Upgrade Plan 212 Portals

Portals (CNR) 20/02/2012

Both iMarine portal ( portal.i-marine.d4science.org) and the d4science.org portal (portal.d4science.org) need to be upgraded.
Packages have be downloaded from the BTRT instance@ENG http://grids16.eng.it/BuildReport/browse/Recent_Builds/org.gcube.2-12-0

Installation

The new version of the portal is going to include all the new Social components that have been integrated in gCube 2.12.

The installation of the social components should be perform as follows:

https://gcube.wiki.gcube-system.org/gcube/index.php/Social_Portal_Extension_Setup (DONE)

Portlet installation

The following portlet need to be installed: (DONE)

org.gcube.messaging.accounting-portlet.1-7-0
org.gcube.messaging.node-accounting-portlet.1-4-0
org.gcube.application.aquamaps.aquamapsportlet.3-0-0
org.gcube.application.aquamaps.aquamapsspeciesview.1-2-0
org.gcube.application.aquamaps.datamanagementfacilityportlet.1-6-0
org.gcube.portlets-user.report-generator-portlet.3-5-0
org.gcube.portlets-user.template-creator.3-5-0
org.gcube.portlets-user.wf-documents-portlet.1-3-0
org.gcube.portlets-user.statistical-manager-portlet.1-1-0
org.gcube.portlets-user.web-application-management-portlet.1-3-0
org.gcube.portlets-user.species-discovery.2-3-0
org.gcube.portlets-user.search-portlet.2-5-1 ( to configure semantic search scopes)
org.gcube.portlets-user.collections-navigator-portlet.1-8-1
org.gcube.portlets-user.user-profile-portlet-new.1-4-0
org.gcube.portlets-user.annotation-front-end-v2.2-3-0-1
org.gcube.portlets-user.content-viewer-portlet.1-7-1-2
org.gcube.portlets-user.results-portlet.4-4-0
org.gcube.portlets-user.time-series-portlet.3-4-0
org.gcube.tools.sam-portlet.1-2-0
org.gcube.portlets-user.codelist-management-portlet.1-2-0
org.gcube.portlets-admin.ir-bootstrapper-portlet.2-0-0
org.gcube.portlets-admin.vre-deployment.3-3-0
org.gcube.portlets-admin.vre-definition.3-6-0
org.gcube.portlets-admin.vre-deployer.1-5-0
org.gcube.portlets-admin.wf-templates-editor.1-1-0
org.gcube.portlets-admin.wf-roles-editor.1-2-0
org.gcube.portlets-admin.collection-explorer.1-5-0
org.gcube.portlets-admin.wf-docs-manager.1-4-0
org.gcube.portlets-admin.runtime-resource-creator.1-1-1
org.gcube.portlets-admin.collections-viewer.1-5-0
org.gcube.portlets-admin.data-transformation-admin-portlet.1-3-1
org.gcube.portlets-admin.ft-index-management-portlet.1-5-0
org.gcube.portlets-admin.fwd-index-management-portlet.1-4-0
org.gcube.portlets-admin.geo-index-management-portlet.1-4-0
org.gcube.portlets-admin.information-space-editor-portlet.2-2-3
org.gcube.portlets-admin.profile-administration-portlet.1-4-0
org.gcube.portlets-admin.search-manager-portlet.1-4-0
org.gcube.portlets-user.geoexplorer-portlet.1-2-2
org.gcube.portlets-user.occurrence-management.1-1-0
org.gcube.portlets-user.time-series-charts-portlet.1-5-0
org.gcube.portlets-user.xsearch-portlet.1-0-1 ( to configure to point to Xearch -Service in production) ( check previous conf)

Libraries installation

Libraries to be deployed under $GLOBUS_LOCATION/lib/_ext (DONE)

occurrence-reconciliation.1-0-1
org.gcube.common.GeoServerInterface.1-9-3-1
org.gcube.content-management.codelist-manager.1-3-1
org.gcube.content-management.storage-manager-core.1-0-2
org.gcube.content-management.storage-manager-wrapper.1-0-2
org.gcube.content-management.storage-resource-link-plugin.1-0-0
org.gcube.content-management.time-series-geo-tools.1.6.1
org.gcube.data-analysis.ecological-engine.1.6.0
org.gcube.data-transformation.data-transformation-handlers.2-4-1
org.gcube.execution.RRGCubePlugins.1-0-0-1
org.gcube.execution.ResourceRegistry.1-3-3
org.gcube.execution.RRGCubeBridge.1-4-0
org.gcube.execution.RRModel.1-4-0
org.gcube.execution.RRPlugins.1-0-1
org.gcube.execution.resourceregistry-configuration-portal.1-0-0
org.gcube.portlets-user.gcube-widgets-library.1-4-0
spql-parser.1-0-0-1
org.gcube.common.ts-charts-datamodel.1-1-0-1
org.gcube.content-management.content-manager-library.2-4-0-1
org.gcube.content-management.gcube-document-library.2-1-0-1
org.gcube.content-management.gcube-model-library.2-1-1-1
org.gcube.content-management.time-series-lexical-matcher.1-2-0-1
org.gcube.content-management.view-manager-stubs.1-1-0-1
org.gcube.dir.master-stubs.1-1-0
org.gcube.index-management.forwardindexlookup-stubs.3-0-0
org.gcube.index-management.forwardindexmanagement-stubs.3-0-0
org.gcube.index-management.forwardindexupdater-stubs.3-0-0
org.gcube.index-management.fulltextindexlookup-stubs.2-1-0
org.gcube.index-management.fulltextindexmanagement-stubs.2-1-0
org.gcube.index-management.fulltextindexupdater-stubs.2-1-0
org.gcube.index-management.geoindexlookup-stubs.2-0-0
org.gcube.index-management.geoindexmanagement-stubs.2-0-0
org.gcube.index-management.geoindexupdater-stubs.2-0-0
org.gcube.index-management.incrementalindexupdater-stubs.1-0-0
org.gcube.information-system.is-cache.1-2-0-1
org.gcube.personalisation.profileadministration-stubs.1-1-0
org.gcube.personalisation.userprofileaccess-stubs.2-1-0
org.gcube.tools.sam-reports.1-1-0
common-clients-2.0.1
common-fw-clients-1.0.0
common-gcore-clients-2.1.0
common-gcore-resources-1.0.0
common-gcore-stubs-1.0.0
discovery-client-1.0.0
org.gcube.application.aquamaps.aquamapsservice-cl.1-0-0
org.gcube.application.aquamaps.aquamapsservice-stubs.4-0-0
org.gcube.application.aquamaps.enhabling.iscrawler.1-4-0
org.gcube.content-management.time-series-stubs.2-4-1
org.gcube.content-management.timeseries-client-library.1-0-0-1
org.gcube.data-analysis.statistical-manager-cl.1.1.0
org.gcube.data-analysis.statistical-manager-stubs.1.1.0
org.gcube.data-transfer.agent-library.1-2-0
org.gcube.data-transformation.data-transformation-stubs.2-2-3
org.gcube.messaging.accounting-portal.1-5-0
org.gcube.messaging.consumer-library.1-6-0
org.gcube.messaging.consumer-stubs.1-8-0
org.gcube.portlets-admin.bdwm-support-library.1-1-0
org.gcube.portlets-user.GISViewer.2-1-3
org.gcube.portlets-user.codelist-interface.1-0-0
org.gcube.portlets-user.codelist-library.1-1-0
org.gcube.portlets-user.csv-import-wizard-workspace-extension.1-0-0
org.gcube.portlets-user.csv-import-wizard.1-0-0
org.gcube.portlets-user.d4Science-reporting-library.2-0-0
org.gcube.portlets-user.gcube-GISViewer.1-2-1
org.gcube.portlets-user.gcube-geoexplorer.1-2-1
org.gcube.portlets-user.geoexplorer.1-2-3
org.gcube.portlets-user.guidedtour-widget.1-1-0
org.gcube.portlets-user.tabular-data-widget.1-1-0
org.gcube.search.G_CQLParser.1-1-0
org.gcube.search.opensearchdatasource-stubs.1-6-1
rg.gcube.search.searchsystemservice-stubs.2-0-3
org.gcube.vo-management.usermanagement-stubs.1-0-0-1
org.gcube.vre-management.softwaregateway-client.1-0-1-1
tree-manager-framework-3.0.0
tree-manager-library-3.0.0
tree-manager-stubs-3.0.0
trees-1.4.0
spd-client-library.2-0-0
streams-2.0.1
org.gcube.vre-management.vremodeler-stubs.2-0-1
spd-plugin-framework.2-0-0
ic-client-1.0.0
org.gcube.vo-management.voms-api.3-5-0
org.gcube.vo-management.voms-admin-stubs.2-0-0-1

Third Party libraries installation

Libraries to be deployed under $GLOBUS_LOCATION/lib/_ext: (DONE)

ormlite-core-4.40.jar
ormlite-jdbc-4.40.jar
commons-net-2.0.jar
datanucleus-api-jdo.jar
datanucleus-cache.jar
datanucleus-enhancer.jar
datanucleus-javaxtime.jar
datanucleus-jdo-query.jar
datanucleus-ldap.jar
datanucleus-management.jar
datanucleus-rdbms.jar
ij140g.jar
iText-2.1.4.jar
javassist-3.12.1.GA.jar
jdo-api.jar
jta.jar
mime-util-2.1.2.jar
objenesis-1.2.jar
jsr107cache-1.0.jar
jsr305-1.3.9.jar
mockito-all-1.8.5.jar
mongo-java-driver-2.6.2.jar
mysql-connector-java-5.1.21-bin.jar
objenesis-1.2.jar
xmlpull-1.1.3.1.jar
json-lib-2.4-jdk15.jar
ezmorph-1.0.6.jar

Configuration

The emptySessionPath="true" parameter must be added to each Connector declared in the conf file $CATALINA_HOME/conf/server.xml

In addition the configuration files for the new version of RR are contained inside the component:

org.gcube.execution.resourceregistry-configuration-portal.1-0-0

The files should replace the configuration files under $GLOBUS_LOCATION/lib/_ext/property_files

ASL HTTP servlet installation and configuration

All ASL servlets are needed to be deployed
- org.gcube.application-support-layer.application-support-layer-http-information-retrieval.1-0-1 ( to rename to aslHttpInformationRetrieval under webapps)
- org.gcube.application-support-layer.application-support-layer-http-infrastructure-login.1-0-2 ( to rename to aslHttpInfrastructureLogin under webapps)
- org.gcube.application-support-layer.application-support-layer-http-content-access.1-0-1 ( to rename to aslHttpContentAccess under webapps)

Installation instructions:

- Create a standard JAAS configuration file with the following content and place it in $CATALINA_HOME/conf/

Gridsphere {
	org.jboss.security.auth.spi.LdapExtLoginModule required
        java.naming.factory.initial=com.sun.jndi.ldap.LdapCtxFactory
        java.naming.provider.url="ldap://ldap.research-infrastructures.eu/"
        java.naming.security.authentication=simple
        bindDN="cn=anonymous,ou=System,dc=research-infrastructures,dc=eu"
        bindCredential=freeToSearch
        baseCtxDN="ou=Organizations,dc=research-infrastructures,dc=eu"
        baseFilter="(uid={0})"
        rolesCtxDN="ou=Groups,ou=DevelopmentPortal,ou=D4ScienceAn e-Infrastructure operated by the D4Science.org initiative.,ou=Applications,dc=research-infrastructures,dc=eu"
        roleFilter="(uniqueMember={1})"
        roleAttributeID="cn"
        roleRecursion="-1"
	;
};

Name it "jaas.config". (You may want to name it differently, the important thing is that in step 3 you use the same file name) This file contains everything is needed to communicate with the D4ScienceAn e-Infrastructure operated by the D4Science.org initiative. LDAP Server, be careful not to change anything in this file, copy and paste as it is in the frame above.

- Make the JVM load the ASL JAAS configuration

Now we have to make the JVM load our JAAS configuration at the time that Tomcat is started. This is done with the java.security.auth.login.config system property.

- Modify $CATALINA_HOME/bin/catalina.sh to include the following:

JAVA_OPTS="$JAVA_OPTS -Djava.security.auth.login.config==$CATALINA_HOME/conf/jaas.config

You should place that two lines of code anywhere but make sure the $CATALINA_HOME is defined already, a good place would be after this piece of code:

 
# Only set CATALINA_HOME if not already set
[ -z "$CATALINA_HOME" ] && CATALINA_HOME=`cd "$PRGDIR/.." ; pwd`
 
if [ -r "$CATALINA_BASE"/bin/setenv.sh ]; then
  . "$CATALINA_BASE"/bin/setenv.sh
elif [ -r "$CATALINA_HOME"/bin/setenv.sh ]; then
  . "$CATALINA_HOME"/bin/setenv.sh
fi
.
.
##Place the two lines here##
echo "Using JAAS Authentication $CATALINA_HOME/conf/jaas.config"
JAVA_OPTS="$JAVA_OPTS -Djava.security.auth.login.config==$CATALINA_HOME/conf/jaas.config"

- ASL uses the UsersManagement service to retrieve information about the scopes, the users, their roles etc. To locate the service a configuration file named UMServiceLocation.config that contains the endpoint reference of the service should placed under $CATALINA_HOME/shared/d4s folder.

- For anonumous access ASL uses the following file for extracting the scope to use aslHTTPScope.config should contain a line with the scope (e.g /d4science.research-infrastructures.eu/FARM/FCPPS). This file should placed under: $CATALINA_HOME/shared/d4s folder.

- Anonymous Access is available for all the functionality offered by the HTTP API. The anonymous access is configurable based on the installation. To allow or prevent users to connect anonymously, the administrator has to register a generic resource in the gCube IS under the relative scope, called OpenAccessConfiguration. An example of the contents of this configuration resource is the following:

/** Configuration file for anonymous access - D4ScienceAn e-Infrastructure operated by the D4Science.org initiative. **/
 
<Functions>
 
            <ShowCollectionInfos>true</ShowCollectionInfos>
 
            <ShowContentInfos>true</ShowContentInfos>
 
            <GetContent>true</GetContent>
 
            <GetMetadata>true</GetMetadata>
 
            <ShowCollections>true</ShowCollections>
 
            <Search>true</Search>
 
            <GetThumbnails>true</GetThumbnails>
 
            <ShowVREs>true</ShowVREs>
 
</Functions>

(This resource is already avaialble for most of the scopes)

Application Profile configurations

The following Application Profiles for the Social Portal should be registered at root scope:

DONE Document Workflow Manager
DONE AquaMaps Species View
DONE AquaMaps
DONE Statistical Manager
Workspace Application (Not needed in 2.12)
DONE My Documents Workflow
AquaMaps Data Management
Templates (Not needed in 2.12)
Reports (Not needed in 2.12)

Upgrade Plan 212 Portals

Contents

Portals (CNR) 20/02/2012

Installation

Portlet installation

Libraries installation

Third Party libraries installation

Configuration

ASL HTTP servlet installation and configuration

Application Profile configurations

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