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Table of Contents
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Revision History

Content changes to this document from the previous to the current level are indicated by revision bars (|) unless a complete rewrite is indicated.

Date

Version

Description

Author

07/29/2008

1.0

Initial document

Kevin Peterson

8/30/2008

1.1

Revised for Security and Exception Handling

Kevin Peterson

Info
titleNote

If this document has been inspected, please indicate the inspection date that each version is based on in the "Change Description and Explanation" area. Entries in this log must be maintained for at least 3 years.

Document Purpose

This document provides the detailed design and implementation of LexBIG Enterprise Vocabulary Service (LexEVS) caGrid Service. It should be noted that the LexEVS Grid Service is no longer part of the caGrid 1.1 infrastructure and will be deployed as a separate unit. This is a change from the previous release of the LexEVS Grid Service.

The LexEVS caGrid service will allow programs to utilize the caGrid 1.2 infrastructure to access LexEVS information that is currently being produced by NCICB.

Implementation Overview

Team Members

The following table lists team members.

Role

Name

Development Lead

Kevin Peterson

Documentation Lead

Kevin Peterson

Project Manager

Tom Johnson

Description

The LexEVS grid service will be used to obtain data accessible via the EVS API 4.2 service, specifically, the Distributed LexBIG services. Please refer to the caCORE EVS API 4.0 technical guide for details on the EVS API 4.2 EVS APIs, and the LexBIG 2.3 Technical and Admin guide for details about LexBIG 2.3.

For more Documentation, Build/Deployment instructions and examples, visit the project documentation home on GForge.

Scope

The LexEVS Grid service will provide programmatic access to the LexBIG domain objects that are available via the LexBIG information model.

The LexEVS grid service will be registered in Cancer Data Standards Repository (caDSR) under the following category:

Category

LexEVS Grid Service

Context

caBIG

Classification Scheme

LexBIG

Version

LexBIG_v2_3_rv1

Architecture

...

The LexEVS Grid Service is implemented to expose the API and Model of LexBIG 2.3. For more information on LexBIG, see

http://informatics.mayo.eduImage Added.

...

LexEVS

...

Grid

...

Service

...

is

...

deployed

...

in

...

a

...

JBoss

...

Application

...

Server,

...

inside

...

of

...

a

...

Globus Web |Application installation. LexEVS Grid Service depends on EVSAPI, which is also deployed to a JBoss container. For more information on the deployment of EVSAPI, see:

Code Block
 (http://www.globus.org/) Web Application installation. LexEVS Grid Service depends on EVSAPI (http://evsapi.nci.nih.gov/), which is also deployed to a JBoss container. For more information on the deployment of EVSAPI, see http://gforge.nci.nih.gov/docman/index.php?group_id=366&selected_doc_group_id=1914&language_id=1

EVSAPI

...

itself

...

depends

...

on

...

an

...

installation

...

of

...

LexBIG.

The diagram below shows the various components of the LexEVS Grid Service System and how they interact.

diagram that shows the various components of the LexEVS Grid Service System and how they interactImage Added

LexEVS Grid Service and EVSAPI need not be deployed to physically separate servers, but it is recommended that if they are co-located on the same server, they should be deployed to separate JBoss containers.

Below is the LexEVS Grid Service Architecture, viewed from inside of the Web Service Container. For more information on how Service Contexts and Resources are used, see the section, Service Contexts and State below.

"diagram showing the LexEVS Grid Service ArchitectureImage Added

LexEVS Grid Service Class Diagram

The LexEVS Grid Service is built on the LexGrid/LexBIG model and implementation. For more information about this model, visit:

Code Block
 (http://informatics.mayo.edu). 

The diagram below shows the various components of the LexEVS Grid Service System and how they interact.

!LexEVS_GridService_System_Components.jpg|alt="diagram that shows the various components of the LexEVS Grid Service System and how they interact"! 

LexEVS Grid Service and EVSAPI need not be deployed to physically separate servers, but it is recommended that if they are co-located on the same server, they should be deployed to separate JBoss containers.

Below is the LexEVS Grid Service Architecture, viewed from inside of the Web Service Container. For more information on how Service Contexts and Resources are used, see the section, [Service Contexts and State|#Service Contexts and State] below.

!LexEVS_GridService_Architecture.jpg|alt="diagram showing the LexEVS Grid Service Architecture, viewed from inside of the Web Service Container"!

h4. LexEVS Grid Service Class Diagram

The LexEVS Grid Service is built on the LexGrid/LexBIG model and implementation.
For more information about this model, visit (LexBIG) https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/LexBIG_Core_Services/LexBIG-2.3/lexbig/lbModel/?root=lexevs
and (LexGrid

and

Code Block
) 
https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/LexBIG_Core_Services/LexBIG-2.3/lgModel/?root=lexevs
{highlight:color=red}(check links: gforge...note that these will be obsolete?){highlight}

Also, visit 2.3/lgModel/?root=lexevs

Also, visit http://informatics.mayo.edu

...

Image Added for

...

background

...

information

...

as

...

well

...

as

...

Class

...

Diagrams,

...

examples,

...

and

...

other

...

information.

...

For

...

information

...

specific

...

to

...

the

...

LexEVS

...

Grid

...

Service,

...

visit:

Code Block
 https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/LexBIG_Core_Services/LexBIG-2.3/lexbig/lbModel.cagrid/?root=lexevs

This

...

link

...

contains

...

Class

...

Diagrams

...

and

...

descriptions

...

for

...

input/output

...

parameters,

...

as

...

well

...

as

...

other

...

information

...

concerning

...

the Silver Level Compliance submission package.

LexEVS Grid Service Sequence Diagram

The sequence diagram for the operation "getSupportedCodingSchemes" is described below:

sequence diagram for getSupportedCodingSchemes operationImage Added

The following diagram shows a General Call Sequence from the client, through the caGrid Service, to the Distributed LexBIG and the returned results:

diagram showing a general call sequenceImage Added

Assumptions

  • The LexEVS service will be based on the latest EVSAPI 4.2 patch release built by NCICB.
  • The LexBIG 2.3 domain model will be loaded in the GME and caDSR.
  • The LexEVS Grid Service will not have any method level security. All security requirements will be handled by the actual deployment of the underlying EVSAPI 4.2 service. Please see the "Security" section below for more information on how the LexEVS Grid Service utilizes this security.
  • The LexEVS Grid Service will not be deployed as a "core" service by caGrid at NCICB as was previously done, but rather will now be deployed as a standalone service.
  • The LexEVS Grid Service release schedule will no longer be coupled to the caGrid deployment schedule as previously done.
  • Multiple version of LexEVS Grid Service may be active at the same instance in time depending solely on the availability of the underlining EVSAPI service.

Dependencies

  • EVSAPI 4.2 service needs to be available and running correctly.
  • The LexBIG 2.3 domain model needs to be registered in caDSR.
  • The LexEVS service and operations will use the Introduce toolkit to generate the appropriate structure for registering the service into caDSR.

Issues

  • None

Third Party Tools

  • Introduce Toolkit
  • Globus Toolkit (4.0.3) or appropriate version supported by caGrid 1.2
  • caGrid 1.2 core infrastructure

Implementation Contents

Server

The LexEVS Grid Service will be deployed as a "stand alone" grid service at NCICB.

Algorithms

None

Batch Processes

None

APIs

The main Service API exposed by the LexEVS Grid service will be the http://informatics.mayo.edu/LexGrid/downloads/javadocGrid/org/LexGrid/LexBIG/cagrid/interfaces/LexBIGServiceGrid.html

...

Image Added Interface.

...

All

...

other

...

APIs

...

will

...

not

...

be

...

directly

...

exposed,

...

but

...

will

...

be

...

made

...

available

...

through

...

Service

...

Contexts.

...

In

...

General,

...

API

...

calls

...

will

...

follow

...

the

...

sequence

...

which

...

is

...

shown

...

in

...

the

...

following

...

diagram:

...

  1. Client

...

  1. invokes

...

  1. caGrid

...

  1. service

...

  1. .

...

  1. caGrid

...

  1. Service

...

  1. uses

...

  1. Distributed

...

  1. LexBIG

...

  1. to

...

  1. implement

...

  1. call.

...

  1. Distributed

...

  1. LexBIG

...

  1. returns

...

  1. requested

...

  1. info

...

  1. to

...

  1. caGrid

...

  1. service.

...

  1. caGrid

...

  1. service

...

  1. sends

...

  1. response

...

  1. to

...

  1. client.

diagram showing the sequence of API callsImage Added

Main Service API

http://informatics.mayo.edu/LexGrid/downloads/javadocGrid/org/LexGrid/LexBIG/cagrid/interfaces/LexBIGServiceGrid.html

...

Image Added

Using the API

To use the LexEVS Grid Services, either org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

or

...

org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...

objects

...

may

...

be

...

instantiated.

...

These

...

are

...

two

...

different

...

Interfaces

...

for

...

accessing

...

the

...

Grid

...

Services.

...

  • org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  • -

...

  • 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

...

  • using

...

  • the

...

  • LexBIG

...

  • API

...

  • to

...

  • used

...

  • 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://...");

...

  • org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...

  • -

...

  • An

...

  • Interface

...

  • for

...

  • interacting

...

  • with

...

  • the

...

  • LexEVS

...

  • Grid

...

  • Services.

...

  • 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://...");

...

getCodingSchemeConcepts

getCodingSchemeConcepts(String,

...

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

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

...

  1. Return

...

  1. the

...

  1. Client

...

  1. Reference

...

  1. to

...

  1. the

...

  1. user.

...

  1. This

...

  1. Reference

...

  1. has

...

  1. the

...

  1. above

...

  1. org.LexGrid.LexBIG.LexBIGService.CodedNodeSet

...

  1. as

...

  1. a

...

  1. Resource.

...

  1. An

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.CodedNodeSetClient

...

  1. object

...

  1. is

...

  1. built

...

  1. from

...

  1. the

...

  1. above

...

  1. Reference.

...

Sample Call:

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Build

...

  1. a

...

  1. org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag

...

  1. containing

...

  1. the

...

  1. Version

...

  1. information

...

  1. for

...

  1. the

...

  1. desired

...

  1. Coding

...

  1. Scheme

...

  1. Code Block

...

  1. CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
    csvt.setVersion("testVersion");

...

  1. Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Coding

...

  1. Scheme

...

  1. name.

...

  1. Code Block

...

  1. CodingSchemeIdentification codingScheme = new CodingSchemeIdentification();
    codingScheme.setCode(code);

...

  1. Invoke the LexBIG caGrid service as follows:
    CodedNodeSetGrid cns = lbs.getCodingSchemeConcepts(codingScheme,

...

  1. 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

  1. Create a Resource on the server and populate it with the requested org.LexGrid.LexBIG.Extensions.Query.Filter

...

  1. Return

...

  1. the

...

  1. Client

...

  1. Reference

...

  1. to

...

  1. the

...

  1. user.

...

  1. This

...

  1. Reference

...

  1. has

...

  1. the

...

  1. above

...

  1. org.LexGrid.LexBIG.Extensions.Query.Filter

...

  1. as

...

  1. a

...

  1. Resource.

...

  1. This

...

  1. client

...

  1. is

...

  1. a

...

  1. Service

...

  1. Context

...

  1. that

...

  1. allows

...

  1. the

...

  1. user

...

  1. to

...

  1. call

...

  1. regular

...

  1. org.LexGrid.LexBIG.Extensions.Query.Filter

...

  1. API

...

  1. calls

...

  1. through

...

  1. the

...

  1. grid

...

  1. service.

...

  1. An

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.client.FilterClient

...

  1. object

...

  1. is

...

  1. built

...

  1. from

...

  1. the

...

  1. above

...

  1. Reference.

...

  1. This

...

  1. FilterClient

...

  1. implements

...

  1. the

...

  1. Interface

...

  1. org.LexGrid.LexBIG.Extensions.Query.Filter.

...

  1. This

...

  1. makes

...

  1. calling

...

  1. Grid

...

  1. Service

...

  1. Calls

...

  1. through

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.client.FilterClient

...

  1. transparent

...

  1. to

...

  1. the

...

  1. end

...

  1. user.

...

Sample Call

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Build

...

  1. an

...

  1. org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Extension

...

  1. name.

...

  1. Code Block

...

  1. ExtensionIdentification extension = new ExtensionIdentification();
    extension.setLexBIGExtensionName(name);

...

  1. Invoke the LexBIG caGrid service as follows:
    Filter filter = lbs.getFilter(extension);

...

getSortAlgorithm

getSortAlgorithm(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.Sort.

...


stubs.types.SortReference

...

Exception

RemoteException

Implementation Details

  1. Create a Resource on the server and populate it with the requested org.LexGrid.LexBIG.Extensions.Query.Sort

...

  1. Return

...

  1. the

...

  1. Client

...

  1. Reference

...

  1. to

...

  1. the

...

  1. user.

...

  1. This

...

  1. Reference

...

  1. has

...

  1. the

...

  1. above

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort.client.SortClient

...

  1. as

...

  1. a

...

  1. Resource.

...

  1. This

...

  1. client

...

  1. is

...

  1. a

...

  1. Service

...

  1. Context

...

  1. that

...

  1. allows

...

  1. the

...

  1. user

...

  1. to

...

  1. call

...

  1. regular

...

  1. org.LexGrid.LexBIG.Extensions.Query.Sort

...

  1. API

...

  1. calls

...

  1. through

...

  1. the

...

  1. grid

...

  1. service.

...

  1. An

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort.client.SortClient

...

  1. object

...

  1. is

...

  1. built

...

  1. from

...

  1. the

...

  1. above

...

  1. Reference.

...

  1. This

...

  1. SortClient

...

  1. implements

...

  1. the

...

  1. Interface

...

  1. org.LexGrid.LexBIG.Extensions.Query.Sort.

...

  1. This

...

  1. makes

...

  1. calling

...

  1. Grid

...

  1. Service

...

  1. Calls

...

  1. through

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort.client.SortClient

...

  1. transparent

...

  1. to

...

  1. the

...

  1. end

...

  1. user.

...

Sample Call

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Build

...

  1. an

...

  1. org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Extension

...

  1. name.

...

  1. Code Block

...

  1. ExtensionIdentification extension = new ExtensionIdentification();
    extension.setLexBIGExtensionName(name);

...

  1. 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

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Invoke

...

  1. the

...

  1. LexBIG

...

  1. caGrid

...

  1. service

...

  1. as

...

  1. follows:

...


  1. ExtensionDescriptionList

...

  1. extDescList

...

  1. =

...

  1. 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

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

...

  1. Return

...

  1. the

...

  1. LexBIGServiceMetadataClient

...

  1. to

...

  1. the

...

  1. user.

...

  1. This

...

  1. LexBIGServiceMetadataClient

...

  1. has

...

  1. the

...

  1. above

...

  1. org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata

...

  1. as

...

  1. a

...

  1. Resource.

...

  1. An

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.LexBIGServiceMetadataClient

...

  1. object

...

  1. is

...

  1. built

...

  1. from

...

  1. the

...

  1. above

...

  1. Reference.

...

Sample Call

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Invoke

...

  1. the

...

  1. LexBIG

...

  1. caGrid

...

  1. service

...

  1. as

...

  1. follows:

...


  1. LexBIGServiceMetadataGrid

...

  1. metadata

...

  1. =

...

  1. 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

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Invoke

...

  1. the

...

  1. LexBIG

...

  1. caGrid

...

  1. service

...

  1. as

...

  1. follows:

...


  1. CodingSchemeRenderingList

...

  1. csrl

...

  1. =

...

  1. 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

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call:

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Invoke

...

  1. the

...

  1. LexBIG

...

  1. caGrid

...

  1. service

...

  1. as

...

  1. follows:

...


  1. Date

...

  1. date

...

  1. =

...

  1. 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

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Build

...

  1. an

...

  1. org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Coding

...

  1. Scheme

...

  1. name.

...

  1. Code Block

...

  1. CodingSchemeIdentification codingScheme = new CodingSchemeIdentification();
    codingScheme.setCode(code);

...

  1. Build a org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag

...

  1. containing

...

  1. the

...

  1. Version

...

  1. information

...

  1. for

...

  1. the

...

  1. desired

...

  1. Coding

...

  1. Scheme

...

  1. Code Block

...

  1. CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
    csvt.setVersion("testVersion");

...

  1. Invoke the LexBIG caGrid service as follows:
    CodedNodeSetGrid cns = lbs.resolveCodingScheme(codingScheme,

...

  1. 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

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

...

  1. Return

...

  1. the

...

  1. Client

...

  1. Reference

...

  1. to

...

  1. the

...

  1. user.

...

  1. This

...

  1. Reference

...

  1. has

...

  1. the

...

  1. above

...

  1. org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph

...

  1. as

...

  1. a

...

  1. Resource.

...

  1. An

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.CodedNodeGraphClient

...

  1. object

...

  1. is

...

  1. built

...

  1. from

...

  1. the

...

  1. above Reference.

Sample Call

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Build

...

  1. an

...

  1. org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Coding

...

  1. Scheme

...

  1. name.

...

  1. Code Block

...

  1. CodingSchemeIdentification codingScheme = new 
    CodingSchemeIdentification();
    codingScheme.setCode(code);

...

  1. Build an org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag

...

  1. containing

...

  1. the

...

  1. Version

...

  1. information

...

  1. for

...

  1. the

...

  1. desired

...

  1. Coding

...

  1. Scheme

...

  1. Code Block

...

  1. CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
    csvt.setVersion("testVersion");

...

  1. Build an org.LexGrid.LexBIG.DataModel.cagrid.RelationContainerIdentification

...

  1. containing

...

  1. the

...

  1. Relation

...

  1. Container

...

  1. information.

...

  1. Code Block

...

  1. RelationContainerIdentification container = new 
    RelationContainerIdentification();
    container.setDc(name);

...

  1. Invoke the LexBIG caGrid service as follows, providing String parameters for the desired Coding Scheme and Relationship Name:
    CodedNodeGraphGrid cng = client.getNodeGraph(codingScheme,

...

  1. csvt,

...

  1. 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:

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call:

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Invoke

...

  1. the

...

  1. LexBIG

...

  1. caGrid

...

  1. service

...

  1. as

...

  1. follows:

...


  1. ModuleDescriptionList

...

  1. mdl

...

  1. =

...

  1. 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.

...


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:

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call:

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Invoke

...

  1. the

...

  1. LexBIG

...

  1. caGrid

...

  1. service

...

  1. as

...

  1. follows:

...


  1. ExtensionDescriptionList

...

  1. edl

...

  1. =

...

  1. 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:

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call:

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Info
    titleNote

    Currently this method will return a LexBIGServiceConvenienceMethods instance.

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Extension

...

  1. name.

...

  1. Code Block

...

  1. ExtensionIdentification extension = new ExtensionIdentification();
    extension.setLexBIGExtensionName("LexBIGServiceConvenienceMethods");

...

  1. Invoke the LexBIG caGrid service as follows:
    LexBIGServiceConvenienceMethodsGrid lbscm = lbs.getGenericExtensions(extension);

...

  1. Return

...

  1. the

...

  1. LexBIGServiceConvenienceMethodsClient

...

  1. to

...

  1. the

...

  1. user.

...

  1. This

...

  1. LexBIGServiceConvenienceMethodsClient

...

  1. has

...

  1. the

...

  1. above

...

  1. org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods

...

  1. as

...

  1. a

...

  1. Resource.

...

  1. An

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.CodedNodeGraphClient

...

  1. object

...

  1. is

...

  1. built

...

  1. from

...

  1. the

...

  1. above

...

  1. 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:

  1. Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.
  2. Return the HistoryServiceClient to the user. This HistoryServiceClient has the above org.LexGrid.LexBIG.History.HistoryService

...

  1. as

...

  1. a

...

  1. Resource.

...

  1. This

...

  1. Client

...

  1. is

...

  1. a

...

  1. Service

...

  1. Context

...

  1. that

...

  1. allows

...

  1. the

...

  1. user

...

  1. to

...

  1. call

...

  1. regular

...

  1. org.LexGrid.LexBIG.History.HistoryService

...

  1. API

...

  1. calls

...

  1. through

...

  1. the

...

  1. grid

...

  1. service.

...

  1. HistoryServiceClient

...

  1. implements

...

  1. the

...

  1. Interface

...

  1. org.LexGrid.LexBIG.History.HistoryService

...

  1. .

...

  1. This

...

  1. makes

...

  1. calling

...

  1. Grid

...

  1. Service

...

  1. Calls

...

  1. through

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.HistoryService.client.HistoryServiceClient

...

  1. transparent

...

  1. to

...

  1. the

...

  1. end

...

  1. user.

...

Sample Call:

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Build

...

  1. an

...

  1. org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Coding

...

  1. Scheme

...

  1. name.

...

  1. Code Block

...

  1. CodingSchemeIdentification codingScheme = new CodingSchemeIdentification();
    codingScheme.setCode(code);

...

  1. 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:

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call:

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Invoke

...

  1. the

...

  1. LexBIG

...

  1. caGrid

...

  1. service

...

  1. as

...

  1. follows:

...


  1. SortDescriptionList

...

  1. sortDescList

...

  1. =

...

  1. 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:

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call:

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Build

...

  1. an

...

  1. org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Coding

...

  1. Scheme

...

  1. name.

...

  1. Code Block

...

  1. CodingSchemeIdentification codingScheme = new CodingSchemeIdentification();
    codingScheme.setCode(code);

...

  1. Build an org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag

...

  1. containing

...

  1. the

...

  1. Version

...

  1. information

...

  1. for

...

  1. the

...

  1. desired

...

  1. Coding

...

  1. Scheme

...

  1. Code Block

...

  1. CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
    csvt.setVersion("testVersion");

...

  1. Invoke the LexBIG caGrid service as follows:
    CodingSchemeCopyRight copyright = lbs.resolveCodingSchemeCopyright(codingScheme,

...

  1. 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:

Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results.

Sample Call:

  1. Connect to the LexBIG caGrid Service using the org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter

...

  1. or

...

  1. org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Build

...

  1. an

...

  1. org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Coding

...

  1. Scheme

...

  1. name.

...

  1. Code Block

...

  1. CodingSchemeIdentification codingScheme = new CodingSchemeIdentification();
    codingScheme.setName("codingScheme");

...

  1. Build an gov.nih.nci.evs.security.SecurityToken

...

  1. containing

...

  1. the

...

  1. security

...

  1. information

...

  1. for

...

  1. the

...

  1. desired

...

  1. Coding

...

  1. Scheme.

...

  1. Code Block

...

  1. SecurityToken metaToken = new SecurityToken();
    metaToken.setAccessToken("token");

...

  1. 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,

...

  1. metaToken);

API Examples

For an example clients, service calls, and SOAP messages, see the LexEVS documentation on GForge.

Example API usage:

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

Code Block
}}  |

h3. API Examples

For an example clients, service calls, and SOAP messages, see http://gforge.nci.nih.gov/docman/index.php?group_id=491&selected_doc_group_id=3880&language_id=1

Example API usage:

*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}

h3. Service Contexts and State

Along with the Main Service (described above), the Server will also host the Service Contexts shown in the following diagram and described in the subsequent sections. These Service Contexts are not meant to be called directly as Grid Services. The main function of these Service Contexts is to provide additional functionality to the Main Service. 

!Service_Context_Operations_Example.jpg|alt="image showing the service contexts, which are detailed in the subsequent sections"!
 
*Service Context Operations Example in Introduce*
{warning:title=Important}Service Contexts are only meant to be called through the Main Service - not directly. Through the Main Service, References to these Service Contexts can be obtained. Calls are made to the Service Contexts through these References.{warning}

*Obtaining a Service Context Reference*
In the figure below, two LexEVS Grid Service Calls are highlighted, 'getCodingSchemeConcepts' and 'getNodeGraph'. These two Grid Service Calls have been selected because they return to the user a "Reference" to a Service Context. For 'getCodingSchemeConcepts', the return type is CodedNodeSetReference (which references the CodedNodeSet Service Context). For 'getNodeGraph', the return type is CodedNodeGraphReference (which references the CodedNodeGraph Service Context).

!Service_Context_Reference.jpg|alt="image that corresponds to the description in the preceding paragraph"!

*Resources*
LexEVS Grid Services use the WS-Resource Framework (WSRF) to allow for stateful calls to the server. When a client requests a Service Context, the client is not only issued a Reference to the Service Context that was requested, but to a unique stateful Resource on the server as well. This Resource is used in the LexEVS Grid Services as a way of statefully holding objects for further use by the client. For more information about how caGrid uses the WS-Resource Framework (WSRF), see 

Service Contexts and State

Along with the Main Service (described above), the Server will also host the Service Contexts shown in the following diagram and described in the subsequent sections. These Service Contexts are not meant to be called directly as Grid Services. The main function of these Service Contexts is to provide additional functionality to the Main Service.

"image showing the service contextsImage Added

Service Context Operations Example in Introduce

Warning
titleImportant

Service Contexts are only meant to be called through the Main Service - not directly. Through the Main Service, References to these Service Contexts can be obtained. Calls are made to the Service Contexts through these References.

Obtaining a Service Context Reference

In the figure below, two LexEVS Grid Service Calls are highlighted, 'getCodingSchemeConcepts' and 'getNodeGraph'. These two Grid Service Calls have been selected because they return to the user a "Reference" to a Service Context. For 'getCodingSchemeConcepts', the return type is CodedNodeSetReference (which references the CodedNodeSet Service Context). For 'getNodeGraph', the return type is CodedNodeGraphReference (which references the CodedNodeGraph Service Context).

image that corresponds to the description in the preceding paragraphImage Added

Resources

LexEVS Grid Services use the WS-Resource Framework (WSRF) to allow for stateful calls to the server. When a client requests a Service Context, the client is not only issued a Reference to the Service Context that was requested, but to a unique stateful Resource on the server as well. This Resource is used in the LexEVS Grid Services as a way of statefully holding objects for further use by the client. For more information about how caGrid uses the WS-Resource Framework (WSRF), see http://www.cagrid.org/wiki/Metadata:WSRF

...

Image Added

For

...

more

...

information

...

on

...

how

...

Resources

...

are

...

implemented

...

in

...

the

...

LexEVS

...

Grid

...

Service, refer to this LexEVSGrid presentation.

Service Context Sequence

The Service Contexts API calls follow this general process:

  1. Client Requests a Service Context, such as a CodedNodeSet.
  2. The Grid Node receives the call and forwards the call to EVSAPI.
  3. EVSAPI calls getCodingSchemeConcepts on the local LexBIG installation and returns a CodedNodeSetImpl object to the Grid Node.
  4. The Grid Node then creates a Resource to store this CodedNodeSetImpl object for future use by the Client.
  5. The Client is then returned a Service Context Client for the CodedNodeSet. This client is associated to the Resource that was created.

image that shows the previously described process of service contexts API callsImage Added

Service Context and Resource Assignment

Info
titleNote

By default, these services are destroyed 5 minutes after creation.

Supported Service Contexts.

CodedNodeSet

http://informatics.mayo.edu/LexGrid/downloads/javadocGrid/org/LexGrid/LexBIG/cagrid/interfaces/CodedNodeSetGrid.html

...

Image Added

To

...

construct

...

a

...

CodedNodeSet,

...

the

...

user

...

calls

...

getCodingSchemeConcepts

...

as

...

described

...

above.

...

When

...

the

...

user

...

creates

...

a

...

CodedNodeSet

...

through

...

the

...

API

...

call

...

getCodingSchemeConcepts,

...

the

...

server

...

creates

...

and

...

stores

...

the

...

CodedNodeSet

...

server-side

...

as

...

a

...

Resource.

...

This

...

Resource

...

is

...

associated

...

with

...

the

...

client

...

and

...

will

...

be

...

accessible

...

only

...

by

...

the

...

client

...

that

...

created

...

it.

...

CodedNodeSet

...

Call

...

Sequence:

...

  1. The

...

  1. user

...

  1. requests

...

  1. a

...

  1. CodedNodeSet

...

  1. using

...

  1. getCodingSchemeConcepts.

...


  1. :RequestCodedNodeSet_Snippet

...

  1. The

...

  1. server

...

  1. calls

...

  1. the

...

  1. Distributed

...

  1. LexBIG

...

  1. getCodingSchemeConcepts

...

  1. method,

...

  1. returning

...

  1. to

...

  1. the

...

  1. server

...

  1. an

...

  1. org.LexGrid.LexBIG.Impl.CodedNodeSetImpl

...

  1. (the

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.LexBIGService.CodedNodeSet)

...

  1. object.

...

  1. The

...

  1. server

...

  1. then

...

  1. creates

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeSet.service.globus.resource.CodedNodeSetResource.

...

  1. This

...

  1. Resource

...

  1. will

...

  1. be

...

  1. used

...

  1. to

...

  1. hold

...

  1. the

...

  1. instance

...

  1. of

...

  1. org.LexGrid.LexBIG.Impl.CodedNodeSetImpl,

...

  1. the

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.LexBIGService.CodedNodeSet

...

  1. that

...

  1. was

...

  1. created

...

  1. above.

...

  1. The

...

  1. server

...

  1. returns

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeSet.stubs.types.CodedNodeSetReference

...

  1. object

...

  1. to

...

  1. the

...

  1. client.

...

  1. This

...

  1. is

...

  1. the

...

  1. reference

...

  1. to

...

  1. the

...

  1. CodedNodeSet

...

  1. Service

...

  1. Context.

...

  1. This

...

  1. object

...

  1. has

...

  1. a

...

  1. direct

...

  1. reference

...

  1. to

...

  1. the

...

  1. Resource

...

  1. created

...

  1. above.

...

  1. The

...

  1. user

...

  1. now

...

  1. uses

...

  1. this

...

  1. client

...

  1. to

...

  1. make

...

  1. transparent

...

  1. Grid

...

  1. calls

...

  1. through

...

  1. the

...

  1. Service

...

  1. Context.

...

  1. The

...

  1. client

...

  1. may

...

  1. continue

...

  1. to

...

  1. make

...

  1. statefull

...

  1. calls

...

  1. to

...

  1. the

...

  1. CodedNodeSetClient

...

  1. and

...

  1. the

...

  1. assigned

...

  1. Resource.

...

  1. These

...

  1. restrictions

...

  1. are

...

  1. separate

...

  1. calls

...

  1. but

...

  1. statefully

...

  1. maintained

...

  1. on

...

  1. the

...

  1. server

...

  1. via

...

  1. the Resource.

CodedNodeGraph

http://informatics.mayo.edu/LexGrid/downloads/javadocGrid/org/LexGrid/LexBIG/cagrid/interfaces/CodedNodeGraphGrid.html

...

Image Added

To

...

construct

...

a

...

CodedNodeGraph,

...

the

...

user

...

calls

...

getNodeGraph

...

as

...

described

...

above.

...

When

...

the

...

user

...

creates

...

a

...

CodedNodeGraph

...

through

...

the

...

API

...

call

...

getNodeGraph,

...

the

...

server

...

creates

...

and

...

stores

...

the

...

CodedNodeGraph

...

server-side

...

as

...

a

...

Resource.

...

This

...

Resource

...

is

...

associated

...

with

...

the

...

client

...

and

...

will

...

be

...

accessible

...

only

...

by

...

the

...

client

...

that

...

created

...

it.

...

CodedNodeGraph

...

Call

...

Sequence:

...

  1. The

...

  1. user

...

  1. requests

...

  1. a

...

  1. CodedNodeGraph

...

  1. using

...

  1. getCodingSchemeConcepts.

...


  1. :RequestCodedNodeGraph_Snippet

...

  1. The

...

  1. server

...

  1. calls

...

  1. the

...

  1. Distributed

...

  1. LexBIG

...

  1. getNodeGraph

...

  1. method,

...

  1. returning

...

  1. to

...

  1. the

...

  1. server

...

  1. an

...

  1. org.LexGrid.LexBIG.Impl.CodedNodeGraphImpl

...

  1. (the

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph)

...

  1. object.

...

  1. The

...

  1. server

...

  1. then

...

  1. creates

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeGraph.service.globus.resource.CodedNodeGraphResource.

...

  1. This

...

  1. Resource

...

  1. will

...

  1. be

...

  1. used

...

  1. to

...

  1. hold

...

  1. the

...

  1. instance

...

  1. of

...

  1. org.LexGrid.LexBIG.Impl.CodedNodeGraphImpl,

...

  1. the

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph

...

  1. that

...

  1. was

...

  1. created

...

  1. above.

...

  1. The

...

  1. server

...

  1. returns

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeGraph.stubs.types.CodedNodeGraphReference

...

  1. object

...

  1. to

...

  1. the

...

  1. client.

...

  1. This

...

  1. is

...

  1. the

...

  1. reference

...

  1. to

...

  1. the

...

  1. CodedNodeGraph

...

  1. Service

...

  1. Context.

...

  1. This

...

  1. object

...

  1. has

...

  1. a

...

  1. direct

...

  1. reference

...

  1. to

...

  1. the

...

  1. Resource

...

  1. created

...

  1. above.

...

  1. The

...

  1. user

...

  1. now

...

  1. uses

...

  1. this

...

  1. client

...

  1. to

...

  1. make

...

  1. transparent

...

  1. Grid

...

  1. calls

...

  1. through

...

  1. the

...

  1. Service

...

  1. Context.

...

  1. The

...

  1. client

...

  1. may

...

  1. continue

...

  1. to

...

  1. make

...

  1. statefull

...

  1. calls

...

  1. to

...

  1. the

...

  1. CodedNodeGraphClient

...

  1. and

...

  1. the

...

  1. assigned

...

  1. Resource.

...

  1. For

...

  1. example,

...

  1. the

...

  1. client

...

  1. may

...

  1. add

...

  1. Restrictions

...

  1. to

...

  1. the

...

  1. CodedNodeGraph

...

  1. before

...

  1. a

...

  1. Resolve:

...


  1. :CodedNodeGraphRestriction_Snippet

...

  1. These

...

  1. restrictions

...

  1. are

...

  1. separate

...

  1. calls

...

  1. but

...

  1. statefully

...

  1. maintained

...

  1. on

...

  1. the

...

  1. server

...

  1. via

...

  1. the

...

  1. Resource

...

  1. .

...

LexBIGServiceConvenienceMethods

...

http://informatics.mayo.edu/LexGrid/downloads/javadocGrid/org/LexGrid/LexBIG/cagrid/interfaces/LexBIGServiceConvenienceMethodsGrid.html

...

Image Added

To

...

construct

...

a

...

LexBIGServiceConvenienceMethods,

...

the

...

user

...

calls

...

getGenericExtensions

...

as

...

described

...

above.

...

When

...

the

...

user

...

creates

...

a

...

LexBIGServiceConvenienceMethods

...

through

...

the

...

API

...

call

...

getGenericExtensions,

...

the

...

server

...

creates

...

and

...

stores

...

the

...

LexBIGServiceConvenienceMethods

...

server-side

...

as

...

a

...

Resource.

...

This

...

Resource

...

is

...

associated

...

with

...

the

...

client

...

and

...

will

...

be

...

accessible

...

only

...

by

...

the

...

client

...

that

...

created

...

it.

...

LexBIGServiceConvenienceMethods

...

Call

...

Sequence:

...

  1. The

...

  1. user

...

  1. requests

...

  1. a

...

  1. LexBIGServiceConvenienceMethods

...

  1. using

...

  1. getGenericExtensions.

...


  1. :RequestLexBIGServiceConvenienceMethods_Snippet

...

  1. The

...

  1. server

...

  1. calls

...

  1. the

...

  1. Distributed

...

  1. LexBIG

...

  1. getGenericExtensions

...

  1. method,

...

  1. returning

...

  1. to

...

  1. the

...

  1. server

...

  1. an

...

  1. org.LexGrid.LexBIG.Impl.Extensions.GenericExtensions.LexBIGServiceConvenienceMethodsImpl

...

  1. (the

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods)

...

  1. object.

...

  1. The

...

  1. server

...

  1. then

...

  1. creates

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceConvenienceMethods.service.globus.resource.LexBIGServiceConvenienceMethodsResource.

...

  1. This

...

  1. Resource

...

  1. will

...

  1. be

...

  1. used

...

  1. to

...

  1. hold

...

  1. the

...

  1. instance

...

  1. of

...

  1. org.LexGrid.LexBIG.Impl.Extensions.GenericExtensions.LexBIGServiceConvenienceMethodsImpl,

...

  1. the

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods

...

  1. that

...

  1. was

...

  1. created

...

  1. above.

...

  1. The

...

  1. server

...

  1. returns

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServicesLexBIGServiceConvenienceMethods.stubs.types.LexBIGServiceConvenienceMethodsReference

...

  1. object

...

  1. to

...

  1. the

...

  1. client.

...

  1. This

...

  1. is

...

  1. the

...

  1. reference

...

  1. to

...

  1. the

...

  1. LexBIGServiceConvenienceMethods

...

  1. Service

...

  1. Context.

...

  1. This

...

  1. object

...

  1. has

...

  1. a

...

  1. direct

...

  1. reference

...

  1. to

...

  1. the

...

  1. Resource

...

  1. created

...

  1. above.

...

  1. This

...

  1. LexBIGServiceConvenienceMethodsClient

...

  1. implements

...

  1. org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods.

...

  1. The

...

  1. user

...

  1. now

...

  1. uses

...

  1. this

...

  1. client

...

  1. to

...

  1. make

...

  1. transparent

...

  1. Grid

...

  1. calls

...

  1. through

...

  1. the

...

  1. Service

...

  1. Context.

...

  1. Because

...

  1. this

...

  1. LexBIGServiceConvenienceMethods

...

  1. implements

...

  1. org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods,

...

  1. API

...

  1. calls

...

  1. will

...

  1. look

...

  1. to

...

  1. the

...

  1. user

...

  1. as

...

  1. being

...

  1. identical

...

  1. to

...

  1. direct

...

  1. LexBIG

...

  1. API

...

  1. calls.

...

  1. The

...

  1. client

...

  1. may

...

  1. continue

...

  1. to

...

  1. make

...

  1. statefull

...

  1. calls

...

  1. to

...

  1. the

...

  1. LexBIGServiceConvenienceMethods

...

  1. Client

...

  1. and

...

  1. the

...

  1. assigned

...

  1. Resource.

...

  1. These

...

  1. API

...

  1. calls

...

  1. are

...

  1. separate

...

  1. calls

...

  1. but

...

  1. statefully

...

  1. maintained

...

  1. on

...

  1. the

...

  1. server

...

  1. via

...

  1. the

...

  1. Resource.

...

LexBIGServiceMetadata

http://informatics.mayo.edu/LexGrid/downloads/javadocGrid/org/LexGrid/LexBIG/cagrid/interfaces/LexBIGServiceMetadataGrid.html

...

Image Added

To

...

construct

...

a

...

LexBIGServiceMetadata,

...

the

...

user

...

calls

...

getServiceMetadata

...

as

...

described

...

above.

...

When

...

the

...

user

...

creates

...

a

...

LexBIGServiceMetadata

...

through

...

the

...

API

...

call

...

getServiceMetadata

...

,

...

the

...

server

...

creates

...

and

...

stores

...

the

...

LexBIGServiceMetadata

...

server-side

...

as

...

a

...

Resource.

...

This

...

Resource

...

is

...

associated

...

with

...

the

...

client

...

and

...

will

...

be

...

accessible

...

only

...

by

...

the

...

client

...

that

...

created

...

it.

...

LexBIGServiceMetadata

...

Call

...

Sequence:

...

  1. The

...

  1. user

...

  1. requests

...

  1. a

...

  1. LexBIGServiceMetadata

...

  1. using

...

  1. getServiceMetadata.

...


  1. :RequestLexBIGServiceMetadata_Snippet

...

  1. The

...

  1. server

...

  1. calls

...

  1. the

...

  1. Distributed

...

  1. LexBIG

...

  1. getServiceMetadata

...

  1. method,

...

  1. returning

...

  1. to

...

  1. the

...

  1. server

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata

...

  1. object.

...

  1. The

...

  1. server

...

  1. then

...

  1. creates

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceMetadata.service.globus.resource.LexBIGServiceMetadataResource.

...

  1. This

...

  1. Resource

...

  1. will

...

  1. be

...

  1. used

...

  1. to

...

  1. hold

...

  1. the

...

  1. instance

...

  1. of

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata.

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceMetadata.stubs.types.LexBIGServiceMetadata

...

  1. object

...

  1. to

...

  1. the

...

  1. client.

...

  1. This

...

  1. is

...

  1. the

...

  1. reference

...

  1. to

...

  1. the

...

  1. LexBIGServiceMetadata

...

  1. Service

...

  1. Context.

...

  1. This

...

  1. object

...

  1. has

...

  1. a

...

  1. direct

...

  1. reference

...

  1. to

...

  1. the

...

  1. Resource

...

  1. created

...

  1. above.

...

  1. The

...

  1. user

...

  1. now

...

  1. uses

...

  1. this

...

  1. client

...

  1. to

...

  1. make

...

  1. transparent

...

  1. Grid

...

  1. calls

...

  1. through

...

  1. the

...

  1. Service

...

  1. Context.

...

  1. The

...

  1. client

...

  1. may

...

  1. continue

...

  1. to

...

  1. make

...

  1. statefull

...

  1. calls

...

  1. to

...

  1. the

...

  1. LexBIGServiceMetadata

...

  1. and

...

  1. the

...

  1. assigned

...

  1. Resource.

...

  1. These

...

  1. API

...

  1. calls

...

  1. are

...

  1. separate

...

  1. calls

...

  1. but

...

  1. statefully

...

  1. maintained

...

  1. on

...

  1. the

...

  1. server

...

  1. via

...

  1. the

...

  1. Resource.

...

HistoryService

http://informatics.mayo.edu/LexGrid/downloads/javadocGrid/org/LexGrid/LexBIG/cagrid/interfaces/HistoryServiceGrid.html

...

Image Added

To

...

construct

...

a

...

HistoryService,

...

the

...

user

...

calls

...

getHistoryService

...

as

...

described

...

above.

...

When

...

the

...

user

...

creates

...

a

...

HistoryService

...

through

...

the

...

API

...

call

...

getHistoryService,

...

the

...

server

...

creates

...

and

...

stores

...

the

...

HistoryService

...

server-side

...

as

...

a

...

Resource.

...

This

...

Resource

...

is

...

associated

...

with

...

the

...

client

...

and

...

will

...

be

...

accessible

...

only

...

by

...

the

...

client

...

that

...

created

...

it.

...

HistoryService

...

Call

...

Sequence:

...

  1. The

...

  1. user

...

  1. requests

...

  1. a

...

  1. HistoryService

...

  1. using

...

  1. getHistoryService

...

  1. .

...


  1. :RequestHistoryService_Snippet

...

  1. The

...

  1. server

...

  1. calls

...

  1. the

...

  1. Distributed

...

  1. LexBIG

...

  1. getHistoryService

...

  1. method,

...

  1. returning

...

  1. to

...

  1. the

...

  1. server

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.History.HistoryService

...

  1. object.

...

  1. The

...

  1. server

...

  1. then

...

  1. creates

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.HistoryService.service.globus.resource.HistoryServiceResource.

...

  1. This

...

  1. Resource

...

  1. will

...

  1. be

...

  1. used

...

  1. to

...

  1. hold

...

  1. the

...

  1. instance

...

  1. of

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.History.HistoryService.

...

  1. The

...

  1. server

...

  1. returns

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceMetadata.stubs.types.LexBIGServiceMetadata

...

  1. object

...

  1. to

...

  1. the

...

  1. client.

...

  1. This

...

  1. is

...

  1. the

...

  1. reference

...

  1. to

...

  1. the

...

  1. HistoryService

...

  1. Service

...

  1. Context.

...

  1. This

...

  1. object

...

  1. has

...

  1. a

...

  1. direct

...

  1. reference

...

  1. to

...

  1. the

...

  1. Resource

...

  1. created

...

  1. above.

...

  1. The

...

  1. user

...

  1. now

...

  1. uses

...

  1. this

...

  1. client

...

  1. to

...

  1. make

...

  1. transparent

...

  1. Grid

...

  1. calls

...

  1. through

...

  1. the

...

  1. Service

...

  1. Context.

...

  1. The

...

  1. client

...

  1. may

...

  1. continue

...

  1. to

...

  1. make

...

  1. statefull

...

  1. calls

...

  1. to

...

  1. the

...

  1. HistoryServiceClient

...

  1. and

...

  1. the

...

  1. assigned

...

  1. Resource.

...

  1. For

...

  1. example,

...

  1. the

...

  1. client

...

  1. may

...

  1. call

...

  1. any

...

  1. method

...

  1. in

...

  1. org.LexGrid.LexBIG.History.HistoryService

...


  1. Example:

...

  1. history.getLatestBaseline();

...

  1. These

...

  1. API

...

  1. calls

...

  1. are

...

  1. separate

...

  1. calls

...

  1. but

...

  1. statefully

...

  1. maintained

...

  1. on

...

  1. the

...

  1. server

...

  1. via

...

  1. the

...

  1. Resource.

...

Sort

http://informatics.mayo.edu/LexGrid/downloads/javadoc/org/LexGrid/LexBIG/Extensions/Query/Sort.html

...

Image Added

To

...

construct

...

a

...

Sort,

...

the

...

user

...

calls

...

getSortAlgorithm

...

as

...

described

...

above.

...

When

...

the

...

user

...

creates

...

a

...

Sort

...

through

...

the

...

API

...

call

...

getSortAlgorithm,

...

the

...

server

...

creates

...

and

...

stores

...

the

...

Sort

...

server-side

...

as

...

a

...

Resource.

...

This

...

Resource

...

is

...

associated

...

with

...

the

...

client

...

and

...

will

...

be

...

accessible

...

only

...

by

...

the

...

client

...

that

...

created

...

it.

...

Sort

...

Call

...

Sequence:

...

  1. The

...

  1. user

...

  1. requests

...

  1. a

...

  1. Sort

...

  1. using

...

  1. getSortAlgorithm

...

  1. .

...


  1. :RequestSort_Snippet

...

  1. The

...

  1. server

...

  1. calls

...

  1. the

...

  1. Distributed

...

  1. LexBIG

...

  1. getSortAlgorithm

...

  1. method,

...

  1. returning

...

  1. to

...

  1. the

...

  1. server

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.Extensions.Query.Sort)

...

  1. object.

...

  1. The

...

  1. server

...

  1. then

...

  1. creates

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort

...

  1. .service.globus.resource.Sort

...

  1. Resource.

...

  1. This

...

  1. Resource

...

  1. will

...

  1. be

...

  1. used

...

  1. to

...

  1. hold

...

  1. the

...

  1. instance

...

  1. of

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.Extensions.Query.Sort.

...

  1. The

...

  1. server

...

  1. returns

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.SortClient

...

  1. object

...

  1. to

...

  1. the

...

  1. client.

...

  1. This

...

  1. is

...

  1. the

...

  1. client

...

  1. to

...

  1. the

...

  1. Sort

...

  1. Service

...

  1. Context.

...

  1. This

...

  1. object

...

  1. has

...

  1. a

...

  1. direct

...

  1. reference

...

  1. to

...

  1. the

...

  1. Resource

...

  1. created

...

  1. above.

...

  1. This

...

  1. SortClient

...

  1. implements

...

  1. org.LexGrid.LexBIG.Extensions.Query.Sort.

...

  1. The

...

  1. user

...

  1. now

...

  1. uses

...

  1. this

...

  1. client

...

  1. to

...

  1. make

...

  1. transparent

...

  1. Grid

...

  1. calls

...

  1. through

...

  1. the

...

  1. Service

...

  1. Context.

...

  1. Because

...

  1. this

...

  1. Sort

...

  1. implements

...

  1. org.LexGrid.LexBIG.Extensions.Query.Sort,

...

  1. API

...

  1. calls

...

  1. will

...

  1. look

...

  1. to

...

  1. the

...

  1. user

...

  1. as

...

  1. being

...

  1. identical

...

  1. to

...

  1. direct

...

  1. LexBIG

...

  1. API

...

  1. calls.

...

  1. The

...

  1. client

...

  1. may

...

  1. continue

...

  1. to

...

  1. make

...

  1. statefull

...

  1. calls

...

  1. to

...

  1. the

...

  1. SortClient

...

  1. and

...

  1. the

...

  1. assigned

...

  1. Resource.

...

  1. For

...

  1. example,

...

  1. the

...

  1. client

...

  1. may

...

  1. call

...

  1. any

...

  1. method

...

  1. in

...

  1. org.LexGrid.LexBIG.Extensions.Query.Sort

...


  1. :RequestSortCompare_Snippet

...

  1. These

...

  1. API

...

  1. calls

...

  1. are

...

  1. separate

...

  1. calls

...

  1. but

...

  1. statefully

...

  1. maintained

...

  1. on

...

  1. the

...

  1. server

...

  1. via

...

  1. the

...

  1. Resource.

...

Filter

http://informatics.mayo.edu/LexGrid/downloads/javadoc/org/LexGrid/LexBIG/Extensions/Query/Filter.htm

...

Image Added

To

...

construct

...

a

...

Filter,

...

the

...

user

...

calls

...

getFilter

...

as

...

described

...

above.

...

When

...

the

...

user

...

creates

...

a

...

Filter

...

through

...

the

...

API

...

call

...

getFilter,

...

the

...

server

...

creates

...

and

...

stores

...

the

...

Sort

...

server-side

...

as

...

a

...

Resource.

...

This

...

Resource

...

is

...

associated

...

with

...

the

...

client

...

and

...

will

...

be

...

accessible

...

only

...

by

...

the

...

client

...

that

...

created

...

it.

...

Filter

...

Call

...

Sequence:

...

  1. The

...

  1. user

...

  1. requests

...

  1. a

...

  1. Filter

...

  1. using

...

  1. getFilter

...


  1. :RequestFilter_Snippet

...

  1. The

...

  1. server

...

  1. calls

...

  1. the

...

  1. Distributed

...

  1. LexBIG

...

  1. getFilter

...

  1. method,

...

  1. returning

...

  1. to

...

  1. the

...

  1. server

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.Extensions.Query.Filter)

...

  1. object.

...

  1. The

...

  1. server

...

  1. then

...

  1. creates

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.service.globus.resource.FilterResource.

...

  1. This

...

  1. Resource

...

  1. will

...

  1. be

...

  1. used

...

  1. to

...

  1. hold

...

  1. the

...

  1. instance

...

  1. of

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.Extensions.Query.Filter.

...

  1. The

...

  1. server

...

  1. returns

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.FilterClient

...

  1. object

...

  1. to

...

  1. the

...

  1. client.

...

  1. This

...

  1. is

...

  1. the

...

  1. client

...

  1. to

...

  1. the

...

  1. Filter

...

  1. Service

...

  1. Context.

...

  1. This

...

  1. object

...

  1. has

...

  1. a

...

  1. direct

...

  1. reference

...

  1. to

...

  1. the

...

  1. Resource

...

  1. created

...

  1. above.

...

  1. This

...

  1. FilterClient

...

  1. implements

...

  1. org.LexGrid.LexBIG.Extensions.Query.Filter.

...

  1. The

...

  1. user

...

  1. now

...

  1. uses

...

  1. this

...

  1. client

...

  1. to

...

  1. make

...

  1. transparent

...

  1. Grid

...

  1. calls

...

  1. through

...

  1. the

...

  1. Service

...

  1. Context.

...

  1. Because

...

  1. this

...

  1. Filter

...

  1. implements

...

  1. org.LexGrid.LexBIG.Extensions.Query.Filter,

...

  1. API

...

  1. calls

...

  1. will

...

  1. look

...

  1. to

...

  1. the

...

  1. user

...

  1. as

...

  1. being

...

  1. identical

...

  1. to

...

  1. direct

...

  1. LexBIG

...

  1. API

...

  1. calls.

...

  1. The

...

  1. client

...

  1. may

...

  1. continue

...

  1. to

...

  1. make

...

  1. statefull

...

  1. calls

...

  1. to

...

  1. the

...

  1. FilterClient

...

  1. and

...

  1. the

...

  1. assigned

...

  1. Resource.

...

  1. For

...

  1. example,

...

  1. the

...

  1. client

...

  1. may

...

  1. call

...

  1. any

...

  1. method

...

  1. in

...

  1. org.LexGrid.LexBIG.Extensions.Query.Filter

...


  1. :RequestFilterMatch_Snippet

...

  1. These

...

  1. API

...

  1. calls

...

  1. are

...

  1. separate

...

  1. calls

...

  1. but

...

  1. statefully

...

  1. maintained

...

  1. on

...

  1. the

...

  1. server

...

  1. via

...

  1. the

...

  1. Resource.

...

ResolvedConceptReferencesIterator

http://informatics.mayo.edu/LexGrid/downloads/javadoc/org/LexGrid/LexBIG/Utility/Iterators/ResolvedConceptReferencesIterator.html

...

Image Added

A

...

ResolvedConceptReferencesIterator

...

is

...

created

...

when

...

a

...

CodedNodeSet

...

or

...

CodedNodeGraph

...

is

...

resolved.

...

It

...

allows

...

results

...

to

...

be

...

returned

...

from

...

the

...

server

...

incrementally

...

instead

...

of

...

all

...

at

...

once.

...

When

...

the

...

user

...

creates

...

a

...

ResolvedConceptReferencesIterator,

...

the

...

server

...

creates

...

and

...

stores

...

the

...

ResolvedConceptReferencesIterator

...

server-side

...

as

...

a

...

Resource.

...

This

...

Resource

...

is

...

associated

...

with

...

the

...

client

...

and

...

will

...

be

...

accessible

...

only

...

by

...

the

...

client

...

that

...

created

...

it.

...

ResolvedConceptReferencesIterator

...

Call

...

Sequence:

...

  1. The

...

  1. user

...

  1. gets

...

  1. a

...

  1. ResolvedConceptReferencesIterator

...

  1. from

...

  1. a

...

  1. Resolve.

...

  1. The

...

  1. server

...

  1. calls

...

  1. the

...

  1. Distributed

...

  1. LexBIG

...

  1. resolve

...

  1. method

...

  1. on

...

  1. the

...

  1. CodedNodeSet,

...

  1. returning

...

  1. to

...

  1. the

...

  1. server

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator

...

  1. object.

...

  1. The

...

  1. server

...

  1. then

...

  1. creates

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.ResolvedConceptReferencesIterator.service.globus.resource.ResolvedConceptReferencesIteratorResource.

...

  1. This

...

  1. Resource

...

  1. will

...

  1. be

...

  1. used

...

  1. to

...

  1. hold

...

  1. the

...

  1. instance

...

  1. of

...

  1. an

...

  1. implementation

...

  1. of

...

  1. org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator.

...

  1. The

...

  1. server

...

  1. returns

...

  1. an

...

  1. org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.ResolvedConceptReferencesIteratorClient

...

  1. object

...

  1. to

...

  1. the

...

  1. client.

...

  1. This

...

  1. is

...

  1. the

...

  1. client

...

  1. to

...

  1. the

...

  1. ResolvedConceptReferencesIterator

...

  1. Service

...

  1. Context.

...

  1. This

...

  1. object

...

  1. has

...

  1. a

...

  1. direct

...

  1. reference

...

  1. to

...

  1. the

...

  1. Resource

...

  1. created

...

  1. above.

...

  1. This

...

  1. ResolvedConceptReferencesIteratorClient

...

  1. implements

...

  1. org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator.

...

  1. The

...

  1. user

...

  1. now

...

  1. uses

...

  1. this

...

  1. client

...

  1. to

...

  1. make

...

  1. transparent

...

  1. Grid

...

  1. calls

...

  1. through

...

  1. the

...

  1. Service

...

  1. Context.

...

  1. Because

...

  1. this

...

  1. ResolvedConceptReferencesIterator

...

  1. implements

...

  1. org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator,

...

  1. API

...

  1. calls

...

  1. will

...

  1. look

...

  1. to

...

  1. the

...

  1. user

...

  1. as

...

  1. being

...

  1. identical

...

  1. to

...

  1. direct

...

  1. LexBIG

...

  1. API

...

  1. calls.

...

  1. The

...

  1. client

...

  1. may

...

  1. continue

...

  1. to

...

  1. make

...

  1. statefull

...

  1. calls

...

  1. to

...

  1. the

...

  1. ResolvedConceptReferencesIteratorClient

...

  1. and

...

  1. the

...

  1. assigned

...

  1. Resource.

...

  1. For

...

  1. example,

...

  1. the

...

  1. client

...

  1. may

...

  1. call

...

  1. any

...

  1. method

...

  1. in

...

  1. org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator

...


  1. :ResolvedConceptReferencesIterator_Snippet

...

  1. These

...

  1. API

...

  1. calls

...

  1. are

...

  1. separate

...

  1. calls

...

  1. but

...

  1. statefully

...

  1. maintained

...

  1. on

...

  1. the

...

  1. server

...

  1. via

...

  1. the

...

  1. Resource.

...

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.

...

:LexGridServiceConnection_Snippet

...

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).

...

Database

...

Changes

...

None

Client

The Introduce toolkit generates a "client"

...

class

...

that

...

will

...

be

...

provided

...

to

...

the

...

users.

...

JSP/HTML

None

Servlet

None

Security Issues

Security in the LexEVS Grid Service is implemented in the Distributed LexBIG layer. The information in this section explains how the LexEVS Grid Services utilize this security implementation. For more information about the Distributed LexBIG Security Implementation, see this documentation:

Code Block


None

h4. Servlet

None

h3. Security Issues

Security in the LexEVS Grid Service is implemented in the Distributed LexBIG layer. The information in this section explains how the LexEVS Grid Services utilize this security implementation. For more information about the Distributed LexBIG Security Implementation, see this documentation: 

http://gforge.nci.nih.gov/tracker/download.php/366/1462/10884/4060/Distributed_LexBIG_%20AccessTo_Licensed_Vocabulary_implemenation.doc
{highlight:color=red}(check link: gforge...note that this will be obsolete?){highlight}

h4. 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: 

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:

...

  1. Connect

...

  1. to

...

  1. the

...

  1. LexBIG

...

  1. caGrid

...

  1. Service

...


  1. LexBIGServiceGrid

...

  1. lbs

...

  1. =

...

  1. new

...

  1. LexBIGServiceGridAdapter(url);

...

  1. Build

...

  1. an

...

  1. org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

...

  1. to

...

  1. hold

...

  1. the

...

  1. Coding

...

  1. Scheme

...

  1. name.

...

  1. Code Block

...

  1. CodingSchemeIdentification codingScheme = new CodingSchemeIdentification();
    codingScheme.setName("codingScheme");

...

  1. Build an gov.nih.nci.evs.security.SecurityToken

...

  1. containing

...

  1. the

...

  1. security

...

  1. information

...

  1. for

...

  1. the

...

  1. desired

...

  1. Coding

...

  1. Scheme.

...

  1. Code Block

...

  1. SecurityToken token = new SecurityToken();
    token.setAccessToken("securityToken");

...

  1. 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,

...

  1. 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

...

of

...

Security

...

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} h3. Performance The LexEVS service will take advantage of all improvements made to the EVSAPI services with the exception of lazy loading. LexEVS grid service, being in nature a web service is currently not taking advantage of lazy loading since objects are transferred as fully populated objects. However, future releases of LexEVS Grid Service may refractor the interface in such as way as to take advantage of some of the benefits brought about by the inclusion of lazy loading in to EVSAPI service. LexEVS Grid Services utilize the performance enhancements of the LexBIG API. For more information about LexBIG performance (which LexEVS Grid Services are dependent on), see

Performance

The LexEVS service will take advantage of all improvements made to the EVSAPI services with the exception of lazy loading. LexEVS grid service, being in nature a web service is currently not taking advantage of lazy loading since objects are transferred as fully populated objects. However, future releases of LexEVS Grid Service may refractor the interface in such as way as to take advantage of some of the benefits brought about by the inclusion of lazy loading in to EVSAPI service.

LexEVS Grid Services utilize the performance enhancements of the LexBIG API.
For more information about LexBIG performance (which LexEVS Grid Services are dependent on), see http://informatics.mayo.edu

...

Image Added

Internationalization

Not Internationalized

Installation / Packaging

The service will be installed and deployed as a "stand alone" service at NCICB.

Migration

Both the current version of LexEVS grid service and a previous version may be "in service" simultaneously if the corresponding underlying EVSAPI service is also "in service" to manage migration of clients.

System Testing

See LexEVS Grid Service Testing Documentation

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