ncats · alx652 · Jul 17, 2025
diff --git a/embedded/project/db.init.sql.tar.gz b/embedded/project/db.init.sql.tar.gz
diff --git a/embedded/project/docker-source/adverse-events/Dockerfile b/embedded/project/docker-source/adverse-events/Dockerfile
@@ -1,39 +1,40 @@
-# Docker mvn build
-FROM maven:3.6.3-jdk-11 as build
+FROM alpine:latest AS build
 
 ARG RELEASE_MODE='public'
 ARG STARTER_MODULE_BRANCH=master
 ARG SUBSTANCES_MODULE_BRANCH=master
 ARG ADVERSE_EVENTS_MODULE_BRANCH=starter
 
+ENV TZ=America/New_York
+
 COPY . .
-COPY . .
-RUN if [ "$RELEASE_MODE" = "development" ]; then \
+RUN if [ -f settings.xml ]; then \
+  mkdir -p /root/.m2; \
+  cp settings.xml /root/.m2/settings.xml; \
+fi && \
+apk add --no-cache git openjdk17 && \
+if [ "$RELEASE_MODE" = "development" ]; then \
   git clone --branch $STARTER_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-starter.git && \
   git clone --branch $SUBSTANCES_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-module-substances.git && \
   git clone --branch $ADVERSE_EVENTS_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-module-adverse-events.git && \
-  cd gsrs-spring-starter &&  mvn clean -U install -DskipTests && \ 
-    sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh && \
-    mvn clean -U install -DskipTests && \
+  cd gsrs-spring-starter &&  ./mvnw clean -U install -DskipTests && \
+    if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+    ./mvnw clean -U install -DskipTests && \
   cd .. && cd gsrs-spring-module-substances && \
-    sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh && \
-    mvn clean -U install -DskipTests && \
-   cd .. && cd gsrs-spring-module-adverse-events && \ 
-    # sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh \
-    mvn clean -U install -DskipTests; \
-fi
-
-RUN rm -rf src/main/resources/application.conf && \
-    rm -rf src/main/resources/adverse-events-env.conf && \
-    rm -rf src/main/resources/adverse-events-env-db.conf && \
-    sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh && \
-    mvn clean -U package -Dwith.packaging=jar -DskipTests
-
-ENV TZ=America/New_York
-RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
-
-RUN mkdir -p /app/data/adverse-events/conf
-RUN mkdir -p /app/data/adverse-events/classes
+    if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+    ./mvnw clean -U install -DskipTests && \
+  cd .. && cd gsrs-spring-module-adverse-events && \
+    if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+    ./mvnw clean -U install -DskipTests && \
+  cd ..; \
+fi && \
+rm -rf src/main/resources/adverse-events-env.conf && \
+rm -rf src/main/resources/adverse-events-env-db.conf && \
+if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+./mvnw clean -U package -Dwith.packaging=jar -DskipTests && \
+ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
+mkdir -p /app/data/adverse-events/conf && \
+mkdir -p /app/data/adverse-events/classes
 
 WORKDIR /app/data/adverse-events
 EXPOSE 8084

diff --git a/embedded/project/docker-source/applications/Dockerfile b/embedded/project/docker-source/applications/Dockerfile
@@ -1,39 +1,40 @@
-# Docker mvn build
-FROM maven:3.6.3-jdk-11 as build
+FROM alpine:latest AS build
 
 ARG RELEASE_MODE='public'
 ARG STARTER_MODULE_BRANCH=master
 ARG SUBSTANCES_MODULE_BRANCH=master
 ARG APPLICATIONS_MODULE_BRANCH=starter
 
+ENV TZ=America/New_York
+
 COPY . .
-COPY . .
-RUN if [ "$RELEASE_MODE" = "development" ]; then \
+RUN if [ -f settings.xml ]; then \
+  mkdir -p /root/.m2; \
+  cp settings.xml /root/.m2/settings.xml; \
+fi && \
+apk add --no-cache git openjdk17 && \
+if [ "$RELEASE_MODE" = "development" ]; then \
   git clone --branch $STARTER_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-starter.git && \
   git clone --branch $SUBSTANCES_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-module-substances.git && \
   git clone --branch $APPLICATIONS_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-module-drug-applications.git && \
-  cd gsrs-spring-starter &&  mvn clean -U install -DskipTests && \ 
-    sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh && \
-    mvn clean -U install -DskipTests && \
+  cd gsrs-spring-starter &&  ./mvnw clean -U install -DskipTests && \
+    if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+    ./mvnw clean -U install -DskipTests && \
   cd .. && cd gsrs-spring-module-substances && \
-    sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh && \
-    mvn clean -U install -DskipTests && \
-   cd .. && cd gsrs-spring-module-drug-applications && \ 
-    # sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh \
-    mvn clean -U install -DskipTests; \
-fi
-
-RUN rm -rf src/main/resources/application.conf && \
-    rm -rf src/main/resources/applications-env.conf && \
-    rm -rf src/main/resources/applications-env-db.conf && \
-    sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh && \
-    mvn clean -U package -Dwith.packaging=jar -DskipTests
-
-ENV TZ=America/New_York
-RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
-
-RUN mkdir -p /app/data/applications/conf
-RUN mkdir -p /app/data/applications/classes
+    if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+    ./mvnw clean -U install -DskipTests && \
+  cd .. && cd gsrs-spring-module-drug-applications && \
+    if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+    ./mvnw clean -U install -DskipTests && \
+  cd ..; \
+fi && \
+rm -rf src/main/resources/applications-env.conf && \
+rm -rf src/main/resources/applications-env-db.conf && \
+if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+./mvnw clean -U package -Dwith.packaging=jar -DskipTests && \
+ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
+mkdir -p /app/data/applications/conf && \
+mkdir -p /app/data/applications/classes
 
 WORKDIR /app/data/applications
 EXPOSE 8084

diff --git a/embedded/project/docker-source/clinical-trials/Dockerfile b/embedded/project/docker-source/clinical-trials/Dockerfile
@@ -1,38 +1,41 @@
-# Docker mvn build
-FROM maven:3.6.3-jdk-11 as build
+
+FROM alpine:latest AS build
 
 ARG RELEASE_MODE='public'
 ARG STARTER_MODULE_BRANCH=master
 ARG SUBSTANCES_MODULE_BRANCH=master
 ARG CLINICAL_TRIALS_MODULE_BRANCH=master
 
+ENV TZ=America/New_York
+
 COPY . .
-RUN if [ "$RELEASE_MODE" = "development" ]; then \
+RUN if [ -f settings.xml ]; then \
+  mkdir -p /root/.m2; \
+  cp settings.xml /root/.m2/settings.xml; \
+fi && \
+apk add --no-cache git openjdk17 && \
+if [ "$RELEASE_MODE" = "development" ]; then \
   git clone --branch $STARTER_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-starter.git && \
   git clone --branch $SUBSTANCES_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-module-substances.git && \
   git clone --branch $CLINICAL_TRIALS_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-module-clinical-trials.git && \
-  cd gsrs-spring-starter &&  mvn clean -U install -DskipTests && \ 
-    sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh && \
-    mvn clean -U install -DskipTests && \
+  cd gsrs-spring-starter &&  ./mvnw clean -U install -DskipTests && \
+    if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+    ./mvnw clean -U install -DskipTests && \
   cd .. && cd gsrs-spring-module-substances && \
-    sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh && \
-    mvn clean -U install -DskipTests && \
-   cd .. && cd gsrs-spring-module-clinical-trials && \ 
-    # sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh \
-    mvn clean -U install -DskipTests; \
-fi
-
-RUN rm -rf src/main/resources/application.conf && \
-    rm -rf src/main/resources/clinical-trials-env.conf && \
-    rm -rf src/main/resources/clinical-trials-env-db.conf && \
-    sed -i.bak -e "s/\.\/mvnw/mvn/g" installExtraJars.sh && sh installExtraJars.sh && \
-    mvn clean -U package -Dwith.packaging=jar -DskipTests
-
-ENV TZ=America/New_York
-RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
-
-RUN mkdir -p /app/data/clinical-trials/conf
-RUN mkdir -p /app/data/clinical-trials/classes
+    if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+    ./mvnw clean -U install -DskipTests && \
+  cd .. && cd gsrs-spring-module-clinical-trials && \
+    if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+    ./mvnw clean -U install -DskipTests && \
+  cd ..; \
+fi && \
+rm -rf src/main/resources/clinical-trials-env.conf && \
+rm -rf src/main/resources/clinical-trials-env-db.conf && \
+if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+./mvnw clean -U package -Dwith.packaging=jar -DskipTests && \
+ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
+mkdir -p /app/data/clinical-trials/conf && \
+mkdir -p /app/data/clinical-trials/classes
 
 WORKDIR /app/data/clinical-trials
 EXPOSE 8089

diff --git a/embedded/project/docker-source/discovery/Dockerfile b/embedded/project/docker-source/discovery/Dockerfile
@@ -1,9 +1,11 @@
-# Docker mvn build
-FROM maven:3.6.3-jdk-11 as build
+
+FROM alpine:latest AS build
 
 COPY . .
 
-RUN mvn clean -U package -Dwith.packaging=jar  -DskipTests
+RUN whoami && cat  /root/.m2/settings.xml
+
+RUN ./mvnw clean -U package -Dwith.packaging=jar  -DskipTests
 
 ENV TZ=America/New_York
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone

diff --git a/embedded/project/docker-source/docker-compose.yml b/embedded/project/docker-source/docker-compose.yml
@@ -1,11 +1,12 @@
-version: '3'
 services:
   adverse-events:
     container_name: adverse-events-emb  
     entrypoint: ["java", "-cp", "/target/adverse-events.jar:classes:conf", "org.springframework.boot.loader.JarLauncher"]
     environment:
       APPLICATION_HOST: http://gateway:9081
       APPLICATION_HOST_PORT: 9081
+      DB_TEST_PASSWORD: ${DB_TEST_PASSWORD}
+      DB_TEST_USERNAME: ${DB_TEST_USERNAME}
       EUREKA_SERVICE_URL: http://discovery:8761/eureka
       IX_HOME: /app/data/adverse-events/ginas.ix
       IX_HOME_SUBSTANCES: /app/data/substances/ginas.ix
@@ -35,6 +36,8 @@ services:
       - 8083:8083
   clinical-trials:
     container_name: clinical-trials-emb
+    depends_on:
+      - substances
     image: gsrs3/gsrs-emb-docker-clinical-trials:0.0.1-SNAPSHOT
     entrypoint: ["java", "-cp", "/target/clinical-trials.jar:classes:conf", "org.springframework.boot.loader.JarLauncher"]
     environment:
@@ -69,24 +72,25 @@ services:
       MS_FRONTEND_SERVER_PORT: 8082
       MS_SERVLET_CONTEXT_PATH_FRONTEND: /
     image: gsrs3/gsrs-emb-docker-frontend:0.0.1-SNAPSHOT
-    volumes:
-      - ../volumes/app-data:/app/data
     ports:
       - 8082:8082
+    volumes:
+      - ../volumes/app-data:/app/data
   gateway:
     container_name: gateway-emb
     entrypoint: ["java", "-cp", "/target/gateway.jar:classes:conf", "org.springframework.boot.loader.JarLauncher"]
-    ports:
-      - 9081:9081
-    image: gsrs3/gsrs-emb-docker-gateway:0.0.1-SNAPSHOT
-    volumes:
-      - ../volumes/app-data:/app/data
     environment:
+      DEBUG: false
       API_BASE_PATH: /ginas/app
       APPLICATION_HOST: http://gateway:9081
       APPLICATION_HOST_PORT: 9081
       EUREKA_SERVICE_URL: http://discovery:8761/eureka
       SERVER_PORT: 9081
+    image: gsrs3/gsrs-emb-docker-gateway:0.0.1-SNAPSHOT
+    ports:
+      - 9081:9081
+    volumes:
+      - ../volumes/app-data:/app/data
   impurities:
     container_name: impurities-emb
     entrypoint: ["java", "-cp", "/target/impurities.jar:classes:conf", "org.springframework.boot.loader.JarLauncher"]
@@ -123,6 +127,8 @@ services:
       - 8090:8090
   products:
     container_name: products-emb
+    depends_on:
+      - substances
     entrypoint: ["java", "-cp", "/target/products.jar:classes:conf", "org.springframework.boot.loader.JarLauncher"]
     environment:
       APPLICATION_HOST: http://gateway:9081
@@ -178,9 +184,9 @@ services:
   mariadb:
     container_name: mariadb-emb
     environment:
-      MARIADB_ROOT_USER: $DB_TEST_USERNAME
-      MARIADB_USER: $DB_TEST_USERNAME
-      MARIADB_ROOT_PASSWORD: $DB_TEST_PASSWORD
+      MARIADB_ROOT_USER: ${DB_TEST_USERNAME}
+      MARIADB_USER: ${DB_TEST_USERNAME}
+      MARIADB_ROOT_PASSWORD: ${DB_TEST_PASSWORD}
     image: mariadb:latest
     ports:
       - "3306:3306"
@@ -194,9 +200,9 @@ services:
     #  "--mysql-native-password=ON",
     command: ["mysqld", "--character-set-server=utf8mb4", "--collation-server=utf8mb4_unicode_ci"]
     environment:
-      MYSQL_ROOT_PASSWORD: $DB_TEST_PASSWORD
-      MYSQL_PASSWORD: $DB_TEST_PASSWORD
-      MYSQL_USER: $DB_TEST_USERNAME
+      MYSQL_ROOT_PASSWORD: ${DB_TEST_PASSWORD}
+      MYSQL_PASSWORD: ${DB_TEST_PASSWORD}
+      MYSQL_USER: ${DB_TEST_USERNAME}
       MYSQL_ALLOW_EMPTY_PASSWORD: "no"
     image: mysql:8.4
     ports:
@@ -209,8 +215,8 @@ services:
     command: postgres -c 'max_connections=1000'
     container_name: postgres-emb
     environment:
-      - POSTGRES_USER=root
-      - POSTGRES_PASSWORD=yourpassword
+      - POSTGRES_USER=${DB_TEST_USERNAME}
+      - POSTGRES_PASSWORD=${DB_TEST_PASSWORD}
     image: postgres:14-alpine
     ports:
       - 5432:5432