diff --git a/doc/release-notes/7418-datasourcedefinition.md b/doc/release-notes/7418-datasourcedefinition.md new file mode 100644 index 00000000000..b8c5561c2c2 --- /dev/null +++ b/doc/release-notes/7418-datasourcedefinition.md @@ -0,0 +1,88 @@ +## 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. + +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 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). + +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 + +- dataverse.db.name +- dataverse.db.user +- dataverse.db.password +- dataverse.db.host +- dataverse.db.port + + + + + +🚨 THIS VERSION OF DATAVERSE **REQUIRES** UPGRADING TO PAYARA 5.2020.6. 🚨 + + + +## Upgrading from earlier releases + +ℹī¸ You need to update the Payara Application Server before continuing here. See above. + +1. Undeploy the previous version. +``` +/asadmin list-applications +/asadmin undeploy dataverse- +``` + +(where `` 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 `${DB_...}`. +(If you are using a PostgreSQL server on `localhost:5432`, you can omit `dataverse.db.host` and `dataverse.db.port`.) + +``` +/asadmin create-system-properties "dataverse.db.user=${DB_USER}" +/asadmin create-system-properties "dataverse.db.host=${DB_HOST}" +/asadmin create-system-properties "dataverse.db.port=${DB_PORT}" +/asadmin create-system-properties "dataverse.db.name=${DB_NAME}" +echo "AS_ADMIN_ALIASPASSWORD=${DB_PASS}" > /tmp/password.txt +/asadmin create-password-alias --passwordfile /tmp/password.txt dataverse.db.password +rm /tmp/password.txt +``` + + + +Now you are safe to delete the old password alias and DB pool: +``` +/asadmin delete-jdbc-connection-pool --cascade=true dvnDbPool +/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/domains/domain1/generated +service payara start +``` + +3. Deploy this version. +``` +/bin/asadmin deploy dataverse-5.3.war +``` + +4. Restart Payara +``` +service payara stop +service payara start +``` diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst index eb98c7d2bdd..4a877eabff7 100644 --- a/doc/sphinx-guides/source/installation/config.rst +++ b/doc/sphinx-guides/source/installation/config.rst @@ -1032,6 +1032,57 @@ 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. + +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. + +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 + +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. + +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 server port to connect to. + +Defaults to ``5432``, the default PostgreSQL port. + +Can also be set via *MicroProfile Config API* sources, e.g. the environment variable ``DATAVERSE_DB_PORT``. + dataverse.rserve.host +++++++++++++++++++++ @@ -1168,7 +1219,7 @@ 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: diff --git a/pom.xml b/pom.xml index bdd60965137..6d7378a7ac2 100644 --- a/pom.xml +++ b/pom.xml @@ -685,6 +685,7 @@ **/*.xml **/firstNames/*.* **/*.xsl + **/*.properties diff --git a/scripts/installer/as-setup.sh b/scripts/installer/as-setup.sh index 2af6e9dd662..1096a12e391 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}" ./asadmin $ASADMIN_OPTS create-jvm-options "\-Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl" diff --git a/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java b/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java index d5f4f8520a7..71b53bd43f2 100644 --- a/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java +++ b/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java @@ -15,7 +15,7 @@ @TransactionManagement(value = TransactionManagementType.BEAN) public class StartupFlywayMigrator { - @Resource(lookup = "jdbc/VDCNetDS") + @Resource(lookup = "java:app/jdbc/dataverse") private DataSource dataSource; @PostConstruct diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java new file mode 100644 index 00000000000..02ba331cdd5 --- /dev/null +++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java @@ -0,0 +1,54 @@ +package edu.harvard.iq.dataverse.util; + +import javax.annotation.Resource; +import javax.annotation.sql.DataSourceDefinition; +import javax.enterprise.inject.Produces; +import javax.inject.Singleton; +import javax.sql.DataSource; + +// Find docs here: https://javaee.github.io/javaee-spec/javadocs/javax/annotation/sql/DataSourceDefinition.html +@Singleton +@DataSourceDefinition( + name = "java:app/jdbc/dataverse", + // The app server (Payara) deploys a managed pool for this data source for us. + // We don't need to deal with this on our own. + // + // HINT: PGSimpleDataSource would work too, but as we use a connection pool, go with a javax.sql.ConnectionPoolDataSource + // HINT: PGXADataSource is unnecessary (no distributed transactions used) and breaks ingest. + className = "org.postgresql.ds.PGConnectionPoolDataSource", + user = "${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") + DataSource ds; + + @Produces + public DataSource getDatasource() { + return ds; + } +} 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..8c475f1c050 --- /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 diff --git a/src/main/resources/META-INF/persistence.xml b/src/main/resources/META-INF/persistence.xml index 8b4e33858ac..45552f36939 100644 --- a/src/main/resources/META-INF/persistence.xml +++ b/src/main/resources/META-INF/persistence.xml @@ -3,7 +3,7 @@ org.eclipse.persistence.jpa.PersistenceProvider - jdbc/VDCNetDS + java:app/jdbc/dataverse @@ -20,15 +20,4 @@ -