org.eaglei.search.provider.ncbi
Class NCBIEUtils

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

public final class NCBIEUtils
extends java.lang.Object

Contains logic for using NCBI EUtils.

Author:

rfrost

Nested Class Summary

static class	NCBIEUtils.DocSummary Simple representation of a DocSum from an eSummary search
static class	NCBIEUtils.ESearchResult Simple representation of an eSearch result
static class	NCBIEUtils.Item
static class	NCBIEUtils.ListItem

Field Summary

static java.lang.String	ID
static java.lang.String	IDLIST

Constructor Summary

NCBIEUtils()

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	buildSummaryURL(NCBIEUtils.ESearchResult result, java.lang.String db, java.lang.String tool)
static org.w3c.dom.Document	executeNCBIRequest(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	parse(java.io.InputStream stream)
static NCBIEUtils.ESearchResult	parseESearchResult(org.w3c.dom.Document doc) Parses an eSearch XML result and returns the IDs.
static java.util.List<NCBIEUtils.DocSummary>	parseESummaryResult(org.w3c.dom.Document doc) Parses an eSummary XML result and returns the IDs.
static java.lang.String	serializeDocument(org.w3c.dom.Document doc)

Methods inherited from class java.lang.Object

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

Field Detail

IDLIST

public static final java.lang.String IDLIST

See Also:

Constant Field Values

ID

public static final java.lang.String ID

See Also:

Constant Field Values

Constructor Detail

NCBIEUtils

public NCBIEUtils()

Method Detail

executeNCBIRequest

public static org.w3c.dom.Document executeNCBIRequest(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.

serializeDocument

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

buildSearchURL

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

buildSummaryURL

public static java.lang.String buildSummaryURL(NCBIEUtils.ESearchResult result,
                                               java.lang.String db,
                                               java.lang.String tool)

parseESearchResult

public static NCBIEUtils.ESearchResult parseESearchResult(org.w3c.dom.Document doc)
                                                   throws java.io.IOException

Parses an eSearch XML result and returns the IDs.

Parameters:

doc - XML Document.

Returns:

List of IDs

Throws:

java.io.IOException

parseESummaryResult

public static java.util.List<NCBIEUtils.DocSummary> parseESummaryResult(org.w3c.dom.Document doc)
                                                                 throws java.io.IOException

Parses an eSummary XML result and returns the IDs.

Parameters:

doc - XML Document.

Returns:

List of IDs

Throws:

java.io.IOException

parse

public static org.w3c.dom.Document parse(java.io.InputStream stream)
                                  throws java.io.IOException

Throws:

java.io.IOException