Bump versions of dependencies.

Also fix some deprecation warnings in modern databind.

Author: Capstan

project.gradle

@@ -30,15 +30,20 @@ project.ext.description = "JSON Patch (RFC 6902) and JSON Merge Patch (RFC 7386)
  * List of dependencies
  */
 dependencies {
-    provided(group: "com.google.code.findbugs", name: "jsr305", version: "2.0.1");
-    compile(group: "com.github.java-json-tools", name: "jackson-coreutils", version: "1.9");
+    provided(group: "com.google.code.findbugs", name: "jsr305", version: "3.0.2");
+    compile(group: "com.google.guava", name: "guava", version: "28.1-android");
+    compile(group: "com.fasterxml.jackson.core", name: "jackson-databind", version: "2.9.9");
+    compile(group: "com.github.java-json-tools", name: "msg-simple", version: "1.2");
+    
+    compile(group: "com.github.java-json-tools", name: "jackson-coreutils", version: "1.11");
     testCompile(group: "org.testng", name: "testng", version: "6.8.7") {
         exclude(group: "junit", module: "junit");
         exclude(group: "org.beanshell", module: "bsh");
         exclude(group: "org.yaml", module: "snakeyaml");
     };
-    testCompile(group: "org.mockito", name: "mockito-core", version: "1.9.5");
-    testCompile(group: "org.assertj", name: "assertj-core", version: "1.7.0");
+    testCompile(group: "org.mockito", name: "mockito-core", version: "2.28.2");
+    // FIXME: update to 3.x once we're off of Java 7
+    testCompile(group: "org.assertj", name: "assertj-core", version: "2.9.1");
 }
 
 javadoc.options {
@@ -48,11 +53,11 @@ javadoc.options {
         addStringOption("-release", "7");
     }
     links("https://docs.oracle.com/javase/7/docs/api/");
-    links("https://www.javadoc.io/doc/com.google.code.findbugs/jsr305/3.0.1/");
-    links("https://fasterxml.github.com/jackson-databind/javadoc/2.2.0/");
-    links("https://fasterxml.github.com/jackson-core/javadoc/2.2.0/");
-    links("https://fasterxml.github.com/jackson-annotations/javadoc/2.2.0/");
-    links("https://www.javadoc.io/doc/com.google.guava/guava/16.0.1/");
-    links("https://fge.github.io/msg-simple/");
-    links("https://fge.github.io/jackson-coreutils/");
+    links("https://www.javadoc.io/doc/com.google.code.findbugs/jsr305/3.0.2/");
+    links("https://fasterxml.github.com/jackson-databind/javadoc/2.9/");
+    links("https://fasterxml.github.com/jackson-core/javadoc/2.9/");
+    links("https://fasterxml.github.com/jackson-annotations/javadoc/2.9/");
+    links("https://www.javadoc.io/doc/com.google.guava/guava/28.1-android/");
+    links("https://java-json-tools.github.io/msg-simple/");
+    links("https://java-json-tools.github.io/jackson-coreutils/");
 }

src/main/java/com/github/fge/jsonpatch/AddOperation.java

@@ -133,7 +133,7 @@ private JsonNode addToObject(final JsonPointer path, final JsonNode node)
     {
         final JsonNode ret = node.deepCopy();
         final ObjectNode target = (ObjectNode) path.parent().get(ret);
-        target.put(Iterables.getLast(path).getToken().getRaw(), value);
+        target.set(Iterables.getLast(path).getToken().getRaw(), value);
         return ret;
     }
 }

src/main/java/com/github/fge/jsonpatch/JsonPatch.java

@@ -126,7 +126,7 @@ public static JsonPatch fromJson(final JsonNode node)
         throws IOException
     {
         BUNDLE.checkNotNull(node, "jsonPatch.nullInput");
-        return JacksonUtils.getReader().withType(JsonPatch.class)
+        return JacksonUtils.getReader().forType(JsonPatch.class)
             .readValue(node);
     }
 

src/main/java/com/github/fge/jsonpatch/ReplaceOperation.java

@@ -73,7 +73,7 @@ public JsonNode apply(final JsonNode node)
         final JsonNode parent = path.parent().get(ret);
         final String rawToken = Iterables.getLast(path).getToken().getRaw();
         if (parent.isObject())
-            ((ObjectNode) parent).put(rawToken, replacement);
+            ((ObjectNode) parent).replace(rawToken, replacement);
         else
             ((ArrayNode) parent).set(Integer.parseInt(rawToken), replacement);
         return ret;

src/main/java/com/github/fge/jsonpatch/mergepatch/JsonMergePatchDeserializer.java

@@ -96,6 +96,7 @@ public JsonMergePatch deserialize(final JsonParser jp,
      * not what we want.
      */
     @Override
+    @SuppressWarnings("deprecation")
     public JsonMergePatch getNullValue()
     {
         return new NonObjectMergePatch(NullNode.getInstance());

src/main/java/com/github/fge/jsonpatch/mergepatch/ObjectMergePatch.java

@@ -84,7 +84,7 @@ public JsonNode apply(final JsonNode input)
              */
             value = Optional.fromNullable(ret.get(key))
                 .or(NullNode.getInstance());
-            ret.put(key, entry.getValue().apply(value));
+            ret.replace(key, entry.getValue().apply(value));
         }
 
         ret.remove(removedMembers);

src/test/java/com/github/fge/jsonpatch/JsonPatchOperationTest.java

@@ -57,7 +57,7 @@ protected JsonPatchOperationTest(final String prefix)
         final JsonNode node = JsonLoader.fromResource(resource);
         errors = node.get("errors");
         ops = node.get("ops");
-        reader = JacksonUtils.getReader().withType(JsonPatchOperation.class);
+        reader = JacksonUtils.getReader().forType(JsonPatchOperation.class);
     }
 
     @DataProvider