org.eaglei.search.provider.ncbi
Class NCBISearchProvider

java.lang.Object
  org.eaglei.search.provider.ncbi.NCBISearchProvider

All Implemented Interfaces:

org.eaglei.search.provider.SearchProvider

Direct Known Subclasses:

NCBIGeneSearchProvider, NCBIMeSHSearchProvider, NCBIProbeSearchProvider, NCBIPubMedSearchProvider, NCBITaxonomySearchProvider

public abstract class NCBISearchProvider
extends java.lang.Object
implements org.eaglei.search.provider.SearchProvider

Abstract implementation of the eagle-i SearchProvider interface that wraps an NCBIDBProvider.

Author:

rfrost

Field Summary

protected org.eaglei.search.provider.ncbi.NCBIDBProvider	dbProvider
protected static boolean	DEBUG
protected org.eaglei.model.EIOntModel	eagleiOntModel
protected org.eaglei.services.InstitutionRegistry	institutionRegistry
protected static org.apache.commons.logging.Log	logger

Constructor Summary

NCBISearchProvider(org.eaglei.search.provider.ncbi.NCBIDBProvider dbProvider, org.eaglei.model.EIOntModel eagleiOntModel, org.eaglei.services.InstitutionRegistry registry)
Creates a new NCBIDBProvider that executes queries against NCBI.

Method Summary

org.eaglei.search.provider.SearchCounts	count(org.eaglei.search.provider.SearchCountRequest countRequest)
protected abstract org.eaglei.search.provider.SearchResult	createSearchResultForDocSummary(org.eaglei.search.provider.ncbi.NCBIEUtils.DocSummary sum)
protected abstract java.lang.String	getQuery(org.eaglei.search.provider.SearchRequest request)
protected java.lang.String	getQuery(org.eaglei.search.provider.SearchRequest request, boolean includeType, java.util.Set<org.eaglei.model.EIURI> typesToIgnore, boolean includeInstitution) Generic query generation logic
abstract org.eaglei.model.EIEntity	getType()
protected static org.eaglei.model.EIURI	getType(org.eaglei.search.provider.SearchRequest request) Gets the type from a SearchRequest.
void	init()
protected boolean	isType(org.eaglei.model.EIURI type, org.eaglei.model.EIURI target) Checks, with inference, if a given type is of another type.
org.eaglei.search.provider.SearchResultSet	query(org.eaglei.search.provider.SearchRequest request)
abstract boolean	shouldAddResults(org.eaglei.search.provider.SearchRequest request)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

protected static final org.apache.commons.logging.Log logger

DEBUG

protected static final boolean DEBUG

dbProvider

protected final org.eaglei.search.provider.ncbi.NCBIDBProvider dbProvider

eagleiOntModel

protected final org.eaglei.model.EIOntModel eagleiOntModel

institutionRegistry

protected final org.eaglei.services.InstitutionRegistry institutionRegistry

Constructor Detail

NCBISearchProvider

public NCBISearchProvider(org.eaglei.search.provider.ncbi.NCBIDBProvider dbProvider,
                          org.eaglei.model.EIOntModel eagleiOntModel,
                          org.eaglei.services.InstitutionRegistry registry)

Creates a new NCBIDBProvider that executes queries against NCBI.

Method Detail

init

public void init()
          throws java.io.IOException

Specified by:

init in interface org.eaglei.search.provider.SearchProvider

Throws:

java.io.IOException

query

public org.eaglei.search.provider.SearchResultSet query(org.eaglei.search.provider.SearchRequest request)
                                                 throws java.io.IOException

Specified by:

query in interface org.eaglei.search.provider.SearchProvider

Throws:

java.io.IOException

count

public org.eaglei.search.provider.SearchCounts count(org.eaglei.search.provider.SearchCountRequest countRequest)
                                              throws java.io.IOException

Specified by:

count in interface org.eaglei.search.provider.SearchProvider

Throws:

java.io.IOException

getType

public abstract org.eaglei.model.EIEntity getType()

shouldAddResults

public abstract boolean shouldAddResults(org.eaglei.search.provider.SearchRequest request)
                                  throws java.io.IOException

Throws:

java.io.IOException

getQuery

protected abstract java.lang.String getQuery(org.eaglei.search.provider.SearchRequest request)
                                      throws java.io.IOException

Throws:

java.io.IOException

createSearchResultForDocSummary

protected abstract org.eaglei.search.provider.SearchResult createSearchResultForDocSummary(org.eaglei.search.provider.ncbi.NCBIEUtils.DocSummary sum)
                                                                                    throws java.io.IOException

Throws:

java.io.IOException

getType

protected static org.eaglei.model.EIURI getType(org.eaglei.search.provider.SearchRequest request)

Gets the type from a SearchRequest.

Parameters:

request - Request

Returns:

Type uri

isType

protected boolean isType(org.eaglei.model.EIURI type,
                         org.eaglei.model.EIURI target)

Checks, with inference, if a given type is of another type.

getQuery

protected java.lang.String getQuery(org.eaglei.search.provider.SearchRequest request,
                                    boolean includeType,
                                    java.util.Set<org.eaglei.model.EIURI> typesToIgnore,
                                    boolean includeInstitution)

Generic query generation logic