org.vivoweb.harvester.fetch
Class NIHFetch

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

Direct Known Subclasses:

NLMJournalFetch, PubmedFetch, PubmedHTTPFetch

public abstract class NIHFetch
extends java.lang.Object

Shared code for modules for fetching NIH data using the SOAP or HTML Interface Based on the example code available at the NIH Website.

Author:

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

Constructor Summary

protected	NIHFetch(ArgList argList, java.lang.String database, java.lang.String outputFile) Constructor
protected	NIHFetch(ArgList argList, java.lang.String database, XMLRecordOutputStream os) Constructor
protected	NIHFetch(java.lang.String emailAddress, java.io.OutputStream outStream, java.lang.String database) Constructor: Primary method for running an NIH Fetch.
protected	NIHFetch(java.lang.String emailAddress, java.lang.String searchTerm, java.lang.String maxRecords, java.lang.String batchSize, java.io.OutputStream outStream, java.lang.String database) Constructor: Primary method for running an NIH Fetch.

Method Summary

void	execute() Executes the task
void	fetchRecords(java.lang.String[] env) Performs an NIH Fetch using a previously defined esearch environment and querykey
void	fetchRecords(java.lang.String[] env, java.lang.String retStart, java.lang.String numRecords) Performs an NIH Fetch using a previously defined esearch environment and querykey
protected abstract 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 java.lang.String	getBatchSize()
protected java.lang.String	getEmailAddress()
protected abstract int	getLatestRecord() Get latest NIH result
protected java.lang.String	getMaxRecords()
protected java.io.OutputStreamWriter	getOsWriter()
protected static ArgParser	getParser(java.lang.String appName, java.lang.String database) Get the ArgParser for this task
protected java.lang.String	getSearchTerm()
protected java.lang.String	getToolName()
java.lang.String[]	runESearch(java.lang.String term) Performs an ESearch against NIH database and returns the query web environment/query key data
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
protected void	setBatchSize(java.lang.String batchSize)
protected void	setEmailAddress(java.lang.String emailAddress)
protected void	setMaxRecords(java.lang.String maxRecords)
protected void	setOsWriter(java.io.OutputStream os) Setter for xmlwriter
protected void	setSearchTerm(java.lang.String searchTerm)

Methods inherited from class java.lang.Object

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

Constructor Detail

NIHFetch

protected NIHFetch(java.lang.String emailAddress,
                   java.io.OutputStream outStream,
                   java.lang.String database)

Constructor: Primary method for running an NIH 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

database - database name

NIHFetch

protected NIHFetch(java.lang.String emailAddress,
                   java.lang.String searchTerm,
                   java.lang.String maxRecords,
                   java.lang.String batchSize,
                   java.io.OutputStream outStream,
                   java.lang.String database)

Constructor: Primary method for running an NIH 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 data

maxRecords - maximum number of records to fetch

batchSize - number of records to fetch per batch

outStream - output stream to write to

database - database name

NIHFetch

protected NIHFetch(ArgList argList,
                   java.lang.String database,
                   XMLRecordOutputStream os)
            throws java.io.IOException

Constructor

Parameters:

argList - parsed argument list

database - database name

os - xml record output stream

Throws:

java.io.IOException - error creating task

NIHFetch

protected NIHFetch(ArgList argList,
                   java.lang.String database,
                   java.lang.String outputFile)
            throws java.io.IOException

Constructor

Parameters:

argList - parsed argument list

database - database name

outputFile - output file path

Throws:

java.io.IOException - error creating task

Method Detail

runESearch

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

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

Parameters:

term - search term to run against database

Returns:

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

Throws:

java.io.IOException - error processing search

runESearch

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

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

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

execute

public void execute()
             throws java.io.IOException

Executes the task

Throws:

java.io.IOException - error processing search

getLatestRecord

protected abstract int getLatestRecord()
                                throws java.io.IOException

Get latest NIH result

Returns:

latest record

Throws:

java.io.IOException - error processing search

fetchRecords

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

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

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

fetchRecords

public void fetchRecords(java.lang.String[] env)
                  throws java.io.IOException

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

Parameters:

env - {WebEnv, QueryKey, number of records found} - from ESearch

Throws:

java.io.IOException - error fetching records

fetchRecords

public void fetchRecords(java.lang.String[] env,
                         java.lang.String retStart,
                         java.lang.String numRecords)
                  throws java.io.IOException

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

Parameters:

env - {WebEnv, QueryKey, number of records found} - from 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

setOsWriter

protected void setOsWriter(java.io.OutputStream os)

Setter for xmlwriter

Parameters:

os - outputstream to write to

getParser

protected static ArgParser getParser(java.lang.String appName,
                                     java.lang.String database)

Get the ArgParser for this task

Parameters:

appName - the application name

database - the database name

Returns:

the ArgParser

getEmailAddress

protected java.lang.String getEmailAddress()

Returns:

the emailAddress

setEmailAddress

protected void setEmailAddress(java.lang.String emailAddress)

Parameters:

emailAddress - the emailAddress to set

getOsWriter

protected java.io.OutputStreamWriter getOsWriter()

Returns:

the osWriter

getSearchTerm

protected java.lang.String getSearchTerm()

Returns:

the searchTerm

setSearchTerm

protected void setSearchTerm(java.lang.String searchTerm)

Parameters:

searchTerm - the searchTerm to set

getMaxRecords

protected java.lang.String getMaxRecords()

Returns:

the maxRecords

setMaxRecords

protected void setMaxRecords(java.lang.String maxRecords)

Parameters:

maxRecords - the maxRecords to set

getBatchSize

protected java.lang.String getBatchSize()

Returns:

the batchSize

setBatchSize

protected void setBatchSize(java.lang.String batchSize)

Parameters:

batchSize - the batchSize to set

getToolName

protected java.lang.String getToolName()

Returns:

the toolName