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Search Algorithm

Code Block

    Name: LuceneQuery
    Version: 1.0
    Description: Search with the Lucene query syntax.  
    See http://lucene.apache.org/java/2_3_2/queryparsersyntax.html

Search Algorithm

Code Block

    Name: DoubleMetaphoneLuceneQuery
    Version: 1.0
    Description: Search with the Lucene query syntax, using a 'sounds like' algorithm.  
    A search for 'atack' will get a hit on 'attack'  
    See http://lucene.apache.org/java/2_3_2/queryparsersyntax.html

Search Algorithm

Code Block

    Name: StemmedLuceneQuery
    Version: 1.0
    Description: Search with the Lucene query syntax, using stemmed terms.  
    A search for 'trees' will get a hit on 'tree'  
    See http://lucene.apache.org/java/2_3_2/queryparsersyntax.html

Search Algorithm

Code Block

    Name: startsWith
    Version: 1.0
    Description: Equivalent to 'term*' (case insensitive)

Search Algorithm

Code Block

    Name: exactMatch
    Version: 1.0
    Description: Exact match (case insensitive)

Search Algorithm

Code Block

    Name: contains
    Version: 1.0
    Description: Equivalent to '* term* *' - in other words - a trailing wildcard on a term 
    (but no leading wild card) and the term can appear at any position.

Search Algorithm

Code Block

    Name: RegExp
    Version: 1.0
    Description: A Regular Expression query.  Searches against the lowercased text, so a 
    regular expression that specifies an uppercase character will never return a match.  
    Additionally, this searches against the entire string as a single token, rather than 
    the tokenized string - so write your regular expression accordingly.  
    Supported syntax is documented here: 
    http://jakarta.apache.org/regexp/apidocs/org/apache/regexp/RE.html

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Programmers access coded concepts by acquiring first a node set or graph. After specifying optional restrictions, the nodes in this set or graph can be resolved as a list of ConceptReference objects which in turn contain references to one or more Concept objects. The following example provides a simple query of concept codes:

Include Page

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ConceptResolution Snippet

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ConceptResolution Snippet

Service Metadata Retrieval

The LexEVS system maintains service metadata which can provide client programs with information about code system content and assigned copyright/licensing information. Below is an brief example showing how to access and print some of this metadata:

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ServiceMetadataRetrieval Snippet

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ServiceMetadataRetrieval Snippet

Combinatorial Queries

One of the most powerful features of the LexEVS architecture is the ability to define multiple search and sort criteria without intermediate retrieval of data from the LexEVS service. Consider the following code snippet:

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CombinatorialQueries Snippet

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CombinatorialQueries Snippet

This example shows a simple yet powerful query to search a code system based on a 'sounds like' match algorithm (the list of all available match algorithms can be listed using the 'ListExtensions -m' admin script).

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Lucene Queries are well documented and can be very powerful. The uninitiated user may need some background on their use however. The user should start here with the official Lucene Query Parser documentation.

Code Block
Link provided for historical purposes http://lucene.apache.org/java/2_3_2/queryparsersyntax.html

Keep in mind that some LexEVS queries such as "startsWith" and "contains" use wild card searches under the covers, so that use of wild cards in this context can cause errors in searches involving these search types.

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The examples and automated test programs provided by the LexEVS installation (see the file breakdown in the section, Overview of the Software #Overview) are available as additional reference materials.

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The LexEVS Graphical User Interface, or GUI, is an optional component of the LexEVS install which will be in the /gui folder of the base LexEVS installation (see file breakdown in the section, Overview of the Software #Overview). The GUI is meant to provide a simple tool to test LexEVS API methods and quickly view the results; almost all public methods defined by the LexEVS API are supported. This guide provides a brief overview of how the GUI can aid programmers in writing code to the LexEVS API.

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LexEVS conforms to the caCORE SDK API - for more information see caCORE SDK 4.1 Programmer's Guide.

QueryOptions

QueryOptions are designed to give the user extra control over the query before it is sent to the system. QueryOptions may be used to modify a query in these ways:

  1. 'CodingScheme' - Restricts the query to the specified Coding Scheme, instead of querying every available Coding Scheme.
  2. CodingSchemeVersionOrTag' - Restricts the query to the specified Version of the Coding Scheme. Note that:
    • This may NOT be specified without also specifying the 'CodingScheme' attribute.
    • If left unset, it will default to the version of the Coding Scheme tagged as "PRODUCTION" in the system.
  3. 'SecurityTokens' - Security Tokens to use with the specified query. These Security Tokens are scoped to the current query ONLY. An subsequent queries will also need to specify the necessary Query Options.

  4. 'LazyLoad' - Some high use-case model Objects have bee 'lazy-load' enabled. This means that some attributes and associations of a model Object may not be fully populated when returned to the user. This allows for faster query times. This defaults to false, meaning that all attributes and associations will be eagerly fetched by the server and model Objects will always be fully populated. To enable this on applicable Objects, set to true.

    Info
    titleNote

    Lazy Loading may only be used in conjunction with specifying a Coding Scheme and Version with the 'CodingScheme' and 'CodingSchemeVersionOrTag' attributes above.

  5. 'ResultPageSize' - the page size of results to return. The higher the number, the more results the system will return to the user at once. The client will request the next group of query results transparenly. This parameter is useful for performance tuning. For example, if a query returns a result of10,000 Objects, a 'ResultPageSize' of '1000' would make 10 calls to the server returning a page of 1000 results each time. If left unset, this value will default to the default set Page Size

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Example 4.1: Query By Example with No Query Options

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QueryByExampleWithNoQueryOptions Snippet

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(Deprecated -- removed in 6.3)
QueryByExampleWithNoQueryOptions Snippet(Deprecated -- removed in 6.3)

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The following table explains specific statements in the code by line number.

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Example 4.2: Query By Example with Query Options

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QueryByExampleWithQueryOptions Snippet

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(Deprecated -- removed in 6.3)
QueryByExampleWithQueryOptions Snippet(Deprecated -- removed in 6.3)

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The following table explains specific statements in the code by line number.

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The Web services interface can be used in any language-specific application that provides a mechanism for consuming XML Web services based on the Simple Object Access Protocol (SOAP). In those environments, connecting to caCORE LexEVS can be as simple as providing the end-point URL. Some platforms and languages require additional client-side code to handle the implementation of the SOAP envelope and the resolution of SOAP types.To view a list of packages that cater to different programming languages, visit http://www.w3.org/TR/SOAP/Image Removed and http://www.soapware.org/Image Removed.

To maximize standards-based interoperability, the caCORE Web service conforms to the Web Services Interoperability Organization (WS-I) basic profile. The WS-I basic profile provides a set of non-proprietary specifications and implementation guidelines that enable interoperability between diverse systems. For more information about WS-I compliance, visit http://www.ws-i.orgImage Removed.

On the server side, Apache Axis is used to provide SOAP-based, inter-application communication. Axis provides the appropriate serialization and deserialization methods for the JavaBeans to achieve an application-independent interface. For more information about Axis, visit http://ws.apache.org/axis/Image Removed.

Configuration

The caCORE/LexEVS WSDL file is located at http://lexevsapi.nci.nih.gov/lexevsapi50/services/lexevsapi50Service?wsdlImage Removed. In addition to describing the protocols, ports, and operations exposed by the caCORE LexEVS Web service, this file can be used by a number of IDEs and tools to generate stubs for caCORE LexEVS objects. This enables code on different platforms to instantiate native objects for use as parameters and return values for the Web service methods. For more information on how to use the WSDL file to generate class stubs, consult the specific documentation for your platform.

The caCORE LexEVS Web services interface has a single end point called <tt>lexevsapi50Service</tt>, which is located at http://lexevsapi.nci.nih.gov/lexevsapi50/services/lexevsapi50ServiceImage Removed. Client applications should use this URL to invoke Web service methods.

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  • GetXML - returns results in an XML format that can be parsed and consumed by most programming languages and many document authoring and management tools.
  • GetHTML - presents result using a simple HTML interface that can be viewed by most modern Internet browsers.

Wiki MarkupWithin the request string of the URL, the criteria element specifies the search criteria using XQuery-like syntax. Within this syntax, square brackets (\[ and \ ]) represent attributes and associated roles of a class, the _at_ symbol (@) signals an attribute name/value pair, and a forward slash character (/) (tick) specifies nested criteria.

Criteria statements in XML-HTTP queries generally use the following syntax (although you can also build more complex statements):

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A number of parameters, such as resultCounter, pageSize, and page, are used internally by the system and are not designed to be set by the user.

When specifying attribute values in the query string, note that use of the following characters generates an error: \
[ \ ] / \ # & amp; %

Info
titleNote

Wiki Markup

Distributed LexEVS API

Overview

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The DLB environment will be configured on the caCORE LexEVS Server (http://lexevsapi.nci.nic.gov/lexevsapi50Image Removed). This will give the server access to the LexEVS database and other resources. The client must therefore go through the caCORE LexEVS server to access any LexEVS data.

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The Mayo Clinic wrote the LexEVS 5.0 API. Documentation describing the LexEVS Service Model is available on the LexGRID Vocabulary Services for caBIG GForge site at https://gforge.nci.nih.gov/frs/?group_id=14Image Removed.archive.

LexEVS Installation and Configuration

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The following code sample shows use of the DLB API to retrieve the list of available coding schemes in the LexEVS repository.

Include Page

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Resolve Coding Scheme
Resolve Coding Scheme

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LexEVS Analytical Grid Service API

The following tables summarize the operations available through the LexEVS Analytical Grid Service. Each of the operations is also defined in detail below. The grid analytical service and related operations are viewable via the caGrid Portal (http://cagrid-portal.nci.nih.govImage Removed).

Using the API

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

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This Interface may be acquired by instantiating LexBIGServiceAdapter with the Grid Service URL as a parameter.

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LexBIGServiceAdapter Snippet

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LexBIGServiceAdapter Snippet

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.

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LexBIGServiceGridAdapter Snippet

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LexBIGServiceGridAdapter Snippet

Method Descriptions

getCodingSchemeConcepts

...

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:

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

    Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Build a org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag containing the Version information for the desired Coding Scheme

    Code Block
    CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag(); 
csvt.setVersion("testVersion");

  3. Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification to hold the Coding Scheme name.

    Code Block
    CodingSchemeIdentification codingScheme = new CodingSchemeIdentification(); 
codingScheme.setCode(code);

  4. Invoke the LexBIG caGrid service as follows:

    Code Block
    CodedNodeSetGrid cns = lbs.getCodingSchemeConcepts(codingScheme, csvt);

...

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:

  • Create a Resource on the server and populate it with the requested org.LexGrid.LexBIG.Extensions.Query.Filter
  • Return the Client Reference to the user. This Reference has the above org.LexGrid.LexBIG.Extensions.Query.Filter as a Resource. This client is a Service Context that allows the user to call regular org.LexGrid.LexBIG.Extensions.Query.Filter API calls through the grid service. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.client.FilterClient object is built from the above Reference. This FilterClient implements the Interface org.LexGrid.LexBIG.Extensions.Query.Filter. This makes calling Grid Service Calls through org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.client.FilterClient transparent to the end user.

    Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification to hold the Extension name.

    Code Block
    ExtensionIdentification extension = new ExtensionIdentification(); 
extension.setLexBIGExtensionName(name);

  3. Invoke the LexEVS caGrid service as follows:

    Code Block
    Filter filter = lbs.getFilter(extension);

...

Description:

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

Input:

org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification

Output:

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

Exception:

RemoteException

Implementation Details:

Implementation:

  • Create a Resource on the server and populate it with the requested org.LexGrid.LexBIG.Extensions.Query.Sort
  • Return the Client Reference to the user. This Reference has the above org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort.client.SortClient as a Resource. This client is a Service Context that allows the user to call regular org.LexGrid.LexBIG.Extensions.Query.Sort API calls through the grid service. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort.client.SortClient object is built from the above Reference. This SortClient implements the Interface org.LexGrid.LexBIG.Extensions.Query.Sort. This makes calling Grid Service Calls through org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort.client.SortClient transparent to the end user.

    Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification to hold the Extension name.

    Code Block
    ExtensionIdentification extension = new ExtensionIdentification(); 
extension.setLexBIGExtensionName(name);

  3. Invoke the LexEVS caGrid service as follows:

    Code Block
    Filter filter = lbs.getSortAlgorithm(extension);

...

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

Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Invoke the LexEVS caGrid service as follows:

    Code Block
     ExtensionDescriptionList extDescList = lbs.getFilterExtensions();

...

Description:

Return an interface to perform system-wide query over metadata for loaded code systems and providers.

Input:

none

Output:

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

Exception:

RemoteException

Implementation Details:

Implementation:

  • Create a Resource on the server and populate it with the requested org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata
  • Return the LexBIGServiceMetadataClient to the user. This LexBIGServiceMetadataClient has the above org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata as a Resource. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.LexBIGServiceMetadataClient object is built from the above Reference.

    Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Invoke the LexEVS caGrid service as follows:

    Code Block
    LexBIGServiceMetadataGrid metadata = lbs.getServiceMetadata();

...

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

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Invoke the LexEVS caGrid service as follows:

    Code Block
    CodingSchemeRenderingList csrl = lbs.getSupportedCodingSchemes();

...

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

Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Invoke the LexEVS caGrid service as follows:

    Code Block
    Date date = lbs.getLastUpdateTime();

...

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

Sample Call:

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

    Code Block
     LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification to hold the Coding Scheme name.

    Code Block
     CodingSchemeIdentification codingScheme = new CodingSchemeIdentification(); 
codingScheme.setCode(code);

  3. Build a org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag containing the Version information for the desired Coding Scheme

    Code Block
     CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag(); 
csvt.setVersion("testVersion");

  4. Invoke the LexEVS caGrid service as follows:

    Code Block
    CodedNodeSetGrid cns = lbs.resolveCodingScheme(codingScheme, csvt);

...

Description:

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

Input:

org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification
org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag
org.LexGrid.LexBIG.DataModel.cagrid.RelationContainerIdentification

Output:

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

Exception:

RemoteException

Implementation Details:

Implementation:

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

    Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification to hold the Coding Scheme name.

    Code Block
    CodingSchemeIdentification codingScheme = new CodingSchemeIdentification(); 
codingScheme.setCode(code);

  3. Build an org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag containing the Version information for the desired Coding Scheme

    Code Block
    
CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag(); 
csvt.setVersion("testVersion");

  4. Build an org.LexGrid.LexBIG.DataModel.cagrid.RelationContainerIdentification containing the Relation Container information.

    Code Block
     RelationContainerIdentification container = new RelationContainerIdentification(); 
container.setDc(name);

  5. Invoke the LexEVS caGrid service as follows, providing String parameters for the desired Coding Scheme and Relationship Name:

    Code Block
    CodedNodeGraphGrid cng = client.getNodeGraph(codingScheme, csvt, container);

...

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

Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Invoke the LexEVS caGrid service as follows:

    Code Block
    ModuleDescriptionList mdl = lbs.getMatchAlgorithms();

...

Description:

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

Info
titleNote

Only generic extensions (base class GenericExtension) will be listed here. All other classes are retrievable at the appropriate interface point (filter, sort, etc).

Input:

none

Output:

org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList

Exception:

RemoteException

Implementation Details:

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

Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Invoke the LexEVS caGrid service as follows:

    Code Block
    ExtensionDescriptionList edl = lbs.getGenericExtensions();

...

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

Sample Call:

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

    Code Block
    
LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
    Info
    titleNote

    Currently this method will return a LexBIGServiceConvenienceMethods instance.

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification to hold the Extension name.

    Code Block
    ExtensionIdentification extension = new ExtensionIdentification(); 
extension.setLexBIGExtensionName("LexBIGServiceConvenienceMethods");

  3. Invoke the LexEVS caGrid service as follows:

    Code Block
    LexBIGServiceConvenienceMethodsGrid lbscm = lbs.getGenericExtensions(extension);
  4. Return the LexBIGServiceConvenienceMethodsClient to the user. This LexBIGServiceConvenienceMethodsClient has the above org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods as a Resource. An org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.CodedNodeGraphClient object is built from the above Reference.

...

Description:

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

Input:

org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification

Output:

org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.HistoryService.stubs.types.HistoryServiceReference

Exception:

RemoteException

Implementation Details:

Implementation:

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

    Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification to hold the Coding Scheme name.

    Code Block
    CodingSchemeIdentification codingScheme = new CodingSchemeIdentification(); 
codingScheme.setCode(code);

  3. Invoke the LexEVS caGrid service as follows:

    Code Block
    HistoryServiceGrid history = lbs.getHistoryService(codingScheme);

...

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

Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Invoke the LexEVS caGrid service as follows:

    Code Block
    SortDescriptionList sortDescList = lbs.getSortAlgorithms(sortContext);

...

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

Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentificationto hold the Coding Scheme name.

    Code Block
    CodingSchemeIdentification codingScheme = new
CodingSchemeIdentification();
codingScheme.setCode(code);

  3. Build an org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTagcontaining the Version information for the desired Coding Scheme

    Code Block
     CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
csvt.setVersion("testVersion");

  4. Invoke the LexEVS caGrid service as follows:

    Code Block
    CodingSchemeCopyRight copyright = lbs.resolveCodingSchemeCopyright(codingScheme, csvt);

...

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

Sample Call:

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

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification to hold the Coding Scheme name.

    Code Block
    CodingSchemeIdentification codingScheme = new
CodingSchemeIdentification(); codingScheme.setName("codingScheme");

  3. Build a gov.nih.nci.evs.security.SecurityTokencontaining the security information for the desired Coding Scheme.

    Code Block
    SecurityToken metaToken = new SecurityToken();
metaToken.setAccessToken("token");

  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(codingScheme, metaToken);

...

The LexEVS Grid Service 4.2 URL is:

Code Block
Link provided for historical purposes http://lexevsapi.nci.nih.gov/wsrf/services/cagrid/LexEVSGridService

...

]

The service is also accessible via the caGRID Portal.

...

Product

Jars

License

Home Page

Apache WS-Addressing

addressing-1.0.jar

adressing 1.0.LICENSE

From Globus 4.0.2 Java Web Services Core lib directory:

http://www.globus.org/toolkit/downloads/4.0.2Image Removed


Source available at

http://ws.apache.org/addressingImage Removed

 

Apache Axis

axis-ant.jar
axis.jar
commons-pool-1.3.jar
commons-logging-1.1.jar
commons-lang-2.2.jar
commons-collections-3.2.jar
commons-codec-1.3.jar
log4j-1.2.8.jar
jaxrpc.jar
saaj.jar
wsdl4j.jar

axis-jars.LICENSE

http://ws.apache.org/axisImage Removed

Apache Xerces

xercesImpl.jar

xerces.LICENSE

http://xerces.apache.org/xerces-jImage Removed

Apache Lucene

lucene-core-2.3.2.jar
lucene-regex-2.3.2.jar
lucene-snowball-2.3.2.jar

Lucene LICENSE

http://lucene.apache.org/Image Removed

ASM
all purpose Java bytecode manipulation and analysis framework

asm.jar

http://asm.objectweb.org/license.htmlImage Removedhttp://asm.objectweb.org/Image Removed

Castor

castor-1.2.jar

http://www.castor.org/license.htmlImage Removedhttp://www.castor.org/index.htmlImage Removed

Globus Toolkit

cog-axis.jar
cog-jglobus.jar

http://www.globus.org/toolkit/legal/4.0/Image Removed

 

Bouncy Castle Crypto APIs

jce-jdk13-125.jar

http://www.bouncycastle.org/licence.htmlImage Removedhttp://www.bouncycastle.org/Image Removed

Open Permis

wsrf_core.jar
wsrf_core_stubs.jar

http://www.openpermis.org/BSDlicenceKent.txtImage Removedhttp://www.openpermis.org/Image Removed

 

Apache WSS4J

wss4j.jar

http://ws.apache.org/wss4j/license.htmlImage Removedhttp://ws.apache.org/wss4j/Image Removed

Spring

spring.jar

Spring LICENSE

http://www.springframework.orgImage Removed

The following table lists the required NCICB/caBIG Libraries.

...

For your convenience, the required libraries are available for download here:

https://gforge.nci.nih.gov/docman/view.php/491/14401/lexevs42-gridsrvc-jarslibs.jarImage Removed.

To programmatically access the LexEVS API Grid Service, these libraries need to be added to your local classpath.

...

Example Client and Service Calls and SOAP Messages

See http://gforge.nci.nih.gov/docman/view.php/491/14252/TestClient.zipImage Removed

Example API

...

Usage

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

Include Page

...

SearchingForConcepts Snippet

...

SearchingForConcepts Snippet

Error Handling

Error Connecting to LexEVS Grid Service

...

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.

Include Page

...

LexGridServiceConnection Snippet

...

LexGridServiceConnection Snippet

This example shows a typical connection to the LexEVS Grid Service, with the two potential Exceptions being caught and handled as necessary.

...

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 . Refer to the Service Contexts and State section in the Design and Architecture Guide 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:

Code Block

Name: SecurityToken
Namespace: gme://caCORE.caCORE/3.2/gov.nih.nci.evs.security
Package: gov.nih.nci.evs.security

...

A client establishes access to a secured vocabulary via the following Grid Service Calls:

  1. Connect to the LexEVS caGrid Service

    Code Block
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);

  2. Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentificationto hold the Coding Scheme name.

    Code Block
    CodingSchemeIdentification codingScheme = new CodingSchemeIdentification();
codingScheme.setName "codingScheme";

  3. Build a gov.nih.nci.evs.security.SecurityTokencontaining the security information for the desired Coding Scheme.

    Code Block
    SecurityToken token = new SecurityToken();
token.setAccessToken("securityToken");

  4. Invoke the LexEVS caGrid service as follows:

    Code Block
    LexBIGServiceGrid lbsg = lbs.setSecurityToken(codingScheme, token);

    This will return a reference to a new "LexBIGServiceGrid" instance that is associated with the security properties that were passed in.

Info
titleNote

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.

...

The LexEVS Data Grid Service is a standard caGrid Data service based on the LexEVS 2009 Model.

caGrid Data Service Documentation

For complete documentation on caGrid Data Services, see caGrid Data Service Documentation.

Querying the System

To query the LexEVS Data Grid Service, use the standard caGrid CQL query method to compose queries. See caGrid Data Service API Documentation for more information.

...

Query for a Concept with a Specific Code

Example: Concept: C12345

Include Page

...

DataGridQueryByCode Snippet

...

(Deprecated -- removed in 6.3)
DataGridQueryByCode Snippet(Deprecated -- removed in 6.3)

...

Query for a Concept with Specific Presentation Text

Example: A concept with a namespace 'SNOMED Clinical Terms' that contains a Presentation equal to 'Heart'

Include Page

...

DataGridQueryByPresentationText Snippet

...

(Deprecated -- removed in 6.3)
DataGridQueryByPresentationText Snippet(Deprecated -- removed in 6.3)

...

Restrict Results to Specific Attributes

Example: Retrieve all of the 'localIds' of any 'SupportedAssociation' in the system.

Include Page

...

DataGridQueryRestrictByAttributes Snippet

...

(Deprecated -- removed in 6.3)
DataGridQueryRestrictByAttributes Snippet(Deprecated -- removed in 6.3)

...

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