Merge pull request #280 from overture-stack/feature/docker-update-1.0.1

Feature/docker update 1.0.2

Author: rtisma

song-docker/client/Dockerfile

@@ -1,7 +1,7 @@
 FROM song_base-ubuntu:latest
 MAINTAINER ICGC <[email protected]>
 
-ENV CLIENT_RELEASE_VERSION 0.3.7
+ENV CLIENT_RELEASE_VERSION 1.0.2
 ENV CLIENT_HOME $DCC_DATA
 ENV DOWNLOAD_URL  https://artifacts.oicr.on.ca/artifactory/dcc-release/org/icgc/dcc/song-client/${CLIENT_RELEASE_VERSION}/song-client-${CLIENT_RELEASE_VERSION}-dist.tar.gz
 ENV TARBALL $DCC_HOME/download.tar.gz

song-docker/db/Dockerfile

@@ -1,7 +1,7 @@
 FROM song_base-db:latest
 MAINTAINER ICGC <[email protected]>
 
-ENV SERVER_RELEASE_VERSION 0.3.7
+ENV SERVER_RELEASE_VERSION 1.0.2
 ENV PGDATA /var/lib/postgresql/data/pgdata
 ENV POSTGRES_INIT_SQL /docker-entrypoint-initdb.d/init.sql
 

song-docker/docker-compose.yml

@@ -98,7 +98,7 @@ services:
       - "./data/client:/opt/dcc/data"
       - "./tools:/opt/dcc/tools"
   object-storage:
-    image: minio/minio:RELEASE.2017-11-22T19-55-46Z
+    image: minio/minio:RELEASE.2018-05-11T00-29-24Z
     network_mode: host
     volumes:
       - "./data/minio:/opt/dcc/data"

song-docker/server/Dockerfile

@@ -4,7 +4,7 @@ MAINTAINER ICGC <[email protected]>
 #
 # Configuration
 #
-ENV SERVER_RELEASE_VERSION 0.3.7
+ENV SERVER_RELEASE_VERSION 1.0.2
 ENV SONG_HOME $DCC_HOME/song-server
 ENV SONG_LOGS $DCC_HOME/song-server/logs
 ENV DOWNLOAD_URL  https://artifacts.oicr.on.ca/artifactory/dcc-release/org/icgc/dcc/song-server/${SERVER_RELEASE_VERSION}/song-server-${SERVER_RELEASE_VERSION}-dist.tar.gz  

song-docker/server/config/application.yml.template

@@ -19,14 +19,36 @@
 #
 
 server:
+  version: 1.0
   port: ${SERVER_PORT}
 
 dcc-storage:
   url: "${STORAGE_SERVER_URL}"
 
+# Hibernate
+spring:
+  jpa:
+    properties:
+      hibernate:
+        dialect: com.marvinformatics.hibernate.json.PostgreSQLJsonDialect
+# disable driver's feature detection. This is required for the following bug in SpringBoot 2.0.0+
+# https://hibernate.atlassian.net/browse/HHH-12368
+        temp.use_jdbc_metadata_defaults: false
+
+# Uncomment this to see the generated SQL stetements
+# logging.level.org.hibernate.SQL: DEBUG
+
+# Uncomment this to see the binding parameters for generated SQL statements
+# logging.level.org.hibernate.type.descriptor.sql: TRACE
+
+
 # Management
 management:
-  port: ${SERVER_MANAGEMENT_PORT}
+  server:
+    port: ${SERVER_MANAGEMENT_PORT}
+
+swagger:
+  alternateUrl: "/api-docs"
 
 id:
   idUrl: "${ID_URL}"
@@ -35,6 +57,7 @@ id:
   persistInMemory: false
 
 validation:
+  delayMs: 30
   threads:
     core: 5
     max: 10
@@ -56,26 +79,35 @@ auth:
     # E.g. TIMEOUT(n) = TIMEOUT(n-1) * MULTIPLIER
     multiplier: 2.0
 
+---
+spring.profiles: async-test
+validation.delayMs: 5000
+
 ---
 spring.profiles: test
 spring:
   profiles:
     include: [dev]
+
 ---
 spring.profiles: dev
 spring:
   profiles:
     include: [fastTest]
   datasource:
-    initialize: true
+    initialization-mode: always
+
+management:
+  server:
+    port: -1
+
+id.persistInMemory: true
 
 auth:
   server:
     prefix: "song"
     suffix: "upload"
 
-validation.delayMs: 3000
-
 # Datasource
 spring.datasource:
   driver-class-name: org.postgresql.Driver
@@ -122,7 +154,7 @@ auth:
 spring:
   profiles: prod
   datasource:
-    initialize: false
+    initialization-mode: never
 
 # Datasource
 spring.datasource:
@@ -134,8 +166,6 @@ spring.datasource:
   max-idle: 1
   min-idle: 1
 
-validation.delayMs: 30
-
 ---
 spring:
   profiles: test

song-docker/storage-client/Dockerfile

@@ -1,4 +1,4 @@
-FROM icgc/icgc-storage-client:1.0.23
+FROM overture/score:1.1.1
 MAINTAINER ICGC <[email protected]>
 
 ENV DCC_HOME /opt/dcc

song-docker/storage-server/Dockerfile

@@ -4,14 +4,14 @@ MAINTAINER ICGC <[email protected]>
 #
 # Configuration
 #
-ENV DCC_STORAGE_HOME $DCC_HOME/dcc-storage-server
-ENV DCC_STORAGE_LOGS $DCC_STORAGE_HOME/logs
+ENV SCORE_SERVER_VERSION 1.1.1
+ENV SCORE_HOME $DCC_HOME/score-server
+ENV SCORE_LOGS $SCORE_HOME/logs
 
 #rtisma-20171002 Temp Hack untill new release
-#ENV DOWNLOAD_URL https://artifacts.oicr.on.ca/artifactory/dcc-release/org/icgc/dcc/dcc-storage-server/[RELEASE]/dcc-storage-server-[RELEASE]-dist.tar.gz
-ENV DOWNLOAD_URL https://artifacts.oicr.on.ca/artifactory/dcc-snapshot/org/icgc/dcc/dcc-storage-server/1.0.24-SNAPSHOT/dcc-storage-server-1.0.24-20171102.202102-7-dist.tar.gz
+ENV DOWNLOAD_URL https://artifacts.oicr.on.ca/artifactory/dcc-release/bio/overture/score-server/${SCORE_SERVER_VERSION}/score-server-${SCORE_SERVER_VERSION}-dist.tar.gz
 
-ENV TARBALL $DCC_HOME/dcc-storage-server.tar.gz
+ENV TARBALL $DCC_HOME/score-server.tar.gz
 ENV DCC_SCRIPTS $DCC_HOME/scripts
 
 ADD config $DCC_CONFIG
@@ -20,22 +20,22 @@ ADD scripts $DCC_SCRIPTS
 
 ENV EXPAND_SCRIPT $DCC_HOME/tools/expand.py
 ENV INPUT_FILE $DCC_CONFIG/application.yml.template
-ENV OUTPUT_FILE $DCC_STORAGE_HOME/conf/application.yml
+ENV OUTPUT_FILE $SCORE_HOME/conf/application.yml
 
 RUN wget $DOWNLOAD_URL -O $TARBALL && \
 	    tar zxvf $TARBALL && \
-	    mv -f $DCC_HOME/dcc-storage-server-*  $DCC_STORAGE_HOME && \
-	    rm -rf $TARBALL $DCC_STORAGE_HOME/conf/application.* && \
-	    mv $DCC_STORAGE_LOGS  ${DCC_STORAGE_LOGS}.bak  && \
-	    ln -s $DCC_HOME/storage_server_logs $DCC_STORAGE_LOGS
-
-		#ln -s $DCC_STORAGE_HOME/conf/application.yml $DCC_STORAGE_HOME/conf/application-secure.yml  && \
-		#ln -s $DCC_STORAGE_HOME/conf/application.yml $DCC_STORAGE_HOME/conf/application-prod.yml  && \
-		#ln -s $DCC_STORAGE_HOME/conf/application.yml $DCC_STORAGE_HOME/conf/application-collaboratory.yml  && \
+	    mv -f $DCC_HOME/score-server-*  $SCORE_HOME && \
+	    rm -rf $TARBALL $SCORE_HOME/conf/application.* && \
+	    mv $SCORE_LOGS  ${SCORE_LOGS}.bak  && \
+	    ln -s $DCC_HOME/storage_server_logs $SCORE_LOGS
+
+		#ln -s $SCORE_HOME/conf/application.yml $SCORE_HOME/conf/application-secure.yml  && \
+		#ln -s $SCORE_HOME/conf/application.yml $SCORE_HOME/conf/application-prod.yml  && \
+		#ln -s $SCORE_HOME/conf/application.yml $SCORE_HOME/conf/application-collaboratory.yml  && \
 #        wrapper.app.parameter.5=--spring.profiles.active=collaboratory,prod,secure \
 CMD python3 $EXPAND_SCRIPT $INPUT_FILE $OUTPUT_FILE && \
 	/bin/bash -c $DCC_SCRIPTS/create-buckets.sh && \
-        $DCC_STORAGE_HOME/bin/dcc-storage-server start  \
+        $SCORE_HOME/bin/dcc-storage-server start  \
 	wrapper.java.additional.2=-Dcom.sun.management.jmxremote.port=${STORAGE_SERVER_JMX_PORT} \
         wrapper.app.parameter.6=--server.port=${STORAGE_SERVER_PORT} \
         wrapper.app.parameter.5=--spring.profiles.active=amazon,collaboratory,prod,secure \

song-python-sdk/README.md

@@ -1,3 +1,4 @@
+
 The SONG Python SDK
 ============================