Updates for a smoother run, partcularly, files will be created with permissions identical to the user running the docker container, which is better for granulation

bin/buildLabkey.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+. $(dirname $0)/env.sh
+docker network create -d bridge $NETWORK
+$DOCKERCOMPOSE -f $COMPOSE up -d --build;
+

config/Dockerfile

@@ -1,17 +0,0 @@
-FROM tomcat:9-jdk17-temurin-focal
-
-RUN apt-get update && apt-get install -y \
-		dirmngr \
-        	gnupg \
-		apt-transport-https \
-		ca-certificates \
-		software-properties-common \
-	&& apt-key adv --keyserver keyserver.ubuntu.com \
-		--recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
-	&& add-apt-repository \
-		'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' \
-	&& apt-get update \
-	&& apt-get install -y r-base \
-	&& rm -rf /var/lib/apt/lists/*
-
-LABEL "name"="tomcatR"

config/db/Dockerfile

@@ -0,0 +1,15 @@
+FROM postgres:14.2
+
+ARG USER_ID
+ARG GROUP_ID
+
+RUN apt-get update && apt-get install -y sudo;
+
+RUN addgroup --gid ${GROUP_ID} labkey
+RUN adduser --gecos 'LabKey' --uid ${USER_ID} --gid ${GROUP_ID} --disabled-password labkey 
+RUN echo 'labkey ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+RUN usermod -G root,sudo labkey
+
+USER labkey
+
+LABEL "name"="postgresqlX"

config/labkey-compose22.3.yaml

@@ -1,22 +1,35 @@
+version: "3.3"
+
 services:
 
-  db:
-    image: postgres:14.2
+  labkey-db:
+#    image: postgres:14.2
+#
+    build:
+            context: ./db
+            args:
+                    USER_ID: ${USER_ID}
+                    GROUP_ID: ${GROUP_ID}
     volumes: 
        - ${POSTGRES_DIR}:/var/lib/postgresql/data
     environment:
        - POSTGRES_USER=postgres
        - POSTGRES_PASSWORD=$PGPASS
+       - POSTGRES_DB=labkey
     ports:
-       - '5432'
-
+       - 5432
 
-  web:
+  labkey-web:
     depends_on:
-        - db
+        - labkey-db
     #image: tomcat:9-jdk17-temurin
-    build: .
+    #
 
+    build: 
+            context: ./web
+            args:
+                    USER_ID: ${USER_ID}
+                    GROUP_ID: ${GROUP_ID}
     volumes:
       - ${LABKEY_DIR}/labkeywebapp:/usr/local/labkey/labkeywebapp
       - ${LABKEY_DIR}/modules:/usr/local/labkey/modules
@@ -33,8 +46,8 @@ services:
       - ${LABKEY_DIR}/tomcat-lib/mail.jar:/usr/local/tomcat/lib/mail.jar
       - ${LABKEY_DIR}/labkey.xml:/usr/local/tomcat/conf/Catalina/localhost/labkey.xml  
     ports:
-      - '8080:8080'
-      - '8443:8443'
+      - 8081:8080
+      - 8444:8443
     
 
 networks:

config/web/Dockerfile

@@ -0,0 +1,29 @@
+FROM tomcat:9-jdk17-temurin-focal
+
+ARG USER_ID
+ARG GROUP_ID
+
+RUN apt-get update && apt-get install -y sudo;
+
+RUN addgroup --gid ${GROUP_ID} labkey
+RUN adduser --gecos 'LabKey' --uid ${USER_ID} --gid ${GROUP_ID} --disabled-password labkey 
+RUN echo 'labkey ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+RUN usermod -G root,sudo labkey
+
+USER labkey
+
+RUN sudo apt-get update && sudo apt-get install -y \
+		dirmngr \
+        	gnupg \
+		apt-transport-https \
+		ca-certificates \
+		software-properties-common \
+	&& sudo apt-key adv --keyserver keyserver.ubuntu.com \
+			--recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
+	&& sudo add-apt-repository \
+		'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' \
+	&& sudo apt-get update \
+	&& sudo apt-get install -y r-base \
+	&& sudo rm -rf /var/lib/apt/lists/*
+
+LABEL "name"="tomcatR"

labkey/labkey.xml → labkey/labkey.xml.template

@@ -4,9 +4,9 @@
     <Resource name="jdbc/labkeyDataSource" auth="Container"
         type="javax.sql.DataSource"
         username="postgres"
-        password="muzikolog"
+        password="verySecret"
         driverClassName="org.postgresql.Driver"
-	url="jdbc:postgresql://db:5432/labkey"
+	url="jdbc:postgresql://labkey-db:5432/labkey"
         maxTotal="20"
         maxIdle="10"
         maxWaitMillis="120000"