Merge pull request #566 from overture-stack/rc/3.1.1

Rc/3.1.1

Author: rtisma

.env

@@ -10,8 +10,7 @@ FROM openjdk:11-jre-stretch as client
 
 ENV SONG_CLIENT_HOME   /song-client
 ENV CLIENT_DIST_DIR    /song-client-dist
-
-ENV TARBALL $DCC_HOME/download.tar.gz
+ENV PATH /usr/local/openjdk-11/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$SONG_CLIENT_HOME/bin
 
 COPY --from=builder /srv/song-client/target/song-client-*-dist.tar.gz /song-client.tar.gz
 

Dockerfile

@@ -5,6 +5,7 @@ FROM openjdk:11-jre-stretch as client
 
 ENV SONG_CLIENT_HOME   /song-client
 ENV CLIENT_DIST_DIR    /song-client-dist
+ENV PATH /usr/local/openjdk-11/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$SONG_CLIENT_HOME/bin
 
 COPY song-client/target/song-client-*-dist.tar.gz  /song-client.tar.gz
 RUN tar zxvf song-client.tar.gz -C /tmp \

Dockerfile.dev

@@ -51,7 +51,7 @@ LOG_DIRS := $(SCORE_SERVER_LOGS_DIR) $(SCORE_CLIENT_LOGS_DIR) $(SONG_SERVER_LOGS
 DOCKER_COMPOSE_CMD := echo "*********** DEMO_MODE = $(DEMO_MODE) **************" \
 	&& echo "*********** FORCE = $(FORCE) **************" \
 	&& DOCKERFILE_NAME=$(DOCKERFILE_NAME) MY_UID=$(MY_UID) MY_GID=$(MY_GID) $(DOCKER_COMPOSE_EXE) -f $(ROOT_DIR)/docker-compose.yml
-SONG_CLIENT_CMD := $(DOCKER_COMPOSE_CMD) run --rm -u $(THIS_USER) song-client bin/sing
+SONG_CLIENT_CMD := $(DOCKER_COMPOSE_CMD) run --rm -u $(THIS_USER) song-client sing
 SCORE_CLIENT_CMD := $(DOCKER_COMPOSE_CMD) run --rm -u $(THIS_USER) score-client bin/score-client
 DC_UP_CMD := $(DOCKER_COMPOSE_CMD) up -d --build
 MVN_CMD := $(MVN_EXE) -f $(ROOT_DIR)/pom.xml
@@ -238,8 +238,8 @@ get-analysis-id:
 test-submit: start-song-server _ping_song_server
 	@echo $(YELLOW)$(INFO_HEADER) "Submitting payload /data/submit/exampleVariantCall.json" $(END)
 	@$(SONG_CLIENT_CMD) submit -f /data/submit/exampleVariantCall.json | tee $(SONG_CLIENT_SUBMIT_RESPONSE_FILE)
-	@cat $(SONG_CLIENT_SUBMIT_RESPONSE_FILE) | grep analysisId | sed 's/.*://' | sed 's/"\|,//g'  > $(SONG_CLIENT_ANALYSIS_ID_FILE)
-	@echo $(YELLOW)$(INFO_HEADER) "Successfully submitted. Cached analysisId: " $$($(GET_ANALYSIS_ID_CMD)) $(END)
+	@cat $(SONG_CLIENT_SUBMIT_RESPONSE_FILE) | grep analysisId | sed -e 's#.*:[^"]*"\([^"]*\)".*#\1#' > $(SONG_CLIENT_ANALYSIS_ID_FILE)
+	@echo $(YELLOW)$(INFO_HEADER) "Successfully submitted. Cached analysisId: '"$$($(GET_ANALYSIS_ID_CMD))"'" $(END)
 
 test-manifest: test-submit
 	@echo $(YELLOW)$(INFO_HEADER) "Creating manifest at /song-client/output" $(END)

Makefile

@@ -89,6 +89,7 @@ services:
       - "./docker/scratch/score-client-logs:/score-client/logs"
       - "./docker/scratch/song-client-output:/song-client/output"
     command: bin/score-client
+    user: "$MY_UID:$MY_GID"
   song-db:
     image: "postgres:9.6"
     environment:
@@ -123,6 +124,7 @@ services:
       - "./docker/scratch/song-client-logs:/song-client/logs"
       - "./docker/scratch/song-client-output:/song-client/output"
     command: bin/sing
+    user: "$MY_UID:$MY_GID"
   song-server:
     build:
       context: ./

docker-compose.yml

@@ -8,4 +8,4 @@ DOCKERFILE_NAME=Dockerfile \
 	MY_GID=$(id -g) \
 	docker-compose \
 	-f ${BASH_SCRIPT_DIR}/../../docker-compose.yml \
-	run --rm song-client bin/sing $@
+	run --rm song-client sing $@

docker/tools/song-client-demo

@@ -8,4 +8,4 @@ DOCKERFILE_NAME=Dockerfile.dev \
 	MY_GID=$(id -g) \
 	docker-compose \
 	-f ${BASH_SCRIPT_DIR}/../..//docker-compose.yml \
-	run --rm song-client bin/sing $@
+	run --rm song-client sing $@

docker/tools/song-client-dev

@@ -21,7 +21,7 @@
     <groupId>bio.overture</groupId>
     <artifactId>song</artifactId>
     <packaging>pom</packaging>
-    <version>3.1.0</version>
+    <version>3.1.1</version>
     <modules>
         <module>song-core</module>
         <module>song-java-sdk</module>

pom.xml

@@ -18,7 +18,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>3.1.0</version>
+		<version>3.1.1</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 
@@ -35,12 +35,12 @@
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-java-sdk</artifactId>
-			<version>3.1.0</version>
+			<version>3.1.1</version>
 		</dependency>
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-core</artifactId>
-			<version>3.1.0</version>
+			<version>3.1.1</version>
 		</dependency>
 
 		<!-- CLI -->

song-client/pom.xml

@@ -29,7 +29,7 @@ elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]];  then
 #    echo Found Java in JAVA_HOME
     _java="$JAVA_HOME/bin/java"
 else
-    echo "Java not found. Sing requires JDK 1.8"
+    echo "Java not found. Sing requires Java 11."
     exit 1
 fi
 
@@ -42,11 +42,13 @@ if [[ "$_java" ]]; then
     fi
 fi
 
-current_dir=$PWD
-fn=$0
-sing_home=$current_dir/`dirname $fn`/../
-
-#         -Dspring.config.location="$sing_home/conf/" \
+here=$(dirname $0)
+if [ "$here" == "." ]; then
+	# This is the case, when the user runs this script from the ./bin directory
+	sing_home=../
+else
+	sing_home=${here%/bin}
+fi
 
 java --illegal-access=deny \
 		 -Dlog.name=song \

song-client/src/main/bin/sing

@@ -19,7 +19,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>3.1.0</version>
+		<version>3.1.1</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

song-core/pom.xml

@@ -18,7 +18,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>3.1.0</version>
+		<version>3.1.1</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

song-java-sdk/pom.xml

@@ -19,7 +19,7 @@
     <parent>
         <artifactId>song</artifactId>
         <groupId>bio.overture</groupId>
-        <version>3.1.0</version>
+        <version>3.1.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -37,7 +37,7 @@
         <dependency>
             <groupId>bio.overture</groupId>
             <artifactId>song-core</artifactId>
-            <version>3.1.0</version>
+            <version>3.1.1</version>
         </dependency>
 
         <!-- Spring -->