gov.nih.nlm.umls.io
Class RichMRFilesConceptOutputStream

java.lang.Object
  gov.nih.nlm.umls.io.RichMRFilesConceptOutputStream

All Implemented Interfaces:

ConceptOutputStream, LocalNullValueSupport

Direct Known Subclasses:

RichMRMetathesaurusOutputStream

public class RichMRFilesConceptOutputStream
extends Object
implements ConceptOutputStream

This ConceptOutputStream generates a subset of "Rich Release Format" MR files.

Author:

Deborah Shapiro

Field Summary

protected boolean	add_unicode_bom
protected static String	file_ext
protected String	mr_dir
protected Map	mr_targets
protected String	null_value
protected static String[]	target_files
protected Map	target_to_output_stream
protected boolean	versioned_output
protected List	warnings

Constructor Summary

RichMRFilesConceptOutputStream()
Instantiates an empty RichMRFilesConceptOutputStream.

Method Summary

void	close() Closes source files that were opened by @link #open(String)}.
void	flush(String file_name) Flushes the given target/output file.
protected long	getFilePosition(String name) DO NOT USE.
String	getNullValue() Returns the null value.
String[]	getWarnings() Returns a String[] of warnings accumulated during processing of the output stream.
boolean	isEmptyValue(String token) Indicates whether or not the specified token is null or contains a null value as defined by being either zero length or a value equal to the null value.
void	open(String mr_dir) Opens all Rich Release Format MR files in the specified directory.
protected BufferedWriter	openTargetFile(String name) Opens the specified file in the directory passed to open(String).
protected void	printLine(String line, String file_name) Prints the given line to the file with the given name.
void	setNullValue(String null_value) Sets the null value to use.
void	writeConcept(Concept concept) Writes a Concept to the appropriate MR files.
protected void	writeMRCOC(Concept concept) Writes MRCOC.RRF entries for a Concept
protected void	writeMRCONSO(Concept concept) Writes MRCONSO.RRF entries for a Concept
protected void	writeMRCXT(Concept concept) Writes MRCXT.RRF entries for a Concept
protected void	writeMRDEF(Concept concept) Writes MRDEF.RRF entries for a Concept
protected void	writeMRHIER(Concept concept) Writes MRHIER entries for a Concept
protected void	writeMRHIST(Concept concept) Writes MRHIST.RRF entries for a Concept
protected void	writeMRMAP(Concept concept) Writes MRMAP.RRF entries for a Concept
protected void	writeMRREL(Concept concept) Writes MRREL.RRF entries for a Concept
protected void	writeMRSAT(Concept concept) Writes MRSAT.RRF entries for a Concept
protected void	writeMRSMAP(Concept concept) Writes MRSMAP.RRF entries for a Concept
protected void	writeMRSTY(Concept concept) Writes MRSTY.RRF entries for a Concept

Methods inherited from class java.lang.Object

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

Field Detail

mr_targets

protected Map mr_targets

target_files

protected static String[] target_files

file_ext

protected static String file_ext

target_to_output_stream

protected Map target_to_output_stream

mr_dir

protected String mr_dir

versioned_output

protected boolean versioned_output

add_unicode_bom

protected boolean add_unicode_bom

warnings

protected List warnings

null_value

protected String null_value

Constructor Detail

RichMRFilesConceptOutputStream

public RichMRFilesConceptOutputStream()

Instantiates an empty RichMRFilesConceptOutputStream.

Method Detail

setNullValue

public void setNullValue(String null_value)

Sets the null value to use. This is needed if release.dat specifies some non-standard null value char sequence.

Specified by:

setNullValue in interface LocalNullValueSupport

Parameters:

null_value - the new null string value

getNullValue

public String getNullValue()

Returns the null value. This is needed if release.dat specifies some non-standard null value char sequence.

Specified by:

getNullValue in interface LocalNullValueSupport

Returns:

the string value for "null"

isEmptyValue

public boolean isEmptyValue(String token)

Indicates whether or not the specified token is null or contains a null value as defined by being either zero length or a value equal to the null value.

Specified by:

isEmptyValue in interface LocalNullValueSupport

open

public void open(String mr_dir)
          throws IOException

Opens all Rich Release Format MR files in the specified directory.

Specified by:

open in interface ConceptOutputStream

Parameters:

mr_dir - the subset directory

Throws:

IOException - if the files cannot be opened

flush

public void flush(String file_name)
           throws IOException

Flushes the given target/output file.

Parameters:

file_name - name of target file

Throws:

IOException

close

public void close()
           throws IOException

Closes source files that were opened by @link #open(String)}.

Specified by:

close in interface ConceptOutputStream

Throws:

IOException - if the files could not be cloesed

printLine

protected void printLine(String line,
                         String file_name)
                  throws IOException

Prints the given line to the file with the given name.

Parameters:

line - the line to be printed

file_name - printing destination

Throws:

IOException

writeConcept

public void writeConcept(Concept concept)
                  throws IOException

Writes a Concept to the appropriate MR files.

Specified by:

writeConcept in interface ConceptOutputStream

Parameters:

concept - the Concept to write

Throws:

IOException - if the files could not be written

writeMRCOC

protected void writeMRCOC(Concept concept)
                   throws IOException

Writes MRCOC.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRCONSO

protected void writeMRCONSO(Concept concept)
                     throws IOException

Writes MRCONSO.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRCXT

protected void writeMRCXT(Concept concept)
                   throws IOException

Writes MRCXT.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRHIER

protected void writeMRHIER(Concept concept)
                    throws IOException

Writes MRHIER entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRDEF

protected void writeMRDEF(Concept concept)
                   throws IOException

Writes MRDEF.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRSTY

protected void writeMRSTY(Concept concept)
                   throws IOException

Writes MRSTY.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRREL

protected void writeMRREL(Concept concept)
                   throws IOException

Writes MRREL.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRSAT

protected void writeMRSAT(Concept concept)
                   throws IOException

Writes MRSAT.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRMAP

protected void writeMRMAP(Concept concept)
                   throws IOException

Writes MRMAP.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRSMAP

protected void writeMRSMAP(Concept concept)
                    throws IOException

Writes MRSMAP.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRHIST

protected void writeMRHIST(Concept concept)
                    throws IOException

Writes MRHIST.RRF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

openTargetFile

protected BufferedWriter openTargetFile(String name)
                                 throws IOException

Opens the specified file in the directory passed to open(String).

Parameters:

name - the filename

Returns:

a BufferedWriter for the file

Throws:

IOException - if the file could not be opened.

getFilePosition

protected long getFilePosition(String name)
                        throws IOException

DO NOT USE.

Parameters:

name - the name

Returns:

the file pos

Throws:

IOException - if anything goes wrong

getWarnings

public String[] getWarnings()

Returns a String[] of warnings accumulated during processing of the output stream.

Specified by:

getWarnings in interface ConceptOutputStream

Returns:

String[] of warnings