org.wandora.application.tools.importers

Class OBOImport

java.lang.Object

org.wandora.application.tools.AbstractWandoraTool

org.wandora.application.tools.importers.AbstractImportTool

org.wandora.application.tools.importers.OBOImport

All Implemented Interfaces:

java.io.Serializable, java.lang.Runnable, WandoraTool, WandoraToolLogger, TopicMapLogger

public class OBOImport
extends AbstractImportTool
implements WandoraTool

OBOImport imports OBO flat file ontology, converts it to a topic map and merges the result to current topic map.

Author:

akivela

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	OBOImport.Category
protected class	OBOImport.Dbxref
protected class	OBOImport.Dbxrefs
protected class	OBOImport.Definition
protected class	OBOImport.Header
class	OBOImport.OBOParser OBOParser class implements parser for OBO flat file format.
protected class	OBOImport.PropertyValue
protected class	OBOImport.RelatedTerm
protected class	OBOImport.Stanza
protected class	OBOImport.Synonym
protected class	OBOImport.TagValuePair

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.ArrayList<java.lang.String>	namespaces

Fields inherited from class org.wandora.application.tools.importers.AbstractImportTool

ASK_SOURCE, askSource, CLOSE_LOGS, closeLogs, CUSTOM_IMPORTER, directMerge, FILE_DIALOG_TITLE_TEXT, FILE_IMPORTER, forceFiles, newLayer, RAW_IMPORTER, resetWandoraFirst, TOPICMAP_DIRECT_MERGE, TOPICMAP_MAKE_NEW_LAYER, TOPICMAP_RESET_FIRST, URL_DIALOG_MESSAGE_TEXT, URL_IMPORTER, WEB_IMPORT, webImport

Fields inherited from interface org.wandora.application.WandoraToolLogger

CLOSE, EXECUTE, INVISIBLE, VISIBLE, WAIT

Constructor Summary

Constructors

Constructor and Description
OBOImport() Creates a new instance of OBOImport
OBOImport(int options)

Method Summary

Modifier and Type	Method and Description
protected void	addNamespace(java.lang.String newNamespace)
void	configure(Wandora admin, Options options, java.lang.String prefix) If the tool is configurable, shows an user interface to configure the tool.
java.lang.String	getDescription() AdminToolManager views tool descriptions while user browses available tools and build user customizable GUI elements such as Tools menu.
javax.swing.Icon	getIcon() All tools may have identifying graphic icon used within tool GUI elements.
java.lang.String	getName() Tools name represent the tool in UI unless the tool has been given explicitly another GUI name.
java.util.ArrayList<java.lang.String>	getNamespaces()
void	importOBO(java.io.InputStream in, TopicMap map)
void	importStream(Wandora wandora, java.lang.String streamName, java.io.InputStream inputStream)
void	initialize(Wandora admin, Options options, java.lang.String prefix) Initializes a tool with options saved in the options.
boolean	isConfigurable() Whether this tool is configurable.
void	writeOptions(Wandora admin, Options options, java.lang.String prefix) If the tool is configurable, saves all current tool options.

Methods inherited from class org.wandora.application.tools.importers.AbstractImportTool

createNewLayer, execute, finalizeImport, getGUIText, getLayerNameFor, getOptions, getType, importFile, importFiles, importUrl, initializeImport, requestImports, setOptions

Methods inherited from class org.wandora.application.tools.AbstractWandoraTool

addUndoMarker, addUndoMarker, allowMultipleInvocations, clearAllThreads, clearThreads, clearThreads, clearToolLock, clearToolLock, clearToolLocks, execute, execute, forceStop, forceStop, getContext, getCurrentLogger, getDefaultLogger, getHistory, getLastLogger, getState, getThreads, getThreads, getToolMenuItem, getToolMenuItem, getTopicName, hlog, interruptAllThreads, interruptThreads, interruptThreads, isRunning, isRunning, lockLog, log, log, log, log, requiresRefresh, run, runInOwnThread, setContext, setDefaultLogger, setLogTitle, setProgress, setProgressMax, setState, setToolLogger, singleLog, singleLog, singleLog, solveContextTopicMap, solveNameForTopicMap

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.wandora.application.WandoraTool

execute, execute, execute, getContext, getToolMenuItem, getType, hlog, isRunning, log, log, log, log, requiresRefresh, setContext, setToolLogger

Methods inherited from interface org.wandora.application.WandoraToolLogger

forceStop, getHistory, getState, lockLog, setLogTitle, setProgress, setProgressMax, setState

Field Detail

namespaces

protected java.util.ArrayList<java.lang.String> namespaces

Constructor Detail

OBOImport

public OBOImport()

Creates a new instance of OBOImport

OBOImport

public OBOImport(int options)

Method Detail

initialize

public void initialize(Wandora admin,
                       Options options,
                       java.lang.String prefix)
                throws TopicMapException

Description copied from class: AbstractWandoraTool

Initializes a tool with options saved in the options. Options for this tool start with the given prefix. What options the tool saves is entirely tool specific.

Specified by:

initialize in interface WandoraTool

Overrides:

initialize in class AbstractWandoraTool

Throws:

TopicMapException

isConfigurable

public boolean isConfigurable()

Description copied from class: AbstractWandoraTool

Whether this tool is configurable. Configurable tools will provide an interface to configure themselves. To make a configurable tool you will need to:

• Implement isConfigurable method and return true there.
• Implement initialize method to initialize the tool with saved options.
• Implement configure method to provide the user interface for configuration and then save the new options.
• Implement writeOptions method to save the current options.

Specified by:

isConfigurable in interface WandoraTool

Overrides:

isConfigurable in class AbstractWandoraTool

Returns:

true if the tool is configurable.

configure

public void configure(Wandora admin,
                      Options options,
                      java.lang.String prefix)
               throws TopicMapException

Description copied from class: AbstractWandoraTool

If the tool is configurable, shows an user interface to configure the tool. The user may edit tool options which this method also need to save. Options specific to this tool should be saved with keys starting with the given prefix.

Specified by:

configure in interface WandoraTool

Overrides:

configure in class AbstractWandoraTool

Throws:

TopicMapException

writeOptions

public void writeOptions(Wandora admin,
                         Options options,
                         java.lang.String prefix)

Description copied from class: AbstractWandoraTool

If the tool is configurable, saves all current tool options. Options specific to this tool should be saved with keys starting with the given prefix.

Specified by:

writeOptions in interface WandoraTool

Overrides:

writeOptions in class AbstractWandoraTool

getName

public java.lang.String getName()

Description copied from class: AbstractWandoraTool

Tools name represent the tool in UI unless the tool has been given explicitly another GUI name. All tools should override this method and return a valid string representing name of the tool.

Specified by:

getName in interface WandoraTool

Overrides:

getName in class AbstractWandoraTool

Returns:

String representing tool's name.

getDescription

public java.lang.String getDescription()

Description copied from class: AbstractWandoraTool

AdminToolManager views tool descriptions while user browses available tools and build user customizable GUI elements such as Tools menu. By default description equals the tool name. All tools should override this method.

Specified by:

getDescription in interface WandoraTool

Overrides:

getDescription in class AbstractWandoraTool

Returns:

String representing tool's description.

getIcon

public javax.swing.Icon getIcon()

Description copied from class: AbstractWandoraTool

All tools may have identifying graphic icon used within tool GUI elements. getIcon should return Icon object of the tool.

Specified by:

getIcon in interface WandoraTool

Overrides:

getIcon in class AbstractImportTool

Returns:

icon for the tool.

getNamespaces

public java.util.ArrayList<java.lang.String> getNamespaces()

addNamespace

protected void addNamespace(java.lang.String newNamespace)

importStream

public void importStream(Wandora wandora,
                         java.lang.String streamName,
                         java.io.InputStream inputStream)

Specified by:

importStream in class AbstractImportTool

importOBO

public void importOBO(java.io.InputStream in,
                      TopicMap map)