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Overview
The cancer Biomedical Informatics Grid, or caBIG®, is a virtual informatics infrastructure that connects data, research tools, scientists, and organizations to leverage their combined strengths and expertise in an open environment with common standards and shared tools. The current test bed architecture of caBIG™, is dubbed caGrid. The software embodiment and corresponding documentation of this architecture constitute the caGrid 1.2 release.
This User Guide addresses the LexEVS Grid Service (version 4.2), from the perspective of a client application developer looking to interface with the referenced analytical grid service.
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The current version of the LexEVS Grid Service is 4.2 and it interfaces with the EVS API 4.2. |
Release History
Version Number | Date | Description |
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1.0 | Unknown | Original release of the EVS Grid Service. Interfaced with caCORE/EVS 3.1. |
4.1 | June 27, 2008 | Follow-on release of EVS Grid Service which interfaces with EVS API 4.1 (based on the EVS 3.2 OM). |
4.2 | October 11, 2008 | Follow-on release of EVS Grid Service 4.1 built on top of LexBIG server 2.3 which interfaces with EVS API 4.2 |
The LexEVS Grid Service
The following table summarizes the operations available through the LexEVS Analytical Grid Service. Each of the operations is also defined in detail below. The grid analytical service and related operations are viewable via the caGrid Portal (http://cagrid-portal.nci.nih.gov).
Using the API
There are two (2) different interfaces for accessing the LexEVS Grid Services:
org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter
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 LexBIG API as much as possible. There is no object wrapping for semantic purposes on this interface. This allows existing applications of the LexBIG API to use Grid Services without code changes.
This Interface may be acquired by instantiating LexBIGServiceAdapter with the Grid Service URL as a parameter.Code Block LexBIGService lbs = new LexBIGServiceAdapter("http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService");
- Option 2, org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter also provides an interface for interacting with the LexEVS Grid Services. However, this Interfaces is the semantically defined interface. All method parameters and return values are defined and annotated as CDEs to be loaded into caDSR. This Interface is intended to be caGrid Silver Level Compliant.
This Interface may be acquired by instantiating LexBIGServiceGridAdapter with the Grid Service URL as a parameter.Code Block LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter("http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService);
Method Descriptions
getCodingSchemeConcepts
getCodingSchemeConcepts(CodingSchemeIdentification, CodingSchemeVersionOrTag) | – |
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Description: | Returns the set of all (or all active) concepts in the specified coding scheme. |
Input: | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag |
Output: | org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeSet.stubs.types.CodedNodeSetReference |
Exception: | RemoteException |
Implementation Details: | Implementation:
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Sample Call | Sample Call
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getFilter
getFilter(ExtensionIdentification) | – |
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Description: | Returns an instance of the filter extension registered with the given name. |
Input: | org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification |
Output: | org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.stubs.types.FilterReference |
Exception: | RemoteException |
Implementation Details: | Implementation:
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Sample Call | Sample Call:
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getSortAlgorithm
getSortAlgorithm(ExtensionIdentification) | – |
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Description: | Returns an instance of the sort extension registered with the given name. |
Input: | org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification |
Output: | org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort |
Exception: | RemoteException |
Implementation Details: | Implementation:
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Sample Call | Sample Call:
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getFilterExtensions
getFilterExtensions() | – |
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Description: | Returns a description of all registered extensions used to provide additional filtering of query results. |
Input: | none |
Output | org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList |
Exception: | RemoteException |
Implementation Details: | Implementation: |
Sample Call | Sample Call:
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getServiceMetadata
getServiceMetadata() | – |
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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. |
Exception: | RemoteException |
Implementation Details: | Implementation:
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Sample Call | Sample Call:
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getSupportedCodingSchemes
getSupportedCodingSchemes() | – |
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Description: | Return a list of coding schemes and versions that are supported by this service, along with their status. |
Input: | none |
Output: | org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList |
Exception: | RemoteException |
Implementation Details: | Implementation: |
Sample Call | Sample Call:
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getLastUpdateTime
getLastUpdateTime() | – |
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Description: | Return the last time that the content of this service was changed; null if no changes have occurred. Tag assignments do not count as service changes for this purpose. |
Input: | none |
Output: | java.util.Date |
Exception: | RemoteException |
Implementation Details: | Implementation: |
Sample Call | Sample Call:
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resolveCodingScheme
resolveCodingScheme(CodingSchemeIdentification, CodingSchemeVersionOrTag) | – |
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Description: | Return detailed coding scheme information given a specific tag or version identifier. |
Input: | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag |
Output: | org.LexGrid.codingSchemes.CodingScheme |
Exception: | RemoteException |
Implementation Details: | Implementation:
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getNodeGraph
getNodeGraph(CodingSchemeIdentification, CodingSchemeVersionOrTag, RelationContainerIdentification) | – |
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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. |
Exception: | RemoteException |
Implementation Details: | Implementation:*
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Sample Call | Sample Call:
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getMatchAlgorithms
getMatchAlgorithms() | – |
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Description: | Returns the node graph as represented in the particular relationship set in the coding scheme. |
Input: | none |
Output: | org.LexGrid.LexBIG.DataModel.Collections.ModuleDescriptionList |
Exception: | RemoteException |
Implementation Details: | Implementation: |
Sample Call | Sample Call:
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getGenericExtensions
getGenericExtensions() | – | |||||
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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) | – | |||||
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Description: | Returns an instance of the application-specific extension registered with the given name. | |||||
Input: | org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification | |||||
Output: | org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList | |||||
Exception: | RemoteException | |||||
Implementation Details: | Implementation:
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getHistoryService
getHistoryService(CodingSchemeIdentification) | – |
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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. |
Exception: | RemoteException |
Implementation Details: | Implementation:
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Sample Call | Sample Call:
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getSortAlgorithms
getSortAlgorithms(SortContext) | – |
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Description: | Returns a description of all registered extensions used to provide additional filtering of query results. |
Input: | org.LexGrid.LexBIG.DataModel.InterfaceElements.types.SortContext |
Output: | org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList |
Exception: | RemoteException |
Implementation Details: | Implementation:
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resolveCodingSchemeCopyright
resolveCodingSchemeCopyright(CodingSchemeIdentification) | – | ||
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Description: | Return coding scheme copyright given a specific tag or version identifier. | ||
Input: | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification | ||
Output: | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeCopyRight | ||
Exception: | RemoteException | ||
Implementation Details: | Implementation:
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setSecurityToken
setSecurityToken(CodingSchemeIdentification, SecurityToken) | – |
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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: | 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:
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Link provided for historical purposes http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService |
The service is also accessible via the caGRID Portal.
Required Libraries
The libraries required for programmatic access to the LexEVS Grid Service are listed in the following tables.
The table below is the Third-Party Software Libraries required for use of the LexEVS API Grid Service.
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 | | ||||
Castor | castor-1.2.jar |
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Globus Toolkit |
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Bouncy Castle Crypto APIs | jce-jdk13-125.jar | ||||
Open Permis |
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Apache | wss4j.jar | ||||
Spring | spring.jar |
The table below lists the NCICB software captured under the caBIG® umbrella.
Library | Associated JARs |
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caGrid Software Libraries | caGrid-ServiceSecurityProvider-client-1.2.jar |
caGrid Software Libraries | caGrid-ServiceSecurityProvider-common-1.2.jar |
caGrid Software Libraries | caGrid-ServiceSecurityProvider-stubs-1.2.jar |
caGrid Software Libraries | caGrid-core-1.2.jar |
caGrid Software Libraries | caGrid-metadata-common-1.2.jar |
caGrid Software Libraries | caGrid-metadata-data-1.2.jar |
caGrid Software Libraries | caGrid-metadata-security-1.2.jar |
caGrid Software Libraries | caGrid-metadatautils-1.2.jar |
EVS API Libaries | evsapi42-beans.jar |
EVS API Libaries | evsapi42-framework.jar |
LexEVS Grid Service Client Library | LexEVSGridService-client.jar |
LexEVS Grid Service Stubs | LexEVSGridService-stubs.jar |
LexEVS Grid Service Common | LexEVSGridService-common.jar |
LexEVS Grid Service Service | LexEVSGridService-service.jar |
LexEVS Grid Service Tests | LexEVSGridService-tests.jar |
caCORE SDK Library | sdk-client-framework.jar |
LexBIG API | lexbig.jar |
Custom Castor Serializer | castor-bean-serializer.jar |
Downloads
For your convenience, the required libraries are available for download on GForge
In order to programmatically access the LexEVS API Grid Service, these libraries need to be added to your local classpath.
Code Examples
For an example client, service calls, and SOAP messages, downoload the TestClient zip file.
Example API Usage
Searching for concepts in NCI Thesaurus containing the string "Gene"
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//Create a Connection to the Grid Service LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(gridServiceURL); //Set up the CodingSchemeIdentification object to define the Coding Scheme CodingSchemeIdentification csid = new CodingSchemeIdentification(); csid.setName("NCI Thesaurus"); //Get the CodedNodeSet for that CodingScheme (This returns a CodedNodeSet Service Context) CodedNodeSetGrid cnsg = lbs.getCodingSchemeConcepts(csid, null); //getCodingSchemeConcepts is a Grid Service Call //Set the text to match MatchCriteria matchText = new MatchCriteria(); matchText.setText("Gene"); //Define a SearchDesignationOption, if any SearchDesignationOption searchOption = new SearchDesignationOption(); //Choose an algorithm to do the matching ExtensionIdentification matchAlgorithm = new ExtensionIdentification(); matchAlgorithm.setLexBIGExtensionName("contains"); //Chose a language LanguageIdentification language = new LanguageIdentification(); language.setIdentifier("en"); //Restrict the CodedNodeSet cnsg.restrictToMatchingDesignations(matchText, searchOption, matchAlgorithm, language); //restrictToMatchingDesignations is a Grid Service Call //Create a SetResolutionPolicy to handle the details of Resolving the CodedNodeSet //Here, we will set the Maximum number of Concepts returned to 10. SetResolutionPolicy resolvePolicy = new SetResolutionPolicy(); resolvePolicy.setMaximumToReturn(10); //Do the resolve ResolvedConceptReferenceList rcrlist = cnsg.resolveToList(resolvePolicy); //resolveToList is a Grid Service Call //Use the returned ResolvedConceptReferenceList to print some details about the concepts found ResolvedConceptReference[] rcref = rcrlist.getResolvedConceptReference(); for (int i = 0; i < rcref.length; i++) { System.out.println(rcref[i].getConceptCode()); System.out.println(rcref[i].getReferencedEntry(). getPresentation()[0].getText().getContent()); } |
Error Handling
Error Connecting to LexEVS Grid Service
When connecting through the Java Client, java.net.ConnectException and org.apache.axis.types.URI.MalformedURIException may be thrown upon an unsuccessful attempt to connect.
A MalformedURIException is thrown in the case if a poorly-formed URL string. In this case, the exception is thrown before an attempt to connect is even made.
If the URL is well-formed, proper connection is tested. If the connection attempt fails, a ConnectException is thrown containing the reason for the failure.
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try{ LexBIGServiceGridAdapter lbsg = new LexBIGServiceGridAdapter("http://localhost:8080/wsrf/services/cagrid/LexEVSGridService"); } catch(java.net.ConnectException e){ //Error Connecting e.printStackTrace(); } catch(org.apache.axis.types.URI.MalformedURIException e){ //URL Syntax Error e.printStackTrace(); } |
This example shows a typical connection to the LexEVS Grid Service, with the two potential Exceptions being caught and handled as necessary.
LexBIG Errors
LexBIG errors will be forwarded through the Distributed LexBIG layer and then on to the Grid layer. Input parameters, along with any other LexBIG (or Distributed LexBIG) errors will be detected on the server, not the client, and forwarded. All Generic LexBIG (or Distributed LexBIG) errors will be forwarded via a RemoteException, with the cause of the error and underlying LexBIG error message included.
Invalid Service Context Access
Service Context Services are not meant to be called directly. If the client attempts to do so, an org.LexGrid.LexBIG.cagrid.LexEVSGridService.CodedNodeSet.stubs.types.InvalidServiceContextAccess
Exception will be thrown. This indicates a call was made to a Service Context without obtaining a Service Context Reference via the Main Service (see the above section Service Contexts and State for more information).
Security Issues
LexEVS Grid Service Security
Certain vocabulary content accessible through the LexEVS Grid Service may require extra authorization to access. Each client is required to supply its own access credentials via Security Tokens. These Security Tokens are implemented by a SecurityToken object:
Name: SecurityToken Namespace: gme://caCORE.caCORE/3.2/gov.nih.nci.evs.security Package: gov.nih.nci.evs.security
Accessing Secure Content
A client establishes access to a secured vocabulary via the following Grid Service Calls:
- Step 1: Connect to the LexBIG caGrid Service
LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
- Step 2: Build an
org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification
to hold the Coding Scheme name.
CodingSchemeIdentification codingScheme = new CodingSchemeIdentification(); codingScheme.setName("codingScheme");
- Step 3: Build an
gov.nih.nci.evs.security.SecurityToken
containing the security information for the desired Coding Scheme.
SecurityToken token = new SecurityToken (); token.setAccessToken("securityToken");
- Step 4: Invoke the LexBIG caGrid service as follows: This will return a reference to a new "LexBIGServiceGrid" instance that is associated with the security properties that were passed in.
LexBIGServiceGrid lbsg = lbs.setSecurityToken(codingScheme, token);
Info title Note The Grid Service "setSecurityToken" returns an
org.LexGrid.LexBIG.cagrid.LexEVSGridService.stubs.types .LexEVSGridServiceReference.LexEVSGridServiceReference
object. This reference must be used to access the secured vocabularies.
Implementation
Each call to "setSecurityToken" sets up a secured connection to Distributed LexBIG with the access privileges included in the SecurityToken parameter. The LexEVSGridServiceReference that is returned to the client contains a unique key identifier to the secure connection that has been created on the server. All subsequent calls the client makes through this LexEVSGridServiceReference will be made securely. If additional SecurityTokens are passed in through the "setSecurityToken" Grid Service, the additional security will be added and maintained.
The "setSecurityToken" Grid Service is a stateful service. This means that after the client sets a SecurityToken, any subsequent call will be applied to that SecurityToken.
Secure connections are not maintained on the server indefinitely, but are based on load conditions. The server will allow 30 unique secure connections to be set up for clients without any time limitations. As additional requests for secure connections are received by the server, connections will be released by the server on an 'oldest first' basis. No connection, however, may be released prior to 5 minutes after its creation.
If no SecurityTokens are passed in by the client, a non-secure Distributed LexBIG connection will be used. The server maintains one (and only one) un-secured Distributed LexBIG connection that is shared by any client not requesting security.
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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. |
Related Links
caGrid page on caBIG website
LexBIG Core Services
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