Package ubic.gemma.core.loader.entrez

Class EntrezXmlUtils

java.lang.Object

ubic.gemma.core.loader.entrez.EntrezXmlUtils

public class EntrezXmlUtils
extends Object

Utilities for manipulating Entrez XML responses.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
EntrezXmlUtils()

Method Summary

Modifier and Type	Method	Description
static Collection<String>	extractFetchIds(Document doc)	Extract IDs from an EFetch call.
static Collection<String>	extractLinkIds(Document doc, String dbfrom, String dbto)	Extract IDs from an ELink call.
static Collection<String>	extractSearchIds(Document doc)	Extract IDs from an ESearch call.
static String	getCookie(Document document)
static int	getCount(Document document)
static EntrezQuery	getQuery(Document doc)
static String	getQueryId(Document document)
static Document	parse(InputStream is)	Parse an XML reply from Entrez.
static Document	parse(InputStream is, String encoding)	Parse an XML reply with a specific character encoding.

Methods inherited from class java.lang.Object

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

Constructor Details

EntrezXmlUtils

public EntrezXmlUtils()

Method Details

parse

public static Document parse(InputStream is)
                      throws IOException

Parse an XML reply from Entrez.

This will check if there are any ERROR tags.

Throws:

IOException

parse

public static Document parse(InputStream is,
 String encoding)
                      throws IOException

Parse an XML reply with a specific character encoding.

This is mainly useful for querying old MINiML documents from NCBI FTP server that are declared as UTF-8 but actually use Windows-1252 encoding.

Throws:

IOException

getQuery

public static EntrezQuery getQuery(Document doc)

getCount

public static int getCount(Document document)

getQueryId

public static String getQueryId(Document document)

getCookie

public static String getCookie(Document document)

extractSearchIds

public static Collection<String> extractSearchIds(Document doc)

Extract IDs from an ESearch call.

See Also:

• EntrezUtils.search(String, EntrezQuery, EntrezRetmode, int, int, String)

extractFetchIds

public static Collection<String> extractFetchIds(Document doc)

Extract IDs from an EFetch call.

The uilist return type must be used in the call.

See Also:

• EntrezUtils.fetch(String, EntrezQuery, EntrezRetmode, String, int, int, String)
• EntrezUtils.fetchById(String, String, EntrezRetmode, String, String)

extractLinkIds

public static Collection<String> extractLinkIds(Document doc,
 String dbfrom,
 String dbto)

Extract IDs from an ELink call.

See Also:

• EntrezUtils.link(String, String, EntrezQuery, String, EntrezRetmode, String)
• EntrezUtils.linkById(String, String, String, String, EntrezRetmode, String)