Deletion section on transformation project and transformation details page

js/source/legacy/CXGN/Transformation.js

@@ -0,0 +1,30 @@
+function deleteTransformationID(transformation_stock_id){
+
+    const confirmation = confirm('Are you sure you want to delete this transformation ID? The deletion cannot be undone.');
+
+    if (confirmation) {
+        jQuery.ajax({
+            url: '/ajax/transformation/delete',
+            data: {'transformation_stock_id' : transformation_stock_id},
+            method: 'POST',
+            destroy: true,
+            beforeSend: function(response) {
+                jQuery('#working_modal').modal('show');
+            },
+            success: function(response) {
+                jQuery('#working_modal').modal('hide');
+                if (response.success == 1) {
+                    alert('Deletion was successful');
+                    location.reload();
+                }
+                if (response.error) {
+                    alert(response.error);
+                }
+            },
+            error: function(response) {
+                jQuery('#working_modal').modal('hide');
+                alert('An error occurred during deletion');
+            }
+        });
+    }
+}

lib/CXGN/Transformation/Transformation.pm

@@ -41,6 +41,27 @@ has 'transformation_stock_id' => (
     is => 'rw',
 );
 
+has 'transformants' => (
+    isa => 'ArrayRef|Undef',
+    is => 'rw',
+    lazy => 1,
+    builder => '_get_transformants',
+);
+
+has 'obsoleted_transformants' => (
+    isa => 'ArrayRef|Undef',
+    is => 'rw',
+    lazy => 1,
+    builder => '_get_obsoleted_transformants',
+);
+
+has 'tracking_identifier' => (
+    isa => 'ArrayRef|Undef',
+    is => 'rw',
+    lazy => 1,
+    builder => '_get_tracking_identifier',
+);
+
 
 sub get_active_transformations_in_project {
     my $self = shift;
@@ -121,7 +142,7 @@ sub get_inactive_transformations_in_project {
 }
 
 
-sub get_transformants {
+sub _get_transformants {
     my $self = shift;
     my $schema = $self->schema();
     my $transformation_stock_id = $self->transformation_stock_id();
@@ -143,11 +164,11 @@ sub get_transformants {
         push @transformants, [$stock_id,  $stock_name]
     }
 
-    return \@transformants;
+    $self->transformants(\@transformants);
 }
 
 
-sub get_obsoleted_transformants {
+sub _get_obsoleted_transformants {
     my $self = shift;
     my $schema = $self->schema();
     my $transformation_stock_id = $self->transformation_stock_id();
@@ -171,7 +192,8 @@ sub get_obsoleted_transformants {
         push @obsoleted_transformants, [$stock_id,  $stock_name, $obsolete_note, $obsolete_date, $sp_person_id]
     }
 
-    return \@obsoleted_transformants;
+    $self->obsoleted_transformants(\@obsoleted_transformants);
+
 }
 
 
@@ -241,7 +263,7 @@ sub get_associated_projects {
 }
 
 
-sub get_tracking_identifier {
+sub _get_tracking_identifier {
     my $self = shift;
     my $schema = $self->schema();
     my $transformation_stock_id = $self->transformation_stock_id();
@@ -256,12 +278,13 @@ sub get_tracking_identifier {
 
     $h->execute($material_of_type_id, $transformation_stock_id);
 
-    my @tracking_identifiers = ();
+    my @tracking_identifier_info = ();
     while (my ($stock_id,  $stock_name) = $h->fetchrow_array()){
-        push @tracking_identifiers, [$stock_id,  $stock_name]
+        push @tracking_identifier_info, [$stock_id,  $stock_name]
     }
 
-    return \@tracking_identifiers;
+    $self->tracking_identifier(\@tracking_identifier_info);
+
 }
 
 
@@ -311,6 +334,114 @@ sub get_default_plant_material {
 }
 
 
+sub delete {
+    my $self = shift;
+    my $schema = $self->schema();
+    my $dbh = $self->schema()->storage()->dbh();
+    my $transformation_stock_id = $self->transformation_stock_id();
+    my $tracking_identifier = $self->tracking_identifier();
+    my $transformants = $self->transformants();
+    my $number_of_transformants = scalar(@$transformants);
+    my $obsoleted_transformants = $self->obsoleted_transformants();
+    my $number_of_obsoleted_transformants = scalar(@$obsoleted_transformants);
+
+    eval {
+        $dbh->begin_work();
+
+        my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", "stock_type")->cvterm_id();
+        my $tracking_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "tracking_identifier", "stock_type")->cvterm_id();
+        my $transformation_experiment_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'transformation_experiment', 'experiment_type')->cvterm_id();
+        my $tracking_experiment_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tracking_activity', 'experiment_type')->cvterm_id();
+
+        if (($number_of_transformants > 0) || ($number_of_obsoleted_transformants > 0)) {
+	        die "Transformation ID has associated transformants. Cannot delete.\n";
+        }
+
+        my $transformation_rs = $schema->resultset("Stock::Stock")->find ({stock_id => $transformation_stock_id, type_id => $transformation_type_id});
+        if (!$transformation_rs) {
+	        die "This stock id is not a transformation ID. Cannot delete.\n";
+        }
+
+        my $transformation_experiment_id;
+        my $nd_q = "SELECT nd_experiment.nd_experiment_id FROM nd_experiment_stock
+            JOIN nd_experiment ON (nd_experiment_stock.nd_experiment_id = nd_experiment.nd_experiment_id)
+            WHERE nd_experiment.type_id = ? AND nd_experiment_stock.stock_id = ?";
+
+        my $nd_h = $schema->storage->dbh()->prepare($nd_q);
+        $nd_h->execute($transformation_experiment_type_id, $transformation_stock_id);
+        my @nd_experiment_ids= $nd_h->fetchrow_array();
+        if (scalar @nd_experiment_ids == 1) {
+            $transformation_experiment_id = $nd_experiment_ids[0];
+        } else {
+            die "Error retrieving experiment id";
+        }
+
+        #delete the nd_experiment_md_files entries
+        my $md_files_q = "DELETE FROM phenome.nd_experiment_md_files WHERE nd_experiment_id = ?";
+        my $md_files_h = $schema->storage->dbh()->prepare($md_files_q);
+        $md_files_h->execute($transformation_experiment_id);
+
+	    # delete the nd_experiment entries
+	    my $q2= "delete from nd_experiment where nd_experiment.nd_experiment_id = ? AND nd_experiment.type_id = ?";
+	    my $h2 = $dbh->prepare($q2);
+	    $h2->execute($transformation_experiment_id, $transformation_experiment_type_id);
+
+	    # delete stock owner entries
+	    #
+	    my $q3 = "delete from phenome.stock_owner where stock_id=?";
+	    my $h3 = $dbh->prepare($q3);
+	    $h3->execute($transformation_stock_id);
+
+	    # delete the stock entries
+	    my $q4 = "delete from stock where stock.stock_id=? and stock.type_id = ?";
+	    my $h4 = $dbh->prepare($q4);
+	    $h4->execute($transformation_stock_id, $transformation_type_id);
+
+        #if linking with tracking tool, delete tracking identifier entry
+        if (scalar @$tracking_identifier > 0) {
+            my $tracking_experiment_id;
+            my $tracking_stock_id = $tracking_identifier->[0]->[0];
+            my $tracking_nd_q = "SELECT nd_experiment.nd_experiment_id FROM nd_experiment_stock
+                JOIN nd_experiment ON (nd_experiment_stock.nd_experiment_id = nd_experiment.nd_experiment_id)
+                WHERE nd_experiment.type_id = ? AND nd_experiment_stock.stock_id = ?";
+
+            my $tracking_nd_h = $schema->storage->dbh()->prepare($tracking_nd_q);
+            $tracking_nd_h->execute($tracking_experiment_type_id, $tracking_stock_id);
+            my @tracking_nd_experiment_ids= $tracking_nd_h->fetchrow_array();
+            if (scalar @tracking_nd_experiment_ids == 1) {
+                $tracking_experiment_id = $tracking_nd_experiment_ids[0];
+            } else {
+                die "Error retrieving experiment id";
+            }
+
+            # delete the tracking nd_experiment entries
+    	    my $tracking_q2= "delete from nd_experiment where nd_experiment.nd_experiment_id = ? AND nd_experiment.type_id = ?";
+    	    my $tracking_h2 = $dbh->prepare($tracking_q2);
+    	    $tracking_h2->execute($tracking_experiment_id, $tracking_experiment_type_id);
+
+    	    # delete tracking stock owner entries
+    	    my $tracking_q3 = "delete from phenome.stock_owner where stock_id=?";
+    	    my $tracking_h3 = $dbh->prepare($tracking_q3);
+    	    $tracking_h3->execute($tracking_stock_id);
+
+    	    # delete the tracking stock entries
+    	    my $tracking_q4 = "delete from stock where stock.stock_id=? and stock.type_id = ?";
+    	    my $tracking_h4 = $dbh->prepare($tracking_q4);
+    	    $h4->execute($tracking_stock_id, $tracking_type_id);
+        }
+    };
+
+    if ($@) {
+	    print STDERR "An error occurred while deleting transformation id ".$transformation_stock_id."$@\n";
+	    $dbh->rollback();
+	    return $@;
+    } else {
+	    $dbh->commit();
+	    return 0;
+    }
+}
+
+
 ###
 1;
 ###

lib/SGN/Controller/AJAX/TrackingActivity.pm

@@ -469,7 +469,7 @@ sub get_activity_summary :Path('/ajax/tracking_activity/summary') :Args(1) {
     my $obsoleted_transformant_count;
     if ($material_stock_type eq 'transformation') {
         my $transformation_obj = CXGN::Transformation::Transformation->new({schema=>$schema, dbh=>$dbh, transformation_stock_id=>$material_stock_id});
-        my $obsoleted_transformants = $transformation_obj->get_obsoleted_transformants();
+        my $obsoleted_transformants = $transformation_obj->obsoleted_transformants();
         if ($obsoleted_transformants) {
             $obsoleted_transformant_count = scalar @$obsoleted_transformants;
         }
@@ -652,26 +652,19 @@ sub update_status_POST : Args(0) {
         return;
     }
 
-    my @user_roles = $c->user->roles();
-    my %has_roles = ();
-    map { $has_roles{$_} = 1; } @user_roles;
-
-    if (! ( (exists($has_roles{$program_name}) && exists($has_roles{submitter})) || exists($has_roles{curator}))) {
-        $c->stash->{rest} = { error => "You need to be either a curator, or a submitter associated with breeding program $program_name to update status." };
-        return;
-    }
-
     my $user_id = $c->user()->get_object()->get_sp_person_id();
 
     my $tracking_identifier_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "tracking_identifier", 'stock_type')->cvterm_id();
     my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", 'stock_type')->cvterm_id();
 
-    my $identifier_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $identifier_id, type_id => $tracking_identifier_type_id });
-    if (!$identifier_rs) {
-        $c->stash->{rest} = { error_string => 'Error. No tracking identifier entry found in the database.' };
-	    return;
-    } else {
-        push @stocks_to_update, $identifier_id;
+    if ($identifier_id ne 'NA') {
+        my $identifier_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $identifier_id, type_id => $tracking_identifier_type_id });
+        if (!$identifier_rs) {
+            $c->stash->{rest} = { error_string => 'Error. No tracking identifier entry found in the database.' };
+    	    return;
+        } else {
+            push @stocks_to_update, $identifier_id;
+        }
     }
 
     my $material_stock_type_id;
@@ -739,15 +732,6 @@ sub reverse_status_POST : Args(0) {
         return;
     }
 
-    my @user_roles = $c->user->roles();
-    my %has_roles = ();
-    map { $has_roles{$_} = 1; } @user_roles;
-
-    if (! ( (exists($has_roles{$program_name}) && exists($has_roles{submitter})) || exists($has_roles{curator}))) {
-        $c->stash->{rest} = { error => "You need to be either a curator, or a submitter associated with breeding program $program_name to update status." };
-        return;
-    }
-
     my $user_id = $c->user()->get_object()->get_sp_person_id();
 
     my $status_type_id;