From 9dfe7b82f16c006abe6b12e94d55e667fdec48ca Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 18 Nov 2020 12:46:28 +0100
Subject: [PATCH 01/22] Provide @DataSourceDefinition for app-level DB config.
 #7418

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.)
---
 .../flyway/StartupFlywayMigrator.java         |  2 +-
 .../iq/dataverse/util/DataSourceProducer.java | 30 +++++++++++++++++++
 src/main/resources/META-INF/persistence.xml   |  2 +-
 3 files changed, 32 insertions(+), 2 deletions(-)
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java

diff --git a/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java b/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java
index d5f4f8520a7..71b53bd43f2 100644
--- a/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java
@@ -15,7 +15,7 @@
 @TransactionManagement(value = TransactionManagementType.BEAN)
 public class StartupFlywayMigrator {
 
-    @Resource(lookup = "jdbc/VDCNetDS")
+    @Resource(lookup = "java:app/jdbc/dataverse")
     private DataSource dataSource;
 
     @PostConstruct
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
new file mode 100644
index 00000000000..f167b62dcd3
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -0,0 +1,30 @@
+package edu.harvard.iq.dataverse.util;
+
+import javax.annotation.Resource;
+import javax.annotation.sql.DataSourceDefinition;
+import javax.enterprise.inject.Produces;
+import javax.inject.Singleton;
+import javax.sql.DataSource;
+
+@Singleton
+@DataSourceDefinition(
+    name = "java:app/jdbc/dataverse",
+    // Using PGXADataSource instead of deprecated PGPoolingDataSource
+    className = "org.postgresql.xa.PGXADataSource",
+    user = "dataverse",
+    password = "${ALIAS=db_password_alias}",
+    serverName = "postgresql",
+    portNumber = 5432,
+    databaseName = "dataverse",
+    minPoolSize = 10,
+    maxPoolSize = 200)
+public class DataSourceProducer {
+    
+    @Resource(lookup="java:app/jdbc/dataverse")
+    DataSource ds;
+    
+    @Produces
+    public DataSource getDatasource() {
+        return ds;
+    }
+}
diff --git a/src/main/resources/META-INF/persistence.xml b/src/main/resources/META-INF/persistence.xml
index 8b4e33858ac..72e61b83374 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/jdbc/dataverse</jta-data-source>
         <properties>
             <!--property name="toplink.logging.level" value="FINE"/-->
 	    <!-- disabling weaving, as an experiment: - L.A. -->

From b92e465d3e1c1f63f631d4337c5ba19f4c864037 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 18 Nov 2020 12:49:38 +0100
Subject: [PATCH 02/22] Make the DataSourceDefinition configureable using
 MicroProfile Config variables in annotation options. #7418 #7000

---
 .../harvard/iq/dataverse/util/DataSourceProducer.java    | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index f167b62dcd3..24f0d8a43fe 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -11,11 +11,10 @@
     name = "java:app/jdbc/dataverse",
     // Using PGXADataSource instead of deprecated PGPoolingDataSource
     className = "org.postgresql.xa.PGXADataSource",
-    user = "dataverse",
-    password = "${ALIAS=db_password_alias}",
-    serverName = "postgresql",
-    portNumber = 5432,
-    databaseName = "dataverse",
+    user = "${MPCONFIG=dataverse.db.user}",
+    password = "${MPCONFIG=dataverse.db.password}",
+    serverName = "${MPCONFIG=dataverse.db.host}",
+    url = "jdbc:postgresql://${MPCONFIG=dataverse.db.host}:${MPCONFIG=dataverse.db.port}/${MPCONFIG=dataverse.db.name}",
     minPoolSize = 10,
     maxPoolSize = 200)
 public class DataSourceProducer {

From 3c92120a37f2f54a6b484aa12072b13d9c3a23a9 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 18 Nov 2020 12:53:07 +0100
Subject: [PATCH 03/22] Add defaults for the database connection using a
 MicroProfile Config file on classpath. #7418 #7000

---
 pom.xml                                                    | 1 +
 src/main/resources/META-INF/microprofile-config.properties | 4 ++++
 2 files changed, 5 insertions(+)
 create mode 100644 src/main/resources/META-INF/microprofile-config.properties

diff --git a/pom.xml b/pom.xml
index 37e78b30933..ca968ff365d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -679,6 +679,7 @@
                     <include>**/*.xml</include>
                     <include>**/firstNames/*.*</include>
                     <include>**/*.xsl</include>
+                    <include>**/*.properties</include>
                 </includes>
             </resource>
         </resources>
diff --git a/src/main/resources/META-INF/microprofile-config.properties b/src/main/resources/META-INF/microprofile-config.properties
new file mode 100644
index 00000000000..ec658cf5c65
--- /dev/null
+++ b/src/main/resources/META-INF/microprofile-config.properties
@@ -0,0 +1,4 @@
+dataverse.db.host=localhost
+dataverse.db.port=5432
+dataverse.db.user=dataverse
+dataverse.db.name=dataverse
\ No newline at end of file

From d05cbaf578cfddaeacc2a84b76f012ea20c06266 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 18 Nov 2020 13:01:32 +0100
Subject: [PATCH 04/22] Remove stale persistence unit from persistence.xml.
 #7418

---
 src/main/resources/META-INF/persistence.xml | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/src/main/resources/META-INF/persistence.xml b/src/main/resources/META-INF/persistence.xml
index 72e61b83374..45552f36939 100644
--- a/src/main/resources/META-INF/persistence.xml
+++ b/src/main/resources/META-INF/persistence.xml
@@ -20,15 +20,4 @@
             <!--<property name="eclipselink.logging.parameters" value="true"/>-->
         </properties>
     </persistence-unit>
-    <!-- the persistence unit below is no longer necessary; needs to be removed 
-	 from gnrs/TestNRS and from here: - L.A. 
-    <persistence-unit name="VDCNet-test" transaction-type="RESOURCE_LOCAL">
-        <provider>oracle.toplink.essentials.ejb.cmp3.EntityManagerFactoryProvider</provider>
-        <properties>
-            <property name="toplink.jdbc.url" value="jdbc:postgresql://localhost:5432/VDCNet-dev"/>
-            <property name="toplink.jdbc.user" value="vdcApp"/>
-            <property name="toplink.jdbc.driver" value="org.postgresql.jdbc3.Jdbc3PoolingDataSource"/>
-            <property name="toplink.jdbc.password" value="secret"/>
-        </properties>
-    </persistence-unit -->
 </persistence>

From 19c5e98324fd468faa26000ecec8b036fa449490 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 18 Nov 2020 13:16:43 +0100
Subject: [PATCH 05/22] Refactor as-setup.sh installer to use the MPCONFIG
 based database connection configuration. #7418

---
 scripts/installer/as-setup.sh | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/scripts/installer/as-setup.sh b/scripts/installer/as-setup.sh
index 84a5f84b677..f7f546b31df 100755
--- a/scripts/installer/as-setup.sh
+++ b/scripts/installer/as-setup.sh
@@ -73,7 +73,7 @@ function preliminary_setup()
   ./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:+DisableExplicitGC"
 
   # alias passwords
-  for alias in "rserve_password_alias ${RSERVE_PASS}" "doi_password_alias ${DOI_PASSWORD}" "db_password_alias ${DB_PASS}"
+  for alias in "rserve_password_alias ${RSERVE_PASS}" "doi_password_alias ${DOI_PASSWORD}" "dataverse.db.password ${DB_PASS}"
   do
       set -- $alias
       echo "AS_ADMIN_ALIASPASSWORD=$2" > /tmp/$1.txt
@@ -150,17 +150,11 @@ function final_setup(){
         ./asadmin $ASADMIN_OPTS delete-jvm-options -Xmx512m
         ./asadmin $ASADMIN_OPTS create-jvm-options "-Xmx${MEM_HEAP_SIZE}m"
 
-
-        ./asadmin $ASADMIN_OPTS create-jdbc-connection-pool --restype javax.sql.DataSource \
-                                        --datasourceclassname org.postgresql.ds.PGPoolingDataSource \
-                                        --property create=true:User=$DB_USER:PortNumber=$DB_PORT:databaseName=$DB_NAME:ServerName=$DB_HOST \
-                                        dvnDbPool
-
-       ./asadmin $ASADMIN_OPTS set resources.jdbc-connection-pool.dvnDbPool.property.password='${ALIAS=db_password_alias}'
-
-        ###
-        # Create data sources
-        ./asadmin $ASADMIN_OPTS create-jdbc-resource --connectionpoolid dvnDbPool jdbc/VDCNetDS
+         # Set up the database connection properties
+        ./asadmin $ASADMIN_OPTS create-system-properties "dataverse.db.user=${DB_USER}"
+        ./asadmin $ASADMIN_OPTS create-system-properties "dataverse.db.host=${DB_HOST}"
+        ./asadmin $ASADMIN_OPTS create-system-properties "dataverse.db.port=${DB_PORT}"
+        ./asadmin $ASADMIN_OPTS create-system-properties "dataverse.db.name=${DB_NAME}"
 
         ###
         # Set up the data source for the timers

From b6468313e6971792eae8a02520ed9acaec78557a Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 18 Nov 2020 13:22:49 +0100
Subject: [PATCH 06/22] Add docs about the new MPCONFIG based database
 properties to config doc. #7418

---
 .../source/installation/config.rst            | 46 ++++++++++++++++++-
 1 file changed, 45 insertions(+), 1 deletion(-)

diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst
index abf710e42e0..9ae5ec8fe7e 100644
--- a/doc/sphinx-guides/source/installation/config.rst
+++ b/doc/sphinx-guides/source/installation/config.rst
@@ -1032,6 +1032,50 @@ dataverse.auth.password-reset-timeout-in-minutes
 
 Users have 60 minutes to change their passwords by default. You can adjust this value here.
 
+dataverse.db.user
++++++++++++++++++
+
+The PostgreSQL user name to connect with.
+
+Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_USER``.
+Defaults to ``dataverse`` (via ``microprofile-config.properties``).
+
+dataverse.db.password
++++++++++++++++++++++
+
+The PostgreSQL users password to connect with.
+
+Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_PASSWORD``.
+Preferrably use a JVM alias, as passwords in environment variables aren't safe!
+
+.. code-block:: shell
+  echo "AS_ADMIN_ALIASPASSWORD=change-me-super-secret" > /tmp/password.txt
+  asadmin create-password-alias --passwordfile /tmp/password.txt dataverse.db.password
+  rm /tmp/password.txt
+dataverse.db.host
++++++++++++++++++
+
+The PostgreSQL server to connect to.
+
+Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_HOST``.
+Defaults to ``localhost`` (via ``microprofile-config.properties``).
+
+dataverse.db.port
++++++++++++++++++
+
+The PostgreSQL servers port to connect to.
+
+Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_PORT``.
+Defaults to ``5432`` (via ``microprofile-config.properties``), the default PostgreSQL port.
+
+dataverse.db.name
++++++++++++++++++
+
+The PostgreSQL database name to use for Dataverse.
+
+Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_NAME``.
+Defaults to ``dataverse`` (via ``microprofile-config.properties``).
+
 dataverse.rserve.host
 +++++++++++++++++++++
 
@@ -1168,7 +1212,7 @@ This JVM setting is also part of **handles** configuration. The Handle.Net insta
 .. _dataverse.handlenet.index:
 
 dataverse.handlenet.index
-+++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++
 If you want to use different index than the default 300
 
 .. _dataverse.timerServer:

From d0a1194d2155e5c06e70386ee2b3f5e6596959b0 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 18 Nov 2020 13:49:10 +0100
Subject: [PATCH 07/22] Add release notes docs, including references to #7417
 and #5345

---
 .../7418-datasourcedefinition.md              | 75 +++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 doc/release-notes/7418-datasourcedefinition.md

diff --git a/doc/release-notes/7418-datasourcedefinition.md b/doc/release-notes/7418-datasourcedefinition.md
new file mode 100644
index 00000000000..7afcddcaf8b
--- /dev/null
+++ b/doc/release-notes/7418-datasourcedefinition.md
@@ -0,0 +1,75 @@
+## Easier Configuration of Database Connections
+
+Dataverse now being able to use up-to-date Java technologies, transforms
+the way how to configure the connection to your PostgreSQL database.
+
+In the past, the configuration of the connection has been quite static
+and not very easy to update. This has been an issue especially for cloud
+and container usage.
+
+Using MicroProfile Config API (#7000, #7418), you can much more easily deposit configuration
+details. For an overview of supported options, please see the
+[installation guide](https://guides.dataverse.org/en/5.3/installation/config.html#jvm-options).
+
+
+<!-- ## Update to Payara Platform 5.2020.6 -->
+<!-- ... -->
+
+<!-- PLACEHOLDER REPLACEMENT TEXT FOR PAYARA UPGRADE NOTE #7417 -->
+🚨 THIS VERSION OF DATAVERSE **REQUIRES** UPGRADING TO PAYARA 5.2020.6. 🚨
+
+<!-- ... -->
+
+## Upgrading from earlier releases
+
+ℹ️ You need to update the Payara Application Server before continuing here. See above.
+
+1. Undeploy the previous version.
+```
+<payara install path>/asadmin list-applications
+<payara install path>/asadmin undeploy dataverse-<version>
+```
+
+(where `<payara install path>` is where Payara 5 is installed, for example: `/usr/local/payara5`)
+
+2. Update your database connection before updating.
+
+Please configure your connection details, replacing all the `${DB_...}`.
+(If you are using a PostgreSQL server on `localhost:5432`, you can omit `dataverse.db.host` and `dataverse.db.port`.)
+
+```
+<payara install path>/asadmin create-system-properties "dataverse.db.user=${DB_USER}"
+<payara install path>/asadmin create-system-properties "dataverse.db.host=${DB_HOST}"
+<payara install path>/asadmin create-system-properties "dataverse.db.port=${DB_PORT}"
+<payara install path>/asadmin create-system-properties "dataverse.db.name=${DB_NAME}"
+echo "AS_ADMIN_ALIASPASSWORD=${DB_PASS}" > /tmp/password.txt
+<payara install path>/asadmin create-password-alias --passwordfile /tmp/password.txt dataverse.db.password
+rm /tmp/password.txt
+```
+
+<!-- PLACE HOLDER FOR EJB TIMER DATABASE RESET NOTE #5345 -->
+
+Now you are safe to delete the old password alias and DB pool:
+```
+<payara install path>/asadmin delete-jdbc-connection-pool --cascade=true dvnDbPool
+<payara install path>/asadmin delete-password-alias db_password_alias
+```
+
+3. Stop payara and remove the generated directory, start.
+```
+service payara stop
+# remove the generated directory:
+rm -rf <payara install path>/payara/domains/domain1/generated
+service payara start
+```
+
+3. Deploy this version.
+```
+<payara install path>/bin/asadmin deploy dataverse-5.3.war
+```
+
+4. Restart Payara
+```
+service payara stop
+service payara start
+```
\ No newline at end of file

From aa1cc0feb4b18f10e5e014085ea662c925ee4b99 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Wed, 25 Nov 2020 11:07:04 -0500
Subject: [PATCH 08/22] fix 'Error in "code-block" directive' #7418

---
 doc/sphinx-guides/source/installation/config.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst
index 9ae5ec8fe7e..71f8b440a9d 100644
--- a/doc/sphinx-guides/source/installation/config.rst
+++ b/doc/sphinx-guides/source/installation/config.rst
@@ -1049,9 +1049,11 @@ Can also be set via *MicroProfile Config API* sources, e. g. environment variabl
 Preferrably use a JVM alias, as passwords in environment variables aren't safe!
 
 .. code-block:: shell
+
   echo "AS_ADMIN_ALIASPASSWORD=change-me-super-secret" > /tmp/password.txt
   asadmin create-password-alias --passwordfile /tmp/password.txt dataverse.db.password
   rm /tmp/password.txt
+
 dataverse.db.host
 +++++++++++++++++
 

From cb4d308beb0209cd758ef43c0633b50cc9d751f5 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Wed, 25 Nov 2020 15:55:18 -0500
Subject: [PATCH 09/22] tweaks, remove mention of
 microprofile-config.properties #7418

src/main/resources/META-INF/microprofile-config.properties is important
for developers to know about but sysadmins following the installation
guide need not concern themselves with it.

Other tweaks in this commit are cosmetic. I de-emphasized the
environment variables by putting them in the bottom.
---
 .../source/installation/config.rst            | 37 +++++++++++--------
 1 file changed, 21 insertions(+), 16 deletions(-)

diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst
index 71f8b440a9d..107ba54c057 100644
--- a/doc/sphinx-guides/source/installation/config.rst
+++ b/doc/sphinx-guides/source/installation/config.rst
@@ -1032,21 +1032,30 @@ dataverse.auth.password-reset-timeout-in-minutes
 
 Users have 60 minutes to change their passwords by default. You can adjust this value here.
 
+dataverse.db.name
++++++++++++++++++
+
+The PostgreSQL database name to use for Dataverse.
+
+Defaults to ``dataverse`` (but the installer sets it to ``dvndb``).
+
+Can also be set via *MicroProfile Config API* sources, e.g. the environment variable ``DATAVERSE_DB_NAME``.
+
 dataverse.db.user
 +++++++++++++++++
 
 The PostgreSQL user name to connect with.
 
-Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_USER``.
-Defaults to ``dataverse`` (via ``microprofile-config.properties``).
+Defaults to ``dataverse`` (but the installer sets it to ``dvnapp``).
+
+Can also be set via *MicroProfile Config API* sources, e.g. the environment variable ``DATAVERSE_DB_USER``.
 
 dataverse.db.password
 +++++++++++++++++++++
 
 The PostgreSQL users password to connect with.
 
-Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_PASSWORD``.
-Preferrably use a JVM alias, as passwords in environment variables aren't safe!
+Preferrably use a JVM alias, as passwords in environment variables aren't safe.
 
 .. code-block:: shell
 
@@ -1054,29 +1063,25 @@ Preferrably use a JVM alias, as passwords in environment variables aren't safe!
   asadmin create-password-alias --passwordfile /tmp/password.txt dataverse.db.password
   rm /tmp/password.txt
 
+Can also be set via *MicroProfile Config API* sources, e.g. the environment variable ``DATAVERSE_DB_PASSWORD``.
+
 dataverse.db.host
 +++++++++++++++++
 
 The PostgreSQL server to connect to.
 
-Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_HOST``.
-Defaults to ``localhost`` (via ``microprofile-config.properties``).
+Defaults to ``localhost``.
+
+Can also be set via *MicroProfile Config API* sources, e.g. the environment variable ``DATAVERSE_DB_HOST``.
 
 dataverse.db.port
 +++++++++++++++++
 
-The PostgreSQL servers port to connect to.
+The PostgreSQL server port to connect to.
 
-Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_PORT``.
-Defaults to ``5432`` (via ``microprofile-config.properties``), the default PostgreSQL port.
-
-dataverse.db.name
-+++++++++++++++++
-
-The PostgreSQL database name to use for Dataverse.
+Defaults to ``5432``, the default PostgreSQL port.
 
-Can also be set via *MicroProfile Config API* sources, e. g. environment variable ``DATAVERSE_DB_NAME``.
-Defaults to ``dataverse`` (via ``microprofile-config.properties``).
+Can also be set via *MicroProfile Config API* sources, e.g. the environment variable ``DATAVERSE_DB_PORT``.
 
 dataverse.rserve.host
 +++++++++++++++++++++

From 9155c0704c2d3dbc75c1976f69d29dd96dd77d75 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <poikilotherm@users.noreply.github.com>
Date: Wed, 25 Nov 2020 22:03:00 +0100
Subject: [PATCH 10/22] Update doc/release-notes/7418-datasourcedefinition.md

Co-authored-by: Philip Durbin <philip_durbin@harvard.edu>
---
 doc/release-notes/7418-datasourcedefinition.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/release-notes/7418-datasourcedefinition.md b/doc/release-notes/7418-datasourcedefinition.md
index 7afcddcaf8b..7b333c4e39b 100644
--- a/doc/release-notes/7418-datasourcedefinition.md
+++ b/doc/release-notes/7418-datasourcedefinition.md
@@ -7,7 +7,7 @@ In the past, the configuration of the connection has been quite static
 and not very easy to update. This has been an issue especially for cloud
 and container usage.
 
-Using MicroProfile Config API (#7000, #7418), you can much more easily deposit configuration
+Using MicroProfile Config API (#7000, #7418), you can much more easily specify configuration
 details. For an overview of supported options, please see the
 [installation guide](https://guides.dataverse.org/en/5.3/installation/config.html#jvm-options).
 
@@ -72,4 +72,4 @@ service payara start
 ```
 service payara stop
 service payara start
-```
\ No newline at end of file
+```

From 06dbef10ac65a8b07d25c3b7506b0362d04030c9 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Tue, 1 Dec 2020 12:25:30 -0500
Subject: [PATCH 11/22] PGXADataSource breaks ingest, use PGPoolingDataSource
 #7418

---
 .../edu/harvard/iq/dataverse/util/DataSourceProducer.java     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index 24f0d8a43fe..bfb64b68188 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -9,8 +9,8 @@
 @Singleton
 @DataSourceDefinition(
     name = "java:app/jdbc/dataverse",
-    // Using PGXADataSource instead of deprecated PGPoolingDataSource
-    className = "org.postgresql.xa.PGXADataSource",
+    // Note that PGPoolingDataSource is deprecated. PGXADataSource breaks ingest.
+    className = "org.postgresql.ds.PGPoolingDataSource",
     user = "${MPCONFIG=dataverse.db.user}",
     password = "${MPCONFIG=dataverse.db.password}",
     serverName = "${MPCONFIG=dataverse.db.host}",

From b1865087ad27a500be18a7a1f89c7d43b5fd3722 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <poikilotherm@users.noreply.github.com>
Date: Tue, 1 Dec 2020 20:37:02 +0100
Subject: [PATCH 12/22] Update
 src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java

---
 .../edu/harvard/iq/dataverse/util/DataSourceProducer.java    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index bfb64b68188..e66de31eecd 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -9,8 +9,9 @@
 @Singleton
 @DataSourceDefinition(
     name = "java:app/jdbc/dataverse",
-    // Note that PGPoolingDataSource is deprecated. PGXADataSource breaks ingest.
-    className = "org.postgresql.ds.PGPoolingDataSource",
+    // App server provides its own pooling, so go with simple data source class.
+    // PGXADataSource is unnecessary (no distributed transactions) and breaks ingest.
+    className = "org.postgresql.ds.PGSimpleDataSource",
     user = "${MPCONFIG=dataverse.db.user}",
     password = "${MPCONFIG=dataverse.db.password}",
     serverName = "${MPCONFIG=dataverse.db.host}",

From 2d0dc6e4d0baedc14671830f4e5fe1d0201f7e4b Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 2 Dec 2020 11:11:16 +0100
Subject: [PATCH 13/22] Remove doubled property usage on DataSourceDefinition
 following Java EE spec on it. #7418

---
 .../java/edu/harvard/iq/dataverse/util/DataSourceProducer.java   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index e66de31eecd..23924092d14 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -14,7 +14,6 @@
     className = "org.postgresql.ds.PGSimpleDataSource",
     user = "${MPCONFIG=dataverse.db.user}",
     password = "${MPCONFIG=dataverse.db.password}",
-    serverName = "${MPCONFIG=dataverse.db.host}",
     url = "jdbc:postgresql://${MPCONFIG=dataverse.db.host}:${MPCONFIG=dataverse.db.port}/${MPCONFIG=dataverse.db.name}",
     minPoolSize = 10,
     maxPoolSize = 200)

From 1c0959b29da894d058814624b7ea9e53baebf400 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 2 Dec 2020 11:25:03 +0100
Subject: [PATCH 14/22] Switch to a javax.sql.ConnectionPoolDataSource class
 for DataSourceDefinition plus add some more inline docs. #7418

---
 .../harvard/iq/dataverse/util/DataSourceProducer.java  | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index 23924092d14..6a975592bd9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -9,9 +9,13 @@
 @Singleton
 @DataSourceDefinition(
     name = "java:app/jdbc/dataverse",
-    // App server provides its own pooling, so go with simple data source class.
-    // PGXADataSource is unnecessary (no distributed transactions) and breaks ingest.
-    className = "org.postgresql.ds.PGSimpleDataSource",
+    //
+    // The app server (Payara) deploys a managed pool for this data source for us.
+    // We don't need to deal with this on our own.
+    //
+    // HINT: PGSimpleDataSource would work too, but as we use a connection pool, go with a javax.sql.ConnectionPoolDataSource
+    // HINT: PGXADataSource is unnecessary (no distributed transactions used) and breaks ingest.
+    className = "org.postgresql.ds.PGConnectionPoolDataSource",
     user = "${MPCONFIG=dataverse.db.user}",
     password = "${MPCONFIG=dataverse.db.password}",
     url = "jdbc:postgresql://${MPCONFIG=dataverse.db.host}:${MPCONFIG=dataverse.db.port}/${MPCONFIG=dataverse.db.name}",

From ea0cf29e0e63945ed22de0d4faf26dc574bd9bec Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 2 Dec 2020 12:51:24 +0100
Subject: [PATCH 15/22] Add more comments about pool sizing and reduce JDBC
 pool to max 100 connections. #7418

---
 .../harvard/iq/dataverse/util/DataSourceProducer.java  | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index 6a975592bd9..32063c0ba92 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -19,8 +19,16 @@
     user = "${MPCONFIG=dataverse.db.user}",
     password = "${MPCONFIG=dataverse.db.password}",
     url = "jdbc:postgresql://${MPCONFIG=dataverse.db.host}:${MPCONFIG=dataverse.db.port}/${MPCONFIG=dataverse.db.name}",
+    //
+    // If we ever need to change these pool settings, we need to remove this class and create the resource
+    // from web.xml. We can use MicroProfile Config in there for these values, impossible to do in the annotation.
+    //
+    // See also https://blog.payara.fish/an-intro-to-connection-pools-in-payara-server-5
+    // Payara DataSourceDefinitionDeployer default value = 8
     minPoolSize = 10,
-    maxPoolSize = 200)
+    // HINT: Payara DataSourceDefinitionDeployer default value = 32
+    // HINT: Harvard Dataverse is fine for a while with 64
+    maxPoolSize = 100)
 public class DataSourceProducer {
     
     @Resource(lookup="java:app/jdbc/dataverse")

From a41e177977e70706179eec2f723fff34b2ba3134 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 2 Dec 2020 12:59:00 +0100
Subject: [PATCH 16/22] Enable special JDBC connection pooling properties for
 debugging and monitoring via MPCONFIG. #7418

---
 .../iq/dataverse/util/DataSourceProducer.java     | 15 ++++++++++++++-
 .../META-INF/microprofile-config.properties       | 13 ++++++++++++-
 2 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index 32063c0ba92..e1d9fcdd572 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -28,7 +28,20 @@
     minPoolSize = 10,
     // HINT: Payara DataSourceDefinitionDeployer default value = 32
     // HINT: Harvard Dataverse is fine for a while with 64
-    maxPoolSize = 100)
+    maxPoolSize = 100,
+    properties = {
+        "fish.payara.is-connection-validation-required=${MPCONFIG=dataverse.db.is-connection-validation-required}",
+        "fish.payara.connection-validation-method=${MPCONFIG=dataverse.db.connection-validation-method}",
+        "fish.payara.validation-table-name=${MPCONFIG=dataverse.db.validation-table-name}",
+        "fish.payara.validation-classname=${MPCONFIG=dataverse.db.validation-classname}",
+        "fish.payara.connection-leak-timeout-in-seconds=${MPCONFIG=dataverse.db.connection-leak-timeout-in-seconds}",
+        "fish.payara.connection-leak-reclaim=${MPCONFIG=dataverse.db.connection-leak-reclaim}",
+        "fish.payara.statement-timeout-in-seconds=${MPCONFIG=dataverse.db.statement-timeout-in-seconds}",
+        "fish.payara.statement-leak-timeout-in-seconds=${MPCONFIG=dataverse.db.statement-leak-timeout-in-seconds}",
+        "fish.payara.statement-leak-reclaim=${MPCONFIG=dataverse.db.statement-leak-reclaim}",
+        "fish.payara.slow-query-threshold-in-seconds=${MPCONFIG=dataverse.db.slow-query-threshold-in-seconds}",
+        "fish.payara.log-jdbc-calls=${MPCONFIG=dataverse.db.log-jdbc-calls}"
+    })
 public class DataSourceProducer {
     
     @Resource(lookup="java:app/jdbc/dataverse")
diff --git a/src/main/resources/META-INF/microprofile-config.properties b/src/main/resources/META-INF/microprofile-config.properties
index ec658cf5c65..d7503817a4c 100644
--- a/src/main/resources/META-INF/microprofile-config.properties
+++ b/src/main/resources/META-INF/microprofile-config.properties
@@ -1,4 +1,15 @@
 dataverse.db.host=localhost
 dataverse.db.port=5432
 dataverse.db.user=dataverse
-dataverse.db.name=dataverse
\ No newline at end of file
+dataverse.db.name=dataverse
+dataverse.db.is-connection-validation-required=false
+dataverse.db.connection-validation-method=table
+dataverse.db.validation-table-name=setting
+dataverse.db.validation-classname=org.glassfish.api.jdbc.validation.PostgresConnectionValidation
+dataverse.db.connection-leak-timeout-in-seconds=0
+dataverse.db.connection-leak-reclaim=false
+dataverse.db.statement-timeout-in-seconds=-1
+dataverse.db.statement-leak-timeout-in-seconds=0
+dataverse.db.statement-leak-reclaim=false
+dataverse.db.slow-query-threshold-in-seconds=-1
+dataverse.db.log-jdbc-calls=false
\ No newline at end of file

From 1a921f6b1b0f1a80a34d5651ad3e883a3c30a69e Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 2 Dec 2020 14:23:49 +0100
Subject: [PATCH 17/22] Make pool resize configurable. #7418

---
 .../iq/dataverse/util/DataSourceProducer.java     | 15 +++++++++++++--
 .../META-INF/microprofile-config.properties       |  3 ++-
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index e1d9fcdd572..bee25f857e6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -8,28 +8,39 @@
 
 @Singleton
 @DataSourceDefinition(
+    // Find docs here: https://javaee.github.io/javaee-spec/javadocs/javax/annotation/sql/DataSourceDefinition.html
+    
     name = "java:app/jdbc/dataverse",
-    //
+    
     // The app server (Payara) deploys a managed pool for this data source for us.
     // We don't need to deal with this on our own.
     //
     // HINT: PGSimpleDataSource would work too, but as we use a connection pool, go with a javax.sql.ConnectionPoolDataSource
     // HINT: PGXADataSource is unnecessary (no distributed transactions used) and breaks ingest.
     className = "org.postgresql.ds.PGConnectionPoolDataSource",
+    
     user = "${MPCONFIG=dataverse.db.user}",
     password = "${MPCONFIG=dataverse.db.password}",
     url = "jdbc:postgresql://${MPCONFIG=dataverse.db.host}:${MPCONFIG=dataverse.db.port}/${MPCONFIG=dataverse.db.name}",
-    //
+    
     // If we ever need to change these pool settings, we need to remove this class and create the resource
     // from web.xml. We can use MicroProfile Config in there for these values, impossible to do in the annotation.
     //
     // See also https://blog.payara.fish/an-intro-to-connection-pools-in-payara-server-5
     // Payara DataSourceDefinitionDeployer default value = 8
     minPoolSize = 10,
+    
     // HINT: Payara DataSourceDefinitionDeployer default value = 32
     // HINT: Harvard Dataverse is fine for a while with 64
     maxPoolSize = 100,
+    
+    // "The number of seconds that a physical connection should remain unused in the pool before the connection is closed for a connection pool. "
+    // Payara DataSourceDefinitionDeployer default value = 300 (seconds)
+    maxIdleTime = 300,
+    
+    // These are documented at https://docs.payara.fish/community/docs/5.2020.6/documentation/payara-server/jdbc/advanced-connection-pool-properties.html#full-list-of-properties
     properties = {
+        "fish.payara.pool-resize-quantity=${MPCONFIG=dataverse.db.pool-resize-quantity}",
         "fish.payara.is-connection-validation-required=${MPCONFIG=dataverse.db.is-connection-validation-required}",
         "fish.payara.connection-validation-method=${MPCONFIG=dataverse.db.connection-validation-method}",
         "fish.payara.validation-table-name=${MPCONFIG=dataverse.db.validation-table-name}",
diff --git a/src/main/resources/META-INF/microprofile-config.properties b/src/main/resources/META-INF/microprofile-config.properties
index d7503817a4c..c562ad7c416 100644
--- a/src/main/resources/META-INF/microprofile-config.properties
+++ b/src/main/resources/META-INF/microprofile-config.properties
@@ -2,6 +2,7 @@ dataverse.db.host=localhost
 dataverse.db.port=5432
 dataverse.db.user=dataverse
 dataverse.db.name=dataverse
+dataverse.db.pool-resize-quantity=2
 dataverse.db.is-connection-validation-required=false
 dataverse.db.connection-validation-method=table
 dataverse.db.validation-table-name=setting
@@ -12,4 +13,4 @@ dataverse.db.statement-timeout-in-seconds=-1
 dataverse.db.statement-leak-timeout-in-seconds=0
 dataverse.db.statement-leak-reclaim=false
 dataverse.db.slow-query-threshold-in-seconds=-1
-dataverse.db.log-jdbc-calls=false
\ No newline at end of file
+dataverse.db.log-jdbc-calls=false

From 83ea82f2d292d88aad3d73aa075eb14692a854ac Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 2 Dec 2020 14:49:03 +0100
Subject: [PATCH 18/22] Reverting the addition of JDBC pooling settings,
 configurable via MPCONFIG. #7418

Due to payara/Payara#5024 this is currently not possible. Needs to be addressed
in a later enhancement when Payara provides a solution.
---
 .../iq/dataverse/util/DataSourceProducer.java |  7 +++++-
 .../META-INF/microprofile-config.properties   | 24 +++++++++----------
 2 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index bee25f857e6..9e85fbe5bd8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -36,9 +36,13 @@
     
     // "The number of seconds that a physical connection should remain unused in the pool before the connection is closed for a connection pool. "
     // Payara DataSourceDefinitionDeployer default value = 300 (seconds)
-    maxIdleTime = 300,
+    maxIdleTime = 300)
     
     // These are documented at https://docs.payara.fish/community/docs/5.2020.6/documentation/payara-server/jdbc/advanced-connection-pool-properties.html#full-list-of-properties
+    //
+    // All these vars cannot be configured via MPCONFIG as Payara doesn't support this (yet). To be enhanced.
+    // See also https://github.com/payara/Payara/issues/5024
+    /*
     properties = {
         "fish.payara.pool-resize-quantity=${MPCONFIG=dataverse.db.pool-resize-quantity}",
         "fish.payara.is-connection-validation-required=${MPCONFIG=dataverse.db.is-connection-validation-required}",
@@ -53,6 +57,7 @@
         "fish.payara.slow-query-threshold-in-seconds=${MPCONFIG=dataverse.db.slow-query-threshold-in-seconds}",
         "fish.payara.log-jdbc-calls=${MPCONFIG=dataverse.db.log-jdbc-calls}"
     })
+    */
 public class DataSourceProducer {
     
     @Resource(lookup="java:app/jdbc/dataverse")
diff --git a/src/main/resources/META-INF/microprofile-config.properties b/src/main/resources/META-INF/microprofile-config.properties
index c562ad7c416..ebccaa5ba87 100644
--- a/src/main/resources/META-INF/microprofile-config.properties
+++ b/src/main/resources/META-INF/microprofile-config.properties
@@ -2,15 +2,15 @@ dataverse.db.host=localhost
 dataverse.db.port=5432
 dataverse.db.user=dataverse
 dataverse.db.name=dataverse
-dataverse.db.pool-resize-quantity=2
-dataverse.db.is-connection-validation-required=false
-dataverse.db.connection-validation-method=table
-dataverse.db.validation-table-name=setting
-dataverse.db.validation-classname=org.glassfish.api.jdbc.validation.PostgresConnectionValidation
-dataverse.db.connection-leak-timeout-in-seconds=0
-dataverse.db.connection-leak-reclaim=false
-dataverse.db.statement-timeout-in-seconds=-1
-dataverse.db.statement-leak-timeout-in-seconds=0
-dataverse.db.statement-leak-reclaim=false
-dataverse.db.slow-query-threshold-in-seconds=-1
-dataverse.db.log-jdbc-calls=false
+#dataverse.db.pool-resize-quantity=2
+#dataverse.db.is-connection-validation-required=false
+#dataverse.db.connection-validation-method=table
+#dataverse.db.validation-table-name=setting
+#dataverse.db.validation-classname=org.glassfish.api.jdbc.validation.PostgresConnectionValidation
+#dataverse.db.connection-leak-timeout-in-seconds=0
+#dataverse.db.connection-leak-reclaim=false
+#dataverse.db.statement-timeout-in-seconds=-1
+#dataverse.db.statement-leak-timeout-in-seconds=0
+#dataverse.db.statement-leak-reclaim=false
+#dataverse.db.slow-query-threshold-in-seconds=-1
+#dataverse.db.log-jdbc-calls=false

From c583909d21daa63b03f82f6aba02965451ef7467 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Thu, 3 Dec 2020 14:45:01 -0500
Subject: [PATCH 19/22] tweak javadoc, default MP config properties #7418

- Show a simple properties example that's easily verifiable by inspecting
server.log (JDBC call debugging).
- Remove MPCONFIG examples that don't work yet (depends on work in
Payara).
---
 .../iq/dataverse/util/DataSourceProducer.java | 28 ++++++-------------
 .../META-INF/microprofile-config.properties   | 12 --------
 2 files changed, 9 insertions(+), 31 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index 9e85fbe5bd8..82936d1919d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -37,27 +37,17 @@
     // "The number of seconds that a physical connection should remain unused in the pool before the connection is closed for a connection pool. "
     // Payara DataSourceDefinitionDeployer default value = 300 (seconds)
     maxIdleTime = 300)
-    
-    // These are documented at https://docs.payara.fish/community/docs/5.2020.6/documentation/payara-server/jdbc/advanced-connection-pool-properties.html#full-list-of-properties
+    // It's possible to add additional properties like this...
+    //
+    //properties = {
+    //    "fish.payara.log-jdbc-calls=true"
+    //})
+    //
+    // ... but at this time we don't think we need any. The full list
+    // of properties can be found at https://docs.payara.fish/community/docs/5.2020.6/documentation/payara-server/jdbc/advanced-connection-pool-properties.html#full-list-of-properties
     //
-    // All these vars cannot be configured via MPCONFIG as Payara doesn't support this (yet). To be enhanced.
+    // All these properties cannot be configured via MPCONFIG as Payara doesn't support this (yet). To be enhanced.
     // See also https://github.com/payara/Payara/issues/5024
-    /*
-    properties = {
-        "fish.payara.pool-resize-quantity=${MPCONFIG=dataverse.db.pool-resize-quantity}",
-        "fish.payara.is-connection-validation-required=${MPCONFIG=dataverse.db.is-connection-validation-required}",
-        "fish.payara.connection-validation-method=${MPCONFIG=dataverse.db.connection-validation-method}",
-        "fish.payara.validation-table-name=${MPCONFIG=dataverse.db.validation-table-name}",
-        "fish.payara.validation-classname=${MPCONFIG=dataverse.db.validation-classname}",
-        "fish.payara.connection-leak-timeout-in-seconds=${MPCONFIG=dataverse.db.connection-leak-timeout-in-seconds}",
-        "fish.payara.connection-leak-reclaim=${MPCONFIG=dataverse.db.connection-leak-reclaim}",
-        "fish.payara.statement-timeout-in-seconds=${MPCONFIG=dataverse.db.statement-timeout-in-seconds}",
-        "fish.payara.statement-leak-timeout-in-seconds=${MPCONFIG=dataverse.db.statement-leak-timeout-in-seconds}",
-        "fish.payara.statement-leak-reclaim=${MPCONFIG=dataverse.db.statement-leak-reclaim}",
-        "fish.payara.slow-query-threshold-in-seconds=${MPCONFIG=dataverse.db.slow-query-threshold-in-seconds}",
-        "fish.payara.log-jdbc-calls=${MPCONFIG=dataverse.db.log-jdbc-calls}"
-    })
-    */
 public class DataSourceProducer {
     
     @Resource(lookup="java:app/jdbc/dataverse")
diff --git a/src/main/resources/META-INF/microprofile-config.properties b/src/main/resources/META-INF/microprofile-config.properties
index ebccaa5ba87..8c475f1c050 100644
--- a/src/main/resources/META-INF/microprofile-config.properties
+++ b/src/main/resources/META-INF/microprofile-config.properties
@@ -2,15 +2,3 @@ dataverse.db.host=localhost
 dataverse.db.port=5432
 dataverse.db.user=dataverse
 dataverse.db.name=dataverse
-#dataverse.db.pool-resize-quantity=2
-#dataverse.db.is-connection-validation-required=false
-#dataverse.db.connection-validation-method=table
-#dataverse.db.validation-table-name=setting
-#dataverse.db.validation-classname=org.glassfish.api.jdbc.validation.PostgresConnectionValidation
-#dataverse.db.connection-leak-timeout-in-seconds=0
-#dataverse.db.connection-leak-reclaim=false
-#dataverse.db.statement-timeout-in-seconds=-1
-#dataverse.db.statement-leak-timeout-in-seconds=0
-#dataverse.db.statement-leak-reclaim=false
-#dataverse.db.slow-query-threshold-in-seconds=-1
-#dataverse.db.log-jdbc-calls=false

From f98c1642f50a1b815251da78b42ea848df4b535b Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Thu, 3 Dec 2020 14:55:47 -0500
Subject: [PATCH 20/22] format with Netbeans #7418

---
 .../iq/dataverse/util/DataSourceProducer.java | 80 +++++++++----------
 1 file changed, 37 insertions(+), 43 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index 82936d1919d..02ba331cdd5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -6,53 +6,47 @@
 import javax.inject.Singleton;
 import javax.sql.DataSource;
 
+// Find docs here: https://javaee.github.io/javaee-spec/javadocs/javax/annotation/sql/DataSourceDefinition.html
 @Singleton
 @DataSourceDefinition(
-    // Find docs here: https://javaee.github.io/javaee-spec/javadocs/javax/annotation/sql/DataSourceDefinition.html
-    
-    name = "java:app/jdbc/dataverse",
-    
-    // The app server (Payara) deploys a managed pool for this data source for us.
-    // We don't need to deal with this on our own.
-    //
-    // HINT: PGSimpleDataSource would work too, but as we use a connection pool, go with a javax.sql.ConnectionPoolDataSource
-    // HINT: PGXADataSource is unnecessary (no distributed transactions used) and breaks ingest.
-    className = "org.postgresql.ds.PGConnectionPoolDataSource",
-    
-    user = "${MPCONFIG=dataverse.db.user}",
-    password = "${MPCONFIG=dataverse.db.password}",
-    url = "jdbc:postgresql://${MPCONFIG=dataverse.db.host}:${MPCONFIG=dataverse.db.port}/${MPCONFIG=dataverse.db.name}",
-    
-    // If we ever need to change these pool settings, we need to remove this class and create the resource
-    // from web.xml. We can use MicroProfile Config in there for these values, impossible to do in the annotation.
-    //
-    // See also https://blog.payara.fish/an-intro-to-connection-pools-in-payara-server-5
-    // Payara DataSourceDefinitionDeployer default value = 8
-    minPoolSize = 10,
-    
-    // HINT: Payara DataSourceDefinitionDeployer default value = 32
-    // HINT: Harvard Dataverse is fine for a while with 64
-    maxPoolSize = 100,
-    
-    // "The number of seconds that a physical connection should remain unused in the pool before the connection is closed for a connection pool. "
-    // Payara DataSourceDefinitionDeployer default value = 300 (seconds)
-    maxIdleTime = 300)
-    // It's possible to add additional properties like this...
-    //
-    //properties = {
-    //    "fish.payara.log-jdbc-calls=true"
-    //})
-    //
-    // ... but at this time we don't think we need any. The full list
-    // of properties can be found at https://docs.payara.fish/community/docs/5.2020.6/documentation/payara-server/jdbc/advanced-connection-pool-properties.html#full-list-of-properties
-    //
-    // All these properties cannot be configured via MPCONFIG as Payara doesn't support this (yet). To be enhanced.
-    // See also https://github.com/payara/Payara/issues/5024
+        name = "java:app/jdbc/dataverse",
+        // The app server (Payara) deploys a managed pool for this data source for us.
+        // We don't need to deal with this on our own.
+        //
+        // HINT: PGSimpleDataSource would work too, but as we use a connection pool, go with a javax.sql.ConnectionPoolDataSource
+        // HINT: PGXADataSource is unnecessary (no distributed transactions used) and breaks ingest.
+        className = "org.postgresql.ds.PGConnectionPoolDataSource",
+        user = "${MPCONFIG=dataverse.db.user}",
+        password = "${MPCONFIG=dataverse.db.password}",
+        url = "jdbc:postgresql://${MPCONFIG=dataverse.db.host}:${MPCONFIG=dataverse.db.port}/${MPCONFIG=dataverse.db.name}",
+        // If we ever need to change these pool settings, we need to remove this class and create the resource
+        // from web.xml. We can use MicroProfile Config in there for these values, impossible to do in the annotation.
+        //
+        // See also https://blog.payara.fish/an-intro-to-connection-pools-in-payara-server-5
+        // Payara DataSourceDefinitionDeployer default value = 8
+        minPoolSize = 10,
+        // HINT: Payara DataSourceDefinitionDeployer default value = 32
+        // HINT: Harvard Dataverse is fine for a while with 64
+        maxPoolSize = 100,
+        // "The number of seconds that a physical connection should remain unused in the pool before the connection is closed for a connection pool. "
+        // Payara DataSourceDefinitionDeployer default value = 300 (seconds)
+        maxIdleTime = 300)
+// It's possible to add additional properties like this...
+//
+//properties = {
+//    "fish.payara.log-jdbc-calls=true"
+//})
+//
+// ... but at this time we don't think we need any. The full list
+// of properties can be found at https://docs.payara.fish/community/docs/5.2020.6/documentation/payara-server/jdbc/advanced-connection-pool-properties.html#full-list-of-properties
+//
+// All these properties cannot be configured via MPCONFIG as Payara doesn't support this (yet). To be enhanced.
+// See also https://github.com/payara/Payara/issues/5024
 public class DataSourceProducer {
-    
-    @Resource(lookup="java:app/jdbc/dataverse")
+
+    @Resource(lookup = "java:app/jdbc/dataverse")
     DataSource ds;
-    
+
     @Produces
     public DataSource getDatasource() {
         return ds;

From d7f3da1f1a13e1b4e3b45a7ecad30a56c70f3c83 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Thu, 3 Dec 2020 15:21:44 -0500
Subject: [PATCH 21/22] mention new JVM options in release notes #7418

---
 doc/release-notes/7418-datasourcedefinition.md | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/doc/release-notes/7418-datasourcedefinition.md b/doc/release-notes/7418-datasourcedefinition.md
index 7b333c4e39b..cb45597d825 100644
--- a/doc/release-notes/7418-datasourcedefinition.md
+++ b/doc/release-notes/7418-datasourcedefinition.md
@@ -1,4 +1,6 @@
-## Easier Configuration of Database Connections
+## Release Highlights
+
+### Easier Configuration of Database Connections
 
 Dataverse now being able to use up-to-date Java technologies, transforms
 the way how to configure the connection to your PostgreSQL database.
@@ -11,6 +13,15 @@ Using MicroProfile Config API (#7000, #7418), you can much more easily specify c
 details. For an overview of supported options, please see the
 [installation guide](https://guides.dataverse.org/en/5.3/installation/config.html#jvm-options).
 
+## Notes for Dataverse Installation Administrators
+
+### New JVM Options
+
+- dataverse.db.name
+- dataverse.db.user
+- dataverse.db.password
+- dataverse.db.host
+- dataverse.db.port
 
 <!-- ## Update to Payara Platform 5.2020.6 -->
 <!-- ... -->

From 7e3498e72353378a0e14730fa7a7ff6b8a364ec6 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Thu, 3 Dec 2020 15:31:01 -0500
Subject: [PATCH 22/22] note that some settings have moved to code #7418

---
 doc/release-notes/7418-datasourcedefinition.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/release-notes/7418-datasourcedefinition.md b/doc/release-notes/7418-datasourcedefinition.md
index cb45597d825..b8c5561c2c2 100644
--- a/doc/release-notes/7418-datasourcedefinition.md
+++ b/doc/release-notes/7418-datasourcedefinition.md
@@ -13,6 +13,8 @@ Using MicroProfile Config API (#7000, #7418), you can much more easily specify c
 details. For an overview of supported options, please see the
 [installation guide](https://guides.dataverse.org/en/5.3/installation/config.html#jvm-options).
 
+Note that some settings have been moved from domain.xml to code such as min and max pool size.
+
 ## Notes for Dataverse Installation Administrators
 
 ### New JVM Options