rework docker

.gitignore

@@ -37,4 +37,6 @@ settings.yaml
 processed/*
 !processed/.gitkeep
 input/*
-!input/.gitkeep
+!input/.gitkeep
+study/*
+!study/.gitkeep

Dockerfile

@@ -3,13 +3,13 @@ FROM maven:3.8.4-openjdk-11-slim as build
 COPY $PWD /mtbimporter
 WORKDIR /mtbimporter
 
-RUN mvn install
+RUN mvn install -Dmaven.javadoc.skip=true -Dmaven.test.skip=true
 
 FROM r-base:4.1.2
 
 RUN apt-get update && apt-get install -y default-jre
 
-RUN wget https://download.docker.com/linux/debian/dists/bullseye/pool/stable/amd64/docker-ce-cli_20.10.7~3-0~debian-bullseye_amd64.deb && dpkg -i docker-ce-cli_20.10.7~3-0~debian-bullseye_amd64.deb && rm docker-ce-cli_20.10.7~3-0~debian-bullseye_amd64.deb
+RUN wget https://download.docker.com/linux/debian/dists/bullseye/pool/stable/amd64/docker-ce-cli_20.10.12~3-0~debian-bullseye_amd64.deb && dpkg -i docker-ce-cli_*.deb && rm docker-ce-cli_*.deb
 
 COPY --from=build /mtbimporter/target/mtbimporter-*-jar-with-dependencies.jar /app/mtbimporter.jar
-CMD ["java", "-jar", "/app/mtbimporter.jar"]
+ENTRYPOINT ["java", "-jar", "/app/mtbimporter.jar"]

docker-compose.yml

@@ -4,10 +4,15 @@ services:
     restart: unless-stopped
     build: ./
     image: ghcr.io/buschlab/mtbimporter:latest
+    command: "/app/settings.yaml"
     volumes:
       - "/var/run/docker.sock:/var/run/docker.sock"
       - "./settings.yaml:/app/settings.yaml"
-
+      - "./input:/app/input"
+      - "./mapper:/mapper"
+      - "./processed:/app/processed"
+      - "./study:/app/study"
+      - "./template:/app/template"
     networks:
      - mtbimporter_net