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Copy of Upgrade FQP

Step 0: Shutdown caGrid 1.2 FQP Service

  1. Connect to your caGrid 1.2 FQP server
  2. Shutdown your Tomcat Container 
     $CATALINA_HOME/bin/shutdown.sh

Step 1: Prepare Host

The caGrid 1.3 Training grid host was installed and configured according to the specifications listed on caGrid 1.3 Host Configuration page.

FQP specific requirements:

  1. Secure Container

Step 2: Prepare Configuration Files

Copy CDS configuration files to new host.

  1. Download and extract https://wiki.cagrid.org/download/attachments/2918098/caGrid-1.3-Configs-NCI.zip.
    1. Copy <target_grid>/FQP/serviceMetadata.xml to $HOME/tmp

Step 3: Install caGrid 1.3 Software

In this step you will use the installer to install and configure caGrid. Be sure to read the following blue info box for special instructions for step 11, 15 and 16 of the installer before proceeding.

Install caGrid and Configure a Secure Container Using the caGrid 1.3 Installer

At Step 11: Make sure you select the correct target grid for your installation
QA: NCI QA Grid for caGrid 1.3
Stage: NCI QA Grid for caGrid 1.3
Production: NCI QA Grid for caGrid 1.3
Training: Training Grid for caGrid 1.3

Step 15: The hostname must be the externally routable name. For example, the Training Grid Master GTS external hostname is mastergts.training.cagrid.org and internal is cagrid-1_3-training-master-gts.cagrid.org. We specified mastergts.training.cagrid.org when creating credentials.

Step 16: Select the option to create credentials with the GAARDS UI

  1. Start GAARDS UI 
      $ cd $CAGRID_HOME $ ant security
  2. Click the "Login" button.
    1. Enter user and password of a user with administration privileges.
  3. Open the "Request Host Certificate" Panel via the "My Account" menu -> "Request Host Certificate".
    1. Type the externally routable hostname of the new FQP service in the "Host" field.
    2. The "Specify directory to Write Credentials" should be your griduser's /home/griduser/.cagrid/certificates directory. This will overwrite the previous credentials.
    3. Click "Request Certificate"
    4. Close the GAARDS UI

At this point, your should set the following environment variables. The last step of the installer provides the paths for these settings:

  1. CAGRID_HOME which points to the location of your 'caGrid' source directory
  2. ANT_HOME which points to the location of your apache-ant-1.7.0 directory
  3. JAVA_HOME which points to the location of your jdk1.5.0_14 directory
  4. GLOBUS_LOCATION which points to the location of your ws-core-4.0.3 directory
  5. CATALINA_HOME which points to the location of your apache-tomcat-5.5.27 directory

Step 4: Configure FQP with prepared configuration files

  1. Copy serviceMetadata.xml 
    $ cp $/tmp/serviceMetadata.xml $CAGRID_HOME/projects/fqp/etc/.

Step 5: Install FQP Service

$ cd $CAGRID_HOME/projects/fqp $ ant deployTomcat

Step 6: Install the Transfer Service

Install the Transfer service. The "no.deployment.validation" option allows us ti skip the deployment validation steps. We can do this because Transfer does not need service metadata.

  1. Go to the Transfer directory
$ cd $CAGRID_HOME/projects/transfer
  1. Edit the Transfer deploy properties to disable service registration
    1. Open 'deploy.properties' for editing
    2. Change the "perform.index.service.registration" setting to false
  2. Deploy the Transfer service.
$ ant -Dno.deployment.validation=true deployTomcat

Step 7: Start Tomcat

Start Tomcat as follows:

  $ $CATALINA_HOME/bin/startup.sh
Check the $CATALINA_HOME/logs/catalina.out file for any errors.

Step 8: Validate

Run a DCQL query against the service

  $ cd $CAGRID_HOME/projects/fqp 
$ ant -Dservice.url=*YOUR_SERVICE_URL* runClient

You should see output similar to the below:

meadowgrain:caGrid/projects/fqp] oster% ant -Dservice.url=https://cagrid-fqp-qa.nci.nih.gov:8443/wsrf/services/cagrid/FederatedQueryProcessor runClient
Buildfile: build.xml

setGlobus:

checkGlobus:
     [echo] Globus: /Users/oster/grid/ws-core-4.0.3

defineClasspaths:

defineExtendedClasspaths:
     [echo] Defining extended classpaths
     [echo] Defining extended classpaths
     [echo] Defining extended classpaths

runClient:
     [echo] Connecting to service: https://cagrid-fqp-qa.nci.nih.gov:8443/wsrf/services/cagrid/FederatedQueryProcessor
     [echo] Issuing query: test/resources/caBIO_Example.xml
     [java] JVM args ignored when same JVM is used.
     [java] Running the Grid Service Client
     [java] Got results from:http://cabio-gridservice.nci.nih.gov:80/wsrf-cabio/services/cagrid/CaBIOSvc
     [java] ===== RESULT [0] =====
     [java] <ns2:Gene id="24998" fullName="BRCA1 associated protein" clusterId="530940" symbol="BRAP" xmlns:ns2="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [1] =====
     [java] <ns3:Gene id="132752" fullName="BRCA1 associated protein" clusterId="153372" symbol="Brap" xmlns:ns3="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [2] =====
     [java] <ns4:Gene id="123666" fullName="Brca1 associated protein 1" clusterId="3779" symbol="Bap1" xmlns:ns4="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [3] =====
     [java] <ns5:Gene id="3924" fullName="BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)" clusterId="106674" symbol="BAP1" xmlns:ns5="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [4] =====
     [java] <ns6:Gene id="44175" fullName="BRCA1 associated RING domain 1" clusterId="591642" symbol="BARD1" xmlns:ns6="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [5] =====
     [java] <ns7:Gene id="124585" fullName="BRCA1 associated RING domain 1" clusterId="10764" symbol="Bard1" xmlns:ns7="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [6] =====
     [java] <ns8:Gene id="25286" fullName="BRCA1 interacting protein C-terminal helicase 1" clusterId="532799" symbol="BRIP1" xmlns:ns8="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [7] =====
     [java] <ns9:Gene id="133858" fullName="BRCA1 interacting protein C-terminal helicase 1" clusterId="186143" symbol="Brip1" xmlns:ns9="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [8] =====
     [java] <ns10:Gene id="32594" fullName="BRCA1/BRCA2-containing complex, subunit 3" clusterId="558537" symbol="BRCC3" xmlns:ns10="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [9] =====
     [java] <ns11:Gene id="135874" fullName="BRCA1/BRCA2-containing complex, subunit 3" clusterId="226957" symbol="Brcc3" xmlns:ns11="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [10] =====
     [java] <ns12:Gene id="14617" fullName="BRCA2 and CDKN1A interacting protein" clusterId="370292" symbol="BCCIP" xmlns:ns12="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [11] =====
     [java] <ns13:Gene id="152936" fullName="BRCA2 and CDKN1A interacting protein" clusterId="389983" symbol="Bccip" xmlns:ns13="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [12] =====
     [java] <ns14:Gene id="78639" fullName="BRCA2 region, mRNA sequence CG011" clusterId="655908" xmlns:ns14="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [13] =====
     [java] <ns15:Gene id="68114" fullName="BRCA2 region, mRNA sequence CG017" clusterId="633948" xmlns:ns15="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [14] =====
     [java] <ns16:Gene id="104212" fullName="BRCA2 region, mRNA sequence GT573" clusterId="684657" xmlns:ns16="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]
     [java] ===== RESULT [15] =====
     [java] <ns17:Gene id="99929" fullName="BRCA2 region, mRNA sequence GT605" clusterId="679846" xmlns:ns17="gme://caCORE.caCORE/3.1/gov.nih.nci.cabio.domain"/>
     [java] ===== END RESULT=====
     [java]
     [java]

BUILD SUCCESSFUL
Total time: 8 seconds

Step 9: Configure FQP to Start Automatically

For the FQP service to be available upon reboot of your server Tomcat must be configured to start automatically.

Tomcat

  1. Configure Tomcat to start automatically: http://tomcat.apache.org/tomcat-5.5-doc/setup.html

Step 10: Update DNS to point to new FQP instance
Last edited by
Sarah Honacki (394 days ago)
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