[BEAM-13616][BEAM-13646] Update vendored calcite 1.28.0 with protobuf 3.19.2

vendor/README.md

@@ -28,6 +28,7 @@ The upgrading of the vendored dependencies should be performed in two steps:
 
 # How to validate the vendored dependencies
 
+## Linkage Tool
 The [linkage tool](https://lists.apache.org/thread.html/eb5d95b9a33d7e32dc9bcd0f7d48ba8711d42bd7ed03b9cf0f1103f1%40%3Cdev.beam.apache.org%3E)
 is useful for the vendored dependency upgrades. It reports the linkage errors across multiple Apache Beam artifact ids.
 
@@ -48,7 +49,7 @@ $ mvn install:install-file \
 $ ./gradlew -PvendoredDependenciesOnly -Ppublishing -PjavaLinkageArtifactIds=beam-vendor-grpc-1_36_0:0.1 :checkJavaLinkage
 ```
 
-## Known Linkage Errors in the Vendored gRPC Dependencies
+### Known Linkage Errors in the Vendored gRPC Dependencies
 
 It's expected that the task outputs some linkage errors.
 While the `checkJavaLinkage` task does not retrieve optional dependencies to avoid bloated
@@ -78,3 +79,38 @@ references to the missing classes. Here are the known linkage errors:
   to be included in the vendored artifact. Slf4j-api is available at Beam's runtime.
 - References to `reactor.blockhound`: When enabled, Netty's BlockHound integration can detect
   unexpected blocking calls. Beam does not use it.
+
+## Create testing PR against new artifacts
+
+Once you've verified using the linkage tool, you can test new artifacts by running unit and integration tests against a PR.
+
+Example PRs:
+- Updating gRPC version (large) https://github.com/apache/beam/pull/16460
+- Updating protobuf for calcite (minor version update): https://github.com/apache/beam/pull/16476
+
+Steps:
+
+1. Generate new artifact files with `publishMavenJavaPublicationToMavenLocal`, e.g.
+
+```
+./gradlew -p vendor/grpc-1_43_2 publishMavenJavaPublicationToMavenLocal -Ppublishing -PvendoredDependenciesOnly
+
+# Copy files (jar/poms/metadata) to your beam repository
+cp -R ~/.m2/repository/org/apache/beam/beam-vendor-grpc-1_43_2/ \
+      $BEAMDIR/tempLib/org/apache/beam/beam-vendor-grpc-1_43_2
+```
+
+2. Add whatever folder (here I use `tempLib`) to the expected project repositories, e.g.
+
+```
+repositories {
+    maven { url "${project.rootDir}/tempLib" }
+    maven {
+      ...
+    }
+}
+```
+
+3. Migrate all references from the old dependency to the new dependency, including imports if needed.
+
+4. Commit any added or changed files and create a PR (can be a draft, as you will not merge this PR) to test on.

vendor/calcite-1_28_0/build.gradle

@@ -16,21 +16,35 @@
  * limitations under the License.
  */
 
+/**
+ * Vendored version of calcite.
+ *
+ * To upgrade:
+ * 1. Use mvn dependency:tree and/or https://search.maven.org/search?q=g:org.apache.calcite%20AND%20a:calcite-core
+ *    to determine dependency tree. You may need to search for optional transitive dependencies
+ *    and determine if they need to be added or upgraded (e.g. protobuf)
+ * 3. Validate built artifacts by running linkage tool
+ *    (https://github.com/apache/beam/tree/master/vendor#how-to-validate-the-vendored-dependencies)
+ *    and unit and integration tests in a PR.
+ */
+
 plugins { id 'org.apache.beam.vendor-java' }
 
 description = "Apache Beam :: Vendored Dependencies :: Calcite 1.28.0"
 
 group = "org.apache.beam"
-version = "0.1"
+version = "0.2"
 
 def calcite_version = "1.28.0"
 def avatica_version = "1.19.0"
+def protobuf_version = "3.19.2"
 def prefix = "org.apache.beam.vendor.calcite.v1_28_0"
 
 List<String> packagesToRelocate = [
         "com.esri",
         "com.fasterxml",
         "com.google.common",
+        "com.google.gson",
         "com.google.protobuf",
         "com.google.thirdparty",
         "com.google.uzaygezen",
@@ -52,6 +66,12 @@ vendorJava(
                 "org.apache.calcite:calcite-core:$calcite_version",
                 "org.apache.calcite:calcite-linq4j:$calcite_version",
                 "org.apache.calcite.avatica:avatica-core:$avatica_version",
+
+                // BEAM-13616: Override the version of protobuf to patch a security vulnerability.
+                // This override can be removed once we upgrade to a newer version of calcite that
+                // depends on protobuf >= 3.19.2.
+                "com.google.protobuf:protobuf-java:$protobuf_version",
+                "com.google.protobuf:protobuf-java-util:$protobuf_version",
         ],
         runtimeDependencies: [
                 library.java.slf4j_api,