gov.nih.nlm.umls.io
Class RichMRFilesConceptInputStream

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

All Implemented Interfaces:

ConceptInputStream, LocalNullValueSupport

Direct Known Subclasses:

MRCXTBuilderOutputStream, RichMRMetathesaurusInputStream

public class RichMRFilesConceptInputStream
extends Object
implements ConceptInputStream

This ConceptInputStream builds Concept objects from a full set of "Rich Release Format" MR files.

Author:

Deborah Shapiro

Field Summary

protected String	add_suffix
protected Map	atom_hm
protected String[]	file_names
protected String	from_rsab
protected String	from_vsab
protected Object[]	install_paths
protected PushBackReader	mrcoc_source
protected int	mrconso_counter
protected int	mrconso_lines
protected PushBackReader	mrconso_source
protected PushBackReader	mrcxt_source
protected PushBackReader	mrdef_source
protected PushBackReader	mrdoc_source
protected PushBackReader	mrhier_source
protected PushBackReader	mrhist_source
protected PushBackReader	mrmap_source
protected PushBackReader	mrrel_source
protected PushBackReader	mrsat_source
protected PushBackReader	mrsty_source
protected String	null_value
protected Map	rel_hm
protected Concept	this_concept
protected String	to_rsab
protected String	to_vsab
protected String[]	tokens
protected List	warnings

Constructor Summary

RichMRFilesConceptInputStream()
Instantiates an empty RichMRFilesConceptInputStream;

Method Summary

void	close() Close files opened during open(String[]).
protected Concept	getAtoms(Concept this_concept, String current_cui) Instantiates Atoms from the MRCONSO.RRF file matching the specified CUI and adds them to the current Concept.
protected void	getAttributes(Concept this_concept, String current_cui) Gets Attributes from the MRSAT.RRF files with the given cui and adds them to the current Concept.
protected void	getComponentHistories(Concept this_concept, String current_cui) Gets ComponentHistorys from the MRHIST.RRF file with the given cui and adds them to the current Concept.
int	getConceptProgress() Returns the percentage of MRCONSO lines that have been processed.
protected void	getContexts(Concept this_concept, String current_cui) Gets Contexts from the MRCXT.RRF and MRHIER.RRF files with the given cui and adds them to this_concept.
protected void	getCoocurrences(Concept this_concept, String current_cui) Gets Coocurrences from the MRCOC.RRF file with the given cui and adds them to the current Concept.
protected void	getDefinitions(Concept this_concept, String current_cui) Gets Definitions from the MRDEF.RRF file with the given cui and adds them to the current Concept.
protected Map	getLineCounts() Reads through MRFILES.RRF to determine the size of MRCONSO.RRF.
protected void	getMappings(Concept this_concept, String current_cui) Gets Mappings from the MRMAP.RRF file with the given cui and adds them to the current Concept.
String	getNullValue() Returns the null value.
protected void	getRelationships(Concept this_concept, String current_cui) Gets Relationships from the MRREL.RRF file with the given cui and adds them to the current Concept.
protected void	getSemanticTypes(Concept this_concept, String current_cui) Gets SemanticTypes from the MRSTY.RRF file with the given cui and adds them to the current Concept.
String[]	getWarnings() Returns a String[] of warnings accumulated during processing of the input 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.
protected Atom	newInstanceFromMRCONSO(String line) Instantiates an Atom from a MRCONSO.RRF line.
protected Context	newInstanceFromMRHIER(String line) Instantiates an Context from a MRHIER.RRF line.
void	open(String[] paths) Opens all of the MR Files in preparation for subsetting.
protected void	openMRFiles() Opens the Rich Release Format MR files.
protected PushBackReader	openSourceFile(String name, boolean fileMustExist) Opens the source file from the most current of the given installation paths in which this source is available.
Concept	readConcept() Returns a Concept containing data from the MR files.
void	setAdditionalSuffix(String suffix) Sets an additional suffix.
void	setNullValue(String null_value) Sets the null value to use.

Methods inherited from class java.lang.Object

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

Field Detail

mrconso_source

protected PushBackReader mrconso_source

mrcxt_source

protected PushBackReader mrcxt_source

mrsty_source

protected PushBackReader mrsty_source

mrdef_source

protected PushBackReader mrdef_source

mrrel_source

protected PushBackReader mrrel_source

mrcoc_source

protected PushBackReader mrcoc_source

mrsat_source

protected PushBackReader mrsat_source

mrhist_source

protected PushBackReader mrhist_source

mrmap_source

protected PushBackReader mrmap_source

mrhier_source

protected PushBackReader mrhier_source

mrdoc_source

protected PushBackReader mrdoc_source

atom_hm

protected Map atom_hm

rel_hm

protected Map rel_hm

file_names

protected String[] file_names

install_paths

protected Object[] install_paths

this_concept

protected Concept this_concept

mrconso_lines

protected int mrconso_lines

mrconso_counter

protected int mrconso_counter

from_rsab

protected String from_rsab

from_vsab

protected String from_vsab

to_rsab

protected String to_rsab

to_vsab

protected String to_vsab

add_suffix

protected String add_suffix

tokens

protected final String[] tokens

warnings

protected List warnings

null_value

protected String null_value

Constructor Detail

RichMRFilesConceptInputStream

public RichMRFilesConceptInputStream()

Instantiates an empty RichMRFilesConceptInputStream;

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[] paths)
          throws IOException

Opens all of the MR Files in preparation for subsetting.

Specified by:

open in interface ConceptInputStream

Parameters:

paths - the sources containing the files

Throws:

IOException - if any files can not be opened

openMRFiles

protected void openMRFiles()
                    throws IOException

Opens the Rich Release Format MR files.

Throws:

IOException - if any files cannot be opened

close

public void close()
           throws IOException

Close files opened during open(String[]).

Specified by:

close in interface ConceptInputStream

Throws:

IOException - if files can not be closed

readConcept

public Concept readConcept()
                    throws IOException

Returns a Concept containing data from the MR files.

Specified by:

readConcept in interface ConceptInputStream

Returns:

a Concept containing data from the MR files

Throws:

IOException - if files could not be read

getConceptProgress

public int getConceptProgress()

Returns the percentage of MRCONSO lines that have been processed.

Specified by:

getConceptProgress in interface ConceptInputStream

Returns:

the percentage of MRCONSO lines that have been processed

openSourceFile

protected PushBackReader openSourceFile(String name,
                                        boolean fileMustExist)
                                 throws IOException

Opens the source file from the most current of the given installation paths in which this source is available.

Parameters:

name - the filename

fileMustExist - true if a FileNotFoundException should be thrown when the file doesn't exist; false otherwise

Returns:

a PushBackReader on the file if it exists. If fileMustExist is false then a PushBackReader enclosing a StringReader of an empty String will be returned.

Throws:

IOException - if the file could not be opened. If fileMustExist is true a FileNotFoundException will be thrown if the specified file doesn't exist.

getLineCounts

protected Map getLineCounts()
                     throws IOException

Reads through MRFILES.RRF to determine the size of MRCONSO.RRF.

Returns:

Map of file names to lines in file

Throws:

IOException - if the file cannot be opened or read

newInstanceFromMRCONSO

protected Atom newInstanceFromMRCONSO(String line)
                               throws IOException

Instantiates an Atom from a MRCONSO.RRF line.

Parameters:

line - a line from MRCONSO.RRF

Returns:

the Atom matching the line

Throws:

IOException - if there is a problem with the file

getAtoms

protected Concept getAtoms(Concept this_concept,
                           String current_cui)
                    throws IOException

Instantiates Atoms from the MRCONSO.RRF file matching the specified CUI and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Returns:

Concept that will contain the Atoms

Throws:

IOException - if anything goes wrong

getAttributes

protected void getAttributes(Concept this_concept,
                             String current_cui)
                      throws IOException

Gets Attributes from the MRSAT.RRF files with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading the file

getContexts

protected void getContexts(Concept this_concept,
                           String current_cui)
                    throws IOException

Gets Contexts from the MRCXT.RRF and MRHIER.RRF files with the given cui and adds them to this_concept.

Parameters:

this_concept - Concept that will contain the Contexts

current_cui - String representation of the cui

Throws:

IOException - if problem reading from MRCXT.RRF or MRHIER.RRF

newInstanceFromMRHIER

protected Context newInstanceFromMRHIER(String line)
                                 throws IOException

Instantiates an Context from a MRHIER.RRF line.

Parameters:

line - a line from MRHIER.RRF

Returns:

the Context matching the line

Throws:

IOException - if there is a problem with the file

getCoocurrences

protected void getCoocurrences(Concept this_concept,
                               String current_cui)
                        throws IOException

Gets Coocurrences from the MRCOC.RRF file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from MRCOC.RRF

getDefinitions

protected void getDefinitions(Concept this_concept,
                              String current_cui)
                       throws IOException

Gets Definitions from the MRDEF.RRF file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from MRDEF.RRF

getSemanticTypes

protected void getSemanticTypes(Concept this_concept,
                                String current_cui)
                         throws IOException

Gets SemanticTypes from the MRSTY.RRF file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from MRSTY.RRF

getRelationships

protected void getRelationships(Concept this_concept,
                                String current_cui)
                         throws IOException

Gets Relationships from the MRREL.RRF file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from MRREL.RRF

getComponentHistories

protected void getComponentHistories(Concept this_concept,
                                     String current_cui)
                              throws IOException

Gets ComponentHistorys from the MRHIST.RRF file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from MRHIST.RRF

getMappings

protected void getMappings(Concept this_concept,
                           String current_cui)
                    throws IOException

Gets Mappings from the MRMAP.RRF file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from MRMAP.RRF

setAdditionalSuffix

public void setAdditionalSuffix(String suffix)

Sets an additional suffix.

Parameters:

suffix - to be added to the .RRF suffix

getWarnings

public String[] getWarnings()

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

Specified by:

getWarnings in interface ConceptInputStream

Returns:

String[] of warnings