From b52d06fa234f1bac3ea4d438879fc40324ed0813 Mon Sep 17 00:00:00 2001
From: Gcolon021 <34667267+Gcolon021@users.noreply.github.com>
Date: Mon, 13 Jan 2025 15:38:39 -0500
Subject: [PATCH] Dockerize maven install (#133)

* Refactor Dockerfiles to use multi-stage builds.
Simplified builds by introducing Maven-based multi-stage builds, consolidating dependencies, and reducing image sizes. Updated entry points to ensure runtime efficiency and maintainability. Transitioned from `ADD` to `COPY` for better clarity and consistency.
---
 docker/pic-sure-hpds-etl/Dockerfile | 50 ++++++++++++++++++-----------
 docker/pic-sure-hpds/Dockerfile     | 17 ++++++++--
 2 files changed, 46 insertions(+), 21 deletions(-)

diff --git a/docker/pic-sure-hpds-etl/Dockerfile b/docker/pic-sure-hpds-etl/Dockerfile
index b375fc13..f160b120 100644
--- a/docker/pic-sure-hpds-etl/Dockerfile
+++ b/docker/pic-sure-hpds-etl/Dockerfile
@@ -1,21 +1,33 @@
+FROM maven:3.9.4-amazoncorretto-21 AS build
+
+RUN yum update -y && yum install -y git && yum clean all
+
+WORKDIR /app
+
+COPY .m2 /root/.m2
+
+COPY . .
+
+RUN mvn clean install -DskipTests
+
 FROM eclipse-temurin:21-alpine
 
-RUN apk add --no-cache --purge -uU bash &&     rm -rf /var/cache/apk/* /tmp/*
-
-RUN apk add --no-cache --purge -uU curl wget unzip gnupg openssl
-
-ADD create_key.sh .
-ADD SQLLoader-jar-with-dependencies.jar .
-ADD CSVLoader-jar-with-dependencies.jar .
-ADD CSVLoaderNewSearch-jar-with-dependencies.jar .
-ADD CSVDumper-jar-with-dependencies.jar .
-ADD VCFLocalLoader-jar-with-dependencies.jar .
-ADD VariantMetadataLoader-jar-with-dependencies.jar .
-ADD UnifiedVCFLocalLoader-jar-with-dependencies.jar .
-ADD MultialleleCounter-jar-with-dependencies.jar .
-ADD RekeyDataset-jar-with-dependencies.jar .
-ADD RemoveConceptFromMetadata-jar-with-dependencies.jar .
-ADD HideAnnotationCategoryValue-jar-with-dependencies.jar .
-ADD SequentialLoader-jar-with-dependencies.jar .
-
-ENTRYPOINT java $JAVA_OPTS -Xmx${HEAPSIZE:-2048}m -jar ${LOADER_NAME:-CSVLoader}-jar-with-dependencies.jar
+RUN apk add --no-cache --purge -uU bash curl wget unzip gnupg openssl && \
+    rm -rf /var/cache/apk/* /tmp/*
+
+WORKDIR /app
+COPY --from=build /app/docker/pic-sure-hpds-etl/SQLLoader-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/CSVLoader-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/CSVLoaderNewSearch-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/CSVDumper-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/VCFLocalLoader-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/VariantMetadataLoader-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/UnifiedVCFLocalLoader-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/MultialleleCounter-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/RekeyDataset-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/RemoveConceptFromMetadata-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/HideAnnotationCategoryValue-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/SequentialLoader-jar-with-dependencies.jar .
+COPY --from=build /app/docker/pic-sure-hpds-etl/create_key.sh .
+
+ENTRYPOINT ["sh", "-c", "java $JAVA_OPTS -Xmx${HEAPSIZE:-2048}m -jar ${LOADER_NAME:-CSVLoader}-jar-with-dependencies.jar"]
diff --git a/docker/pic-sure-hpds/Dockerfile b/docker/pic-sure-hpds/Dockerfile
index fca99d31..6d973a83 100644
--- a/docker/pic-sure-hpds/Dockerfile
+++ b/docker/pic-sure-hpds/Dockerfile
@@ -1,6 +1,19 @@
+FROM maven:3.9.4-amazoncorretto-21 AS build
+
+RUN yum update -y && yum install -y git && yum clean all
+
+WORKDIR /app
+
+COPY .m2 /root/.m2
+
+COPY . .
+
+RUN mvn clean install -DskipTests
+
 FROM amazoncorretto:21.0.1-alpine3.18
 
-# Copy jar and access token from maven build
-ADD service-3.0.0-SNAPSHOT.jar /service.jar
+WORKDIR /app
+
+COPY --from=build /app/service/target/service-*-SNAPSHOT.jar /service.jar
 
 ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /service.jar"]
\ No newline at end of file