Merge pull request #717 from overture-stack/rc/4.5.1

Release Candidate 4.5.1

Author: joneubank

pom.xml

@@ -21,7 +21,7 @@
     <groupId>bio.overture</groupId>
     <artifactId>song</artifactId>
     <packaging>pom</packaging>
-    <version>4.5.0</version>
+    <version>4.5.1</version>
     <modules>
         <module>song-core</module>
         <module>song-java-sdk</module>

song-client/pom.xml

@@ -18,7 +18,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>4.5.0</version>
+		<version>4.5.1</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 
@@ -35,12 +35,12 @@
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-java-sdk</artifactId>
-			<version>4.5.0</version>
+			<version>4.5.1</version>
 		</dependency>
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-core</artifactId>
-			<version>4.5.0</version>
+			<version>4.5.1</version>
 		</dependency>
 
 		<!-- CLI -->

song-core/pom.xml

@@ -19,7 +19,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>4.5.0</version>
+		<version>4.5.1</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

song-java-sdk/pom.xml

@@ -18,7 +18,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>4.5.0</version>
+		<version>4.5.1</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

song-server/pom.xml

@@ -19,7 +19,7 @@
     <parent>
         <artifactId>song</artifactId>
         <groupId>bio.overture</groupId>
-        <version>4.5.0</version>
+        <version>4.5.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -37,7 +37,7 @@
         <dependency>
             <groupId>bio.overture</groupId>
             <artifactId>song-core</artifactId>
-            <version>4.5.0</version>
+            <version>4.5.1</version>
         </dependency>
 
         <!-- Spring -->

song-server/src/main/java/bio/overture/song/server/service/analysis/AnalysisServiceImpl.java

@@ -300,15 +300,22 @@ public Analysis publish(
     checkAnalysisAndStudyRelated(studyId, id);
 
     val a = unsecuredDeepRead(id);
+
+    // Validations before publishing
     val analysisSchema = a.getAnalysisSchema();
     checkAnalysisTypeVersion(analysisSchema);
     val files = a.getFiles();
     checkMissingFiles(id, files);
     val file2storageObjectMap = getStorageObjectsForFiles(files);
     checkMismatchingFileSizes(id, file2storageObjectMap);
     checkMismatchingFileMd5sums(id, file2storageObjectMap, ignoreUndefinedMd5);
+
+    // Publish
     checkedUpdateState(id, PUBLISHED);
 
+    // Recalculate publish times now that it has a new PUBLISHED state in history
+    a.populatePublishTimes();
+    
     return a;
   }