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Step by Step Guide to Install caArray 2.x Grid Service (caArray 2.2 and Under)

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Topic: caArray Installation and Upgrade

Release: Up to caArray 2.2

Date entered: 01/26/2009

Question

Step by Step Guide to Install caArray 2.x Grid Service (caArray 2.2 and Under)

Answer

Introduction

There are three components installed during caArray's installation process: UPT, caArray and caArray Grid Service (refer to caArray001 - Is UPT required for caArray or other application tools in LSD Bundle?). UPT is a mandatory application used for caArray's user access control. The caGrid Service is used to advertise your caArray application on the NCI caGrid Portal. The caGrid Portal provides a visual display of the services that are running on the caGrid infrastructure and the institutions that are participating in the caBIG program. You can easily find caBIG services, participants, and points of contact on the caGrid Portal. You can also query caGrid data services, share your queries, and search for the queries of other community members. Advertising your caGrid Service on caGrid Portal is optional. You may choose to participate at a later time, or you may choose not to participate at all.

The official caGrid Service configuration steps can be found in caArray Installation Guide (page 23). This knowledge base entry offers a supplemental step by step installation guide based on our hands-on experience here at Columbia University.

Prerequisite

caArray 2.x application must be running prior to the activation of your caGrid service on the caGrid Portal. However, the grid service is not required for the caArray application to run.

Abbreviation Used

The following abbreviations will be used through the text:

Abbreviation

Comment

<installation_directory>

The location where you keep the files downloaded.
Example: /app_data1/caArray2.1

Code Block
<application_base_path> = ${application.base.path}

The location where you are going to install caArray and caGrid service.
Example: /app_data1/caarray_app/caarray

Code Block
<grid.home> = ${application.base.path}

The location for the caGrid service files, see step 2
It is predefined in install.properties file.

Step 1. Make appropriate changes to install.properties file

File Location: <installation_directory>/install.properties

...

Property

Comments

application.base.path=/app_data1/caarray_app/caarray

The location where you are going to install caArray (i.e. the deployment of caGrid service and caArray application).
It need to be pre-created before installation start.
Important: <application_base_path> must be different from
<installation_directory> or the installation will fail.

grid.index URL =http://cagrid-index.nci.nih.gov:8080/wsrf/services/DefaultIndexService

NCI caGrid service's production webserver name

domain.name=afapp1.c2b2.columbia.edu

Our private DNS name where the caArray is installed.

grid.static.grid.hostname=localhost

We use localhost here because our caGrid service is on the same machine as caArray (a default configuration).
The caGrid service's hostname must be used if it is installed on a different machine from caArray application.

grid.static.grid.port=80

Our publicly accessible port to DMZ Zone

Step 2. Run ant to compile source code

File location: <installation_directory>/ant

...

Directory

Comments

Code Block
grid.home=${application.base.path}/jboss-4.0.4.GA

For caGrid service (created during the deployment)

Code Block
jboss.home=${application.base.path}/jboss-4.0.5.GA

For Jboss service (created during the deployment)

Step 3. Make appropriate changes to web.xml file

File Location: <grid.home>/server/default/deploy/wsrf.war/WEB-INF/web.xml

...

The port used in web.xml should be the port from the publicly accessible address, not the port on the internal server.

Step 4. Make appropriate changes to server-config.wsdd

File Location: <grid.home>/server/default/deploy/wsrf.war/WEB-INF/etc/globus_wsrf_core/server-config.wsdd

...

Code Block
 	<parameter name="logicalHost" value="caarraygrid.c2b2.columbia.edu"/>

Step 5. Make appropriate changes to CaArraySvc_registration.xml

File Location: <grid.home>/server/default/deploy/wsrf.war/WEB-INF/etc/cagrid_CaArraySvc/CaArraySvc_registration.xml

...

Code Block
 	<ServiceGroupEPR>
  <wsa:Address>http://cagrid-index.nci.nih.gov:8080/wsrf/services/DefaultIndexService</wsa:Address>
  	</ServiceGroupEPR>

Step 6. Make appropriate changes to serviceMetadata.xml

File Location: <grid.home>/server/default/deploy/wsrf.war/WEB-INF/etc/cagrid_CaArraySvc/serviceMetadata.xml

...

Code Block
  <ns1:hostingResearchCenter>
  <ns14:ResearchCenter displayName="Columbia University Medical Center"  shortName="CUMC"
  xmlns:ns14="gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata.common">
  <ns14:Address country="US" locality="New York" postalCode="10032" stateProvince="NY" street1="My Street1." street2=""/>
  <ns14:pointOfContactCollection>
  <ns14:PointOfContact affiliation="Columbia University Medical Center" email="my_contact@my.organization"
  firstName="My FirstName" lastName="My LastName" phoneNumber="My Phone" role="DBA"/>
  </ns14:pointOfContactCollection>
  </ns14:ResearchCenter>
  </ns1:hostingResearchCenter>

Step 7. Restart JBoss server for grid service

Code Block
 	cd $\{application.base.path\}/jboss-4.0.4.GA/bin
 	nohup ./run.sh &amp;

Step 8. Testing caGrid Service Installed

The table below summarizes four methods we used to test if our newly installed caGrid Service (caarraygrid) works properly:

Objects

Procedures

Results

Does caarraygrid Registered in NCI Index?

Following Information should be returned:<ns8:Address xmlns:ns8="http://schemas.xmlsoap.org/ws/2004/03/addressing">

http://caarraygrid.c2b2.columbia.edu:80/wsrf/services/cagrid/CaArraySvc

</ns8:Address>

Is our registration accurate with ServiceMetaData?

It should return our contact information, such as:<ns1:ServiceMetadata xmlns:ns1="gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata">
<ns1:serviceDescription>
<ns2:Service description="" name="CaArraySvc" version="1.1"
xmlns:ns2="gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata.service">
<ns2:pointOfContactCollection>
<ns3:PointOfContact affiliation="Columbia University Medical Center" ....

Is there any data returned with DomainModel?

It should return some of our data from caArray, such as: <ns1:DomainModel projectDescription="Version 2.0 caArray Model" projectLongName="caArray"
projectShortName="caArray" projectVersion="2"
xmlns:ns1="gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata.dataservice">
<ns1:exposedUMLAssociationCollection>
<ns1:UMLAssociation bidirectional="false">
<ns1:targetUMLAssociationEdge>
<ns1:UMLAssociationEdge maxCardinality="1" minCardinality="0" roleName="annotation">
<ns1:UMLClassReference refid="5423786E-6C04-59EA-E044-0003BA3F9857"/> ....

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="87b176cecf939f66-c927f534-46904813-89d39cd8-2a3b0fe8415d4055710ccdca"><ac:plain-text-body><![CDATA[

Can I see my caGrid Service online?

  • Go to [http://cagrid-portal.nci.nih.gov/web/guest/home

http://cagrid-portal.nci.nih.gov/web/guest/home] Click the "SERVICES" tab -> "Search" tab -> ['Keyword' = "caarraygrid" and 'Search Fields' = "URL" ] -> "Search" button

Checking that caGrid is online]]></ac:plain-text-body></ac:structured-macro>
Screenshot showing Checking that caGrid is online

Have a comment?

Please leave your comment in the caArray End User Forum.

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