From e1b3f429d6a18e19ab3563d5b3be0cbb58de31a9 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Mon, 26 Nov 2018 13:07:33 +0100
Subject: [PATCH] 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                      |  4 +++-
 conf/docker/app/init_2_configure.sh             | 17 +++++++++++++++++
 pom.xml                                         |  6 +++++-
 src/main/resources/META-INF/persistence.xml     |  2 +-
 src/main/webapp/WEB-INF/glassfish-resources.xml | 17 +++++++++++++++++
 5 files changed, 43 insertions(+), 3 deletions(-)
 create mode 100644 conf/docker/app/init_2_configure.sh
 create mode 100644 src/main/webapp/WEB-INF/glassfish-resources.xml

diff --git a/conf/docker/app/Dockerfile b/conf/docker/app/Dockerfile
index 2dfa6f3dbe4..359a4bd8377 100644
--- a/conf/docker/app/Dockerfile
+++ b/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 ${DEPLOY_DIR}
\ No newline at end of file
+COPY maven/${project.build.finalName}.war ${DEPLOY_DIR}
+
+COPY --chown=payara init_2_configure.sh ${SCRIPT_DIR}
\ No newline at end of file
diff --git a/conf/docker/app/init_2_configure.sh b/conf/docker/app/init_2_configure.sh
new file mode 100644
index 00000000000..35d1d0a1cf4
--- /dev/null
+++ b/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}
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 3f20d00c0b0..8be16a6dc24 100644
--- a/pom.xml
+++ b/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>
diff --git a/src/main/resources/META-INF/persistence.xml b/src/main/resources/META-INF/persistence.xml
index 8b4e33858ac..85da2f1c4d6 100644
--- a/src/main/resources/META-INF/persistence.xml
+++ b/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. -->
diff --git a/src/main/webapp/WEB-INF/glassfish-resources.xml b/src/main/webapp/WEB-INF/glassfish-resources.xml
new file mode 100644
index 00000000000..d5286b3c609
--- /dev/null
+++ b/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>
\ No newline at end of file