edu.iastate.jtm.jmed
Class PubMedQuerier

java.lang.Object
  edu.iastate.jtm.jmed.PubMedQuerier

public class PubMedQuerier
extends java.lang.Object

Get number of hits and/or PMID list from PubMed.

Author:

dingjing

Field Summary

static int	CONNECT_FAIL
static int	FETCH_LIMIT
static int	FIRST_DEFAULT
static int	NOT_FOUND
static int	QUERY_FAIL

Constructor Summary

PubMedQuerier()

PubMedQuerier(int db)

PubMedQuerier(int db, java.lang.String tool, java.lang.String email)

PubMedQuerier(org.dom4j.io.SAXReader xmlParser)

PubMedQuerier(org.dom4j.io.SAXReader xmlParser, int db)

PubMedQuerier(java.lang.String tool, java.lang.String email)

Method Summary

java.lang.String	appendTerm(java.lang.String pre, java.lang.String suf, java.lang.String op, boolean quote)
java.lang.String	combineTerms(java.util.List terms, java.lang.String op, java.lang.String[] fields, boolean quote, boolean exclude0)
java.lang.String	combineTerms(java.lang.String[] terms, int count, java.lang.String op, java.lang.String[] fields, boolean quote, boolean exclude0) Concatenate a list of terms into a single query.
org.dom4j.Element	getErrorList()
int	getHits()
org.dom4j.Element	getTranslation()
boolean	hasMorePmids()
boolean	isIndexed()
static void	main(java.lang.String[] args) For test.
void	retrieveAll(java.io.File output) Retrieve all PMIDs to a single file.
void	retrieveAll(java.util.List pmids)
void	retrieveAll(java.lang.String[] pmids) Retrieve all PMIDs to an array.
void	retrieveAll(java.lang.String prefix, int size) Retrieve all PMIDs to multiple files.
java.lang.String[]	retrieveBatch() Retrieve a batch of PMIDs, and store them in a new array.
int	retrieveBatch(java.util.List pmids)
int	retrieveBatch(java.lang.String[] pmids, int offset) Retrieve a batch of PMIDs into an array starting at offset.
int	sendQuery(java.lang.String queryTerm)
int	sendQuery(java.lang.String queryTerm, boolean asis)
int	sendQuery(java.lang.String queryTerm, Limits limits)
int	sendQuery(java.lang.String queryTerm, Limits limits, boolean asis) Send a query to PubMed.
void	setBatchSize(int bs)
void	setFirstSize(int fs)
void	setHasAbstract(boolean ha)
void	setIgnoreError(boolean ie)
void	setIgnoreWarning(boolean iw)
void	setOutputOriginal(boolean o)
void	setQuotedQuery(boolean q)
void	setVerbose(boolean v) Set verbose mode.

Methods inherited from class java.lang.Object

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

Field Detail

NOT_FOUND

public static final int NOT_FOUND

See Also:

Constant Field Values

QUERY_FAIL

public static final int QUERY_FAIL

See Also:

Constant Field Values

CONNECT_FAIL

public static final int CONNECT_FAIL

See Also:

Constant Field Values

FETCH_LIMIT

public static final int FETCH_LIMIT

See Also:

Constant Field Values

FIRST_DEFAULT

public static final int FIRST_DEFAULT

See Also:

Constant Field Values

Constructor Detail

PubMedQuerier

public PubMedQuerier(int db)
              throws java.io.UnsupportedEncodingException,
                     org.xml.sax.SAXException

Throws:

java.io.UnsupportedEncodingException

org.xml.sax.SAXException

PubMedQuerier

public PubMedQuerier()
              throws org.xml.sax.SAXException,
                     java.io.UnsupportedEncodingException

Throws:

org.xml.sax.SAXException

java.io.UnsupportedEncodingException

PubMedQuerier

public PubMedQuerier(org.dom4j.io.SAXReader xmlParser,
                     int db)
              throws java.io.UnsupportedEncodingException

Throws:

java.io.UnsupportedEncodingException

PubMedQuerier

public PubMedQuerier(org.dom4j.io.SAXReader xmlParser)
              throws java.io.UnsupportedEncodingException

Throws:

java.io.UnsupportedEncodingException

PubMedQuerier

public PubMedQuerier(int db,
                     java.lang.String tool,
                     java.lang.String email)
              throws java.io.UnsupportedEncodingException,
                     org.xml.sax.SAXException

Throws:

java.io.UnsupportedEncodingException

org.xml.sax.SAXException

PubMedQuerier

public PubMedQuerier(java.lang.String tool,
                     java.lang.String email)
              throws java.io.UnsupportedEncodingException,
                     org.xml.sax.SAXException

Throws:

java.io.UnsupportedEncodingException

org.xml.sax.SAXException

Method Detail

setVerbose

public void setVerbose(boolean v)

Set verbose mode.

Parameters:

v - verbose mode

setQuotedQuery

public void setQuotedQuery(boolean q)

setOutputOriginal

public void setOutputOriginal(boolean o)

setIgnoreError

public void setIgnoreError(boolean ie)

setIgnoreWarning

public void setIgnoreWarning(boolean iw)

setBatchSize

public void setBatchSize(int bs)

setFirstSize

public void setFirstSize(int fs)

setHasAbstract

public void setHasAbstract(boolean ha)

combineTerms

public java.lang.String combineTerms(java.lang.String[] terms,
                                     int count,
                                     java.lang.String op,
                                     java.lang.String[] fields,
                                     boolean quote,
                                     boolean exclude0)

Concatenate a list of terms into a single query.

Parameters:

terms - list of terms

count - list size

op - operator "AND" or "OR"

fields - field after each term

quote - whether quote term or not

exclude0 - whether or not exclude 0 hits terms

Returns:

query string

combineTerms

public java.lang.String combineTerms(java.util.List terms,
                                     java.lang.String op,
                                     java.lang.String[] fields,
                                     boolean quote,
                                     boolean exclude0)

appendTerm

public java.lang.String appendTerm(java.lang.String pre,
                                   java.lang.String suf,
                                   java.lang.String op,
                                   boolean quote)

sendQuery

public int sendQuery(java.lang.String queryTerm,
                     Limits limits)

sendQuery

public int sendQuery(java.lang.String queryTerm,
                     Limits limits,
                     boolean asis)

Send a query to PubMed.

Parameters:

queryTerm -

limits -

outputOriginal -

Returns:

# of hits if successful.

sendQuery

public int sendQuery(java.lang.String queryTerm)

sendQuery

public int sendQuery(java.lang.String queryTerm,
                     boolean asis)

getHits

public int getHits()

getTranslation

public org.dom4j.Element getTranslation()

getErrorList

public org.dom4j.Element getErrorList()

isIndexed

public boolean isIndexed()

hasMorePmids

public boolean hasMorePmids()

retrieveBatch

public java.lang.String[] retrieveBatch()
                                 throws org.dom4j.DocumentException,
                                        java.io.IOException

Retrieve a batch of PMIDs, and store them in a new array.

Returns:

The new array of PMIDs

Throws:

org.dom4j.DocumentException

java.io.IOException

retrieveBatch

public int retrieveBatch(java.lang.String[] pmids,
                         int offset)
                  throws org.dom4j.DocumentException,
                         java.io.IOException

Retrieve a batch of PMIDs into an array starting at offset.

Parameters:

pmids - the array to store PMIDs.

offset - starting position in the array.

Returns:

number of PMIDs retrieved.

Throws:

org.dom4j.DocumentException

java.io.IOException

retrieveBatch

public int retrieveBatch(java.util.List pmids)
                  throws org.dom4j.DocumentException,
                         java.io.IOException

Throws:

org.dom4j.DocumentException

java.io.IOException

retrieveAll

public void retrieveAll(java.lang.String[] pmids)
                 throws org.dom4j.DocumentException,
                        java.io.IOException

Retrieve all PMIDs to an array.

Parameters:

pmids - array to store the PMIDs.

Throws:

org.dom4j.DocumentException

java.io.IOException

retrieveAll

public void retrieveAll(java.util.List pmids)
                 throws org.dom4j.DocumentException,
                        java.io.IOException

Throws:

org.dom4j.DocumentException

java.io.IOException

retrieveAll

public void retrieveAll(java.io.File output)
                 throws org.dom4j.DocumentException,
                        java.io.IOException

Retrieve all PMIDs to a single file.

Parameters:

output - output file

Throws:

org.dom4j.DocumentException

java.io.IOException

retrieveAll

public void retrieveAll(java.lang.String prefix,
                        int size)
                 throws org.dom4j.DocumentException,
                        java.io.IOException

Retrieve all PMIDs to multiple files.

Parameters:

prefix - prefix of output filenames

size - number of PMIDs per file

Throws:

org.dom4j.DocumentException

java.io.IOException

main

public static void main(java.lang.String[] args)

For test.

Parameters:

args - the command line arguments