EuBrazilOpenBIO VO 2.16.0

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gHN Upgrade Instructions

The upgrade to the latest version of GHNgCube Hosting Node. (v 3.8.0) and gCube (2.16.0) requires Site Manager to apply the following upgrade instructions

Clean and upgrade

  • Clean and upgrade to GHNgCube Hosting Node. v 3.8.0 using the following instructions
  • upgrade to GHNgCube Hosting Node. v 3.8.0 using the following instructions

EUBrazilOpenBio VOVirtual Organization;

GHNs

GHNgCube Hosting Node. to upgrade following this instructions:

  • (CNR) db2.p.d4science.research-infrastructures.eu:8080
  • (CNR) geoserver.d4science-ii.research-infrastructures.eu:9000
  • (CNR) geoserver2.d4science.research-infrastructures.eu:9000
  • (CNR) geoserver3.d4science.research-infrastructures.eu:9000
  • (CNR) geoserver4.d4science.research-infrastructures.eu:9000
  • (UPV) gcube01.i3m.upv.es:8080
  • (UPV) gcube01.i3m.upv.es:8081
  • (UPV) gcube01.i3m.upv.es:8082
  • (UPV) gcube01.i3m.upv.es:8083
  • (UPV) gcube02.i3m.upv.es:8080
  • (UPV) gcube02.i3m.upv.es:8081
  • (UPV) gcube02.i3m.upv.es:8082
  • (UPV) gcube02.i3m.upv.es:8083
  • (UPV) gcube03.i3m.upv.es:8080
  • (UPV) gcube03.i3m.upv.es:8081
  • (UPV) gcube03.i3m.upv.es:8082
  • (UPV) gcube03.i3m.upv.es:8083
  • (UPV) gcube04.i3m.upv.es:8080
  • (UPV) gcube04.i3m.upv.es:8081
  • (UPV) gcube04.i3m.upv.es:8082
  • (UPV) gcube04.i3m.upv.es:8083
  • (UPV) gcube05.i3m.upv.es:8080
  • (UPV) gcube05.i3m.upv.es:8081
  • (UPV) gcube05.i3m.upv.es:8082
  • (UPV) gcube05.i3m.upv.es:8083
  • (UFF) sn10.ic.uff.br:8080

GHNgCube Hosting Node. to clean following this instructions:

  • (CNR) node8.p.d4science.research-infrastructures.eu:8000
  • (CNR) node12.p.d4science.research-infrastructures.eu:8080
  • (CNR) node16.p.d4science.research-infrastructures.eu:8080
  • (CNR) node19.p.d4science.research-infrastructures.eu:8080
  • (CNR) node21.p.d4science.research-infrastructures.eu:8080
  • (CNR) node34.p.d4science.research-infrastructures.eu:8080
  • (CNR) node77.p.d4science.research-infrastructures.eu:8080

Service Deployment

  • (CNR) db2.p.d4science.research-infrastructures.eu:8080 : upgrade EcologicalModeling
  • (CNR) node8.p.d4science.research-infrastructures.eu:8000 : deploy VREModeler, Personalization
  • (CNR) node16.p.d4science.research-infrastructures.eu:8080 : deploy DataTransformation,ExecutionEngine
  • (CNR) node19.p.d4science.research-infrastructures.eu:8080 : deploy CouchBase, FWIndex
  • (CNR) node21.p.d4science.research-infrastructures.eu:8080 : deploy FTIndex
  • (CNR) node34.p.d4science.research-infrastructures.eu:8080 : deploy TM and plugins
  • (CNR) node77.p.d4science.research-infrastructures.eu:8080 ; deploy SPD and plugins

Portal

GHNgCube Hosting Node. upgrade

  • upgrade to GHNgCube Hosting Node. v 3.8.0 using the following instructions

Components installation

Artifact can be downloaded using the following instructions:

  • Install Artifact dowloaded tool
svn export  https://svn.d4science.research-infrastructures.eu/gcube/trunk/tools/artifact-downloader/
  • run the client as follows
mkdir artifacts

./ArtifactDownloader ./2.16.0/list_components  http://grids16.eng.it/BuildReport/bdownload/Recent_Builds/org.gcube.2-16-0/latest/reports/org.gcube-org.gcube.2-16-0-tar.gz.txt./artifacts http://grids16.eng.it/BuildReport/bdownload/Recent_Builds/org.gcube.2-16-0/latest

Portlets

to Upgrade:

  • org.gcube.data-transfer.scheduler-portlet.2-0-0
  • org.gcube.portlets-admin.ir-bootstrapper-portlet.2-3-0
  • org.gcube.portlets-admin.users-management-portlet.1-8-2
  • org.gcube.portlets-admin.collection-explorer.1-6-0
  • org.gcube.portlets-admin.collections-viewer.2-0-0
  • org.gcube.portlets-user.geoexplorer-portlet.2-2-0
  • org.gcube.portlets-user.workspace-portlet.6-3-0
  • org.gcube.portlets-user.messages.0-3-0
  • org.gcube.portlets-user.species-discovery.3-3-0
  • org.gcube.portlets-user.xsearch-portlet.1-1-0
  • org.gcube.portlets-user.search-portlet.3-1-0
  • org.gcube.portlets-user.results-portlet.5-2-0
  • org.gcube.portlets-user.shareupdates.0-5-0
  • org.gcube.portlets-user.notifications.0-4-0
  • org.gcube.portlets-user.newsfeed-1-1-0
  • org.gcube.application.aquamaps.aquamapsportlet.3-0-2
  • org.gcube.application.aquamaps.aquamapsspeciesview.1-2-2
  • org.gcube.application.aquamaps.datamanagementfacilityportlet.1-6-2
  • org.gcube.portlets-user.report-generator-portlet.4-4-0
  • org.gcube.portlets-user.template-creator.4-4-0
  • org.gcube.portlets-user.time-series-portlet.3-4-2
  • org.gcube.portlets-admin.wf-roles-editor.1-3-0
  • org.gcube.portlets-user.socialprofile.0-2-0
  • org.gcube.portlets-admin.information-space-editor-portlet.2-4-0
  • org.gcube.portlets-user.join-new-environment-1-2-0

Given the name changes, layouts must also be revised to add the new portlet

new portlet:

  • org.gcube.portlets-user.trendylyzer-portlet.1-0-0

to remove:

  • Task-manager
  • Datatransformation-admin-portlet
  • geo-index-management-portlet
  • AnnotationsPortlet
  • VREVirtual Research Environment.-Deployer
  • ContentViewerPortlet
  • applicationSupportLayerHttp

the following portlet need also to be reinstalled because of changes on workspace-light-tree

  • org.gcube.portlets-user.codelist-management-portlet
  • org.gcube.portlets-admin.wf-docs-manager
  • org.gcube.portlets-user.occurrence-management


Openbio specific portlets:

  • ENM portlet
  • Cross Mapping

Libraries

Libraries to be upgraded under $GLOBUS_LOCATION/lib/_ext

  • org.gcube.data-analysis.ecological-engine.1.7.0
  • org.gcube.common.GeoServerInterface.1-10-2
  • org.gcube.data-transfer.agent-library.2-0-0
  • org.gcube.data-transfer.scheduler-library.2-0-0
  • org.gcube.data-transfer.common.2-0-0
  • org.gcube.execution.RRModel.1-4-1
  • org.gcube.execution.ResourceRegistry.1-3-5
  • org.gcube.content-management.storage-manager-wrapper.2.0.2
  • org.gcube.content-management.storage-manager-core.2.0.2
  • org.gcube.portlets-user.GISViewer.3-1-1
  • org.gcube.portlets-user.geoexplorer.2-3-0
  • org.gcube.portlets-user.gcube-geoexplorer.2-3-0
  • org.gcube.portlets-user.wsmail-widget.1-2-0
  • org.gcube.application.aquamaps.aquamapsservice-cl.2-0-0
  • org.gcube.application.aquamaps.aquamapsservice-stubs.4-2-0
  • org.gcube.index-management.forwardindexnode-stubs
  • org.gcube.index-management.fulltextindexnode-stubs
  • spd-client-library.3-1-0
  • spd-model-library.2-1-0
  • spd-plugin-framework.2-3-0
  • spql-parser.2-1-0


Libraries to be upgraded under $GLOBUS_LOCATION/lib/_social-library/

  • org.gcube.portal.social-networking-library.1-3-0


Libraries to be upgraded under $GLOBUS_LOCATION/lib/_home-library

  • org.gcube.portlets-user.home-library.4-6-0
  • org.gcube.portlets-user.home-library-jcr.1-6-0
  • org.gcube.portlets-user.workspace-portlet-tree.6-3-0
  • org.gcube.portlets-user.workspace-portlet-lighttree.2-10-0

Libraries to be upgraded under $GLOBUS_LOCATION/lib/_application-support-layer

  • org.gcube.application-support-layer.application-support-layer-oai_ore.1-1-0
  • org.gcube.application-support-layer.application-support-layer-core.3-4-0
  • org.gcube.application-support-layer.application-support-layer-search.4-1-0
  • org.gcube.application-support-layer.application-support-layer-content.5-1-0
  • org.gcube.application-support-layer.social.0-5-0

libs to remove from GLOBUS_LOCATION/lib/ext

  • org.gcube.dir.master.stubs.jar
  • org.gcube.indexmanagement.forwardindexlookup.stubs.jar
  • org.gcube.indexmanagement.forwardindexmanagement.stubs.jar
  • org.gcube.indexmanagement.forwardindexupdater.stubs.jar
  • org.gcube.indexmanagement.fulltextindexmanagement.stubs.jar
  • org.gcube.indexmanagement.fulltextindexupdater.stubs.jar
  • org.gcube.indexmanagement.geoindexlookup.stubs.jar
  • org.gcube.indexmanagement.geoindexmanagement.stubs.jar
  • org.gcube.indexmanagement.geoindexupdater.stubs.jar
  • org.gcube.indexmanagement.incrementalindexupdater.stubs.jar
  • org.gcube.contentmanagement.storagelayer.storagemanagementservice.stubs.jar
  • viewmanager-stubs-1.1.0-2.13.0.jar
  • gcubedocumentlibrary-2.1.0-2.13.0.jar
  • gcubemodellibrary-2.1.1-2.13.0.jar
  • contentmanagementlibrary-1.7.0-2.13.0.jar
  • contentmanager-stubs-2.4.0-2.13.0.jar
  • iscrawler-1.5.0-2.14.0.jar

Libraries to remove from $GLOBUS_LOCATION/lib/_application-support-layer

  • org.gcube.application-support-layer.application-support-layer-storagemanagement

External components:

  • nekohtml-1.9.6.2.jar

Configuration

  • ASL Search requires a new configuration file : $CARTALINA_HOME/conf/excluded_fields.properties
  • containing : excluded_browsable_field_names=gDocCollectionLang,gDocCollectionID
  • New configuration for mail notifications to be included in the file: $CATALINA_HOME/conf/gcube-data.properties
    • for iMarine portal : portalinstancename=iMarine Gateway
    • for D4ScienceAn e-Infrastructure operated by the D4Science.org initiative..org portal : portalinstancename=D4ScienceAn e-Infrastructure operated by the D4Science.org initiative..org Gateway

The following tabs should be removed from the layouts:

  • GeoIndex
  • DataTransformation
  • Annotation ( hidden)
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