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title
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titleContents of this Page
Table of Contents
minLevel2

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.

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.gov).

...

Using the API

There are two (2)

...

different

...

interfaces

...

for

...

accessing

...

the

...

LexEVS

...

Grid

...

Services:

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. 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:
 Implementation: 
  • Step 1: Create a Resource on the server and populate it with the requested org.LexGrid.LexBIG.LexBIGService.CodedNodeSet
...
  • .
  • Step 2: Return the Client Reference to the user. This Reference has the above org.LexGrid.LexBIG.LexBIGService.CodedNodeSet
...
  •  as 
...
  •  a 
...
  •  Resource. 
...
  •  An 
...
  • org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.CodedNodeSetClient
...
  •  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 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:
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:
 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:
org.LexGrid.LexBIG.DataModel.cagrid.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 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.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.
Input:
org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification
...
Output:
...
org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.
...

HistoryService.stubs.types.HistoryServiceReference
...
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.
  • 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.History.HistoryService
...
  • . 
...
  •  This 
...
  •  makes 
...
  •  calling 
...
  •  Grid 
...
  •  Service 
...
  •  Calls 
...
  •  through 
...
  • org.LexGrid.LexBIG.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.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: 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:
 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: 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:
 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);
...
setSecurityToken
setSecurityToken(CodingSchemeIdentification, 
...
 SecurityToken)
...
–
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:
 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.setName("codingScheme");
...
  • Step 3: Build an gov.nih.nci.evs.security.SecurityToken
...
  •  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  

{code}
http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService
{code}

The service is also accessible via the [caGRID Portal|http://cagrid-portallexevsapi.nci.nih.gov/wsrf/webservices/guest/home;jsessionid=AEEE79C27E8EDB4EC0117C2CE8857D49].


h3. Required Libraries

The libraries required for programmatic access to the LexEVS Grid Service are listed in the following tables. 

The table below is the Third-Party Software Libraries required for use of the LexEVS API Grid Service. 

|| Product || Jars || License || Home Page ||
| Apache WS-Addressing | 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.
The table below is the Third-Party Software Libraries required for use of the LexEVS API Grid Service.
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
...
The table below lists the NCICB software captured under the caBIG® umbrella.
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 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, downoload the TestClient zip file.
Example API Usage
Searching for concepts in NCI Thesaurus containing the string "Gene"
 Code Block
 |


h3. 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. 


h3. Code Examples

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


h4. Example API usage

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

{code}//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()); 
}
{code}


h2. Error Handling


h3. Error Connecting to LexEVS Grid Service

When connecting through the Java Client, 
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.


{
 Code Block
}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();
}{code}


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);
...
  •  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.
...
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.


{:=
 Info
title
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.
 
{info}
 
h2. Related Links
[caGrid 1.2 Website:|https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/]
[LexBIG Core Services|https://gforge.nci.nih.gov/frs/?group_id=491]


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