Merge pull request #4341 from solgenomics/topic/rename_accession_ui

add a bulk accession rename feature

docs/03_managing_breeding_data/03_03.md

@@ -113,6 +113,21 @@ Grafted accessions can be used like any other accession, for example, they can b
 
 Note that you shouldn't create new grafts based on other grafts. The scion accession and the rootstock accession have to be different, otherwise they will not be created.
 
+3.3.5 Bulk renaming of accessions
+---
+
+Accessions can be renamed in bulk using the rename accessions feature. To rename accessions, prepare a tab delimited file with two columns: the first column should have the header "old name" and contain the accession names that need to be changed. The second column should have the header "new name" and contain the names that the accessions in column 1 should be renamed to.
+
+The accession renaming feature is available from the Manage->Accessions page. Click on the "Rename Accessions" button. The first step is the upload of the file with a verification step. The verification step checks whether all the accession names in column 1 exist in the database, and whether all the accession names given in column 2 do NOT exist in the database. Only if both conditions are met, will the "rename" button become active, otherwise an error message is displayed listing the offending accession names.
+
+Optionally, the old name can be automatically added as a synonym to the renamed accession, using the checkbox on the submit form. This option is clicked by default. Unclick the checkbox to NOT save any old names as synonyms.
+
+Note that accession renaming should not be undertaken lightly. This feature is intended for special use cases, such as where accessions are created in a nursery with a name that is different from the accession name in the downstream breeding program.
+
+It can also be used to rename accessions in bulk that have spelling mistakes and other issues. Please note however, that the tool does not make any attempt to change the names of associated elements, such a plots, that may have been constructed using accession names.
+
+Because of the many implications of accession renaming, the feature is limited to accounts with the curator role.
+
 
 
 

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

@@ -0,0 +1,120 @@
+/*jslint browser: true, devel: true */
+
+/**
+
+=head1 UploadRenameAccessions.js
+
+Dialogs for uploading accessions to be renamed
+
+
+=head1 AUTHORS
+
+Lukas Mueller <lam87@cornell.edu>, based on code by
+Jeremy D. Edwards <jde22@cornell.edu>
+
+=cut
+
+*/
+
+
+var $j = jQuery.noConflict();
+
+jQuery(document).ready(function ($) {
+
+    $('#upload_rename_accessions_link').click(function () {
+        open_upload_rename_accessions_dialog();
+    });
+
+    $("#upload_rename_accessions_dialog_submit").click( function () {
+        $('#upload_rename_accessions_dialog').modal("hide");
+        upload_rename_accessions_file();
+    });
+
+ //    $("#rename_accessions_upload_spreadsheet_format_info_link").click( function () {
+ //       $('#upload_rename_accessions_dialog').modal("hide");
+ //       $("#rename_accessions_upload_spreadsheet_format_info_dialog" ).modal("show");
+ //   });
+
+    var archived_filename;
+    $('#upload_rename_accessions_form').iframePostForm({
+        json: false,
+        post: function () {
+            var uploadedRenameAccessionsFile = $("#rename_accessions_uploaded_file").val();
+            $('#working_modal').modal("show");
+            if (uploadedRenameAccessionsFile === '') {
+                $('#working_modal').modal("hide");
+                alert("No file selected");
+            }
+        },
+        complete: function (r) {
+    	    var clean_r = r.replace('<pre>', '');
+	    clean_r = clean_r.replace('</pre>', '');
+	    console.log(clean_r);
+	    var response = JSON.parse(clean_r);
+            $('#working_modal').modal("hide");
+
+            var html;
+
+            if (response.error) {
+                html = '<h3>The Following Issues Were Identified</h3><p class="bg-warning">'+response.error+'</p>';
+		$('#upload_rename_accessions_store').prop("disabled", true);
+            }
+            else {
+
+                archived_filename = response.archived_filename_with_path;
+
+		$('#upload_rename_accessions_store').prop("disabled", false);
+                html = '<h3>There Were No Issues Identified</h3>Please click the "Rename" button to renamee the accessions in the database.';
+            }
+            $("#upload_rename_accessions_validate_display tbody").html(html);
+            $("#upload_rename_accessions_validate_display").modal('show');
+        }
+    });
+
+    function upload_rename_accessions_file() {
+        var uploadFile = $("#rename_accessions_uploaded_file").val();
+        $('#upload_rename_accessions_form').attr("action", "/ajax/rename_accessions/upload_verify");
+        if (uploadFile === '') {
+            alert("Please select a file");
+            return;
+        }
+        $("#upload_rename_accessions_form").submit();
+    }
+
+    function open_upload_rename_accessions_dialog() {
+        $('#upload_rename_accessions_dialog').modal("show");
+    }
+
+    jQuery('#upload_rename_accessions_store').click(function(){
+
+
+        jQuery.ajax( {
+            url: '/ajax/rename_accessions/upload_store',
+            data: {
+                'archived_filename':archived_filename,
+		'store_old_name_as_synonym' : jQuery('#store_old_name_as_synonym').val()
+            },
+            beforeSend: function(){
+                jQuery('#working_modal').modal('show');
+            },
+            success: function(response) {
+                jQuery('#working_modal').modal('hide');
+                if (response.error) {
+                    alert('An Error Occured: No accessions were renamed! Try Fixing Your File For The Issues Identified In the Validation. '+response.error);
+                }
+                else {
+		    //alert("RESPONSE: "+JSON.stringify(response));
+                    jQuery('#rename_accessions_upload_success_dialog_message').modal('show');
+		    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');
+		alert('An error occurred storing the accession data. None were renamed.'+response.responseText);
+            }
+        });
+    });
+
+});

lib/CXGN/Stock.pm

@@ -479,6 +479,7 @@ has 'subjects' => (
     is => 'rw',
 );
 
+
 sub BUILD {
     my $self = shift;
 
@@ -489,6 +490,18 @@ sub BUILD {
         $self->stock($stock);
         $self->stock_id($stock->stock_id);
     }
+    elsif ($self->uniquename) {
+	$stock = $self->schema()->resultset("Stock::Stock")->find( { uniquename => $self->uniquename() });
+	if (!$stock) {
+	    print STDERR "Can't find stock ".$self->uniquename.". Generating empty object.\n";
+	}
+	else {
+	    $self->stock($stock);
+	    $self->stock_id($stock->stock_id);
+	}
+    }
+
+
     if (defined $stock && !$self->is_saving) {
         $self->organism_id($stock->organism_id);
 #	my $organism = $self->schema()->resultset("Organism::Organism")->find( { organism_id => $stock->organism_id() });
@@ -521,6 +534,8 @@ sub BUILD {
 
 	$self->subjects(\@subjects);
     }
+
+
     return $self;
 }
 
@@ -537,6 +552,7 @@ sub _retrieve_stock_owner {
     $self->owners(\@owners);
 }
 
+
 =head2 store()
 
  Usage: $self->store