vub.starlab.ontoserver.database
Class DatabaseAPI

java.lang.Object
  |
  +--vub.starlab.ontoserver.database.DatabaseAPI

All Implemented Interfaces:

IDatabaseAPI, IDatabaseInsertionAPI, IDatabaseRetrievalAPI

public class DatabaseAPI

extends java.lang.Object

implements IDatabaseInsertionAPI, IDatabaseRetrievalAPI

Constructor Summary

DatabaseAPI()

DatabaseAPI(java.lang.String DriverName, java.lang.String URL)

Method Summary

int	addConcept(java.lang.String description, java.lang.String sourceName, java.lang.String key) Method adds a new concept to the ontology
void	addContextInOntology(java.lang.String ContextLabel, int ConceptId, java.lang.String OntoName) This method adds a new context in an existing ontology.
void	addContextInOntology(java.lang.String ContextLabel, java.lang.String ConceptDescription, java.lang.String SourceName, java.lang.String Key, java.lang.String OntoName)
void	addLexonInContext(java.lang.String TermLabel1, java.lang.String TermLabel2, java.lang.String Role, java.lang.String Context, java.lang.String OntoName) This method adds a (term - relation - term) triple in an existing context in an existing ontology.
void	addOntology(java.lang.String OntologyName, java.lang.String ContributorUserName, java.lang.String OwnerUserName, java.lang.String Status, java.lang.String Documentation) This method adds a new ontology.
void	addTermInContext(java.lang.String TermLabel, int ConceptId, java.lang.String Context, java.lang.String OntoName) This method adds a term in an existing context in an existing ontology.
void	addTermInContext(java.lang.String TermLabel, java.lang.String ConceptDescription, java.lang.String ConceptSourceName, java.lang.String Key, java.lang.String Context, java.lang.String OntoName)
void	addUserAccount(java.lang.String UserName, java.lang.String Name, java.lang.String Email, java.lang.String PassWord, boolean Administrator, java.lang.String Affiliation) This method adds a new user
void	addVersion(java.lang.String OntoName, java.lang.String CreatedDate, java.lang.String Documentation, java.lang.String CreatorUserName, java.lang.String VersionLabel) This method adds a new version.
void	closeConnection() This method is called when all database operations are finished, and a connection to the database is not longer required.
void	establishConnection()
void	establishConnection(java.lang.String DriverName, java.lang.String URL) This method should be called before calling any other method of this interface.
IContext	getContextDetail(java.lang.String ontologyName, java.lang.String contextIdentifyingTerm) This method returns the details associated with a context.
OntologyObjectCollection	getContexts(java.lang.String ontologyName) This method retrieves all contexts for a stored ontology present the ontology server.
OntologyObjectCollection	getLexons(java.lang.String ontologyName, java.lang.String contextIdentifyingTerm) This method retrieves all lexons for a context within a stored ontology As parameters, the ontology name and the context name for which you want to retrieve the lexons are required.
OntologyObjectCollection	getOntologies() This method retrieves all ontologies currently stored in the ontology server.
IOntology	getOntologyDetail(java.lang.String ontoName) This method returns the details associated with an ontology.
ITerm	getTermDetail(java.lang.String ontologyName, java.lang.String contextIdentifyingTerm, java.lang.String term) This method returns the details associated with a term.
OntologyObjectCollection	getTerms(java.lang.String ontologyName, java.lang.String contextIdentifyingTerm) This method retrieves all terms for a context withing a stored ontology present the ontology server.
IUser	getUserDetail(java.lang.String userName) This method returns the details associated with a user.
OntologyObjectCollection	getUsers() This method retrieves all users currently registered in the ontology server.

Methods inherited from class java.lang.Object

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

Constructor Detail

DatabaseAPI

public DatabaseAPI()

DatabaseAPI

public DatabaseAPI(java.lang.String DriverName,
                   java.lang.String URL)

Method Detail

establishConnection

public void establishConnection(java.lang.String DriverName,
                                java.lang.String URL)

Description copied from interface: IDatabaseAPI

This method should be called before calling any other method of this interface. It opens de connection to the database. Method expects as parameters the driver that should be used to establish the connection, and an URL, which is a java conventional string consisting of jdbc:<subprotocol >:<subname>, mostly this URL is suplied by the driver vendor. As an example, the URL could be "jdbc:odbc:name_of_datasource".

Specified by:

establishConnection in interface IDatabaseAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseAPI

Parameters:

DriverName - the name of the driver, for example, when using the jdbc-odbc bridge, this DriverName would be "sun.jdbc.odbc.JdbcOdbcDriver"

URL - a java conventional string consisting of jdbc:<subprotocol >:<subname>, mostly this URL is suplied by the driver, for example, when using the jdbc-odbc bridge, this URL would be "jdbc:odbc:name_of_datasource"

See Also:

IDatabaseAPI.closeConnection()

closeConnection

public void closeConnection()

Description copied from interface: IDatabaseAPI

This method is called when all database operations are finished, and a connection to the database is not longer required. Java.sql.* junk is cleaned up before exiting.

Specified by:

closeConnection in interface IDatabaseAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseAPI

See Also:

IDatabaseAPI.establishConnection(String, String)

addUserAccount

public void addUserAccount(java.lang.String UserName,
                           java.lang.String Name,
                           java.lang.String Email,
                           java.lang.String PassWord,
                           boolean Administrator,
                           java.lang.String Affiliation)
                    throws UserAccountAlreadyExistsException

Description copied from interface: IDatabaseInsertionAPI

This method adds a new user

Specified by:

addUserAccount in interface IDatabaseInsertionAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseInsertionAPI

Parameters:

UserName - the username for the new user

Name - the name for the new user

Email - the email adres for the new user

PassWord - the password for the new user

Administrator - denoting if the user does or does not have administrator access

Affiliation - the affiliation for the new user

Throws:

UserAccountAlreadyExistsException - exception is thrown when the user already exists

addContextInOntology

public void addContextInOntology(java.lang.String ContextLabel,
                                 java.lang.String ConceptDescription,
                                 java.lang.String SourceName,
                                 java.lang.String Key,
                                 java.lang.String OntoName)
                          throws ContextAlreadyExistsException

addContextInOntology

public void addContextInOntology(java.lang.String ContextLabel,
                                 int ConceptId,
                                 java.lang.String OntoName)
                          throws ContextAlreadyExistsException

Description copied from interface: IDatabaseInsertionAPI

This method adds a new context in an existing ontology. (the context is also added in the meta-context for this ontology)

Specified by:

addContextInOntology in interface IDatabaseInsertionAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseInsertionAPI

Parameters:

ContextLabel - the name for the new context

ConceptId - the id of the concept which is associated with the term specifying the ontology

OntoName - the name for the ontology

Throws:

ContextAlreadyExistsException - exception is thrown when the context was already present in the ontology

addConcept

public int addConcept(java.lang.String description,
                      java.lang.String sourceName,
                      java.lang.String key)

Description copied from interface: IDatabaseInsertionAPI

Method adds a new concept to the ontology

Specified by:

addConcept in interface IDatabaseInsertionAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseInsertionAPI

Parameters:

description - the description for the concept

sourceName - the name of the source where the concept originates from

key - an identification of the key which was used for the description, which should give a hint on how the description parameter should be interpreted

Returns:

int the Id for the concept which you just added

See Also:

addTermInContext

public void addTermInContext(java.lang.String TermLabel,
                             int ConceptId,
                             java.lang.String Context,
                             java.lang.String OntoName)
                      throws ContextNotFoundException

Description copied from interface: IDatabaseInsertionAPI

This method adds a term in an existing context in an existing ontology. If the Context is not found within that ontology, an exception is thrown.

Specified by:

addTermInContext in interface IDatabaseInsertionAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseInsertionAPI

Parameters:

TermLabel - the name of the term you want to add

ConceptId - the id of the concept which is associated with the term you want to add

Context - the name for the context in which you want to add the term

OntoName - the name for the ontology

Returns:

Throws:

-

See Also:

addTermInContext

public void addTermInContext(java.lang.String TermLabel,
                             java.lang.String ConceptDescription,
                             java.lang.String ConceptSourceName,
                             java.lang.String Key,
                             java.lang.String Context,
                             java.lang.String OntoName)
                      throws ContextNotFoundException

addLexonInContext

public void addLexonInContext(java.lang.String TermLabel1,
                              java.lang.String TermLabel2,
                              java.lang.String Role,
                              java.lang.String Context,
                              java.lang.String OntoName)
                       throws ContextNotFoundException

Description copied from interface: IDatabaseInsertionAPI

This method adds a (term - relation - term) triple in an existing context in an existing ontology. If the context is not found within that ontology, an exception is thrown. Note that the error mechanisme is not yet fully implemented, a OntologyNotFoundException should also be thrown here one day

Specified by:

addLexonInContext in interface IDatabaseInsertionAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseInsertionAPI

Parameters:

TermLabel1 - the label of the first term in the lexon triple

TermLabel2 - the label of the second term in the lexon triple

Role - the rolename for the lexon triple

Context - the name of the context in which you want to add the triple

OntoName - the name of the ontology

Throws:

ContextNotFoundException - exception thrown when the context in which you want to insert is not found

addOntology

public void addOntology(java.lang.String OntologyName,
                        java.lang.String ContributorUserName,
                        java.lang.String OwnerUserName,
                        java.lang.String Status,
                        java.lang.String Documentation)
                 throws OntologyAlreadyExistsException

Description copied from interface: IDatabaseInsertionAPI

This method adds a new ontology. Note that the addOntology method also adds a meta-context for this ontology (a context with contextlabel "Context")

Specified by:

addOntology in interface IDatabaseInsertionAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseInsertionAPI

Parameters:

OntologyName - the name for the new ontology

ContributorUserName - the username of the person who contributed the ontology

OwnerUserName - the username of the owner of this ontology

Status - the status of the new ontology

Documentation - some documentation for the new ontology

Throws:

OntologyAlreadyExistsException - exception thrown when the ontology already exists

addVersion

public void addVersion(java.lang.String OntoName,
                       java.lang.String CreatedDate,
                       java.lang.String Documentation,
                       java.lang.String CreatorUserName,
                       java.lang.String VersionLabel)
                throws VersionAlreadyExistsException

Description copied from interface: IDatabaseInsertionAPI

This method adds a new version. There is no version management yet, this method just assigns a new version every time it is called.

Specified by:

addVersion in interface IDatabaseInsertionAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseInsertionAPI

Parameters:

OntoName - the name of the ontology for which you want to add a version

CreatedDate - the date from this version

Documentation - documentation which may be supplied

CreatorUserName - the username of the user creating this new version

VersionLabel - the label for the version

Throws:

VersionAlreadyExistsException - cannot occur yet, as there is no version management in the current version

establishConnection

public void establishConnection()

getOntologies

public OntologyObjectCollection getOntologies()

Description copied from interface: IDatabaseRetrievalAPI

This method retrieves all ontologies currently stored in the ontology server. The method returns an OntologyObjectCollection, which in its turn contains objects implementing the IOntology interface: objects retrieved from the OntologyObjectCollection must be casted to the IOntology type

Specified by:

getOntologies in interface IDatabaseRetrievalAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseRetrievalAPI

Returns:

OntologyObjectCollection a collection designed to contain object implementing the IOntologyObject interface

See Also:

OntologyObjectCollection, OntologyObjectIterator, OntologyCollectionIterator, IOntology

getOntologyDetail

public IOntology getOntologyDetail(java.lang.String ontoName)
                            throws OntologyNotFoundException

Description copied from interface: IDatabaseRetrievalAPI

This method returns the details associated with an ontology. The return object implements the IOntology interface, and contains the ontology details. This method expects as parameters an ontology name, the ontology for which you want the details. If the ontology is not found, an OntologyNotFoundException is returned.

Specified by:

getOntologyDetail in interface IDatabaseRetrievalAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseRetrievalAPI

Parameters:

ontoName - the name of the ontology for which you want the details

Returns:

IOntology an object implementing the IOntology interface

Throws:

OntologyNotFoundException - exception thrown when the ontology is not found

See Also:

IOntology, OntologyNotFoundException

getUsers

public OntologyObjectCollection getUsers()

Description copied from interface: IDatabaseRetrievalAPI

This method retrieves all users currently registered in the ontology server. The method returns an OntologyObjectCollection, which in its turn contains objects implementing the IUser interface: objects retrieved from the OntologyObjectCollection must be casted to the IUser type

Specified by:

getUsers in interface IDatabaseRetrievalAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseRetrievalAPI

Returns:

OntologyObjectCollection a collection designed to contain object implementing the IOntologyObject interface

See Also:

OntologyObjectCollection, OntologyObjectIterator, UserCollectionIterator, IUser

getUserDetail

public IUser getUserDetail(java.lang.String userName)
                    throws UserNotFoundException

Description copied from interface: IDatabaseRetrievalAPI

This method returns the details associated with a user. The return object implements the IUser interface, and contains the user details. This method expects as a parameter a username, the username for the person you want the details from. If the user is not found, an UserNotFoundException is returned.

Specified by:

getUserDetail in interface IDatabaseRetrievalAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseRetrievalAPI

Parameters:

userName - the username for which you want the details

Returns:

IUser an object implementing the IUser interface

Throws:

UserNotFoundException - exception thrown when the user is not found

See Also:

IUser, UserNotFoundException

getContexts

public OntologyObjectCollection getContexts(java.lang.String ontologyName)

Description copied from interface: IDatabaseRetrievalAPI

This method retrieves all contexts for a stored ontology present the ontology server. As parameters, the ontology name for which you want retrieve its contexts is required. The method returns an OntologyObjectCollection, which in its turn contains objects implementing the IContext interface: objects retrieved from the OntologyObjectCollection must be casted to the IContext type

Specified by:

getContexts in interface IDatabaseRetrievalAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseRetrievalAPI

Parameters:

ontologyName - the name of the ontology for which you want the contexts

Returns:

OntologyObjectCollection a collection designed to contain object implementing the IOntologyObject interface

See Also:

OntologyObjectCollection, OntologyObjectIterator, ContextCollectionIterator, IContext

getContextDetail

public IContext getContextDetail(java.lang.String ontologyName,
                                 java.lang.String contextIdentifyingTerm)
                          throws ContextNotFoundException

Description copied from interface: IDatabaseRetrievalAPI

This method returns the details associated with a context. The return object implements the IContext interface, and contains the context details. This method expects as parameters an ontology name and the context name for which you want the details. If the context is not found, an ContextNotFoundException is returned.

Specified by:

getContextDetail in interface IDatabaseRetrievalAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseRetrievalAPI

Parameters:

userName - the username for which you want the details

Returns:

IContext an object implementing the IContext interface

Throws:

ContextNotFoundException - exception thrown when the context is not found

See Also:

IContext, ContextNotFoundException

getLexons

public OntologyObjectCollection getLexons(java.lang.String ontologyName,
                                          java.lang.String contextIdentifyingTerm)
                                   throws ContextNotFoundException

Description copied from interface: IDatabaseRetrievalAPI

This method retrieves all lexons for a context within a stored ontology As parameters, the ontology name and the context name for which you want to retrieve the lexons are required. The method returns an OntologyObjectCollection, which in its turn contains objects implementing the ILexon interface: objects retrieved from the OntologyObjectCollection must be casted to the ILexon type

Specified by:

getLexons in interface IDatabaseRetrievalAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseRetrievalAPI

Parameters:

ontologyName - the name of the ontology

contextIdentifyingTerm - the name of the context

Returns:

OntologyObjectCollection a collection designed to contain object implementing the IOntologyObject interface

See Also:

OntologyObjectCollection, OntologyObjectIterator, LexonCollectionIterator, ILexon

getTerms

public OntologyObjectCollection getTerms(java.lang.String ontologyName,
                                         java.lang.String contextIdentifyingTerm)
                                  throws ContextNotFoundException

Description copied from interface: IDatabaseRetrievalAPI

This method retrieves all terms for a context withing a stored ontology present the ontology server. As parameters, the ontology name and a context are required for which you want to retrieve the terms are required. The method returns an OntologyObjectCollection, which in its turn contains objects implementing the IContext interface: objects retrieved from the OntologyObjectCollection must be casted to the ITerm type

Specified by:

getTerms in interface IDatabaseRetrievalAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseRetrievalAPI

Parameters:

ontologyName - the name of the ontology for which you want the contexts

contextIdentifyingTerm - the name of the term specifying the context

Returns:

OntologyObjectCollection a collection designed to contain object implementing the IOntologyObject interface

See Also:

OntologyObjectCollection, OntologyObjectIterator, TermCollectionIterator, ITerm

getTermDetail

public ITerm getTermDetail(java.lang.String ontologyName,
                           java.lang.String contextIdentifyingTerm,
                           java.lang.String term)
                    throws ContextNotFoundException,
                           TermNotFoundException

Description copied from interface: IDatabaseRetrievalAPI

This method returns the details associated with a term. The return object implements the ITerm interface, and contains the term details. This method expects as parameters an ontology name, a term identifying the context within this ontology, and the term for which you want to retrieve the details. If the context is not found within this ontology, a ContextNotFoundException is returned. NOTE: error throwing is not yet fully implemented here

Specified by:

getTermDetail in interface IDatabaseRetrievalAPI

Following copied from interface: vub.starlab.ontoserver.database.IDatabaseRetrievalAPI

Parameters:

ontologyName - the name of the ontology for which you want the contexts

contextIdentifyingTerm - the name of the term specifying the context

term - the term for which you want to retrieve the details

Returns:

IContext an object implementing the IContext interface

Throws:

ContextNotFoundException - exception thrown when the context is not found

ContextNotFoundException - exception thrown when the term is not found

See Also:

ITerm, ContextNotFoundException, TermNotFoundException