overture-stack · Aug 9, 2019 · Sep 23, 2019 · Oct 1, 2019 · Oct 1, 2019 · Oct 5, 2019
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM openjdk:8u121-jdk-alpine
+FROM openjdk:12-alpine
 
 ARG MAVEN_VERSION=3.5.4
 ARG SHA=ce50b1c91364cb77efe3776f756a6d92b76d9038b0a0782f7d53acf1e997a14d

diff --git a/Jenkinsfile b/Jenkinsfile
@@ -1,2 +1,20 @@
-@Library(value="oicr", changelog=false) _
-rollcall{}
+@Library(value="kids-first/aws-infra-jenkins-shared-libraries", changelog=false) _
+ecs_service_type_1_standard {
+    projectName = "rollcall"
+    environments = "dev,qa,prd"
+    docker_image_type = "alpine"
+    docker_workdir_path = "/srv/rollcall"
+    entrypoint_command = "/srv/rollcall/exec/run.sh"
+    quick_deploy = "true"
+    internal_app = "true"
+    external_config_repo = "false"
+    container_port = "9001"
+    vcpu_container             = "2048"
+    memory_container           = "4096"
+    vcpu_task                  = "2048"
+    memory_task                = "4096"
+    health_check_path = "/swagger-ui.html"
+    dependencies = "ecr"
+    friendly_dns_name = "rollcall"
+    publish_to_public_repo = "true"
+}
diff --git a/README.md b/README.md
@@ -46,6 +46,7 @@ This problem is what Rollcall helps solve by introducing concepts like data rele
 
 ## Index Naming
 
+
 The thing that Rollcall is opinionated about is the way indices are named. So opinionated in fact that it uses a grammer file to describe the index naming grammer. 
 
 It can be found here: [IndexName.g4](src/main/antlr4/bio/overture/rollcall/antlr4/IndexName.g4)

diff --git a/docker/scripts/run.sh b/docker/scripts/run.sh
@@ -26,11 +26,17 @@ if [  -z ${ES_CLUSTER_NAME+x} ]; then
     exit 1
 fi
 
+if [  -z ${c+x} ]; then
+    echo "The env variable ES_SCHEME is undefined"
+    exit 1
+fi
+
 CONF_DIR=/conf
 mkdir $CONF_DIR
 CONFIG_FILE=${CONF_DIR}/application.properties
 echo "elasticsearch.host=$ES_HOST" > $CONFIG_FILE
 echo "elasticsearch.port=$ES_PORT" >> $CONFIG_FILE
+echo "elasticsearch.scheme=$ES_SCHEME" >> $CONFIG_FILE
 echo "elasticsearch.cluster-name=$ES_CLUSTER_NAME" >> $CONFIG_FILE
 
 java -Dspring.config.location=classpath:/application.yml,file:${CONFIG_FILE}  -jar $JAR_PATH

diff --git a/pom.xml b/pom.xml
@@ -42,6 +42,8 @@
         <java.version>11</java.version>
         <antlr4.version>4.7</antlr4.version>
         <antlr4-maven.version>4.7</antlr4-maven.version>
+        <jaxb-api.version>2.3.1</jaxb-api.version>
+        <log4j2.version>2.16.0</log4j2.version>
     </properties>
 
     <dependencies>
@@ -82,6 +84,16 @@
             <artifactId>spring-security-jwt</artifactId>
             <version>1.0.9.RELEASE</version>
         </dependency>
+        <dependency>
+            <groupId>com.auth0</groupId>
+            <artifactId>auth0-spring-security-api</artifactId>
+            <version>1.2.6</version>
+        </dependency>
+        <dependency>
+            <groupId>com.auth0</groupId>
+            <artifactId>java-jwt</artifactId>
+            <version>3.8.3</version>
+        </dependency>
 
         <!-- Lombok -->
         <dependency>
@@ -98,27 +110,32 @@
         </dependency>
 
         <!-- Elasticsearch -->
+        <!-- Dong go beyond : https://github.com/elastic/elasticsearch/issues/41647-->
         <dependency>
             <groupId>org.elasticsearch</groupId>
             <artifactId>elasticsearch</artifactId>
             <version>6.3.1</version>
         </dependency>
         <dependency>
             <groupId>org.elasticsearch.client</groupId>
-            <artifactId>elasticsearch-rest-high-level-client</artifactId>
+            <artifactId>elasticsearch-rest-client</artifactId>
             <version>6.3.1</version>
         </dependency>
         <dependency>
             <groupId>org.elasticsearch.client</groupId>
-            <artifactId>transport</artifactId>
-            <version>6.3.1</version>
-        </dependency>
-        <dependency>
-            <groupId>org.elasticsearch.plugin</groupId>
-            <artifactId>transport-netty4-client</artifactId>
+            <artifactId>elasticsearch-rest-high-level-client</artifactId>
             <version>6.3.1</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.elasticsearch.client</groupId>
+                    <artifactId>elasticsearch-rest-client</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.elasticsearch</groupId>
+                    <artifactId>elasticsearch</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
-
         <!-- Swagger -->
         <dependency>
             <groupId>io.springfox</groupId>
@@ -135,7 +152,13 @@
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>testcontainers</artifactId>
-            <version>1.8.2</version>
+            <version>1.14.3</version>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>elasticsearch</artifactId>
+            <version>1.14.3</version>
+            <scope>test</scope>
         </dependency>
 
         <dependency>
@@ -145,6 +168,18 @@
             <scope>test</scope>
         </dependency>
 
+
+        <!-- JAXB 2.3.for jdk11 -->
+        <dependency>
+            <groupId>javax.xml.bind</groupId>
+            <artifactId>jaxb-api</artifactId>
+            <version>${jaxb-api.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jaxb</groupId>
+            <artifactId>jaxb-runtime</artifactId>
+            <version>${jaxb-api.version}</version>
+        </dependency>
     </dependencies>
 
     <build>

diff --git a/src/main/java/bio/overture/rollcall/RollcallApplication.java b/src/main/java/bio/overture/rollcall/RollcallApplication.java
@@ -20,9 +20,10 @@
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.autoconfigure.data.elasticsearch.ElasticsearchAutoConfiguration;
 import org.springframework.boot.autoconfigure.elasticsearch.rest.RestClientAutoConfiguration;
 
-@SpringBootApplication(exclude = {RestClientAutoConfiguration.class})
+@SpringBootApplication(exclude = {ElasticsearchAutoConfiguration.class, RestClientAutoConfiguration.class})
 public class RollcallApplication {
 
   public static void main(String[] args) {

diff --git a/src/main/java/bio/overture/rollcall/config/ElasticsearchConfig.java b/src/main/java/bio/overture/rollcall/config/ElasticsearchConfig.java
@@ -22,10 +22,6 @@
 import org.apache.http.HttpHost;
 import org.elasticsearch.client.RestClient;
 import org.elasticsearch.client.RestHighLevelClient;
-import org.elasticsearch.client.transport.TransportClient;
-import org.elasticsearch.common.settings.Settings;
-import org.elasticsearch.common.transport.TransportAddress;
-import org.elasticsearch.transport.client.PreBuiltTransportClient;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -43,6 +39,9 @@ public class ElasticsearchConfig {
   @Value("${elasticsearch.port}")
   private int port;
 
+  @Value("${elasticsearch.scheme}")
+  private String scheme;
+
   @Value("${elasticsearch.cluster-name}")
   private String clusterName;
 
@@ -51,18 +50,10 @@ public class ElasticsearchConfig {
   public RestHighLevelClient restClient() {
     return new RestHighLevelClient(
       RestClient.builder(
-        new HttpHost(InetAddress.getByName(host), port)
+        new HttpHost(InetAddress.getByName(host), port, scheme)
       )
     );
   }
 
-  @Bean
-  @SneakyThrows
-  public TransportClient transportClient() {
-    return new PreBuiltTransportClient(Settings.builder()
-        .put(CLUSTER_NAME, clusterName)
-        .build())
-      .addTransportAddress(new TransportAddress(InetAddress.getByName(host), port));
-  }
 
 }
diff --git a/src/main/java/bio/overture/rollcall/config/WebSecurityConfig.java b/src/main/java/bio/overture/rollcall/config/WebSecurityConfig.java
@@ -19,120 +19,70 @@
 package bio.overture.rollcall.config;
 
 import bio.overture.rollcall.jwt.JWTAuthorizationFilter;
-import bio.overture.rollcall.jwt.JWTTokenConverter;
+import com.auth0.spring.security.api.JwtWebSecurityConfigurer;
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
-import lombok.val;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.web.servlet.FilterRegistrationBean;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Profile;
 import org.springframework.core.Ordered;
-import org.springframework.core.io.ResourceLoader;
 import org.springframework.http.HttpMethod;
 import org.springframework.security.config.annotation.web.builders.HttpSecurity;
 import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
+import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
 import org.springframework.security.oauth2.config.annotation.web.configuration.EnableResourceServer;
-import org.springframework.security.oauth2.config.annotation.web.configuration.ResourceServerConfigurerAdapter;
-import org.springframework.security.oauth2.config.annotation.web.configurers.ResourceServerSecurityConfigurer;
-import org.springframework.security.oauth2.provider.token.DefaultTokenServices;
-import org.springframework.security.oauth2.provider.token.TokenStore;
-import org.springframework.security.oauth2.provider.token.store.JwtAccessTokenConverter;
-import org.springframework.security.oauth2.provider.token.store.JwtTokenStore;
 import org.springframework.security.web.authentication.www.BasicAuthenticationFilter;
 import org.springframework.web.cors.CorsConfiguration;
 import org.springframework.web.cors.UrlBasedCorsConfigurationSource;
 
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
 import java.util.Collections;
 
 @Slf4j
 @EnableWebSecurity
 @EnableResourceServer
 @Profile("!test")
-public class WebSecurityConfig extends ResourceServerConfigurerAdapter {
+public class WebSecurityConfig extends WebSecurityConfigurerAdapter {
+
+    @Value("${auth0.apiAudience}")
+    private String audience;
+
+    @Value("${auth0.issuer}")
+    private String issuer;
+
+    @Override
+    @SneakyThrows
+    public void configure(HttpSecurity http) {
+        JwtWebSecurityConfigurer
+                .forRS256(audience, issuer)
+                .configure(http)
+                .authorizeRequests()
+                .antMatchers("/swagger**", "/swagger-resources/**", "/v2/api**", "/webjars/**").permitAll()
+                .and()
+                .authorizeRequests()
+                .antMatchers(HttpMethod.POST).authenticated()
+                .and()
+                .authorizeRequests()
+                .anyRequest().authenticated()
+                .and()
+                .addFilterAfter(new JWTAuthorizationFilter(), BasicAuthenticationFilter.class);
+
+    }
+
+    @Bean
+    @SuppressWarnings("unchecked")
+    public FilterRegistrationBean simpleCorsFilter() {
+        UrlBasedCorsConfigurationSource source = new UrlBasedCorsConfigurationSource();
+        CorsConfiguration config = new CorsConfiguration();
+        config.setAllowCredentials(true);
+        config.setAllowedOrigins(Collections.singletonList("*"));
+        config.setAllowedMethods(Collections.singletonList("*"));
+        config.setAllowedHeaders(Collections.singletonList("*"));
+        source.registerCorsConfiguration("/**", config);
+        FilterRegistrationBean bean = new FilterRegistrationBean(new org.springframework.web.filter.CorsFilter(source));
+        bean.setOrder(Ordered.HIGHEST_PRECEDENCE);
+        return bean;
+    }
 
-  @Autowired // Field injection bad, but clean in this spot.
-  private ResourceLoader resourceLoader;
-
-  @Value("${auth.jwt.publicKeyUrl}")
-  private String publicKeyUrl;
-
-  @Override
-  @SneakyThrows
-  public void configure(HttpSecurity http) {
-    http
-      .authorizeRequests()
-      .antMatchers(HttpMethod.OPTIONS, "/aliases/*").permitAll()
-      .antMatchers(HttpMethod.OPTIONS, "/indices/*").permitAll()
-      .antMatchers("/health").permitAll()
-      .antMatchers("/isAlive").permitAll()
-      .antMatchers("/upload/**").permitAll()
-      .antMatchers("/download/**").permitAll()
-      .antMatchers("/entities/**").permitAll()
-      .antMatchers("/swagger**", "/swagger-resources/**", "/v2/api**", "/webjars/**").permitAll()
-      .and()
-      .authorizeRequests()
-      .anyRequest().authenticated()
-      .and()
-      .addFilterAfter(new JWTAuthorizationFilter(), BasicAuthenticationFilter.class);
-  }
-
-  @Bean
-  @SuppressWarnings("unchecked")
-  public FilterRegistrationBean simpleCorsFilter() {
-    UrlBasedCorsConfigurationSource source = new UrlBasedCorsConfigurationSource();
-    CorsConfiguration config = new CorsConfiguration();
-    config.setAllowCredentials(true);
-    config.setAllowedOrigins(Collections.singletonList("*"));
-    config.setAllowedMethods(Collections.singletonList("*"));
-    config.setAllowedHeaders(Collections.singletonList("*"));
-    source.registerCorsConfiguration("/**", config);
-    FilterRegistrationBean bean = new FilterRegistrationBean(new org.springframework.web.filter.CorsFilter(source));
-    bean.setOrder(Ordered.HIGHEST_PRECEDENCE);
-    return bean;
-  }
-
-  @Override
-  public void configure(ResourceServerSecurityConfigurer config) {
-    config.tokenServices(tokenServices());
-  }
-
-  @Bean
-  public TokenStore tokenStore() {
-    return new JwtTokenStore(accessTokenConverter());
-  }
-
-  @Bean
-  @SneakyThrows
-  public JwtAccessTokenConverter accessTokenConverter() {
-    return new JWTTokenConverter(fetchJWTPublicKey());
-  }
-
-
-  @Bean
-  public DefaultTokenServices tokenServices() {
-    val defaultTokenServices = new DefaultTokenServices();
-    defaultTokenServices.setTokenStore(tokenStore());
-    return defaultTokenServices;
-  }
-
-  /**
-   * Call EGO server for public key to use when verifying JWTs
-   * Pass this value to the JWTTokenConverter
-   */
-  @SneakyThrows
-  private String fetchJWTPublicKey() {
-    val publicKeyResource = resourceLoader.getResource(publicKeyUrl);
-
-    val stringBuilder = new StringBuilder();
-    val reader = new BufferedReader(
-      new InputStreamReader(publicKeyResource.getInputStream()));
-
-    reader.lines().forEach(stringBuilder::append);
-    return stringBuilder.toString();
-  }
 
 }
Original file line number	Diff line number	Diff line change
		@@ -46,6 +46,7 @@ This problem is what Rollcall helps solve by introducing concepts like data rele

		## Index Naming


		The thing that Rollcall is opinionated about is the way indices are named. So opinionated in fact that it uses a grammer file to describe the index naming grammer.

		It can be found here: [IndexName.g4](src/main/antlr4/bio/overture/rollcall/antlr4/IndexName.g4)