org.vivoweb.harvester.fetch
Class PubmedFetch

java.lang.Object
  org.vivoweb.harvester.fetch.NIHFetch
      org.vivoweb.harvester.fetch.PubmedFetch

public class PubmedFetch
extends NIHFetch

Module for fetching PubMed Citations using the PubMed SOAP Interface Based on the example code available at the PubMed Website.

Author:

Stephen V. Williams (swilliams@ctrip.ufl.edu), Dale R. Scheppler (dscheppler@ctrip.ufl.edu), Christopher Haines (hainesc@ctrip.ufl.edu)

Field Summary

protected static XMLRecordOutputStream

baseXMLROS a base xmlrecordoutputstream

Constructor Summary

PubmedFetch(ArgList argList)
Constructor

PubmedFetch(java.lang.String[] args)
Constructor

PubmedFetch(java.lang.String emailAddress, java.io.OutputStream outStream)
Constructor: Primary method for running a PubMed Fetch.

PubmedFetch(java.lang.String emailAddress, java.lang.String searchTerm, java.lang.String maxRecords, java.lang.String batchSize, java.io.OutputStream outStream)
Constructor: Primary method for running a PubMed Fetch.

PubmedFetch(java.lang.String emailAddress, java.lang.String searchTerm, java.lang.String maxRecords, java.lang.String batchSize, RecordHandler rh)
Constructor: Primary method for running a PubMed Fetch.

Method Summary

void	fetchRecords(java.lang.String WebEnv, java.lang.String QueryKey, java.lang.String retStart, java.lang.String numRecords) Performs an NIH Fetch using a previously defined esearch environment and querykey
protected int	getLatestRecord() Get latest NIH result
static void	main(java.lang.String... args) Main method

Methods inherited from class org.vivoweb.harvester.fetch.NIHFetch

execute, fetchRecords, fetchRecords, getBatchSize, getEmailAddress, getMaxRecords, getOsWriter, getParser, getSearchTerm, getToolName, runESearch, runESearch, setBatchSize, setEmailAddress, setMaxRecords, setOsWriter, setSearchTerm

Methods inherited from class java.lang.Object

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

Field Detail

baseXMLROS

protected static XMLRecordOutputStream baseXMLROS

a base xmlrecordoutputstream

Constructor Detail

PubmedFetch

public PubmedFetch(java.lang.String emailAddress,
                   java.io.OutputStream outStream)
            throws java.io.IOException

Constructor: Primary method for running a PubMed Fetch. The email address of the person responsible for this install of the program is required by NIH guidelines so the person can be contacted if there is a problem, such as sending too many queries too quickly.

Parameters:

emailAddress - contact email address of the person responsible for this install of the VIVO Harvester

outStream - output stream to write to

Throws:

java.io.IOException - error finding latest record

PubmedFetch

public PubmedFetch(java.lang.String emailAddress,
                   java.lang.String searchTerm,
                   java.lang.String maxRecords,
                   java.lang.String batchSize,
                   java.io.OutputStream outStream)

Constructor: Primary method for running a PubMed Fetch. The email address of the person responsible for this install of the program is required by NIH guidelines so the person can be contacted if there is a problem, such as sending too many queries too quickly.

Parameters:

emailAddress - contact email address of the person responsible for this install of the VIVO Harvester

searchTerm - query to run on pubmed data

maxRecords - maximum number of records to fetch

batchSize - number of records to fetch per batch

outStream - output stream to write to

PubmedFetch

public PubmedFetch(java.lang.String emailAddress,
                   java.lang.String searchTerm,
                   java.lang.String maxRecords,
                   java.lang.String batchSize,
                   RecordHandler rh)

Constructor: Primary method for running a PubMed Fetch. The email address of the person responsible for this install of the program is required by NIH guidelines so the person can be contacted if there is a problem, such as sending too many queries too quickly.

Parameters:

emailAddress - contact email address of the person responsible for this install of the VIVO Harvester

searchTerm - query to run on pubmed data

maxRecords - maximum number of records to fetch

batchSize - number of records to fetch per batch

rh - record handler to write to

PubmedFetch

public PubmedFetch(java.lang.String[] args)
            throws java.io.IOException

Constructor

Parameters:

args - commandline argument

Throws:

java.io.IOException - error creating task

PubmedFetch

public PubmedFetch(ArgList argList)
            throws java.io.IOException

Constructor

Parameters:

argList - parsed argument list

Throws:

java.io.IOException - error creating task

Method Detail

fetchRecords

public void fetchRecords(java.lang.String WebEnv,
                         java.lang.String QueryKey,
                         java.lang.String retStart,
                         java.lang.String numRecords)
                  throws java.io.IOException

Description copied from class: NIHFetch

Performs an NIH Fetch using a previously defined esearch environment and querykey

Specified by:

fetchRecords in class NIHFetch

Parameters:

WebEnv - web environment from an ESearch

QueryKey - query key from an ESearch

retStart - record number (out of the total - eg: '1200' out of 15000 records), not the record ID

numRecords - The number of records to fetch

Throws:

java.io.IOException - error fetching records

getLatestRecord

protected int getLatestRecord()
                       throws java.io.IOException

Description copied from class: NIHFetch

Get latest NIH result

Specified by:

getLatestRecord in class NIHFetch

Returns:

latest record

Throws:

java.io.IOException - error processing search

main

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

Main method

Parameters:

args - commandline arguments