Repackage application as a runnable WAR

The previous build created a fat JAR that could only be run from the command line. This commit modifies the Gradle configuration to build a WAR that can be run inside an application server. Command-line behaviour is preserved by the Spring Boot Gradle plugin which adds provided dependencies to the WAR.

  Resolves issue #31.

shim-server/build.gradle

@@ -5,19 +5,20 @@ buildscript {
     }
 
     ext {
-        springBootVersion = "1.3.0.RELEASE"
+        springBootVersion = "1.3.1.RELEASE"
     }
 
     dependencies {
         classpath "org.springframework.boot:spring-boot-gradle-plugin:${springBootVersion}"
     }
 }
 
+apply plugin: 'war'
 apply plugin: 'spring-boot'
 
 version = shimmerVersion
 
-jar {
+war {
     baseName = 'shimmer'
 }
 
@@ -29,10 +30,6 @@ ext {
     signpostVersion = '1.2.1.2'
 }
 
-configurations {
-    compile.exclude module: "spring-boot-starter-tomcat"
-}
-
 dependencies {
     compile project(':java-shim-sdk')
     compile "commons-io:commons-io:2.4"
@@ -49,33 +46,53 @@ dependencies {
     compile "oauth.signpost:signpost-commonshttp4:${signpostVersion}"
     compile "oauth.signpost:signpost-core:${signpostVersion}"
     compile "org.springframework.boot:spring-boot-autoconfigure"
-    compile "org.springframework.boot:spring-boot-starter-jetty"
     compile "org.springframework.data:spring-data-mongodb"
     compile "org.springframework.security.oauth:spring-security-oauth"
     compile "org.springframework.security.oauth:spring-security-oauth2"
     compile "org.springframework:spring-web"
     compile "org.springframework:spring-webmvc"
     compile "javax.validation:validation-api:1.1.0.Final"
-    compile "org.codehaus.woodstox:woodstox-core-asl:4.4.1" // required to print XML
 
-    testCompile 'org.testng:testng:6.8.21' // slowly migrate to TestNG
+    testCompile "org.hamcrest:hamcrest-core"
+    testCompile "org.hamcrest:hamcrest-library"
     testCompile "junit:junit"
     testCompile "org.mockito:mockito-core"
-    testCompile "org.springframework.boot:spring-boot-starter-test"
+    testCompile "org.springframework:spring-test"
+    testCompile "org.testng:testng:6.8.21" // slowly migrate to TestNG
 
     runtime "org.glassfish:javax.el"
     runtime 'org.slf4j:jcl-over-slf4j'
     runtime 'org.slf4j:log4j-over-slf4j'
     runtime 'ch.qos.logback:logback-classic'
     runtime "org.yaml:snakeyaml"
+
+    /* Servlet API and Jetty dependencies shouldn't be included in the `lib` directory of the assembled WAR file,
+       as they'll conflict with existing classes in the application server's classpath. To prevent them from being
+       copied into the WAR file, their scope is set to `providedCompile` or `providedRuntime` as defined
+       by the Gradle WAR plugin.
+
+       In order to make the WAR executable from the command line, the Spring Boot Gradle plugin copies the
+       dependencies to a different directory in the WAR file called `lib-provided`, which is ignored by the application
+       server but contributes classes to the classpath when running with `java -jar`.
+
+       Unfortunately, IntelliJ's Spring Boot run configuration doesn't include dependencies with provided scope in the
+       application classpath, and the application fails to start because of missing classes. This is tracked
+       at https://youtrack.jetbrains.com/issue/IDEA-107048. To get around this, you can either use a Gradle run
+       configuration and set it to execute the `bootRun` task. Or you can use the Spring Boot run configuration
+       and toggle the comments on the following four lines.
+    */
+    providedCompile "javax.servlet:javax.servlet-api"
+    providedRuntime "org.springframework.boot:spring-boot-starter-jetty"
+    // compile "javax.servlet:javax.servlet-api"
+    // runtime "org.springframework.boot:spring-boot-starter-jetty"
 }
 
-task copyArchiveJarToDockerContext(dependsOn: assemble, type: Copy) {
+task copyWarToDockerContext(dependsOn: assemble, type: Copy) {
     from 'build/libs'
     into 'docker'
-    include "${jar.archiveName}"
+    include "${war.archiveName}"
     rename { String fileName ->
-        fileName.replace("${jar.archiveName}", "${jar.baseName}.jar")
+        fileName.replace("${war.archiveName}", "${war.baseName}.war")
     }
 }
-build.dependsOn copyArchiveJarToDockerContext
+build.dependsOn copyWarToDockerContext

shim-server/docker/Dockerfile

@@ -4,7 +4,7 @@ MAINTAINER Emerson Farrugia <[email protected]>
 ENV SERVER_PREFIX /opt/omh/shimmer
 
 RUN mkdir -p $SERVER_PREFIX
-ADD shimmer.jar $SERVER_PREFIX/
+ADD shimmer.war $SERVER_PREFIX/
 EXPOSE 8083
 
-CMD /usr/bin/java -jar $SERVER_PREFIX/shimmer.jar --spring.config.location=file:$SERVER_PREFIX/
+CMD /usr/bin/java -jar $SERVER_PREFIX/shimmer.war --spring.config.location=file:$SERVER_PREFIX/

shim-server/src/main/java/org/openmhealth/shimmer/Application.java

@@ -19,12 +19,12 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.builder.SpringApplicationBuilder;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.boot.context.web.SpringBootServletInitializer;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.ComponentScan;
 import org.springframework.data.mongodb.repository.config.EnableMongoRepositories;
-import org.springframework.security.config.annotation.web.builders.HttpSecurity;
-import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
 
 import static org.openmhealth.schema.configuration.JacksonConfiguration.newObjectMapper;
 
@@ -34,22 +34,17 @@
  */
 @SpringBootApplication
 @EnableConfigurationProperties
-@EnableMongoRepositories("org.openmhealth.shim") // FIXME confirm
-@ComponentScan(basePackages = {"org.openmhealth.shim", "org.openmhealth.shimmer"}) // FIXME confirm
-public class Application extends WebSecurityConfigurerAdapter {
+@EnableMongoRepositories("org.openmhealth.shim")
+@ComponentScan(basePackages = {"org.openmhealth.shim", "org.openmhealth.shimmer"})
+public class Application extends SpringBootServletInitializer {
 
-    public static void main(String[] args) {
-        SpringApplication.run(Application.class, args);
-    }
-
-    // TODO refactor authentication
     @Override
-    protected void configure(HttpSecurity http) throws Exception {
+    protected SpringApplicationBuilder configure(SpringApplicationBuilder application) {
+        return application.sources(Application.class);
+    }
 
-        /**
-         * Allow full anonymous authentication.
-         */
-        http.csrf().disable().authorizeRequests().anyRequest().permitAll();
+    public static void main(String[] args) {
+        SpringApplication.run(Application.class, args);
     }
 
     // TODO look into Jackson2ObjectMapperBuilder to support Spring Boot configuration, e.g. for indentation

shim-server/src/main/java/org/openmhealth/shimmer/common/configuration/SecurityConfiguration.java

@@ -0,0 +1,24 @@
+package org.openmhealth.shimmer.common.configuration;
+
+import org.springframework.context.annotation.Configuration;
+import org.springframework.security.config.annotation.web.builders.HttpSecurity;
+import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
+
+
+/**
+ * TODO this is just a refactoring of existing code, needs to be revised
+ *
+ * @author Emerson Farrugia
+ */
+@Configuration
+public class SecurityConfiguration extends WebSecurityConfigurerAdapter {
+
+    @Override
+    protected void configure(HttpSecurity http) throws Exception {
+
+        /**
+         * Allow full anonymous authentication.
+         */
+        http.csrf().disable().authorizeRequests().anyRequest().permitAll();
+    }
+}

shim-server/src/main/resources/application.yaml

@@ -1,10 +1,6 @@
 spring:
   application:
-    name: Open mHealth shim server
-  # this is necessary to prevent proxy errors due https://github.com/spring-projects/spring-boot/issues/1929
-  dao:
-    exceptiontranslation:
-      enabled: false
+    name: Shimmer
   data:
     mongodb:
       uri: mongodb://mongo:27017/omh_dsu
@@ -17,16 +13,16 @@ security:
   basic:
     enabled: false
 logging:
-  file: omh-shims.log
+  file: shimmer.log
 
 openmhealth:
   shim:
     server:
       callbackUrlBase: http://localhost:8083
 
-    #NOTE: Un-comment and fill in the clientId/clientSecret with your credentials if you're not using the UI
-    #NOTE: Un-comment and set partnerAccess to true if your credentials for a given API have partner access
-    #NOTE: Un-comment and fill in your serialValues for iHealth, otherwise the iHealth shim will not work correctly
+    #NOTE: Uncomment and fill in the clientId/clientSecret with your credentials if you're not using the UI
+    #NOTE: Uncomment and set partnerAccess to true if your credentials for a given API have partner access
+    #NOTE: Uncomment and fill in your serialValues for iHealth, otherwise the iHealth shim will not work correctly
     #ihealth:
     #  serialValues:
     #    SC: [YOUR_SC_VALUE]