Merge pull request #703 from overture-stack/rc/4.4.0

Release Candidate 4.4.0

Jenkinsfile

@@ -36,7 +36,7 @@ spec:
   containers:
   - name: jdk
     tty: true
-    image: openjdk:11
+    image: adoptopenjdk/openjdk11:jdk-11.0.6_10-alpine
     env: 
       - name: DOCKER_HOST 
         value: tcp://localhost:2375 
@@ -194,5 +194,39 @@ spec:
                 rtUpload(serverId: 'artifactory', spec: fileSet)
             }
         }
+
+		stage('Deploy to Overture QA') {
+			when {
+				branch "develop"
+			}
+			steps {
+				build(job: "/Overture.bio/provision/helm", parameters: [
+						[$class: 'StringParameterValue', name: 'OVERTURE_ENV', value: 'qa' ],
+						[$class: 'StringParameterValue', name: 'OVERTURE_CHART_NAME', value: 'song'],
+						[$class: 'StringParameterValue', name: 'OVERTURE_RELEASE_NAME', value: 'song'],
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_CHART_VERSION', value: ''], // use latest
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_REPO_URL', value: "https://overture-stack.github.io/charts-server/"],
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_REUSE_VALUES', value: "true" ],
+						[$class: 'StringParameterValue', name: 'OVERTURE_ARGS_LINE', value: "--set-string image.tag=${commit}" ]
+				])
+			}
+		}
+
+		stage('Deploy to Overture Staging') {
+			when {
+				branch "master"
+			}
+			steps {
+				build(job: "/Overture.bio/provision/helm", parameters: [
+						[$class: 'StringParameterValue', name: 'OVERTURE_ENV', value: 'staging' ],
+						[$class: 'StringParameterValue', name: 'OVERTURE_CHART_NAME', value: 'song'],
+						[$class: 'StringParameterValue', name: 'OVERTURE_RELEASE_NAME', value: 'song'],
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_CHART_VERSION', value: ''], // use latest
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_REPO_URL', value: "https://overture-stack.github.io/charts-server/"],
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_REUSE_VALUES', value: "true" ],
+						[$class: 'StringParameterValue', name: 'OVERTURE_ARGS_LINE', value: "--set-string image.tag=${version}" ]
+				])
+			}
+		}
     }
 }

docker-compose.yml

@@ -1,7 +1,7 @@
 version: '3.7'
 services:
   ego-api:
-    image: "overture/ego:3.1.0"
+    image: "overture/ego:3.4.0"
     environment:
       SERVER_PORT: 8080
       SPRING_DATASOURCE_URL: jdbc:postgresql://ego-postgres:5432/ego?stringtype=unspecified
@@ -10,11 +10,11 @@ services:
       SPRING_FLYWAY_ENABLED: "true"
       SPRING_FLYWAY_LOCATIONS: "classpath:flyway/sql,classpath:db/migration"
       SPRING_PROFILES: demo, auth
+      JWT_DURATIONMS: 300000 # expire tokens in 5 min for local testing
     expose:
       - "8080"
     ports:
       - "9082:8080"
-    command: java -jar /srv/ego/install/ego.jar
     depends_on:
       - ego-postgres
   ego-postgres:
@@ -43,10 +43,10 @@ services:
     ports:
       - "8085:9000"
   score-server:
-    image: overture/score-server:5.0.0
+    image: overture/score-server:5.1.0
     user: "$MY_UID:$MY_GID"
     environment:
-      SPRING_PROFILES_ACTIVE: amazon,collaboratory,prod,secure
+      SPRING_PROFILES_ACTIVE: amazon,collaboratory,prod,secure,jwt
       SERVER_PORT: 8080
       OBJECT_SENTINEL: heliograph
       BUCKET_NAME_OBJECT: oicr.icgc.test
@@ -57,6 +57,7 @@ services:
       S3_ACCESSKEY: minio
       S3_SECRETKEY: minio123
       S3_SIGV4ENABLED: "true"
+      AUTH_JWT_PUBLICKEYURL: http://ego-api:8080/oauth/token/public_key
       AUTH_SERVER_URL: http://ego-api:8080/o/check_api_key/
       AUTH_SERVER_CLIENTID: score
       AUTH_SERVER_CLIENTSECRET: scoresecret
@@ -144,7 +145,8 @@ services:
       target: server
     environment:
       SERVER_PORT: 8080
-      SPRING_PROFILES_ACTIVE: "prod,secure,default"
+      SPRING_PROFILES_ACTIVE: "prod,secure,default,jwt,score-client-cred"
+      AUTH_JWT_PUBLICKEYURL: http://ego-api:8080/oauth/token/public_key
       AUTH_SERVER_URL: http://ego-api:8080/o/check_api_key/
       AUTH_SERVER_CLIENTID: song
       AUTH_SERVER_TOKENNAME: apiKey
@@ -153,7 +155,10 @@ services:
       AUTH_SERVER_SCOPE_STUDY_SUFFIX: .WRITE
       AUTH_SERVER_SCOPE_SYSTEM: song.WRITE
       SCORE_URL: http://score-server:8080
-      SCORE_ACCESSTOKEN: f69b726d-d40f-4261-b105-1ec7e6bf04d5
+      SCORE_CLIENTCREDENTIALS_ID: songToScore
+      SCORE_CLIENTCREDENTIALS_SECRET: songToScoreSecret
+      SCORE_CLIENTCREDENTIALS_TOKENURL: http://ego-api:8080/oauth/token
+      SCORE_CLIENTCREDENTIALS_SYSTEMSCOPE: "score.WRITE"
       MANAGEMENT_SERVER_PORT: 8081
       SPRING_DATASOURCE_USERNAME: postgres
       SPRING_DATASOURCE_PASSWORD: password

docker/ego-init/init.sql

@@ -295,6 +295,7 @@ ALTER TABLE public.userpermission OWNER TO postgres;
 --
 
 COPY public.egoapplication (name, clientid, clientsecret, redirecturi, description, status, id, type) FROM stdin;
+song-to-score	songToScore	songToScoreSecret	http://example.com	song-to-score	APPROVED	77f1ef78-7495-4b4a-982a-6b9532dc69fb	CLIENT
 \.
 
 
@@ -344,6 +345,7 @@ COPY public.flyway_schema_history (installed_rank, version, description, type, s
 --
 
 COPY public.groupapplication (group_id, application_id) FROM stdin;
+f2885e96-f74e-4f7a-b935-fb48b18e761d	77f1ef78-7495-4b4a-982a-6b9532dc69fb
 \.
 
 

pom.xml

@@ -21,7 +21,7 @@
     <groupId>bio.overture</groupId>
     <artifactId>song</artifactId>
     <packaging>pom</packaging>
-    <version>4.3.0</version>
+    <version>4.4.0</version>
     <modules>
         <module>song-core</module>
         <module>song-java-sdk</module>
@@ -176,6 +176,11 @@
                 <artifactId>jackson-datatype-guava</artifactId>
                 <version>${jackson.version}</version>
             </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.datatype</groupId>
+                <artifactId>jackson-datatype-jsr310</artifactId>
+                <version>${jackson.version}</version>
+            </dependency>
             <dependency>
                 <groupId>com.fasterxml.jackson.dataformat</groupId>
                 <artifactId>jackson-dataformat-yaml</artifactId>

song-client/pom.xml

@@ -18,7 +18,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>4.3.0</version>
+		<version>4.4.0</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 
@@ -35,12 +35,12 @@
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-java-sdk</artifactId>
-			<version>4.3.0</version>
+			<version>4.4.0</version>
 		</dependency>
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-core</artifactId>
-			<version>4.3.0</version>
+			<version>4.4.0</version>
 		</dependency>
 
 		<!-- CLI -->

song-core/pom.xml

@@ -19,7 +19,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>4.3.0</version>
+		<version>4.4.0</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 
@@ -65,6 +65,10 @@
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-annotations</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>com.fasterxml.jackson.datatype</groupId>
+			<artifactId>jackson-datatype-jsr310</artifactId>
+		</dependency>
 
 		<!-- Utilities -->
 		<dependency>

song-core/src/main/java/bio/overture/song/core/model/Analysis.java

@@ -1,7 +1,9 @@
 package bio.overture.song.core.model;
 
 import bio.overture.song.core.model.enums.AnalysisStates;
+import java.time.LocalDateTime;
 import java.util.List;
+import java.util.SortedSet;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
@@ -23,4 +25,12 @@ public class Analysis extends DynamicData {
   private AnalysisTypeId analysisType;
   private List<CompositeSample> samples;
   private List<FileDTO> files;
+
+  private LocalDateTime createdAt;
+  private LocalDateTime updatedAt;
+
+  private LocalDateTime firstPublishedAt;
+  private LocalDateTime publishedAt;
+
+  private SortedSet<AnalysisStateChange> analysisStateHistory;
 }

song-core/src/main/java/bio/overture/song/core/model/AnalysisStateChange.java

@@ -0,0 +1,21 @@
+package bio.overture.song.core.model;
+
+import java.time.LocalDateTime;
+import lombok.*;
+
+@Data
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+@ToString(callSuper = true)
+@EqualsAndHashCode(callSuper = true)
+public class AnalysisStateChange extends DynamicData implements Comparable<AnalysisStateChange> {
+  private String initialState;
+  private String updatedState;
+  private LocalDateTime updatedAt;
+
+  @Override
+  public int compareTo(AnalysisStateChange o) {
+    return this.getUpdatedAt().compareTo(o.getUpdatedAt());
+  }
+}

song-core/src/main/java/bio/overture/song/core/model/AnalysisType.java

@@ -2,6 +2,7 @@
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.JsonNode;
+import java.time.LocalDateTime;
 import javax.validation.constraints.NotNull;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
@@ -16,6 +17,7 @@ public class AnalysisType {
 
   @NotNull private String name;
   @NotNull private Integer version;
+  private LocalDateTime createdAt;
 
   @JsonInclude(JsonInclude.Include.NON_NULL)
   private JsonNode schema;

song-core/src/main/java/bio/overture/song/core/model/enums/AnalysisActions.java

@@ -0,0 +1,43 @@
+package bio.overture.song.core.model.enums;
+
+import static java.lang.String.format;
+import static java.util.Arrays.stream;
+import static java.util.stream.Collectors.toUnmodifiableSet;
+
+import bio.overture.song.core.utils.Streams;
+import java.util.Collection;
+import java.util.Set;
+import lombok.NonNull;
+
+public enum AnalysisActions {
+    PUBLISH,
+    UNPUBLISH,
+    SUPPRESS,
+    CREATE;
+
+    private static final Set<String> SET =
+            Streams.stream(values()).map(AnalysisActions::toString).collect(toUnmodifiableSet());
+
+    public String toString() {
+        return this.name();
+    }
+
+    public static AnalysisActions resolveAnalysisActions(@NonNull String analysisAction) {
+        return Streams.stream(values())
+                .filter(x -> x.toString().equals(analysisAction))
+                .findFirst()
+                .orElseThrow(
+                        () ->
+                                new IllegalStateException(
+                                        format("The analysis action '%s' cannot be resolved", analysisAction)));
+    }
+
+    public static String[] toStringArray() {
+        return stream(values()).map(Enum::name).toArray(String[]::new);
+    }
+
+    public static Set<String> findIncorrectAnalysisActions(
+            @NonNull Collection<String> analysisActions) {
+        return analysisActions.stream().filter(x -> !SET.contains(x)).collect(toUnmodifiableSet());
+    }
+}

song-core/src/main/java/bio/overture/song/core/utils/JsonUtils.java

@@ -31,9 +31,14 @@
 import com.fasterxml.jackson.databind.deser.std.StringDeserializer;
 import com.fasterxml.jackson.databind.module.SimpleModule;
 import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import com.fasterxml.jackson.datatype.jsr310.deser.LocalDateTimeDeserializer;
+import com.fasterxml.jackson.datatype.jsr310.ser.LocalDateTimeSerializer;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URL;
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
 import java.util.Map;
 import lombok.NonNull;
 import lombok.SneakyThrows;
@@ -48,10 +53,22 @@ public class JsonUtils {
   protected static final ObjectMapper mapper = mapper();
 
   public static ObjectMapper mapper() {
+    val mapper = new ObjectMapper();
+
+    /* Register Moduless */
     val specialModule = new SimpleModule();
     specialModule.addDeserializer(String.class, SpecialStringJsonDeserializer.instance);
 
-    val mapper = new ObjectMapper().registerModule(specialModule);
+    val isoDateFormatter = DateTimeFormatter.ISO_DATE_TIME;
+    val dateTimeDeserializer = new LocalDateTimeDeserializer(isoDateFormatter);
+    val dateTimeSerializer = new LocalDateTimeSerializer(isoDateFormatter);
+
+    val javaTimeModule = new JavaTimeModule();
+    javaTimeModule.addDeserializer(LocalDateTime.class, dateTimeDeserializer);
+    javaTimeModule.addSerializer(LocalDateTime.class, dateTimeSerializer);
+
+    mapper.registerModule(specialModule);
+    mapper.registerModule(javaTimeModule);
 
     mapper.disable(DeserializationFeature.FAIL_ON_MISSING_CREATOR_PROPERTIES);
     mapper.disable(DeserializationFeature.FAIL_ON_UNRESOLVED_OBJECT_IDS);

song-java-sdk/pom.xml

@@ -18,7 +18,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>4.3.0</version>
+		<version>4.4.0</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

song-server/pom.xml

@@ -19,7 +19,7 @@
     <parent>
         <artifactId>song</artifactId>
         <groupId>bio.overture</groupId>
-        <version>4.3.0</version>
+        <version>4.4.0</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -37,7 +37,7 @@
         <dependency>
             <groupId>bio.overture</groupId>
             <artifactId>song-core</artifactId>
-            <version>4.3.0</version>
+            <version>4.4.0</version>
         </dependency>
 
         <!-- Spring -->

song-server/src/main/java/bio/overture/song/server/ServerMain.java

@@ -16,6 +16,8 @@
  */
 package bio.overture.song.server;
 
+import java.util.TimeZone;
+import javax.annotation.PostConstruct;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.security.servlet.SecurityAutoConfiguration;
@@ -24,6 +26,11 @@
 @SpringBootApplication(exclude = {SecurityAutoConfiguration.class})
 public class ServerMain {
 
+  @PostConstruct
+  public void init() {
+    TimeZone.setDefault(TimeZone.getTimeZone("UTC"));
+  }
+
   public static void main(String... args) {
     SpringApplication.run(ServerMain.class, args);
   }