,
+        optional_columns => \@OPTIONAL_COLUMNS
+    );
+    my $parsed = $parser->parse();
+    my $parsed_errors = $parsed->{'errors'};
+    my $parsed_data = $parsed->{'data'};
+    my $parsed_values = $parsed->{'values'};
+    my $additional_columns = $parsed->{'additional_columns'};
+
+    # Return file parsing errors
+    if ( $parsed_errors && scalar(@$parsed_errors) > 0 ) {
+        $errors{'error_messages'} = $parsed_errors;
+        $self->_set_parse_errors(\%errors);
+        return;
+    }
+
+    # Unsupported column headers
+    if ( $additional_columns && scalar(@$additional_columns) > 0 ) {
+        $errors{'error_messages'} = [ 'The following column headers are not supported: ' . join(', ', @$additional_columns) ];
+        $self->_set_parse_errors(\%errors);
+        return;
+    }
+
+    # Maps to track row/col positions
+    my %seen_positions;    # check that each row_number/col_number pair is used only once
+
+    foreach my $data (@$parsed_data) {
+        my $row = $data->{'_row'};
+        my $plot_name = $data->{'plot_name'};
+        my $row_number = $data->{'row_number'};
+        my $col_number = $data->{'col_number'};
+
+        # Row Number: must be a positive integer
+        if (!($row_number =~ /^\d+?$/)) {
+            push @error_messages, "Row $row: row_number <strong>$row_number</strong> must be a positive integer.";
+        }
+
+        # Col Number: must be a positive integer
+        if (!($col_number =~ /^\d+?$/)) {
+            push @error_messages, "Row $row: col_number <strong>$col_number</strong> must be a positive integer.";
+        }
+
+        # Track row/col positions to check for duplicates
+        my $position_key = "$row_number-$col_number";
+        if ( !exists $seen_positions{$position_key} ) {
+            $seen_positions{$position_key} = [$plot_name];
+        }
+        else {
+            push @{$seen_positions{$position_key}}, $plot_name;
+        }
+    }
+
+    # Plot Names: must exist in the database as plots
+    my $plot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot', 'stock_type')->cvterm_id();
+    my @plot_names = @{$parsed_values->{'plot_name'}};
+    my @missing_plots;
+    my %plot_trial_map;  # map of plot_name => trial_id
+
+    foreach my $plot_name (@plot_names) {
+        my $rs = $schema->resultset("Stock::Stock")->search({
+            'me.uniquename' => $plot_name,
+            'me.type_id' => $plot_cvterm_id,
+            'me.is_obsolete' => { '!=' => 't' }
+        });
+
+        if ($rs->count() == 0) {
+            push @missing_plots, $plot_name;
+        }
+        else {
+            # Get the trial that this plot belongs to
+            my $plot_stock = $rs->first();
+            my $plot_id = $plot_stock->stock_id();
+
+            # Get trial from plot
+            my $plot_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot_of', 'stock_relationship')->cvterm_id();
+            my $project_rs = $schema->resultset("Project::Project")->search({
+                'nd_experiment_stocks.stock_id' => $plot_id,
+                'nd_experiment_projects.nd_experiment_id' => { -ident => 'nd_experiment_stocks.nd_experiment_id' }
+            }, {
+                join => { 'nd_experiment_projects' => { 'nd_experiment' => 'nd_experiment_stocks' } }
+            });
+
+            if ($project_rs->count() > 0) {
+                my $trial = $project_rs->first();
+                my $trial_id = $trial->project_id();
+                $plot_trial_map{$plot_name} = $trial_id;
+            }
+        }
+    }
+
+    # Report missing plots
+    if (scalar(@missing_plots) > 0) {
+        push @error_messages, "Plot name(s) <strong>".join(', ',@missing_plots)."</strong> do not exist in the database as plots.";
+    }
+
+    # Check that all plots belong to the same trial
+    my @trial_ids = uniq values %plot_trial_map;
+    if (scalar(@trial_ids) > 1) {
+        push @error_messages, "All plots must belong to the same trial. Found plots from multiple trials.";
+    }
+    elsif (scalar(@trial_ids) == 0 && scalar(@missing_plots) == 0) {
+        push @error_messages, "Could not determine trial for the provided plots.";
+    }
+
+    # Check for unique row/col positions
+    foreach my $position_key (keys %seen_positions) {
+        my $plots = $seen_positions{$position_key};
+        my $count = scalar(@$plots);
+        if ( $count > 1 ) {
+            my @pos = split('-', $position_key);
+            push @error_messages, "Position row=" . $pos[0] . " col=" . $pos[1] . " is assigned to multiple plots: <strong>" . join(', ', @$plots) . "</strong>. Each position can only be occupied once.";
+        }
+    }
+
+    if (scalar(@error_messages) >= 1) {
+        $errors{'error_messages'} = \@error_messages;
+        $self->_set_parse_errors(\%errors);
+        return;
+    }
+
+    $self->_set_validated_data($parsed);
+    return 1; #returns true if validation is passed
+}
+
+sub _parse_with_plugin {
+    my $self = shift;
+    my $schema = $self->get_chado_schema();
+    my $parsed = $self->_get_validated_data();
+    my $data = $parsed->{'data'};
+
+    # Get plot stock type cvterm
+    my $plot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot', 'stock_type')->cvterm_id();
+
+    my %spatial_layout_data;
+
+    foreach my $d (@$data) {
+        my $plot_name = $d->{'plot_name'};
+        my $row_number = $d->{'row_number'};
+        my $col_number = $d->{'col_number'};
+
+        # Get plot stock_id from plot_name
+        my $rs = $schema->resultset("Stock::Stock")->search({
+            'uniquename' => $plot_name,
+            'type_id' => $plot_cvterm_id,
+            'is_obsolete' => { '!=' => 't' }
+        });
+
+        if ($rs->count() > 0) {
+            my $plot_stock = $rs->first();
+            my $plot_id = $plot_stock->stock_id();
+
+            # Store the spatial layout information
+            $spatial_layout_data{$plot_id} = {
+                plot_name => $plot_name,
+                row_number => $row_number,
+                col_number => $col_number
+            };
+        }
+    }
+
+
+    $self->_set_parsed_data(\%spatial_layout_data);
+
+    return 1;
+}
+
+1;
diff --git a/lib/SGN/Controller/AJAX/TrialMetadata.pm b/lib/SGN/Controller/AJAX/TrialMetadata.pm
index 8117f014e2..2cffc0aa17 100644
--- a/lib/SGN/Controller/AJAX/TrialMetadata.pm
+++ b/lib/SGN/Controller/AJAX/TrialMetadata.pm
@@ -39,6 +39,7 @@ use List::Util qw(max);
 use CXGN::Trial::TrialLayout;
 use CXGN::BreedersToolbox::Projects;
 use Sort::Key::Natural qw(natkeysort);
+use CXGN::Trial::ParseUpload;
 
 
 BEGIN { extends 'Catalyst::Controller::REST' }
@@ -3678,36 +3679,66 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
     $md5 = $uploader->get_md5($archived_filename_with_path);
     unlink $upload_tempfile;
 
-    my $error_string = '';
-   # open file and remove return of line
-    open(my $F, "< :encoding(UTF-8)", $archived_filename_with_path) || die "Can't open archive file $archived_filename_with_path";
+#     my $error_string = '';
+#    # open file and remove return of line
+#     open(my $F, "< :encoding(UTF-8)", $archived_filename_with_path) || die "Can't open archive file $archived_filename_with_path";
+#     my $schema = $c->dbic_schema("Bio::Chado::Schema", undef, $user_id);
+#     my $header = <$F>;
+#     while (<$F>) {
+#     	chomp;
+#     	$_ =~ s/\r//g;
+#     	my ($plot,$row,$col) = split /\t/ ;
+#     	my $rs = $schema->resultset("Stock::Stock")->search({uniquename=> $plot });
+#     	if ($rs->count()== 1) {
+#       	my $r =  $rs->first();
+#       	print STDERR "The plots $plot was found.\n Loading row $row col $col\n";
+#       	$r->create_stockprops({row_number => $row, col_number => $col});
+#       }
+#       else {
+#       	print STDERR "WARNING! $plot was not found in the database.\n";
+#         $error_string .= "WARNING! $plot was not found in the database.";
+#       }
+#     }
+
+#     if ($error_string){
+#         $c->stash->{rest} = {error_string => $error_string};
+#         $c->detach();
+#     }
+
     my $schema = $c->dbic_schema("Bio::Chado::Schema", undef, $user_id);
-    my $header = <$F>;
-    while (<$F>) {
-    	chomp;
-    	$_ =~ s/\r//g;
-    	my ($plot,$row,$col) = split /\t/ ;
-    	my $rs = $schema->resultset("Stock::Stock")->search({uniquename=> $plot });
-    	if ($rs->count()== 1) {
-      	my $r =  $rs->first();
-      	print STDERR "The plots $plot was found.\n Loading row $row col $col\n";
-      	$r->create_stockprops({row_number => $row, col_number => $col});
-      }
-      else {
-      	print STDERR "WARNING! $plot was not found in the database.\n";
-        $error_string .= "WARNING! $plot was not found in the database.";
-      }
-    }
 
-    if ($error_string){
-        $c->stash->{rest} = {error_string => $error_string};
-        $c->detach();
+    my $parser = CXGN::Trial::ParseUpload->new({
+        chado_schema => $schema,
+        trial_id => $trial_id,
+        filename => $archived_filename_with_path
+    });
+    $parser->load_plugin('TrialSpatialLayoutGeneric');
+
+    my $parsed_data = $parser->parse();
+
+    if (!$parsed_data || $parser->has_parse_errors()) {
+        my $return_error = '';
+
+        if (! $parser->has_parse_errors() ){
+            $return_error = "Parsing failed, but we could not get parsing errors...";
+            $c->stash->{rest} = {error_string => $return_error,};
+        }
+        else {
+            my $parse_errors = $parser->get_parse_errors();
+
+            foreach my $error_string (@{$parse_errors->{'error_messages'}}){
+                $return_error=$return_error.$error_string."<br>";
+            }
+        }
+
+        $c->stash->{rest} = {error_string => $return_error};
+        return;
     }
 
     my $dbh = $c->dbc->dbh();
     my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );
     my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'phenotypes', 'concurrent', $c->config->{basepath});
-    my $trial_layout = CXGN::Trial::TrialLayout->new({ schema => $c->dbic_schema("Bio::Chado::Schema", undef, $user_id), trial_id => $trial_id, experiment_type => 'field_layout' });
+    my $trial_layout = CXGN::Trial::TrialLayout->new({ schema => $schema, trial_id => $trial_id, experiment_type => 'field_layout' });
     $trial_layout->generate_and_cache_layout();
 
     $c->stash->{rest} = {success => 1};

From 6e60699c092673f44a5d5453aeec631573b8a78f Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Fri, 13 Feb 2026 09:23:05 -0500
Subject: [PATCH 03/18] Finish up generic upload error handling

---
 js/source/legacy/CXGN/Trial.js                | 58 +++++++---------
 .../Plugin/TrialSpatialLayoutGeneric.pm       | 66 +++++++------------
 lib/SGN/Controller/AJAX/TrialMetadata.pm      | 45 +++++--------
 3 files changed, 66 insertions(+), 103 deletions(-)

diff --git a/js/source/legacy/CXGN/Trial.js b/js/source/legacy/CXGN/Trial.js
index 24c0c9463d..db3b53e14e 100644
--- a/js/source/legacy/CXGN/Trial.js
+++ b/js/source/legacy/CXGN/Trial.js
@@ -642,49 +642,39 @@ jQuery(document).ready(function ($) {
     $('#upload_trial_coordinates_form').iframePostForm({
         json: true,
         post: function () {
-                var uploadedtrialcoordFile = $("#trial_coordinates_uploaded_file").val();
+            var uploadedtrialcoordFile = $("#trial_coordinates_uploaded_file").val();
             $('#working_modal').modal("show");
-                if (uploadedtrialcoordFile === '') {
-            $('#working_modal').modal("hide");
-            alert("No file selected");
-                }
+            if (uploadedtrialcoordFile === '') {
+                $('#working_modal').modal("hide");
+                alert("No file selected");
+            }
         },
         complete: function (response) {
             $('#working_modal').modal("hide");
 
-            try {
-                // Check if response exists and is valid
-                if (!response) {
-                    alert("Error: No response received from server. Please try again.");
-                    return;
-                }
-
-                if (response.error_string) {
-                    $("#upload_trial_coord_error_display tbody").html('');
-                    $("#upload_trial_coord_error_display tbody").append(response.error_string);
-                    jQuery('#upload_trial_coord_error_display').modal('show');
-                    return;
-                }
+            // Check if response exists and is valid
+            if (!response || typeof response !== 'object') {
+                alert("Error: No response received from server. Please try again.");
+                return;
+            }
 
-                if (response.error) {
-                    alert(response.error);
-                    return;
-                }
+            if (response.error) {
+                $("#upload_trial_coord_error_display tbody").html('');
+                $("#upload_trial_coord_error_display tbody").append(response.error);
+                jQuery('#upload_trial_coord_error_display').modal('show');
+                return;
+            }
 
-                if (response.success) {
-                    $('#trial_coord_upload_success_dialog_message').modal("show");
-                    //alert("File uploaded successfully");
-                    return;
-                }
+            if (response.success) {
+                $('#trial_coord_upload_success_dialog_message').modal("show");
+                //alert("File uploaded successfully");
+                return;
+            }
 
-                // Catch-all for unexpected responses
-                console.error("Unexpected server response:", response);
-                alert("An unexpected error occurred. The server response was not in the expected format. Please check the console for details or contact support.");
+            // Catch-all for unexpected responses
+            console.error("Unexpected server response:", response);
+            alert("An unexpected error occurred. The server response was not in the expected format. Please check the console for details or contact support.");
 
-            } catch (e) {
-                console.error("Error processing server response:", e);
-                alert("An error occurred while processing the server response: " + e.message);
-            }
         }
     });
 
diff --git a/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm b/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm
index 84ea09255b..e88b9463ea 100644
--- a/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm
+++ b/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm
@@ -6,6 +6,7 @@ use CXGN::File::Parse;
 use SGN::Model::Cvterm;
 use CXGN::List::Validate;
 use CXGN::Stock;
+use CXGN::Project;
 
 my @REQUIRED_COLUMNS = qw|plot_name row_number col_number|;
 my @OPTIONAL_COLUMNS = qw||;
@@ -15,6 +16,7 @@ sub _validate_with_plugin {
     my $self = shift;
     my $filename = $self->get_filename();
     my $schema = $self->get_chado_schema();
+    my $trial_id = $self->get_trial_id();
 
     # List validator
     my $validator = CXGN::List::Validate->new();
@@ -80,43 +82,9 @@ sub _validate_with_plugin {
         }
     }
 
-    # Plot Names: must exist in the database as plots
-    my $plot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot', 'stock_type')->cvterm_id();
+    # Plots must exist
     my @plot_names = @{$parsed_values->{'plot_name'}};
-    my @missing_plots;
-    my %plot_trial_map;  # map of plot_name => trial_id
-
-    foreach my $plot_name (@plot_names) {
-        my $rs = $schema->resultset("Stock::Stock")->search({
-            'me.uniquename' => $plot_name,
-            'me.type_id' => $plot_cvterm_id,
-            'me.is_obsolete' => { '!=' => 't' }
-        });
-
-        if ($rs->count() == 0) {
-            push @missing_plots, $plot_name;
-        }
-        else {
-            # Get the trial that this plot belongs to
-            my $plot_stock = $rs->first();
-            my $plot_id = $plot_stock->stock_id();
-
-            # Get trial from plot
-            my $plot_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot_of', 'stock_relationship')->cvterm_id();
-            my $project_rs = $schema->resultset("Project::Project")->search({
-                'nd_experiment_stocks.stock_id' => $plot_id,
-                'nd_experiment_projects.nd_experiment_id' => { -ident => 'nd_experiment_stocks.nd_experiment_id' }
-            }, {
-                join => { 'nd_experiment_projects' => { 'nd_experiment' => 'nd_experiment_stocks' } }
-            });
-
-            if ($project_rs->count() > 0) {
-                my $trial = $project_rs->first();
-                my $trial_id = $trial->project_id();
-                $plot_trial_map{$plot_name} = $trial_id;
-            }
-        }
-    }
+    my @missing_plots = @{$validator->validate($schema, 'plots', \@plot_names)->{'missing'}};
 
     # Report missing plots
     if (scalar(@missing_plots) > 0) {
@@ -124,12 +92,23 @@ sub _validate_with_plugin {
     }
 
     # Check that all plots belong to the same trial
-    my @trial_ids = uniq values %plot_trial_map;
-    if (scalar(@trial_ids) > 1) {
-        push @error_messages, "All plots must belong to the same trial. Found plots from multiple trials.";
+    my $trial = CXGN::Project->new({
+        bcs_schema => $schema,
+        trial_id => $trial_id
+    });
+
+    my %trial_plots = map {$_->[1] => 1} @{$trial->get_plots()};
+
+    my @mismatched_plots;
+
+    foreach my $plot (@plot_names) {
+        if (!defined($trial_plots{$plot})) {
+            push @mismatched_plots, $plot;
+        }
     }
-    elsif (scalar(@trial_ids) == 0 && scalar(@missing_plots) == 0) {
-        push @error_messages, "Could not determine trial for the provided plots.";
+
+    if (scalar(@mismatched_plots) > 0) {
+        push @error_messages, "All plots must belong to ".$trial->get_name().". ";
     }
 
     # Check for unique row/col positions
@@ -189,7 +168,10 @@ sub _parse_with_plugin {
     }
 
 
-    $self->_set_parsed_data(\%spatial_layout_data);
+    $self->_set_parsed_data({
+        trial_id => $self->get_trial_id(),
+        spatial_layout => \%spatial_layout_data
+    });
 
     return 1;
 }
diff --git a/lib/SGN/Controller/AJAX/TrialMetadata.pm b/lib/SGN/Controller/AJAX/TrialMetadata.pm
index 2cffc0aa17..51b5da3351 100644
--- a/lib/SGN/Controller/AJAX/TrialMetadata.pm
+++ b/lib/SGN/Controller/AJAX/TrialMetadata.pm
@@ -3679,32 +3679,6 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
     $md5 = $uploader->get_md5($archived_filename_with_path);
     unlink $upload_tempfile;
 
-#     my $error_string = '';
-#    # open file and remove return of line
-#     open(my $F, "< :encoding(UTF-8)", $archived_filename_with_path) || die "Can't open archive file $archived_filename_with_path";
-#     my $schema = $c->dbic_schema("Bio::Chado::Schema", undef, $user_id);
-#     my $header = <$F>;
-#     while (<$F>) {
-#     	chomp;
-#     	$_ =~ s/\r//g;
-#     	my ($plot,$row,$col) = split /\t/ ;
-#     	my $rs = $schema->resultset("Stock::Stock")->search({uniquename=> $plot });
-#     	if ($rs->count()== 1) {
-#       	my $r =  $rs->first();
-#       	print STDERR "The plots $plot was found.\n Loading row $row col $col\n";
-#       	$r->create_stockprops({row_number => $row, col_number => $col});
-#       }
-#       else {
-#       	print STDERR "WARNING! $plot was not found in the database.\n";
-#         $error_string .= "WARNING! $plot was not found in the database.";
-#       }
-#     }
-
-#     if ($error_string){
-#         $c->stash->{rest} = {error_string => $error_string};
-#         $c->detach();
-#     }
-
     my $schema = $c->dbic_schema("Bio::Chado::Schema", undef, $user_id);
 
     my $parser = CXGN::Trial::ParseUpload->new({
@@ -3731,7 +3705,24 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
             }
         }
 
-        $c->stash->{rest} = {error_string => $return_error};
+        $c->stash->{rest} = {error => $return_error};
+        return;
+    }
+
+    # store all row/column data here
+    eval {
+        foreach my $plot_id (keys(%{$parsed_data->{spatial_layout}})) {
+            my $plot_name = $parsed_data->{spatial_layout}->{$plot_id}->{plot_name};
+            my $row = $parsed_data->{spatial_layout}->{$plot_id}->{row_number};
+            my $col = $parsed_data->{spatial_layout}->{$plot_id}->{col_number};
+
+            my $rs = $schema->resultset("Stock::Stock")->search({uniquename=> $plot_name });
+            my $r = $rs->first();
+            $r->create_stockprops({row_number => $row, col_number => $col});
+        }
+    };
+    if ($@) {
+        $c->stash->{rest} = {error => "The upload was successful, but an error occurred trying to save the row and column data: $@\n"};
         return;
     }
 

From ec979db52a6c9cecb84f94b861236d1f3f23e02e Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Fri, 13 Feb 2026 10:58:29 -0500
Subject: [PATCH 04/18] Add job recording for spatial layout upload

---
 lib/CXGN/Job.pm                          |  2 +-
 lib/SGN/Controller/AJAX/TrialMetadata.pm | 31 +++++++++++++++++++++++-
 2 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/lib/CXGN/Job.pm b/lib/CXGN/Job.pm
index 04f0b0de1e..9c717f617c 100644
--- a/lib/CXGN/Job.pm
+++ b/lib/CXGN/Job.pm
@@ -217,7 +217,7 @@ The command submitted to be run.
 
 =cut
 
-has 'cmd' => (isa => 'Str', is => 'rw');
+has 'cmd' => (isa => 'Maybe[Str]', is => 'rw');
 
 =head2 logfile()
 
diff --git a/lib/SGN/Controller/AJAX/TrialMetadata.pm b/lib/SGN/Controller/AJAX/TrialMetadata.pm
index 51b5da3351..addfebf726 100644
--- a/lib/SGN/Controller/AJAX/TrialMetadata.pm
+++ b/lib/SGN/Controller/AJAX/TrialMetadata.pm
@@ -40,6 +40,7 @@ use CXGN::Trial::TrialLayout;
 use CXGN::BreedersToolbox::Projects;
 use Sort::Key::Natural qw(natkeysort);
 use CXGN::Trial::ParseUpload;
+use CXGN::Job;
 
 
 BEGIN { extends 'Catalyst::Controller::REST' }
@@ -3681,6 +3682,25 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
 
     my $schema = $c->dbic_schema("Bio::Chado::Schema", undef, $user_id);
 
+    my $trial_obj = CXGN::Project->new({
+        bcs_schema => $schema,
+        trial_id => $trial_id
+    });
+
+    my $job = CXGN::Job->new({
+        sp_person_id => $user_id,
+        schema => $schema,
+        people_schema => $c->dbic_schema("CXGN::People::Schema"),
+        name => $trial_obj->get_name()." spatial layout upload",
+        job_type => 'upload',
+        cmd => "",
+        finish_logfile => $c->config->{job_finish_log},
+        submit_page =>  $c->request->headers->referer,
+        results_page =>  $c->request->headers->referer
+    });
+
+    $job->update_status("submitted");
+
     my $parser = CXGN::Trial::ParseUpload->new({
         chado_schema => $schema,
         trial_id => $trial_id,
@@ -3695,7 +3715,6 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
 
         if (! $parser->has_parse_errors() ){
             $return_error = "Parsing failed, but we could not get parsing errors...";
-            $c->stash->{rest} = {error_string => $return_error,};
         }
         else {
             my $parse_errors = $parser->get_parse_errors();
@@ -3706,6 +3725,10 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
         }
 
         $c->stash->{rest} = {error => $return_error};
+        $job->additional_args({
+            error => $return_error
+        });
+        $job->update_status("failed");
         return;
     }
 
@@ -3723,6 +3746,10 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
     };
     if ($@) {
         $c->stash->{rest} = {error => "The upload was successful, but an error occurred trying to save the row and column data: $@\n"};
+        $job->additional_args({
+            error => $@
+        });
+        $job->update_status("failed");
         return;
     }
 
@@ -3732,6 +3759,8 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
     my $trial_layout = CXGN::Trial::TrialLayout->new({ schema => $schema, trial_id => $trial_id, experiment_type => 'field_layout' });
     $trial_layout->generate_and_cache_layout();
 
+    $job->update_status("finished");
+
     $c->stash->{rest} = {success => 1};
 }
 

From 833206c483497d7b30ea571f6900aaaa271a9415 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Fri, 13 Feb 2026 12:48:02 -0500
Subject: [PATCH 05/18] Change file format note

---
 mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas b/mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas
index c13da688f2..b4679a0329 100644
--- a/mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas
+++ b/mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas
@@ -89,11 +89,10 @@ $trial_name
         <div class="container-fluid">
 
 <b>
-trial coordinates may be uploaded in tab-delimited text file format
+Trial coordinates may be uploaded as tab-separated values (.tsv), comma-separated values (.csv), excel (.xls/.xlsx), and open document format (.ods).
 </b>
 <br>
-(.xls or .xlsx formats are NOT supported)
-<br><br>
+<br>
 <b>
   Header:
 </b>

From d1754d8215b0a231c9d27763b6ade6f47dbd4d1a Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Fri, 13 Feb 2026 15:02:04 -0500
Subject: [PATCH 06/18] Add test file

---
 t/data/trial/field_coord_upload_bad_input.csv | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 t/data/trial/field_coord_upload_bad_input.csv

diff --git a/t/data/trial/field_coord_upload_bad_input.csv b/t/data/trial/field_coord_upload_bad_input.csv
new file mode 100644
index 0000000000..eece114465
--- /dev/null
+++ b/t/data/trial/field_coord_upload_bad_input.csv
@@ -0,0 +1,16 @@
+plot_name,row_number,col_number
+test_trial21_badplotname,1,1
+test_trial22,1,1
+test_trial23,1,3
+test_trial24,2,1
+test_trial25,2,2
+test_trial26,2,3
+test_trial27,3,1
+test_trial28,3,2
+test_trial29,3,3
+test_trial210,4,1
+test_trial211,4,2
+test_trial212,4,3
+test_trial213,5,1
+test_trial214,5,2
+test_trial215,5,3

From ffe69f7370612af04ebac0490142515c963bc88c Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Fri, 13 Feb 2026 16:22:45 -0500
Subject: [PATCH 07/18] Change schema statement

---
 lib/SGN/Controller/AJAX/TrialMetadata.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/SGN/Controller/AJAX/TrialMetadata.pm b/lib/SGN/Controller/AJAX/TrialMetadata.pm
index addfebf726..454f44d096 100644
--- a/lib/SGN/Controller/AJAX/TrialMetadata.pm
+++ b/lib/SGN/Controller/AJAX/TrialMetadata.pm
@@ -3756,7 +3756,7 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
     my $dbh = $c->dbc->dbh();
     my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );
     my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'phenotypes', 'concurrent', $c->config->{basepath});
-    my $trial_layout = CXGN::Trial::TrialLayout->new({ schema => $schema, trial_id => $trial_id, experiment_type => 'field_layout' });
+    my $trial_layout = CXGN::Trial::TrialLayout->new({ schema => $c->dbic_schema("Bio::Chado::Schema", undef, $user_id), trial_id => $trial_id, experiment_type => 'field_layout' });
     $trial_layout->generate_and_cache_layout();
 
     $job->update_status("finished");

From cb88f171cf34ae35cfb7433e6880c2444fba3df3 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Mon, 16 Feb 2026 11:55:01 -0500
Subject: [PATCH 08/18] Change file separators, monkey with test

---
 t/data/trial/field_coord_upload.csv           | 32 +++++++++----------
 t/data/trial/field_coord_upload.txt           | 16 ++++++++++
 .../CXGN/DownloadFieldMapSpreadsheet.t        |  2 +-
 3 files changed, 33 insertions(+), 17 deletions(-)
 create mode 100644 t/data/trial/field_coord_upload.txt

diff --git a/t/data/trial/field_coord_upload.csv b/t/data/trial/field_coord_upload.csv
index 1aad5f4f49..3da36b8dfa 100644
--- a/t/data/trial/field_coord_upload.csv
+++ b/t/data/trial/field_coord_upload.csv
@@ -1,16 +1,16 @@
-plot_name	row_number	col_number
-test_trial21	1	1
-test_trial22	1	2
-test_trial23	1	3
-test_trial24	2	1
-test_trial25	2	2
-test_trial26	2	3
-test_trial27	3	1
-test_trial28	3	2
-test_trial29	3	3
-test_trial210	4	1
-test_trial211	4	2
-test_trial212	4	3
-test_trial213	5	1
-test_trial214	5	2
-test_trial215	5	3
+plot_name,row_number,col_number
+test_trial21,1,1
+test_trial22,1,2
+test_trial23,1,3
+test_trial24,2,1
+test_trial25,2,2
+test_trial26,2,3
+test_trial27,3,1
+test_trial28,3,2
+test_trial29,3,3
+test_trial210,4,1
+test_trial211,4,2
+test_trial212,4,3
+test_trial213,5,1
+test_trial214,5,2
+test_trial215,5,3
diff --git a/t/data/trial/field_coord_upload.txt b/t/data/trial/field_coord_upload.txt
new file mode 100644
index 0000000000..1aad5f4f49
--- /dev/null
+++ b/t/data/trial/field_coord_upload.txt
@@ -0,0 +1,16 @@
+plot_name	row_number	col_number
+test_trial21	1	1
+test_trial22	1	2
+test_trial23	1	3
+test_trial24	2	1
+test_trial25	2	2
+test_trial26	2	3
+test_trial27	3	1
+test_trial28	3	2
+test_trial29	3	3
+test_trial210	4	1
+test_trial211	4	2
+test_trial212	4	3
+test_trial213	5	1
+test_trial214	5	2
+test_trial215	5	3
diff --git a/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t b/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t
index cebd6ac2a2..773bee3832 100644
--- a/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t
+++ b/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t
@@ -31,7 +31,7 @@ $response = $ua->post(
         'http://localhost:3010/ajax/breeders/trial/coordsupload',
         Content_Type => 'form-data',
         Content => [
-            trial_coordinates_uploaded_file => [ $file, 'coords_upload', Content_Type => 'application/vnd.ms-excel', ],
+            trial_coordinates_uploaded_file => [ $file, 'coords_upload', Content_Type => 'application/octet-stream', ],
             "trial_coordinates_upload_trial_id"=>$trial_id,
             "sgn_session_id"=>$sgn_session_id
         ]

From 4430fb56d1e3e30261bc6c3dfd74c14634dc3363 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Mon, 16 Feb 2026 14:24:57 -0500
Subject: [PATCH 09/18] Debugging

---
 lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm | 3 ++-
 lib/SGN/Controller/AJAX/TrialMetadata.pm                       | 3 +++
 t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t              | 3 +++
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm b/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm
index e88b9463ea..b8cedcbd7c 100644
--- a/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm
+++ b/lib/CXGN/Trial/ParseUpload/Plugin/TrialSpatialLayoutGeneric.pm
@@ -7,6 +7,7 @@ use SGN::Model::Cvterm;
 use CXGN::List::Validate;
 use CXGN::Stock;
 use CXGN::Project;
+use Data::Dumper;
 
 my @REQUIRED_COLUMNS = qw|plot_name row_number col_number|;
 my @OPTIONAL_COLUMNS = qw||;
@@ -167,9 +168,9 @@ sub _parse_with_plugin {
         }
     }
 
+    # print STDERR Dumper \%spatial_layout_data;
 
     $self->_set_parsed_data({
-        trial_id => $self->get_trial_id(),
         spatial_layout => \%spatial_layout_data
     });
 
diff --git a/lib/SGN/Controller/AJAX/TrialMetadata.pm b/lib/SGN/Controller/AJAX/TrialMetadata.pm
index 2d6b587dab..41b0481306 100644
--- a/lib/SGN/Controller/AJAX/TrialMetadata.pm
+++ b/lib/SGN/Controller/AJAX/TrialMetadata.pm
@@ -3730,6 +3730,7 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
             error => $return_error
         });
         $job->update_status("failed");
+        $c->detach();
         return;
     }
 
@@ -3754,6 +3755,8 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
         return;
     }
 
+    # print STDERR Dumper $parsed_data->{spatial_layout};
+
     my $dbh = $c->dbc->dbh();
     my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );
     my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'phenotypes', 'concurrent', $c->config->{basepath});
diff --git a/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t b/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t
index 773bee3832..9620aafa6f 100644
--- a/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t
+++ b/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t
@@ -26,6 +26,7 @@ print STDERR $sgn_session_id."\n";
 my $trial_id = $schema->resultset('Project::Project')->find({name=>'test_trial'})->project_id();
 
 my $file = $test->config->{basepath}."/t/data/trial/field_coord_upload.csv";
+print STDERR "Upload file path: $file \n";
 my $ua = LWP::UserAgent->new;
 $response = $ua->post(
         'http://localhost:3010/ajax/breeders/trial/coordsupload',
@@ -37,6 +38,8 @@ $response = $ua->post(
         ]
     );
 
+sleep(20);
+
 #print STDERR Dumper $response;
 ok($response->is_success);
 my $message = $response->decoded_content;

From 274a3eed4818e962789c3b203911f8992885e285 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Tue, 17 Feb 2026 11:44:25 -0500
Subject: [PATCH 10/18] Fix test

---
 lib/SGN/Controller/AJAX/TrialMetadata.pm      |  4 +-
 ...oord_upload.txt => field_coord_upload.tsv} |  0
 .../CXGN/DownloadFieldMapSpreadsheet.t        | 37 +++++++++++++++++--
 3 files changed, 37 insertions(+), 4 deletions(-)
 rename t/data/trial/{field_coord_upload.txt => field_coord_upload.tsv} (100%)

diff --git a/lib/SGN/Controller/AJAX/TrialMetadata.pm b/lib/SGN/Controller/AJAX/TrialMetadata.pm
index 41b0481306..e030871f1d 100644
--- a/lib/SGN/Controller/AJAX/TrialMetadata.pm
+++ b/lib/SGN/Controller/AJAX/TrialMetadata.pm
@@ -3678,6 +3678,8 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
     	return;
     }
 
+    # print STDERR "Proceeding with $archived_filename_with_path \n";
+
     $md5 = $uploader->get_md5($archived_filename_with_path);
     unlink $upload_tempfile;
 
@@ -3759,7 +3761,7 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
 
     my $dbh = $c->dbc->dbh();
     my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );
-    my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'phenotypes', 'concurrent', $c->config->{basepath});
+    my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'stockprop', 'concurrent', $c->config->{basepath});
     my $trial_layout = CXGN::Trial::TrialLayout->new({ schema => $c->dbic_schema("Bio::Chado::Schema", undef, $user_id), trial_id => $trial_id, experiment_type => 'field_layout' });
     $trial_layout->generate_and_cache_layout();
 
diff --git a/t/data/trial/field_coord_upload.txt b/t/data/trial/field_coord_upload.tsv
similarity index 100%
rename from t/data/trial/field_coord_upload.txt
rename to t/data/trial/field_coord_upload.tsv
diff --git a/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t b/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t
index 9620aafa6f..e245c10a20 100644
--- a/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t
+++ b/t/unit_fixture/CXGN/DownloadFieldMapSpreadsheet.t
@@ -32,19 +32,50 @@ $response = $ua->post(
         'http://localhost:3010/ajax/breeders/trial/coordsupload',
         Content_Type => 'form-data',
         Content => [
-            trial_coordinates_uploaded_file => [ $file, 'coords_upload', Content_Type => 'application/octet-stream', ],
+            trial_coordinates_uploaded_file => [ $file, 'field_coord_upload.csv', Content_Type => 'text/csv', ],
             "trial_coordinates_upload_trial_id"=>$trial_id,
             "sgn_session_id"=>$sgn_session_id
         ]
     );
 
-sleep(20);
+ok($response->is_success);
+
+$file = $test->config->{basepath}."/t/data/trial/field_coord_upload.tsv";
+print STDERR "Upload file path: $file \n";
+$ua = LWP::UserAgent->new;
+$response = $ua->post(
+        'http://localhost:3010/ajax/breeders/trial/coordsupload',
+        Content_Type => 'form-data',
+        Content => [
+            trial_coordinates_uploaded_file => [ $file, 'field_coord_upload.tsv', Content_Type => 'text/csv', ],
+            "trial_coordinates_upload_trial_id"=>$trial_id,
+            "sgn_session_id"=>$sgn_session_id
+        ]
+    );
+
+ok($response->is_success);
+
+#test bad file input
+$file = $test->config->{basepath}."/t/data/trial/field_coord_upload_bad_input.csv";
+print STDERR "Upload file path: $file \n";
+$ua = LWP::UserAgent->new;
+$response = $ua->post(
+        'http://localhost:3010/ajax/breeders/trial/coordsupload',
+        Content_Type => 'form-data',
+        Content => [
+            trial_coordinates_uploaded_file => [ $file, 'field_coord_upload_bad_input.csv', Content_Type => 'text/csv', ],
+            "trial_coordinates_upload_trial_id"=>$trial_id,
+            "sgn_session_id"=>$sgn_session_id
+        ]
+    );
 
-#print STDERR Dumper $response;
 ok($response->is_success);
 my $message = $response->decoded_content;
 my $message_hash = decode_json $message;
 print STDERR Dumper $message_hash;
+my $messages = $message_hash->{error};
+ok($messages =~ m/do not exist in the database as plots/gi);
+ok($messages =~ m/assigned to multiple plots/gi);
 
 my $trial_layout_download = CXGN::Trial::TrialLayoutDownload->new({
     schema => $schema,

From b485145087d474d94fbf91d5a89075e7929f0048 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Tue, 17 Feb 2026 15:55:52 -0500
Subject: [PATCH 11/18] Fix selenium test

---
 ...trial_coords.csv => T100_trial_coords.tsv} |  0
 t/selenium2/02_trial/trial_detail.t           | 42 ++++++++++---------
 2 files changed, 22 insertions(+), 20 deletions(-)
 rename t/data/trial/{T100_trial_coords.csv => T100_trial_coords.tsv} (100%)

diff --git a/t/data/trial/T100_trial_coords.csv b/t/data/trial/T100_trial_coords.tsv
similarity index 100%
rename from t/data/trial/T100_trial_coords.csv
rename to t/data/trial/T100_trial_coords.tsv
diff --git a/t/selenium2/02_trial/trial_detail.t b/t/selenium2/02_trial/trial_detail.t
index 4b16abbe63..a9d425ff0e 100644
--- a/t/selenium2/02_trial/trial_detail.t
+++ b/t/selenium2/02_trial/trial_detail.t
@@ -1,7 +1,7 @@
 use lib 't/lib';
 use strict;
 
-use Test::More 'tests' => 178;
+use Test::More 'tests' => 172;
 
 use SGN::Test::WWW::WebDriver;
 use SGN::Test::Fixture;
@@ -125,34 +125,36 @@ $t->while_logged_in_as("curator", sub {
         $t->find_element_ok("delete_field_map_hm_link", "id", "click on delete previous coordinate")->click();
         sleep(1);
 
-        $t->find_element_ok("delete_field_coords_ok_button", "id", "click on delete previous coordinate - confirm")->click();
-        sleep(15);
+        $t->accept_alert_ok("click on delete previous coordinate - confirm");
+        sleep(25);
 
-        $t->find_element_ok("dismiss_delete_field_map_dialog", "id", "click on confirmation of delete")->click();
-        sleep(10);
+        $t->accept_alert_ok("click on confirmation of delete");
+        sleep(15);
 
         #Upload Trial Coordinates
-        my $heatmap_onswitch = $t->find_element_ok("pheno_heatmap_onswitch", "id", "click to open pheno heatmap panel");
-        $heatmap_onswitch->click();
-        sleep(3);
+        if ($file eq "T100_trial_layout.xls") { #the coords upload file only works on the first trial, no need to test that feature again
+            my $heatmap_onswitch = $t->find_element_ok("pheno_heatmap_onswitch", "id", "click to open pheno heatmap panel");
+            $heatmap_onswitch->click();
+            sleep(8);
 
-        $t->find_element_ok("heatmap_upload_trial_coords_link", "id", "click on upload_trial_coords_link ")->click();
+            $t->find_element_ok("heatmap_upload_trial_coords_link", "id", "click on upload_trial_coords_link ")->click();
 
-        my $upload_input = $t->find_element_ok("trial_coordinates_uploaded_file", "id", "find file input");
+            my $upload_input = $t->find_element_ok("trial_coordinates_uploaded_file", "id", "find file input");
 
-        my $filename = $f->config->{basepath} . "/t/data/trial/T100_trial_coords.csv";
-        $t->driver()->upload_file($filename);
-        $upload_input->send_keys($filename);
-        sleep(1);
+            my $filename = $f->config->{basepath} . "/t/data/trial/T100_trial_coords.tsv";
+            $t->driver()->upload_file($filename);
+            $upload_input->send_keys($filename);
+            sleep(1);
 
-        $t->find_element_ok("upload_trial_coords_ok_button", "id", "submit upload trial coords file ")->click();
-        sleep(15);
+            $t->find_element_ok("upload_trial_coords_ok_button", "id", "submit upload trial coords file ")->click();
+            sleep(15);
 
-        $t->find_element_ok("trial_coord_upload_success_dialog_message_cancel", "id", "close success msg")->click();
-        sleep(1);
+            $t->find_element_ok("trial_coord_upload_success_dialog_message_cancel", "id", "close success msg")->click();
+            sleep(1);
 
-        $t->find_element_ok("upload_trial_coords_cancel_button", "id", "close upload modal")->click();
-        sleep(5);
+            $t->find_element_ok("upload_trial_coords_cancel_button", "id", "close upload modal")->click();
+            sleep(5);
+        }
 
         my $trial_details = $t->find_element_ok(
             'trial_details_content',

From aa3a4653e699fc8f7683bf563ea05f1355355f51 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Wed, 18 Feb 2026 10:26:02 -0500
Subject: [PATCH 12/18] Fix another selenium test

---
 t/data/trial/upload_trial_coords_file.csv  | 32 +++++++++++-----------
 t/selenium2/breeders/upload_trial_coords.t |  4 +--
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/t/data/trial/upload_trial_coords_file.csv b/t/data/trial/upload_trial_coords_file.csv
index 13238734d5..852deb4862 100644
--- a/t/data/trial/upload_trial_coords_file.csv
+++ b/t/data/trial/upload_trial_coords_file.csv
@@ -1,16 +1,16 @@
-plot_name	row_number	col_number
-test_trial21	1	1
-test_trial22	1	2
-test_trial23	1	3
-test_trial24	1	4
-test_trial25	1	5
-test_trial26	2	5
-test_trial27	2	4
-test_trial28	2	3
-test_trial29	2	2
-test_trial210	2	1
-test_trial211	3	1
-test_trial212	3	2
-test_trial213	3	3
-test_trial214	3	4
-test_trial215	3	5
+plot_name,row_number,col_number
+test_trial21,1,1
+test_trial22,1,2
+test_trial23,1,3
+test_trial24,1,4
+test_trial25,1,5
+test_trial26,2,5
+test_trial27,2,4
+test_trial28,2,3
+test_trial29,2,2
+test_trial210,2,1
+test_trial211,3,1
+test_trial212,3,2
+test_trial213,3,3
+test_trial214,3,4
+test_trial215,3,5
diff --git a/t/selenium2/breeders/upload_trial_coords.t b/t/selenium2/breeders/upload_trial_coords.t
index d9b9cd215c..441b456868 100644
--- a/t/selenium2/breeders/upload_trial_coords.t
+++ b/t/selenium2/breeders/upload_trial_coords.t
@@ -17,7 +17,7 @@ $t->while_logged_in_as("submitter", sub {
     my $heatmap_onswitch = $t->find_element_ok("pheno_heatmap_onswitch",  "id",  "click to open pheno heatmap panel");
 
     $heatmap_onswitch->click();
-    sleep(3);
+    sleep(5);
 
     $t->find_element_ok("heatmap_upload_trial_coords_link", "id", "click on upload_trial_coords_link ")->click();
 
@@ -54,7 +54,7 @@ $t->while_logged_in_as("submitter", sub {
     $t->find_element_ok("delete_field_map_hm_link", "id", "find a delete coordinates after upload button and click")->click();
     sleep(1);
 
-    $t->find_element_ok("delete_field_coords_ok_button", "id", "find confirm deletion of coordinates after upload");
+    $t->accept_alert_ok("find confirm deletion of coordinates after upload");
     }
 );
 

From 1c4e2e5362a1fec529985da1c78ec250d6e799d2 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Wed, 18 Feb 2026 10:31:04 -0500
Subject: [PATCH 13/18] Appease the linter

---
 t/selenium2/breeders/upload_trial_coords.t | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/t/selenium2/breeders/upload_trial_coords.t b/t/selenium2/breeders/upload_trial_coords.t
index 441b456868..290ccdae76 100644
--- a/t/selenium2/breeders/upload_trial_coords.t
+++ b/t/selenium2/breeders/upload_trial_coords.t
@@ -5,6 +5,8 @@ use Test::More 'tests' => 12;
 use SGN::Test::WWW::WebDriver;
 use SGN::Test::Fixture;
 
+use strict;
+
 my $f = SGN::Test::Fixture->new();
 my $t = SGN::Test::WWW::WebDriver->new();
 

From 1d85c59c1d2cdd2ca48bbdac4ca0dcf0146081a6 Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Mon, 23 Feb 2026 10:24:58 -0500
Subject: [PATCH 14/18] Use mason component to display supported file types for
 a generic file parser upload

---
 mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas b/mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas
index b4679a0329..0ad5153aa1 100644
--- a/mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas
+++ b/mason/breeders_toolbox/trial/trial_coords_upload_dialogs.mas
@@ -88,9 +88,7 @@ $trial_name
       <div class="modal-body">
         <div class="container-fluid">
 
-<b>
-Trial coordinates may be uploaded as tab-separated values (.tsv), comma-separated values (.csv), excel (.xls/.xlsx), and open document format (.ods).
-</b>
+<& /help/file_upload_type.mas, type => "Trial Coordinates" &>
 <br>
 <br>
 <b>

From a5aec802974e1171c58da66b50be2bcbffdc8fc8 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Mon, 23 Feb 2026 10:37:55 -0500
Subject: [PATCH 15/18] Use update_or_create to save stockprops

---
 lib/SGN/Controller/AJAX/TrialMetadata.pm | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/lib/SGN/Controller/AJAX/TrialMetadata.pm b/lib/SGN/Controller/AJAX/TrialMetadata.pm
index e030871f1d..0ad0108699 100644
--- a/lib/SGN/Controller/AJAX/TrialMetadata.pm
+++ b/lib/SGN/Controller/AJAX/TrialMetadata.pm
@@ -26,6 +26,7 @@ use Try::Tiny;
 use CXGN::BreederSearch;
 use CXGN::Page::FormattingHelpers qw / html_optional_show /;
 use SGN::Image;
+use SGN::Model::Cvterm;
 use CXGN::Trial::TrialLayoutDownload;
 use CXGN::Genotype::DownloadFactory;
 use POSIX qw | !qsort !bsearch |;
@@ -3736,16 +3737,17 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
         return;
     }
 
+    my $row_number_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'row_number', 'stock_property');
+    my $col_number_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'col_number', 'stock_property');
+
     # store all row/column data here
     eval {
         foreach my $plot_id (keys(%{$parsed_data->{spatial_layout}})) {
-            my $plot_name = $parsed_data->{spatial_layout}->{$plot_id}->{plot_name};
             my $row = $parsed_data->{spatial_layout}->{$plot_id}->{row_number};
             my $col = $parsed_data->{spatial_layout}->{$plot_id}->{col_number};
 
-            my $rs = $schema->resultset("Stock::Stock")->search({uniquename=> $plot_name });
-            my $r = $rs->first();
-            $r->create_stockprops({row_number => $row, col_number => $col});
+            $schema->resultset("Stock::Stockprop")->update_or_create({ type_id=>$row_number_cvterm->cvterm_id, stock_id=>$plot_id, rank=>0, value=>$row },{ key=>'stockprop_c1' }); 
+            $schema->resultset("Stock::Stockprop")->update_or_create({ type_id=>$col_number_cvterm->cvterm_id, stock_id=>$plot_id, rank=>0, value=>$col },{ key=>'stockprop_c1' });
         }
     };
     if ($@) {
@@ -3762,7 +3764,7 @@ sub upload_trial_coordinates : Path('/ajax/breeders/trial/coordsupload') Args(0)
     my $dbh = $c->dbc->dbh();
     my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );
     my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'stockprop', 'concurrent', $c->config->{basepath});
-    my $trial_layout = CXGN::Trial::TrialLayout->new({ schema => $c->dbic_schema("Bio::Chado::Schema", undef, $user_id), trial_id => $trial_id, experiment_type => 'field_layout' });
+    my $trial_layout = CXGN::Trial::TrialLayout->new({ schema => $schema, trial_id => $trial_id, experiment_type => 'field_layout' });
     $trial_layout->generate_and_cache_layout();
 
     $job->update_status("finished");

From de47424b3c5d667ff9ccfb031c12da4920156ab6 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Fri, 27 Feb 2026 12:15:20 -0500
Subject: [PATCH 16/18] Add a page refresh after upload is done

---
 js/source/legacy/CXGN/Trial.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/js/source/legacy/CXGN/Trial.js b/js/source/legacy/CXGN/Trial.js
index db3b53e14e..765e050aac 100644
--- a/js/source/legacy/CXGN/Trial.js
+++ b/js/source/legacy/CXGN/Trial.js
@@ -667,7 +667,9 @@ jQuery(document).ready(function ($) {
 
             if (response.success) {
                 $('#trial_coord_upload_success_dialog_message').modal("show");
-                //alert("File uploaded successfully");
+                $('#trial_coord_upload_success_dialog_message_cancel').on('click', function() {
+                    location.reload();
+                });
                 return;
             }
 

From 3b9fd4d6912d6c9a54690582c5317ba46ea6cbc8 Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Fri, 27 Feb 2026 14:07:02 -0500
Subject: [PATCH 17/18] Fix selenium tests

---
 t/selenium2/02_trial/trial_detail.t        | 5 +----
 t/selenium2/breeders/upload_trial_coords.t | 5 +----
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/t/selenium2/02_trial/trial_detail.t b/t/selenium2/02_trial/trial_detail.t
index a9d425ff0e..027dd147cd 100644
--- a/t/selenium2/02_trial/trial_detail.t
+++ b/t/selenium2/02_trial/trial_detail.t
@@ -150,10 +150,7 @@ $t->while_logged_in_as("curator", sub {
             sleep(15);
 
             $t->find_element_ok("trial_coord_upload_success_dialog_message_cancel", "id", "close success msg")->click();
-            sleep(1);
-
-            $t->find_element_ok("upload_trial_coords_cancel_button", "id", "close upload modal")->click();
-            sleep(5);
+            sleep(10); #wait for page to refresh
         }
 
         my $trial_details = $t->find_element_ok(
diff --git a/t/selenium2/breeders/upload_trial_coords.t b/t/selenium2/breeders/upload_trial_coords.t
index 290ccdae76..d22b5c50c4 100644
--- a/t/selenium2/breeders/upload_trial_coords.t
+++ b/t/selenium2/breeders/upload_trial_coords.t
@@ -36,10 +36,7 @@ $t->while_logged_in_as("submitter", sub {
     sleep(15);
 
     $t->find_element_ok("trial_coord_upload_success_dialog_message_cancel", "id", "close success msg")->click();
-    sleep(1);
-
-    $t->find_element_ok("upload_trial_coords_cancel_button", "id", "close upload modal")->click();
-    sleep(1);
+    sleep(10);
 
     # RELOAD PAGE TO CHECK IF SUCCESS
     $t->get_ok('/breeders/trial/137');

From 308827a04a64f79c1b37bc64cea5afe94e300a9b Mon Sep 17 00:00:00 2001
From: ryan-preble <rsp98@cornell.edu>
Date: Fri, 27 Feb 2026 15:13:29 -0500
Subject: [PATCH 18/18] Forgot to change the number of tests in plan

---
 t/selenium2/02_trial/trial_detail.t        | 2 +-
 t/selenium2/breeders/upload_trial_coords.t | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/t/selenium2/02_trial/trial_detail.t b/t/selenium2/02_trial/trial_detail.t
index 027dd147cd..190a69cd10 100644
--- a/t/selenium2/02_trial/trial_detail.t
+++ b/t/selenium2/02_trial/trial_detail.t
@@ -1,7 +1,7 @@
 use lib 't/lib';
 use strict;
 
-use Test::More 'tests' => 172;
+use Test::More 'tests' => 171;
 
 use SGN::Test::WWW::WebDriver;
 use SGN::Test::Fixture;
diff --git a/t/selenium2/breeders/upload_trial_coords.t b/t/selenium2/breeders/upload_trial_coords.t
index d22b5c50c4..721c59a624 100644
--- a/t/selenium2/breeders/upload_trial_coords.t
+++ b/t/selenium2/breeders/upload_trial_coords.t
@@ -1,6 +1,6 @@
 use lib 't/lib';
 
-use Test::More 'tests' => 12;
+use Test::More 'tests' => 11;
 
 use SGN::Test::WWW::WebDriver;
 use SGN::Test::Fixture;