org.vivoweb.harvester.fetch
Class PubmedHTTPFetch

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

public class PubmedHTTPFetch
extends NIHFetch

Module for fetching PubMed Citations using the PubMed HTTP 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)

Constructor Summary

PubmedHTTPFetch(ArgList argList)
Constructor

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

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

PubmedHTTPFetch(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.

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
java.lang.String[]	runESearch(java.lang.String term, boolean logMessage) Performs an ESearch against NIH database and returns the query web environment/query key data

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

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

Methods inherited from class java.lang.Object

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

Constructor Detail

PubmedHTTPFetch

public PubmedHTTPFetch(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

PubmedHTTPFetch

public PubmedHTTPFetch(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

PubmedHTTPFetch

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

Constructor

Parameters:

args - commandline arguments

Throws:

java.io.IOException - error creating task

PubmedHTTPFetch

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

Constructor

Parameters:

argList - parsed argument list

Throws:

java.io.IOException - error creating task

Method Detail

runESearch

public java.lang.String[] runESearch(java.lang.String term,
                                     boolean logMessage)
                              throws java.io.IOException

Description copied from class: NIHFetch

Performs an ESearch against NIH database and returns the query web environment/query key data

Overrides:

runESearch in class NIHFetch

Parameters:

term - search term to run against database

logMessage - do we write log messages

Returns:

String[] = {WebEnv, QueryKey, number of records found, first record ID} from the search

Throws:

java.io.IOException - error processing search

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