Merge pull request #238 from medizininformatik-initiative/feature/237…

…-Minor-suggestions-to-improve-the-container-image

#237 - Minor suggestions to improve the container image

.github/integration-test/docker-compose.yml

@@ -8,6 +8,7 @@ services:
     depends_on:
       - dataportal-postgres
     environment:
+      JAVA_OPTS: ""
       QUERYRESULT_PUBLIC_KEY: "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"
       # ----- app
       QUERY_VALIDATION_ENABLED: "true"

.github/scripts/check-if-running-as-user-10001.sh

@@ -0,0 +1,10 @@
+#!/bin/bash -e
+
+if docker exec -u0 dataportal-backend pgrep -u 10001 java > /dev/null
+then
+    echo "Java process is running as user 10001"
+    exit 0
+else
+    echo "Java process is not running as user 10001"
+    exit 1
+fi

.github/workflows/ci.yml

@@ -17,11 +17,31 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up JDK 21
+      - name: Docker Meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+            type=sha
+          labels: |
+            maintainer=medizininformatik-initiative
+            org.opencontainers.image.authors=medizininformatik-initiative
+            org.opencontainers.image.source=https://github.com/medizininformatik-initiative/feasibility-backend
+            org.opencontainers.image.vendor=medizininformatik-initiative
+            org.opencontainers.image.title=dataportal backend
+            org.opencontainers.image.description=The backend for the dataportal, including feasibility query execution as well as data selection and extraction.
+
+      - name: Set up JDK 22
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: 21
+          java-version: 22
 
       - name: Cache Local Maven Repo
         uses: actions/cache@v4
@@ -159,8 +179,8 @@ jobs:
       - name: Wait for Dataportal Backend
         run: .github/scripts/wait-for-url.sh  http://localhost:8091/actuator/health
 
-      - name: Check if Dataportal Backend is correctly running with the dataportal user
-        run: .github/scripts/check-if-running-as-dataportal-user.sh
+      - name: Check if Dataportal Backend is correctly running with the user with id 10001
+        run: .github/scripts/check-if-running-as-user-10001.sh
 
       - name: Wait for Blaze
         run: .github/scripts/wait-for-url.sh  http://localhost:8082/health
@@ -203,11 +223,11 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up JDK 21
+    - name: Set up JDK 22
       uses: actions/setup-java@v4
       with:
         distribution: 'temurin'
-        java-version: 21
+        java-version: 22
 
     - name: Cache Local Maven Repo
       uses: actions/cache@v4

Dockerfile

@@ -1,17 +1,6 @@
-FROM eclipse-temurin:17-jre
-
-RUN apt update -yqq && apt upgrade -yqq && \
-    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/
+FROM eclipse-temurin:22-jre-alpine@sha256:d8ac5f15b7dc0a91bdfb89422f900383469e5de12dcce3949f145d713f455b34
 
 WORKDIR /opt/dataportal-backend
-COPY ./target/*.jar ./dataportal-backend.jar
-COPY ontology ontology
-
-RUN groupadd --system dataportal && useradd --system dataportal -g dataportal
-RUN mkdir logging
-RUN chown -R dataportal:dataportal /opt/dataportal-backend
-
-USER dataportal:dataportal
 
 ARG VERSION=6.0.0
 ENV APP_VERSION=${VERSION}
@@ -23,22 +12,17 @@ ENV CERTIFICATE_PATH=/opt/dataportal-backend/certs
 ENV TRUSTSTORE_PATH=/opt/dataportal-backend/truststore
 ENV TRUSTSTORE_FILE=self-signed-truststore.jks
 
-RUN mkdir -p $CERTIFICATE_PATH $TRUSTSTORE_PATH
-RUN chown dataportal:dataportal $CERTIFICATE_PATH $TRUSTSTORE_PATH
+RUN mkdir logging && \
+    mkdir -p $CERTIFICATE_PATH $TRUSTSTORE_PATH && \
+    chown -R 10001:10001 /opt/dataportal-backend && \
+    chown 10001:10001 $CERTIFICATE_PATH $TRUSTSTORE_PATH && \
+    apk --no-cache add curl bash
+USER 10001
 
 HEALTHCHECK --interval=5s --start-period=10s CMD curl -s -f http://localhost:8090/actuator/health || exit 1
 
+COPY ./target/*.jar ./dataportal-backend.jar
+COPY ontology ontology
 COPY ./docker-entrypoint.sh /
-ENTRYPOINT ["/bin/bash", "/docker-entrypoint.sh"]
 
-ARG GIT_REF=""
-ARG BUILD_TIME=""
-LABEL maintainer="medizininformatik-initiative" \
-    org.opencontainers.image.created=${BUILD_TIME} \
-    org.opencontainers.image.authors="medizininformatik-initiative" \
-    org.opencontainers.image.source="https://github.com/medizininformatik-initiative/feasibility-backend" \
-    org.opencontainers.image.version=${VERSION} \
-    org.opencontainers.image.revision=${GIT_REF} \
-    org.opencontainers.image.vendor="medizininformatik-initiative" \
-    org.opencontainers.image.title="dataportal backend" \
-    org.opencontainers.image.description="Provides backend functions for the dataportal"
+ENTRYPOINT ["/bin/bash", "/docker-entrypoint.sh"]

docker-compose.yml

@@ -13,6 +13,7 @@ services:
       init-elasticsearch:
         condition: service_completed_successfully
     environment:
+      JAVA_OPTS: ${DATAPORTAL_BACKEND_JAVA_OPTS}
       # ----- app
       QUERY_VALIDATION_ENABLED: ${DATAPORTAL_BACKEND_QUERY_VALIDATION_ENABLED:-true}
       CQL_TRANSLATE_ENABLED: ${DATAPORTAL_BACKEND_CQL_TRANSLATE_ENABLED:-true}
@@ -31,8 +32,8 @@ services:
       # ---- ontology
       ONTOLOGY_FILES_FOLDER_UI: ${DATAPORTAL_BACKEND_ONTOLOGY_FILES_FOLDER:-/opt/dataportal-backend/ontology}
       ONTOLOGY_DB_MIGRATION_FOLDER: ${DATAPORTAL_BACKEND_ONTOLOGY_DB_MIGRATION_FOLDER:-/opt/dataportal-backend/ontology/migration}
-      MAPPINGS_FILE: ${DATAPORTAL_BACKEND_ONTOLOGY_FILES_FOLDER:-/opt/dataportal-backend/ontology}/codex-term-code-mapping.json
-      CONCEPT_TREE_FILE: ${DATAPORTAL_BACKEND_ONTOLOGY_FILES_FOLDER:-/opt/dataportal-backend/ontology}/codex-code-tree.json
+      MAPPINGS_FILE: ${DATAPORTAL_BACKEND_ONTOLOGY_FILES_FOLDER:-/opt/dataportal-backend/ontology}/mapping_cql.json
+      CONCEPT_TREE_FILE: ${DATAPORTAL_BACKEND_ONTOLOGY_FILES_FOLDER:-/opt/dataportal-backend/ontology}/mapping_tree.json
       # ---- auth
       KEYCLOAK_ENABLED: ${DATAPORTAL_BACKEND_KEYCLOAK_ENABLED:-true}
       KEYCLOAK_BASE_URL: ${DATAPORTAL_BACKEND_KEYCLOAK_BASE_URL:-http://keycloak:8080}
@@ -82,20 +83,18 @@ services:
       PRIVACY_QUOTA_READ_DETAILED_OBFUSCATED_INTERVALSECONDS: ${DATAPORTAL_BACKEND_PRIVACY_QUOTA_READ_DETAILED_OBFUSCATED_INTERVALSECONDS:-7200}
       PRIVACY_THRESHOLD_RESULTS: ${DATAPORTAL_BACKEND_PRIVACY_THRESHOLD_RESULTS:-20}
       PRIVACY_THRESHOLD_SITES: ${DATAPORTAL_BACKEND_PRIVACY_THRESHOLD_SITES:-3}
-      PRIVACY_THRESHOLD_SITES_RESULT: ${DATAPORTAL_BACKEND_PRIVACY_THRESHOLD_SITES_RESULT}
+      PRIVACY_THRESHOLD_SITES_RESULT: ${DATAPORTAL_BACKEND_PRIVACY_THRESHOLD_SITES_RESULT:-0}
       QUERYRESULT_DISABLE_LOG_FILE_ENCRYPTION: "true"
       # ---- Elastic Search
-      ELASTIC_SEARCH_ENABLED: ${DATAPORTAL_BACKEND_ELASTIC_SEARCH_ENABLED}
-      ELASTIC_SEARCH_HOST: ${DATAPORTAL_BACKEND_ELASTIC_SEARCH_HOST}
-      ELASTIC_SEARCH_FILTER: ${DATAPORTAL_BACKEND_ELASTIC_SEARCH_FILTER}
+      ELASTIC_SEARCH_ENABLED: ${DATAPORTAL_BACKEND_ELASTIC_SEARCH_ENABLED:-true}
+      ELASTIC_SEARCH_HOST: ${DATAPORTAL_BACKEND_ELASTIC_SEARCH_HOST:-dataportal-elastic}
+      ELASTIC_SEARCH_FILTER: ${DATAPORTAL_BACKEND_ELASTIC_SEARCH_FILTER:-context,terminology,kds_module}
       # ---- logging
       LOG_LEVEL_SQL: ${DATAPORTAL_BACKEND_LOG_LEVEL_SQL:-warn}
       LOG_LEVEL: ${DATAPORTAL_BACKEND_LOG_LEVEL:-warn}
     volumes:
-      - ${DATAPORTAL_BACKEND_LOCAL_CONCEPT_TREE_PATH:-./ontology/dataportal-code-tree.json}:${DATAPORTAL_BACKEND_ONTOLOGY_FILES_FOLDER:-/opt/dataportal-backend/ontology}/dataportal-code-tree.json
-      - ${DATAPORTAL_BACKEND_LOCAL_TERM_CODE_MAPPING_PATH:-./ontology/dataportal-term-code-mapping.json}:${DATAPORTAL_BACKEND_ONTOLOGY_FILES_FOLDER:-/opt/dataportal-backend/ontology}/dataportal-term-code-mapping.json
-      - ${DATAPORTAL_BACKEND_DSF_SECURITY_DIR:-/dev/null}:/opt/dataportal-backend/dsf-security/
-      - ${DATAPORTAL_BACKEND_ONTOLOGY_DB_MIGRATION_FOLDER:-../ontology/migration}:/opt/dataportal-backend/ontology/migration
+      - ${DATAPORTAL_BACKEND_CERTS_PATH:-../certs}:/opt/dataportal-security
+      - ./certs:/opt/dataportal-backend/certs
 
   dataportal-postgres:
     container_name: dataportal-postgres

docker-entrypoint.sh

@@ -28,8 +28,11 @@ if [ ! "${#ca_files[@]}" -eq 0 ]; then
 
     done
 
+    echo "### JAVA_OPTS is set to $JAVA_OPTS"
+
     java $JAVA_OPTS -Djavax.net.ssl.trustStore="$TRUSTSTORE_FILE" -Djavax.net.ssl.trustStorePassword="$TRUSTSTORE_PASS" -jar dataportal-backend.jar
 else
     echo "# No CA *.pem cert files found in /opt/dataportal-backend/certs -> starting dataportal backend without own CAs"
+    echo "### JAVA_OPTS is set to $JAVA_OPTS"
     java $JAVA_OPTS -jar dataportal-backend.jar
 fi