Merge pull request #6809 from IQSS/6761-payara-installer-update

6761 payara installer update

conf/jhove/jhove.conf

@@ -3,7 +3,7 @@
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xmlns="http://hul.harvard.edu/ois/xml/ns/jhove/jhoveConfig"
  xsi:schemaLocation="http://hul.harvard.edu/ois/xml/ns/jhove/jhoveConfig
-                     file:///usr/local/glassfish4/glassfish/domains/domain1/config/jhoveConfig.xsd">
+                     file:///usr/local/payara5/glassfish/domains/domain1/config/jhoveConfig.xsd">
  <jhoveHome>/usr/local/src/jhove</jhoveHome>
  <defaultEncoding>utf-8</defaultEncoding>
  <tempDirectory>/tmp</tempDirectory>

scripts/installer/Makefile

@@ -1,35 +1,37 @@
 INSTALLER_ZIP_DIR=dvinstall
 DISTRIBUTION_WAR_FILE=${INSTALLER_ZIP_DIR}/dataverse.war
-GLASSFISH_SETUP_SCRIPT=${INSTALLER_ZIP_DIR}/glassfish-setup.sh
+GLASSFISH_SETUP_SCRIPT=${INSTALLER_ZIP_DIR}/as-setup.sh
 POSTGRES_DRIVERS=${INSTALLER_ZIP_DIR}/pgdriver
+JSF_PATCH_DIR=${INSTALLER_ZIP_DIR}/jsfpatch
 API_SCRIPTS=${INSTALLER_ZIP_DIR}/setup-datasetfields.sh ${INSTALLER_ZIP_DIR}/setup-users.sh ${INSTALLER_ZIP_DIR}/setup-builtin-roles.sh ${INSTALLER_ZIP_DIR}/setup-dvs.sh ${INSTALLER_ZIP_DIR}/data ${INSTALLER_ZIP_DIR}/setup-identity-providers.sh  ${INSTALLER_ZIP_DIR}/setup-all.sh ${INSTALLER_ZIP_DIR}/post-install-api-block.sh
 DB_SCRIPT=${INSTALLER_ZIP_DIR}/reference_data.sql
 JHOVE_CONFIG=${INSTALLER_ZIP_DIR}/jhove.conf
 JHOVE_SCHEMA=${INSTALLER_ZIP_DIR}/jhoveConfig.xsd
 SOLR_SCHEMA=${INSTALLER_ZIP_DIR}/schema.xml ${INSTALLER_ZIP_DIR}/schema_dv_mdb_fields.xml ${INSTALLER_ZIP_DIR}/schema_dv_mdb_copies.xml ${INSTALLER_ZIP_DIR}/updateSchemaMDB.sh
 SOLR_CONFIG=${INSTALLER_ZIP_DIR}/solrconfig.xml
-PYTHON_FILES=${INSTALLER_ZIP_DIR}/README_python.txt ${INSTALLER_ZIP_DIR}/installConfig.py ${INSTALLER_ZIP_DIR}/installUtils.py ${INSTALLER_ZIP_DIR}/install.py ${INSTALLER_ZIP_DIR}/installGlassfish.py ${INSTALLER_ZIP_DIR}/requirements.txt ${INSTALLER_ZIP_DIR}/default.config ${INSTALLER_ZIP_DIR}/interactive.config
+PYTHON_FILES=${INSTALLER_ZIP_DIR}/README_python.txt ${INSTALLER_ZIP_DIR}/installConfig.py ${INSTALLER_ZIP_DIR}/installUtils.py ${INSTALLER_ZIP_DIR}/install.py ${INSTALLER_ZIP_DIR}/installAppServer.py ${INSTALLER_ZIP_DIR}/requirements.txt ${INSTALLER_ZIP_DIR}/default.config ${INSTALLER_ZIP_DIR}/interactive.config
 INSTALL_SCRIPT=${INSTALLER_ZIP_DIR}/install
 
 installer:	dvinstall.zip
 
 clean: 
 	/bin/rm -rf ${INSTALLER_ZIP_DIR} dvinstall.zip
 
-dvinstall.zip:	${GLASSFISH_SETUP_SCRIPT} ${POSTGRES_DRIVERS} ${DISTRIBUTION_WAR_FILE} ${API_SCRIPTS} ${DB_SCRIPT} ${JHOVE_CONFIG} ${JHOVE_SCHEMA} ${SOLR_SCHEMA} ${SOLR_CONFIG} ${PYTHON_FILES} ${INSTALL_SCRIPT}
+dvinstall.zip:	${GLASSFISH_SETUP_SCRIPT} ${POSTGRES_DRIVERS} ${JSF_PATCH_DIR} ${DISTRIBUTION_WAR_FILE} ${API_SCRIPTS} ${DB_SCRIPT} ${JHOVE_CONFIG} ${JHOVE_SCHEMA} ${SOLR_SCHEMA} ${SOLR_CONFIG} ${PYTHON_FILES} ${INSTALL_SCRIPT}
 	@echo making installer...
-	zip -r dvinstall.zip ${GLASSFISH_SETUP_SCRIPT} ${POSTGRES_DRIVERS} ${DISTRIBUTION_WAR_FILE} ${API_SCRIPTS} ${DB_SCRIPT} ${JHOVE_CONFIG} ${JHOVE_SCHEMA} ${SOLR_SCHEMA} ${SOLR_CONFIG} ${PYTHON_FILES} ${INSTALL_SCRIPT}
+	zip -r dvinstall.zip ${GLASSFISH_SETUP_SCRIPT} ${POSTGRES_DRIVERS} ${JSF_PATCH_DIR} ${DISTRIBUTION_WAR_FILE} ${API_SCRIPTS} ${DB_SCRIPT} ${JHOVE_CONFIG} ${JHOVE_SCHEMA} ${SOLR_SCHEMA} ${SOLR_CONFIG} ${PYTHON_FILES} ${INSTALL_SCRIPT}
 	@echo 
 	@echo "Done!"
 
-${INSTALL_SCRIPT}: install
-	@echo copying the installer script
+${INSTALLER_ZIP_DIR}:
 	mkdir -p ${INSTALLER_ZIP_DIR}
+
+${INSTALL_SCRIPT}: install ${INSTALLER_ZIP_DIR}
+	@echo copying the installer script
 	/bin/cp install ${INSTALLER_ZIP_DIR}
 
 ${DISTRIBUTION_WAR_FILE}: 
 	@echo copying war file...
-	@mkdir -p ${INSTALLER_ZIP_DIR}
 	@VERSION_NUMBER=`grep -m1 '<version>' ../../pom.xml | sed 's/ *<\/*version>//g'`; export VERSION_NUMBER; \
 	BUILT_WAR_FILE=../../target/dataverse-$$VERSION_NUMBER.war; export BUILT_WAR_FILE; \
 	if [ -f $$BUILT_WAR_FILE ]; \
@@ -41,47 +43,44 @@ ${DISTRIBUTION_WAR_FILE}:
 		exit 1; \
 	fi
 
-${GLASSFISH_SETUP_SCRIPT}:	glassfish-setup.sh
+${GLASSFISH_SETUP_SCRIPT}:	as-setup.sh ${INSTALLER_ZIP_DIR}
 	@echo copying glassfish setup
-	mkdir -p ${INSTALLER_ZIP_DIR}
-	/bin/cp glassfish-setup.sh ${INSTALLER_ZIP_DIR}
+	/bin/cp as-setup.sh ${INSTALLER_ZIP_DIR}
 
 ${POSTGRES_DRIVERS}:	 pgdriver/postgresql-42.2.12.jar
+	mkdir -p ${POSTGRES_DRIVERS}
 	@echo copying postgres driver
-	@mkdir -p ${POSTGRES_DRIVERS}
-	/bin/cp pgdriver/postgresql-42.2.12.jar ${INSTALLER_ZIP_DIR}/pgdriver
+	/bin/cp pgdriver/postgresql-42.2.12.jar ${POSTGRES_DRIVERS}
+
+${JSF_PATCH_DIR}: jsfpatch/jakarta.faces_dv.jar
+	mkdir -p ${JSF_PATCH_DIR}
+	@echo copying jsf patch
+	/bin/cp jsfpatch/jakarta.faces_dv.jar ${JSF_PATCH_DIR}
 
-${API_SCRIPTS}:	../api/setup-datasetfields.sh ../api/setup-users.sh ../api/setup-dvs.sh ../api/setup-identity-providers.sh ../api/setup-all.sh ../api/post-install-api-block.sh ../api/setup-builtin-roles.sh ../api/data
+${API_SCRIPTS}:	../api/setup-datasetfields.sh ../api/setup-users.sh ../api/setup-dvs.sh ../api/setup-identity-providers.sh ../api/setup-all.sh ../api/post-install-api-block.sh ../api/setup-builtin-roles.sh ../api/data ${INSTALLER_ZIP_DIR}
 	@echo copying api scripts
-	@mkdir -p ${INSTALLER_ZIP_DIR}
 	/bin/cp -R ../api/setup-datasetfields.sh ../api/setup-users.sh ../api/setup-dvs.sh ../api/setup-identity-providers.sh ../api/setup-all.sh ../api/post-install-api-block.sh ../api/setup-builtin-roles.sh ../api/data ${INSTALLER_ZIP_DIR}
 
-${DB_SCRIPT}:	../database/reference_data.sql
+${DB_SCRIPT}:	../database/reference_data.sql ${INSTALLER_ZIP_DIR}
 	@echo copying reference data sql script
-	@mkdir -p ${INSTALLER_ZIP_DIR}
 	/bin/cp ../database/reference_data.sql ${INSTALLER_ZIP_DIR}
 
-${JHOVE_CONFIG}:	../../conf/jhove/jhove.conf
+${JHOVE_CONFIG}:	../../conf/jhove/jhove.conf ${INSTALLER_ZIP_DIR}
 	@echo copying jhove config file
-	@mkdir -p ${INSTALLER_ZIP_DIR}
 	/bin/cp ../../conf/jhove/jhove.conf ${INSTALLER_ZIP_DIR}
 
-${JHOVE_SCHEMA}:	../../conf/jhove/jhoveConfig.xsd
+${JHOVE_SCHEMA}:	../../conf/jhove/jhoveConfig.xsd ${INSTALLER_ZIP_DIR}
 	@echo copying jhove schema file
-	@mkdir -p ${INSTALLER_ZIP_DIR}
 	/bin/cp ../../conf/jhove/jhoveConfig.xsd ${INSTALLER_ZIP_DIR}
 
-${SOLR_SCHEMA}:		../../conf/solr/7.7.2/schema.xml ../../conf/solr/7.7.2/schema_dv_mdb_fields.xml ../../conf/solr/7.7.2/schema_dv_mdb_copies.xml ../../conf/solr/7.7.2/updateSchemaMDB.sh
+${SOLR_SCHEMA}:		../../conf/solr/7.7.2/schema.xml ../../conf/solr/7.7.2/schema_dv_mdb_fields.xml ../../conf/solr/7.7.2/schema_dv_mdb_copies.xml ../../conf/solr/7.7.2/updateSchemaMDB.sh ${INSTALLER_ZIP_DIR}
 	@echo copying Solr schema file
-	@mkdir -p ${INSTALLER_ZIP_DIR}
 	/bin/cp ../../conf/solr/7.7.2/schema*.xml ../../conf/solr/7.7.2/updateSchemaMDB.sh ${INSTALLER_ZIP_DIR}
 
-${SOLR_CONFIG}:		../../conf/solr/7.7.2/solrconfig.xml
+${SOLR_CONFIG}:		../../conf/solr/7.7.2/solrconfig.xml ${INSTALLER_ZIP_DIR}
 	@echo copying Solr config file
-	@mkdir -p ${INSTALLER_ZIP_DIR}
 	/bin/cp ../../conf/solr/7.7.2/solrconfig.xml ${INSTALLER_ZIP_DIR}
 
-${PYTHON_FILES}: README_python.txt install.py installConfig.py installGlassfish.py installUtils.py requirements.txt default.config interactive.config
+${PYTHON_FILES}: README_python.txt install.py installConfig.py installAppServer.py installUtils.py requirements.txt default.config interactive.config ${INSTALLER_ZIP_DIR}
 	@echo copying Python installer files
-	@mkdir -p ${INSTALLER_ZIP_DIR}
-	/bin/cp README_python.txt install.py installConfig.py installGlassfish.py installUtils.py requirements.txt default.config interactive.config ${INSTALLER_ZIP_DIR}
+	/bin/cp README_python.txt install.py installConfig.py installAppServer.py installUtils.py requirements.txt default.config interactive.config ${INSTALLER_ZIP_DIR}

scripts/installer/README_python.txt

@@ -16,20 +16,28 @@ backward compatibility, for now, but please use version 2.7 or newer.
 
 
 The extra module psycopg2 (PostgreSQL client) is required. The
-installer has been tested with psycopg2 version 2.8.4.
+installer has been tested with psycopg2 version 2.8.4. 
 
-Install the module with 
+We recommend that you try installing the "binary", pre-built version of the package:
 
-pip install psycopg2 
+pip install psycopg2-binary
 
-(or "pip3 install psycopg2" if you intend to use python3 and it's
+(or "pip3 install psycopg2-binary" if you intend to use python3 and it's
 installed separately on your system)
 
-In order to build the module, pip will need to execute pg_config,
-PostgreSQL configuration utility. Make sure it is in your PATH. If you
-have multiple versions of PostgresQL installed, make sure the version
-that you will be using with Dataverse is the first on your PATH. For
-example,
+If for whatever reason the binary psycopg2 package doesn't run
+properly on your system, you can try the more complex process of
+making pip build it from sources:
+
+pip3 install psycopg2
+
+This will require compilers to be properly installed on your system.
+(On MacOS, you'll need XCode installed). 
+In order to link with the PostgresQL libraries, pip will need to
+execute pg_config, PostgreSQL configuration utility. Make sure it is
+in your PATH. If you have multiple versions of PostgresQL installed,
+make sure the version that you will be using with Dataverse is the
+first on your PATH. For example,
 
    PATH=/usr/pgsql-9.6/bin:$PATH; export PATH
 

scripts/installer/glassfish-setup.sh → scripts/installer/as-setup.sh

@@ -5,7 +5,9 @@
 # as environmental variables: 
 # (no defaults for these values are provided here!)
 #
-# glassfish configuration: 
+# app. server (payara) configuration: 
+# the variables used by this script still has the word "glassfish" in them.
+# this is kept as legacy, just to avoid unncessary changes.
 # GLASSFISH_ROOT
 # GLASSFISH_DOMAIN
 # ASADMIN_OPTS
@@ -49,14 +51,25 @@ function preliminary_setup()
 {
     # undeploy the app, if running: 
 
-  ./asadmin $ASADMIN_OPTS undeploy dataverse-4.0
+  ./asadmin $ASADMIN_OPTS undeploy dataverse
 
   # avoid OutOfMemoryError: PermGen per http://eugenedvorkin.com/java-lang-outofmemoryerror-permgen-space-error-during-deployment-to-glassfish/
   #./asadmin $ASADMIN_OPTS list-jvm-options
-  ./asadmin $ASADMIN_OPTS delete-jvm-options "-XX\:MaxPermSize=192m"
-  ./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:MaxPermSize=512m"
-  ./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:PermSize=256m"
-  ./asadmin $ASADMIN_OPTS delete-jvm-options -client
+  # Note that these JVM options are different for Payara5 and Glassfish4:
+  # old Glassfish4 options: (commented out)
+  #./asadmin $ASADMIN_OPTS delete-jvm-options "-XX\:MaxPermSize=192m"
+  #./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:MaxPermSize=512m"
+  #./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:PermSize=256m"
+  # payara5 ships with the "-server" option already in domain.xml, so no need:
+  #./asadmin $ASADMIN_OPTS delete-jvm-options -client
+
+  # new Payara5 options: (thanks to donsizemore@unc.edu)
+  ./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:MaxMetaspaceSize=512m"
+  ./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:MetaspaceSize=256m"
+  ./asadmin $ASADMIN_OPTS create-jvm-options "-Dfish.payara.classloading.delegate=false"
+  ./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:+UseG1GC"
+  ./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:+UseStringDeduplication"
+  ./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}"
@@ -67,8 +80,8 @@ function preliminary_setup()
       rm /tmp/$1.txt
   done
 
-    ###
-  # Add the necessary JVM options: 
+  ###
+  # Add the Dataverse-specific JVM options: 
   # 
   # location of the datafiles temp directory: 
   # (defaults to dataverse/files in the users home directory, ${FILES_DIR}/temp if this is set)
@@ -82,8 +95,9 @@ function preliminary_setup()
   ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddataverse.rserve.port=${RSERVE_PORT}"
   ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddataverse.rserve.user=${RSERVE_USER}"
   ./asadmin $ASADMIN_OPTS create-jvm-options '\-Ddataverse.rserve.password=${ALIAS=rserve_password_alias}'
-  # Data Deposit API options
+  # The host and url addresses this Dataverse will be using:
   ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddataverse.fqdn=${HOST_ADDRESS}"
+  ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddataverse.siteUrl=http\://\${dataverse.fqdn}\:8080"
   # password reset token timeout in minutes
   ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddataverse.auth.password-reset-timeout-in-minutes=60"
 
@@ -167,18 +181,18 @@ function final_setup(){
 
 if [ "$DOCKER_BUILD" = "true" ]
   then
-    FILES_DIR="/usr/local/glassfish4/glassfish/domains/domain1/files"
+    FILES_DIR="/usr/local/payara5/glassfish/domains/domain1/files"
     RSERVE_HOST="localhost"
     RSERVE_PORT="6311"
     RSERVE_USER="rserve"
     RSERVE_PASS="rserve"
     HOST_ADDRESS="localhost\:8080"
-    pushd /usr/local/glassfish4/glassfish/bin/
+    pushd /usr/local/payara5/glassfish/bin/
     ./asadmin start-domain domain1
     preliminary_setup
-    chmod -R 777 /usr/local/glassfish4/
-    rm -rf /usr/local/glassfish4/glassfish/domains/domain1/generated 
-    rm -rf /usr/local/glassfish4/glassfish/domains/domain1/applications
+    chmod -R 777 /usr/local/payara5/
+    rm -rf /usr/local/payara5/glassfish/domains/domain1/generated 
+    rm -rf /usr/local/payara5/glassfish/domains/domain1/applications
     popd
     exit 0
 fi
@@ -288,11 +302,11 @@ if [ ! -d "$DOMAIN_DIR" ]
     exit 2
 fi
 
-echo "Setting up your glassfish4 to support Dataverse"
-echo "Glassfish directory: "$GLASSFISH_ROOT
+echo "Setting up your app. server (Payara5) to support Dataverse"
+echo "Payara directory: "$GLASSFISH_ROOT
 echo "Domain directory:    "$DOMAIN_DIR
 
-# Move to the glassfish dir
+# Move to the payara dir
 pushd $GLASSFISH_BIN_DIR
 
 ###
@@ -331,6 +345,6 @@ echo Updates done. Restarting...
 # Clean up
 popd
 
-echo "Glassfish setup complete"
+echo "Payara setup complete"
 date
 

scripts/installer/default.config

@@ -1,7 +1,7 @@
 [glassfish]
 HOST_DNS_ADDRESS = localhost
-GLASSFISH_USER = glassfish
-GLASSFISH_DIRECTORY = /usr/local/glassfish4
+GLASSFISH_USER = dataverse
+GLASSFISH_DIRECTORY = /usr/local/payara5
 GLASSFISH_ADMIN_USER = admin
 GLASSFISH_ADMIN_PASSWORD = secret
 GLASSFISH_HEAP = 2048