make headers consistent and check for correctness of headers, fix typos, adapt test files to new headers.

Author: lukasmueller

js/source/legacy/CXGN/BreedersToolbox/UploadRenameAccessions.js

@@ -105,14 +105,14 @@ jQuery(document).ready(function ($) {
                 else {
 		    //alert("RESPONSE: "+JSON.stringify(response));
                     jQuery('#rename_accessions_upload_success_dialog_message').modal('show');
-		    jQuery('#list_of_uploaded_rename_accessions').val(response.renamed_accessions);
+		    var renamed_accessions_html = response.renamed_accessions.join("<br />");
+		    jQuery('#list_of_uploaded_rename_accessions').html(renamed_accessions_html);
 		    //jQuery('#list_of_already_uploaded_rename_accessions').val(response.grafts_already_present);
                 }
             },
             error: function(response) {
                 jQuery('#working_modal').modal('hide');
-		jQuery('#list_of_rename_accessions_with_problems').html(response.list_of_grafts_with_problems);
-                alert('An error occurred storing the accession data. None were renamed.'+response.responseText);
+		alert('An error occurred storing the accession data. None were renamed.'+response.responseText);
             }
         });
     });

lib/SGN/Controller/AJAX/Accessions/Rename.pm

@@ -187,36 +187,36 @@ sub upload_rename_accessions_store : Path('/ajax/rename_accessions/upload_store'
     my $schema = $c->dbic_schema("Bio::Chado::Schema");
 
     my ($header, $rename) = $self->_get_rename_accessions_from_file($c, $archived_filename);
-    
+
     my $info = $self->validate_rename_accessions($c, $header, $rename);
 
     print STDERR "FILE CONTENTS: ".Dumper($rename);
 
     my @renamed_accessions;
     my @accessions_already_present;
     my @error_accessions;
-
+    
     if (exists($info->{accessions_already_present}) && defined($info->{accessions_already_present})) {
 	@accessions_already_present = @{$info->{accessions_already_present}};
     }
     my $error;
 
     foreach my $g (@$rename) {
 	my ($old_accession_name, $new_accession_name) = @$g;
-
-
+	
+	
 	my $stock = CXGN::Stock->new( { schema => $schema, uniquename => $old_accession_name });
-
+	
 	$stock->uniquename($new_accession_name);
-
+	
 	if ($store_old_name_as_synonym eq "on") {
 	    print STDERR "Storing old name ($old_accession_name) as synonym for $new_accession_name.\n";
 	    $stock->add_synonym($old_accession_name);
 	}
 	else {
 	    print STDERR "Synonym storing not requested. \n";
 	}
-
+	
 	$stock->store();
 
 	if (exists($info->{errors}) && defined($info->{error}) && $info->{error} ne ''){
@@ -228,7 +228,7 @@ sub upload_rename_accessions_store : Path('/ajax/rename_accessions/upload_store'
     }
 
     if (@error_accessions){
-        $c->stash->{rest} = { error => join(", ",@error_accessions) };
+	$c->stash->{rest} = { error => join(", ",@error_accessions) };
         $c->detach();
     }
     $c->stash->{rest} = { success => 1, renamed_accession_count => \@renamed_accessions, renamed_accessions => $rename };
@@ -243,9 +243,9 @@ sub _get_rename_accessions_from_file {
     my $header = <$F>;
     $header =~ s/\r//g;
     chomp($header);
-
+    
     my @header = split/\t/, $header;
-
+    
     foreach my $h (@header) {
 	$h =~ s/^\s+|\s+$//g
     }
@@ -261,39 +261,48 @@ sub _get_rename_accessions_from_file {
 	$new_accession_name =~ s/^\s+|\s+$//g; # trim also
 	push @rename, [ $old_accession_name, $new_accession_name ];
     }
-
-    return \@header, \@rename;
+    
+    return (\@header, \@rename);
 }
 
+
 sub validate_rename_accessions {
     my $self = shift;
     my $c = shift;
     my $header = shift;
     my $rename = shift;
-
+    
+    my $error = "";
+    
+    if ($header->[0] ne "old_name") {
+	$error = "Column 1 header must be old_name. "; 
+    }
+    if ($header->[1] ne "new_name") {
+	$error .= "Column 2 header must be new_name. ";
+    }
+    
     my @must_exist = map { $_->[0] } @$rename;
-
+    
     my @must_not_exist = map { $_->[1] } @$rename;
-
+    
     $self->schema( $c->dbic_schema("Bio::Chado::Schema") );
     print STDERR "INPUT MUST EXIST: ".Dumper(\@must_exist);
     print STDERR "INPUT MUST NOT EXIST: ".Dumper(\@must_not_exist);
     my $list_validate = CXGN::List::Validate->new();
 
-
     my $must_exist_data = $list_validate->validate( $self->schema, 'accessions', \@must_exist );
-
+    
     print STDERR "MUST EXIST: ".Dumper($must_exist_data);
-
+    
     my $must_not_exist_data = $list_validate->validate( $self->schema, 'accessions', \@must_not_exist );
-
+    
     my @missing = ();
     if (ref($must_not_exist_data->{missing})) { 
 	@missing = @{$must_not_exist_data->{missing}};
     }
-
+    
     print STDERR "MUST NOT EXIST MISSING: ".Dumper(\@missing);
-
+    
     my @must_not_exist_but_present = ();
     foreach my $m (@must_not_exist) {
 	print STDERR "checking $m...\n";
@@ -302,10 +311,10 @@ sub validate_rename_accessions {
 	    push @must_not_exist_but_present, $m;
 	}
     }
-
+    
     print STDERR "MUST NOT EXIST BUT PRESENT: ".Dumper(\@must_not_exist_but_present);
 
-    return { must_exist_missing => $must_exist_data->{missing}, must_not_exist_present => \@must_not_exist_but_present };
+    return { error => $error, must_exist_missing => $must_exist_data->{missing}, must_not_exist_present => \@must_not_exist_but_present };
 }
 
 

mason/breeders_toolbox/upload_accession_rename_dialog.mas

@@ -38,7 +38,8 @@
  	  <h2>The accession renaming list upload was successful.</h2>
 
 	  Successfully renamed:<br />
-	  <div id="list_of_uploaded_rename_accessions">
+	  <div class="bg-success" id="list_of_uploaded_rename_accessions">
+	       [loading...]
 	  </div>
 	  <br />
 
@@ -113,8 +114,8 @@
 
 	  <h4>Required fields:</h4>
 	  <ul>
-            <li>old accession name (exact name MUST exist in the database)</li>
-            <li>new accession name (must NOT exist in the database)</li>
+            <li>old_name (exact name MUST exist in the database)</li>
+            <li>new_name (must NOT exist in the database)</li>
 	  </ul>
 	</div>
       </div>

t/data/stock/renaming/accession_renaming_1.csv

@@ -1,3 +1,3 @@
-old name	new name
+old_name	new_name
 test_accession1	test_accession100
 test_accession2	test_accession200

t/data/stock/renaming/accession_renaming_2.csv

@@ -1,3 +1,3 @@
-old name	new name
+old_name	new_name
 test_accession100	test_accession1
 test_accession200	test_accession2

t/data/stock/renaming/accession_renaming_3.csv

@@ -1,3 +1,3 @@
-old name	new name
+old_name	new_name
 test_accession227	test_accession228
 test_accession2	test_accession3