NIH | National Cancer Institute | NCI Wiki  

Versions Compared

Old Version 51

changes.mady.by.user Unknown User (wileyal)

Saved on

compared with

New Version Current

changes.mady.by.user Unknown User (wileyal)

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Migration of unmigrated content due to installation of a new plugin
Scrollbar
iconsfalse

Include Page
wikicontent:Included No Longer Updated Panel
wikicontent:Included No Longer Updated Panel

...

Page info
title
title

Panel
titleContents of this Page
Table of Contents
minLevel2

...

The cancer Biomedical Informatics Grid, or caBIG®, is a virtual informatics infrastructure that connects data, research tools, scientists, and organizations to leverage their combined strengths and expertise in an open environment with common standards and shared tools. The current test bed architecture of caBIG™, caBIG® is dubbed caGrid. The software embodiment and corresponding documentation of this architecture constitute the caGrid 1.2 release.

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter or
  2. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

  • Option 1, org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter provides an interface for interacting with the LexEVS Grid Services. This Interface is intended to mirror the existing LexBIG API as much as possible. There is no object wrapping for semantic purposes on this interface. This allows existing applications of the LexBIG API to use Grid Services without code changes.
    This Interface may be acquired by instantiating LexBIGServiceAdapter with the Grid Service URL as a parameter.

    Code Block
    LexBIGService lbs = new LexBIGServiceAdapter("http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService");

  • Option 2, org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter also provides an interface for interacting with the LexEVS Grid Services. However, this Interfaces is the semantically defined interface. All method parameters and return values are defined and annotated as CDEs to be loaded into caDSR. This Interface is intended to be caGrid Silver Level Compliant.
    This Interface may be acquired by instantiating LexBIGServiceGridAdapter with the Grid Service URL as a parameter.

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter("http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService);

...

getGenericExtensions(ExtensionIdentification)

–

Description:

Returns an instance of the application-specific extension registered with the given name.

Input:

org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification

Output:

org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList

Exception:

RemoteException

Implementation Details:

Implementation :
Step 1: Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.
Sample Call :

  • Step 1: Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter or org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

    Info
    titleNote

    Currently this method will return a LexBIGServiceConvenienceMethods instance.

  • Step 2: Build an org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification to hold the Extension name. ExtensionIdentification extension = new ExtensionIdentification(); extension.setLexBIGExtensionName("LexBIGServiceConvenienceMethods");
  • Step 3: Invoke the LexBIG caGrid service as follows: LexBIGServiceConvenienceMethodsGrid lbscm = lbs.getGenericExtensions(extension);
  • Step 4: Return the LexBIGServiceConvenienceMethodsClient to the user. This LexBIGServiceConvenienceMethodsClient has the above org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods as a Resource. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.CodedNodeGraphClient object is built from the above Reference.

...

resolveCodingSchemeCopyright(CodingSchemeIdentification)

–

Description:

Return coding scheme copyright given a specific tag or version identifier.

Input:

org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

Output:

org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeCopyRight

Exception:

RemoteException

Implementation Details:

Implementation :
Step 1: Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server}}, and forward the results.
Sample Call :

  • Step 1: Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter or org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  • Step 2: Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification to hold the Coding Scheme name.
    CodingSchemeIdentification codingScheme = new

    Code Block
    CodingSchemeIdentification();

    codingScheme.setCode;

  • Step 3: Build an org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag containing the Version information for the desired Coding Scheme
    CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag(); csvt.setVersion("testVersion");
  • Step 4: Invoke the LexBIG caGrid service as follows: CodingSchemeCopyRight copyright = lbs.resolveCodingSchemeCopyright(codingScheme, csvt);

...

The LexEVS Grid Service 4.2 URL is:

Code Block

Link provided for historical purposes http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService

...

Product

Jars

License

Home Page

Apache WS-Addressing

addressing-1.0.jar

adressing 1.0.LICENSE

From Globus 4.0.2 Java Web Services Core lib directory: http://www.globus.org/toolkit/downloads/4.0.2
Source available at:

Code Block

Link provided for historical purposes http://ws.apache.org/addressing

Apache Axis

  • axis-ant.jar
  • axis.jar
  • commons-pool-1.3.jar
  • commons-logging-1.1.jar
  • commons-lang-2.2.jar
  • commons-collections-3.2.jar
  • commons-codec-1.3.jar
  • log4j-1.2.8.jar
  • jaxrpc.jar
  • saaj.jar
  • wsdl4j.jar

axis-jars.LICENSE

http://ws.apache.org/axis

Apache Xerces

xercesImpl.jar

xerces.LICENSE

http://xerces.apache.org/xerces-j

Apache Lucene

  • lucene-core-2.3.2.jar
  • lucene-regex-2.3.2.jar
  • lucene-snowball-2.3.2.jar

Lucene LICENSE

http://lucene.apache.org/

ASM - all purpose Java bytecode manipulation and analysis framework

asm.jar

http://asm.objectweb.org/license.html

http://asm.objectweb.org/

Castor

castor-1.2.jar

http://www.castor.org/license.html

Code Block

Link provided for historical purposes http://www.castor.org/index.html

Globus Toolkit

  • cog-axis.jar
  • cog-jglobus.jar

http://www.globus.org/toolkit/legal/4.0/

–

Bouncy Castle Crypto APIs

jce-jdk13-125.jar

http://www.bouncycastle.org/licence.html

http://www.bouncycastle.org/

Open Permis

  • wsrf_core.jar
  • wsrf_core_stubs.jar

http://www.openpermis.org/BSDlicenceKent.txt

http://www.openpermis.org/

Apache
WSS4J

wss4j.jar

http://ws.apache.org/wss4j/license.html

http://ws.apache.org/wss4j/

Spring

spring.jar

Spring LICENSE

http://www.springframework.org

...

For your convenience, the required libraries are available for download on GForge

In order to programmatically access the LexEVS API Grid Service, these libraries need to be added to your local classpath.

...

For an example client, service calls, and SOAP messages, downoload the TestClient zip file.

Example API Usage

Searching for concepts in NCI Thesaurus containing the string "Gene"

...

  • Step 1: Connect to the LexBIG caGrid Service LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
  • Step 2: Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification to hold the Coding Scheme name.
    CodingSchemeIdentification codingScheme = new CodingSchemeIdentification(); codingScheme.setName("codingScheme");
  • Step 3: Build an gov.nih.nci.evs.security.SecurityToken containing the security information for the desired Coding Scheme.
    SecurityToken token = new SecurityToken (); token.setAccessToken("securityToken");

  • Step 4: Invoke the LexBIG caGrid service as follows: This will return a reference to a new "LexBIGServiceGrid" instance that is associated with the security properties that were passed in.
    LexBIGServiceGrid lbsg = lbs.setSecurityToken(codingScheme, token);

    Info
    titleNote

    The Grid Service "setSecurityToken" returns an org.LexGrid.LexBIG.cagrid.LexEVSGridService.stubs.types .LexEVSGridServiceReference.LexEVSGridServiceReference object. This reference must be used to access the secured vocabularies.

...

Info
titleNote

All non-secured information accessed by the LexEVS Grid Service is publicly available from NCICB and users are expected to follow the licensing requirements currently in place for accessing and using NCI EVS information.

...

...

Scrollbar
iconsfalse