refactor: Docker setup

Dockerfile

@@ -0,0 +1,43 @@
+FROM maven:3.8.4-openjdk-17 as maven
+
+# copy source code and POM
+
+WORKDIR /usr/src/morph-xr2rml
+
+COPY morph-base morph-base
+COPY morph-core morph-core
+COPY morph-xr2rml-dist morph-xr2rml-dist
+COPY morph-xr2rml-lang morph-xr2rml-lang
+COPY morph-xr2rml-mongo morph-xr2rml-mongo
+COPY morph-xr2rml-rdb morph-xr2rml-rdb
+COPY pom.xml pom.xml
+
+RUN mvn clean install
+
+# find the fat JAR file and copy it to a fixed location
+RUN JAR_FILE=$(ls morph-xr2rml-dist/target/*jar-with-dependencies.jar) && \
+    cp "$JAR_FILE" morph-xr2rml-dist/target/dist.jar
+
+# ==================================================================================================
+
+FROM openjdk:11-jdk-bullseye
+
+RUN apt-get update -y && \
+    apt-get install -y && \
+    rm -rf /var/lib/apt/lists/*
+
+ENV XR2RML="/morph-xr2rml"
+RUN mkdir -p $XR2RML
+WORKDIR "$XR2RML"
+
+# copy the JAR file from the build stage
+COPY --from=maven /usr/src/morph-xr2rml/morph-xr2rml-dist/target/dist.jar "$XR2RML"
+
+ENV CONFIG="$XR2RML/config"
+ENV OUTPUT="$XR2RML/output"
+ENV LOG="$XR2RML/log"
+RUN mkdir -p "$CONFIG" "$OUTPUT" "$LOG"
+
+# Morph-xR2RML is not run at container startup, only when the run_xr2rml.sh script is run from outside.
+# So instead just use sleep so that the container never kicks out.
+CMD ["sleep", "infinity"]

docker/docker-compose.yml → docker-compose.mongo.yml

@@ -1,27 +1,17 @@
 version: '3.2'
-services:
+networks:
+  xr2rml-net:
+    driver: bridge
 
+services:
   morph-xr2rml:
-    image: frmichel/morph-xr2rml:v1.3.2
-    container_name: morph-xr2rml
     networks:
       - xr2rml-net
-    volumes:
-      - "./xr2rml_config:/xr2rml_config"
-      - "./xr2rml_output:/xr2rml_output"
-      - "./log:/log"
-
   mongo-xr2rml:
     image: mongo:4.4.6
-    container_name: mongo-xr2rml    
     networks:
       - xr2rml-net
     volumes:
       - "./mongo_db:/data/db"
       - "./mongo_tools:/mongo_tools"
       - "./mongo_import:/mongo_import"
-
-networks:
-  xr2rml-net:
-    driver: bridge
-

docker-compose.yml

@@ -0,0 +1,8 @@
+version: '3.2'
+services:
+  morph-xr2rml:
+    build: .
+    volumes:
+      - "./xr2rml_config:/xr2rml_config"
+      - "./xr2rml_output:/xr2rml_output"
+      - "./log:/log"