org.eaglei.search.provider.nif
Class NIFQueryUtil

java.lang.Object
  org.eaglei.search.provider.nif.NIFQueryUtil

public final class NIFQueryUtil
extends java.lang.Object

Contains logic for using NIF ESearch.

Author:

rfrost, tbashor

Nested Class Summary

static class

NIFQueryUtil.ESearchResult Simple representation of an eSearch result and, optionally, the results of a subsequent set of sSummary or eFetch calls.

Field Summary

static java.lang.String	DB
static java.lang.String	EUTILS_URL
static java.lang.String	ID
static java.lang.String	ID_PARAM
static java.lang.String	IDLIST
static java.lang.String	RETMAX
static java.lang.String	RETMODE
static java.lang.String	RETSTART
static java.lang.String	TERM
static java.lang.String	TOOL

Constructor Summary

NIFQueryUtil()

Method Summary

static java.lang.String	buildSearchURL(java.lang.String query, java.lang.String db, java.lang.String tool, int start, int max)
static java.lang.String	buildServiceURL(java.lang.String serviceURL, java.util.List<java.lang.String> ids, java.lang.String db, int max, java.lang.String tool) Builds a query URL for executing an eUtils service that retrieves information for a set of IDs.
static org.w3c.dom.Document	executeNIFRequest(java.lang.String url) Executes an NCBI request at the specified eUtils URL and returns the XML response as a DOM Document
static org.w3c.dom.Document	search(java.lang.String query, java.lang.String db, java.lang.String tool, int startIndex, int maxResults) Executes an NCBI search.
static java.lang.String	serializeDocument(org.w3c.dom.Document doc) Utility method to serialize an XML document.

Methods inherited from class java.lang.Object

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

Field Detail

EUTILS_URL

public static final java.lang.String EUTILS_URL

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Constant Field Values

DB

public static final java.lang.String DB

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Constant Field Values

TERM

public static final java.lang.String TERM

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Constant Field Values

RETMAX

public static final java.lang.String RETMAX

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Constant Field Values

RETSTART

public static final java.lang.String RETSTART

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Constant Field Values

TOOL

public static final java.lang.String TOOL

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Constant Field Values

ID_PARAM

public static final java.lang.String ID_PARAM

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Constant Field Values

RETMODE

public static final java.lang.String RETMODE

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Constant Field Values

IDLIST

public static final java.lang.String IDLIST

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Constant Field Values

ID

public static final java.lang.String ID

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Constant Field Values

Constructor Detail

NIFQueryUtil

public NIFQueryUtil()

Method Detail

search

public static org.w3c.dom.Document search(java.lang.String query,
                                          java.lang.String db,
                                          java.lang.String tool,
                                          int startIndex,
                                          int maxResults)
                                   throws java.io.IOException

Executes an NCBI search.

Throws:

java.io.IOException

buildSearchURL

public static java.lang.String buildSearchURL(java.lang.String query,
                                              java.lang.String db,
                                              java.lang.String tool,
                                              int start,
                                              int max)

executeNIFRequest

public static org.w3c.dom.Document executeNIFRequest(java.lang.String url)
                                              throws java.io.IOException

Executes an NCBI request at the specified eUtils URL and returns the XML response as a DOM Document

Parameters:

url - eUtils URL with all params.

Returns:

Response as DOM Document.

Throws:

java.io.IOException - Thrown if there is an error.

buildServiceURL

public static java.lang.String buildServiceURL(java.lang.String serviceURL,
                                               java.util.List<java.lang.String> ids,
                                               java.lang.String db,
                                               int max,
                                               java.lang.String tool)

Builds a query URL for executing an eUtils service that retrieves information for a set of IDs.

Parameters:

serviceURL - Base URL for the service

ids - IDs of artifacts whose information is being retrieved

db - The target db

max - Max number of results

tool - The source tool

Returns:

Query URL.

serializeDocument

public static java.lang.String serializeDocument(org.w3c.dom.Document doc)

Utility method to serialize an XML document.

Parameters:

doc - The DOM document.

Returns:

String serialization.