Upgrade Plan 290

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gHN Upgrade Instructions

It should be carried as follows:

1) Download the upgrade script from 

wget http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/ghn-distribution/upgrade-scripts/upgrade-ghn-3-3-0.sh

and make it executable: 

chmod 700 upgrade-ghn-3-3-0.sh

2) Verify that the GLOBUS_LOCATION environment variable is correctly set 

echo $GLOBUS_LOCATION

3) Run the upgrade script with the following arguments:

  • <port>: The port where the container runs.
  • <restart/norestart>: tells if the container has to be restarted or not after the upgrade
./upgrade-ghn-3-3-0.sh <port> <restart/norestart>

Notes:

  • The script ask for the removal of previous GHNgCube Hosting Node. logs ( recommended )

4) Verify the upgrade operation using the infrastructure monitoring tools 

http://monitor.d4science.research-infrastructures.eu

Infrastructure (13 Jun AM)

Infrastructure Enabling Services (13 Jun AM)

GHNgCube Hosting Node. to upgrade:

gHNs:

  • DONE (CERN) node1.p.d4science.research-infrastructures.eu:8000: upgrade node ( restart )
  • DONE (CERN) node1.p.d4science.research-infrastructures.eu:8080: upgrade node ( restart )
  • DONE (CERN) node2.p.d4science.research-infrastructures.eu:8080: upgrade node ( restart )
  • DONE (CERN) node17.p.d4science.research-infrastructures.eu:8080: upgrade node ( restart )
  • DONE (CERN) node11.p.d4science.research-infrastructures.eu:8080: upgrade node ( restart )

Other nodes:

  • DONE (CERN) node67.p.d4science.research-infrastructures.eu: MongoDB server installation
  • DONE (CERN) node58.p.d4science.research-infrastructures.eu: MongoDB server installation
  • DONE (CERN) node73.p.d4science.research-infrastructures.eu: MongoDB server installation
  • DONE (CERN) message-broker.d4science.research-infrastructures.eu : Upgrade to ActiveMQ 5.6 and switch to use KahaDB for persistent messages

Services

  • DONE (CERN) node2.p.d4science.research-infrastructures.eu:8080: upgrade IS-Registry
  • DONE (CERN) node1.p.d4science.research-infrastructures.eu:8000: upgrade RM
  • DONE (CERN) node11.p.d4science.research-infrastructures.eu:8080: install Software Gateway
  • DONE (CERN) node17.p.d4science.research-infrastructures.eu:8080: upgrade Messaging Consumer

Configuration

  • DONE (CERN) profile from gCube 2.9.0 registration in production
  • DONE (CERN) Generic Resource describing the MongoDB configuration.
  • DONE (CERN) Generic Resource describing the Nexus Server URL
  • DONE (CERN) Add SG GHNgCube Hosting Node. and RI to all VOVirtual Organization; scopes

gCubeApps VOVirtual Organization;

gCubeApps Enabling Services (13 Jun AM)

gHNs:

  • DONE (CERN) node66.p.d4science.research-infrastructures.eu:8000: upgrade node (restart)
  • DONE (CERN) node66.p.d4science.research-infrastructures.eu:8080: upgrade node (restart)
  • DONE (CERN) node65.p.d4science.research-infrastructures.eu:8080: upgrade node (restart)


Services:

  • DONE (CERN) node65.p.d4science.research-infrastructures.eu:8080: upgrade IS-Registry
  • DONE (CERN) node66.p.d4science.research-infrastructures.eu:8080: upgrade RM

Configuration:

The following RuntimeResource must be configured

  • DONE Geo Server
  • DONE GeoNetwork
  • DONE RStudio
  • DONE TimeSeries Database
  • DONE Ecological Modeling Database
  • DONE PostGis Database
  • DONE Obis database
  • DONE Species Link
  • DONE Worms
  • DONE CoL
  • DONE Maven Repository
  • Transect

gCubeApps VOVirtual Organization;/VREVirtual Research Environment. Services (13 June AM)

gHNs:

  • DONE (CERN) node36.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) rstudio.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node39.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node47.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node49.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node53.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node54.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node59.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node60.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node61.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node62.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node63.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)
  • DONE (CERN) node64.p.d4science.research-infrastructures.eu:8080 : upgrade node (restart)


Services:

  • DONE (CERN) node47.p.d4science.research-infrastructures.eu:8080 : deploy Species Discovery
  • DONE(CERN) node49.p.d4science.research-infrastructures.eu:8080 : upgrade Aquamaps service
  • DONE (CERN) node59.p.d4science.research-infrastructures.eu:8080 : upgrade TS service
    • DONE org.gcube.content-management.time-series.2-3-0
    • DONE org.gcube.content-management.time-series-geo-tools.1-4-0
    • DONE org.gcube.common.TSDBInterface.1-3-0
    • DONE org.gcube.common.TSPostgresImplementation.1-3-0
    • DONE org.gcube.common.GeoServerInterface.1-8-0
    • DONE org.gcube.data-analysis.ecological-engine.1-2-0
    • DONE org.gcube.content-management.codelist-manager.1-2-0
  • DONE (CERN) node64.p.d4science.research-infrastructures.eu:8080 : upgrade VREModeler
  • DONE (CERN) node60.p.d4science.research-infrastructures.eu:8080 : upgrade RM
  • DONE (CERN) node61.p.d4science.research-infrastructures.eu:8080 : upgrade RM
  • DONE (CERN) node62.p.d4science.research-infrastructures.eu:8080 : upgrade RM
  • DONE (CERN) node63.p.d4science.research-infrastructures.eu:8080 : upgrade RM

new VREVirtual Research Environment.:

A new VREVirtual Research Environment. is going to be deployed ( BiodiversityResearchEnvironment, but is still not clear)  :

  • (CNR) node39.p.d4science.research-infrastructures.eu:8080 : deploy RM

WebApp Deployment VREVirtual Research Environment.:

  • DONE (CERN) Deployment of the RUService Webapp. The releted RI need to be added to all gCubeApps scopes and as well to FARM VOs VREs.

Portals (13 June PM)

D4ScienceAn e-Infrastructure operated by the D4Science.org initiative..org portal

The D4ScienceAn e-Infrastructure operated by the D4Science.org initiative..org portal [1] will first be upgraded in order to give access to the gCubeApps env. The portal will be fully upgraded with the artifacts coming from gCube 2.9.0.

Home Library conf

From this version of gCube, the homelibrary with JackRabbit Repo will be used and for that reason a JackRabbit repo need to be deployed on the infra:

  • DONE (CNR) node76.p.d4science.research-infrastructures.eu : Deployment and configuration of a JackRabbit repo
  • DONE (CNR) Runtime Resource for JackRabbit to be configured
  • DONE (CNR) Importing User data from local repo @ iMarine portal to Jack Rabbit repo

Maven installation

The new War Management portlet has introduced a dependency towards Maven client.

In order to install the maven client on ubuntu node please type : 

sudo apt-get install maven2

once installed, the settings for gcube maven repository should be configured inside the file $HOME/.m2/settings.xml. Please check with the infrastructure-managers those settings

Portal upgrade

The portal is going to be upgraded to the portal-bundle-2-1-0.

In addition the following upgrades will be performed by CNR:

new portlets:

  • DONE org.gcube.portlets-user.species-discovery.1-0-0
  • DONE org.gcube.application.aquamaps.aquamapsspeciesview.1-0-0

upgraded portlets:

  • DONE org.gcube.messaging.accounting-portlet.1-6-0
  • DONE org.gcube.messaging.monitoring-portlet.1-2-0
  • DONE org.gcube.messaging.node-accounting-portlet.1-4-0
  • DONE org.gcube.portlets-user.template-generator.3-4-0
  • DONE org.gcube.portlets-user.report-generator-portlet.3-4-0
  • DONE org.gcube.portlets-user.results-portlet.4-4-0
  • DONE org.gcube.portlets-user.time-series-portlet.3-3-0
  • DONE org.gcube.portlets-user.codelist-management-portlet.1-1-0
  • DONE org.gcube.portlets-user.geoexplorer.1-1-0
  • DONE org.gcube.portlets-user.gcube-geoexplorer.1-1-0
  • DONE org.gcube.portlets-user.geoexplorer-portlet.1-1-0
  • DONE org.gcube.portlets-user.workspace-portlet.5-0-0
  • DONE org.gcube.portlets-user.war-management-portlet.1-1-1
  • DONE org.gcube.portlets-user.web-application-management-portlet.1-1-1
  • DONE org.gcube.portlets-user.wf-documents-portlet.1-1-0
  • DONE org.gcube.application.aquamaps.aquamapsportlet.2-8-0
  • DONE org.gcube.application.aquamaps.datamanagementfacilityportlet.1-4-0
  • DONE org.gcube.portlets-admin.runtime-resource-creator.1-1-0

upgraded libraries:

  • DONE org.gcube.portlets-user.war-management-widget.1-1-0
  • DONE org.gcube.portlets-user.GISViewer.2-0-0
  • DONE org.gcube.portlets-user.gcube-GISViewer.1-1-0
  • DONE org.gcube.application.aquamaps.enhabling.iscrawler.1-2-0
  • DONE org.gcube.messaging.accounting-portal.1-4-0
  • DONE org.gcube.messaging.consumer-library.1-5-0
  • DONE org.gcube.application.aquamaps.aquamapsservice-stubs.3-2-0
  • DONE org.gcube.common.GeoServerInterface.1-8-0

new libraries:

  • DONE species-products-discovery-stubs.1-0-0
  • DONE tree-manager-stubs-1.0.0
  • DONE tree-manager-library-1.0.0
  • DONE tree-manager-framework-1.0.0
  • DONE streams-.1.0.0
  • DONE trees-1.0.0
  • DONE common-gcore-clients-1.0.0
  • DONE common-clients-1.0.0
  • DONE org.gcube.vre-management.softwaregateway-client.1-0-0

iMarine Portal

Regarding the iMarine portal [2], only a subset of the components will be upgraded, cause the FARM VOVirtual Organization; is not going to be upgraded for the moment.


Portal upgrade

new portlets:

  • DONE org.gcube.application.aquamaps.aquamapsspeciesview.1-0-0

upgraded portlets:

  • DONE org.gcube.portlets-user.time-series-portlet.3-3-0
  • DONE org.gcube.portlets-user.codelist-management-portlet.1-1-0
  • DONE org.gcube.portlets-user.geoexplorer-portlet.1-1-0
  • DONE org.gcube.application.aquamaps.aquamapsportlet.2-8-0
  • DONE org.gcube.application.aquamaps.datamanagementfacilityportlet.1-4-0
  • DONE org.gcube.portlets-admin.resource-management-portlet.2-0-0
  • DONE org.gcube.portlets-admin.runtime-resource-creator.1-1-0

upgraded libraries:

  • DONE org.gcube.common.GeoServerInterface.1-8-0
  • DONE org.gcube.portlets-user.geoexplorer.1-1-0
  • DONE org.gcube.portlets-user.gcube-geoexplorer.1-1-0
  • DONE org.gcube.portlets-user.GISViewer.2-0-0
  • DONE org.gcube.portlets-user.gcube-GISViewer.1-1-0
  • DONE org.gcube.application.aquamaps.enhabling.iscrawler.1-2-0
  • DONE org.gcube.application.aquamaps.aquamapsservice-stubs.3-2-0

Notes

Infrastructure components released

New Services Upgraded services New Libraries Upgraded libraries New plugins
tree-manager-1.0.0 org.gcube.index-management.geoindexupdater.2-1-0 streams-1.0.0 org.gcube.messaging.accounting-portal.1-4-0 tree-repository-1.0.0
species-products-discovery.1-0-0 org.gcube.index-management.fulltextindexupdater.2-2-0 trees-1.0.0 org.gcube.messaging.consumer-library.1-5-0 obis-spd-plugin.1-0-0
org.gcube.data-transfer.agent-service.1-0-0 org.gcube.messaging.consumer.1-7-0 tree-manager-stubs-1.0.0 org.gcube.messaging.messages.1-4-0 gbif-spd-plugin.1-0-0
org.gcube.vre-management.softwaregateway.1-0-0 org.gcube.application.aquamaps.aquamapsservice.3-2-0 tree-manager-library-1.0.0 org.gcube.application.aquamaps.aquamapsservice-stubs.3-2-0 worms-spd-plugin.1-0-0
org.gcube.content-management.content-manager.2-5-0 tree-manager-framework-1.0.0 org.gcube.application.aquamaps-publisher-library.2-1-0 brazilianflora-spd-plugin.1-0-0
org.gcube.content-management.time-series.2-3-0 species-products-discovery-stubs.1-0-0 org.gcube.content-management.time-series-geo-tools.1-4-0 specieslink-spd-plugin.1-0-0
org.gcube.vre-management.ghnmanager.1-5-0 org.gcube.data-transfer.agent-library.1-0-0 org.gcube.content-management.geo-utils-custom.1.2.0
org.gcube.vre-management.deployer.2-3-0 org.gcube.data-transfer.agent-stubs.1-0-0 org.gcube.content-management.codelist-manager.1-2-0
org.gcube.vre-management.resourcemanager.1-1-0 org.gcube.data-transfer.common.1-0-0 org.gcube.vre-management.ghnmanager-stubs.1-5-0
org.gcube.vre-management.vremodeler.1-6-2 org.gcube.content-management.storage-manager-core.1-0-0 org.gcube.vre-management.deployer-stubs.2-3-0
org.gcube.information-system.glite-bridge.1-0-3 org.gcube.content-management.storage-manager-wrapper.1-0-0 org.gcube.vre-management.resourcemanager-stubs.1-1-0
org.gcube.execution.WorkflowEngineService.1-2-1 org.gcube.vre-management.softwaregateway-stubs.1-0-0 gcf.1-4-0
org.gcube.data-transformation.data-transformation.2-2-0 org.gcube.vre-management.softwaregateway-client.1-0-0 org.gcube.common.utils.encryption.1-0-1
common-clients-1.0.0 org.gcube.common.TSDBInterface.1-3-0
common-gcore-clients-1.0.0 org.gcube.common.TSPostgresImplementation.1-3-0
org.gcube.common.tapir-parser.1-0-0 org.gcube.common.GeoServerInterface.1-8-0
org.gcube.data-analysis.ruserservice.1.0.0 org.gcube.information-system.is-publisher.2-2-0
org.gcube.execution.gRS2Broker.1-0-0 org.gcube.data-analysis.ecological-engine.1-2-0
org.gcube.execution.WorkflowDTSAdaptor.1-0-0 org.gcube.execution.MadgikCommons.1-1-0
org.gcube.execution.gRS2.1-3-0
org.gcube.execution.gRSBridge.1-2-0
org.gcube.execution.InformationSystem.1-3-0
org.gcube.execution.EnvironmentProvider.1-2-0
org.gcube.execution.GCubeEnvironmentProvider.1-3-0
org.gcube.execution.Environment-servicearchive.1-3-0
org.gcube.execution.ExecutionEngine.1-1-5
org.gcube.execution.WorkflowEngine.1-2-1
org.gcube.execution.WorkflowEngineService.Stubs.1-2-1
org.gcube.execution.WorkflowEngineServiceClient.1-2-1
org.gcube.data-transformation.data-transformation-handlers.2-3-0
org.gcube.data-transformation.data-transformation-library.2-0-0
org.gcube.data-transformation.data-transformation-programs.1-3-2
org.gcube.data-transformation.data-transformation-stubs.2-2-0

Portal components released

New Libraries Upgraded libraries New portlets Upgraded portlets
org.gcube.application-support-layer-http-access-management.1-0-0 org.gcube.application-support-layer.application-support-layer-content.4-1-1 org.gcube.portlets-user.species-discovery.1-0-0 org.gcube.portlets-admin.resource-management-portlet.2-0-0
org.gcube.application-support-layer.application-support-layer-http-infrastructure-login.1-0-0 org.gcube.application-support-layer.application-support-layer-core.3-1-2 org.gcube.application.aquamaps.aquamapsspeciesview.1-0-0 org.gcube.messaging.accounting-portlet.1-6-0
org.gcube.portlets-user.home-library-jcr.1-0-0 org.gcube.application-support-layer.application-support-layer-http.4-1-3 org.gcube.messaging.monitoring-portlet.1-2-0
species-products-discovery-stubs.1-0-0 org.gcube.portlets-user.home-library.4-0-0 org.gcube.messaging.node-accounting-portlet.1-4-0
tree-manager-stubs-1.0.0 org.gcube.portlets-user.war-management-widget.1-1-0 org.gcube.portlets-user.template-generator.3-4-0
tree-manager-library-1.0.0 org.gcube.portlets-user.workspace-portlet-lighttree.2-6-0 org.gcube.portlets-user.report-generator-portlet.3-4-0
tree-manager-framework-1.0.0 org.gcube.portlets-user.GISViewer.2-0-0 org.gcube.portlets-user.results-portlet.4-4-0
streams-.1.0.0 org.gcube.portlets-user.gcube-GISViewer.1-1-0 org.gcube.portlets-user.time-series-portlet.3-3-0
trees-1.0.0 org.gcube.application.aquamaps.enhabling.iscrawler.1-2-0 org.gcube.portlets-user.codelist-management-portlet.1-1-0
common-gcore-clients-1.0.0 org.gcube.portlets-user.workspace-portlet-tree.5-0-0 org.gcube.portlets-user.geoexplorer.1-1-0
common-clients-1.0.0 org.gcube.portal.custom-portal-handler.1-1-0 org.gcube.portlets-user.gcube-geoexplorer.1-1-0
org.gcube.vre-management.softwaregateway-client.1-0-0 org.gcube.messaging.accounting-portal.1-4-0 org.gcube.portlets-user.geoexplorer-portlet.1-1-0
org.gcube.messaging.consumer-library.1-5-0 org.gcube.portlets-user.workspace-portlet.5-0-0
org.gcube.application.aquamaps.aquamapsservice-stubs.3-2-0 org.gcube.portlets-user.war-management-portlet.1-1-1
org.gcube.portlets-user.web-application-management-portlet.1-1-1
org.gcube.portlets-user.gcube-loggedin-portlet.1-6-0
org.gcube.portlets-user.wf-documents-portlet.1-1-0
org.gcube.application.aquamaps.aquamapsportlet.2-8-0
org.gcube.application.aquamaps.datamanagementfacilityportlet.1-4-0
org.gcube.portlets-admin.runtime-resource-creator.1-1-0
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