Update to Dropwizard 4.x

.github/workflows/ci-build-manual.yml

@@ -0,0 +1,65 @@
+name: Build and push a development version on docker 
+
+on:
+  workflow_dispatch:
+    inputs:
+      custom_tag:
+        type: string
+        description: Docker image tag
+        required: true
+        default: "latest-develop"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
+      with:
+        java-version: '17.0.10+7'
+        distribution: 'temurin'
+        cache: 'gradle'
+    - name: Build with Gradle
+      run: ./gradlew build -x test
+
+  docker-build:
+    needs: [ build ]
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Create more disk space
+        run: |
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /opt/ghc
+          sudo rm -rf "/usr/local/share/boost"
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+          sudo rm -rf /opt/hostedtoolcache
+          sudo rm -rf /opt/google/chrome 
+          sudo rm -rf /opt/microsoft/msedge 
+          sudo rm -rf /opt/microsoft/powershell 
+          sudo rm -rf /opt/pipx 
+          sudo rm -rf /usr/lib/mono 
+          sudo rm -rf /usr/local/julia* 
+          sudo rm -rf /usr/local/lib/android 
+          sudo rm -rf /usr/local/lib/node_modules 
+          sudo rm -rf /usr/local/share/chromium 
+          sudo rm -rf /usr/local/share/powershell 
+          sudo rm -rf /usr/share/dotnet 
+          sudo rm -rf /usr/share/swift
+      - uses: actions/checkout@v4
+      - name: Build and push
+        id: docker_build
+        uses: mr-smithers-excellent/docker-build-push@v6
+        with:
+          dockerfile: Dockerfile.software
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+          image: lfoppiano/software-mentions
+          registry: docker.io
+          pushImage: true
+          tags:  |
+            latest-develop, ${{ github.event.inputs.custom_tag}}
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/ci-build.yml

@@ -0,0 +1,71 @@
+name: Build unstable
+
+on: [push]
+
+concurrency: 
+  group: gradle
+#  cancel-in-progress: true
+
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
+      with:
+        java-version: '17.0.10+7'
+        distribution: 'temurin'
+        cache: 'gradle'
+    - name: Build with Gradle
+      run: ./gradlew build -x test
+
+#    - name: Test with Gradle Jacoco and Coveralls
+#      run: ./gradlew test jacocoTestReport coveralls --no-daemon
+#
+#    - name: Coveralls GitHub Action
+#      uses: coverallsapp/github-action@v2
+#      with:
+#        github-token: ${{ secrets.GITHUB_TOKEN }}
+#        format: jacoco
+
+  docker-build:
+    needs: [ build ]
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Create more disk space
+        run: |
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /opt/ghc
+          sudo rm -rf "/usr/local/share/boost"
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+          sudo rm -rf /opt/hostedtoolcache
+          sudo rm -rf /opt/google/chrome 
+          sudo rm -rf /opt/microsoft/msedge 
+          sudo rm -rf /opt/microsoft/powershell 
+          sudo rm -rf /opt/pipx 
+          sudo rm -rf /usr/lib/mono 
+          sudo rm -rf /usr/local/julia* 
+          sudo rm -rf /usr/local/lib/android 
+          sudo rm -rf /usr/local/lib/node_modules 
+          sudo rm -rf /usr/local/share/chromium 
+          sudo rm -rf /usr/local/share/powershell 
+          sudo rm -rf /usr/share/dotnet 
+          sudo rm -rf /usr/share/swift
+      - uses: actions/checkout@v4
+      - name: Build and push
+        id: docker_build
+        uses: mr-smithers-excellent/docker-build-push@v6
+        with:
+          dockerfile: Dockerfile.software
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+          image: lfoppiano/software-mentions
+          registry: docker.io
+          pushImage: ${{ github.event_name != 'pull_request' }}
+          tags: latest-develop
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

Dockerfile.software

@@ -7,146 +7,87 @@ FROM openjdk:17-jdk-slim as builder
 USER root
 
 RUN apt-get update && \
-    apt-get -y --no-install-recommends install unzip
+    apt-get -y --no-install-recommends install apt-utils libxml2 git-lfs unzip wget
 
-WORKDIR /opt/grobid-source
-
-# gradle
-COPY gradle/ ./gradle/
-COPY gradlew ./
-COPY gradle.properties ./
-COPY build.gradle ./
-COPY settings.gradle ./
-
-# source
-COPY software-mentions/ ./software-mentions/
-COPY grobid-home/ ./grobid-home/
-COPY grobid-core/ ./grobid-core/
-COPY grobid-service/ ./grobid-service/
-COPY grobid-trainer/ ./grobid-trainer/
-
-# cleaning unused native libraries before packaging
-RUN rm -rf grobid-home/pdf2xml
-RUN rm -rf grobid-home/pdfalto/lin-32
-RUN rm -rf grobid-home/pdfalto/mac-64
-RUN rm -rf grobid-home/pdfalto/win-*
-RUN rm -rf grobid-home/lib/lin-32
-RUN rm -rf grobid-home/lib/win-*
-RUN rm -rf grobid-home/lib/mac-64
-
-# cleaning unused datasets stuff
-RUN rm -rf software-mentions/resources/dataset
+WORKDIR /opt/grobid
 
-RUN ./gradlew clean assemble install --no-daemon  --info --stacktrace
+RUN mkdir -p software-mentions-source grobid-home/models
+COPY src software-mentions-source/src
+COPY settings.gradle software-mentions-source/
+COPY resources/config/config-docker.yml software-mentions-source/resources/config/config.yml
+COPY resources/models software-mentions-source/resources/models
+COPY resources/lexicon software-mentions-source/resources/lexicon
+COPY build.gradle software-mentions-source/
+COPY gradle software-mentions-source/gradle/
+COPY gradlew software-mentions-source/
+#COPY .git software-mentions-source/.git
+COPY localLibs software-mentions-source/localLibs
+
+# Preparing models
+WORKDIR /opt/grobid/software-mentions-source
+RUN rm -rf /opt/grobid/grobid-home/models/*
+RUN ./gradlew clean assemble -x shadowJar --no-daemon  --stacktrace --info
+RUN git lfs install
+RUN ./gradlew installModels  --no-daemon --info --stacktrace \
+    && rm -f /opt/grobid/grobid-home/models/*.zip
+
+# Preparing distribution
+WORKDIR /opt/grobid
+RUN rm -f /opt/grobid/software-mentions-source/build/distributions/software-mentions-shadow* \
+  && unzip -o /opt/grobid/software-mentions-source/build/distributions/software-mentions-*.zip -d software-mentions_distribution \
+  && mv software-mentions_distribution/software-mentions-* software-mentions \
+  && rm -rf /opt/grobid/software-mentions-source/build
 
-WORKDIR ./software-mentions/
-RUN ./gradlew clean install --no-daemon  --info --stacktrace
+# install Pub2TEI
+WORKDIR /opt/
+RUN wget https://github.com/kermitt2/Pub2TEI/archive/refs/heads/master.zip && \
+    unzip master.zip &&  \
+    mv Pub2TEI-master Pub2TEI && \
+    rm master.zip
 
-WORKDIR /opt/grobid
-RUN unzip -o /opt/grobid-source/grobid-service/build/distributions/grobid-service-*.zip && \
-    mv grobid-service* grobid-service
-RUN unzip -o /opt/grobid-source/grobid-home/build/distributions/grobid-home-*.zip && \
-    chmod -R 755 /opt/grobid/grobid-home/pdfalto
-RUN rm -rf grobid-source
 
 # -------------------
 # build runtime image
 # -------------------
 
-# use NVIDIA Container Toolkit to automatically recognize possible GPU drivers on the host machine
-FROM tensorflow/tensorflow:2.7.0-gpu
+FROM lfoppiano/grobid:0.8.1-full as runtime
 
 # setting locale is likely useless but to be sure
 ENV LANG C.UTF-8
 
-# update NVIDIA Cuda key (following a key rotation in April 2022)
-RUN apt-get install -y wget
-RUN apt-key del 7fa2af80
-RUN rm /etc/apt/sources.list.d/cuda.list
-RUN rm /etc/apt/sources.list.d/nvidia-ml.list
-RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
-RUN dpkg -i cuda-keyring_1.0-1_all.deb
-
-# install JRE, python and other dependencies
-RUN apt-get update && \
-    apt-get -y --no-install-recommends install apt-utils build-essential gcc libxml2 libfontconfig unzip curl \
-    openjdk-17-jre-headless openjdk-17-jdk ca-certificates-java \
-    musl gfortran \
-    python3 python3-pip python3-setuptools python3-dev \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/*
-
 WORKDIR /opt/grobid
+RUN rm -rf /opt/grobid/grobid-home/models/*-with_ELMo \
+    && rm -rf /opt/grobid/grobid-service \
+    && ln -sf software-mentions/resources/ resources
 
-COPY --from=builder /opt/grobid .
-
-RUN python3 -m pip install pip --upgrade
+# the last command above is just a hack to make the lexicon loader working
 
-# install DeLFT via pypi
-RUN pip3 install requests delft==0.3.3
-# link the data directory to /data
-# the current working directory will most likely be /opt/grobid
-RUN mkdir -p /data \
-    && ln -s /data /opt/grobid/data \
-    && ln -s /data ./data
+COPY --from=builder /opt/grobid/grobid-home/models ./grobid-home/models
+COPY --from=builder /opt/grobid/software-mentions ./software-mentions/
+COPY --from=builder /opt/grobid/software-mentions-source/resources/config/config.yml ./software-mentions/resources/config/config.yml
+COPY --from=builder /opt/grobid/software-mentions-source/resources/lexicon/ ./software-mentions/resources/lexicon/
 
-# disable python warnings (and fix logging)
-ENV PYTHONWARNINGS="ignore"
+COPY --from=builder /opt/grobid/software-mentions /opt/grobid/software-mentions
+COPY --from=builder /opt/Pub2TEI /opt/Pub2TEI
 
-WORKDIR /opt/grobid
+VOLUME ["/opt/grobid/grobid-home/tmp"]
 
-ENV JAVA_OPTS=-Xmx4g
+#WORKDIR /opt/grobid
 
-# install jep (and temporarily the matching JDK)
-ENV JDK_URL=https://download.java.net/java/GA/jdk17.0.2/dfd4a8d0985749f896bed50d7138ee7f/8/GPL/openjdk-17.0.2_linux-x64_bin.tar.gz
-RUN curl --fail --show-error --location -q ${JDK_URL} -o /tmp/openjdk.tar.gz 
-RUN mkdir /tmp/jdk-17 
-RUN tar xvfz /tmp/openjdk.tar.gz --directory /tmp/jdk-17 --strip-components 1 --no-same-owner 
-RUN /tmp/jdk-17/bin/javac -version
-RUN JAVA_HOME=/tmp/jdk-17 pip3 install jep==4.0.2 
-RUN rm -f /tmp/openjdk.tar.gz 
-RUN rm -rf /tmp/jdk-17
-ENV LD_LIBRARY_PATH=/usr/local/lib/python3.8/dist-packages/jep:grobid-home/lib/lin-64:grobid-home/lib/lin-64/jep:${LD_LIBRARY_PATH}
-# remove libjep.so because we are providing our own version in the virtual env above
-RUN rm /opt/grobid/grobid-home/lib/lin-64/jep/libjep.so
-
-# preload embeddings 
-
-COPY --from=builder /opt/grobid-source/grobid-home/scripts/preload_embeddings.py .
-COPY --from=builder /opt/grobid-source/grobid-home/config/resources-registry.json .
-#RUN python3 preload_embeddings.py --embedding word2vec --registry ./resources-registry.json
-RUN ln -s /opt/grobid /opt/delft
-
-COPY --from=builder /opt/grobid-source/software-mentions /opt/grobid/software-mentions
-COPY --from=builder /root/.m2/repository/org /opt/grobid/software-mentions/lib/org
-
-# install Pub2TEI
-WORKDIR /opt/
-RUN wget https://github.com/kermitt2/Pub2TEI/archive/refs/heads/master.zip
-RUN unzip master.zip
-RUN mv Pub2TEI-master Pub2TEI
-
-WORKDIR /opt/grobid/software-mentions
-
-RUN mkdir /opt/grobid/delft
-RUN mkdir /opt/grobid/delft/delft
-COPY --from=builder /opt/grobid-source/grobid-home/config/resources-registry.json /opt/grobid/delft/delft/resources-registry.json
-
-# trigger gradle wrapper install
-RUN ./gradlew --version
-
-# install all the ML models
-RUN ./gradlew copyModels installModels  && rm -rf resources/models && rm -f /opt/grobid/grobid-home/models/software/model.wapiti.gz && rm -f /opt/grobid/grobid-home/models/software-BERT-0.3.2.zip && rm -f /opt/grobid/grobid-home/models/context_bert-0.3.2.zip && rm -f /opt/grobid/grobid-home/models/context_used_bert-0.3.2.zip && rm -f /opt/grobid/grobid-home/models/context_shared_bert-0.3.2.zip && rm -f /opt/grobid/grobid-home/models/context_creation_bert-0.3.2.zip
-
-RUN ./gradlew clean assemble install --no-daemon --stacktrace --info -x test
-
-CMD ["sh", "-c", "java --add-opens java.base/java.lang=ALL-UNNAMED -jar build/libs/software-mentions-0.8.0-onejar.jar server resources/config/config.yml"]
+# this will build and load embeddings on the image forever (only if required by the config) :)
+# LF: AFAIK this is not needed at the moment as all the models are running with bert, but might
+# be a solution if we want to support the GRU version
+# RUN python3 preload_embeddings.py --registry ./resources-registry.json --embedding word2vec
 
 ARG GROBID_VERSION
+ENV GROBID_VERSION=${GROBID_VERSION:-latest}
+ENV SOFTWARE_MENTIONS_OPTS "-Djava.library.path=/opt/grobid/grobid-home/lib/lin-64:/usr/local/lib/python3.8/dist-packages/jep --add-opens java.base/java.lang=ALL-UNNAMED"
+
+CMD ["./software-mentions/bin/software-mentions", "server", "software-mentions/resources/config/config.yml"]
 
 LABEL \
     authors="The contributors" \
     org.label-schema.name="software-mentions" \
     org.label-schema.description="Image with software-mentions service" \
     org.label-schema.url="https://github.com/softcite/software-mentions" \
-    org.label-schema.version=${GROBID_VERSION}
+    org.label-schema.version=${GROBID_VERSION}