picklist field (single and multivalued) silent validation and fix

Author: ddooley

lib/DataHarmonizer.js

@@ -1597,17 +1597,22 @@ class DataHarmonizer {
 
       if (field.sources) {
         const options = field.sources.flatMap((source) => {
-          return Object.values(field.permissible_values[source]).reduce(
-            (acc, item) => {
-              acc.push({
-                label: titleOverText(item),
-                value: titleOverText(item),
-                _id: item.text,
-              });
-              return acc;
-            },
-            []
-          );
+          if (field.permissible_values[source])
+            return Object.values(field.permissible_values[source]).reduce(
+              (acc, item) => {
+                acc.push({
+                  label: titleOverText(item),
+                  value: titleOverText(item),
+                  _id: item.text,
+                });
+                return acc;
+              },
+              []
+            );
+          else {
+            alert("Schema Error: Slot mentions enumeration " + source + " but this was not found in enumeration dictionary, or it has no selections");
+            return [];
+          }
         });
 
         col.source = options;
@@ -2780,11 +2785,13 @@ class DataHarmonizer {
             if (field.multivalued === true) {
               const [, update] = validateValsAgainstVocab(cellVal, field);
               if (update) {
+                data[row][col] = update;
                 cellChanges.push([row, col, update, 'thisChange']);
               }
             } else {
               const [, update] = validateValAgainstVocab(cellVal, field);
               if (update) {
+                data[row][col] = update;
                 cellChanges.push([row, col, update, 'thisChange']);
               }
             }

web/templates/influenza/schema.json

@@ -301,8 +301,8 @@
       "title": "umbrella bioproject accession menu",
       "from_schema": "https://example.com/Influenza"
     },
-    "null value menu": {
-      "name": "null value menu",
+    "NullValueMenu": {
+      "name": "NullValueMenu",
       "title": "null value menu",
       "from_schema": "https://example.com/Influenza",
       "permissible_values": {
@@ -531,7 +531,15 @@
     "PresamplingActivityMenu": {
       "name": "PresamplingActivityMenu",
       "title": "presampling activity menu",
-      "from_schema": "https://example.com/Influenza"
+      "from_schema": "https://example.com/Influenza",
+      "permissible_values": {
+        "Post-infection convalescence": {
+          "text": "Post-infection convalescence"
+        },
+        "Vaccination": {
+          "text": "Vaccination"
+        }
+      }
     },
     "VaccineNameMenu": {
       "name": "VaccineNameMenu",

web/templates/influenza/schema.yaml

@@ -1716,8 +1716,8 @@ enums:
     name: UmbrellaBioprojectAccessionMenu
     title: umbrella bioproject accession menu
     permissible_values: {}
-  null value menu:
-    name: null value menu
+  NullValueMenu:
+    name: NullValueMenu
     title: null value menu
     permissible_values:
       Not Applicable:
@@ -1878,7 +1878,11 @@ enums:
   PresamplingActivityMenu:
     name: PresamplingActivityMenu
     title: presampling activity menu
-    permissible_values: {}
+    permissible_values:
+      Post-infection convalescence:
+        text: Post-infection convalescence
+      Vaccination:
+        text: Vaccination
   VaccineNameMenu:
     name: VaccineNameMenu
     title: vaccine name menu

web/templates/influenza/schema_enums.tsv

@@ -2,7 +2,7 @@ title	name	meaning	menu_1	menu_2	menu_3	menu_4	menu_5	description	EXPORT_GISAID
 
 umbrella bioproject accession menu	UmbrellaBioprojectAccessionMenu												
 
-null value menu		GENEPIO:0001619	Not Applicable										
+null value menu	NullValueMenu	GENEPIO:0001619	Not Applicable										
 		GENEPIO:0001618	Missing										
 		GENEPIO:0001620	Not Collected										
 		GENEPIO:0001668	Not Provided										
@@ -60,8 +60,8 @@ Related specimen relationship type menu	RelatedSpecimenRelationshipTypeMenu	HP:0
 			Sequencing/bioinformatics methods development/validation 										
 			Specimen sampling methods testing										
 
-presampling activity menu	PresamplingActivityMenu	Post-infection convalescence											
-		Vaccination											
+presampling activity menu	PresamplingActivityMenu		Post-infection convalescence										
+			Vaccination