Update build.gradle files to correspond with pom.xml changes within m…

…aster branch up to f10399d

build.gradle

@@ -74,6 +74,7 @@ ext.library = [
     datastore_v1_proto_client: "com.google.cloud.datastore:datastore-v1-proto-client:1.4.0",
     datastore_v1_protos: "com.google.cloud.datastore:datastore-v1-protos:1.3.0",
     error_prone_annotations: "com.google.errorprone:error_prone_annotations:2.0.15",
+    findbugs_annotations: "com.github.stephenc.findbugs:findbugs-annotations:1.3.9-1",
     findbugs_jsr305: "com.google.code.findbugs:jsr305:3.0.1",
     gax_grpc: "com.google.api:gax-grpc:0.20.0",
     google_api_client: "com.google.api-client:google-api-client:$google_clients_version",
@@ -83,7 +84,7 @@ ext.library = [
     google_api_services_bigquery: "com.google.apis:google-api-services-bigquery:v2-rev355-$google_clients_version",
     google_api_services_clouddebugger: "com.google.apis:google-api-services-clouddebugger:v2-rev8-$google_clients_version",
     google_api_services_cloudresourcemanager: "com.google.apis:google-api-services-cloudresourcemanager:v1-rev6-$google_clients_version",
-    google_api_services_dataflow: "com.google.apis:google-api-services-dataflow:v1b3-rev214-$google_clients_version",
+    google_api_services_dataflow: "com.google.apis:google-api-services-dataflow:v1b3-rev218-$google_clients_version",
     google_api_services_pubsub: "com.google.apis:google-api-services-pubsub:v1-rev10-$google_clients_version",
     google_api_services_storage: "com.google.apis:google-api-services-storage:v1-rev71-$google_clients_version",
     google_auth_library_credentials: "com.google.auth:google-auth-library-credentials:$google_auth_version",
@@ -254,6 +255,9 @@ rat {
     // Proto/grpc generated wrappers
     "**/apache_beam/portability/api/*_pb2*.py",
     "**/go/pkg/beam/model/**/*.pb.go",
+
+    // VCF test files
+    "**/apache_beam/testing/data/vcf/*",
   ]
 }
 check.dependsOn rat

runners/core-construction-java/build.gradle

@@ -31,6 +31,7 @@ test {
 
 dependencies {
   compile library.java.guava
+  compileOnly librarj.java.findbugs_annotations
   shadow project(path: ":beam-model-parent:beam-model-pipeline", configuration: "shadow")
   shadow project(path: ":beam-model-parent:beam-model-job-management", configuration: "shadow")
   shadow project(path: ":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-core", configuration: "shadow")

runners/core-java/build.gradle

@@ -31,6 +31,7 @@ test {
 
 dependencies {
   compile library.java.guava
+  compileOnly library.java.findbugs_annotations
   shadow project(path: ":beam-model-parent:beam-model-pipeline", configuration: "shadow")
   shadow project(path: ":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-core", configuration: "shadow")
   shadow project(path: ":beam-model-parent:beam-model-fn-execution", configuration: "shadow")

runners/direct-java/build.gradle

@@ -64,6 +64,7 @@ shadowJar {
   relocate "org.apache.beam.runners.core", "org.apache.beam." + project.name.replace("-", ".") + ".repackaged.runners.core"
   relocate "org.apache.beam.model", "org.apache.beam." + project.name.replace("-", ".") + ".repackaged.model"
   relocate "com.google.protobuf", "org.apache.beam." + project.name.replace("-", ".") + ".repackaged.com.google.protobuf"
+  relocate "javax.annotation", "org.apache.beam." + project.name.replace("-", ".") + ".repackaged.javax.annotation"
 }
 
 task packageTests(type: Jar) {

runners/google-cloud-dataflow-java/build.gradle

@@ -36,7 +36,7 @@ processResources {
   filter org.apache.tools.ant.filters.ReplaceTokens, tokens: [
     'dataflow.legacy_environment_major_version' : '6',
     'dataflow.fnapi_environment_major_version' : '1',
-    'dataflow.container_version' : 'beam-master-20170926'
+    'dataflow.container_version' : 'beam-master-20171113'
   ]
 }
 

runners/java-fn-execution/build.gradle

@@ -17,7 +17,7 @@
  */
 
 apply from: project(":").file("build_rules.gradle")
-applyJavaNature(javaVersion: 1.8)
+applyJavaNature()
 
 description = "Apache Beam :: Runners :: Java Fn Execution"
 
@@ -30,6 +30,14 @@ description = "Apache Beam :: Runners :: Java Fn Execution"
  */
 evaluationDependsOn(":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-fn-execution")
 
+configurations.all {
+  // Fn Execution contains shared utilities for Runners and Harnesses which use            
+  // the Portability framework. Runner-side interactions must not require a
+  // dependency on any particular SDK, so this library must not introduce such an
+  // edge.
+  exclude group: "org.apache.beam", module: "beam-sdks-java-core"
+}
+
 dependencies {
   compile library.java.guava
   shadow project(path: ":beam-model-parent:beam-model-pipeline", configuration: "shadow")
@@ -38,10 +46,12 @@ dependencies {
   shadow library.java.grpc_core
   shadow library.java.grpc_stub
   shadow library.java.grpc_netty
+  shadow library.java.slf4j_api
   testCompile project(":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-fn-execution").sourceSets.test.output
   testCompile library.java.junit
   testCompile library.java.hamcrest_core
   testCompile library.java.hamcrest_library
+  testCompile library.java.mockito_core
 }
 
 task packageTests(type: Jar) {

sdks/java/core/build.gradle

@@ -53,7 +53,7 @@ dependencies {
   compile library.java.byte_buddy
   compile library.java.commons_compress
   compile library.java.commons_lang3
-  compileOnly "com.github.stephenc.findbugs:findbugs-annotations:1.3.9-1"
+  compileOnly library.java.findbugs_annotations
   shadow library.java.jackson_core
   shadow library.java.jackson_annotations
   shadow library.java.jackson_databind

sdks/java/extensions/sql/build.gradle

@@ -33,6 +33,8 @@ dependencies {
   compile "org.apache.calcite:calcite-core:$calcite_version"
   compile "org.apache.calcite:calcite-linq4j:$calcite_version"
   compile "org.apache.calcite.avatica:avatica-core:$avatica_version"
+  compile "com.alibaba:fastjson:1.2.12"
+  compileOnly library.java.findbugs_jsr305
   shadow project(path: ":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-core", configuration: "shadow")
   shadow project(path: ":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-extensions-parent:beam-sdks-java-extensions-join-library", configuration: "shadow")
   shadow library.java.slf4j_api
@@ -44,8 +46,11 @@ dependencies {
   testCompile library.java.slf4j_jdk14
   testCompile library.java.junit
   testCompile library.java.hamcrest_core
+  testCompile library.java.mockito_core
 }
 
+// TODO: Add support for generating fmpp
+
 shadowJar {
   dependencies {
     include(dependency("org.apache.calcite:.*"))

sdks/java/fn-execution/build.gradle

@@ -17,9 +17,17 @@
  */
 
 apply from: project(":").file("build_rules.gradle")
-applyJavaNature(javaVersion: 1.8)
+applyJavaNature()
 
-description = "Apache Beam :: SDKs :: Java :: Harness Core"
+description = "Apache Beam :: SDKs :: Java :: Fn Execution"
+
+configurations.all {
+  // Fn Execution contains shared utilities for Runners and Harnesses which use
+  // the Portability framework. Runner-side interactions must not require a
+  // dependency on any particular SDK, so this library must not introduce such an
+  // edge.
+  exclude group: "org.apache.beam", module: "beam-sdks-java-core"
+}
 
 dependencies {
   compile library.java.guava

sdks/java/io/file-based-io-tests/build.gradle

@@ -0,0 +1,48 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * License); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an AS IS BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+apply from: project(":").file("build_rules.gradle")
+applyJavaNature()
+
+description = "Apache Beam :: SDKs :: Java :: File-based-io-tests"
+
+/*
+ * We need to rely on manually specifying these evaluationDependsOn to ensure that
+ * the following projects are evaluated before we evaluate this project. This is because
+ * we are attempting to reference the "sourceSets.test.output" directly.
+ * TODO: Swap to generating test artifacts which we can then rely on instead of
+ * the test outputs directly.
+ */
+evaluationDependsOn(":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-common")
+
+dependencies {
+  shadowTest project(":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-core")
+  shadowTest project(":beam-runners-parent:beam-runners-direct-java").sourceSets.test.output
+  shadowTest project(":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-common")
+  shadowTest project(":beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-common").sourceSets.test.output
+  shadowTest library.java.guava
+  shadowTest library.java.junit
+  shadowTest library.java.hamcrest_core
+}
+
+task packageTests(type: Jar) {
+  from sourceSets.test.output
+  classifier = "tests"
+}
+
+artifacts.archives packageTests

settings.gradle

@@ -50,6 +50,7 @@ include ':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-s
 include ':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-redis'
 include ':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-solr'
 include ':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-tika'
+include ':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-file-based-io-tests'
 include ':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-xml'
 include ':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent'
 include ':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-maven-archetypes-parent:beam-sdks-java-maven-archetypes-starter'
@@ -125,6 +126,7 @@ project(':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-s
 project(':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-redis').projectDir = "$rootDir/sdks/java/io/redis" as File
 project(':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-solr').projectDir = "$rootDir/sdks/java/io/solr" as File
 project(':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-tika').projectDir = "$rootDir/sdks/java/io/tika" as File
+project(':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-file-based-io-tests').projectDir = "$rootDir/sdks/java/io/file-based-io-tests" as File
 project(':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent:beam-sdks-java-io-xml').projectDir = "$rootDir/sdks/java/io/xml" as File
 project(':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-io-parent').projectDir = "$rootDir/sdks/java/io" as File
 project(':beam-sdks-parent:beam-sdks-java-parent:beam-sdks-java-maven-archetypes-parent:beam-sdks-java-maven-archetypes-starter').projectDir = "$rootDir/sdks/java/maven-archetypes/starter" as File