it.uniroma2.art.semanticturkey.ontology

Class STOntologyManager<T extends RDFModel>

java.lang.Object

it.uniroma2.art.semanticturkey.ontology.STOntologyManager<T>

public abstract class STOntologyManager<T extends RDFModel>
extends Object

A class managing high level operations (such as recursive ontology import, gussing namespace-prefix mappings etc..) which are usually not automated by a triple store.

The namespace-prefix mapping has a double management

• prefixes for imported ontologies are guessed by means of some heuristics and then directly added to the loaded triple store manager. These "guesses" will be typically shown with a lighter color on user interfaces, denoting their setting being chosen automatically
• the namespace-prefix mapping APIs in this class allow for the definition of custom mappings. These are persisted on the project associated to this OntologyManager and will be reloaded each time the project is open. These custom mappings will usually be evident in the UI as user-specified mappings

Note that, at the level of this OntologyManager, there is no track of which mappings were already present in the loaded triple store and which ones have been guessed by OntologyManager. Only those explicitly selected by the user are made evident

Author:

Armando Stellato

Field Summary

Fields

Modifier and Type	Field and Description
protected HashSet<String>	applicationOntologiesNamespace This set contains namespaces of ontologies adopted by the application or its extension to model their own behavior.
protected HashSet<ARTURIResource>	applicationOntologiesNG This set contains named graphs adopted by the application or its extension to model their own behavior.
protected HashMap<ARTURIResource,ImportStatus>	importsStatusMap importStatusMap is a map pointing to structures (ImportStatus) telling the import status (LOCAL, WEB, NULL, FAILED) of a ontology which should be imported by the main graph, and the location of its file in case it is a LOCAL import Some notes: I was thinking about making this map a persistence object.
protected static org.slf4j.Logger	logger
protected T	model
protected OWLArtModelFactory<? extends ModelConfiguration>	modelFactory
protected NSPrefixMappings	nsPrefixMappings
protected Project<T>	proj
protected com.google.common.collect.HashMultimap<ImportModality,ARTResource>	refreshedOntologies this map tells whether a given ontology import has been refreshed or not this information can't be accessed: through supportOntologies/applicationOntologies/listofExplicitOWLImports: since these are declarations of the intention to import an ontology, but do not reflect its true import of data by checking availability of the ontology as a Named Graph in the ontology triples.
protected HashSet<String>	supportOntologiesNamespace Triples with predicate having a namespace contained in this set should be never shown to the user (whether he is in user or admin mode) typical examples of ontologies in this set are those needed by specific triple stores to handle reasoning note that these ontologies are declared to be support ontologies, but the developer must still check whether they are imported or not
protected HashSet<ARTURIResource>	supportOntologiesNG this set contains named graphs containing triples that should be never shown to the user (whether he is in user or admin mode) typical examples of ontologies in this set are those needed by specific triple stores to handle reasoning note that these ontologies are declared to be support ontologies, but the developer must still check whether they are imported or not
protected File	tripleStoreDir

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	STOntologyManager(Project<T> project, ModelFactory<? extends ModelConfiguration> fact)

Method Summary

Methods

Modifier and Type	Method and Description
void	addOntologyImportFromLocalFile(String baseURI, String fromLocalFilePath, String toLocalFile) as for addOntologyImportFromLocalFile(baseURI, fromLocalFilePath, toLocalFile, true)
void	addOntologyImportFromLocalFile(String baseURI, String fromLocalFilePath, String toLocalFile, ImportModality modality, boolean updateImportStatement)
void	addOntologyImportFromMirror(String baseURI, String mirFileString) as for addOntologyImportFromMirror(baseURI, mirFileString, true)
void	addOntologyImportFromMirror(String baseURI, String mirFileString, ImportModality modality, boolean updateImportStatement)
void	addOntologyImportFromWeb(String baseURI, String sourceURL, RDFFormat rdfFormat) as for #addOntologyImportFromWeb(String, String, {@link ImportModality.USER}, true )
void	addOntologyImportFromWeb(String baseURI, String sourceURL, RDFFormat rdfFormat, ImportModality modality, boolean updateImportStatement) imports an ontology from the Web
void	addOntologyImportFromWebToMirror(String baseURI, String sourceURL, String toLocalFile, RDFFormat rdfFormat) as for addOntologyImportFromWebToMirror(baseURI, sourceURL, toLocalFile, true)
void	addOntologyImportFromWebToMirror(String baseURI, String sourceURL, String toLocalFile, RDFFormat rdfFormat, ImportModality modality, boolean updateImportStatement) as for addOntologyImportFromWeb(String, String, RDFFormat, ImportModality, boolean) with the exception that the imported ontology is stored in the mirror
protected boolean	availableNG(ARTResource ont) tells if named graph ont is present in the current ontology
void	clearData()
Set<ARTURIResource>	computeImportsClosure(ARTURIResource ont) computes and returns the transitive closure of the owl:imports relationship over the managed ontology starting from import ont
protected void	computeImportsClosure(ARTURIResource ont, HashSet<ARTURIResource> importClosure) computes the transitive closure of the owl:imports relationship over the managed ontology starting from import ont, storing all computed imports in importClosure
Set<ARTURIResource>	computeImportsClosure(Set<ImportModality> mods) computes and returns the transitive closure of the owl:imports relationship over the managed ontology along all ontology imports declared under modalities mods
void	declareApplicationOntology(ARTURIResource ont, boolean ng, boolean ns) can be used by ST extensions to declare use of application ontologies for supporting their functionalities if ng is true, this prevents triples in the namedgraph of this ontology to be shown (when ST is in user mode) if ns is true, this prevents triples having a predicate with namespace matching the name of ontology ont to be shown (again, when ST is in user mode) One of the two boolean arguments must obviously be true, otherwise this declaration has no effect
protected abstract void	declareSupportOntologies() need to be implemented by specific Ontology Manager to declare support ontologies which need to be loaded by them.
protected void	declareSupportOntology(ARTURIResource ont, boolean ng, boolean ns) can be used by implementations of this class to declare use of support ontologies for supporting their functionalities if ng is true, this prevents triples in the namedgraph of this ontology to be shown if ns is true, this prevents triples having a predicate with namespace matching the name of ontology ont to be shown One of the two boolean arguments must obviously be true, otherwise this declaration has no effect
void	downloadImportedOntologyFromWeb(String baseURI, String altURL) downloads an ontology which is in the import list as a FAILED import from web (needs to specify an alternative URL, because the baseURI failed)
void	downloadImportedOntologyFromWebToMirror(String baseURI, String altURL, String toLocalFile) downloads an ontology which is in the import list as a FAILED import from web to the mirror (needs to specify an alternative URL, because the baseURI failed)
Collection<ARTURIResource>	getApplicationOntologies()
Collection<ARTURIResource>	getDeclaredImports(ImportModality mod) retrieves the list of imports for the given ImportModality note that these are imports declared (it is not assured that they have been imported successfully) for example, getImportSet(ImportModality.USER) retrieves the set of all ontology imports set by the user
abstract String	getId()
void	getImportedOntologyFromLocalFile(String baseURI, String fromLocalFilePath, String toLocalFile) downloads an ontology which is in the import list as a FAILED import, from a local file
ImportStatus	getImportStatus(String baseURI)
Map<String,String>	getNSPrefixMappings(boolean explicit)
T	getOntModel()
Collection<ARTURIResource>	getOntologyImports() gets the set of ontologies imported by the user
static Set<ImportModality>	getOtherModalities(ImportModality mod)
OWLModel	getOWLModel() this is really not general at the moment.
Collection<ARTURIResource>	getSupportOntologies()
static OntTempFile	getTempFileEntry() this method is used to get the path of a new temp file to be used for whatever reason (the file is stored in the default temp file directory of Semantic Turkey
void	guessMissingPrefix(String ns)
void	guessMissingPrefixes()
boolean	hasDeclaredImport(ARTURIResource ont, ImportModality mod) checks if ontology ont has been explicitly imported with modality mod in the managed ontology
void	initializeMappingsPersistence(NSPrefixMappings nsPrefixMappings)
boolean	isApplicationNG(ARTURIResource ontology)
boolean	isApplicationOntNamespace(String ns)
boolean	isImportedInAnotherModality(ARTURIResource ont, ImportModality mod)
protected boolean	isRefreshedOntology(ARTURIResource ont)
boolean	isSupportNG(ARTURIResource ontology)
boolean	isSupportOntNamespace(String ns)
void	loadOntologyData(File inputFile, String baseURI, RDFFormat format)
void	loadOntologyData(File inputFile, String baseURI, RDFFormat format, ARTResource graph) this method adds RDF data directly to the ontology being edited (i.e. it is not a read-only import of an external ontology that the working ontology depends on, but a mass add of RDF triples to the main graph of the working ontology)
void	mirrorOntology(String baseURI, String toLocalFile) mirrors an ontology which has already been successfully imported from the web
void	printImportsStatus()
void	removeDeclaredImport(ARTURIResource ont, ImportModality mod) removes an ontology import declaration from the given ImportModality mod.
void	removeImportDeclaration(ARTURIResource ont) as for removeDeclaredImport(ARTURIResource, ImportModality) with second argument = ImportModality.USER this method thus removes an import declared by the user
void	removeNSPrefixMapping(String namespace)
void	removeOntologyImport(String uriToBeRemoved) as for removeOntologyImport(String, ImportModality) with second argument = ImportModality.USER
void	removeOntologyImport(String uriToBeRemoved, ImportModality mod) removes an import from the managed ontology.
void	renameNG(ARTURIResource oldNG, ARTURIResource newNG) renames an existing NG to a new name (actually, moves all o the data from the old one to the new one, and deletes the triples in the old one)
void	setNSPrefixMapping(String prefix, String namespace)
T	startOntModel(String baseuri, File directoryFile, ModelConfiguration modelConfiguration)
Document	writeRDFonDOMDocument(OWLModel r)
void	writeRDFOnFile(File outPutFile, RDFFormat format) as writeRDFOnFile(File, RDFFormat, boolean) with last argument = false;
void	writeRDFOnFile(File outPutFile, RDFFormat format, boolean multigraph)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static org.slf4j.Logger logger

model

protected T extends RDFModel model

modelFactory

protected OWLArtModelFactory<? extends ModelConfiguration> modelFactory

nsPrefixMappings

protected NSPrefixMappings nsPrefixMappings

tripleStoreDir

protected File tripleStoreDir

proj

protected Project<T extends RDFModel> proj

refreshedOntologies

protected com.google.common.collect.HashMultimap<ImportModality,ARTResource> refreshedOntologies

this map tells whether a given ontology import has been refreshed or not
this information can't be accessed:

• through supportOntologies/applicationOntologies/listofExplicitOWLImports: since these are declarations of the intention to import an ontology, but do not reflect its true import of data
• by checking availability of the ontology as a Named Graph in the ontology triples. The reason is that when the ontology is being declared as a WEB resource, then it needs to be refreshed from the WEB, even if its content is already present as a NG, every time the project is loaded

for these reasons, this map is used to formally acknowledge the fact that the a ontology has been loaded/refreshed for the current working session

supportOntologiesNG

protected HashSet<ARTURIResource> supportOntologiesNG

this set contains named graphs containing triples that should be never shown to the user (whether he is in user or admin mode)
typical examples of ontologies in this set are those needed by specific triple stores to handle reasoning
note that these ontologies are declared to be support ontologies, but the developer must still check whether they are imported or not

supportOntologiesNamespace

protected HashSet<String> supportOntologiesNamespace

Triples with predicate having a namespace contained in this set should be never shown to the user (whether he is in user or admin mode)
typical examples of ontologies in this set are those needed by specific triple stores to handle reasoning
note that these ontologies are declared to be support ontologies, but the developer must still check whether they are imported or not

applicationOntologiesNG

protected HashSet<ARTURIResource> applicationOntologiesNG

This set contains named graphs adopted by the application or its extension to model their own behavior.
The triples associated to these NG should be hidden to the user unless in admin mode
The base application ontology for Semantic Turkey is annotation.owl
note that these ontologies are declared to be application ontologies, but the developer must still check whether they are imported or not

applicationOntologiesNamespace

protected HashSet<String> applicationOntologiesNamespace

This set contains namespaces of ontologies adopted by the application or its extension to model their own behavior.
Triples with predicate having a namespace contained in this set should be hidden to the user unless in admin mode.
The base application ontology for Semantic Turkey is annotation.owl
note that these ontologies are declared to be application ontologies, but the developer must still check whether they are imported or not

importsStatusMap

protected HashMap<ARTURIResource,ImportStatus> importsStatusMap

importStatusMap is a map pointing to structures (ImportStatus) telling the import status (LOCAL, WEB, NULL, FAILED) of a ontology which should be imported by the main graph, and the location of its file in case it is a LOCAL import Some notes: I was thinking about making this map a persistence object. However, I would rather use the following strategy, which considers the introduction of quad store repositories and a straight use of the mirror

• once loaded the model, STOntologyManager checks all imports
• this could be done in two ways:
  • through: owlModel.listOntologyImports(owlModel.createURIResource(owlModel.getBaseURI()))
  • or through: owlModel.listOntologyImports(NodeFilters.ANY);

• the second one gets all imports in a row, so it is faster, but the first one allows you to stop other imports should another import they depend on be no more able to work

  I would use the first one, but I should also make sure that, when an import is explicitly removed, then all imports depending exclusively on it are also removed. They *should*, since they are written in the imported ontology, which is on another named graph, and which is deleted when the import is removed. So I only need to check that the cascade of imported ontologies is removed (and only if these are not in turn imported by another part of the imported tree)

• then it checks if the related URI is present in the mirror and in the NAMED GRAPHS. Then you have the following 4 possibilities
  • MIRROR & NO_NG: it loads it from the mirror (strange situation, this should not happen: if you have an import, then also the data should have already been loaded)
  • MIRROR & NG: the ontology is actually loaded as expected, however the system checks if the timestamp of the mirror is more recent than that of the project (it is in a global property of the project) and in affirmative case it deletes the old named graph and then loads it again from the mirror file (otherwise it keeps the one already in the graph)
  • NO_MIRROR & NO_NG: load it from the web, if available put status=WEB, otherwise put status=FAILED
  • NO_MIRROR & NG: remove the NG, then behave as: NO_MIRROR & NO_NG (this is used for ontologies imported from the WEB and not mirrored, in this case the system behaves as the ontology is never present (though it is persisted in the NG). For this reason the associated NG is deleted and the ontology is loaded back from the WEB. Thus, keeping an imported ontology as WEB is good as it is always refreshed, but it also needs always a connection, and in case of projects with large amounts data, will slow down the project initialization due to the reloading of all the ontologies marked as WEB

Constructor Detail

STOntologyManager

protected STOntologyManager(Project<T> project,
                 ModelFactory<? extends ModelConfiguration> fact)

Method Detail

startOntModel

public T startOntModel(String baseuri,
              File directoryFile,
              ModelConfiguration modelConfiguration)
                                 throws ModelCreationException

Parameters:

baseuri - the baseuri of the repository

repositoryDirectory - the baseuri of

Returns:

Throws:

RepositoryCreationException

ModelCreationException

getId

public abstract String getId()

clearData

public void clearData()
               throws ModelCreationException,
                      ModelUpdateException

Throws:

ModelCreationException

ModelUpdateException

initializeMappingsPersistence

public void initializeMappingsPersistence(NSPrefixMappings nsPrefixMappings)
                                   throws ModelUpdateException,
                                          ModelAccessException

Throws:

ModelUpdateException

ModelAccessException

getDeclaredImports

public Collection<ARTURIResource> getDeclaredImports(ImportModality mod)
                                              throws ModelAccessException

retrieves the list of imports for the given ImportModality
note that these are imports declared (it is not assured that they have been imported successfully)

for example, getImportSet(ImportModality.USER) retrieves the set of all ontology imports set by the user

Parameters:

mod -

Returns:

Throws:

ModelAccessException

getOntologyImports

public Collection<ARTURIResource> getOntologyImports()
                                              throws ModelAccessException

gets the set of ontologies imported by the user

Returns:

Throws:

ModelAccessException

hasDeclaredImport

public boolean hasDeclaredImport(ARTURIResource ont,
                        ImportModality mod)
                          throws ModelAccessException

checks if ontology ont has been explicitly imported with modality mod in the managed ontology

Parameters:

ont -

mod -

Returns:

Throws:

ModelAccessException

isImportedInAnotherModality

public boolean isImportedInAnotherModality(ARTURIResource ont,
                                  ImportModality mod)
                                    throws ModelAccessException

Throws:

ModelAccessException

availableNG

protected boolean availableNG(ARTResource ont)
                       throws ModelAccessException

tells if named graph ont is present in the current ontology

Parameters:

ont -

Returns:

Throws:

ModelAccessException

isRefreshedOntology

protected boolean isRefreshedOntology(ARTURIResource ont)

getApplicationOntologies

public Collection<ARTURIResource> getApplicationOntologies()

getSupportOntologies

public Collection<ARTURIResource> getSupportOntologies()

isSupportNG

public boolean isSupportNG(ARTURIResource ontology)

isSupportOntNamespace

public boolean isSupportOntNamespace(String ns)

isApplicationNG

public boolean isApplicationNG(ARTURIResource ontology)

isApplicationOntNamespace

public boolean isApplicationOntNamespace(String ns)

declareApplicationOntology

public void declareApplicationOntology(ARTURIResource ont,
                              boolean ng,
                              boolean ns)

can be used by ST extensions to declare use of application ontologies for supporting their functionalities
if ng is true, this prevents triples in the namedgraph of this ontology to be shown (when ST is in user mode)
if ns is true, this prevents triples having a predicate with namespace matching the name of ontology ont to be shown (again, when ST is in user mode)
One of the two boolean arguments must obviously be true, otherwise this declaration has no effect

Parameters:

ont -

ng -

ns -

declareSupportOntology

protected void declareSupportOntology(ARTURIResource ont,
                          boolean ng,
                          boolean ns)

can be used by implementations of this class to declare use of support ontologies for supporting their functionalities
if ng is true, this prevents triples in the namedgraph of this ontology to be shown
if ns is true, this prevents triples having a predicate with namespace matching the name of ontology ont to be shown
One of the two boolean arguments must obviously be true, otherwise this declaration has no effect

Parameters:

ont -

ng -

ns -

declareSupportOntologies

protected abstract void declareSupportOntologies()

need to be implemented by specific Ontology Manager to declare support ontologies which need to be loaded by them. These are expected to be automatically loaded by the specific Ontology Manager implementation, so they just need to be declared with this method

addOntologyImportFromLocalFile

public void addOntologyImportFromLocalFile(String baseURI,
                                  String fromLocalFilePath,
                                  String toLocalFile)
                                    throws MalformedURLException,
                                           ModelUpdateException

as for addOntologyImportFromLocalFile(baseURI, fromLocalFilePath, toLocalFile, true)

Parameters:

baseURI -

fromLocalFilePath -

toLocalFile -

Throws:

MalformedURLException

ModelUpdateException

addOntologyImportFromLocalFile

public void addOntologyImportFromLocalFile(String baseURI,
                                  String fromLocalFilePath,
                                  String toLocalFile,
                                  ImportModality modality,
                                  boolean updateImportStatement)
                                    throws MalformedURLException,
                                           ModelUpdateException

Throws:

MalformedURLException

ModelUpdateException

addOntologyImportFromMirror

public void addOntologyImportFromMirror(String baseURI,
                               String mirFileString)
                                 throws MalformedURLException,
                                        ModelUpdateException

as for addOntologyImportFromMirror(baseURI, mirFileString, true)

Parameters:

baseURI -

mirFileString -

Throws:

MalformedURLException

ModelUpdateException

addOntologyImportFromMirror

public void addOntologyImportFromMirror(String baseURI,
                               String mirFileString,
                               ImportModality modality,
                               boolean updateImportStatement)
                                 throws ModelUpdateException

Throws:

ModelUpdateException

addOntologyImportFromWeb

public void addOntologyImportFromWeb(String baseURI,
                            String sourceURL,
                            RDFFormat rdfFormat)
                              throws MalformedURLException,
                                     ModelUpdateException

as for #addOntologyImportFromWeb(String, String, {@link ImportModality.USER}, true )

Parameters:

baseURI -

sourceURL -

Throws:

MalformedURLException

ModelUpdateException

addOntologyImportFromWeb

public void addOntologyImportFromWeb(String baseURI,
                            String sourceURL,
                            RDFFormat rdfFormat,
                            ImportModality modality,
                            boolean updateImportStatement)
                              throws ModelUpdateException

imports an ontology from the Web

Parameters:

baseURI - the baseuri of the ontology to be imported.

sourceURL - the alternative url, in case the baseuri is not the physical location for the ontology

rdfFormat - the serialization format of the rdf content to be parsed. null will result in the format being inferred from file extension or mime type, as for OWLART API

modality - one of ImportModality.USER or ImportModality.APPLICATION

updateImportStatement - this tells if the method is (likely to be) invoked (variable set to true) to explicitly import an ontology (such as when invoked following a import user request) or (variable set to false) when an ontology needs to be added for whatever reason (like reloading it from the web because it is already available as a WEB import)

Throws:

ModelUpdateException

addOntologyImportFromWebToMirror

public void addOntologyImportFromWebToMirror(String baseURI,
                                    String sourceURL,
                                    String toLocalFile,
                                    RDFFormat rdfFormat)
                                      throws MalformedURLException,
                                             ModelUpdateException

as for addOntologyImportFromWebToMirror(baseURI, sourceURL, toLocalFile, true)

Parameters:

baseURI -

sourceURL -

toLocalFile -

Throws:

MalformedURLException

ModelUpdateException

addOntologyImportFromWebToMirror

public void addOntologyImportFromWebToMirror(String baseURI,
                                    String sourceURL,
                                    String toLocalFile,
                                    RDFFormat rdfFormat,
                                    ImportModality modality,
                                    boolean updateImportStatement)
                                      throws MalformedURLException,
                                             ModelUpdateException

as for addOntologyImportFromWeb(String, String, RDFFormat, ImportModality, boolean) with the exception that the imported ontology is stored in the mirror

Throws:

MalformedURLException

ModelUpdateException

renameNG

public void renameNG(ARTURIResource oldNG,
            ARTURIResource newNG)
              throws ModelAccessException,
                     ModelUpdateException

renames an existing NG to a new name (actually, moves all o the data from the old one to the new one, and deletes the triples in the old one)

Parameters:

oldNG -

newNG -

Throws:

ModelAccessException

ModelUpdateException

removeDeclaredImport

public void removeDeclaredImport(ARTURIResource ont,
                        ImportModality mod)
                          throws ModelUpdateException

removes an ontology import declaration from the given ImportModality mod. Note that this removes only the import declaration, though it does not remove the RDF data (if any) associated to that named graph

Parameters:

ont -

mod -

Throws:

ModelUpdateException

removeImportDeclaration

public void removeImportDeclaration(ARTURIResource ont)
                             throws ModelUpdateException

as for removeDeclaredImport(ARTURIResource, ImportModality) with second argument = ImportModality.USER
this method thus removes an import declared by the user

Parameters:

ont -

mod -

Throws:

ModelUpdateException

removeOntologyImport

public void removeOntologyImport(String uriToBeRemoved)
                          throws IOException,
                                 ModelUpdateException,
                                 ModelAccessException

as for removeOntologyImport(String, ImportModality) with second argument = ImportModality.USER

Parameters:

uriToBeRemoved -

Throws:

IOException

ModelUpdateException

ModelAccessException

removeOntologyImport

public void removeOntologyImport(String uriToBeRemoved,
                        ImportModality mod)
                          throws IOException,
                                 ModelUpdateException,
                                 ModelAccessException

removes an import from the managed ontology.
This implies:

• removing uriToBeRemoved from the import declaration for USER ontologies or from the list of APPLICATION ontologies
• removing the RDF data associated to its named graph
• doing the above for any ontology which is imported by uriToBeRemoved and is not imported by other ontologies nor available as an APPLICATION ontology

Parameters:

uriToBeRemoved -

mod -

Throws:

IOException

ModelUpdateException

ModelAccessException

getOtherModalities

public static Set<ImportModality> getOtherModalities(ImportModality mod)

computeImportsClosure

public Set<ARTURIResource> computeImportsClosure(Set<ImportModality> mods)
                                          throws ModelAccessException,
                                                 ModelUpdateException

computes and returns the transitive closure of the owl:imports relationship over the managed ontology along all ontology imports declared under modalities mods

Parameters:

mods -

Returns:

Throws:

ModelAccessException

ModelUpdateException

computeImportsClosure

public Set<ARTURIResource> computeImportsClosure(ARTURIResource ont)
                                          throws ModelAccessException

computes and returns the transitive closure of the owl:imports relationship over the managed ontology starting from import ont

Parameters:

ont -

Returns:

Throws:

ModelAccessException

computeImportsClosure

protected void computeImportsClosure(ARTURIResource ont,
                         HashSet<ARTURIResource> importClosure)
                              throws ModelAccessException

computes the transitive closure of the owl:imports relationship over the managed ontology starting from import ont, storing all computed imports in importClosure

Parameters:

ont -

importClosure -

Throws:

ModelAccessException

downloadImportedOntologyFromWebToMirror

public void downloadImportedOntologyFromWebToMirror(String baseURI,
                                           String altURL,
                                           String toLocalFile)
                                             throws ModelUpdateException,
                                                    ImportManagementException

downloads an ontology which is in the import list as a FAILED import from web to the mirror (needs to specify an alternative URL, because the baseURI failed)

Parameters:

method -

baseURI -

fromLocalFilePath -

localFile -

Throws:

RepositoryUpdateException

ImportManagementException

ModelUpdateException

downloadImportedOntologyFromWeb

public void downloadImportedOntologyFromWeb(String baseURI,
                                   String altURL)
                                     throws MalformedURLException,
                                            ModelUpdateException,
                                            ImportManagementException

downloads an ontology which is in the import list as a FAILED import from web (needs to specify an alternative URL, because the baseURI failed)

Parameters:

altURL -

Throws:

MalformedURLException

RepositoryUpdateException

ImportManagementException

ModelUpdateException

getImportedOntologyFromLocalFile

public void getImportedOntologyFromLocalFile(String baseURI,
                                    String fromLocalFilePath,
                                    String toLocalFile)
                                      throws MalformedURLException,
                                             ModelUpdateException,
                                             ImportManagementException

downloads an ontology which is in the import list as a FAILED import, from a local file

Parameters:

altURL -

fromLocalFilePath -

toLocalFile -

Throws:

MalformedURLException

RepositoryUpdateException

ImportManagementException

ModelUpdateException

mirrorOntology

public void mirrorOntology(String baseURI,
                  String toLocalFile)
                    throws ImportManagementException,
                           ModelUpdateException

mirrors an ontology which has already been successfully imported from the web

Throws:

ImportManagementException

RepositoryUpdateException

ModelUpdateException

getImportStatus

public ImportStatus getImportStatus(String baseURI)

printImportsStatus

public void printImportsStatus()

loadOntologyData

public void loadOntologyData(File inputFile,
                    String baseURI,
                    RDFFormat format,
                    ARTResource graph)
                      throws FileNotFoundException,
                             IOException,
                             ModelAccessException,
                             ModelUpdateException,
                             UnsupportedRDFFormatException

this method adds RDF data directly to the ontology being edited (i.e. it is not a read-only import of an external ontology that the working ontology depends on, but a mass add of RDF triples to the main graph of the working ontology)

Parameters:

inputFile - the RDF file from which RDF data is being loaded

baseURI - the baseURI to be used when importing relative names from loaded RDF data

Throws:

FileNotFoundException

IOException

ModelAccessException

ModelUpdateException

UnsupportedRDFFormatException

loadOntologyData

public void loadOntologyData(File inputFile,
                    String baseURI,
                    RDFFormat format)
                      throws FileNotFoundException,
                             IOException,
                             ModelAccessException,
                             ModelUpdateException,
                             UnsupportedRDFFormatException

Throws:

FileNotFoundException

IOException

ModelAccessException

ModelUpdateException

UnsupportedRDFFormatException

writeRDFOnFile

public void writeRDFOnFile(File outPutFile,
                  RDFFormat format)
                    throws IOException,
                           ModelAccessException,
                           UnsupportedRDFFormatException

as writeRDFOnFile(File, RDFFormat, boolean) with last argument = false;

Parameters:

outPutFile -

format -

Throws:

UnsupportedRDFFormatException

ModelAccessException

IOException

Exception

writeRDFOnFile

public void writeRDFOnFile(File outPutFile,
                  RDFFormat format,
                  boolean multigraph)
                    throws IOException,
                           ModelAccessException,
                           UnsupportedRDFFormatException

Throws:

IOException

ModelAccessException

UnsupportedRDFFormatException

writeRDFonDOMDocument

public Document writeRDFonDOMDocument(OWLModel r)
                               throws Exception

Throws:

Exception

getNSPrefixMappings

public Map<String,String> getNSPrefixMappings(boolean explicit)
                                       throws ModelAccessException

Parameters:

explicit - specifies if the full mapping provided by the OWL Art API implementation or the sole mappings expressed by the user should be returned

Returns:

a copy of the internal mapping from prefixes to namespaces (as strings).

Throws:

ModelAccessException

setNSPrefixMapping

public void setNSPrefixMapping(String prefix,
                      String namespace)
                        throws NSPrefixMappingUpdateException,
                               ModelUpdateException

Throws:

NSPrefixMappingUpdateException

ModelUpdateException

removeNSPrefixMapping

public void removeNSPrefixMapping(String namespace)
                           throws NSPrefixMappingUpdateException,
                                  ModelUpdateException

Throws:

NSPrefixMappingUpdateException

ModelUpdateException

guessMissingPrefixes

public void guessMissingPrefixes()
                          throws ModelAccessException,
                                 ModelUpdateException

Throws:

ModelAccessException

ModelUpdateException

guessMissingPrefix

public void guessMissingPrefix(String ns)
                        throws ModelAccessException,
                               ModelUpdateException

Throws:

ModelAccessException

ModelUpdateException

getTempFileEntry

public static OntTempFile getTempFileEntry()

this method is used to get the path of a new temp file to be used for whatever reason (the file is stored in the default temp file directory of Semantic Turkey

Returns:

the path to the temp file

getOntModel

public T getOntModel()

getOWLModel

public OWLModel getOWLModel()

this is really not general at the moment. It assumes a project is either OWL or SKOS (which is what happens at the moment). in the future, this class will be subclassed with a class having OWL or SKOS models and this method will only be available there. So, in the case of OWL, the model itself will be returned, while in the case of SKOS, the OWLModel will be returned through SKOSModel.getOWLModel() method

Returns: