From e2ec6aee768d0ed0ed2ffc5bf5f3f7f2df32af2c Mon Sep 17 00:00:00 2001
From: khartmann <kevin.hartmann@oicr.on.ca>
Date: Mon, 9 Dec 2019 12:48:21 -0500
Subject: [PATCH 1/3] Bugfix: sing now computes it's parent directory correctly
 Enhancement: docker client now runs as a song user that has the sing binary
 in the PATH environment variable

---
 Dockerfile                    | 5 +++--
 song-client/src/main/bin/sing | 8 +++-----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index a1de5ea87..76bce0036 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -10,10 +10,10 @@ 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
+RUN groupadd -r song && useradd -r -g song song
 
 RUN tar zxvf song-client.tar.gz -C /tmp \
 	&& rm -rf song-client.tar.gz \
@@ -27,6 +27,7 @@ RUN tar zxvf song-client.tar.gz -C /tmp \
 
 # Set working directory for convenience with interactive usage
 WORKDIR $SONG_CLIENT_HOME
+USER song 
 
 ###############################################################################################################
 
diff --git a/song-client/src/main/bin/sing b/song-client/src/main/bin/sing
index cbd6ece6c..aa8256d29 100755
--- a/song-client/src/main/bin/sing
+++ b/song-client/src/main/bin/sing
@@ -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
 
@@ -42,10 +42,8 @@ if [[ "$_java" ]]; then
     fi
 fi
 
-current_dir=$PWD
-fn=$0
-sing_home=$current_dir/`dirname $fn`/../
-
+here=$(dirname $0)
+sing_home=${here%/bin}
 #         -Dspring.config.location="$sing_home/conf/" \
 
 java --illegal-access=deny \

From 070e498a80f498175bbdb00be85dd827efb3615b Mon Sep 17 00:00:00 2001
From: khartmann <kevin.hartmann@oicr.on.ca>
Date: Mon, 9 Dec 2019 16:05:26 -0500
Subject: [PATCH 2/3] PER PR

---
 .env                           | 2 --
 Dockerfile                     | 2 --
 Dockerfile.dev                 | 1 +
 docker-compose.yml             | 2 ++
 docker/tools/score-client-demo | 2 +-
 docker/tools/score-client-dev  | 2 +-
 docker/tools/song-client-demo  | 2 +-
 docker/tools/song-client-dev   | 2 +-
 8 files changed, 7 insertions(+), 8 deletions(-)
 delete mode 100644 .env

diff --git a/.env b/.env
deleted file mode 100644
index f3a17455e..000000000
--- a/.env
+++ /dev/null
@@ -1,2 +0,0 @@
-COMPOSE_PROJECT_NAME=song
-
diff --git a/Dockerfile b/Dockerfile
index 76bce0036..c09a81a98 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,7 +13,6 @@ 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 --from=builder /srv/song-client/target/song-client-*-dist.tar.gz /song-client.tar.gz
-RUN groupadd -r song && useradd -r -g song song
 
 RUN tar zxvf song-client.tar.gz -C /tmp \
 	&& rm -rf song-client.tar.gz \
@@ -27,7 +26,6 @@ RUN tar zxvf song-client.tar.gz -C /tmp \
 
 # Set working directory for convenience with interactive usage
 WORKDIR $SONG_CLIENT_HOME
-USER song 
 
 ###############################################################################################################
 
diff --git a/Dockerfile.dev b/Dockerfile.dev
index 8939cc2ee..c1ee811be 100644
--- a/Dockerfile.dev
+++ b/Dockerfile.dev
@@ -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 \
diff --git a/docker-compose.yml b/docker-compose.yml
index 491c88c6f..24401dd15 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -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: ./
diff --git a/docker/tools/score-client-demo b/docker/tools/score-client-demo
index c033e261d..6bce5dad6 100755
--- a/docker/tools/score-client-demo
+++ b/docker/tools/score-client-demo
@@ -6,4 +6,4 @@ BASH_SCRIPT_DIR=$( dirname  "${BASH_SCRIPT}")
 DOCKERFILE_NAME=Dockerfile \
 	docker-compose \
 	-f ${BASH_SCRIPT_DIR}/../../docker-compose.yml \
-	run --rm score-client bin/score-client $@
+	run --rm score-client score-client $@
diff --git a/docker/tools/score-client-dev b/docker/tools/score-client-dev
index 7f294d5ab..8b43c3ada 100755
--- a/docker/tools/score-client-dev
+++ b/docker/tools/score-client-dev
@@ -6,4 +6,4 @@ BASH_SCRIPT_DIR=$( dirname  "${BASH_SCRIPT}")
 DOCKERFILE_NAME=Dockerfile.dev \
 	docker-compose \
 	-f ${BASH_SCRIPT_DIR}/../../docker-compose.yml \
-	run --rm score-client bin/score-client $@
+	run --rm score-client score-client $@
diff --git a/docker/tools/song-client-demo b/docker/tools/song-client-demo
index d30d7af94..0e70ed3d8 100755
--- a/docker/tools/song-client-demo
+++ b/docker/tools/song-client-demo
@@ -8,4 +8,4 @@ DOCKERFILE_NAME=Dockerfile \
 	MY_GID=$(id -g) \
 	docker-compose \
 	-f ${BASH_SCRIPT_DIR}/../../docker-compose.yml \
-	run --rm song-client bin/sing $@
+	run --rm song-client sing $@
diff --git a/docker/tools/song-client-dev b/docker/tools/song-client-dev
index 6e5f9f1a2..6e179e667 100755
--- a/docker/tools/song-client-dev
+++ b/docker/tools/song-client-dev
@@ -8,4 +8,4 @@ DOCKERFILE_NAME=Dockerfile.dev \
 	MY_GID=$(id -g) \
 	docker-compose \
 	-f ${BASH_SCRIPT_DIR}/../..//docker-compose.yml \
-	run --rm song-client bin/sing $@
+	run --rm song-client sing $@

From be2860d239725b7d802c6d0e8e1eeda318833732 Mon Sep 17 00:00:00 2001
From: khartmann <kevin.hartmann@oicr.on.ca>
Date: Tue, 10 Dec 2019 11:39:03 -0500
Subject: [PATCH 3/3] 1) Fixes as per PR 2) Bugfix: sed command wasn't
 generating correct analysisId.

---
 Makefile                       | 6 +++---
 docker/tools/score-client-demo | 2 +-
 docker/tools/score-client-dev  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index fb3af24e7..7b6250493 100644
--- a/Makefile
+++ b/Makefile
@@ -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" $(END)
diff --git a/docker/tools/score-client-demo b/docker/tools/score-client-demo
index 6bce5dad6..c033e261d 100755
--- a/docker/tools/score-client-demo
+++ b/docker/tools/score-client-demo
@@ -6,4 +6,4 @@ BASH_SCRIPT_DIR=$( dirname  "${BASH_SCRIPT}")
 DOCKERFILE_NAME=Dockerfile \
 	docker-compose \
 	-f ${BASH_SCRIPT_DIR}/../../docker-compose.yml \
-	run --rm score-client score-client $@
+	run --rm score-client bin/score-client $@
diff --git a/docker/tools/score-client-dev b/docker/tools/score-client-dev
index 8b43c3ada..7f294d5ab 100755
--- a/docker/tools/score-client-dev
+++ b/docker/tools/score-client-dev
@@ -6,4 +6,4 @@ BASH_SCRIPT_DIR=$( dirname  "${BASH_SCRIPT}")
 DOCKERFILE_NAME=Dockerfile.dev \
 	docker-compose \
 	-f ${BASH_SCRIPT_DIR}/../../docker-compose.yml \
-	run --rm score-client score-client $@
+	run --rm score-client bin/score-client $@