From 8e6037f92cafe146963eddbafccc57ab1d44bcb4 Mon Sep 17 00:00:00 2001 From: Dusan Andric Date: Tue, 13 Jul 2021 12:15:55 -0400 Subject: [PATCH 1/9] next snapshot --- pom.xml | 2 +- score-client/pom.xml | 2 +- score-core/pom.xml | 2 +- score-fs/pom.xml | 2 +- score-server/pom.xml | 2 +- score-test/pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pom.xml b/pom.xml index 61f696b3..a5ca4f72 100644 --- 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 bio.overture score - 5.5.0 + 5.6.0-SNAPSHOT pom ${project.artifactId} diff --git a/score-client/pom.xml b/score-client/pom.xml index f87a86d5..ddc26349 100644 --- 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 bio.overture score - 5.5.0 + 5.6.0-SNAPSHOT ../pom.xml diff --git a/score-core/pom.xml b/score-core/pom.xml index 77bc79d5..fa4ea514 100644 --- 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 bio.overture score - 5.5.0 + 5.6.0-SNAPSHOT ../pom.xml diff --git a/score-fs/pom.xml b/score-fs/pom.xml index 04448b0c..9509879b 100644 --- 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 bio.overture score - 5.5.0 + 5.6.0-SNAPSHOT ../pom.xml diff --git a/score-server/pom.xml b/score-server/pom.xml index d7705645..20392730 100644 --- 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 bio.overture score - 5.5.0 + 5.6.0-SNAPSHOT ../pom.xml diff --git a/score-test/pom.xml b/score-test/pom.xml index 41d3537c..653a9921 100644 --- 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 bio.overture score - 5.5.0 + 5.6.0-SNAPSHOT ../pom.xml From 4ff86bccc8987c7e6f61d579a7932998e7d56e62 Mon Sep 17 00:00:00 2001 From: Yelizar Alturmessov Date: Fri, 16 Jul 2021 08:58:44 -0400 Subject: [PATCH 2/9] Jenkinsfile update Replace docker socket mount with docker host env vars. --- Jenkinsfile | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index 462563e7..8ef805c8 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -60,14 +60,10 @@ 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 volumes: - - name: docker-sock - hostPath: - path: /var/run/docker.sock - type: File - name: docker-graph-storage emptyDir: {} - name: maven-cache From 08f4febd78e42758d8017a45705b3e470c0fc640 Mon Sep 17 00:00:00 2001 From: Yelizar Alturmessov Date: Fri, 16 Jul 2021 11:29:35 -0400 Subject: [PATCH 3/9] Jenkinsfile update Set explicit UIDs for containers. --- Jenkinsfile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Jenkinsfile b/Jenkinsfile index 8ef805c8..4a08850b 100644 --- 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 @@ -63,6 +64,8 @@ spec: env: - name: DOCKER_HOST value: tcp://localhost:2375 + securityContext: + runAsUser: 1000 volumes: - name: docker-graph-storage emptyDir: {} From e2c9dd785cd8574e39bf875df6c4ca98658aedf3 Mon Sep 17 00:00:00 2001 From: Yelizar Alturmessov <65674408+yalturmes@users.noreply.github.com> Date: Wed, 21 Jul 2021 10:45:53 -0400 Subject: [PATCH 4/9] Update Jenkinsfile Set explicit HOME env var for docker client container. --- Jenkinsfile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index 4a08850b..70e692be 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -62,8 +62,10 @@ spec: image: docker:18-git tty: true env: - - name: DOCKER_HOST - value: tcp://localhost:2375 + - name: DOCKER_HOST + value: tcp://localhost:2375 + - name: HOME + value: /home/jenkins/agent securityContext: runAsUser: 1000 volumes: From 66f4fe2d9cfb1feb6fb0bd90153c677231c47fc5 Mon Sep 17 00:00:00 2001 From: Dusan Andric Date: Thu, 29 Jul 2021 10:57:08 -0400 Subject: [PATCH 5/9] updated azure storage version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a5ca4f72..be00d636 100644 --- a/pom.xml +++ b/pom.xml @@ -239,7 +239,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S 1.11.219 - 4.4.0 + 8.6.6 1.69 From 61ccba46a1a1026354049424cb97f238bd4aa411 Mon Sep 17 00:00:00 2001 From: Dusan Andric Date: Thu, 29 Jul 2021 10:57:08 -0400 Subject: [PATCH 6/9] updated azure storage version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a5ca4f72..be00d636 100644 --- a/pom.xml +++ b/pom.xml @@ -239,7 +239,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S 1.11.219 - 4.4.0 + 8.6.6 1.69 From 7e9144d802da073d4db6e05b5ff8b865644a6af7 Mon Sep 17 00:00:00 2001 From: Dusan Andric Date: Thu, 29 Jul 2021 15:48:48 -0400 Subject: [PATCH 7/9] fixes opens on internal jdk packages --- score-client/src/main/bin/score-client | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/score-client/src/main/bin/score-client b/score-client/src/main/bin/score-client index 77401333..f8fa645c 100755 --- 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 \ From 9709f0232af7bd2e4ae5d0c070e7e578e7814c8d Mon Sep 17 00:00:00 2001 From: Dusan Andric Date: Tue, 3 Aug 2021 14:57:34 -0400 Subject: [PATCH 8/9] sets block size on blob client. --- .../overture/score/client/upload/azure/AzureUploadService.java | 1 + 1 file changed, 1 insertion(+) 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 index 54558807..83978b44 100644 --- 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(); From 46411d1432a0822d5d0fec832f00a26979adb406 Mon Sep 17 00:00:00 2001 From: Dusan Andric Date: Tue, 3 Aug 2021 16:08:24 -0400 Subject: [PATCH 9/9] 5.6.0 release --- pom.xml | 2 +- score-client/pom.xml | 2 +- score-core/pom.xml | 2 +- score-fs/pom.xml | 2 +- score-server/pom.xml | 2 +- score-test/pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pom.xml b/pom.xml index be00d636..f23345ea 100644 --- 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 bio.overture score - 5.6.0-SNAPSHOT + 5.6.0 pom ${project.artifactId} diff --git a/score-client/pom.xml b/score-client/pom.xml index ddc26349..614c8fa0 100644 --- 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 bio.overture score - 5.6.0-SNAPSHOT + 5.6.0 ../pom.xml diff --git a/score-core/pom.xml b/score-core/pom.xml index fa4ea514..caa5c9c8 100644 --- 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 bio.overture score - 5.6.0-SNAPSHOT + 5.6.0 ../pom.xml diff --git a/score-fs/pom.xml b/score-fs/pom.xml index 9509879b..97d7fad5 100644 --- 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 bio.overture score - 5.6.0-SNAPSHOT + 5.6.0 ../pom.xml diff --git a/score-server/pom.xml b/score-server/pom.xml index 20392730..9d121a80 100644 --- 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 bio.overture score - 5.6.0-SNAPSHOT + 5.6.0 ../pom.xml diff --git a/score-test/pom.xml b/score-test/pom.xml index 653a9921..31598b55 100644 --- 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 bio.overture score - 5.6.0-SNAPSHOT + 5.6.0 ../pom.xml