From ec8c7faee8f1f6bf3aac33b6f26fce25a1c1ffe7 Mon Sep 17 00:00:00 2001
From: titima15 <tt15@cornell.edu>
Date: Sat, 13 Aug 2022 01:14:26 +0000
Subject: [PATCH] improve validation

---
 .../Plugin/GenotypeTrialCoordinateTemplate.pm      | 44 +++++++++++++++-------
 .../Trial/ParseUpload/Plugin/GenotypeTrialXLS.pm   | 15 ++++++++
 2 files changed, 46 insertions(+), 13 deletions(-)

diff --git a/lib/CXGN/Trial/ParseUpload/Plugin/GenotypeTrialCoordinateTemplate.pm b/lib/CXGN/Trial/ParseUpload/Plugin/GenotypeTrialCoordinateTemplate.pm
index ace480d63..0a296dc37 100644
--- a/lib/CXGN/Trial/ParseUpload/Plugin/GenotypeTrialCoordinateTemplate.pm
+++ b/lib/CXGN/Trial/ParseUpload/Plugin/GenotypeTrialCoordinateTemplate.pm
@@ -60,26 +60,44 @@ sub _validate_with_plugin {
         }
     }
 
+    my $value_header = $columns[0];
+    $value_header =~ s/^\s+|\s+$//g;
+    my $column_header = $columns[1];
+    $column_header =~ s/^\s+|\s+$//g;
+    my $row_header = $columns[2];
+    $row_header =~ s/^\s+|\s+$//g;
+    my $identification_header = $columns[3];
+    $identification_header =~ s/^\s+|\s+$//g;
+    my $person_header = $columns[4];
+    $person_header =~ s/^\s+|\s+$//g;
+    my $date_header = $columns[5];
+    $date_header =~ s/^\s+|\s+$//g;
+    my $facility_identifier_header;
     if ($include_facility_identifiers) {
-        if ($columns[0] ne "Value" ||
-            $columns[1] ne "Column" ||
-            $columns[2] ne "Row" ||
-            $columns[3] ne "Identification" ||
-            $columns[4] ne "Person" ||
-            $columns[5] ne "Date" ||
-            $columns[6] ne "Facility Identifier") {
+        $facility_identifier_header = $columns[6];
+        $facility_identifier_header =~ s/^\s+|\s+$//g;
+    }
+
+    if ($include_facility_identifiers) {
+        if ($value_header ne "Value" ||
+            $column_header ne "Column" ||
+            $row_header ne "Row" ||
+            $identification_header ne "Identification" ||
+            $person_header ne "Person" ||
+            $date_header ne "Date" ||
+            $facility_identifier_header ne "Facility Identifier") {
             push @error_messages, 'File contents incorrect. Header row must contain: "Value","Column","Row","Identification","Person","Date", Facility Identifier';
             $errors{'error_messages'} = \@error_messages;
             $self->_set_parse_errors(\%errors);
             return;
         }
     } else {
-        if ($columns[0] ne "Value" ||
-            $columns[1] ne "Column" ||
-            $columns[2] ne "Row" ||
-            $columns[3] ne "Identification" ||
-            $columns[4] ne "Person" ||
-            $columns[5] ne "Date" ) {
+        if ($value_header ne "Value" ||
+            $column_header ne "Column" ||
+            $row_header ne "Row" ||
+            $identification_header ne "Identification" ||
+            $person_header ne "Person" ||
+            $date_header ne "Date" ) {
             push @error_messages, 'File contents incorrect. Header row must contain: "Value","Column","Row","Identification","Person","Date"';
             $errors{'error_messages'} = \@error_messages;
             $self->_set_parse_errors(\%errors);
diff --git a/lib/CXGN/Trial/ParseUpload/Plugin/GenotypeTrialXLS.pm b/lib/CXGN/Trial/ParseUpload/Plugin/GenotypeTrialXLS.pm
index 531703dc5..196902822 100644
--- a/lib/CXGN/Trial/ParseUpload/Plugin/GenotypeTrialXLS.pm
+++ b/lib/CXGN/Trial/ParseUpload/Plugin/GenotypeTrialXLS.pm
@@ -64,49 +64,64 @@ sub _validate_with_plugin {
 
     if ($worksheet->get_cell(0,0)) {
         $date_head  = $worksheet->get_cell(0,0)->value();
+        $date_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,1)) {
         $sample_id_head  = $worksheet->get_cell(0,1)->value();
+        $sample_id_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,2)) {
         $well_A01_head  = $worksheet->get_cell(0,2)->value();
+        $well_A01_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,3)) {
         $row_head  = $worksheet->get_cell(0,3)->value();
+        $row_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,4)) {
         $column_head  = $worksheet->get_cell(0,4)->value();
+        $column_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,5)) {
         $source_observation_unit_name_head  = $worksheet->get_cell(0,5)->value();
+        $source_observation_unit_name_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,6)) {
         $ncbi_taxonomy_id_head  = $worksheet->get_cell(0,6)->value();
+        $ncbi_taxonomy_id_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,7)) {
         $dna_person_head  = $worksheet->get_cell(0,7)->value();
+        $dna_person_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,8)) {
         $notes_head  = $worksheet->get_cell(0,8)->value();
+        $notes_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,9)) {
         $tissue_type_head  = $worksheet->get_cell(0,9)->value();
+        $tissue_type_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,10)) {
         $extraction_head  = $worksheet->get_cell(0,10)->value();
+        $extraction_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,11)) {
         $concentration_head = $worksheet->get_cell(0,11)->value();
+        $concentration_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,12)) {
         $volume_head = $worksheet->get_cell(0,12)->value();
+        $volumn_head =~ s/^\s+|\s+$//g;
     }
     if ($worksheet->get_cell(0,13)) {
         $is_blank_head = $worksheet->get_cell(0,13)->value();
+        $is_blank_head =~ s/^\s+|\s+$//g;
     }
     if ($include_facility_identifiers){
         if ($worksheet->get_cell(0,14)) {
             $facility_identifier_head = $worksheet->get_cell(0,14)->value();
+            $facility_identifier_head =~ s/^\s+|\s+$//g;
         }
     }
 
-- 
2.11.4.GIT