Improve/variant creation form

src/ajax/check_hgvs_dialogue.php

@@ -114,12 +114,15 @@
     // We could not validate this variant, but the problem
     //  lies with us. We will accept this variant and the
     //  uncertainty that comes with it.
+    // Just to be sure, we remove the reference sequence here,
+    //  because it might still be stuck to the variant
+    //  description from the mapping process.
     var oInput = $(\'input[name="' . $sFieldName . '"]\');
-    oInput.val("' . addslashes($sVariant) . '").attr("class", "warn");
+    oInput.val("' . substr(strstr(addslashes($sVariant), ':'), 1) . '").attr("class", "warn");
     oInput.siblings("img:first").attr({src: "gfx/check_orange.png", title: "Your variant could not be (in)validated..."});
     $(this).dialog("close");
 }};
-');
+'); // Fixme; Use lovd_removeRefSeq once the necessary code has been pulled in (from the branch feat/checkHGVSTool)
 
 
 // Create a PHP function to easily update the dialogue.
@@ -409,7 +412,8 @@ function update_images_per_step($sStep, $sImage)
         // We will have to allow these variants into the database.
         update_images_per_step('statusMapping', 'gfx/cross.png');
         update_dialogue(
-            '<br>Something went wrong on our side, which means we could not map nor validate your variant.',
+            '<br>This variant type is not supported by VariantValidator.' .
+            ' Therefore, we can only check the syntax and not perform the mapping.',
             'oButtonOKCouldBeValid'
         );
         exit;
@@ -575,17 +579,26 @@ function update_images_per_step($sStep, $sImage)
     }
 
 
-    // Fill in all fields that remained empty.
+    // Fill and deactivate all fields that remained empty.
+    // Some fields might not have been filled after the mapping. Some
+    //  unknown issues have occurred here, most likely concerning the
+    //  reference sequence. Because we want to allow users to fill in
+    //  these fields without that resulting in a reset of all values,
+    //  we will deactivate the onChanges for these fields and warn the
+    //  user.
     print('
     // Fill in all fields that remained empty.
-    $(\'#variantForm input[name*="VariantOnGenome"]\').each(function(e){
-        if($(this).val()==="") {
-            $(this).val("g.?");
-        }
-    });
-    $(\'#variantForm input[name*="VariantOnTranscript"]\').each(function(e){
-        if($(this).val()==="" && !$(this).attr("name").endsWith("Exon")) {
-            $(this).val("c.?");
+    $(\'#variantForm input[name*="VariantOn"]\').each(function(e){
+        sName = $(this).attr("name");
+        if ($(this).val() === ""
+            && !(sName.endsWith("Exon") || sName.endsWith("DBID") || sName.endsWith("Reference"))) {
+            if (sName.includes("Genome")) {
+                $(this).val("g.?");
+            } else {
+                $(this).val((sName.endsWith("DNA")? "c" : (sName.endsWith("RNA")? "r" : "p")) + ".?");
+            }
+            $(this).off("change").attr("class", "warn");
+            $(this).siblings("img:first").attr({src: "gfx/check_orange.png", title: "Variant mapping failed! The HGVS check of this field is turned off to allow changes to be made freely. To turn the checks back on, refresh the page."});
         }
     });
     ');