edu.cornell.med.icb.synonyms.util
Class SynonymClImportTool

java.lang.Object
  edu.cornell.med.icb.synonyms.util.SynonymClImportTool

public final class SynonymClImportTool
extends Object

Import abbreviations and DYMs from twease query logs using the command line.

Author:

Kevin Dorff

Field Summary

static int	HUGO_ALIASES Hugo_Aliases are stored in this position of the array.
static int	HUGO_MIN_SYMBOL_LENGTH The minimum length acceptable for Hugo symbols.
static int	HUGO_NAME Hugo_Name are stored in this position of the array.
static int	HUGO_PREVSYMBOLS Hugo_PrevSymbols are stored in this position of the array.
static int	HUGO_SYMBOL Hugo_Symbol are stored in this position of the array.

Constructor Summary

SynonymClImportTool()
Constructor.

SynonymClImportTool(String persistenceUnit)
Constructor.

Method Summary

int	getHugoLineCount() Import value: number of hugo lines processed.
int	getMeshBaseTermsCount() Import value: number of mesh base terms processed.
SynonymImportTool	getSynonymImportTool()
int	getTweaseImportBadParseCount() Import value: number of twease queries that couldn't be parsed.
int	getTweaseImportQueryCount() Import value: number of twease queries imported.
int	getTweaseImportTermCount() Import value: number of twease terms found.
int	getTweaseImportTermRepeatCount() Import value: number of twease repeat terms found.
void	hugoImport(String filename) Import a Hugo TSV file.
void	initializeQueryExecutor() Initialze the QueryExecutor.
static void	main(String[] args) Command line interface to SynonymImportTool.
void	meshImport(String filename) Import the MeSH data.
protected List<Synonym>	processHugoDataLine(String line, int[] header, int minSymbolLen) Process a Hugo data line for synonyms.
void	tweaseQueryLogImport(String filename, boolean importRelated, boolean importDym, boolean importAbbr) Import the abbreviations and DYM's for all the phrases and terms in the specified twease query logs.

Methods inherited from class java.lang.Object

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

Field Detail

HUGO_SYMBOL

public static final int HUGO_SYMBOL

Hugo_Symbol are stored in this position of the array.

See Also:

Constant Field Values

HUGO_NAME

public static final int HUGO_NAME

Hugo_Name are stored in this position of the array.

See Also:

Constant Field Values

HUGO_PREVSYMBOLS

public static final int HUGO_PREVSYMBOLS

Hugo_PrevSymbols are stored in this position of the array.

See Also:

Constant Field Values

HUGO_ALIASES

public static final int HUGO_ALIASES

Hugo_Aliases are stored in this position of the array.

See Also:

Constant Field Values

HUGO_MIN_SYMBOL_LENGTH

public static final int HUGO_MIN_SYMBOL_LENGTH

The minimum length acceptable for Hugo symbols.

See Also:

Constant Field Values

Constructor Detail

SynonymClImportTool

public SynonymClImportTool(String persistenceUnit)

Constructor.

Parameters:

persistenceUnit - the jpa persistence-unit name to use.

SynonymClImportTool

public SynonymClImportTool()

Constructor.

Method Detail

getSynonymImportTool

public SynonymImportTool getSynonymImportTool()

hugoImport

public void hugoImport(String filename)
                throws IOException

Import a Hugo TSV file.

Parameters:

filename - twease query log

Throws:

IOException - problem reading the file

processHugoDataLine

protected List<Synonym> processHugoDataLine(String line,
                                            int[] header,
                                            int minSymbolLen)

Process a Hugo data line for synonyms.

Parameters:

line - the line of data to use

header - the positions of the columns of iterest

minSymbolLen - the minimum length of a symbol to accept

Returns:

List[Synonym] the synonyms found for this line

meshImport

public void meshImport(String filename)
                throws FileNotFoundException,
                       javax.xml.stream.XMLStreamException

Import the MeSH data.

Parameters:

filename - MeSH XML file of data

Throws:

FileNotFoundException - specified twease query log does not exist

javax.xml.stream.XMLStreamException - problem processing the xml file

tweaseQueryLogImport

public void tweaseQueryLogImport(String filename,
                                 boolean importRelated,
                                 boolean importDym,
                                 boolean importAbbr)
                          throws FileNotFoundException,
                                 javax.xml.stream.XMLStreamException

Import the abbreviations and DYM's for all the phrases and terms in the specified twease query logs.

Parameters:

filename - twease query log

importRelated - set to true to import "Related" synonyms

importDym - set to true to import "DYM" synonyms

importAbbr - set to true to import "Abbr" synonyms

Throws:

FileNotFoundException - specified twease query log does not exist

javax.xml.stream.XMLStreamException - problem processing the xml file

initializeQueryExecutor

public void initializeQueryExecutor()
                             throws twease.query.TweaseException,
                                    org.apache.commons.configuration.ConfigurationException,
                                    IllegalAccessException,
                                    textractor.database.TextractorDatabaseException,
                                    IOException,
                                    InstantiationException,
                                    InvocationTargetException,
                                    NoSuchMethodException,
                                    URISyntaxException,
                                    ClassNotFoundException

Initialze the QueryExecutor.

Throws:

twease.query.TweaseException - exception

org.apache.commons.configuration.ConfigurationException - exception

IllegalAccessException - exception

textractor.database.TextractorDatabaseException - exception

IOException - exception

InstantiationException - exception

InvocationTargetException - exception

NoSuchMethodException - exception

ClassNotFoundException

URISyntaxException

getTweaseImportQueryCount

public int getTweaseImportQueryCount()

Import value: number of twease queries imported.

Returns:

value

getTweaseImportBadParseCount

public int getTweaseImportBadParseCount()

Import value: number of twease queries that couldn't be parsed.

Returns:

value

getTweaseImportTermCount

public int getTweaseImportTermCount()

Import value: number of twease terms found.

Returns:

value

getTweaseImportTermRepeatCount

public int getTweaseImportTermRepeatCount()

Import value: number of twease repeat terms found.

Returns:

value

getHugoLineCount

public int getHugoLineCount()

Import value: number of hugo lines processed.

Returns:

value

getMeshBaseTermsCount

public int getMeshBaseTermsCount()

Import value: number of mesh base terms processed.

Returns:

value

main

public static void main(String[] args)

Command line interface to SynonymImportTool.

Parameters:

args - command line arguments