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Composition Setup
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=TOC} {toc:minLevel=2} {cloak}{panel} *Topic*: caArray Installation and Upgrade *Release*: Up to caArray 2.2 *Date entered*:
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Topic: caArray Installation and Upgrade

Release: Up to caArray 2.2

Date entered: 01/26/2009

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Question

Step by Step Guide to Install caArray 2.x

...

Grid

...

Service

...

(caArray

...

2.2

...

and

...

Under)

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Answer

Have a comment?

Please leave your comment in the caArray End User Forum.

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There are three components installed during caArray's installation process: UPT, caArray and caArray Grid Service (refer to caArray001). 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 
...
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
...
Image Added
 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
...
> 
...
 <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
}
 	<param-name>defaultPort</param-name>
 	<param-value>80</param-value>
{code}
	
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: 
...
http://caarraygrid.c2b2.columbia.edu:80/wsrf/services/cagrid/CaArraySvc
...
Image Added
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
}
 	<parameter name="logicalHost" value="caarraygrid.c2b2.columbia.edu"/>
{code}

h3. Step 
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
 

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

h3. Step 
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
}
  <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>
{code}


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>
{code}

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


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

h3. Step 
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:
...