fix: remove jsonb_array and fix jsonb data types such that it can be used in schema design and graphql api

apps/catalogue/src/components/detailView/SectionArrayValue.vue

@@ -48,7 +48,6 @@ export default {
         DATE_ARRAY: "StringDisplay",
         DATETIME: "StringDisplay",
         DATETIME_ARRAY: "StringDisplay",
-        JSONB_ARRAY: "ObjectDisplay",
         ONTOLOGY_ARRAY: "OntologyFieldValue",
       }[this.metadata.columnType];
     },

apps/catalogue/src/components/detailView/SectionField.vue

@@ -88,7 +88,6 @@ export default {
         DECIMAL_ARRAY: "SectionArrayValue",
         DATE_ARRAY: "SectionArrayValue",
         DATETIME_ARRAY: "SectionArrayValue",
-        JSONB_ARRAY: "SectionArrayValue",
         ONTOLOGY_ARRAY: "SectionArrayValue",
         REF_ARRAY: "RefArrayFieldValue",
         REF: "RefFieldValue",

apps/metadata-utils/src/types.ts

@@ -31,7 +31,6 @@ export type CellValueType =
   | "DATETIME_ARRAY"
   | "PERIOD"
   | "JSONB"
-  | "JSONB_ARRAY"
   | "REF"
   | "REF_ARRAY"
   | "REFBACK"

apps/schema/src/columnTypes.js

@@ -16,6 +16,7 @@ export default [
   "HYPERLINK_ARRAY",
   "INT",
   "INT_ARRAY",
+  "JSONB",
   "LONG",
   "LONG_ARRAY",
   "ONTOLOGY",

backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlTableFieldFactory.java

@@ -196,7 +196,6 @@ private void createTableField(Column col, GraphQLObjectType.Builder tableBuilder
       case DATETIME_ARRAY:
       case PERIOD_ARRAY:
       case UUID_ARRAY:
-      case JSONB_ARRAY:
         tableBuilder.field(
             GraphQLFieldDefinition.newFieldDefinition()
                 .name(id)

backend/molgenis-emx2-io/src/main/java/org/molgenis/emx2/io/emx1/Emx1Attribute.java

@@ -280,7 +280,6 @@ private static String getEmx1Type(Column c) {
           INT_ARRAY,
           DATE_ARRAY,
           DATETIME_ARRAY,
-          JSONB_ARRAY,
           DECIMAL_ARRAY:
         return "array types unsupported in emx1: " + c.getColumnType();
       default:

backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/RDFService.java

@@ -437,7 +437,6 @@ private CoreDatatype.XSD columnTypeToXSD(final ColumnType columnType) {
               EMAIL_ARRAY,
               HEADING,
               JSONB,
-              JSONB_ARRAY,
               STRING,
               STRING_ARRAY,
               TEXT,

backend/molgenis-emx2-sql/src/main/java/org/molgenis/emx2/sql/SqlQuery.java

@@ -1159,7 +1159,6 @@ private Condition whereCondition(
       case DATE_ARRAY -> whereConditionArrayEquals(name, operator, toDateArray(values));
       case DATETIME_ARRAY -> whereConditionArrayEquals(name, operator, toDateTimeArray(values));
       case PERIOD_ARRAY -> whereConditionArrayEquals(name, operator, toYearToSecondArray(values));
-      case JSONB_ARRAY -> whereConditionArrayEquals(name, operator, toJsonbArray(values));
       case REF -> whereConditionRefEquals(name, operator, values);
       default ->
           throw new SqlQueryException(

backend/molgenis-emx2-sql/src/main/java/org/molgenis/emx2/sql/SqlTypeUtils.java

@@ -180,7 +180,6 @@ public static Object getTypedValue(Column c, Row row) {
       case PERIOD -> row.getPeriod(name);
       case PERIOD_ARRAY -> row.getPeriodArray(name);
       case JSONB -> row.getJsonb(name);
-      case JSONB_ARRAY -> row.getJsonbArray(name);
       default ->
           throw new UnsupportedOperationException(
               "Unsupported columnType found:" + c.getColumnType());

backend/molgenis-emx2-sql/src/test/java/org/molgenis/emx2/sql/TestCreateArrayDataTypes.java

@@ -80,13 +80,6 @@ public void testTextArray() {
         });
   }
 
-  @Test
-  public void testJSON() {
-    executeTest(
-        JSONB_ARRAY,
-        new String[] {"{\"key\":\"value1\"}", "{\"key\":\"value2\"}", "{\"key\":\"value3\"}"});
-  }
-
   //  @Test
   //  public void testBool()  {
   //    executeTest(BOOL_ARRAY, new Boolean[] {null, true, false});

backend/molgenis-emx2-sql/src/test/java/org/molgenis/emx2/sql/TestCreateForeignKeysArrays.java

@@ -67,13 +67,6 @@ public void testTextRef() {
         });
   }
 
-  @Test
-  public void testJSONRef() {
-    executeTest(
-        ColumnType.JSONB,
-        new String[] {"{\"key\": \"value1\"}", "{\"key\": \"value2\"}", "{\"key\": \"value3\"}"});
-  }
-
   private void executeTest(ColumnType columnType, Object[] testValues) {
 
     Schema schema = db.dropCreateSchema("TestRefArray" + columnType.toString().toUpperCase());

backend/molgenis-emx2/src/main/java/org/molgenis/emx2/ColumnType.java

@@ -37,7 +37,6 @@ public enum ColumnType {
 
   // COMPOSITE
   JSONB(org.jooq.JSONB.class),
-  JSONB_ARRAY(org.jooq.JSONB[].class),
 
   // RELATIONSHIP
   REF(Object.class),

backend/molgenis-emx2/src/main/java/org/molgenis/emx2/Row.java

@@ -171,10 +171,6 @@ public JSONB getJsonb(String name) {
     return TypeUtils.toJsonb(values.get(name));
   }
 
-  public JSONB[] getJsonbArray(String name) {
-    return TypeUtils.toJsonbArray(values.get(name));
-  }
-
   public Row setString(String name, String value) {
     this.values.put(name, value);
     return this;
@@ -344,8 +340,6 @@ public <T> T get(String name, Class<T> type) {
         return (T) getStringArray(name);
       case "JSONB":
         return (T) getJsonb(name);
-      case "JSONB[]":
-        return (T) getJsonbArray(name);
       case "Integer":
         return (T) getInteger(name);
       case "Integer[]":

backend/molgenis-emx2/src/main/java/org/molgenis/emx2/utils/TypeUtils.java

@@ -1,6 +1,5 @@
 package org.molgenis.emx2.utils;
 
-import java.io.Serializable;
 import java.lang.reflect.Array;
 import java.math.BigDecimal;
 import java.sql.Timestamp;
@@ -260,26 +259,10 @@ public static JSONB toJsonb(Object v) {
     return (JSONB) v;
   }
 
-  public static JSONB[] toJsonbArray(Object v) {
+  public static JSONB[] toJsonbArray(Object[] values) {
     // non standard so not using the generic function
-    if (v == null) return null; // NOSONAR
-    if (v instanceof String) {
-      String value = toString(v);
-      if (value != null) {
-        v = List.of(JSONB.valueOf(value));
-      } else {
-        return null;
-      }
-    }
-    if (v instanceof String[]) {
-      v = toStringArray(v);
-    }
-    if (v instanceof Serializable[]) v = List.of((Serializable[]) v);
-    if (v instanceof Object[]) v = List.of((Object[]) v);
-    if (v instanceof List) {
-      return ((List<Object>) v).stream().map(TypeUtils::toJsonb).toArray(JSONB[]::new);
-    }
-    return (JSONB[]) v;
+    if (values == null) return null; // NOSONAR
+    return Arrays.stream(values).map(TypeUtils::toJsonb).toArray(JSONB[]::new);
   }
 
   public static String toText(Object v) {
@@ -320,7 +303,6 @@ public static ColumnType getArrayType(ColumnType columnType) {
       case DATE -> ColumnType.DATE_ARRAY;
       case DATETIME -> ColumnType.DATETIME_ARRAY;
       case PERIOD -> ColumnType.PERIOD_ARRAY;
-      case JSONB -> ColumnType.JSONB_ARRAY;
       default ->
           throw new UnsupportedOperationException(
               "Unsupported array columnType found:" + columnType);
@@ -392,7 +374,6 @@ public static DataType toJooqType(ColumnType type) {
       case PERIOD_ARRAY ->
           SQLDataType.INTERVAL.asConvertedDataType(new PeriodConverter()).getArrayDataType();
       case JSONB -> SQLDataType.JSONB;
-      case JSONB_ARRAY -> SQLDataType.JSONB.getArrayDataType();
       default ->
           // should never happen
           throw new IllegalArgumentException("jooqTypeOf(type) : unsupported type '" + type + "'");
@@ -422,7 +403,7 @@ public static Object getTypedValue(Object v, ColumnType columnType) {
       case PERIOD -> TypeUtils.toPeriod(v);
       case PERIOD_ARRAY -> TypeUtils.toPeriodArray(v);
       case JSONB -> TypeUtils.toJsonb(v);
-      case JSONB_ARRAY -> TypeUtils.toJsonbArray(v);
+
       default ->
           throw new UnsupportedOperationException(
               "Unsupported columnType columnType found:" + columnType);

backend/molgenis-emx2/src/test/java/org/molgenis/emx2/TestTypeUtils.java

@@ -7,7 +7,6 @@
 import java.util.Arrays;
 import java.util.List;
 import java.util.UUID;
-import org.jooq.JSONB;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.utils.TypeUtils;
 
@@ -22,9 +21,6 @@ public void test() {
     executeTest(ColumnType.DATE_ARRAY, new LocalDate[] {LocalDate.now(), LocalDate.now()});
     executeTest(
         ColumnType.DATETIME_ARRAY, new LocalDateTime[] {LocalDateTime.now(), LocalDateTime.now()});
-    executeTest(
-        ColumnType.JSONB_ARRAY,
-        new JSONB[] {JSONB.valueOf("{name:\"blaat\"}"), JSONB.valueOf("{name2:\"blaat2\"}")});
 
     // test null string is trimmed to null correctly
     for (ColumnType type : ColumnType.values()) {