EuBrazilOpenBIO VO 2.17.0

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gHN Upgrade Instructions

The upgrade to the latest version of GHNgCube Hosting Node. (v 3.8.1) and gCube (2.17.0) requires Site Manager to apply the following upgrade instructions

Clean and upgrade

  • Clean and upgrade to GHNgCube Hosting Node. v 3.8.1 using the following instructions
  • upgrade to GHNgCube Hosting Node. v 3.8.1 using the following instructions

EUBrazilOpenBio VOVirtual Organization;

GHNs

GHNgCube Hosting Node. to upgrade following this instructions: ( NOTE not mandatory upgrade)

  • geoserver.d4science.org:9000
  • geoserver2.d4science.org:9000
  • geoserver3.d4science.org:9000
  • geoserver4.d4science.org:9000
  • node77.p.d4science.research-infrastructures.eu:8080
  • DONE node34.p.d4science.research-infrastructures.eu:8080

GHNgCube Hosting Node. to clean following this instructions:

  • DONE db2.p.d4science.research-infrastructures.eu:8080
  • DONE node8.p.d4science.research-infrastructures.eu:8000
  • DONE node12.p.d4science.research-infrastructures.eu:8080
  • DONE node16.p.d4science.research-infrastructures.eu:8080
  • DONE node19.p.d4science.research-infrastructures.eu:8080
  • DONE node21.p.d4science.research-infrastructures.eu:8080
  • (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

new GHNgCube Hosting Node. to install:

  • DONE (CNR) node24.d4science.org:8080

Service Deployment

  • DONE db2.p.d4science.research-infrastructures.eu:8080 : deploy SM, install VOVirtual Organization; keys
  • DONE node8.p.d4science.research-infrastructures.eu:8000 : deploy VREModeler
  • DONE node12.p.d4science.research-infrastructures.eu:8080 : deploy Personalization
  • DONE node16.p.d4science.research-infrastructures.eu:8080 : deploy DataTransformation,ExecutionEngine
  • DONE node19.p.d4science.research-infrastructures.eu:8080 : deploy CouchBase, FWIndex
  • DONE node21.p.d4science.research-infrastructures.eu:8080 : deploy FTIndex
  • DONE node34.p.d4science.research-infrastructures.eu:8080 : updrade OAI-TM plugin
  • DONE node24.d4science.org:8080 : deploy Search , ExecutionEngine ( add ghn to SpeciesLab scope)

Portal

GHNgCube Hosting Node. upgrade

  • upgrade to GHNgCube Hosting Node. v 3.8.1 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 under artifact-downloader folder

./ArtifactDownloader ./2.17.0/list_components  http://grids16.eng.it/BuildReport/bdownload/Recent_Builds/org.gcube.2-17-0/latest/reports/org.gcube-org.gcube.2-17-0-tar.gz.txt ./artifacts http://grids16.eng.it/BuildReport/bdownload/Recent_Builds/org.gcube.2-17-0/latest

Portlets

to Upgrade:

  • org.gcube.messaging.accounting-portlet.1-9-0
  • org.gcube.messaging.node-accounting-portlet.1-5-0
  • org.gcube.data-transfer.storagemanager-portlet.1-1-0
  • org.gcube.portlets-admin.collection-explorer.2-0-0
  • org.gcube.portlets-admin.collections-viewer.2-1-0
  • org.gcube.portlets-admin.resource-management-portlet.5-1-0
  • org.gcube.portlets-admin.runtime-resource-creator.1-4-0
  • org.gcube.portlets-admin.vre-definition.4-1-0
  • org.gcube.portlets-admin.vre-deployer.3-0-0
  • org.gcube.portlets-admin.vre-manager.5-0-0
  • org.gcube.portlets-admin.users-management-portlet.1-9-0
  • org.gcube.portlets-admin.search-manager-portlet.1-5-0
  • org.gcube.portlets-admin.roles-management-portlet.1-6-0
  • org.gcube.portlets-admin.ir-bootstrapper-portlet.2-4-0
  • org.gcube.portlets-admin.fwd-index-management-portlet.2-1-0
  • org.gcube.portlets-admin.ft-index-management-portlet.2-2-0
  • org.gcube.portlets-admin.information-space-editor-portlet.2-5-0
  • org.gcube.portlets-user.geoexplorer-portlet.2-4-0
  • org.gcube.portlets-user.workspace-portlet.6-5-0
  • org.gcube.portlets-user.messages.0-4-0
  • org.gcube.portlets-user.species-discovery.3-5-0
  • org.gcube.portlets-user.xsearch-portlet.1-1-1
  • org.gcube.portlets-user.statistical-manager-portlet.1-2-3
  • org.gcube.portlets-user.gcube-loggedin-portlet.2-2-0
  • org.gcube.portlets-user.gcube-login-portlet.2-0-0
  • org.gcube.portlets-user.join-new-environment.1-3-0
  • org.gcube.portlets-user.newsfeed.1-4-0
  • org.gcube.portlets-user.notifications.1-0-0
  • org.gcube.portlets-user.socialprofile.0-3-0
  • org.gcube.portlets-user.collections-navigator-portlet.2-1-0
  • org.gcube.portlets-user.search-portlet.3-2-0
  • org.gcube.portlets-user.results-portlet.5-3-0
  • org.gcube.portlets-user.user-profile-portlet-new.1-6-0
  • org.gcube.portlets-user.occurrence-management.2-0-0
  • org.gcube.portlets-user.shareupdates-1-0-0
  • org.gcube.portlets-user.myvres.1-0-0
  • ENM portlet (from Eric)
  • Cross mapping (from Eric)

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

new portlet:

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


to remove cause replaced by mavenized version

  • RuntimeResourceCreator-portlet
  • CollectionExplorer
  • CollectionsNavigatorPortlet
  • GCubeLogin
  • nodeaccountingui
  • OccurrenceManagement
  • InformationSpaceEditor
  • UserProfileEditingPortlet

Servlets

servlet to install uner $CATALINA_HOME/webapp

  • org.gcube.application-support-layer.application-support-layer-http-information-retrieval.1-4-0
  • org.gcube.application-support-layer.application-support-layer-http-content-access.1-2-0
  • org.gcube.application-support-layer.application-support-layer-http-infrastructure-login.1-1-0
  • org.gcube.application-support-layer-http-access-management.1-1-0

Libraries

DONE Libraries to upgrade/install under $GLOBUS_LOCATION/lib/_ext

  • org.gcube.portal.portal-manager.1-0-0
  • org.gcube.portal.custom-portal-handler.1-3-0
  • org.gcube.vre-management.resourcemanager-client.1-0-0
  • org.gcube.vre-management.vremodeler-client-library.1-0-0
  • org.gcube.search.opensearchdatasource-client-library.1-0-0
  • org.gcube.vre-management.ghnmanager-client.1-0-0
  • org.gcube.search.search-client-library.1-0-1
  • org.gcube.portlets-widgets.application-news-widget.1-3-0
  • org.gcube.portlets-widgets.guided-tour-widget.1-4-0
  • org.gcube.portlets-widgets.pickuser-widget.0-4-0 NOT NEEDED In the context
  • org.gcube.portlets-widgets.report-exporter-widget.1-1-0 NOT NEEDED In the context
  • org.gcube.portlets-widgets.switch-button-widget.1-0-0 NOT NEEDED In the context
  • org.gcube.portlets-widgets.user-selection-dialog.1-0-0 NOT NEEDED In the context
  • org.gcube.portlets-widgets.wsmail-widget.1-4-0 NOT NEEDED In the context
  • org.gcube.portlets-admin.software-upload-wizard.1-2-0 NOT NEEDED In the context
  • org.gcube.portlets-admin.resource-sweeper.2-0-0 NOT NEEDED In the context
  • org.gcube.portlets-admin.ishealth-monitor.1-1-0 NOT NEEDED In the context
  • org.gcube.portlets-admin.rmp-common-library.2-0-0 NOT NEEDED In the context
  • org.gcube.portlets-admin.activation-record-widget.1-2-0 NOT NEEDED In the context
  • org.gcube.data-analysis.ecological-engine-external-algorithms.1.1.1
  • org.gcube.data-analysis.ecological-geospatial-extensions.1.1.0 NOT FOUND
  • org.gcube.data-analysis.statistical-manager-cl.1.1.3
  • org.gcube.portlets-user.GISViewer.3-3-0
  • org.gcube.portlets-user.gcube-GISViewer.2-1-0
  • org.gcube.portlets-user.geoexplorer.2-5-0
  • org.gcube.portlets-user.gcube-geoexplorer.2-5-0
  • gis-interface.2-0-1
  • geonetwork.2-0-1
  • org.gcube.portlets-user.gcube-widgets-library.1-7-0 NOT NEEDED Build Time Solo
  • org.gcube.portlets-user.csv-import-wizard.1-2-0
  • occurrence-reconciliation.2-0-0
  • org.gcube.index-management.forwardindexnode-client-library.1-2-0
  • org.gcube.index-management.fulltextindexnode-client-library.1-2-0
  • org.gcube.data-transformation.data-transformation-client-library.3-0-0 NOT FOUND
  • org.gcube.execution.RRPlugins.1-0-2
  • org.gcube.execution.RRModel.1-5-0
  • org.gcube.execution.RRGCubeBridge.1-5-0
  • org.gcube.execution.ResourceRegistry.1-4-0 NOT FOUND
  • org.gcube.execution.rrconfprovider-portal.1-0-0 (from Maven) DONE OK
  • common-clients-2.1.0
  • common-gcore-clients-2.2.0
  • common-fw-clients-1.1.0
  • org.gcube.messaging.consumer-library.2-1-0
  • spd-client-library.3-1-1
  • org.gcube.content-management.storage-resource-link-plugin.1-1-0
  • org.gcube.content-management.storage-manager-core.2.0.3
  • org.gcube.vre-management.vremodeler-utils.1-0-0
  • org.gcube.portlets-user.csv-import-wizard-workspace-extension.1-2-0 (from Maven)
  • org.gcube.data-analysis.statistical-manager-stubs.1-1-4

DONE Libraries to be upgraded under $GLOBUS_LOCATION/lib/

  • registry-publisher-1.2.1


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

  • org.gcube.portal.social-networking-library.1-4-0


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

  • org.gcube.common.home-library.1-0-0
  • org.gcube.common.home-library-jcr.1-0-0
  • org.gcube.portlets-user.workspace-application-handler.1-1-0
  • org.gcube.portlets-user.workspace-portlet-tree.6-5-0
  • org.gucbe.portlets-widgets.workspace-light-tree.2-13-0


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

  • org.gcube.application-support-layer.application-support-layer-core.4-0-0
  • org.gcube.application-support-layer.application-support-layer-search.5-0-0
  • org.gcube.application-support-layer.application-support-layer-content.6-0-0
  • org.gcube.application-support-layer.gcube-search-library.1-2-0
  • org.gcube.application-support-layer.social.0-7-1
  • org.gcube.application-support-layer.application-support-layer-vremanagement.5-0-0
  • org.gcube.application-support-layer.application-support-layer-userprofile.4-0-0


DONE Libraries to remove from GLOBUS_LOCATION/lib/_ext

  • org.gcube.tools.sam.reports.jar
  • org.gcube.application.aquamaps.aquamapsservice-stubs
  • org.gcube.application-support-layer.application-support-layer-oai_ore
  • org.gcube.indexmanagement.fulltextindexlookup.stubs.jar
  • org.gcube.personalization.profileadministration.stubs.jar
  • org.gcube.personalization.userprofileaccess.stubs.jar
  • profileadministration-stubs-2.0.0-2.15.0.jar
  • searchsystemservice-stubs-2.0.3-2.12.0.jar
  • tree-manager-stubs-3.0.0-2.12.0.jar
  • userprofileaccess-stubs-3.0.0-2.15.0.jar
  • vremodeler-stubs-2.0.1-2.12.0.jar
  • opensearchdatasource-stubs-1.6.2-2.15.0.jar
  • data-transformation-service-stubs-2.2.3-2.12.0.jar


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

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

DONE Libraries to remove from $GLOBUS_LOCATION/lib/_home-library

  • org.gcube.portlets-user.home-library
  • org.gcube.portlets-user.home-library-jcr


DONE External components:

  • gwt-fix-2.5.1-gxt2.jar
  • gwt-servlet-deps.jar
  • gwt-servlet.jar
  • gwt-user-2.5.1.jar NOT DONE

Configuration

  • the infrastructure.properties file should be created under $CATALINA_HOME/conf :

for EUBrazilOpenBio portal the content should be 

infrastructure=d4science.research-infrastructures.eu
scopes=EUBrazilOpenBio


  • symmetric keys for d4science.research-infrastructures.eu scope and EUBrazilOpenBio should be installed under $GLOBUS_LOCATION , they can be downloaded from http://goo.gl/EKDwqd
  • The ResourceRegistry property files bundle have to be downloaded from [1] and unpacked under the $GLOBUS_LOCATION/lib/_ext folder
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