Merge pull request #372 from overture-stack/develop

Merges develop into master for new stable.
overture-stack · Aug 2, 2019 · e68b6ae · e68b6ae
2 parents 75d92d3 + 21d2552
commit e68b6ae
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Showing 81 changed files with 3,534 additions and 3,529 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -3,7 +3,7 @@ executorType: machine
 jobs:
   test:
     docker:
-      - image: circleci/openjdk:8-jdk
+      - image: circleci/openjdk:11-jdk
 
     working_directory: ~/repo
 

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM java:8-jdk
+FROM openjdk:11.0.3-jdk
 
 ARG MAVEN_VERSION=3.5.3
 ARG SHA=b52956373fab1dd4277926507ab189fb797b3bc51a2a267a193c931fffad8408

diff --git a/README.md b/README.md
@@ -14,7 +14,7 @@
 [![Slack](http://slack.overture.bio/badge.svg)](http://slack.overture.bio)
 
 ## Table of Contents
-
+- [Documentation](#documentation)
 - [Introduction](#introduction)
 - [Features](#features)
 - [Tech Stack](#tech-stack)
@@ -27,6 +27,10 @@
 - [Shoutouts](#shoutouts)
   - [Browserstack](#browserstack)
 
+## Documentation
+
+Explore documentation with the Ego [Read the Docs](https://ego.readthedocs.io/en/latest/).
+
 ## Introduction
 
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

diff --git a/pom.xml b/pom.xml
@@ -5,23 +5,24 @@
 
     <groupId>bio.overture</groupId>
     <artifactId>ego</artifactId>
-    <version>2.2.1</version>
+    <version>2.2.2-SNAPSHOT</version>
 
     <name>ego</name>
     <description>OAuth 2.0 Authorization service that supports multiple OpenID Connect Providers</description>
 
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.0.2.RELEASE</version>
+        <version>2.1.4.RELEASE</version>
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <java.version>1.8</java.version>
+        <java.version>11</java.version>
         <mapstruct.version>1.2.0.Final</mapstruct.version>
+        <grpc.version>1.19.0</grpc.version>
     </properties>
 
     <dependencies>
@@ -59,8 +60,10 @@
         <dependency>
             <groupId>org.projectlombok</groupId>
             <artifactId>lombok</artifactId>
+            <version>1.18.8</version>
             <optional>true</optional>
         </dependency>
+
         <dependency>
             <groupId>io.springfox</groupId>
             <artifactId>springfox-swagger2</artifactId>
@@ -124,17 +127,17 @@
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>testcontainers</artifactId>
-            <version>1.7.2</version>
+            <version>1.10.0</version>
         </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>jdbc</artifactId>
-            <version>1.7.2</version>
+            <version>1.10.0</version>
         </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>postgresql</artifactId>
-            <version>1.7.2</version>
+            <version>1.10.0</version>
         </dependency>
         <dependency>
             <groupId>commons-io</groupId>
@@ -159,7 +162,7 @@
         <dependency>
             <groupId>com.google.api-client</groupId>
             <artifactId>google-api-client</artifactId>
-            <version>1.23.0</version>
+            <version>1.28.0</version>
         </dependency>
 
         <!-- Json Web Tokens -->
@@ -172,16 +175,10 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.9.8</version>
+            <version>2.9.9.1</version>
         </dependency>
 
         <!-- Testing -->
-        <dependency>
-            <groupId>org.assertj</groupId>
-            <artifactId>assertj-core</artifactId>
-            <version>3.11.1</version>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>net.javacrumbs.json-unit</groupId>
             <artifactId>json-unit-fluent</artifactId>
@@ -239,6 +236,39 @@
             <version>${mapstruct.version}</version>
         </dependency>
 
+        <!-- gRPC -->
+        <dependency>
+            <groupId>io.grpc</groupId>
+            <artifactId>grpc-netty-shaded</artifactId>
+            <version>${grpc.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>io.grpc</groupId>
+            <artifactId>grpc-protobuf</artifactId>
+            <version>${grpc.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>io.grpc</groupId>
+            <artifactId>grpc-stub</artifactId>
+            <version>${grpc.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
+            <version>27.1-jre</version>
+        </dependency>
+        <dependency>
+            <groupId>io.grpc</groupId>
+            <artifactId>grpc-services</artifactId>
+            <version>${grpc.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>io.grpc</groupId>
+            <artifactId>grpc-testing</artifactId>
+            <version>${grpc.version}</version>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-devtools</artifactId>
@@ -251,9 +281,22 @@
             <version>1.2</version>
         </dependency>
 
+        <dependency>
+            <groupId>org.glassfish.jaxb</groupId>
+            <artifactId>jaxb-runtime</artifactId>
+        </dependency>
+
     </dependencies>
 
     <build>
+        <extensions>
+            <extension>
+                <groupId>kr.motd.maven</groupId>
+                <artifactId>os-maven-plugin</artifactId>
+                <version>1.5.0.Final</version>
+            </extension>
+        </extensions>
+
         <plugins>
             <plugin>
                 <groupId>com.coveo</groupId>
@@ -300,6 +343,26 @@
                     </execution>
                 </executions>
             </plugin>
+
+            <plugin>
+                <groupId>org.xolstice.maven.plugins</groupId>
+                <artifactId>protobuf-maven-plugin</artifactId>
+                <version>0.5.1</version>
+                <configuration>
+                    <protocArtifact>com.google.protobuf:protoc:3.6.1:exe:${os.detected.classifier}</protocArtifact>
+                    <protoSourceRoot>${basedir}/src/main/proto</protoSourceRoot>
+                    <pluginId>grpc-java</pluginId>
+                    <pluginArtifact>io.grpc:protoc-gen-grpc-java:1.19.0:exe:${os.detected.classifier}</pluginArtifact>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>compile</goal>
+                            <goal>compile-custom</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
         <resources>
             <resource>

diff --git a/src/main/java/bio/overture/ego/controller/PolicyController.java b/src/main/java/bio/overture/ego/controller/PolicyController.java
@@ -89,6 +89,12 @@ public PolicyController(
         dataType = "string",
         paramType = "query",
         value = "Search for ids containing this text"),
+    @ApiImplicitParam(
+        name = Fields.NAME,
+        required = false,
+        dataType = "string",
+        paramType = "query",
+        value = "Search for polices whose names containing this text"),
     @ApiImplicitParam(
         name = LIMIT,
         required = false,

diff --git a/src/main/java/bio/overture/ego/controller/UserController.java b/src/main/java/bio/overture/ego/controller/UserController.java
@@ -386,18 +386,18 @@ public void deleteGroupsFromUser(
   public @ResponseBody User addApplicationsToUser(
       @RequestHeader(value = HttpHeaders.AUTHORIZATION, required = true) final String accessToken,
       @PathVariable(value = "id", required = true) UUID id,
-      @RequestBody(required = true) List<UUID> appIds) {
-    return userService.addUserToApps(id, appIds);
+      @RequestBody(required = true) List<UUID> applicationIds) {
+    return userService.associateApplicationsWithUser(id, applicationIds);
   }
 
   @AdminScoped
-  @RequestMapping(method = RequestMethod.DELETE, value = "/{id}/applications/{appIds}")
+  @RequestMapping(method = RequestMethod.DELETE, value = "/{id}/applications/{applicationIds}")
   @ApiResponses(value = {@ApiResponse(code = 200, message = "Delete Applications from User")})
   @ResponseStatus(value = HttpStatus.OK)
   public void deleteApplicationsFromUser(
       @RequestHeader(value = HttpHeaders.AUTHORIZATION, required = true) final String accessToken,
       @PathVariable(value = "id", required = true) UUID id,
-      @PathVariable(value = "appIds", required = true) List<UUID> appIds) {
-    userService.deleteUserFromApps(id, appIds);
+      @PathVariable(value = "applicationIds", required = true) List<UUID> applicationIds) {
+    userService.disassociateApplicationsFromUser(id, applicationIds);
   }
 }
diff --git a/src/main/java/bio/overture/ego/grpc/GrpcServer.java b/src/main/java/bio/overture/ego/grpc/GrpcServer.java
@@ -0,0 +1,71 @@
+package bio.overture.ego.grpc;
+
+import bio.overture.ego.grpc.interceptor.AuthInterceptor;
+import bio.overture.ego.grpc.service.UserServiceGrpcImpl;
+import io.grpc.Server;
+import io.grpc.ServerBuilder;
+import io.grpc.ServerInterceptors;
+import java.util.Optional;
+import lombok.NonNull;
+import lombok.extern.slf4j.Slf4j;
+import lombok.val;
+import org.springframework.beans.factory.DisposableBean;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.CommandLineRunner;
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Component;
+
+@Slf4j
+@Component
+@Profile("grpc")
+public class GrpcServer implements CommandLineRunner, DisposableBean {
+
+  @Value("${grpc.port}")
+  private int port;
+
+  private Server server;
+
+  private final AuthInterceptor authInterceptor;
+  private final UserServiceGrpcImpl userServiceImpl;
+
+  @Autowired
+  public GrpcServer(
+      @NonNull AuthInterceptor authInterceptor, @NonNull UserServiceGrpcImpl userServiceImpl) {
+
+    this.authInterceptor = authInterceptor;
+
+    this.userServiceImpl = userServiceImpl;
+  }
+
+  @Override
+  public void run(String... args) throws Exception {
+
+    val userService = ServerInterceptors.intercept(userServiceImpl, authInterceptor);
+
+    server = ServerBuilder.forPort(port).addService(userService).build().start();
+
+    log.info("gRPC Server started, listening on " + port);
+    startDaemonAwaitThread();
+  }
+
+  private void startDaemonAwaitThread() {
+    Thread awaitThread =
+        new Thread(
+            () -> {
+              try {
+                this.server.awaitTermination();
+              } catch (InterruptedException e) {
+                log.error("gRPC server stopped.", e);
+              }
+            });
+    awaitThread.start();
+  }
+
+  @Override
+  public final void destroy() throws Exception {
+    log.info("Shutting down gRPC server ...");
+    Optional.ofNullable(server).ifPresent(Server::shutdown);
+    log.info("gRPC server stopped.");
+  }
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,7 +3,7 @@ executorType: machine @@
     jobs:
       test:
         docker:
-          - image: circleci/openjdk:8-jdk
+          - image: circleci/openjdk:11-jdk
         working_directory: ~/repo
@@ Expand Down @@