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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™, caBIG® is dubbed caGrid. The software embodiment and corresponding documentation of this architecture constitute the caGrid 1.2 release.
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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);
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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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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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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
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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 |
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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 |
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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.
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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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- 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.
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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
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