DCJ-515: Fix json parsing for dataset updates (#2358)

DataBiosphere · Jul 15, 2024 · e03a530 · e03a530
1 parent ea6a428
commit e03a530
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Showing 4 changed files with 103 additions and 6 deletions.
diff --git a/src/main/java/org/broadinstitute/consent/http/models/DatasetUpdate.java b/src/main/java/org/broadinstitute/consent/http/models/DatasetUpdate.java
@@ -1,12 +1,22 @@
 package org.broadinstitute.consent.http.models;
 
+import com.google.gson.Gson;
 import java.util.List;
+import org.broadinstitute.consent.http.util.gson.GsonUtil;
 
-public record DatasetUpdate (
+public record DatasetUpdate(
     String name,
     Integer dacId,
     List<DatasetProperty> properties
-){
+) {
+
+  private static final Gson GSON = GsonUtil.gsonBuilderWithAdapters().create();
+
+  public DatasetUpdate(String json) {
+    this(GSON.fromJson(json, DatasetUpdate.class).getName(),
+        GSON.fromJson(json, DatasetUpdate.class).getDacId(),
+        GSON.fromJson(json, DatasetUpdate.class).getDatasetProperties());
+  }
 
   public String getName() {
     return this.name;

diff --git a/src/main/java/org/broadinstitute/consent/http/resources/DatasetResource.java b/src/main/java/org/broadinstitute/consent/http/resources/DatasetResource.java
@@ -233,12 +233,10 @@ public Response updateByDatasetUpdate(
       @FormDataParam("dataset") String json) {
 
     try {
-
-      DatasetUpdate update = new Gson().fromJson(json, DatasetUpdate.class);
-
-      if (Objects.isNull(update)) {
+      if (json == null || json.isEmpty()) {
         throw new BadRequestException("Dataset is required");
       }
+      DatasetUpdate update = new DatasetUpdate(json);
 
       Dataset datasetExists = datasetService.findDatasetById(datasetId);
       if (Objects.isNull(datasetExists)) {

diff --git a/src/main/java/org/broadinstitute/consent/http/util/gson/GsonUtil.java b/src/main/java/org/broadinstitute/consent/http/util/gson/GsonUtil.java
@@ -3,6 +3,7 @@
 import com.google.cloud.storage.BlobId;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
+import com.google.gson.ToNumberPolicy;
 import java.sql.Timestamp;
 import java.time.Instant;
 import java.util.Date;
@@ -29,6 +30,7 @@ public static Gson buildGsonNullSerializer() {
 
   public static GsonBuilder gsonBuilderWithAdapters() {
     return new GsonBuilder()
+        .setObjectToNumberStrategy(ToNumberPolicy.LONG_OR_DOUBLE)
         .registerTypeAdapter(
             Instant.class,
             new InstantTypeAdapter())

diff --git a/src/test/java/org/broadinstitute/consent/http/models/DatasetUpdateTest.java b/src/test/java/org/broadinstitute/consent/http/models/DatasetUpdateTest.java
@@ -0,0 +1,87 @@
+package org.broadinstitute.consent.http.models;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNull;
+
+import com.google.gson.Gson;
+import com.google.gson.reflect.TypeToken;
+import java.util.ArrayList;
+import java.util.List;
+import org.broadinstitute.consent.http.models.dataset_registration_v1.FileTypeObject;
+import org.broadinstitute.consent.http.models.dataset_registration_v1.FileTypeObject.FileType;
+import org.junit.jupiter.api.Test;
+
+public class DatasetUpdateTest {
+
+  @Test
+  void testDatasetUpdate() {
+    String json = """
+        {
+          "name": "Test Dataset Update",
+          "dacId": 1,
+          "properties": [
+            {
+              "propertyName": "string value",
+              "propertyValue": "TDR Location"
+            },
+            {
+              "propertyName": "long value",
+              "propertyValue": 12
+            },
+            {
+              "propertyName": "boolean value",
+              "propertyValue": true
+            },
+            {
+              "propertyName": "double value",
+              "propertyValue": 10.001
+            },
+            {
+              "propertyName": "File Types",
+              "propertyValue": [{"fileType":"ARRAYS","functionalEquivalence":"testing"}]
+            }
+          ]
+        }""";
+    DatasetUpdate update = new DatasetUpdate(json);
+
+    List<DatasetProperty> props = update.getDatasetProperties();
+    assertEquals("TDR Location", getPropByName("string value", props).getPropertyValue());
+    assertEquals(12L, getPropByName("long value", props).getPropertyValue());
+    assertEquals(true, getPropByName("boolean value", props).getPropertyValue());
+    assertEquals(10.001D, getPropByName("double value", props).getPropertyValue());
+
+    // Parsing the object value of this prop is a little complicated due to JSON serialization
+    DatasetProperty fileTypeProp = getPropByName("File Types", props);
+    java.lang.reflect.Type listOfFileTypes = new TypeToken<ArrayList<FileTypeObject>>() {}.getType();
+    Gson gson = new Gson();
+    List<FileTypeObject> fileTypes = gson.fromJson(fileTypeProp.getPropertyValueAsString(), listOfFileTypes);
+    assertFalse(fileTypes.isEmpty());
+    FileTypeObject type = fileTypes.get(0);
+    assertEquals(FileType.ARRAYS, type.getFileType());
+  }
+
+  private DatasetProperty getPropByName(String name, List<DatasetProperty> props ) {
+    return props.stream().filter(p -> p.getPropertyName().equals(name)).findFirst().orElse(null);
+  }
+
+  @Test
+  void testDatasetUpdateNullValues() {
+    String json = """
+        {
+          "not_a_name": "Test Dataset Update",
+          "not_a_dac_id": 1,
+          "no_properties": [
+            {
+              "propertyName": "string value",
+              "propertyValue": "TDR Location"
+            }
+          ]
+        }""";
+    DatasetUpdate update = new DatasetUpdate(json);
+    assertNull(update.getName());
+    assertNull(update.getDacId());
+    assertNull(update.getDatasetProperties());
+  }
+
+}