Add Dockerfile

Dockerfile

@@ -0,0 +1,52 @@
+# Stage 1: Build the application
+FROM maven:3.9.6-amazoncorretto-21 as builder
+
+# Set the working directory in the Maven image
+WORKDIR /app
+
+# Copy the java source files and the pom.xml file into the image
+COPY src ./src
+COPY pom.xml .
+
+# Build the application
+RUN mvn clean package
+
+FROM python:3.11
+
+# Install any needed packages specified in requirements.txt
+COPY requirements.txt ./
+RUN pip install --no-cache-dir -r requirements.txt
+
+# Install Perl. Some scripts are written in perl
+RUN apt-get update && apt-get install -y perl
+
+COPY scripts/ scripts/
+RUN chmod -R a+x /scripts/
+
+# Set the working directory in the container
+WORKDIR /scripts/
+
+ENV PORTAL_HOME=/
+
+COPY --from=builder /app/core-*.jar /
+# Set environment variables for Java version and installation paths
+ENV JAVA_VERSION 21
+ENV JAVA_HOME /usr/java/openjre-$JAVA_VERSION
+
+# Install necessary packages for adding repositories over HTTPS
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends apt-transport-https ca-certificates wget dirmngr gnupg software-properties-common && \
+    rm -rf /var/lib/apt/lists/*
+
+# Download and install OpenJRE 21
+# Note: The exact URL might change based on the latest available version, so replace it with the correct URL for JRE 21
+RUN mkdir -p "$JAVA_HOME" && \
+    wget -O jdk21.tar.gz "https://download.oracle.com/java/21/latest/jdk-21_linux-x64_bin.tar.gz" && \
+    tar xvf jdk21.tar.gz --strip-components=1 -C "$JAVA_HOME" && \
+    rm jdk21.tar.gz
+
+# Add java to PATH
+ENV PATH $JAVA_HOME/bin:$PATH
+
+# This file is empty. It has to be overriden by bind mounting the actual application.properties
+RUN touch /application.properties

README.md

@@ -82,3 +82,16 @@ The script will search for `core-*.jar` in the root of the project:
 ```bash
 python scripts/importer/metaImport.py -s tests/test_data/study_es_0 -p tests/test_data/api_json_unit_tests -o
 ```
+
+## Running in docker
+
+Build docker image with:
+```bash
+docker build -t cbioportal-core .
+```
+
+Example of how to start the loading:
+```bash
+docker run -it -v $(pwd)/data/:/data/ -v $(pwd)/application.properties:/application.properties cbioportal-core python importer/metaImport.py -s /data/study_es_0 -p /data/api_json -o
+```
+