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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


{code}
 	<param-name>defaultPort</param-name>
 	<param-value>80</param-value>
{code}


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


{code}
 	<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


{code}
  <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


{code}
  <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


{code}
 	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:
...
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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