org.ecoinformatics.seek.ecogrid

Class EcogridWriter

java.lang.Object

ptolemy.kernel.util.NamedObj

ptolemy.kernel.InstantiableNamedObj

ptolemy.kernel.Entity<T>

ptolemy.kernel.ComponentEntity<T>

ptolemy.actor.AtomicActor<TypedIOPort>

ptolemy.actor.TypedAtomicActor

org.ecoinformatics.seek.ecogrid.EcogridWriter

All Implemented Interfaces:

java.lang.Cloneable, Actor, Executable, FiringsRecordable, Initializable, TypedActor, Changeable, Debuggable, DebugListener, Derivable, Instantiable, ModelErrorHandler, MoMLExportable, Moveable, Nameable

public class EcogridWriter
extends TypedAtomicActor

The EcogridWriter actor writes a data file and the EML metadata describing that data file to a remote EcoGrid repositiory. Identifiers for the data and metadata are created and these IDs are sent to the output ports. These IDs might be used for future access to the data and metadata files. Note also that the ID of the data file is inserted into the metadata file as a reference (i.e., a pointer from the metadata to the data). The EcoGrid is a distributed network providing scientists access to ecological, biodiversity, and environmental data and analytic resources. The EcoGrid can be used to store ecological data, or to model or analyze it via remote EcoGrid services. Ecological Metadata Language (EML) is a standard set of terms and definitions used to describe ecological data. For example, EML metadata might contain infomation about a data set's units of measurement, date of collection, location, etc.

Author:

tao

Nested Class Summary

Nested classes/interfaces inherited from class ptolemy.kernel.Entity

Entity.ContainedObjectsIterator

Field Summary

Fields

Modifier and Type	Field and Description
StringParameter	authenURLParam Ecogrid service URL for authenticating user
TypedIOPort	dataDocidPort Broadcasts the data docid, which is generated by the actor for future reference.
protected static boolean	isDebugging
protected static org.apache.commons.logging.Log	log
StringParameter	metadataDesParam Ecogrid service URL for receiving metadata and data
TypedIOPort	metadataDocidPort An output port that broadcasts the metadata doc ID, which is generated by the actor for future reference.
TypedIOPort	metadataPort Accepts a string of metadata describing the data file.
StringParameter	passwordParam Password for this user
TypedIOPort	sourceDataPort Can be used in lieu of supplying a file name to dataFileNamePort.
TypedIOPort	sourceFileNamePort Accepts the file name and path of the local data file to upload to the EcoGrid service.
StringParameter	usernameParam User name for authenticatication.

Fields inherited from class ptolemy.actor.TypedAtomicActor

_typesValid

Fields inherited from class ptolemy.actor.AtomicActor

_actorFiringListeners, _initializables, _notifyingActorFiring, _stopRequested

Fields inherited from class ptolemy.kernel.util.NamedObj

_changeListeners, _changeLock, _changeRequests, _debugging, _debugListeners, _deferChangeRequests, _elementName, _isPersistent, _verbose, _workspace, ATTRIBUTES, CLASSNAME, COMPLETE, CONTENTS, DEEP, FULLNAME, LINKS

Fields inherited from interface ptolemy.actor.Executable

COMPLETED, NOT_READY, STOP_ITERATING

Constructor Summary

Constructors

Constructor and Description
EcogridWriter(CompositeEntity container, java.lang.String name)

Method Summary

Modifier and Type	Method and Description
void	attributeChanged(Attribute attribute) Determine the attribute changed value
void	fire() Output the data lines into an array.
boolean	prefire() Return true.

Methods inherited from class ptolemy.actor.TypedAtomicActor

_containedTypeConstraints, _customTypeConstraints, _defaultTypeConstraints, _fireAt, _fireAt, attributeTypeChanged, clone, clone, isBackwardTypeInferenceEnabled, newPort, typeConstraintList, typeConstraints

Methods inherited from class ptolemy.actor.AtomicActor

_actorFiring, _actorFiring, _declareDelayDependency, addActorFiringListener, addInitializable, connectionsChanged, createReceivers, declareDelayDependency, getCausalityInterface, getDirector, getExecutiveDirector, getManager, initialize, inputPortList, isFireFunctional, isStrict, iterate, newReceiver, outputPortList, postfire, preinitialize, pruneDependencies, recordFiring, removeActorFiringListener, removeDependency, removeInitializable, setContainer, stop, stopFire, terminate, wrapup

Methods inherited from class ptolemy.kernel.ComponentEntity

_adjustDeferrals, _checkContainer, _getContainedObject, _propagateExistence, getContainer, instantiate, isAtomic, isOpaque, moveDown, moveToFirst, moveToIndex, moveToLast, moveUp, propagateExistence, setName

Methods inherited from class ptolemy.kernel.Entity

_addPort, _description, _exportMoMLContents, _removePort, _validateSettables, connectedPortList, connectedPorts, containedObjectsIterator, getAttribute, getPort, getPorts, linkedRelationList, linkedRelations, portList, removeAllPorts, setClassDefinition, uniqueName

Methods inherited from class ptolemy.kernel.InstantiableNamedObj

_setParent, exportMoML, getChildren, getElementName, getParent, getPrototypeList, isClassDefinition, isWithinClassDefinition

Methods inherited from class ptolemy.kernel.util.NamedObj

_addAttribute, _adjustOverride, _attachText, _cloneFixAttributeFields, _containedDecorators, _copyChangeRequestList, _debug, _debug, _debug, _debug, _debug, _executeChangeRequests, _getIndentPrefix, _isMoMLSuppressed, _markContentsDerived, _notifyHierarchyListenersAfterChange, _notifyHierarchyListenersBeforeChange, _propagateValue, _removeAttribute, _splitName, _stripNumericSuffix, addChangeListener, addDebugListener, addHierarchyListener, attributeDeleted, attributeList, attributeList, decorators, deepContains, depthInHierarchy, description, description, event, executeChangeRequests, exportMoML, exportMoML, exportMoML, exportMoML, exportMoMLPlain, getAttribute, getAttributes, getChangeListeners, getClassName, getDecoratorAttribute, getDecoratorAttributes, getDerivedLevel, getDerivedList, getDisplayName, getFullName, getModelErrorHandler, getName, getName, getSource, handleModelError, isDeferringChangeRequests, isOverridden, isPersistent, lazyContainedObjectsIterator, message, notifyOfNameChange, propagateValue, propagateValues, removeAttribute, removeChangeListener, removeDebugListener, removeHierarchyListener, requestChange, setClassName, setDeferringChangeRequests, setDerivedLevel, setDisplayName, setModelErrorHandler, setPersistent, setSource, sortContainedObjects, toplevel, toString, validateSettables, workspace

Methods inherited from class java.lang.Object

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

Methods inherited from interface ptolemy.actor.Actor

createReceivers, getCausalityInterface, getDirector, getExecutiveDirector, getManager, inputPortList, newReceiver, outputPortList

Methods inherited from interface ptolemy.actor.Executable

isFireFunctional, isStrict, iterate, postfire, stop, stopFire, terminate

Methods inherited from interface ptolemy.actor.Initializable

addInitializable, initialize, preinitialize, removeInitializable, wrapup

Methods inherited from interface ptolemy.kernel.util.Nameable

description, getContainer, getDisplayName, getFullName, getName, getName, setName

Methods inherited from interface ptolemy.kernel.util.Derivable

getDerivedLevel, getDerivedList, propagateValue

Field Detail

sourceFileNamePort

public TypedIOPort sourceFileNamePort

Accepts the file name and path of the local data file to upload to the EcoGrid service. WARNING: This port is ignored if you supply data to dataPort.

sourceDataPort

public TypedIOPort sourceDataPort

Can be used in lieu of supplying a file name to dataFileNamePort. The byte[] of the input object will be uploaded.

metadataPort

public TypedIOPort metadataPort

Accepts a string of metadata describing the data file. This string will be uploaded to Ecogrid service as metadata

metadataDocidPort

public TypedIOPort metadataDocidPort

An output port that broadcasts the metadata doc ID, which is generated by the actor for future reference.

dataDocidPort

public TypedIOPort dataDocidPort

Broadcasts the data docid, which is generated by the actor for future reference.

log

protected static final org.apache.commons.logging.Log log

isDebugging

protected static final boolean isDebugging

metadataDesParam

public StringParameter metadataDesParam

Ecogrid service URL for receiving metadata and data

authenURLParam

public StringParameter authenURLParam

Ecogrid service URL for authenticating user

usernameParam

public StringParameter usernameParam

User name for authenticatication. For example, it is a DN for knb ldap server. uid=smith,o=NCEAS,dc=eocinformatics,dc=org

passwordParam

public StringParameter passwordParam

Password for this user

Constructor Detail

EcogridWriter

public EcogridWriter(CompositeEntity container,
                     java.lang.String name)
              throws IllegalActionException,
                     NameDuplicationException

Throws:

IllegalActionException

NameDuplicationException

Method Detail

attributeChanged

public void attributeChanged(Attribute attribute)
                      throws IllegalActionException

Determine the attribute changed value

Overrides:

attributeChanged in class NamedObj

Parameters:

attribute - The attribute that changed.

Throws:

IllegalActionException - If the output type is not recognized.

prefire

public boolean prefire()
                throws IllegalActionException

Description copied from class: AtomicActor

Return true. Derived classes override this method to define operations to be performed at the beginning of every iteration of its execution, prior the invocation of the fire() method. Derived classes may also use it to check preconditions for an iteration, if there are any.

Specified by:

prefire in interface Executable

Overrides:

prefire in class AtomicActor<TypedIOPort>

Returns:

Description of the Returned Value

Throws:

IllegalActionException - Description of Exception

Since:

fire

public void fire()
          throws IllegalActionException

Output the data lines into an array.

Specified by:

fire in interface Executable

Overrides:

fire in class AtomicActor<TypedIOPort>

Throws:

IllegalActionException - If there's no director.