Package com.semedy.reasoner.api.edb

Class ExtensionalDB

java.lang.Object

com.semedy.reasoner.api.edb.ExtensionalDB

All Implemented Interfaces:

Closeable, AutoCloseable

public class ExtensionalDB
extends Object
implements Closeable

Extensional database is a container for all facts.
It contains a list of edb tuples for each predicate containing all facts for that predicate.
edb tuples may be scanned, index structures may be generated etc.

Constructor Summary

Constructors

Constructor	Description
ExtensionalDB()	a no name main memory edb without transactions
ExtensionalDB(String edbdir, String tempdir, String logDir, Configuration.StorageType storage, Set<String> excludedPredicates, long maxtermstoload, boolean compress, List<Literal> partition, boolean transactionLog, String[] indexedprops, Configuration config)
ExtensionalDB(List<Literal> partitions, Configuration config)

Method Summary

Modifier and Type	Method	Description
void	addRelation(String pname, Relation T)	add a whole relation R to a predicate
boolean	addTuple(String predicate, TupleBuffer tuple)	add tuple to edb.
void	addTupleToIndices(String predicate, long[] codes, Object[] terms)	add tuple to edb indices
void	backup(String edbDir, String backupfile)	create a backup for the extensional database
void	backupOld(String backupfile, SymbolTable symbolTable)	Deprecated.
void	bulkExport(InterruptFlag interrupt, List<Filter> filters, String resultdirectory, SymbolTable symbolTable)	Bulk export of facts for predicate symbols to raw files in result directory
void	bulkLoadFiles(List<File>[] files, Map<String,Long> counts, Map<String,String> indexToPredicates, String tempdir, SymbolTable symbols)
boolean	checkSanity()	checks sanity of all bplus trees
void	clear()	remove all facts
void	clearJoinCaches()	clear join caches of all relations
void	close()	Closes the extensional database.
InvertedIndices	createIndex(SymbolTable symbols, long propCode)	create indices for property
List<Relation>	createRelation(String predicate)	Create a relation for predicate p.
List<Relation>	createRelation(String predicate, int number)	Create a relation for predicate p.
Schemas	createSchemas(SymbolTable symbols)	Create a cache for the hierarchy
void	delete()	delete all facts and release all files
void	exportNQuads(List<String> predicates, Writer writer, SymbolTable symbolTable, String iri)	export of facts for predicate symbols to N-Quads file
void	exportOOLogic(InterruptFlag interrupt, List<Filter> filters, Writer writer, SymbolTable symbolTable)	export of facts for predicate symbols to OO-logic file
void	exportOOLogic(InterruptFlag interrupt, List<Filter> filters, Writer writer, SymbolTable symbolTable, String module)	export of facts for predicate symbols to OO-logic file.
void	exportOOLogic(InterruptFlag interrupt, List<Filter> filters, String resultFile, SymbolTable symbolTable)	export of facts for predicate symbols to OO-logic file
void	exportOOLogic(InterruptFlag interrupt, List<Filter> filters, String resultFile, SymbolTable symbolTable, String module)	export of facts for predicate symbols to OO-logic file.
void	flush()
InvertedIndices	getInvertedIndices()	get all inverted indices
InvertedIndices	getInvertedIndices(String property)	get inverted indices
LoaderProvider	getLoaderProvider()	get loaders for different file formats, like json, nquads, csv
List<String>	getPredicates()	returns a list of all predicates in the extensional database
List<Relation>	getRelations(String predicate)	return a list of all relations for predicate p (can be more than one)
Schemas	getSchemas()	get schema information
void	indexTransactionBegin()	transaction begin for indices
void	indexTransactionCommit()	transaction commit for indices
void	indexTransactionRollback()	transaction rollback for indices
boolean	isEmpty()	Is the extensional database empty?
boolean	isEmpty(String p)	Is the relation for predicate empty?
boolean	isPersistent()	Is it a persistent extensional database?
void	loadFactsFiles(List<String> files, boolean deleteold, SymbolTable symbolTable, ExternalDataTypeProvider datatypes, BuiltinProvider builtins)	reads facts files in ordinary predicate form
void	loadFiles(List<String> files, SymbolTable symbols, ExternalDataTypeProvider dataTypes)	load all kind of files (besides OO-logic files)
void	recreateIndices(SymbolTable symbols)	recreate indices for properties
void	removeRelation(String predicate)	removes all relations for predicate p
boolean	removeTuple(String predicate, TupleBuffer tuple)	remove a tuple from edb.
void	removeTupleFromIndices(String predicate, long[] codes, Object[] terms)	remove tuple from edb indices
void	reOpen()	reopens a closed extensional database
void	restore(String backupfile, String edbDir)	restore the edb from a backup file.
void	restore(List<String> predicatesToRestore, boolean restoreSymbolTable, String edbdir, String workdir, String logDir, String backupfile, ExternalDataTypeProvider datatypes, int maxTermLength)	restore single predicates and/or symbol table from a backup file.
void	restoreOld(String edbdir, String workdir, String logdir, String backupfile, ExternalDataTypeProvider datatypes, int maxTermLength)	restore the edb from a backup file.
void	selectMixedRelations()	load all mixed relations into RAM.
void	setRelationFactory(RelationFactory f)	Store factory for creating stores inside extensional db This allows for instance to keep some relations in main memory and other ones as persistent relations

Methods inherited from class java.lang.Object

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

Constructor Details

ExtensionalDB

public ExtensionalDB()
              throws IOException,
SemReasonerException

a no name main memory edb without transactions

Throws:

IOException

SemReasonerException

ExtensionalDB

public ExtensionalDB(List<Literal> partitions,
 Configuration config)
              throws IOException,
SemReasonerException

Throws:

IOException

SemReasonerException

ExtensionalDB

public ExtensionalDB(String edbdir,
 String tempdir,
 String logDir,
 Configuration.StorageType storage,
 Set<String> excludedPredicates,
 long maxtermstoload,
 boolean compress,
 List<Literal> partition,
 boolean transactionLog,
 String[] indexedprops,
 Configuration config)
              throws IOException,
SemReasonerException

Throws:

IOException

SemReasonerException

Method Details

selectMixedRelations

public void selectMixedRelations()
                          throws EDBException,
IOException

load all mixed relations into RAM.
Swap out all bplus nodes afterwards.

Throws:

EDBException

IOException

getInvertedIndices

public InvertedIndices getInvertedIndices()

get all inverted indices

Returns:

getLoaderProvider

public LoaderProvider getLoaderProvider()

get loaders for different file formats, like json, nquads, csv

Returns:

getInvertedIndices

public InvertedIndices getInvertedIndices(String property)

get inverted indices

Returns:

recreateIndices

public void recreateIndices(SymbolTable symbols)
                     throws IOException,
SemReasonerException

recreate indices for properties

Parameters:

symbols -

Throws:

IOException

SemReasonerException

createIndex

public InvertedIndices createIndex(SymbolTable symbols,
 long propCode)
                            throws IOException,
SemReasonerException

create indices for property

Parameters:

symbols -

Throws:

IOException

SemReasonerException

createSchemas

public Schemas createSchemas(SymbolTable symbols)
                      throws IOException,
SemReasonerException

Create a cache for the hierarchy

Throws:

IOException

SemReasonerException

getSchemas

public Schemas getSchemas()

get schema information

Returns:

checkSanity

public boolean checkSanity()
                    throws IOException,
EDBException

checks sanity of all bplus trees

Returns:

Throws:

IOException

EDBException

reOpen

public void reOpen()
            throws IOException,
SemReasonerException

reopens a closed extensional database

Throws:

IOException

SemReasonerException

close

public void close()
           throws IOException

Closes the extensional database. Must be called at the end to finalize the db correctly

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Throws:

IOException

flush

public void flush()
           throws IOException

Throws:

IOException

getPredicates

public List<String> getPredicates()

returns a list of all predicates in the extensional database

createRelation

public List<Relation> createRelation(String predicate)
                              throws EDBException,
IOException

Create a relation for predicate p.
A predicate is given by the name and the arity: name|arity
Example: p|2

Parameters:

predicate - , full qualified predicate name

Returns:

created relation

Throws:

EDBException

IOException

createRelation

public List<Relation> createRelation(String predicate,
 int number)
                              throws EDBException,
IOException

Create a relation for predicate p.
A predicate is given by the name and the arity: name|arity
Example: p|2

Parameters:

predicate - , full qualified predicate name

Returns:

created relation

Throws:

EDBException

IOException

removeRelation

public void removeRelation(String predicate)
                    throws EDBException,
IOException

removes all relations for predicate p

Parameters:

predicate - , full qualified predicate name

Throws:

EDBException

IOException

getRelations

public List<Relation> getRelations(String predicate)

return a list of all relations for predicate p (can be more than one)

Parameters:

predicate - , full qualified predicate name

Returns:

addRelation

public void addRelation(String pname,
 Relation T)
                 throws IOException,
SemReasonerException

add a whole relation R to a predicate

Parameters:

pname - , predicate the relation is added to

T - relation to be added

Throws:

IOException

SemReasonerException

isEmpty

public boolean isEmpty()
                throws EDBException,
IOException

Is the extensional database empty?

Returns:

Throws:

EDBException

IOException

See Also:

• isEmpty()

isEmpty

public boolean isEmpty(String p)
                throws EDBException

Is the relation for predicate empty?

Returns:

Throws:

EDBException

See Also:

• isEmpty()

isPersistent

public boolean isPersistent()

Is it a persistent extensional database?

Returns:

See Also:

• isPersistent()

clear

public void clear()
           throws IOException,
EDBException

remove all facts

Throws:

IOException

EDBException

delete

public void delete()
            throws EDBException

delete all facts and release all files

Throws:

EDBException

clearJoinCaches

public void clearJoinCaches()
                     throws IOException,
EDBException

clear join caches of all relations

Throws:

IOException

EDBException

bulkLoadFiles

public void bulkLoadFiles(List<File>[] files,
 Map<String,Long> counts,
 Map<String,String> indexToPredicates,
 String tempdir,
 SymbolTable symbols)
                   throws IOException,
SemReasonerException,
InterruptedException

Throws:

IOException

SemReasonerException

InterruptedException

loadFactsFiles

public void loadFactsFiles(List<String> files,
 boolean deleteold,
 SymbolTable symbolTable,
 ExternalDataTypeProvider datatypes,
 BuiltinProvider builtins)
                    throws IOException,
DatatypeConfigurationException,
SemReasonerException

reads facts files in ordinary predicate form

Parameters:

files - , files to be loaded

deleteold - , delete old facts

symbolTable - , symbol table

datatypes - , external data types

builtins - , the available builtins

Throws:

IOException

DatatypeConfigurationException

SemReasonerException

loadFiles

public void loadFiles(List<String> files,
 SymbolTable symbols,
 ExternalDataTypeProvider dataTypes)
               throws IOException,
InterruptedException,
SemReasonerException

load all kind of files (besides OO-logic files)

Parameters:

files -

symbols -

dataTypes -

Throws:

IOException

InterruptedException

SemReasonerException

restoreOld

public void restoreOld(String edbdir,
 String workdir,
 String logdir,
 String backupfile,
 ExternalDataTypeProvider datatypes,
 int maxTermLength)
                throws InterruptedException,
IOException,
SemReasonerException

restore the edb from a backup file.
Clear the edb directory first.
Caution! the current edb may be damaged
Caution! also the backup may be damaged

Parameters:

edbdir - , the directory for the edb

workdir - , a directory for temporary files

logdir - , a directory for logging files

backupfile - , the input file (backupfile)

datatypes - , the external data types

maxTermLength - , the max term length to distinguish terms

Throws:

InterruptedException

IOException

SemReasonerException

restore

public void restore(String backupfile,
 String edbDir)
             throws InterruptedException,
IOException,
SemReasonerException

restore the edb from a backup file.
Clear the edb directory first.
Caution! the current edb may be damaged
Caution! also the backup may be damaged

Parameters:

edbDir - , the directory for the edb

backupfile - , the input file (backupfile)

Throws:

InterruptedException

IOException

SemReasonerException

restore

public void restore(List<String> predicatesToRestore,
 boolean restoreSymbolTable,
 String edbdir,
 String workdir,
 String logDir,
 String backupfile,
 ExternalDataTypeProvider datatypes,
 int maxTermLength)
             throws InterruptedException,
IOException,
SemReasonerException

restore single predicates and/or symbol table from a backup file.
Delete the predicate files and/or symbol table in edb first
Caution! the current edb may be damaged
Caution! also the backup may be damaged

Parameters:

edbdir - , the directory for the edb

workdir - , a directory for temporary files

backupfile - , the input file (backupfile)

Throws:

InterruptedException

IOException

SemReasonerException

backup

public void backup(String edbDir,
 String backupfile)
            throws SemReasonerException,
IOException,
EDBException

create a backup for the extensional database

Parameters:

backupfile -

Throws:

IOException

EDBException

SemReasonerException

EDBException

backupOld

@Deprecated
public void backupOld(String backupfile,
 SymbolTable symbolTable)
               throws SemReasonerException,
IOException,
EDBException

Deprecated.

create a backup for the extensional database

Parameters:

backupfile -

symbolTable -

Throws:

IOException

EDBException

SemReasonerException

EDBException

bulkExport

public void bulkExport(InterruptFlag interrupt,
 List<Filter> filters,
 String resultdirectory,
 SymbolTable symbolTable)
                throws InterruptedException,
SemReasonerException

Bulk export of facts for predicate symbols to raw files in result directory

Parameters:

interrupt - , flag to support interrupting the export process

filters - , predicates together with filters for export

resultdirectory -

symbolTable -

Throws:

InterruptedException

SemReasonerException

exportOOLogic

public void exportOOLogic(InterruptFlag interrupt,
 List<Filter> filters,
 String resultFile,
 SymbolTable symbolTable,
 String module)
                   throws InterruptedException,
IOException,
SemReasonerException

export of facts for predicate symbols to OO-logic file.
Fill into a module, if module is not yet given

Parameters:

interrupt - , flag to interrupt export

filters - , the predicates to be exported, e.g. value|3, member|2 together with filters

resultFile -

symbolTable -

module -

Throws:

InterruptedException

IOException

FileNotFoundException

SemReasonerException

exportOOLogic

public void exportOOLogic(InterruptFlag interrupt,
 List<Filter> filters,
 Writer writer,
 SymbolTable symbolTable,
 String module)
                   throws InterruptedException,
IOException,
SemReasonerException

export of facts for predicate symbols to OO-logic file.
Fill into a module, if module is not yet given

Parameters:

interrupt - , flag to interrupt export

filters - , the predicates to be exported, e.g. value|3, member|2 together with filters

writer - , the writer to write to

symbolTable - , the symbols

module - , the module to added, may be null

Throws:

InterruptedException

IOException

FileNotFoundException

SemReasonerException

exportOOLogic

public void exportOOLogic(InterruptFlag interrupt,
 List<Filter> filters,
 String resultFile,
 SymbolTable symbolTable)
                   throws InterruptedException,
IOException,
SemReasonerException

export of facts for predicate symbols to OO-logic file

Parameters:

interrupt - , flag to interrupt export

filters - , the predicates to be exported, e.g. value|3, member|2 together with filters

resultFile -

symbolTable -

Throws:

InterruptedException

IOException

FileNotFoundException

SemReasonerException

exportOOLogic

public void exportOOLogic(InterruptFlag interrupt,
 List<Filter> filters,
 Writer writer,
 SymbolTable symbolTable)
                   throws InterruptedException,
IOException,
SemReasonerException

export of facts for predicate symbols to OO-logic file

Parameters:

interrupt - , flag to interrupt export

filters - , the predicates to be exported, e.g. value|3, member|2 together with filters

writer -

symbolTable -

Throws:

InterruptedException

IOException

FileNotFoundException

SemReasonerException

exportNQuads

public void exportNQuads(List<String> predicates,
 Writer writer,
 SymbolTable symbolTable,
 String iri)
                  throws InterruptedException,
IOException,
SemReasonerException

export of facts for predicate symbols to N-Quads file

Parameters:

predicates -

writer -

symbolTable -

iri - , an iri if there is none

Throws:

InterruptedException

IOException

FileNotFoundException

SemReasonerException

setRelationFactory

public void setRelationFactory(RelationFactory f)

Store factory for creating stores inside extensional db
This allows for instance to keep some relations in main memory and other ones as persistent relations

Parameters:

f -

indexTransactionBegin

public void indexTransactionBegin()
                           throws IOException

transaction begin for indices

Throws:

IOException

indexTransactionCommit

public void indexTransactionCommit()
                            throws IOException

transaction commit for indices

Throws:

IOException

indexTransactionRollback

public void indexTransactionRollback()
                              throws IOException

transaction rollback for indices

Throws:

IOException

addTupleToIndices

public void addTupleToIndices(String predicate,
 long[] codes,
 Object[] terms)
                       throws EDBException,
IOException

add tuple to edb indices

Parameters:

codes -

terms - unencoded terms in tuple

Throws:

IOException

EDBException

removeTupleFromIndices

public void removeTupleFromIndices(String predicate,
 long[] codes,
 Object[] terms)
                            throws EDBException,
IOException

remove tuple from edb indices

Parameters:

codes -

terms - unencoded terms in tuple

Throws:

IOException

EDBException

addTuple

public boolean addTuple(String predicate,
 TupleBuffer tuple)
                 throws IOException,
SemReasonerException

add tuple to edb.
use partitioning

Parameters:

tuple -

Throws:

IOException

SemReasonerException

removeTuple

public boolean removeTuple(String predicate,
 TupleBuffer tuple)
                    throws IOException,
SemReasonerException

remove a tuple from edb.
use partitioning

Parameters:

tuple -

Throws:

IOException

SemReasonerException