port [zjsonpatch](https://github.com/flipkart-incubator/zjsonpatch) v…

…ersion [0.4.12](https://github.com/flipkart-incubator/zjsonpatch/releases/tag/0.4.12)

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,70 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '34 20 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://git.io/codeql-language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.gitignore

@@ -4,3 +4,4 @@ target/*
 .settings/*
 .DS_Store
 /target/
+.idea

NOTICE

@@ -1,5 +1,5 @@
 bsonpatch library
-Copyright 2017,2018 eBay, Inc.
+Copyright 2017,2018,2022 eBay, Inc.
 
 This product includes software developed at
 eBay, Inc. (https://www.ebay.com/).

README.md

@@ -1,14 +1,15 @@
-# This is an implementation of  [RFC 6902 JSON Patch](http://tools.ietf.org/html/rfc6902) written in Java.
+# This is an implementation of  [RFC 6902 JSON Patch](https://datatracker.ietf.org/doc/html/rfc6902) written in Java.
 
 This [JSON Patch](http://jsonpatch.com) implementation works directly with [BSON documents](http://bsonspec.org/) using the [MongoDB Java driver implementation of BSON](https://www.mongodb.com/json-and-bson). 
 
 The code here was ported (copied, renamed, repackaged, modified) from the [zjsonpatch project](https://github.com/flipkart-incubator/zjsonpatch).
 
 ## Description & Use-Cases
-- Java Library to find / apply JSON Patches according to [RFC 6902](http://tools.ietf.org/html/rfc6902).
+- Java Library to find / apply JSON Patches according to [RFC 6902](https://datatracker.ietf.org/doc/html/rfc6902).
 - JSON Patch defines a JSON document structure for representing changes to a JSON document.
 - It can be used to avoid sending a whole document when only a part has changed, thus reducing network bandwidth requirements if data (in JSON format) is required to send across multiple systems over network or in case of multi DC transfer.
-- This library compares two [BsonValue](http://mongodb.github.io/mongo-java-driver/3.6/javadoc/org/bson/BsonValue.html) inputs and produces a [BsonArray](http://mongodb.github.io/mongo-java-driver/3.6/javadoc/org/bson/BsonArray.html) of the changes.
+- When used in combination with the HTTP PATCH method as per [RFC 5789 HTTP PATCH](https://datatracker.ietf.org/doc/html/rfc5789), it will do partial updates for HTTP APIs in a standard  way.
+- This library compares two [BsonValue](https://mongodb.github.io/mongo-java-driver/3.12/javadoc/org/bson/BsonValue.html) inputs and produces a [BsonArray](https://mongodb.github.io/mongo-java-driver/3.12/javadoc/org/bson/BsonArray.html) of the changes.
 
 
 ### Compatible with : Java 8 and above all versions
@@ -20,15 +21,15 @@ The code here was ported (copied, renamed, repackaged, modified) from the [zjson
 
 ### How to use:
 
-### Current Version : 0.4.9
+### Current Version : 0.4.12
 
 Add following to `<dependencies/>` section of your pom.xml -
 
 ```xml
 <dependency>
   <groupId>com.ebay.bsonpatch</groupId>
   <artifactId>bsonpatch</artifactId>
-  <version>0.4.9</version>
+  <version>0.4.12</version>
 </dependency>
 ```
 
@@ -42,7 +43,7 @@ Computes and returns a JSON `patch` (as a BsonArray) from `source`  to `target`,
 Both `source` and `target` must be either valid BSON objects or arrays or values. 
 Further, if resultant `patch` is applied to `source`, it will yield `target`.
 
-The algorithm which computes this JsonPatch currently generates following operations as per [RFC 6902](https://tools.ietf.org/html/rfc6902) -  
+The algorithm which computes this JsonPatch currently generates following operations as per [RFC 6902](https://datatracker.ietf.org/doc/html/rfc6902#section-4) -  
  - `add`
  - `remove`
  - `replace`

pom.xml

@@ -6,7 +6,7 @@
 
 	<groupId>com.ebay.bsonpatch</groupId>
 	<artifactId>bsonpatch</artifactId>
-	<version>0.4.9</version>
+	<version>0.4.12</version>
 	<packaging>jar</packaging>
 
 	<name>${project.groupId}:${project.artifactId}</name>
@@ -47,7 +47,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.8.1</version>
+				<version>3.10.1</version>
 				<configuration>
 					<source>1.8</source>
 					<target>1.8</target>
@@ -61,7 +61,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>
-				<version>3.0.1</version>
+				<version>3.2.1</version>
 				<executions>
 					<execution>
 						<id>attach-sources</id>
@@ -118,7 +118,7 @@
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-javadoc-plugin</artifactId>
-						<version>2.10.4</version>
+						<version>3.3.2</version>
 						<executions>
 							<execution>
 								<id>attach-javadocs</id>
@@ -137,25 +137,25 @@
 		<dependency>
 			<groupId>org.mongodb</groupId>
 			<artifactId>mongo-java-driver</artifactId>
-			<version>3.11.2</version>
+			<version>3.12.10</version>
 		</dependency>
 		<dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-collections4</artifactId>
-            <version>4.2</version>
+            <version>4.3</version>
         </dependency>
        	<!-- For IOUtils.toString(inputStream, charset) and StringBuilderWriter -->
 		<dependency>
 			<scope>test</scope>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.6</version>
+			<version>2.7</version>
 		</dependency>
 		<dependency>
 			<scope>test</scope>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
-			<version>4.12</version>
+			<version>4.13.1</version>
 		</dependency>
 	</dependencies>
 </project>

src/main/java/com/ebay/bsonpatch/BsonDiff.java

@@ -48,20 +48,29 @@ public static BsonArray asBson(final BsonValue source, final BsonValue target) {
 
     public static BsonArray asBson(final BsonValue source, final BsonValue target, EnumSet<DiffFlags> flags) {
         BsonDiff diff = new BsonDiff(flags);
-
-        // generating diffs in the order of their occurrence
-        diff.generateDiffs(JsonPointer.ROOT, source, target);
-
-        if (!flags.contains(DiffFlags.OMIT_MOVE_OPERATION)) {        
-	         // Merging remove & add to move operation
-        	diff.introduceMoveOperation();
+        if (source == null && target != null) {
+            // return add node at root pointing to the target
+            diff.diffs.add(Diff.generateDiff(Operation.ADD, JsonPointer.ROOT, target));
         }
-
-        if (!flags.contains(DiffFlags.OMIT_COPY_OPERATION)) {
-	         // Introduce copy operation
-        	diff.introduceCopyOperation(source, target);
+        if (source != null && target == null) {
+            // return remove node at root pointing to the source
+            diff.diffs.add(Diff.generateDiff(Operation.REMOVE, JsonPointer.ROOT, source));
         }
+        if (source != null && target != null) {
+            diff.generateDiffs(JsonPointer.ROOT, source, target);
+
+            if (!flags.contains(DiffFlags.OMIT_MOVE_OPERATION))
+                // Merging remove & add to move operation
+                diff.introduceMoveOperation();
+
+            if (!flags.contains(DiffFlags.OMIT_COPY_OPERATION))
+                 // Introduce copy operation
+                diff.introduceCopyOperation(source, target);
 
+            if (flags.contains(DiffFlags.ADD_EXPLICIT_REMOVE_ADD_ON_REPLACE))
+                // Split replace into remove and add instructions
+                diff.introduceExplicitRemoveAndAddOperation();
+        }
         return diff.getBsonNodes();
     }
 
@@ -212,6 +221,26 @@ private void introduceMoveOperation() {
         }
     }
 
+    /**
+     * This method splits a {@link Operation#REPLACE} operation within a diff into a {@link Operation#REMOVE}
+     * and {@link Operation#ADD} in order, respectively.
+     * Does nothing if {@link Operation#REPLACE} op does not contain a from value
+     */
+    private void introduceExplicitRemoveAndAddOperation() {
+        List<Diff> updatedDiffs = new ArrayList<Diff>();
+        for (Diff diff : diffs) {
+            if (!diff.getOperation().equals(Operation.REPLACE) || diff.getSrcValue() == null) {
+                updatedDiffs.add(diff);
+                continue;
+            }
+            //Split into two #REMOVE and #ADD
+            updatedDiffs.add(new Diff(Operation.REMOVE, diff.getPath(), diff.getSrcValue()));
+            updatedDiffs.add(new Diff(Operation.ADD, diff.getPath(), diff.getValue()));
+        }
+        diffs.clear();
+        diffs.addAll(updatedDiffs);
+    }
+
     //Note : only to be used for arrays
     //Finds the longest common Ancestor ending at Array
     private static JsonPointer computeRelativePath(JsonPointer path, int startIdx, int endIdx, List<Diff> diffs) {

src/main/java/com/ebay/bsonpatch/CompatibilityFlags.java

@@ -24,7 +24,8 @@
 public enum CompatibilityFlags {
 	MISSING_VALUES_AS_NULLS,
 	REMOVE_NONE_EXISTING_ARRAY_ELEMENT,
-    ALLOW_MISSING_TARGET_OBJECT_ON_REPLACE;
+    ALLOW_MISSING_TARGET_OBJECT_ON_REPLACE,
+    FORBID_REMOVE_MISSING_OBJECT;
 
     public static EnumSet<CompatibilityFlags> defaults() {
         return EnumSet.noneOf(CompatibilityFlags.class);

src/main/java/com/ebay/bsonpatch/DiffFlags.java

@@ -22,6 +22,7 @@
 import java.util.EnumSet;
 
 public enum DiffFlags {
+
     /**
      * This flag omits the <i>value</i> field on remove operations.
      * This is a default flag.
@@ -51,14 +52,32 @@ public enum DiffFlags {
      * <i>fromValue</i> represents the the value replaced by a {@link Operation#REPLACE}
      * operation, in other words, the original value. This can be useful for debugging
      * output or custom processing of the diffs by downstream systems.
-     *
      * Please note that this is a non-standard extension to RFC 6902 and will not affect
      * how patches produced by this library are processed by this or other libraries.
      *
      * @since 0.4.1
      */
     ADD_ORIGINAL_VALUE_ON_REPLACE,
-
+
+    /**
+     * This flag normalizes a {@link Operation#REPLACE} operation into its respective
+     * {@link Operation#REMOVE} and {@link Operation#ADD} operations. Although it adds
+     * a redundant step, this can be useful for auditing systems in which immutability
+     * is a requirement.
+     * <p>
+     * For the flag to work, {@link DiffFlags#ADD_ORIGINAL_VALUE_ON_REPLACE} has to be
+     * enabled as the new instructions in the patch need to grab the old <i>fromValue</i>
+     * {@code "op": "replace", "fromValue": "F1", "value": "F2" }
+     * The above instruction will be split into
+     * {@code "op":"remove", "value":"F1" } and {@code "op":"add", "value":"F2"} respectively.
+     * <p>
+     * Please note that this is a non-standard extension to RFC 6902 and will not affect
+     * how patches produced by this library are processed by this or other libraries.
+     *
+     * @since 0.4.11
+     */
+    ADD_EXPLICIT_REMOVE_ADD_ON_REPLACE,
+
     /**
      * This flag instructs the diff generator to emit {@link Operation#TEST} operations
      * that validate the state of the source document before each mutation. This can be

src/main/java/com/ebay/bsonpatch/InPlaceApplyProcessor.java

@@ -125,13 +125,17 @@ public void remove(JsonPointer path) throws JsonPointerEvaluationException {
 
         BsonValue parentNode = path.getParent().evaluate(target);
         JsonPointer.RefToken token = path.last();
-        if (parentNode.isDocument())
+        if (parentNode.isDocument()) {
+            if (flags.contains(CompatibilityFlags.FORBID_REMOVE_MISSING_OBJECT) && !parentNode.asDocument().containsKey(token.getField()))
+                throw new BsonPatchApplicationException(
+                        "Missing field " + token.getField(), Operation.REMOVE, path.getParent());
             parentNode.asDocument().remove(token.getField());
+        }
         else if (parentNode.isArray()) {
-            if (!flags.contains(CompatibilityFlags.REMOVE_NONE_EXISTING_ARRAY_ELEMENT) && token.getIndex() >= parentNode.asArray().size()) {
-            	
+            if (!flags.contains(CompatibilityFlags.REMOVE_NONE_EXISTING_ARRAY_ELEMENT) &&
+                    token.getIndex() >= parentNode.asArray().size()) {
                 throw new BsonPatchApplicationException(
-                        "Array index " + token.getIndex() + " out of bounds", Operation.REPLACE, path.getParent());
+                        "Array index " + token.getIndex() + " out of bounds", Operation.REMOVE, path.getParent());
             } else if (token.getIndex() >= parentNode.asArray().size()) {
             	// do nothing, don't get upset about index out of bounds if REMOVE_NONE_EXISTING_ARRAY_ELEMENT set 
             	// can't just call remove on BsonArray because it throws index out of bounds exception
@@ -140,7 +144,7 @@ else if (parentNode.isArray()) {
             }
         } else {
             throw new BsonPatchApplicationException(
-                    "Cannot reference past scalar value", Operation.REPLACE, path.getParent());
+                    "Cannot reference past scalar value", Operation.REMOVE, path.getParent());
         }
     }
 

src/test/java/com/ebay/bsonpatch/CompatibilityTest.java

@@ -20,6 +20,7 @@
 package com.ebay.bsonpatch;
 
 import static com.ebay.bsonpatch.CompatibilityFlags.ALLOW_MISSING_TARGET_OBJECT_ON_REPLACE;
+import static com.ebay.bsonpatch.CompatibilityFlags.FORBID_REMOVE_MISSING_OBJECT;
 import static com.ebay.bsonpatch.CompatibilityFlags.MISSING_VALUES_AS_NULLS;
 import static com.ebay.bsonpatch.CompatibilityFlags.REMOVE_NONE_EXISTING_ARRAY_ELEMENT;
 import static org.hamcrest.core.IsEqual.equalTo;
@@ -30,6 +31,7 @@
 
 import org.bson.BsonArray;
 import org.bson.BsonDocument;
+import org.bson.BsonValue;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -39,13 +41,15 @@ public class CompatibilityTest {
     BsonArray replaceNodeWithMissingValue;
     BsonArray removeNoneExistingArrayElement;
     BsonArray replaceNode;
+    BsonArray removeNode;
 
     @Before
     public void setUp() throws Exception {
     	addNodeWithMissingValue = BsonArray.parse("[{\"op\":\"add\",\"path\":\"/a\"}]");
         replaceNodeWithMissingValue = BsonArray.parse("[{\"op\":\"replace\",\"path\":\"/a\"}]");
         removeNoneExistingArrayElement = BsonArray.parse("[{\"op\": \"remove\",\"path\": \"/b/0\"}]");
         replaceNode = BsonArray.parse("[{\"op\":\"replace\",\"path\":\"/a\",\"value\":true}]");
+        removeNode = BsonArray.parse("[{\"op\":\"remove\",\"path\":\"/b\"}]");
     }
 
     @Test
@@ -87,4 +91,17 @@ public void withFlagReplaceShouldAddValueWhenMissingInTarget() throws Exception
     	BsonDocument result = BsonPatch.apply(replaceNode, BsonDocument.parse("{}"), EnumSet.of(ALLOW_MISSING_TARGET_OBJECT_ON_REPLACE)).asDocument();
         assertThat(result, equalTo(expected));
     }
-}
+
+    @Test(expected = BsonPatchApplicationException.class)
+    public void withFlagRemoveMissingValueShouldThrow() throws Exception {
+        BsonDocument source = BsonDocument.parse("{\"a\": true}");
+        BsonPatch.apply(removeNode, source, EnumSet.of(FORBID_REMOVE_MISSING_OBJECT));
+    }
+
+    @Test
+    public void withFlagRemoveShouldRemove() throws Exception {
+        BsonDocument source = BsonDocument.parse("{\"b\": true}");
+        BsonDocument expected = BsonDocument.parse("{}");
+        BsonValue result = BsonPatch.apply(removeNode, source, EnumSet.of(FORBID_REMOVE_MISSING_OBJECT));
+        assertThat(result, equalTo(expected));
+    }}