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Introduction
This document is a section of the LexEVS 5.x Programmer's Guide.
The following table summarizes the operations available through the LexEVS Analytical Grid Service. Each of the operations is also defined in detail below. The grid analytical service and related operations are viewable via the caGrid Portal (http://cagrid-portal.nci.nih.gov)..
Using the API
There are two (2) different interfaces for accessing the LexEVS Grid Services:
org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter
, ororg.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 LexEVS API as much as possible. There is no object wrapping for semantic purposes on this interface. This allows existing applications of the LexEVS 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-analytical50.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-analytical50.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. |
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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: |
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Input: | Implementation: | |
Description: | Returns an instance of the filter extension registered with the given name. | |
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Exception: | RemoteException | |
Implementation Details: |
getSortAlgorithm
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Sample Call; | ||||
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Description: | Returns an instance of the sort extension registered with the given name. | |||
Input: | Sample Call:
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Exception: | RemoteException | |||
Implementation Details: |
getFilterExtensions
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Description: | Returns a description of all registered extensions used to provide additional filtering of query results. | |||
Input: | none | |||
Output |
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Exception: | RemoteException | |||
Implementation Details: |
Implementation:
Step 1: Call this method on the associated LexEVS Service instance (or Distributed LexEVS instance) on the server, and forward the results.
Sample Call:
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getFilter
getFilter(ExtensionIdentification)
Description: | Returns an instance of the filter extension registered with the given name. |
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Input: | org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification |
Output: | org.LexGrid.LexBIG.cagrid |
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.LexBIGCaGridServices.Filter.stubs.types.FilterReference | |
Exception: | RemoteException |
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Implementation Details: | Implementation :
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LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
Step 2: Invoke the LexEVS caGrid service as follows:
ExtensionDescriptionList extDescList = lbs.getFilterExtensions(); |
getServiceMetadata
Description: | Return an interface to perform system-wide query over metadata for loaded code systems and providers. |
Input: | none |
Output: |
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
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Sample Call:
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getSupportedCodingSchemes
getSortAlgorithm
getSortAlgorithm(ExtensionIdentification)
Description: | Returns an instance of the sort extension registered with the given name | Description: | Return a list of coding schemes and versions that are supported by this service, along with their status. |
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Input: | none org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification | ||
Output: | org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList.cagrid.LexBIGCaGridServices.Sort. | ||
Exception: | RemoteException | ||
Implementation Details: | Implementation:
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Sample Call:
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Sample Call: | Sample Call:
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LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
Step 2: Invoke the LexEVS caGrid service as follows:
CodingSchemeRenderingList csrl = lbs.getSupportedCodingSchemes(); |
getLastUpdateTime
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Description:
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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.
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Input:
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none
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Output:
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java.util.Date
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Exception:
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RemoteException
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Implementation Details:
Implementation:
Step 1: Call this method on the associated LexEVS Service instance (or Distributed LexEVS instance) on the server, and forward the results.
Sample Call:
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getFilterExtensions
getFilterExtensions()
Description: | Returns a description of all registered extensions used to provide additional filtering of query results |
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Date date = lbs.getLastUpdateTime(); |
resolveCodingScheme
Description: | Return detailed coding scheme information given a specific tag or version identifier. | ||
Input: | none | ||
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Output | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag | Output: | org.LexGrid.codingSchemes.CodingScheme Collections.ExtensionDescriptionList |
Exception: | RemoteException | ||
Implementation Details: |
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Implementation: | ||
Description: | Returns the node graph as represented in the particular relationship set in the coding scheme. | |
Step 1: Call this method on the associated LexEVS Service instance (or Distributed LexEVS instance) on the server, and forward the results.
| Input: |
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Output: | ''org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices. | |
Exception: | RemoteException | |
Implementation Details: |
getMatchAlgorithms
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getServiceMetadata
getServiceMetadata()
Description: | Return an interface to perform system-wide query over metadata for loaded code systems and providers | Description: | Returns the node graph as represented in the particular relationship set in the coding scheme. |
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Input: | none | ||
Output: | org.LexGrid.LexBIG.DataModel.Collections.ModuleDescriptionListcagrid.LexBIGCaGridServices.LexBIGServiceMetadata. | ||
Exception: | RemoteException | ||
Implementation Details: | Implementation:
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Sample Call:
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Sample Call: | Sample Call: '
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getSupportedCodingSchemes
getSupportedCodingSchemes()
Description: | Return a list of coding schemes and versions that are supported by this service, along with their status. |
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LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
Step 2: Invoke the LexEVS caGrid service as follows:
ModuleDescriptionList mdl = lbs.getMatchAlgorithms(); |
getGenericExtensions
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Description:
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Returns a description of all registered extensions used to implement application-specific behavior that is centrally accessible from a LexBIGService.
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Input: | none | ||
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Output: | org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionListCodingSchemeRenderingList | ||
Exception: | RemoteException | ||
Implementation Details: | Implementation:
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getLastUpdateTime
getLastUpdateTime()
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Description: | Returns an instance of the application-specific extension registered with the given nameReturn 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. |
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Input: | org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification none |
Output: | orgjava.LexGrid.LexBIG.DataModel.Collections.SortDescriptionListutil.Date |
Exception: | RemoteException |
Implementation Details: |
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Implementation: | ||||
Description: | Resolve a reference to the history api servicing the given coding scheme. | |||
Step 1: Call this method on the associated LexEVS Service instance (or Distributed LexEVS instance) on the server, and forward the results.
| Input: |
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HistoryService.stubs.types.HistoryServiceReference |
Exception: | RemoteException | |||
Implementation Details: |
getSortAlgorithms
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resolveCodingScheme
resolveCodingScheme(CodingSchemeIdentification, CodingSchemeVersionOrTag)
Description: | Return detailed coding scheme information given a specific tag or version identifier | Description: | Returns a description of all registered extensions used to provide additional filtering of query results. |
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Input: | org.LexGrid.LexBIG.DataModel.InterfaceElements.types.SortContextcagrid.CodingSchemeIdentification, org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag | ||
Output: | org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionListcodingSchemes.CodingScheme | ||
Exception: | RemoteException | ||
Implementation Details: |
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Implementation: | ||||||
Description: | Return coding scheme copyright given a specific tag or version identifier. | |||||
Step 1: Call this method on the associated LexEVS Service instance (or Distributed LexEVS instance) on the server, and forward the results.
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Exception: | RemoteException | |||||
Implementation Details: |
setSecurityToken
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Description: | Sets the Security Token for the given Coding Scheme. | |
Input: | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, gov.nih.nci.evs.security.SecurityToken | |
Output: |
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Exception: | RemoteException | |
Implementation Details: | ||
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getNodeGraph
getNodeGraph(CodingSchemeIdentification, CodingSchemeVersionOrTag, RelationContainerIdentification)
Description: | Returns the node graph as represented in the particular relationship set in the coding scheme. | ||||||||||
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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. | ||||||||||
Exception: | RemoteException | ||||||||||
Implementation Details: | Implementation:
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Sample Call: | Sample Call :
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getMatchAlgorithms
getMatchAlgorithms()
Description: | Returns the node graph as represented in the particular relationship set in the coding scheme. | ||||
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Input: | none | ||||
Output: | org.LexGrid.LexBIG.DataModel.Collections.ModuleDescriptionList | ||||
Exception: | RemoteException | ||||
Implementation Details: | Implementation:
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getGenericExtensions
getGenericExtensions()
Description: | Returns a description of all registered extensions used to implement application-specific behavior that is centrally accessible from a LexBIGService.
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Input: | none | |||||
Output: | org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList | |||||
Exception: | RemoteException | |||||
Implementation Details: | Implementation:
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getGenericExtension
getGenericExtensions(ExtensionIdentification)
Description: | Returns an instance of the application-specific extension registered with the given name. | |||||||
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Input: | org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification | |||||||
Output: | org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList | |||||||
Exception: | RemoteException | |||||||
Implementation Details: | Implementation :
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getHistoryService
getHistoryService(CodingSchemeIdentification)
Description: | Resolve a reference to the history api servicing the given coding scheme. | ||||
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Input: | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification | ||||
Output: | org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices. | ||||
Exception: | RemoteException | ||||
Implementation Details: | Implementation :
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Sample Call: | Sample Call :
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getSortAlgorithms
getSortAlgorithms(SortContext)
Description: | Returns a description of all registered extensions used to provide additional filtering of query results. | ||
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Input: | org.LexGrid.LexBIG.DataModel.InterfaceElements.types.SortContext | ||
Output: | org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList | ||
Exception: | RemoteException | ||
Implementation Details: | Implementation :
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resolveCodingSchemeCopyright
resolveCodingSchemeCopyright(CodingSchemeIdentification)
Description: | Return coding scheme copyright given a specific tag or version identifier. | ||||||
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Input: | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification | ||||||
Output: | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeCopyRight | ||||||
Exception: | RemoteException | ||||||
Implementation Details: | Implementation :
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setSecurityToken
setSecurityToken(CodingSchemeIdentification, SecurityToken)
Description: | Sets the Security Token for the given Coding Scheme. | ||||||||
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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 :
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Usage Instructions
Service URL
The LexEVS Grid Service 4.2 URL is: http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService.
The service is also accessible via the caGRID Portal.
Required Libraries
The libraries required for programmatic access to the LexEVS Grid Service are listed in the tables below. The 3rd Party Software Libraries required for use of the LexEVS API Grid Service are listed in Table 4.1 and the NCICB software captured under the caBIG® umbrella are listed in Table 4.2.Table 4.1 3rd Party Librariesthe following table.
Product | Jars | License | Home Page |
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Apache WS-Addressing | addressing-1.0.jar | From Globus 4.0.2 Java Web Services Core lib directory: http://www.globus.org/toolkit/downloads/4.0.2
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Apache Axis |
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Apache Xerces | xercesImpl.jar | http://xerces.apache.org/xerces-j | |
Apache Lucene |
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ASM - all purpose Java bytecode manipulation and analysis framework | asm.jar | http://asm.objectweb.org/license.html | |||||||
Castor | castor-1.2.jar |
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Globus Toolkit |
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Bouncy Castle Crypto APIs | jce-jdk13-125.jar | http://www.bouncycastle.org/licence.html | |
Open Permis |
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Apache | wss4j.jar | http://ws.apache.org/wss4j/license.html | |
Spring | spring.jar | http://www.springframework.org |
The following table lists the Table 4.2 NCICB/caBIG Libraries.
Library | Associated JARs |
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caGrid Software Libraries | caGrid-ServiceSecurityProvider-client-1.2.jar |
| caGrid-ServiceSecurityProvider-common-1.2.jar |
| caGrid-ServiceSecurityProvider-stubs-1.2.jar |
| caGrid-core-1.2.jar |
| caGrid-metadata-common-1.2.jar |
| caGrid-metadata-data-1.2.jar |
| caGrid-metadata-security-1.2.jar |
| caGrid-metadatautils-1.2.jar |
EVS API Libaries | evsapi42-beans.jar |
| evsapi42-framework.jar |
LexEVS Grid Service Client Library | LexEVSGridService-client.jar |
LexEVS Grid Service Stubs | LexEVSGridService-stubs.jar |
LexEVS Grid Service Common | LexEVSGridService-common.jar |
LexEVS Grid Service Service | LexEVSGridService-service.jar |
LexEVS Grid Service Tests | LexEVSGridService-tests.jar |
caCORE SDK Library | sdk-client-framework.jar |
LexEVS API | lexbig.jar |
Custom Castor Serializer | castor-bean-serializer.jar |
Downloads
For your convenience, the required libraries are available for download here:
https://gforge.nci.nih.gov/docman/view.php/491/14401/lexevs42-gridsrvc-jarslibs.jar.
In order to programmatically access the LexEVS API Grid Service, these libraries need to be added to your local classpath.
Code Examples
Example
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Client and Service Calls and SOAP
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Messages
See http://gforge.nci.nih.gov/docman/view.php/491/14252/TestClient.zip
Example API
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Usage
Example 1: Searching for concepts in NCI Thesaurus containing the string "Gene"
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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.
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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.
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This example shows a typical connection to the LexEVS Grid Service, with the two potential Exceptions being caught and handled as necessary.
LexEVS Errors
LexEVS errors will be forwarded through the Distributed LexEVS layer and then on to the Grid layer. Input parameters, along with any other LexEVS (or Distributed LexEVS) errors will be detected on the server, not the client, and forwarded. All Generic LexEVS (or Distributed LexEVS) errors will be forwarded via a RemoteException, with the cause of the error and underlying LexEVS error message included.
Invalid Service Context Access
Service Context Services are not meant to be called directly. If the client attempts to do so, an org.LexGrid.LexBIG.cagrid.LexEVSGridService.CodedNodeSet.stubs.types.InvalidServiceContextAccess Exception will be thrown. This indicates a call was made to a Service Context without obtaining a Service Context Reference via the Main Service (see the above section Service Contexts and State for more information).
Security Issues
LexEVS Grid Service Security
Certain vocabulary content accessible through the LexEVS Grid Service may require extra authorization to access. Each client is required to supply its own access credentials via Security Tokens. These Security Tokens are implemented by a SecurityToken object:
<font color="000FFF">Name{Name: SecurityToken
Namespace: gme://caCORE.caCORE/3.2/gov.nih.nci.evs.security
Package: gov.nih.nci.evs.
security</font>security
Accessing Secure Content
A client establishes access to a secured vocabulary via the following Grid Service Calls:
- Step 1: Connect to the LexEVS caGrid Service
LexBIGServiceGrid lbs = new
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- LexBIGServiceGridAdapter(url);
Step 2:Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification to hold the Coding Scheme name.
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Code Block CodingSchemeIdentification codingScheme = new CodingSchemeIdentification();
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codingScheme.setName(
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codingScheme"
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Step 3:Build an gov.nih.nci.evs.security.SecurityToken containing the security information for the desired Coding Scheme.
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Code Block SecurityToken token = new SecurityToken (); token.setAccessToken("securityToken");
Step 4:Invoke the LexEVS 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.
Code Block LexBIGServiceGrid lbsg = lbs.setSecurityToken(
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codingScheme, token);
It is important to note that the Grid Service "setSecurityToken" returns an
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_org.LexGrid.LexBIG.cagrid.LexEVSGridService.stubs.types
.LexEVSGridServiceReference.LexEVSGridServiceReference
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_ object. This reference must be used to access the secured vocabularies.
Implementation
Each call to "setSecurityToken" sets up a secured connection to Distributed LexEVS 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.
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If no SecurityTokens are passed in by the client, a non-secure Distributed LexEVS connection will be used. The server maintains one (and only one) un-secured Distributed LexEVS connection that is shared by any client not requesting security.NOTE:
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All non-secured information accessed by the LexEVS Grid Service is publicly available from NCICB and users are expected to follow the licensing requirements currently in place for accessing and using NCI EVS information. |
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