Build complete application in Dockerfile.

This ensures container building process is build-environment agnostic.

Dockerfile

@@ -1,9 +1,55 @@
-FROM openjdk:8-jre-alpine
+ARG WORKDIR=/wb_names
+ARG APPJAR_BUILDPATH=build/wb-names-app.jar
 
-ARG uberjar_path=
-ADD $uberjar_path /srv/app.jar
+### Stage 1: build UI
+FROM node:12 AS BUILD_UI_STAGE
+
+ARG WORKDIR
+
+WORKDIR $WORKDIR
+COPY Makefile ./
+COPY client/ ./client/
+COPY scripts/ ./scripts/
+
+RUN --mount=type=secret,id=make-secrets-file,required=true \
+    make build-ui SECRETS_SRC=/run/secrets/make-secrets-file APP_PROFILE=prod
+
+### Stage 2: build API (and include UI components)
+FROM clojure:temurin-8-tools-deps-jammy as BUILD_API_STAGE
+
+ARG WORKDIR
+ARG APPJAR_BUILDPATH
+
+RUN apt update && apt upgrade -y && apt install -y maven unzip
+
+#Install clojure manually (com.datomic/datomic-pro 1.0.6165 is not stored on maven central)
+COPY build/datomic-pro-1.0.6165.zip datomic-pro-1.0.6165.zip
+RUN unzip datomic-pro-1.0.6165.zip \
+     && cd datomic-pro-1.0.6165/ \
+     && bin/maven-install
+
+WORKDIR $WORKDIR
+COPY Makefile ./
+COPY src/wormbase/ src/wormbase/
+COPY resources/ ./resources/
+COPY deps.edn ./
+COPY project.clj ./
+COPY scripts/ ./scripts/
+COPY --from=BUILD_UI_STAGE $WORKDIR/client/ $WORKDIR/client/
+
+RUN make build-app-jar APP_JAR_PATH=$APPJAR_BUILDPATH
+
+### Stage 3: build final application image
+FROM openjdk:8-jre-alpine as APPLICATION_IMAGE_STAGE
+
+ARG WORKDIR
+ARG APPJAR_BUILDPATH
+
+RUN apk update && apk upgrade
+
+COPY --from=BUILD_API_STAGE $WORKDIR/$APPJAR_BUILDPATH /srv/wb-names-app.jar
 
 # Expose necessary ports
 EXPOSE 3000
 
-CMD ["java", "-cp", "/srv/app.jar", "clojure.main", "-m", "wormbase.names.service"]
+CMD ["java", "-cp", "/srv/wb-names-app.jar", "clojure.main", "-m", "wormbase.names.service"]

Makefile

@@ -91,11 +91,14 @@ build/:
 	mkdir build/
 
 .PHONY: build
-build: ENV.VERSION_TAG clean build/ ui-build build/${DEPLOY_JAR} \
+build: build/ ENV.VERSION_TAG ${STORE_SECRETS_FILE} \
        $(call print-help,build,\
-       Build the docker images from using the current git revision.)
+       Build the docker images from the current git revision.)
+	@aws s3 cp s3://wormbase/datomic-pro/distro/datomic-pro-1.0.6165.zip build/
 	@docker build -t ${ECR_REPO_NAME}:${VERSION_TAG} \
-		--build-arg uberjar_path=build/${DEPLOY_JAR} .
+		--secret id=make-secrets-file,src=${STORE_SECRETS_FILE} \
+		.
+	@rm ${STORE_SECRETS_FILE}
 
 .PHONY: build-ui
 build-ui: ENV.GOOGLE_OAUTH_CLIENT_ID \