gov.nih.nlm.mms.browser
Class RRFBrowsableInputStream

java.lang.Object
  gov.nih.nlm.mms.browser.RRFBrowsableInputStream

All Implemented Interfaces:

BrowsableInputStream, LocalNullValueSupport

public class RRFBrowsableInputStream
extends Object
implements BrowsableInputStream, LocalNullValueSupport

Rich Release Format implementation of BrowsableInputStream. For this class to be usable the directory must be set with setDirectory(String).

Constructor Summary

RRFBrowsableInputStream()
Constructor.

Method Summary

void	buildIndexes(ProgressMonitor pm) Builds the indexes in the RRFBrowsableInputStream.
boolean	buildIndexesNeeded() Indicates if indexes in the RRFBrowsableInputStream need to be built.
void	close() Closes the RRFBrowsableInputStream.
boolean	containsConcept(String cui) Indicates if the RRFBrowsableInputStream contains the concept specified by the CUI.
int	countChildren(Context context) Returns the number of children for the given Context.
int	countSiblings(Context context) Returns the number of siblings for the given Context.
boolean	directoryContainsExpectedData() Indicates if directory of RRFBrowsableInputStream contains RRF data.
Atom[]	findAtomsByCodeSab(String code, Set sources) Looks up the given code in the CODE_SAB_MRCONSO.x index file and returns the Atom[] of Atoms that have the given code and that are in any of the given Sources.
Context[]	findChildren(Context context, SearchOptions options) Returns a Context[] of children for the given context.
Context[]	findSiblings(Context context, SearchOptions options) Returns a Context[] of siblings for the given context.
Set	findWordMatches(String word, Language language) Finds WordSearchResults of Concepts with Strings containing the specified word.
Color	getColor() Returns the name of the color associated with this input format.
String	getDirectory() Gets directory of RRFBrowsableInputStream.
String	getName() Returns the name of the Input Format.
String	getNullValue() Returns the null value.
List	getPrecedenceOrder() Gets the list of source TTYs in precedence order.
String[]	getPreexpandedRawFiles() Returns list of file names that should be preexpanded to show user initial content when concepts are first opened in browser.
Map	getRawConceptWithLinks(String cui, LinkGenerator link_gen) Returns a Map that has concept data RRF filename String objects as keys and have String[] values which are the lines in the file matching the specified CUI.
Map	getRawHistoryData(String cui) Returns a Map that has history filename String objects as keys and have String[] values which are the lines of the file that provide historical information for the specified CUI.
Map	getRawMetadata() Returns a Map that has metadata filename String objects as keys and have String[] values which are the lines of the file that are relevant to the query.
String	getReleaseVersion() Returns the release version
List	getSourceList() Returns the List of included sources.
int	getWordFrequency(String word, Language language) Gets number of strings in which a word appears.
boolean	hasChildren(Context context) Indicates if given Context has children.
boolean	hasSiblings(Context context) Indicates if the given Context has siblings.
void	initializeMetadata() Initializes metadata from MRDOC.RRF and MRSAB.RRF files.
protected boolean	initializeMetadataNeeded() Indicates if metadata classes need to be initialized.
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() Opens the RRFBrowsableInputStream.
Atom	readAtom(String aui, AtomDataSelector selector) Looks up the given AUI in the index file and returns the Atom that contains the given AUI.
Concept	readConcept(String cui, ConceptDataSelector selector) Populates a Concept with the amount of information specified by a ConceptDataSelector.
ReleaseMetadata	readReleaseMetadata() Returns the ReleaseMetadata containing data from MRSAB.RRF, MRCUI.RRF, MRAUI.RRF, and MRDOC.RRF.
void	setDirectory(String newDirectory) Sets directory of RRFBrowsableInputStream.
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

Constructor Detail

RRFBrowsableInputStream

public RRFBrowsableInputStream()

Constructor.

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

getDirectory

public String getDirectory()

Gets directory of RRFBrowsableInputStream.

Specified by:

getDirectory in interface BrowsableInputStream

Returns:

directory of RRFBrowsableInputStream.

setDirectory

public void setDirectory(String newDirectory)

Sets directory of RRFBrowsableInputStream.

Specified by:

setDirectory in interface BrowsableInputStream

Parameters:

newDirectory - directory of RRFBrowsableInputStream

directoryContainsExpectedData

public boolean directoryContainsExpectedData()

Indicates if directory of RRFBrowsableInputStream contains RRF data.

Specified by:

directoryContainsExpectedData in interface BrowsableInputStream

Returns:

true if the directory set by setDirectory(String) contains RRF data, otherwise false.

open

public void open()
          throws IOException

Opens the RRFBrowsableInputStream.

Specified by:

open in interface BrowsableInputStream

Throws:

IOException - if there is a problem opening the RRFBrowsableInputStream.

close

public void close()
           throws IOException

Closes the RRFBrowsableInputStream.

Specified by:

close in interface BrowsableInputStream

Throws:

IOException - if there is a problem closing the RRFBrowsableInputStream.

initializeMetadataNeeded

protected boolean initializeMetadataNeeded()

Indicates if metadata classes need to be initialized.

Returns:

true if the metadata classes need to be initialized; false otherwise.

See Also:

initializeMetadata()

initializeMetadata

public void initializeMetadata()
                        throws IOException

Initializes metadata from MRDOC.RRF and MRSAB.RRF files. The following metadata classes are initialized:

• AttributeName
• CoocurrenceType
• Language
• AdditionalRelationshipLabel
• RelationshipLabel
• SourceIdentifierType
• StringType
• Suppressible
• TermStatus
• TermType
• TermTypeGroup

Specified by:

initializeMetadata in interface BrowsableInputStream

Throws:

IOException

readReleaseMetadata

public ReleaseMetadata readReleaseMetadata()
                                    throws IOException

Returns the ReleaseMetadata containing data from MRSAB.RRF, MRCUI.RRF, MRAUI.RRF, and MRDOC.RRF.

Specified by:

readReleaseMetadata in interface BrowsableInputStream

Returns:

the ReleaseMetadata

Throws:

IOException - if the files could not be read.

buildIndexesNeeded

public boolean buildIndexesNeeded()

Indicates if indexes in the RRFBrowsableInputStream need to be built.

Specified by:

buildIndexesNeeded in interface BrowsableInputStream

Returns:

true if indexes needed to be built; false otherwise.

buildIndexes

public void buildIndexes(ProgressMonitor pm)
                  throws IOException

Builds the indexes in the RRFBrowsableInputStream.

Specified by:

buildIndexes in interface BrowsableInputStream

Parameters:

pm - ProgressMonitor for displaying progress of the operation

Throws:

IOException

getPrecedenceOrder

public List getPrecedenceOrder()

Gets the list of source TTYs in precedence order.

Specified by:

getPrecedenceOrder in interface BrowsableInputStream

Returns:

List of source TTYs in precedence order.

getSourceList

public List getSourceList()

Returns the List of included sources.

Specified by:

getSourceList in interface BrowsableInputStream

Returns:

included source List.

getName

public String getName()

Returns the name of the Input Format.

Specified by:

getName in interface BrowsableInputStream

Returns:

input format name

getColor

public Color getColor()

Returns the name of the color associated with this input format.

Specified by:

getColor in interface BrowsableInputStream

Returns:

input format color

getReleaseVersion

public String getReleaseVersion()

Returns the release version

Specified by:

getReleaseVersion in interface BrowsableInputStream

Returns:

release version

readConcept

public Concept readConcept(String cui,
                           ConceptDataSelector selector)
                    throws IOException

Populates a Concept with the amount of information specified by a ConceptDataSelector.

Specified by:

readConcept in interface BrowsableInputStream

Parameters:

cui - CUI (concept unique identifier) of the Concept desired

selector - ConceptDataSelector

Returns:

a populated Concept according to the specified ConceptDataSelector.

Throws:

IOException

readAtom

public Atom readAtom(String aui,
                     AtomDataSelector selector)
              throws IOException

Looks up the given AUI in the index file and returns the Atom that contains the given AUI.

Specified by:

readAtom in interface BrowsableInputStream

Parameters:

aui - AUI to be searched for

selector - AtomDataSelector specifying how to populate the Atom

Returns:

the Atom containing the AUI, populated according to the AtomDataSelector.

Throws:

IOException

getRawConceptWithLinks

public Map getRawConceptWithLinks(String cui,
                                  LinkGenerator link_gen)
                           throws IOException

Returns a Map that has concept data RRF filename String objects as keys and have String[] values which are the lines in the file matching the specified CUI.

Specified by:

getRawConceptWithLinks in interface BrowsableInputStream

Parameters:

cui - UMLS CUI

link_gen - LinkGenerator used to insert hyperlinks to referenced CUIs and AUIs

Returns:

a Map from each RRF file name to an array of the lines in that file matching the specified CUI.

Throws:

IOException

getRawHistoryData

public Map getRawHistoryData(String cui)
                      throws IOException

Returns a Map that has history filename String objects as keys and have String[] values which are the lines of the file that provide historical information for the specified CUI.

Specified by:

getRawHistoryData in interface BrowsableInputStream

Parameters:

cui - UMLS CUI

Returns:

a Map that has history filename String objects as keys and have String[] values which are the lines of the file that provide historical information for the specified CUI

Throws:

IOException

getRawMetadata

public Map getRawMetadata()
                   throws IOException

Returns a Map that has metadata filename String objects as keys and have String[] values which are the lines of the file that are relevant to the query.

Specified by:

getRawMetadata in interface BrowsableInputStream

Returns:

a Map that has metadata filename String objects as keys and have String[] values which are the lines of the file that are relevant to the query.

Throws:

IOException

containsConcept

public boolean containsConcept(String cui)
                        throws IOException

Indicates if the RRFBrowsableInputStream contains the concept specified by the CUI.

Specified by:

containsConcept in interface BrowsableInputStream

Parameters:

cui - CUI of the concept in question

Returns:

true if the data set contains the concept specified by the CUI.

Throws:

IOException

countSiblings

public int countSiblings(Context context)
                  throws IOException

Description copied from interface: BrowsableInputStream

Returns the number of siblings for the given Context.

Specified by:

countSiblings in interface BrowsableInputStream

Returns:

number of siblings

Throws:

IOException

hasSiblings

public boolean hasSiblings(Context context)
                    throws IOException

Description copied from interface: BrowsableInputStream

Indicates if the given Context has siblings.

Specified by:

hasSiblings in interface BrowsableInputStream

Returns:

true if context has siblings false otherwise

Throws:

IOException

findSiblings

public Context[] findSiblings(Context context,
                              SearchOptions options)
                       throws IOException

Description copied from interface: BrowsableInputStream

Returns a Context[] of siblings for the given context.

Specified by:

findSiblings in interface BrowsableInputStream

options - SearchOptions specify parameters

Returns:

array of siblings

Throws:

IOException

countChildren

public int countChildren(Context context)
                  throws IOException

Description copied from interface: BrowsableInputStream

Returns the number of children for the given Context.

Specified by:

countChildren in interface BrowsableInputStream

Returns:

count of children

Throws:

IOException

hasChildren

public boolean hasChildren(Context context)
                    throws IOException

Description copied from interface: BrowsableInputStream

Indicates if given Context has children.

Specified by:

hasChildren in interface BrowsableInputStream

Returns:

true if context has children false otherwise

Throws:

IOException

findChildren

public Context[] findChildren(Context context,
                              SearchOptions options)
                       throws IOException

Description copied from interface: BrowsableInputStream

Returns a Context[] of children for the given context.

Specified by:

findChildren in interface BrowsableInputStream

options - SearchOptions specify parameters

Returns:

Context[]

Throws:

IOException

findWordMatches

public Set findWordMatches(String word,
                           Language language)
                    throws IOException,
                           InterruptedException

Finds WordSearchResults of Concepts with Strings containing the specified word.

Specified by:

findWordMatches in interface BrowsableInputStream

Parameters:

word - search word or partial search word with wild card '*' at end

language - Language of strings to be found

Returns:

Set of WordSearchResults consisting of matches on the specified word.

Throws:

IOException

InterruptedException

getWordFrequency

public int getWordFrequency(String word,
                            Language language)
                     throws IOException

Gets number of strings in which a word appears.

Specified by:

getWordFrequency in interface BrowsableInputStream

Parameters:

word - word or partial word followed by a wild card character '*'.

language - Language of strings to search

Returns:

number of strings in which a word appears.

Throws:

IOException

findAtomsByCodeSab

public Atom[] findAtomsByCodeSab(String code,
                                 Set sources)
                          throws IOException

Looks up the given code in the CODE_SAB_MRCONSO.x index file and returns the Atom[] of Atoms that have the given code and that are in any of the given Sources.

Specified by:

findAtomsByCodeSab in interface BrowsableInputStream

Parameters:

code - to be searched for

sources - Set of sources that returned Atoms may belong to

Returns:

Atom[] of Atoms with the given code and in one of the given sources

Throws:

IOException

getPreexpandedRawFiles

public String[] getPreexpandedRawFiles()

Returns list of file names that should be preexpanded to show user initial content when concepts are first opened in browser.

Specified by:

getPreexpandedRawFiles in interface BrowsableInputStream

Returns:

list of files whose data should be preexpanded