Make things work with development release mode

embedded/project/docker-source/adverse-events/Dockerfile

@@ -4,8 +4,8 @@ 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
+ARG TZ=America/New_York
+ENV TZ=${TZ}
 
 COPY . .
 RUN if [ -f settings.xml ]; then \
@@ -14,24 +14,29 @@ RUN if [ -f settings.xml ]; then \
 fi && \
 apk add --no-cache git openjdk17 && \
 if [ "$RELEASE_MODE" = "development" ]; then \
+  echo "RELEASE_MODE: "$RELEASE_MODE && \
+  echo "STARTER_MODULE_BRANCH: "$STARTER_MODULE_BRANCH && \
+  echo "SUBSTANCES_MODULE_BRANCH: "$SUBSTANCES_MODULE_BRANCH && \
+  echo "ADVERSE_EVENTS_MODULE_BRANCH: "$ADVERSE_EVENTS_MODULE_BRANCH && \
   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 $ADVERSE_EVENTS_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-module-adverse-events.git && \
-  cd gsrs-spring-starter &&  ./mvnw clean -U install -DskipTests && \
+  cd gsrs-spring-starter && \
     if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-    ./mvnw clean -U install -DskipTests && \
-  cd .. && cd gsrs-spring-module-substances && \
+    sh ./mvnw clean -U install -DskipTests && \
+  cd ../gsrs-spring-module-substances && \
     if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-    ./mvnw clean -U install -DskipTests && \
-  cd .. && cd gsrs-spring-module-adverse-events && \
+    sh ./mvnw clean -U install -DskipTests && \
+  cd ../gsrs-spring-module-adverse-events && \
     if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-    ./mvnw clean -U install -DskipTests && \
+    sh ./mvnw clean -U install -DskipTests && \
   cd ..; \
 fi && \
 rm -rf src/main/resources/adverse-events-env.conf && \
 rm -rf src/main/resources/adverse-events-env-db.conf && \
+rm -rf src/main/resources/adverse-events.conf && \
 if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-./mvnw clean -U package -Dwith.packaging=jar -DskipTests && \
+sh ./mvnw clean -U package -Dwith.packaging=jar -DskipTests && \
 ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
 mkdir -p /app/data/adverse-events/conf && \
 mkdir -p /app/data/adverse-events/classes

embedded/project/docker-source/applications/Dockerfile

@@ -4,8 +4,8 @@ ARG RELEASE_MODE='public'
 ARG STARTER_MODULE_BRANCH=master
 ARG SUBSTANCES_MODULE_BRANCH=master
 ARG APPLICATIONS_MODULE_BRANCH=starter
-
-ENV TZ=America/New_York
+ARG TZ=America/New_York
+ENV TZ=${TZ}
 
 COPY . .
 RUN if [ -f settings.xml ]; then \
@@ -14,22 +14,27 @@ RUN if [ -f settings.xml ]; then \
 fi && \
 apk add --no-cache git openjdk17 && \
 if [ "$RELEASE_MODE" = "development" ]; then \
+  echo "RELEASE_MODE: "$RELEASE_MODE && \
+  echo "STARTER_MODULE_BRANCH: "$STARTER_MODULE_BRANCH && \
+  echo "SUBSTANCES_MODULE_BRANCH: "$SUBSTANCES_MODULE_BRANCH && \
+  echo "APPLICATIONS_MODULE_BRANCH: "$APPLICATIONS_MODULE_BRANCH && \
   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 $APPLICATIONS_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-module-drug-applications.git && \
-  cd gsrs-spring-starter &&  ./mvnw clean -U install -DskipTests && \
+  cd gsrs-spring-starter && \
     if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-    ./mvnw clean -U install -DskipTests && \
-  cd .. && cd gsrs-spring-module-substances && \
+    sh ./mvnw clean -U install -DskipTests && \
+  cd ../gsrs-spring-module-substances && \
     if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-    ./mvnw clean -U install -DskipTests && \
-  cd .. && cd gsrs-spring-module-drug-applications && \
+    sh ./mvnw clean -U install -DskipTests && \
+  cd ../gsrs-spring-module-drug-applications && \
     if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-    ./mvnw clean -U install -DskipTests && \
+    sh ./mvnw clean -U install -DskipTests && \
   cd ..; \
 fi && \
 rm -rf src/main/resources/applications-env.conf && \
 rm -rf src/main/resources/applications-env-db.conf && \
+rm -rf src/main/resources/applications.conf && \
 if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
 ./mvnw clean -U package -Dwith.packaging=jar -DskipTests && \
 ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \

embedded/project/docker-source/clinical-trials/Dockerfile

@@ -5,8 +5,8 @@ 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
+ARG TZ=America/New_York
+ENV TZ=${TZ}
 
 COPY . .
 RUN if [ -f settings.xml ]; then \
@@ -15,22 +15,27 @@ RUN if [ -f settings.xml ]; then \
 fi && \
 apk add --no-cache git openjdk17 && \
 if [ "$RELEASE_MODE" = "development" ]; then \
+  echo "RELEASE_MODE: "$RELEASE_MODE && \
+  echo "STARTER_MODULE_BRANCH: "$STARTER_MODULE_BRANCH && \
+  echo "SUBSTANCES_MODULE_BRANCH: "$SUBSTANCES_MODULE_BRANCH && \
+  echo "CLINICAL_TRIALS_MODULE_BRANCH: "$CLINICAL_TRIALS_MODULE_BRANCH && \
   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 $CLINICAL_TRIALS_MODULE_BRANCH --depth 2 https://github.com/ncats/gsrs-spring-module-clinical-trials.git && \
-  cd gsrs-spring-starter &&  ./mvnw clean -U install -DskipTests && \
+  cd gsrs-spring-starter && \
     if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-    ./mvnw clean -U install -DskipTests && \
-  cd .. && cd gsrs-spring-module-substances && \
+    sh ./mvnw clean -U install -DskipTests && \
+  cd ../gsrs-spring-module-substances && \
     if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-    ./mvnw clean -U install -DskipTests && \
-  cd .. && cd gsrs-spring-module-clinical-trials && \
+    sh ./mvnw clean -U install -DskipTests && \
+  cd ../gsrs-spring-module-clinical-trials && \
     if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
-    ./mvnw clean -U install -DskipTests && \
+    sh ./mvnw clean -U install -DskipTests && \
   cd ..; \
 fi && \
 rm -rf src/main/resources/clinical-trials-env.conf && \
 rm -rf src/main/resources/clinical-trials-env-db.conf && \
+rm -rf src/main/resources/clinical-trials.conf && \
 if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
 ./mvnw clean -U package -Dwith.packaging=jar -DskipTests && \
 ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \

embedded/project/docker-source/discovery/Dockerfile

@@ -1,18 +1,26 @@
 
 FROM alpine:latest AS build
 
-COPY . .
-
-RUN whoami && cat  /root/.m2/settings.xml
+ARG RELEASE_MODE='public'
+ARG TZ=America/New_York
+ENV TZ=${TZ}
 
-RUN ./mvnw clean -U package -Dwith.packaging=jar  -DskipTests
+COPY . .
 
-ENV TZ=America/New_York
-RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+RUN if [ -f settings.xml ]; then \
+  mkdir -p /root/.m2; \
+  cp settings.xml /root/.m2/settings.xml; \ 
+fi && \
+apk add --no-cache git openjdk17 && \
+rm -rf src/main/resources/discovery-env.conf && \
+rm -rf src/main/resources/discovery.conf && \
+if [ -f "installExtraJars.sh" ]; then sh installExtraJars.sh; fi && \
+sh ./mvnw clean -U package -Dwith.packaging=jar -DskipTests && \
+ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
+mkdir -p /app/data/discovery  && \
+mkdir -p /app/data/discovery/conf  && \
+mkdir -p /app/data/discovery/classes
 
-RUN mkdir -p /app/discovery
-RUN mkdir -p /app/data/discovery/conf
-RUN mkdir -p /app/data/discovery/classes
 WORKDIR /app/data/discovery
 EXPOSE 8761
 ENTRYPOINT ["java", "-cp", "/target/discovery.jar:classes:conf", "org.springframework.boot.loader.JarLauncher"]

embedded/project/docker-source/docker-notes.md

@@ -3,9 +3,16 @@
 ## Terminal Environment
 
 ```
+cd gsrs3-docker-deployments/embedded
 
 export embedded_root_dir=$(pwd)
-export gsrs_ci_dir=$embedded_root_dir/project/gsrs3-main-deployment
+
+
+
+export gsrs_ci_dir=$embedded_root_dir/project/gsrs-ci
+# or ...
+# export gsrs_ci_dir=$embedded_root_dir/project/gsrs3-main-deployment
+
 export DOCKER_SOURCE=$embedded_root_dir/project/docker-source
 export HOST_VOLUMES=$embedded_root_dir/project/volumes
 
@@ -16,6 +23,17 @@ export DB_TEST_PASSWORD=yourpassword
 export RELEASE_MODE=public
 
 export BUILD_VERSION=v2025.0429.1
+
+# As needed, only use if in development mode
+export STARTER_MODULE_BRANCH='master'
+export SUBSTANCES_MODULE_BRANCH='master'
+export ADVERSE_EVENTS_MODULE_BRANCH='starter'
+export APPLICATIONS_MODULE_BRANCH='starter'
+export CLINICAL_TRIALS_MODULE_BRANCH='master'
+export IMPURITIES_MODULE_BRANCH='starter'
+export INVITRO_PHARMACOLOGY_MODULE_BRANCH='master'
+export PRODUCTS_MODULE_BRANCH='starter'
+export SSG4M_MODULE_BRANCH='master'
 ```
 
 ## Purpose
@@ -55,11 +73,15 @@ First you'll need to build your images (see below)
 
 # The docker-compose.yml file should require one of these but does not yet do so.
 
-# If you need to use sudo, put the sudo before the db credentials.
-
 cd gsrs-ci
 
-export DATABASE=postgresql 
+export DATABASE=mariadb
+DB_TEST_USERNAME=root DB_TEST_PASSWORD=yourpassword \
+docker-compose -f $DOCKER_SOURCE/docker-compose.yml up \
+$DATABASE frontend gateway substances products
+
+# If you need to use sudo, put the sudo before the db credentials.
+export DATABASE=postgresql
 sudo \
 DB_TEST_USERNAME=root DB_TEST_PASSWORD=yourpassword \
 docker-compose -f $DOCKER_SOURCE/docker-compose.yml up \
@@ -112,9 +134,8 @@ See if environment variables are interpolated as expected.
 ```
 export DATABASE=postgresql 
 sudo \
-DB_TEST_USERNAME=root DB_TEST_PASSWORD=XXXXXX \
-docker-compose -f ../docker-source/docker-compose.yml up \
-config
+DB_TEST_USERNAME=root DB_TEST_PASSWORD=yourpassword \
+docker-compose -f $DOCKER_SOURCE/docker-compose.yml config
 ```
 
 ## Override the frontend config.json
@@ -130,14 +151,16 @@ $HOST_VOLUMES/app-data/frontend/classes/static/assets/data/config.json
 ```
 # Run these in the gsrs-ci/<service> corresponding folder
 
-# Make sure you have set a value RELEASE_MODE (development|public). This will determine whether a `Dockerfile` looks for code in Github or Maven. 
+# Make sure you have set a value RELEASE_MODE (development|public). This will determine whether a `Dockerfile` looks for code in Github or Maven Central.
+
+# A settings.xml file may be required, we are trying to make it no so.
 
 # ==== 
 
 cd gsrs-ci
 
 cd substances
-cp ../../settings.xml . 
+# cp ../../settings.xml . 
  docker build -f $DOCKER_SOURCE/substances/Dockerfile \
 --platform linux/x86_64 \
 --no-cache --progress=plain \
@@ -150,9 +173,21 @@ cp ../../settings.xml .
 # On substances 
 # --platform linux/x86_64  -- because got errors related to ehcache-failsafe.xml and Error loading shared library ld-linux-aarch64.so
 
+# Experimental, may not work, not currently used by FDA
+# not included in gsrs3-main-deployment
+cd ..
+cd discovery
+# cp ../../settings.xml .
+docker build -f $DOCKER_SOURCE/discovery/Dockerfile \
+--no-cache --progress=plain \
+--build-arg RELEASE_MODE=$RELEASE_MODE \
+--build-arg BUILD_VERSION=$BUILD_VERSION \
+-t gsrs3/gsrs-emb-docker-discovery:0.0.1-SNAPSHOT .
+
+
 cd ..
 cd gateway
-cp ../../settings.xml .
+# cp ../../settings.xml .
 docker build -f $DOCKER_SOURCE/gateway/Dockerfile \
 --no-cache --progress=plain \
 --build-arg RELEASE_MODE=$RELEASE_MODE \
@@ -161,7 +196,7 @@ docker build -f $DOCKER_SOURCE/gateway/Dockerfile \
 
 cd ..
 cd frontend
-cp ../../settings.xml .
+# cp ../../settings.xml .
 # export FRONTEND_TAG='development_3.0'
 export FRONTEND_TAG='GSRSv3.1.2PUB'
 docker build -f $DOCKER_SOURCE/frontend/Dockerfile \
@@ -186,7 +221,7 @@ docker build -f $DOCKER_SOURCE/adverse-events/Dockerfile \
 
 cd ..
 cd applications
-cp ../../settings.xml .
+# cp ../../settings.xml .
 docker build -f $DOCKER_SOURCE/applications/Dockerfile \
 --no-cache --progress=plain \
 --build-arg RELEASE_MODE=$RELEASE_MODE \
@@ -198,7 +233,7 @@ docker build -f $DOCKER_SOURCE/applications/Dockerfile \
 
 cd ..
 cd clinical-trials
-cp ../../settings.xml .
+# cp ../../settings.xml .
 docker build -f $DOCKER_SOURCE/clinical-trials/Dockerfile \
 --no-cache --progress=plain \
 --build-arg RELEASE_MODE=$RELEASE_MODE \
@@ -210,7 +245,7 @@ docker build -f $DOCKER_SOURCE/clinical-trials/Dockerfile \
 
 cd ..
 cd impurities
-cp ../../settings.xml .
+# cp ../../settings.xml .
 docker build -f $DOCKER_SOURCE/impurities/Dockerfile \
 --no-cache --progress=plain \
 --build-arg RELEASE_MODE=$RELEASE_MODE \
@@ -222,7 +257,7 @@ docker build -f $DOCKER_SOURCE/impurities/Dockerfile \
 
 cd ..
 cd invitro-pharmacology
-cp ../../settings.xml .
+# cp ../../settings.xml .
 docker build -f $DOCKER_SOURCE/invitro-pharmacology/Dockerfile \
  --no-cache --progress=plain \
 --build-arg RELEASE_MODE=$RELEASE_MODE \
@@ -234,7 +269,7 @@ docker build -f $DOCKER_SOURCE/invitro-pharmacology/Dockerfile \
 
 cd ..
 cd products
-cp ../../settings.xml .
+# cp ../../settings.xml .
 docker build -f $DOCKER_SOURCE/products/Dockerfile \
 --no-cache --progress=plain \
 --build-arg RELEASE_MODE=$RELEASE_MODE \
@@ -246,7 +281,7 @@ docker build -f $DOCKER_SOURCE/products/Dockerfile \
 
 cd ..
 cd ssg4m
-cp ../../settings.xml .
+# cp ../../settings.xml .
 docker build -f $DOCKER_SOURCE/ssg4m/Dockerfile \
 --no-cache --progress=plain \
 --build-arg RELEASE_MODE=$RELEASE_MODE \
@@ -270,20 +305,22 @@ tar -xvzf db.init.sql.tar.gz
 Before committing to Git, clean up folders from test instances
 
 ```
-rm -r ./volumes/app-data/adverse-events/ginas.ix
-rm -r ./volumes/app-data/applications/ginas.ix
-rm -r ./volumes/app-data/clinical-trials/ginas.ix
-rm -r ./volumes/app-data/impurities/ginas.ix
-rm -r ./volumes/app-data/invitro-pharmacology/ginas.ix
-rm -r ./volumes/app-data/substances/ginas.ix
+rm -r $HOST_VOLUMES/app-data/adverse-events/ginas.ix
+rm -r $HOST_VOLUMES/app-data/applications/ginas.ix
+rm -r $HOST_VOLUMES/app-data/clinical-trials/ginas.ix
+rm -r $HOST_VOLUMES/app-data/impurities/ginas.ix
+rm -r $HOST_VOLUMES/app-data/invitro-pharmacology/ginas.ix
+rm -r $HOST_VOLUMES/app-data/products/ginas.ix
+rm -r $HOST_VOLUMES/app-data/substances/ginas.ix
 ```
 
 ## Wipe databases
 
 ```
-rm -r ./volumes/app-data/db/mariadb/info && mkdir -p ./volumes/app-data/db/mariadb/info
-rm -r ./volumes/app-data/db/postgresql/info && mkdir -p ./volumes/app-data/db/postgresql/info
-rm -r ./volumes/app-data/db/mysql/info && mkdir -p ./volumes/app-data/db/mysql/info
+
+rm -r $HOST_VOLUMES/$app-data/db/mariadb/info && mkdir -p ./volumes/app-data/db/mariadb/info
+rm -r $HOST_VOLUMES/app-data/db/postgresql/info && mkdir -p ./volumes/app-data/db/postgresql/info
+rm -r  $HOST_VOLUMES/app-data/db/mysql/info && mkdir -p ./volumes/app-data/db/mysql/info
 ```
 
 ## Find more files to exclude from commits or clean up