Create JDBC connection from glassfish-resources.xml

This commit is a first test to apply database configuration and
credentials to the application server without using a config
on domain level but on application level.

Most certainly, this is only compatible with Payara 5.x as
Glassfish 5.x is unknown to support system properties in
config files and it certainly does not support password aliases.

The JNDI names have been changed to be conform with Java EE 7.
See https://github.com/javaee-samples/javaee7-samples/tree/master/jpa/datasourcedefinition-applicationxml-pu
and others for working examples. (Staying with the old name
was not successfull.)

conf/docker/app/Dockerfile

@@ -7,4 +7,6 @@ ARG LIB_PATH="${PAYARA_DIR}/glassfish/domains/${DOMAIN_NAME}/lib/"
 
 COPY --chown=payara maven/lib/* ${LIB_PATH}
 
-COPY maven/${project.build.finalName}.war ${DEPLOY_DIR}
+COPY maven/${project.build.finalName}.war ${DEPLOY_DIR}
+
+COPY --chown=payara init_2_configure.sh ${SCRIPT_DIR}

conf/docker/app/init_2_configure.sh

@@ -0,0 +1,17 @@
+#!/usr/bin/env sh
+
+# TEST FOR POSTBOOT: THIS WILL NEED TO BE ENHANCED WITH A) ENV VARS
+#                    AND B) SECRETS FILE...
+
+echo "AS_ADMIN_ALIASPASSWORD=test1234" > ${PAYARA_DIR}/dbpass
+
+cat > ${POSTBOOT_COMMANDS}.tmp << 'EOF'
+create-system-properties "postgres.host=postgres"
+create-system-properties "postgres.port=5432"
+create-system-properties "postgres.database=dataverse
+create-system-properties "postgres.user=dataverse"
+create-password-alias    "postgres-pass" --passwordfile ${PAYARA_DIR}/dbpass
+EOF
+
+echo "$(cat ${POSTBOOT_COMMANDS}.tmp | cat - ${POSTBOOT_COMMANDS} )" > ${POSTBOOT_COMMANDS}
+cat ${POSTBOOT_COMMANDS}

pom.xml

@@ -706,7 +706,11 @@
             <dependencies>
                 <!-- Adding this as a dependency will copy it to the domains /lib folder, where it needs to be. -->
                 <!-- FIXME: Gassfish should be capable to load the driver directly from the WAR, too. That would render
-                            the installer a tiny bit simpler and make distribution easier. Needs testing. -->
+                            the installer a tiny bit simpler and make distribution easier.
+                            Needs testing. See also:
+                            https://github.com/eclipse-ee4j/glassfish/issues/19451
+                            https://github.com/eclipse-ee4j/glassfish/issues/20944
+                            -->
                 <dependency>
                     <groupId>org.postgresql</groupId>
                     <artifactId>postgresql</artifactId>

src/main/resources/META-INF/persistence.xml

@@ -3,7 +3,7 @@
     <persistence-unit name="VDCNet-ejbPU" transaction-type="JTA">
         <!-- provider>oracle.toplink.essentials.ejb.cmp3.EntityManagerFactoryProvider</provider-->
         <provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>
-        <jta-data-source>jdbc/VDCNetDS</jta-data-source>
+        <jta-data-source>java:app/DV/VDCNetDS</jta-data-source>
         <properties>
             <!--property name="toplink.logging.level" value="FINE"/-->
 	    <!-- disabling weaving, as an experiment: - L.A. -->

src/main/webapp/WEB-INF/glassfish-resources.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE resources PUBLIC "-//GlassFish.org//DTD GlassFish Application Server 3.1 Resource Definitions//EN" "http://glassfish.org/dtds/glassfish-resources_1_5.dtd">
+<resources>
+  <!-- Java DataBase Connection Configuration -->
+  <jdbc-connection-pool
+      res-type="javax.sql.DataSource"
+      datasource-classname="org.postgresql.ds.PGPoolingDataSource"
+      name="dvnDbPool">
+    <property name="serverName" value="${postgres.host}"/>
+    <property name="portNumber" value="${postgres.port}"/>
+    <property name="databaseName" value="${postgres.database}"/>
+    <property name="User" value="${postgres.user}"/>
+    <property name="Password" value="${ALIAS=postgres-pass}"/>
+    <property name="create" value="true" />
+  </jdbc-connection-pool>
+  <jdbc-resource jndi-name="java:app/DV/VDCNetDS" pool-name="dvnDbPool"/>
+</resources>