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

Topic: caArray Installation and Upgrade

Release: Up to caArray 2.2

Date entered: 01/26/2009

Panel
titleContents of this Page
Table of Contents
minLevel2

Introduction

There are three components installed during caArray's installation process: UPT, caArray and caArray Grid Service (refer to caArray 001 - 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) (login required). 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
...
This is the step to configure Install.properties 
...
 file 
...
 before 
...
 the 
...
 deployment 
...
 of 
...
 caArray 
...
 Grid 
...
 service 
...
 begins. 
...
 caGrid 
...
 service 
...
 and 
...
 caArray 
...
 share 
...
 the 
...
 same 
...
 Install.properties 
...
 file.
...
It 
...
 is 
...
 important 
...
 to 
...
 specify 
...
 following 
...
 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
During the compiling process, Java class files will be deployed into following two directories, as defined in Install.properties file:
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
 Code Block


{panel}
 	<param-name>defaultPort</param-name>
 	<param-value>80</param-value>
{panel}
	
The 
The web.xml 
...
 file 
...
 contains 
...
 the 
...
 port 
...
 and 
...
 protocol 
...
 your 
...
 grid 
...
 service 
...
 will 
...
 be 
...
 advertised 
...
 as. 
...
 The 
...
 port 
...
 defined 
...
 here 
...
 should 
...
 be 
...
 the 
...
 same 
...
 publicly 
...
 accessible 
...
 port 
...
 as 
...
 defined 
...
 in 
...
 your 
...
 property 
...
 file 
...
 (grid.static.grid.port 
...
 in 
...
Step 
...
 1
...
). 
...
 It 
...
 is 
...
 port 
...
 80 
...
 in 
...
 our 
...
 case, 
...
 as 
...
 defined 
...
 in 
...
 our 
...
 property 
...
file.
caArray Application and Port Forwarding 
 caArray Application and Port Forwarding as explained in the text that followsImage Added
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.
...
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
...
This 
...
 is 
...
 to 
...
 add 
...
 your 
...
 caGrid 
...
 service's 
...
 publicly 
...
accessible DNS 
...
 name 
...
 into 
...
 configuration 
...
 file.
 Code Block

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

h3. *Step 5*. Make appropriate changes to 
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
...
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
 

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

h3. *Step 6*.  Make appropriate changes to 
Step 6. Make appropriate changes to serviceMetadata.xml
...
File 
...
 Location:
...
 <grid.home>/server/default/deploy/wsrf.war/WEB-INF/etc/cagrid_CaArraySvc/serviceMetadata.xml
...
This 
...
 file 
...
 contains 
...
 the 
...
 contact 
...
 information 
...
 for 
...
 your 
...
 caGrid 
...
 service. 
...
 Your 
...
 caGrid 
...
 Service 
...
 will 
...
 not 
...
 be 
...
 recognized 
...
 in 
...
the caGrid 
...
 Portal 
...
 without 
...
 the 
...
 proper 
...
 identification 
...
 defined 
...
 here.
The following is in the top of the file.
 Code Block
 

*  *Top of file *

{panel}
  <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>
{panel}

* *Bottom of file* ...

{
The following is at the bottom of the file.
 Code Block
panel}
  <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
{panel}

h3. *Step 7*.  Restart JBoss server for grid service:

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

h3. *Step 8*.  Testing caGrid Service Installed
Table below summarizes 4 methods we used to test if our newly installed caGrid Service (*caarraygrid*) works properly:

|| Objects|| Procedures ||Results ||
| 
Does *caarraygrid* Registered in NCI Index? | grep 'caarraygrid' |
| 
Is our registration accurate with ServiceMetaData? | 
* 	
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?
  • 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 onlineImage Added
Have a comment?
Please leave your comment in the caArray End User Forum.
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