Merge pull request #316 from overture-stack/rc/5.6.0

Rc/5.6.0
overture-stack · Aug 4, 2021 · 881b970 · 881b970
2 parents afade0a + 46411d1
commit 881b970
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Showing 9 changed files with 20 additions and 15 deletions.
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -49,6 +49,7 @@ spec:
     image: docker:18.06-dind
     securityContext: 
         privileged: true 
+        runAsUser: 0
     volumeMounts: 
       - name: docker-graph-storage 
         mountPath: /var/lib/docker 
@@ -60,14 +61,14 @@ 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: {}
   - name: maven-cache

diff --git a/pom.xml b/pom.xml
@@ -20,7 +20,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
 
   <groupId>bio.overture</groupId>
   <artifactId>score</artifactId>
-  <version>5.5.0</version>
+  <version>5.6.0</version>
   <packaging>pom</packaging>
 
   <name>${project.artifactId}</name>
@@ -239,7 +239,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
     <!-- Versions - Amazon -->
     <aws-java-sdk.version>1.11.219</aws-java-sdk.version>
 
-    <azure-storage.version>4.4.0</azure-storage.version>
+    <azure-storage.version>8.6.6</azure-storage.version>
 
     <!-- Versions - Utilities -->
     <jcommander.version>1.69</jcommander.version>

diff --git a/score-client/pom.xml b/score-client/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.5.0</version>
+    <version>5.6.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-client/src/main/bin/score-client b/score-client/src/main/bin/score-client
@@ -48,7 +48,10 @@ BASE_DIR=`dirname $0`/..; export BASE_DIR
 # Installation directory
 CLIENT_DIR="$(cd ${BASE_DIR} && pwd -P)"
 
-exec java -Xmx3G --illegal-access=deny \
+exec java -Xmx3G \
+	--add-opens=java.base/jdk.internal.ref=ALL-UNNAMED \
+	--add-opens=java.base/java.nio=ALL-UNNAMED \
+	--illegal-access=deny \
 	-Dlogging.path=${BASE_DIR}/logs \
 	-Dspring.config.additional-location=${CLIENT_DIR}/conf/ \
 	-Dlogging.config=${CLIENT_DIR}/conf/logback.xml \

diff --git a/score-client/src/main/java/bio/overture/score/client/upload/azure/AzureUploadService.java b/score-client/src/main/java/bio/overture/score/client/upload/azure/AzureUploadService.java
@@ -122,6 +122,7 @@ public void eventOccurred(RetryingEvent eventArg) {
 
       val options = new BlobRequestOptions();
       options.setConcurrentRequestCount(parallelUploads);
+      blob.setStreamWriteSizeInBytes(BLOCK_SIZE);
 
       progress.start();
       progress.startTransfer();

diff --git a/score-core/pom.xml b/score-core/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.5.0</version>
+    <version>5.6.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-fs/pom.xml b/score-fs/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.5.0</version>
+    <version>5.6.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-server/pom.xml b/score-server/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.5.0</version>
+    <version>5.6.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-test/pom.xml b/score-test/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.5.0</version>
+    <version>5.6.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>