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

...

Info
titleNote

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.govImage Removed).

Using the API

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

  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);

Method Descriptions

getCodingSchemeConcepts

getCodingSchemeConcepts(CodingSchemeIdentification, CodingSchemeVersionOrTag)

–

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:

...

Input:

Implementation:

Description:

Returns an instance of the filter extension registered with the given name.

Description:

Returns an instance of the sort extension registered with the given name.

Input:

  • Step 1: Create a Resource on the server and populate it with the requested org.LexGrid.LexBIG.
DataModel
  • LexBIGService.
cagrid
  • CodedNodeSet.
ExtensionIdentification

Output:

org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.stubs.types.FilterReference

Exception:

RemoteException

Implementation Details:

getSortAlgorithm

  • Step 2: Return the Client Reference to the user. This Reference has the above org.LexGrid.LexBIG.
DataModel.cagrid.ExtensionIdentification

Output:

''
  • LexBIGService.CodedNodeSet as a Resource. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.
Sort.
stubs.types.SortReference''

Exception:

RemoteException

Implementation Details:

getFilterExtensions

  • service.CodedNodeSetClient object is built from the above Reference.

Sample Call

Description:

Returns a description of all registered extensions used to provide additional filtering of query results.

Input:

none

Output

Sample Call

  • Step 1: Connect to the LexBIG caGrid Service using the
    org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter
    or
  • org.LexGrid.LexBIG.
DataModel
  • cagrid.
Collections
  • adapters.
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:

...

  • LexBIGServiceGridAdapter
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
  • Step 2: Build a org.LexGrid.LexBIG.

...

  • DataModel.

...

  • Core.CodingSchemeVersionOrTag containing the Version information for the desired Coding Scheme
    CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag(); csvt.setVersion("testVersion");
  • Step 3: Build an org.LexGrid.LexBIG.DataModel.cagrid.

...

  • CodingSchemeIdentification to hold the Coding Scheme name.
    CodingSchemeIdentification codingScheme = new CodingSchemeIdentification(); codingScheme.setCode(code);
  • Step

...

  • 4: Invoke the LexBIG caGrid service as follows:

...

  • CodedNodeSetGrid cns = lbs.

...

  • getCodingSchemeConcepts(codingScheme, csvt);

...

getFilter

getFilter(ExtensionIdentification)

–

...

Description:

Return an interface to perform system-wide query over metadata for loaded code systems and providersReturns an instance of the filter extension registered with the given name.

Input:

none org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification

Output:

org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceMetadataFilter.
stubs.types.LexBIGServiceMetadataReferenceFilterReference

Exception:

RemoteException

Implementation Details:

Implementation:

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

...

  • Extensions.Query.Filter.

...

  • Step 2: Return the

...

  • Client Reference to the user. This

...

  • Reference has the above org.LexGrid.LexBIG.

...

  • Extensions.Query.

...

  • Filter as a Resource. This client is a Service Context that allows the user to call regular org.LexGrid.LexBIG.Extensions.Query.Filter API calls through the grid service. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.

...

  • Filter.client.FilterClient}} object is built from the above Reference. This FilterClient implements the Interface org.LexGrid.LexBIG.Extensions.Query.Filter. This makes calling Grid Service Calls through org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.client.FilterClient transparent to the end user.

Sample Call

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.ExtensionIdentification to hold the Extension name.
    ExtensionIdentification extension = new ExtensionIdentification(); extension.setLexBIGExtensionName(name);
  • Step 3: Invoke the LexBIG caGrid service as follows:
    Filter filter = lbs.getFilter(extension);

getSortAlgorithm

getSortAlgorithm(ExtensionIdentification)

–

Description:

Returns an instance of the sort extension registered with the given name.

Input:

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.CodingSchemeRenderingListcagrid.ExtensionIdentification

Output:

org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort
stubs.types.SortReference

Exception:

RemoteException

Implementation Details:

Implementation :

  • Step 1:

...

  • Create a Resource on the server

...

  • and

...

Sample Call:

...

  • populate it with the requested org.LexGrid.LexBIG.Extensions.Query.Sort
  • Step 2: Return the Client Reference to the user. This Reference has the above org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort.client.SortClient as a Resource. This client is a Service Context that allows the user to call regular org.LexGrid.LexBIG.Extensions.

...

  • Query.Sort API calls through the grid service. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.

...

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:

  • Sort.client.SortClient object is built from the above Reference. This SortClient implements the Interface org.LexGrid.LexBIG.Extensions.Query.Sort. This makes calling Grid Service Calls through org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort.client.SortClient transparent to the end user.

Sample Call

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.ExtensionIdentification to hold the Extension name.
    ExtensionIdentification extension = new ExtensionIdentification(); extension.setLexBIGExtensionName(name);
  • Step 3: Invoke the LexBIG caGrid service as follows:
    Filter filter = lbs.getSortAlgorithm(extension);

getFilterExtensions

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

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

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

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

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

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

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

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

resolveCodingScheme(CodingSchemeIdentification, CodingSchemeVersionOrTag)

–

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:

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 CodingSchemeIdentification(); codingScheme.setCode(code);
  • Step 3: Build a 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: CodedNodeSetGrid cns = lbs.resolveCodingScheme(codingScheme, csvt);

getNodeGraph

getNodeGraph(CodingSchemeIdentification, CodingSchemeVersionOrTag, RelationContainerIdentification)

–

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:

Implementation :*

  • Step 1: Create a Resource on the server and populate it with the requested org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph.
  • Step 2: Return the Client Reference to the user. This Reference has the above org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph as a Resource. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.CodedNodeGraphClient object is built from the above Reference.

Sample Call

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 CodingSchemeIdentification(); codingScheme.setCode(code);
  • 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: Build an org.LexGrid.LexBIG.DataModel.cagrid.RelationContainerIdentification containing the Relation Container information.
    RelationContainerIdentification container = new RelationContainerIdentification(); container.setDc(name);
  • Step 5: Invoke the LexBIG caGrid service as follows, providing String parameters for the desired Coding Scheme and Relationship Name: CodedNodeGraphGrid cng = client.getNodeGraph(codingScheme, csvt, container);

getMatchAlgorithms

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

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

getGenericExtensions()

–

Description:

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

Info
titleNote

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

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.

getHistoryService

getHistoryService(CodingSchemeIdentification)

–

Description:

Resolve a reference to the history api servicing the given coding scheme

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,

Output:

org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag

Output:

org.LexGrid.codingSchemes.CodingScheme cagrid.LexBIGCaGridServices.
HistoryService.stubs.types.HistoryServiceReference

Exception:

RemoteException

Implementation Details:

...

Input:

Implementation :

Description:

Returns the node graph as represented in the particular relationship set in the coding scheme.

  • Step 1: Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.
  • Step 2: Return the HistoryServiceClient to the user. This HistoryServiceClient has the above org.LexGrid.LexBIG.History.HistoryService as a Resource. This Client is a Service Context that allows the user to call regular org.LexGrid.LexBIG.History.HistoryService API calls through the grid service. HistoryServiceClient implements the Interface
  • org.LexGrid.LexBIG.
DataModel
  • History.
cagrid.CodingSchemeIdentification,
  • HistoryService. This makes calling Grid Service Calls through org.LexGrid.LexBIG
.DataModel.Core.CodingSchemeVersionOrTag,
  • .cagrid.LexBIGCaGridServices.HistoryService.client.HistoryServiceClient transparent to the end user.

Sample Call

Sample Call :

  • Step 1: Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.
DataModel
  • cagrid.
cagrid.RelationContainerIdentification

Output:

Description:

Returns the node graph as represented in the particular relationship set in the coding scheme.

Input:

none

Output:

''
  • adapters.LexBIGServiceAdapter or org.LexGrid.LexBIG.cagrid.
LexBIGCaGridServices
  • adapters.

CodedNodeGraph.stubs.types.CodedNodeGraphReference''

Exception:

RemoteException

Implementation Details:

getMatchAlgorithms

  • LexBIGServiceGridAdapter
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
  • Step 2: Build an
  • 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:

...

  • .cagrid.CodingSchemeIdentification to hold the Coding Scheme name.
    CodingSchemeIdentification codingScheme = new CodingSchemeIdentification(); codingScheme.setCode(code);
  • Step 3: Invoke the LexBIG caGrid service as follows: HistoryServiceGrid history = lbs.getHistoryService(codingScheme);

getSortAlgorithms

getSortAlgorithms(SortContext)

–

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:

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:

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.
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:

...

  • cagrid.adapters.LexBIGServiceGridAdapter
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
  • Step 2: Invoke the LexBIG caGrid service as follows: SortDescriptionList sortDescList = lbs.getSortAlgorithms(sortContext);

resolveCodingSchemeCopyright

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:

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:

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.
DataModel
  • cagrid.
cagrid.ExtensionIdentification

Output:

Description:

Resolve a reference to the history api servicing the given coding scheme.

Input:

  • adapters.LexBIGServiceAdapter or org.LexGrid.LexBIG.
DataModel
  • cagrid.
Collections
  • adapters.
SortDescriptionList

Exception:

RemoteException

Implementation Details:

getHistoryService

  • LexBIGServiceGridAdapter
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  • Step 2: Build an

  • org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

Output:

  • to hold the Coding Scheme name.
    CodingSchemeIdentification codingScheme = new

    Code Block
    CodingSchemeIdentification();

    codingScheme.setCode;

  • Step 3: Build an org.LexGrid.LexBIG.
cagrid
  • DataModel.
LexBIGCaGridServices.
HistoryService.stubs.types.HistoryServiceReference

Exception:

RemoteException

Implementation Details:

getSortAlgorithms

  • 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);

setSecurityToken

setSecurityToken(CodingSchemeIdentification, SecurityToken)

–

Description:

Sets the Security Token for the given Coding Scheme

Description:

Returns a description of all registered extensions used to provide additional filtering of query results.

Input:

org.LexGrid.LexBIG.DataModel.InterfaceElements.types.SortContext.cagrid.CodingSchemeIdentification, gov.nih.nci.evs.security.SecurityToken

Output:

org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList.cagrid.LexEVSGridService.stubs.types.LexEVSGridServiceReference.LexEVSGridServiceReference

Exception:

RemoteException

Implementation Details:

...

Input:

Implementation :

Description:

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

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.
DataModel
  • cagrid.adapters.
cagrid.CodingSchemeIdentification

Output:

Description:

Sets the Security Token for the given Coding Scheme.

Input:

org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification,
  • LexBIGServiceGridAdapter.
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
  • Step 2: Build an org.LexGrid.LexBIG.DataModel.cagrid.
CodingSchemeCopyRight

Exception:

RemoteException

Implementation Details:

setSecurityToken

  • CodingSchemeIdentification to hold the Coding Scheme name.
    CodingSchemeIdentification codingScheme = new
    CodingSchemeIdentification(); codingScheme.setName("codingScheme");
  • Step 3: Build an
  • gov.nih.nci.evs.security.SecurityToken

Output:

org.LexGrid.LexBIG.cagrid.LexEVSGridService.stubs.types.LexEVSGridServiceReference.LexEVSGridServiceReference

Exception:

RemoteException

Implementation Details:

  • containing the security information for the desired Coding Scheme.
    SecurityToken metaToken = new SecurityToken();
    metaToken.setAccessToken("token");
  • 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, metaToken);

Usage Instructions

Service URL

The LexEVS Grid Service 4.2 URL is:

Code Block
Link provided for historical purposes 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 following tables below. The 3rd

The table below is the Third-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

Image Removed


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-jImage Removed

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

Image Removed

http://asm.objectweb.org/

Image Removed

Castor

castor-1.2.jar

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

Image Removed

Code Block
Link provided for historical purposes http://www.castor.org/index.html
Image Removed

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

Image Removed

http://www.bouncycastle.org/

Image Removed

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

Image Removed

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

Image Removed

Spring

spring.jar

Spring LICENSE

http://www.springframework.org

Image Removed

The table below lists the NCICB software captured under the caBIG® umbrella.Table 4.2 NCICB/caBIG Libraries

Library

Associated JARs

caGrid Software Libraries

caGrid-ServiceSecurityProvider-client-1.2.jar

caGrid Software Libraries

caGrid-ServiceSecurityProvider-common-1.2.jar

caGrid Software Libraries

caGrid-ServiceSecurityProvider-stubs-1.2.jar

caGrid Software Libraries

caGrid-core-1.2.jar

caGrid Software Libraries

caGrid-metadata-common-1.2.jar

caGrid Software Libraries

caGrid-metadata-data-1.2.jar

caGrid Software Libraries

caGrid-metadata-security-1.2.jar

caGrid Software Libraries

caGrid-metadatautils-1.2.jar

EVS API Libaries

evsapi42-beans.jar

EVS API Libaries

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.jarImage Removed. for download on GForge

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.zipImage Removed downoload the TestClient zip file.

Example API

...

Usage

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

Code Block
//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.

...

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:

<font color="000FFF">NameName: SecurityToken
Namespace: gme://caCORE.caCORE/3.2/gov.nih.nci.evs.security
Package: gov.nih.nci.evs.security</font>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);

    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.

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.

...

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.

...

...

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