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Readme to generate the jar file and integrate it in an other directory - IntelliJ IDE 2023.1

A. Generation

1. JAR (already done for you)

You can find it in the /jar directory, but you can run this command if you'd like to generate a new one:

example@john:~$ mvn install

2. Uber JAR

You'll sometimes need a Fat/Uber JAR bundling all the dependencies JMEOS needs internally (such as jnr.ffi) so you don't have to manage them yourself (e.g. when creating a Jupyter Notebook using JMEOS). This command will generate a Fat Jar in the /jar directory alongside the classic Jar

  example@john:~$ mvn package

Here's an article explaining everything about Fat/Uber, Thin, Skinny and Hollow JARs: https://dzone.com/articles/the-skinny-on-fat-thin-hollow-and-uber

In the end, the structure of your personal project should look like this:
my-project/
├── Dockerfile
├── pom.xml
├── lib/
│ └── JMEOS-fat.jar
└── src/main/java/org/example/Main.java

B. Integration

1. Copy of the Jar

Copy the generated src/jar/JMEOS-fat.jar file into the new project repository you desire. It is recommended to put it into a specific directory (ex: src/lib).

2. Add dependency

Open the pom.xml file (if using Maven) or a the build.gradle (if using Gradle) and add the jmeos dependency.
For Maven:

<dependency>
  <groupId>org.jmeos</groupId>
  <artifactId>jmeos</artifactId>
  <version>1.0-SNAPSHOT</version>
</dependency>

3. Install the dependency

Since JMEOS is not available on Maven Central, you need to register it in your local Maven repository so that the dependency can be resolved:
Linux:

example@john:~$ mvn install:install-file -Dfile=$path_to_jar_file/JMEOS-fat.jar -DgroupId=org.jmeos -DartifactId=jmeos -Dversion=1.0-SNAPSHOT -Dpackaging=jar

Windows:

example@john:~$ mvn install:install-file -Dfile="$absolute_path_to_jar_file/JMEOS-fat.jar" -DgroupId="org.jmeos" -DartifactId=jmeos -Dversion="1.0-SNAPSHOT" -Dpackaging=jar

where $path_to_jar_file is the absolute path to the .jar file previously copied and placed in your project.

You just need to refresh Maven with the "Reload all Maven Projects" button, and you should see all the dependencies appear in the "External Libraries" of your project.

C. Running

On Windows, your project using JMEOS may not run well using an IDE. Therefore, using Docker will simplify the process.

Here's an example of a Dockerfile for a basic fresh project with no other dependencies:

FROM debian:bookworm-slim

RUN apt-get update \
  && apt-get install -y git curl gnupg build-essential cmake \
     postgresql-server-dev-15 libproj-dev libjson-c-dev postgis \
  && export GNUPGHOME="$(mktemp -d)" \
  && curl -fL https://apt.corretto.aws/corretto.key | gpg --batch --import \
  && gpg --batch --export '6DC3636DAE534049C8B94623A122542AB04F24E3' > /usr/share/keyrings/corretto.gpg \
  && rm -r "$GNUPGHOME" \
  && unset GNUPGHOME \
  && echo "deb [signed-by=/usr/share/keyrings/corretto.gpg] https://apt.corretto.aws stable main" > /etc/apt/sources.list.d/corretto.list \
  && apt-get update \
  && apt-get install -y java-21-amazon-corretto-jdk

# Compile MobilityDB with MEOS (generates libmeos.so)
RUN git clone https://github.com/MobilityDB/MobilityDB.git -b master /usr/local/src/MobilityDB
RUN mkdir -p /usr/local/src/MobilityDB/build
RUN cd /usr/local/src/MobilityDB/build && \
    cmake -DMEOS=ON -DALL=ON .. && \
    make -j$(nproc) && \
    make install && \
    ldconfig

# Maven
ENV MAVEN_HOME=/usr/share/maven
ENV MAVEN_CONFIG="/root/.m2"
COPY --from=maven:3.9.6-eclipse-temurin-11 ${MAVEN_HOME} ${MAVEN_HOME}
COPY --from=maven:3.9.6-eclipse-temurin-11 /usr/local/bin/mvn-entrypoint.sh /usr/local/bin/mvn-entrypoint.sh
COPY --from=maven:3.9.6-eclipse-temurin-11 /usr/share/maven/ref/settings-docker.xml /usr/share/maven/ref/settings-docker.xml
RUN ln -s ${MAVEN_HOME}/bin/mvn /usr/bin/mvn

# Install JMEOS in the local Maven repository
# (edit the JMEOS.jar path if needed at the root of your project)
COPY lib/JMEOS-fat.jar /tmp/JMEOS-fat.jar
RUN mvn install:install-file \
    -Dfile=/tmp/JMEOS-fat.jar \
    -DgroupId=org.jmeos \
    -DartifactId=jmeos \
    -Dversion=1.0-SNAPSHOT \
    -Dpackaging=jar

WORKDIR /app
COPY pom.xml .
# dependencies cache
RUN mvn dependency:go-offline -q   
COPY src ./src
RUN mvn package

ENV LD_LIBRARY_PATH=/usr/local/lib

# Entrypoint
CMD ["java", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "-Djava.library.path=/usr/local/lib", "-cp", "target/untitled-1.0-SNAPSHOT.jar:/tmp/JMEOS-fat.jar", "org.example.Main"]

Note:

  • build MobilityDB from master with -DALL=ON, as above. The jar's GeneratedFunctions is emitted from the catalog of master with every family on, so a library built from a release branch, or without the family flag, lacks symbols the jar names — the call fails at run time rather than at build time:
    RUN git clone https://github.com/MobilityDB/MobilityDB.git -b master
    cmake -DMEOS=ON -DALL=ON .. && \
  • do not forget to adapt the entrypoint parameters to your project:
    • the parameters of target/ here depending on the artifactId and version of your pom, here:
      target/untitled-1.0-SNAPSHOT.jar:/tmp/JMEOS-fat.jar"
    • the program you're trying to run, here:
      "org.example.Main"