Merge pull request #620 from overture-stack/rc/5.0.0

Release 5.0.0
upgrade spring boot
upgrade spring cloud version
fix profiles
fix vault
update to new spring data page-able interface

Author: blabadi

Jenkinsfile

@@ -24,6 +24,7 @@ spec:
     image: docker:18.06-dind
     securityContext: 
         privileged: true 
+        runAsUser: 0
     volumeMounts: 
       - name: docker-graph-storage 
         mountPath: /var/lib/docker 
@@ -35,14 +36,14 @@ spec:
   - name: docker
     image: docker:18-git
     tty: true
-    volumeMounts:
-    - mountPath: /var/run/docker.sock
-      name: docker-sock
+    env: 
+    - name: DOCKER_HOST 
+      value: tcp://localhost:2375
+    - name: HOME
+      value: /home/jenkins/agent
+  securityContext:
+    runAsUser: 1000
   volumes:
-  - name: docker-sock
-    hostPath:
-      path: /var/run/docker.sock
-      type: File
   - name: docker-graph-storage 
     emptyDir: {}
 """

docker-compose-all.yml

@@ -0,0 +1,31 @@
+version: '3.7'
+services:
+  api:
+    build:
+      context: ./
+      dockerfile: Dockerfile
+    restart: always
+    environment:
+      SERVER_PORT: 8080
+      SPRING_DATASOURCE_URL: jdbc:postgresql://postgres:5432/ego?stringtype=unspecified
+      SPRING_DATASOURCE_USERNAME: postgres
+      SPRING_DATASOURCE_PASSWORD: password
+      SPRING_FLYWAY_ENABLED: "true"
+      SPRING_FLYWAY_LOCATIONS: "classpath:flyway/sql,classpath:db/migration"
+      SPRING_PROFILES: demo, auth
+    expose:
+      - "8080"
+    ports:
+      - "$API_HOST_PORT:8080"
+    depends_on:
+      - postgres
+  postgres:
+    image: postgres:12.6
+    restart: always
+    environment:
+      - POSTGRES_DB=ego
+      - POSTGRES_PASSWORD=password
+    expose:
+      - "5432"
+    ports:
+      - "8432:5432"

docker-compose.yml

@@ -1,24 +1,12 @@
 version: '3.7'
 services:
-  api:
-    build:
-      context: ./
-      dockerfile: Dockerfile
-    restart: always
+  ego-ui:
+    image: overture/ego-ui:edge
+    network_mode: host
     environment:
-      SERVER_PORT: 8080
-      SPRING_DATASOURCE_URL: jdbc:postgresql://postgres:5432/ego?stringtype=unspecified
-      SPRING_DATASOURCE_USERNAME: postgres
-      SPRING_DATASOURCE_PASSWORD: password
-      SPRING_FLYWAY_ENABLED: "true"
-      SPRING_FLYWAY_LOCATIONS: "classpath:flyway/sql,classpath:db/migration"
-      SPRING_PROFILES: demo, auth
-    expose:
-      - "8080"
-    ports:
-      - "$API_HOST_PORT:8080"
-    depends_on:
-      - postgres
+      REACT_APP_API: http://localhost:8081
+      REACT_APP_EGO_CLIENT_ID: ego-ui
+
   postgres:
     image: postgres:12.6
     restart: always
@@ -28,4 +16,5 @@ services:
     expose:
       - "5432"
     ports:
-      - "8432:5432"
+      - "5432:5432"
+

pom.xml

@@ -5,15 +5,15 @@
 
     <groupId>bio.overture</groupId>
     <artifactId>ego</artifactId>
-    <version>4.5.2</version>
+    <version>5.0.0</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>2.1.8.RELEASE</version>
+        <version>2.5.6</version>
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
 
@@ -87,6 +87,7 @@
             <artifactId>spring-boot-starter-test</artifactId>
             <scope>test</scope>
         </dependency>
+
         <dependency>
             <groupId>org.springframework.security</groupId>
             <artifactId>spring-security-test</artifactId>
@@ -106,7 +107,10 @@
             <groupId>org.springframework.session</groupId>
             <artifactId>spring-session-core</artifactId>
         </dependency>
-
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-validation</artifactId>
+        </dependency>
         <!-- JDBC -->
         <dependency>
             <groupId>com.h2database</groupId>
@@ -292,6 +296,12 @@
             <scope>test</scope>
         </dependency>
 
+        <dependency>
+            <groupId>org.junit.vintage</groupId>
+            <artifactId>junit-vintage-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-devtools</artifactId>
@@ -416,7 +426,7 @@
             <dependency>
                 <groupId>org.springframework.cloud</groupId>
                 <artifactId>spring-cloud-dependencies</artifactId>
-                <version>Greenwich.SR2</version>
+                <version>2020.0.4</version>
                 <type>pom</type>
                 <scope>import</scope>
             </dependency>

src/main/java/bio/overture/ego/controller/resolver/PageableResolver.java

@@ -96,7 +96,7 @@ public Sort getSort() {
         // TODO: this is a hack for now to provide default sort on id field
         // ideally we should not be making assumption about field name as "id" - it will break if
         // field doesn't exist
-        return new Sort(direction, StringUtils.isEmpty(sort) ? "id" : sort);
+        return Sort.by(direction, StringUtils.isEmpty(sort) ? "id" : sort);
       }
 
       @Override
@@ -114,6 +114,11 @@ public Pageable first() {
         return null;
       }
 
+      @Override
+      public Pageable withPage(int pageNumber) {
+        throw new RuntimeException("Not implemented");
+      }
+
       @Override
       public boolean hasPrevious() {
         return false;

src/main/java/bio/overture/ego/grpc/ProtoUtils.java

@@ -87,6 +87,11 @@ public Pageable first() {
         return null;
       }
 
+      @Override
+      public Pageable withPage(int pageNumber) {
+        throw new RuntimeException("Not implemented");
+      }
+
       @Override
       public boolean hasPrevious() {
         return false;
@@ -97,7 +102,7 @@ public boolean hasPrevious() {
   public static Sort parseSort(String sort) {
     if (sort.isEmpty()) {
       // Sort results by creation time, ensure static order for the page_token to refer to
-      return new Sort(Sort.Direction.ASC, JavaFields.CREATEDAT);
+      return Sort.by(Sort.Direction.ASC, JavaFields.CREATEDAT);
     } else {
       val orders =
           Arrays.stream(sort.split(","))

src/main/java/bio/overture/ego/model/exceptions/ExceptionHandlers.java

@@ -2,8 +2,11 @@
 
 import static java.lang.String.format;
 import static org.springframework.http.HttpStatus.BAD_REQUEST;
+import static org.springframework.http.HttpStatus.NOT_FOUND;
 
 import bio.overture.ego.utils.Joiners;
+import java.util.Date;
+import java.util.Map;
 import javax.servlet.http.HttpServletRequest;
 import javax.validation.ConstraintViolationException;
 import lombok.extern.slf4j.Slf4j;
@@ -17,6 +20,21 @@
 @ControllerAdvice
 public class ExceptionHandlers {
 
+  @ExceptionHandler(NotFoundException.class)
+  public ResponseEntity<Object> handleConstraintViolationException(
+      HttpServletRequest req, NotFoundException ex) {
+    val message = ex.getMessage();
+    log.error(message);
+    return new ResponseEntity<Object>(
+        Map.of(
+            "message", ex.getMessage(),
+            "timestamp", new Date(),
+            "path", req.getServletPath(),
+            "error", NOT_FOUND.getReasonPhrase()),
+        new HttpHeaders(),
+        NOT_FOUND);
+  }
+
   @ExceptionHandler(ConstraintViolationException.class)
   public ResponseEntity<Object> handleConstraintViolationException(
       HttpServletRequest req, ConstraintViolationException ex) {

src/main/java/bio/overture/ego/utils/IgnoreCaseSortDecorator.java

@@ -4,6 +4,7 @@
 import static org.springframework.util.StringUtils.isEmpty;
 
 import java.util.Map;
+import java.util.Optional;
 import lombok.NonNull;
 import lombok.RequiredArgsConstructor;
 import lombok.val;
@@ -29,11 +30,26 @@ public Sort getSort() {
     return Sort.by(orders);
   }
 
+  @Override
+  public Sort getSortOr(Sort sort) {
+    return delegate.getSortOr(sort);
+  }
+
   private String getSortField(String sort) {
     val mapValue = SORT_MAP.get(sort);
     return isEmpty(mapValue) ? sort : mapValue;
   }
 
+  @Override
+  public boolean isPaged() {
+    return delegate.isPaged();
+  }
+
+  @Override
+  public boolean isUnpaged() {
+    return delegate.isUnpaged();
+  }
+
   /** Delegated methods */
   @Override
   public int getPageNumber() {
@@ -65,8 +81,18 @@ public Pageable first() {
     return delegate.first();
   }
 
+  @Override
+  public Pageable withPage(int pageNumber) {
+    return delegate.withPage(pageNumber);
+  }
+
   @Override
   public boolean hasPrevious() {
     return delegate.hasPrevious();
   }
+
+  @Override
+  public Optional<Pageable> toOptional() {
+    return Optional.of(delegate);
+  }
 }

src/main/resources/application.yml

@@ -38,14 +38,16 @@ spring.main.allow-bean-definition-overriding: true
 spring.datasource:
   driver-class-name: org.postgresql.Driver
   url: jdbc:postgresql://localhost:5432/ego?stringtype=unspecified
-
   username: postgres
   password: password
   max-active: 10
   max-idle: 1
   min-idle: 1
 
 spring:
+  cloud:
+    vault:
+      enabled: false
   flyway:
     enabled: false
     placeholders:
@@ -198,7 +200,9 @@ initialization:
 # Profile - "jks"
 ###############################################################################
 spring:
-  profiles: jks
+  config:
+    activate:
+      on-profile: jks
 
 token:
   key-store: src/main/resources/ego-jwt.jks
@@ -210,8 +214,9 @@ token:
 # Profile - "auth"
 ###############################################################################
 spring:
-  profiles: auth
-  profiles.include: secure
+  config:
+    activate:
+      on-profile: auth
 
 # security
 auth:
@@ -231,7 +236,9 @@ logging:
 # Profile - "demo"
 ###############################################################################
 spring:
-  profiles: grpc
+  config:
+    activate:
+      on-profile: grpc
 
 grpc:
   port: 50051
@@ -241,14 +248,17 @@ grpc:
 # Profile - "demo"
 ###############################################################################
 spring:
-  profiles: demo
-
+  config:
+    activate:
+      on-profile: demo
 ---
 ###############################################################################
 # Profile - "test"
 ###############################################################################
 spring:
-  profiles: test
+  config:
+    activate:
+      on-profile: test
 
 # To log the httpRequests and httpResponses for the controllers, set to true
 logging.test.controller.enable: false