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

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

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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

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

Code Block

 	<param-name>defaultPort</param-name>
 	<param-value>80</param-value>

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Our caGrid service server physically resides on an internal server (afapp1.c2b2.columbia.edu:18080) behind the firewall. This address, however, is not reachable from outside of Columbia University's network. Our publicly accessible address (a logical hostname) is:

Code Block
Historical link
http://caarraygrid.c2b2.columbia.edu:80/wsrf/services/cagrid/CaArraySvc

Since our caGrid service is actually running on the internal server's port 18080, a proxy server will forward any incoming request from the publicly accessible port 80 to port 18080 on the internal host.

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This is to add your caGrid service's publicly accessible DNS name into configuration file.

Code Block

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

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This file has the URL to the Index Server where you can see if your service is advertised. Make sure it contains following:

Code Block

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

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The following is in the top of the file.

Code Block

  <ns2:pointOfContactCollection>
  <ns3:PointOfContact affiliation="Columbia University Medical Center"  email="my_contact@my.organization"
  firstName="My FirstName" lastName="My LastName" phoneNumber="My Phone" role="DBA"
  xmlns:ns3="gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata.common"/>
  </ns2:pointOfContactCollection>

The following is at the bottom of the file.

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;

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Objects

Procedures

Results

Does caarraygrid Registered in NCI Index?

  • export GLOBUS_LOCATION=/app_data1/ws-core-4.0.3
  • cd /app_data1/ws-core-4.0.3/bin
  • ./wsrf-query -a -z none -s http://cagrid-index.nci.nih.gov:8080/wsrf/services/DefaultIndexService | grep 'caarraygrid'

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?

  • ./wsrf-get-property -a -z none -s http://caarraygrid.c2b2.columbia.edu:80/wsrf/services/cagrid/CaArraySvc {gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata}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?

  • ./wsrf-get-property -a -z none -s http://caarraygrid.c2b2.columbia.edu:80/wsrf/services/cagrid/CaArraySvc {gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata.dataservice}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"/> ....

Can I see my caGrid Service online?

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

Checking that caGrid is online
Screenshot showing Checking that caGrid is online

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Please leave your comment in the caArray End User Forum.

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