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Overview

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™, is dubbed caGrid. The software embodiment and corresponding documentation of this architecture constitute the caGrid 1.2 release.

This User Guide addresses the LexEVS Grid Service (version 4.2), from the perspective of a client application developer looking to interface with the referenced analytical grid service.

NOTE: The current version of the LexEVS Grid Service is 4.2 and it interfaces with the EVS API 4.2

Release History

Version Number	Date	Description
1.0	Unknown	Original release of the EVS Grid Service. Interfaced with caCORE/EVS 3.1.
4.1	June 27, 2008	Follow-on release of EVS Grid Service which interfaces with EVS API 4.1 (based on the EVS 3.2 OM).
4.2	October 11, 2008	Follow-on release of EVS Grid Service 4.1 built on top of LexBIG server 2.3 which interfaces with EVS API 4.2

The LexEVS Grid Service

The following table summarizes the operations available through the LexEVS Analytical Grid Service. Each of the operations is also defined in detail below. The grid analytical service and related operations are viewable via the caGrid Portal (http://cagrid-portal.nci.nih.gov).

Using the API

There are two (2) different interfaces for accessing the LexEVS Grid Services:

org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter, or
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.

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.

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

Method Descriptions

getCodingSchemeConcepts

Description:	Returns the set of all (or all active) concepts in the specified coding scheme.
Input:	org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag
Output:	org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeSet.stubs.types.CodedNodeSetReference
Exception:	RemoteException
Implementation Details:

getFilter

Description:	Returns an instance of the filter extension registered with the given name.
Input:	org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification
Output:	org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.stubs.types.FilterReference
Exception:	RemoteException
Implementation Details:

getSortAlgorithm

Description:	Returns an instance of the sort extension registered with the given name.
Input:	org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification
Output:	''org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort. stubs.types.SortReference''
Exception:	RemoteException
Implementation Details:

getFilterExtensions

Description:	Returns a description of all registered extensions used to provide additional filtering of query results.
Input:	none
Output	org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList
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: Invoke the LexBIG caGrid service as follows:

ExtensionDescriptionList extDescList = lbs.getFilterExtensions(); |

getServiceMetadata

Description:	Return an interface to perform system-wide query over metadata for loaded code systems and providers.
Input:	none
Output:	org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceMetadata. stubs.types.LexBIGServiceMetadataReference
Exception:	RemoteException
Implementation Details:

Implementation:

Step 1: Create a Resource on the server and populate it with the requested org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata

Step 2: Return the LexBIGServiceMetadataClient to the user. This LexBIGServiceMetadataClient has the above org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata as a Resource. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.LexBIGServiceMetadataClient object is built from the above Reference.

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: Invoke the LexBIG caGrid service as follows:

LexBIGServiceMetadataGrid metadata = lbs.getServiceMetadata(); |

getSupportedCodingSchemes

Description:	Return a list of coding schemes and versions that are supported by this service, along with their status.
Input:	none
Output:	org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList
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: Invoke the LexBIG caGrid service as follows:

CodingSchemeRenderingList csrl = lbs.getSupportedCodingSchemes(); |

getLastUpdateTime

Description:	Return the last time that the content of this service was changed; null if no changes have occurred. Tag assignments do not count as service changes for this purpose.
Input:	none
Output:	java.util.Date
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: Invoke the LexBIG caGrid service as follows:

Date date = lbs.getLastUpdateTime(); |

resolveCodingScheme

Description:	Return detailed coding scheme information given a specific tag or version identifier.
Input:	org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag
Output:	org.LexGrid.codingSchemes.CodingScheme
Exception:	RemoteException
Implementation Details:

getNodeGraph

Description:	Returns the node graph as represented in the particular relationship set in the coding scheme.
Input:	org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag, org.LexGrid.LexBIG.DataModel.cagrid.RelationContainerIdentification
Output:	''org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices. CodedNodeGraph.stubs.types.CodedNodeGraphReference''
Exception:	RemoteException
Implementation Details:

getMatchAlgorithms

Description:	Returns the node graph as represented in the particular relationship set in the coding scheme.
Input:	none
Output:	org.LexGrid.LexBIG.DataModel.Collections.ModuleDescriptionList
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: Invoke the LexBIG caGrid service as follows:
ModuleDescriptionList mdl = lbs.getMatchAlgorithms(); |

getGenericExtensions

Description:

Returns a description of all registered extensions used to implement application-specific behavior that is centrally accessible from a LexBIGService.

Note that only generic extensions (base class GenericExtension) will be listed here. All other classes are retrievable at the appropriate interface point (filter, sort, etc). |

Input:	none
Output:	org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList
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: Invoke the LexBIG caGrid service as follows:
ExtensionDescriptionList edl = lbs.getGenericExtensions(); |

getGenericExtension

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:

getHistoryService

Description:	Resolve a reference to the history api servicing the given coding scheme.
Input:	org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification
Output:	org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices. HistoryService.stubs.types.HistoryServiceReference
Exception:	RemoteException
Implementation Details:

getSortAlgorithms

Description:	Returns a description of all registered extensions used to provide additional filtering of query results.
Input:	org.LexGrid.LexBIG.DataModel.InterfaceElements.types.SortContext
Output:	org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList
Exception:	RemoteException
Implementation Details:

resolveCodingSchemeCopyright

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:

setSecurityToken

Description:	Sets the Security Token for the given Coding Scheme.
Input:	org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, gov.nih.nci.evs.security.SecurityToken
Output:	org.LexGrid.LexBIG.cagrid.LexEVSGridService.stubs.types.LexEVSGridServiceReference.LexEVSGridServiceReference
Exception:	RemoteException
Implementation Details:

Usage Instructions

Service URL

The LexEVS Grid Service 4.2 URL is: http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService.

The service is also accessible via the caGRID Portal.

Required Libraries

The libraries required for programmatic access to the LexEVS Grid Service are listed in the tables below. The 3rd Party Software Libraries required for use of the LexEVS API Grid Service are listed in Table 4.1 and the NCICB software captured under the caBIG umbrella are listed in Table 4.2.

Table 4.1 3rd Party Libraries

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 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	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

Table 4.2 NCICB/caBIG Libraries

Library	Associated JARs
caGrid Software Libraries	caGrid-ServiceSecurityProvider-client-1.2.jar
caGrid-ServiceSecurityProvider-common-1.2.jar
caGrid-ServiceSecurityProvider-stubs-1.2.jar
caGrid-core-1.2.jar
caGrid-metadata-common-1.2.jar
caGrid-metadata-data-1.2.jar
caGrid-metadata-security-1.2.jar
caGrid-metadatautils-1.2.jar
EVS API Libaries	evsapi42-beans.jar
evsapi42-framework.jar
LexEVS Grid Service Client Library	LexEVSGridService-client.jar
LexEVS Grid Service Stubs	LexEVSGridService-stubs.jar
LexEVS Grid Service Common	LexEVSGridService-common.jar
LexEVS Grid Service Service	LexEVSGridService-service.jar
LexEVS Grid Service Tests	LexEVSGridService-tests.jar
caCORE SDK Library	sdk-client-framework.jar
LexBIG API	lexbig.jar
Custom Castor Serializer	castor-bean-serializer.jar

Downloads

For your convenience, the required libraries are available for download here:

https://gforge.nci.nih.gov/docman/view.php/491/14401/lexevs42-gridsrvc-jars.jar.

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

Code Examples

For an example client, service calls, and SOAP messages, see http://gforge.nci.nih.gov/docman/view.php/491/14252/TestClient.zip

Example API usage

Example 1: Searching for concepts in NCI Thesaurus containing the string "Gene"

//Create a Connection to the Grid Service
LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(gridServiceURL);
 
//Set up the CodingSchemeIdentification object to define the Coding Scheme
CodingSchemeIdentification csid = new CodingSchemeIdentification();
csid.setName("NCI Thesaurus");
 
//Get the CodedNodeSet for that CodingScheme (This returns a CodedNodeSet Service Context) 
CodedNodeSetGrid cnsg = lbs.getCodingSchemeConcepts(csid, null); //getCodingSchemeConcepts is a Grid Service Call
 
//Set the text to match
MatchCriteria matchText = new MatchCriteria();
matchText.setText("Gene");
 
//Define a SearchDesignationOption, if any
SearchDesignationOption searchOption = new SearchDesignationOption();
 
//Choose an algorithm to do the matching
ExtensionIdentification matchAlgorithm = new ExtensionIdentification();
matchAlgorithm.setLexBIGExtensionName("contains");
 
//Chose a language
LanguageIdentification language = new LanguageIdentification();
language.setIdentifier("en");
 
//Restrict the CodedNodeSet
cnsg.restrictToMatchingDesignations(matchText, searchOption, matchAlgorithm, language); 
//restrictToMatchingDesignations is a Grid Service Call
 
//Create a SetResolutionPolicy to handle the details of Resolving the CodedNodeSet
//Here, we will set the Maximum number of Concepts returned to 10.
SetResolutionPolicy resolvePolicy = new SetResolutionPolicy();
resolvePolicy.setMaximumToReturn(10);
 
//Do the resolve
ResolvedConceptReferenceList rcrlist = cnsg.resolveToList(resolvePolicy); //resolveToList is a Grid Service Call
 
//Use the returned ResolvedConceptReferenceList to print some details about the concepts found
ResolvedConceptReference[] rcref = rcrlist.getResolvedConceptReference();
for (int i = 0; i < rcref.length; i++) {
	System.out.println(rcref[i].getConceptCode());
	System.out.println(rcref[i].getReferencedEntry().
		getPresentation()[0].getText().getContent()); 
}

Error Handling

Error Connecting to LexEVS Grid Service

When connecting through the Java Client, java.net.ConnectException and org.apache.axis.types.URI.MalformedURIException may be thrown upon an unsuccessful attempt to connect.

A MalformedURIException is thrown in the case if a poorly-formed URL string. In this case, the exception is thrown before an attempt to connect is even made.

If the URL is well-formed, proper connection is tested. If the connection attempt fails, a ConnectException is thrown containing the reason for the failure.

try{
LexBIGServiceGridAdapter lbsg = new LexBIGServiceGridAdapter("http://localhost:8080/wsrf/services/cagrid/LexEVSGridService");
} catch(java.net.ConnectException e){
	//Error Connecting
	e.printStackTrace();
} catch(org.apache.axis.types.URI.MalformedURIException e){
	//URL Syntax Error
	e.printStackTrace();
}

This example shows a typical connection to the LexEVS Grid Service, with the two potential Exceptions being caught and handled as necessary.

LexBIG Errors

LexBIG errors will be forwarded through the Distributed LexBIG layer and then on to the Grid layer. Input parameters, along with any other LexBIG (or Distributed LexBIG) errors will be detected on the server, not the client, and forwarded. All Generic LexBIG (or Distributed LexBIG) errors will be forwarded via a RemoteException, with the cause of the error and underlying LexBIG error message included.

Invalid Service Context Access

Service Context Services are not meant to be called directly. If the client attempts to do so, an org.LexGrid.LexBIG.cagrid.LexEVSGridService.CodedNodeSet.stubs.types.InvalidServiceContextAccess Exception will be thrown. This indicates a call was made to a Service Context without obtaining a Service Context Reference via the Main Service (see the above section Service Contexts and State for more information).

Security Issues

LexEVS Grid Service Security

Certain vocabulary content accessible through the LexEVS Grid Service may require extra authorization to access. Each client is required to supply its own access credentials via Security Tokens. These Security Tokens are implemented by a SecurityToken object:

Name: SecurityToken
Namespace: gme://caCORE.caCORE/3.2/gov.nih.nci.evs.security
Package: gov.nih.nci.evs.security

Accessing Secure Content

A client establishes access to a secured vocabulary via the following Grid Service Calls:

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);

It is important to note that 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.

Implementation

Each call to "setSecurityToken" sets up a secured connection to Distributed LexBIG with the access privileges included in the SecurityToken parameter. The LexEVSGridServiceReference that is returned to the client contains a unique key identifier to the secure connection that has been created on the server. All subsequent calls the client makes through this LexEVSGridServiceReference will be made securely. If additional SecurityTokens are passed in through the "setSecurityToken" Grid Service, the additional security will be added and maintained.

The "setSecurityToken" Grid Service is a stateful service. This means that after the client sets a SecurityToken, any subsequent call will be applied to that SecurityToken.

Secure connections are not maintained on the server indefinitely, but are based on load conditions. The server will allow 30 unique secure connections to be set up for clients without any time limitations. As additional requests for secure connections are received by the server, connections will be released by the server on an 'oldest first' basis. No connection, however, may be released prior to 5 minutes after its creation.

If no SecurityTokens are passed in by the client, a non-secure Distributed LexBIG connection will be used. The server maintains one (and only one) un-secured Distributed LexBIG connection that is shared by any client not requesting security.

NOTE:

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.

Content

Space Tools

Overview

Release History

The LexEVS Grid Service

Using the API

Method Descriptions

getCodingSchemeConcepts

getFilter

getSortAlgorithm

getFilterExtensions

getServiceMetadata

getSupportedCodingSchemes

getLastUpdateTime

resolveCodingScheme

getNodeGraph

getMatchAlgorithms

getGenericExtensions

getGenericExtension

getHistoryService

getSortAlgorithms

resolveCodingSchemeCopyright

setSecurityToken

Usage Instructions

Service URL

Required Libraries

Downloads

Code Examples

Example API usage

Error Handling

Error Connecting to LexEVS Grid Service

LexBIG Errors

Invalid Service Context Access

Security Issues

Related Links

Content

Space Tools

LexEVS Grid Service 4.2 User Guide

Overview

Release History

The LexEVS Grid Service

Using the API

Method Descriptions

getCodingSchemeConcepts

getFilter

getSortAlgorithm

getFilterExtensions

getServiceMetadata

getSupportedCodingSchemes

getLastUpdateTime

resolveCodingScheme

getNodeGraph

getMatchAlgorithms

getGenericExtensions

getGenericExtension

getHistoryService

getSortAlgorithms

resolveCodingSchemeCopyright

setSecurityToken

Usage Instructions

Service URL

Required Libraries

Downloads

Code Examples

Example API usage

Error Handling

Error Connecting to LexEVS Grid Service

LexBIG Errors

Invalid Service Context Access

Security Issues

Related Links