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Data Service Development without caDSR and GME

Contents

Overview

On August 7, 2009, several grid services were decommissioned that affect some features of caGrid 1.1 and 1.2 Introduce extensions. The following is a list of the decommissioned grid services:

  1. CaBIOSvc 3.1 Data Service (Includes caBIO, caDSR and EVS services): http://cabio-gridservice.nci.nih.gov:80/wsrf-cabio/services/cagrid/CaBIOSvc
  2. CaBIO32GridSvc 3.2 Data Service (Includes caBIO only): http://cabiogrid32.nci.nih.gov/wsrf/services/cagrid/CaBIO32GridSvc <http://cabiogrid32.nci.nih.gov/wsrf/services/cagrid/CaBIO32GridSvc>
  3. CaDSRService 1.0 Analytical Service: http://cagrid-service.nci.nih.gov:8080/wsrf/services/cagrid/CaDSRService
  4. EVSGridService 1.0 Analytical Service: http://cagrid-service.nci.nih.gov:8080/wsrf/services/cagrid/EVSGridService

The following Training Grid services were disabled on Monday, August 10th:

  1. caDSR: http://gme.training.cagrid.org:8080/wsrf/services/cagrid/CaDSRService
  2. EVS: http://evs.training.cagrid.org:8080/wsrf/services/cagrid/EVSGridService
  3. GME: http://gme.training.cagrid.org:8080/wsrf/services/cagrid/GlobalModelExchange

In response to these changes, the caGrid Knowledge Center updated 3 Introduce extensions and has provided this article to allow caGrid 1.1 and 1.2 service developers to continue using their current software for Data Service creation without experiencing exceptions.

Important:
  • caGrid 1.3 supports the new services that have replaced the decommissioned services. caGrid 1.1 and 1.2 users who desire the functionality of these grid services in Introduce may want to consider upgrading their services to caGrid 1.3.
  • This can be done by installing and building caGrid 1.3, then opening your service for modification in the 1.3 version of Introduce. You will be asked if you want to upgrade your service (Please, backup your 1.2 services first).

Article Applies To

Data Service developers using caGrid 1.1 or 1.2 that are configured to use a grid that does not have caDSR or GME grid services available.

  • Training Grid
  • NCI Production Grid

Updated Introduce Extensions:

caGrid 1.1

  • caGrid Metadata Editor Extensions (1.1.1): Uses caDSR service.
  • caGrid Metadata Service Extension (1.1.1): Calls caDSR to annotate metadata. Log message updated to mention deprecation of caDSR service. Extension will produce an unannotated metadata file. This functionality has been in existence in caGrid 1.2 and has not been altered.
  • caGrid Data Service Extensions (1.1.2): The caCORE SDK Data Service extension provides the ability to select a domain model from caDSR and to select a schema from GME. This version of the extension will remove the caDSR lookup option from the Domain Model Selection and the GME lookup option from the Schema Selection portions of the Data Service creation wizard.

caGrid 1.2

  • caGrid Metadata Editor Extensions (1.2.1): Uses caDSR service.
  • caGrid Metadata Service Extension (1.2.1): Calls caDSR to annotate metadata. Log message updated to mention deprecation of caDSR service. Extension will produce an unannotated metadata file. This functionality has been in existence in caGRid 1.2 and has not been altered.
  • caGrid Data Service Extensions (1.2.2): The caCORE SDK Data Service extension provides the ability to select a domain model from caDSR and to select a schema from GME. This version of the extension will remove the caDSR lookup option from the Domain Model Selection and the GME lookup option from the Schema Selection portions of the Data Service creation wizard. SDK Data Style instructions

Updating Introduce to Avoid caDSR and GME Errors During Data Service Creation

Step 1: Extension Removal

For developers using a Grid without caDSR and GME services, it is safe to remove the caDSR and GME extensions from Introduce. You will be required to update the caGrid project.properties file to prevent re-installation of the caDSR extension.

Important Note: $CAGRID_LOCATION is used as the location of caGrid. It is not an environment variable.
  1. Manually Delete the Extensions:
    1. $CAGRID_LOCATION/introduce/extensions/caDSR-discover
    2. $CAGRID_LOCATION/introduce/extensions/gme-discovery
  2. Prevent caDSR Extension re-installation using one of the following:
    1. Checkout the newest version of $CAGRID_LOCATION/caGrid/projects.properties from the caGrid Source Repository
    2. Update your local file following the steps below:
      1. Open $CAGRID_LOCATION/caGrid/projects.properties in an editor
      2. Find the introduce.extension.projects.list section
      3. Remove the cadsr, entry
      4. Save the file

Step 2: Remove caDSR and GME URLS from target grid configuration

The caGRid 'ant -Dtarget.grid=<gridname> configure' task reads the grid configuration for the specified grid and automatically populates several service URLS into caGrid services for you. Because caDSR and GME are decomissioned, these entries must be removed for the Training and Production Grids following the steps below.

Option 1: Manually Remove the service URLS

  1. Select the file appropriate for your installation
    Distribution File Location
    caGrid 1.1 Training $CAGRID_LOCATION/caGrid/share/resources/target_grids/training/service_urls.properties
    caGrid 1.1 Production $CAGRID_LOCATION/caGrid/share/resources/target_grids/nci_prod/service_urls.properties
    caGrid 1.2 Training $CAGRID_LOCATION/caGrid/repository/cagrid/target_grids/training-1.2/service_urls.properties
    caGrid 1.2 Production $CAGRID_LOCATION/caGrid/repository/cagrid/target_grids/nci_prod-1.2/service_urls.properties
  2. Open the file.
  3. Remove the URLs for cadsr and gme so that the lines look like this: 
    cagrid.master.cadsr.service.url=
cagrid.master.gme.service.url=
  4. Save the file.

Option 2: Update from SVN

Checkout the newest version of the Training or Production target grid URLs from the caGrid Source Repository

  1. caGrid 1.1 Training 
    svn checkout https://ncisvn.nci.nih.gov/svn/cagrid/branches/caGrid-1_1_release/cagrid-1-0/caGrid/share/resources/target_grids/training/service_urls.properties


  2. caGrid 1.1 Production 
    svn checkout https://ncisvn.nci.nih.gov/svn/cagrid/branches/caGrid-1_1_release/cagrid-1-0/caGrid/share/resources/target_grids/nci_prod/service_urls.properties


  3. caGrid 1.2 Training 
    svn checkout https://ncisvn.nci.nih.gov/svn/cagrid/tags/caGrid-1_2_release_1_2_0_1/cagrid-1-0/caGrid/repository/caGrid/target_grid/training-1.2/service_urls.properties


  4. caGrid 1.2 Production 
    svn checkout https://ncisvn.nci.nih.gov/svn/cagrid/tags/caGrid-1_2_release_1_2_0_1/cagrid-1-0/caGrid/repository/caGrid/target_grid/nci_prod-1.2/service_urls.properties


Step 3: 'Configure' your caGrid Installation

Run the 'ant configure' task to ensure that the caDSR and GME URLs are removed from your caGrid distribution.

  1. Open a command prompt
  2. Change directory to your caGrid location, shown here as $CAGRID_LOCATION 
    > cd $CAGRID_LOCATION


  3. Run the configure command
    1. caGrid 1.1 Training 
      > ant -Dtarget.grid=training configure


    2. caGrid 1.1 Production 
      > ant -Dtarget.grid=nci_prod configure


    3. caGrid 1.2 Training 
      > ant -Dtarget.grid=training-1.2 configure


    4. caGrid 1.2 Production 
      > ant -Dtarget.grid=nci_prod-1.2 configure

Step 4: Download Introduce Updates and Remove caDSR/GME URLS

Option 1: Introduce 1.1

  1. From the command line, open > Introduce using the 'ant introduce' command. 
    > ant introduce


  2. In Introduce, select the Help->Check for Updates menu item.
  3. In the Introduce Update Manager, click > the Look for Updates button.
  4. Select >the following extension updates:
    1. CaGrid Metadata Service Extension (1.1.1)
    2. CaGrid Data Service Extensions (1.1.2)
    3. CaGrid Metadata Editor Extensions (1.1.1)
  5. Click > Next
  6. Introduce will download the updates and then restart.
  7. Click > the Configuration menu and select > the Preferences menu item
  8. In the left-hand Topic list, select > Service URLs
    1. Remove > the Cancer Data Standards Repository (caDSR) URL
    2. Remove > the Global Model Exchange URL
    3. Click > Apply, then Click > Done

Option 2: Introduce 1.2

  1. From the command line, open > Introduce using the 'ant introduce' command.
  2. In Introduce, select the Help->Introduce Software Update item.
  3. In the Introduce Update Manager, click the Look for Updates button.
  4. Select the following extensions
    1. CaGrid Metadata Service Extension (1.2.1)
    2. CaGrid Data Service Extensions (1.2.2)
    3. CaGrid Metadata Editor Extensions (1.2.1)
  5. Click > Next
  6. Introduce will download the updates and then restart.
  7. Click > the Configure menu and select > the Configure Introduce menu item.
  8. In the left-hand Topic list, select > Service URLs
    1. If populated, Remove > the Cancer Data Standards Repository (caDSR) URL
    2. If populated, Remove > the Global Model Exchange URL
    3. Click > Apply, then Click > Done

Update Existing Data Service to Not use a caDSR Model

SCENARIO: You have an existing caCORE Data Service that was created when the caDSR service was available. Now, you would like to modify the service.

To enable modification of caCORE Data Services in Introduce you will want to perform the following steps:

  1. Open > your services introduce.xml file for editing.
  2. Find > the CadsrInformation element in the file
  3. Change >the useSuppliedModel attribute to "true" or add useSuppliedModel="true" 
    <ns9:CadsrInformation noDomainModel="false" projectVersion="1.0" useSuppliedModel="true" xsi:type="ns9:CadsrInformation">


  4. Save the file.

Data Extension View Changes

Data Model Selection

With the caDSR URL removed, you will now see a different view during Data Service creation using a caCORE data model.

  1. Introduce Data Service Creation with configured caDSR URL:


  2. Introduce Data Service Creation without configure caDSR URL:

    Select the caCORE Domain Model from File

Schema Selection

With the GME URL removed, you will now see a different view during Data Service creation using a caCORE a Schema.

  1. Introduce Data Service Creation with configured GME URL:

    Select the schema from GME


  2. Introduce Data Service Creation without configure GME URL:

    Select the schema from File
Last edited by
Kim Leonard (709 days ago) , ...
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