6593 payara docs

doc/sphinx-guides/source/_static/admin/counter-processor-config.yaml

@@ -1,8 +1,8 @@
 # currently no other option but to have daily logs and have year-month-day format in the name with
 # 4-digit year and 2-digit month and day
-# /usr/local/glassfish4/glassfish/domains/domain1/logs/counter_2019-01-11.log
+# /usr/local/payara5/glassfish/domains/domain1/logs/counter_2019-01-11.log
 #log_name_pattern: sample_logs/counter_(yyyy-mm-dd).log
-log_name_pattern: /usr/local/glassfish4/glassfish/domains/domain1/logs/counter_(yyyy-mm-dd).log
+log_name_pattern: /usr/local/payara5/glassfish/domains/domain1/logs/counter_(yyyy-mm-dd).log
 
 # path_types regular expressions allow matching to classify page urls as either an investigation or request
 # based on specific URL structure for your system.
@@ -42,7 +42,7 @@ year_month: 2019-01
 # Don't put the filename extension, the code will tack on the tsv or json extension for you.
 # Output formats are either tsv or json currently.  TSV is currently broken until anyone accepts reports in that format.
 # FIXME: "/tmp" is fine for a quick test but pick another directory that
-# the "counter" user can write to and that the "glassfish" user can read from.
+# the "counter" user can write to and that the "dataverse" user can read from.
 output_file: /tmp/make-data-count-report
 output_format: json
 

doc/sphinx-guides/source/_static/installation/files/etc/httpd/conf.d/ssl.conf

@@ -223,14 +223,14 @@ CustomLog logs/ssl_request_log \
 #  Require all granted
 #</Location>
 
-# don't pass paths used by rApache and TwoRavens to Glassfish
+# don't pass paths used by rApache and TwoRavens to app server
 ProxyPassMatch ^/RApacheInfo$ !
 ProxyPassMatch ^/custom !
 ProxyPassMatch ^/dataexplore !
-# don't pass paths used by Shibboleth to Glassfish
+# don't pass paths used by Shibboleth to app server
 ProxyPassMatch ^/Shibboleth.sso !
 ProxyPassMatch ^/shibboleth-ds !
-# pass everything else to Glassfish
+# pass everything else to app server
 ProxyPass / ajp://localhost:8009/
 
 <Location /shib.xhtml>

doc/sphinx-guides/source/_static/installation/files/etc/init.d/glassfish.init.root → doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.root

@@ -1,34 +1,34 @@
 #! /bin/sh
 # chkconfig: 2345 99 01
-# description: GlassFish App Server
+# description: Payara App Server
 
 set -e
 
-ASADMIN=/usr/local/glassfish4/bin/asadmin
+ASADMIN=/usr/local/payara5/bin/asadmin
 
 case "$1" in
   start)
-        echo -n "Starting GlassFish server: glassfish"
+        echo -n "Starting Payara"
         # Increase file descriptor limit:
         ulimit -n 32768
         # Allow "memory overcommit":
         # (basically, this allows to run exec() calls from inside the
         # app, without the Unix fork() call physically hogging 2X
-        # the amount of memory glassfish is already using)
+        # the amount of memory Payara is already using)
         echo 1 > /proc/sys/vm/overcommit_memory
 
         #echo
-        #echo "GLASSFISH IS UNDER MAINTENANCE;"
+        #echo "PAYARA IS UNDER MAINTENANCE;"
         #echo "PLEASE DO NOT USE service init script."
         #echo
 	LANG=en_US.UTF-8; export LANG
         $ASADMIN start-domain domain1
         echo "."
         ;;
   stop)
-        echo -n "Stopping GlassFish server: glassfish"
+        echo -n "Stopping Payara"
         #echo
-        #echo "GLASSFISH IS UNDER MAINTENANCE;"
+        #echo "PAYARA IS UNDER MAINTENANCE;"
         #echo "PLEASE DO NOT USE service init script."
         #echo
 
@@ -37,7 +37,7 @@ case "$1" in
         ;;
 
   *)
-        echo "Usage: /etc/init.d/glassfish {start|stop}"
+        echo "Usage: /etc/init.d/payara {start|stop}"
         exit 1
 esac
 

doc/sphinx-guides/source/_static/installation/files/etc/init.d/glassfish.init.service → doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.service

@@ -1,33 +1,33 @@
 #! /bin/sh
 # chkconfig: 2345 80 01
-# description: GlassFish App Server
+# description: Payara App Server
 set -e
 
-ASADMIN=/usr/local/glassfish4/bin/asadmin
-GF_USER=glassfish
+ASADMIN=/usr/local/payara5/bin/asadmin
+APP_SERVER_USER=dataverse
 
 case "$1" in
   start)
-        echo -n "Starting GlassFish server: glassfish"
+        echo -n "Starting Payara"
         # Increase file descriptor limit:
         ulimit -n 32768
         # Allow "memory overcommit":
         # (basically, this allows to run exec() calls from inside the
         # app, without the Unix fork() call physically hogging 2X
-        # the amount of memory glassfish is already using)
+        # the amount of memory Payara is already using)
         echo 1 > /proc/sys/vm/overcommit_memory
 	LANG=en_US.UTF-8; export LANG
 
-        sudo -u $GF_USER $ASADMIN start-domain domain1
+        sudo -u $APP_SERVER_USER $ASADMIN start-domain domain1
         ;;
   stop)
-        echo -n "Stopping GlassFish server: glassfish"
+        echo -n "Stopping Payara"
 
-        sudo -u $GF_USER $ASADMIN stop-domain domain1
+        sudo -u $APP_SERVER_USER $ASADMIN stop-domain domain1
         echo "."
          ;;
   *)
-        echo "Usage: /etc/init.d/glassfish {start|stop}"
+        echo "Usage: /etc/init.d/payara {start|stop}"
 
         exit 1
 esac

doc/sphinx-guides/source/_static/installation/files/etc/systemd/payara.service

@@ -0,0 +1,16 @@
+[Unit]
+Description = Payara Server
+After = syslog.target network.target
+
+[Service]
+Type = forking
+ExecStart = /usr/bin/java -jar /usr/local/payara5/glassfish/lib/client/appserver-cli.jar start-domain
+ExecStop = /usr/bin/java -jar /usr/local/payara5/glassfish/lib/client/appserver-cli.jar stop-domain
+ExecReload = /usr/bin/java -jar /usr/local/payara5/glassfish/lib/client/appserver-cli.jar restart-domain
+User=dataverse
+LimitNOFILE=32768
+Environment="LANG=en_US.UTF-8"
+TimeoutStartSec=120s
+
+[Install]
+WantedBy = multi-user.target

doc/sphinx-guides/source/_static/util/clear_timer.sh

@@ -5,29 +5,28 @@
 # assumes this script is being run as root, and that the postgres user had passwordless 
 # access to the database (local sockets, or appropriate environmental variables).
 
-# will restart glassfish if it's stopped; comment out the `start-domain` command at the end
+# will restart Payara if it's stopped; comment out the `start-domain` command at the end
 # if you'd like to avoid that.
 
-# directory where glassfish is installed
-GLASSFISH_DIR=/usr/local/glassfish4
+# directory where Payara is installed
+PAYARA_DIR=/usr/local/payara5
 
-# directory within glassfish (defaults)
-DV_DIR=${GLASSFISH_DIR}/glassfish/domains/domain1
+# directory within Payara (defaults)
+DV_DIR=${PAYARA_DIR}/glassfish/domains/domain1
 
 # name of dataverse database
 DV_DB=dvndb
 
 # OS user for the database
 DB_USER=postgres
 
-# stop the glassfish domain (generates a warning if glassfish is stopped)
-${GLASSFISH_DIR}/bin/asadmin stop-domain
+# stop the domain (generates a warning if app server is stopped)
+${PAYARA_DIR}/bin/asadmin stop-domain
 
-rm -rf ${GLASSFISH_DIR}/${DV_DIR}/generated/
-rm -rf ${GLASSFISH_DIR}/${DV_DIR}/osgi-cache/felix
+rm -rf ${PAYARA_DIR}/${DV_DIR}/generated/
+rm -rf ${PAYARA_DIR}/${DV_DIR}/osgi-cache/felix
 
 sudo -u ${DB_USER} psql ${DV_DB} -c 'delete from "EJB__TIMER__TBL"';
 
-# restart the domain (also generates a warning if glassfish is stopped)
-${GLASSFISH_DIR}/bin/asadmin start-domain
-
+# restart the domain (also generates a warning if app server is stopped)
+${PAYARA_DIR}/bin/asadmin start-domain

doc/sphinx-guides/source/admin/harvestclients.rst

@@ -24,6 +24,6 @@ The process of creating a new, or editing an existing client, is largely self-ex
 What if a Run Fails?
 ~~~~~~~~~~~~~~~~~~~~
 
-Each harvesting client run logs a separate file per run to Glassfish's default logging directory (``/usr/local/glassfish4/glassfish/domains/domain1/logs/`` unless you've changed it). Look for filenames in the format  ``harvest_TARGET_YYYY_MM_DD_timestamp.log`` to get a better idea of what's going wrong.
+Each harvesting client run logs a separate file per run to the app server's default logging directory (``/usr/local/payara5/glassfish/domains/domain1/logs/`` unless you've changed it). Look for filenames in the format  ``harvest_TARGET_YYYY_MM_DD_timestamp.log`` to get a better idea of what's going wrong.
 
 Note that you'll want to run a minimum Dataverse version of 4.6, optimally 4.18, for the best OAI-PMH interoperability.

doc/sphinx-guides/source/admin/make-data-count.rst

@@ -100,7 +100,7 @@ Soon we will be setting up a cron job to run nightly but we start with a single
 
 * If you are running Counter Processor for the first time in the middle of a month, you will need create blank log files for the previous days. e.g.:
 
-  * ``cd /usr/local/glassfish4/glassfish/domains/domain1/logs``
+  * ``cd /usr/local/payara5/glassfish/domains/domain1/logs``
 
   * ``touch counter_2019-02-01.log``
 

doc/sphinx-guides/source/admin/metadatacustomization.rst

@@ -546,7 +546,7 @@ Loading TSV files into Dataverse
 
 A number of TSV files are loaded into Dataverse on every new installation, becoming the metadata blocks you see in the UI. For the list of metadata blocks that are included with Dataverse out of the box, see the :doc:`/user/appendix` section of the User Guide.
 
-Along with TSV file, there are corresponding ResourceBundle property files with key=value pair `here <https://github.com/IQSS/dataverse/tree/develop/src/main/java>`__.  To add other language files, see the :doc:`/installation/config` for dataverse.lang.directory JVM Options section, and add a file, for example: "citation_lang.properties" to the path you specified for the ``dataverse.lang.directory`` JVM option, and then restart Glassfish.
+Along with TSV file, there are corresponding ResourceBundle property files with key=value pair `here <https://github.com/IQSS/dataverse/tree/develop/src/main/java>`__.  To add other language files, see the :doc:`/installation/config` for dataverse.lang.directory JVM Options section, and add a file, for example: "citation_lang.properties" to the path you specified for the ``dataverse.lang.directory`` JVM option, and then restart the app server.
 
 If you are improving an existing metadata block, the Dataverse installation process will load the TSV for you, assuming you edited the TSV file in place. The TSV file for the Citation metadata block, for example, can be found at ``scripts/api/data/metadatablocks/citation.tsv``.
 If any of the below mentioned property values are changed, corresponsing ResourceBundle property file has to be edited and stored under ``dataverse.lang.directory`` location

doc/sphinx-guides/source/admin/metadataexport.rst

@@ -28,7 +28,7 @@ Note, that creating, modifying, or re-exporting an OAI set will also attempt to
 Export Failures
 ---------------
 
-An export batch job, whether started via the API, or by the application timer, will leave a detailed log in your configured logs directory. This is the same location where your main Glassfish server.log is found. The name of the log file is ``export_[timestamp].log`` - for example, *export_2016-08-23T03-35-23.log*. The log will contain the numbers of datasets processed successfully and those for which metadata export failed, with some information on the failures detected. Please attach this log file if you need to contact Dataverse support about metadata export problems.
+An export batch job, whether started via the API, or by the application timer, will leave a detailed log in your configured logs directory. This is the same location where your main app server logs are found. The name of the log file is ``export_[timestamp].log`` - for example, *export_2016-08-23T03-35-23.log*. The log will contain the numbers of datasets processed successfully and those for which metadata export failed, with some information on the failures detected. Please attach this log file if you need to contact Dataverse support about metadata export problems.
 
 Downloading Metadata via GUI
 ----------------------------

doc/sphinx-guides/source/admin/monitoring.rst

@@ -36,7 +36,7 @@ Create a username/password (i.e. "admin" for both):
 
 ``htpasswd /etc/munin/munin-htpasswd admin``
 
-Assuming you are fronting Glassfish with Apache, prevent Apache from proxying "/munin" traffic to Glassfish by adding the following line to your Apache config:
+Assuming you are fronting your app server with Apache, prevent Apache from proxying "/munin" traffic to the app server by adding the following line to your Apache config:
 
 ``ProxyPassMatch ^/munin !``
 
@@ -90,12 +90,12 @@ Process the logs:
 
 Please note that load balancers (such as Amazon's ELB) might interfer with the ``LogFormat`` mentioned above.  To start troubleshooting errors such as ``AWStats did not find any valid log lines that match your LogFormat parameter``, you might need to bump up the value of ``NbOfLinesForCorruptedLog`` in the config files above and re-try while you interate on your Apache and AWStats config.
 
-Please note that the Dataverse team has attempted to parse Glassfish logs using AWStats but it didn't seem to just work and posts have been made at https://stackoverflow.com/questions/49134154/what-logformat-definition-does-awstats-require-to-parse-glassfish-http-access-logs and https://sourceforge.net/p/awstats/discussion/43428/thread/9b1befda/ that can be followed up on some day.
+Please note that the Dataverse team has attempted to parse Glassfish/Payara logs using AWStats but it didn't seem to just work and posts have been made at https://stackoverflow.com/questions/49134154/what-logformat-definition-does-awstats-require-to-parse-glassfish-http-access-logs and https://sourceforge.net/p/awstats/discussion/43428/thread/9b1befda/ that can be followed up on some day.
 
-Database Connection Pool used by Glassfish
-------------------------------------------
+Database Connection Pool Used by App Server
+-------------------------------------------
 
-https://github.com/IQSS/dataverse/issues/2595 contains some information on enabling monitoring of Glassfish, which is disabled by default. It's a TODO to document what to do here if there is sufficient interest.
+https://github.com/IQSS/dataverse/issues/2595 contains some information on enabling monitoring of app servers, which is disabled by default. It's a TODO to document what to do here if there is sufficient interest.
 
 
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