A B C D E F G H I J L M N O P R S T U V W X

A

AbstractAdaptor - Class in com.petpet.c3po.api.adaptor

The abstract adaptor class provides an encapsulation of a meta data adaptor.

AbstractAdaptor() - Constructor for class com.petpet.c3po.api.adaptor.AbstractAdaptor

AbstractCLICommand - Class in com.petpet.c3po.command

An abstract CLI command that has some helper methods for implementing commands.

AbstractCLICommand() - Constructor for class com.petpet.c3po.command.AbstractCLICommand

ActionLog - Class in com.petpet.c3po.api.model

A basic model class that stores the information of the last action done on a collection and the date that the action was executed.

ActionLog(String, String) - Constructor for class com.petpet.c3po.api.model.ActionLog

Creates an action log with the current date.

ActionLog(String, String, Date) - Constructor for class com.petpet.c3po.api.model.ActionLog

Creates an action log.

ActionLogHelper - Class in com.petpet.c3po.utils

A helper class to record and read the last action done over a collection of elements.

ActionLogHelper(PersistenceLayer) - Constructor for class com.petpet.c3po.utils.ActionLogHelper

Creates an action log helper.

addFilterCondition(FilterCondition) - Method in class com.petpet.c3po.api.model.helper.Filter

Adds a new filter condition unless it is null or it already exists.

addIdentityTool(String, String) - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

Adds the given tool information to the format sources list.

addValue(MetadataRecord) - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

Adds a value to the list of values.

AGGREGATE_FINALIZE - Static variable in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

A finalize function for the aggregation map reduce job, to calculate the average, standard deviation and variance.

AGGREGATE_MAP - Static variable in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

A javascript Map function for calculating the min, max, sum, avg, sd and var of a numeric property.

AGGREGATE_REDUCE - Static variable in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

The reduce of the aggregation functions.

ANALYSIS_ACTION - Static variable in class com.petpet.c3po.api.model.ActionLog

A constant denoting that the last action over a collection has just done some analysis over it and hasn't changed the data.

API_VERSION - Static variable in class com.petpet.c3po.common.Constants

The version of the api module.

AssignCollectionToElementRule - Class in com.petpet.c3po.adaptor.rules

This PostProcessingRule applies the given collection to every Element that is processed.

AssignCollectionToElementRule(String) - Constructor for class com.petpet.c3po.adaptor.rules.AssignCollectionToElementRule

Creates the rule.

B

BetweenFilterCondition - Class in com.petpet.c3po.api.model.helper

A filter condition that represent a between x and y condition, e.g.

BetweenFilterCondition(String, BetweenFilterCondition.Operator, Object, BetweenFilterCondition.Operator, Object) - Constructor for class com.petpet.c3po.api.model.helper.BetweenFilterCondition

Creates a between filter condition.

BetweenFilterCondition.Operator - Enum in com.petpet.c3po.api.model.helper

The different supported operators.

C

C3PO - Class in com.petpet.c3po

This is the entry point for the command line interface.

C3PO() - Constructor for class com.petpet.c3po.C3PO

Creates the CLI and initializes the maps with all commands and parameters.

C3POConfigurationException - Exception in com.petpet.c3po.utils.exceptions

A simple exception to be thrown when a (internal) configuration error occurrs.

C3POConfigurationException() - Constructor for exception com.petpet.c3po.utils.exceptions.C3POConfigurationException

C3POConfigurationException(String) - Constructor for exception com.petpet.c3po.utils.exceptions.C3POConfigurationException

C3POConfigurationException(String, Throwable) - Constructor for exception com.petpet.c3po.utils.exceptions.C3POConfigurationException

C3POConfigurationException(Throwable) - Constructor for exception com.petpet.c3po.utils.exceptions.C3POConfigurationException

C3POFileAppender - Class in com.petpet.c3po.utils

A log file appender.

C3POFileAppender() - Constructor for class com.petpet.c3po.utils.C3POFileAppender

C3POPersistenceException - Exception in com.petpet.c3po.utils.exceptions

A simple exception that is thrown if something goes wrong in the persistence layer.

C3POPersistenceException() - Constructor for exception com.petpet.c3po.utils.exceptions.C3POPersistenceException

C3POPersistenceException(String) - Constructor for exception com.petpet.c3po.utils.exceptions.C3POPersistenceException

C3POPersistenceException(String, Throwable) - Constructor for exception com.petpet.c3po.utils.exceptions.C3POPersistenceException

C3POPersistenceException(Throwable) - Constructor for exception com.petpet.c3po.utils.exceptions.C3POPersistenceException

Cache - Interface in com.petpet.c3po.api.dao

A simple cache that allows easy retrieval of common objects as properties and sources of meta data, but also putting any kind of object or clearing it..

cleanup() - Method in class com.petpet.c3po.command.AbstractCLICommand

Cleans up the database and logs an error if an exception occurs.

clear() - Method in interface com.petpet.c3po.api.dao.Cache

Clears the cache.

clear() - Method in class com.petpet.c3po.dao.DBCache

Clears the cache.

clearCache() - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Clears the current cache of the application.

clearCache() - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Clears the current cache of the application.

clearCache() - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Clears the DBCache and removes all internally managed mongo collection that store cached results.

close() - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

This method will be called once before the applications ends running.

close() - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

This method will be called once before the applications ends running.

close() - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

If the connection is open, then this method closes it.

CNF_ADAPTORS_COUNT - Static variable in class com.petpet.c3po.common.Constants

The thread count configuration for the adaptor workers.

CNF_CONSOLIDATORS_COUNT - Static variable in class com.petpet.c3po.common.Constants

The thread count configuration for the consolidator workers.

CNF_ELEMENT_IDENTIFIER_RULE - Static variable in class com.petpet.c3po.common.Constants

The key for the create element identifier processing rule.

CNF_EMPTY_VALUE_RULE - Static variable in class com.petpet.c3po.common.Constants

The key for the empty value processing rule.

CNF_HTML_INFO_RULE - Static variable in class com.petpet.c3po.common.Constants

The key for the html info processing rule.

CNF_INFER_DATE_RULE - Static variable in class com.petpet.c3po.common.Constants

The key for the infer date processing rule.

CNF_PERSISTENCE - Static variable in class com.petpet.c3po.common.Constants

A config identifier for the persistence layer class.

CNF_VERSION_RESOLUTION_RULE - Static variable in class com.petpet.c3po.common.Constants

The key for the format version resolution processing rule.

com.petpet.c3po - package com.petpet.c3po

This package contains the CLI.

com.petpet.c3po.adaptor.fits - package com.petpet.c3po.adaptor.fits

This package contains all classes needed for the FITS meta data Adaptor.

com.petpet.c3po.adaptor.rules - package com.petpet.c3po.adaptor.rules

This package contains pre and post processing rules.

com.petpet.c3po.adaptor.tika - package com.petpet.c3po.adaptor.tika

This package contains all classes needed for the Apache TIKA meta data Adaptor.

com.petpet.c3po.analysis - package com.petpet.c3po.analysis

This package contains helper classes and components for doing analysis and aggregations of the data stored within C3PO.

com.petpet.c3po.api.adaptor - package com.petpet.c3po.api.adaptor

This package contains meta data adaptor relevant interfaces.

com.petpet.c3po.api.dao - package com.petpet.c3po.api.dao

This package contains some interfaces for the extension of C3POs data store back-end.

com.petpet.c3po.api.gatherer - package com.petpet.c3po.api.gatherer

This package contains some interfaces for the extension of C3POs meta data gatherers.

com.petpet.c3po.api.model - package com.petpet.c3po.api.model

This package contains the basic model of C3PO that has to be supported by any underlying back-end implementation of the persistence layer.

com.petpet.c3po.api.model.helper - package com.petpet.c3po.api.model.helper

This package contains some helper model classes of C3PO that do not have to be serialized to the back-end data store, but are used by the core module.

com.petpet.c3po.command - package com.petpet.c3po.command

This package contains all CLI commands.

com.petpet.c3po.common - package com.petpet.c3po.common

This package contains some common classes such as constants.

com.petpet.c3po.controller - package com.petpet.c3po.controller

This package contains the persistence layer implementations.

com.petpet.c3po.dao - package com.petpet.c3po.dao

This package contains controller classes that tie the whole processing workflow together.

com.petpet.c3po.dao.mongo - package com.petpet.c3po.dao.mongo

This package contains all classes needed for the Mongo Persistence Layer.

com.petpet.c3po.gatherer - package com.petpet.c3po.gatherer

This package contains MetaDataGatherer implementations.

com.petpet.c3po.parameters - package com.petpet.c3po.parameters

This package contains all CLI parameter wrappers.

com.petpet.c3po.parameters.validation - package com.petpet.c3po.parameters.validation

This package contains some CLI parameter validators.

com.petpet.c3po.utils - package com.petpet.c3po.utils

This package contains some CLI utility classes.

com.petpet.c3po.utils.exceptions - package com.petpet.c3po.utils.exceptions

This package contains some exceptions.

Command - Interface in com.petpet.c3po.command

A command interface for the CLI.

Configurator - Class in com.petpet.c3po.utils

Configures the application based on a configuration file.

configure() - Method in class com.petpet.c3po.adaptor.fits.FITSAdaptor

This method will be called once before the adaptor is started and gives the implementing class a chance to configure itself.

configure() - Method in class com.petpet.c3po.adaptor.tika.TIKAAdaptor

This method will be called once before the adaptor is started and gives the implementing class a chance to configure itself.

configure() - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

This method will be called once before the adaptor is started and gives the implementing class a chance to configure itself.

configure() - Method in class com.petpet.c3po.utils.Configurator

Configures the application in the following order:
1.

Consolidator - Class in com.petpet.c3po.controller

The consolidator is a class (worker thread) that processes parsed elements and stores them to the data base.

Consolidator(PersistenceLayer, Queue<Element>) - Constructor for class com.petpet.c3po.controller.Consolidator

Creates the consolidator worker.

Constants - Class in com.petpet.c3po.common

contains(String) - Method in class com.petpet.c3po.api.model.helper.Filter

Returns true if this filter has at least one FilterCondition with the given field.

contains(FilterCondition) - Method in class com.petpet.c3po.api.model.helper.Filter

Checks if it contains the given FilterCondition.

Controller - Class in com.petpet.c3po.controller

A controller that manages the operations coming as input from the client applications.

Controller(Configurator) - Constructor for class com.petpet.c3po.controller.Controller

This constructors sets the persistence layer, initializes the processing queue and the LocalFileGatherer;

CORE_VERSION - Static variable in class com.petpet.c3po.common.Constants

The version of the core module.

count(Class<T>, Filter) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Counts the number of objects of the given type that match the filter.

count(Class<T>, Filter) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Counts the number of objects of the given type that match the filter.

count(Class<T>, Filter) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Counts the number of objects of the given type that match the filter.

createElement(String, String) - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

Creates new element and sets the element field.

CreateElementIdentifierRule - Class in com.petpet.c3po.adaptor.rules

A PostProcessingRule that creates an element uid if it was not created by adaptor for some reason.

CreateElementIdentifierRule() - Constructor for class com.petpet.c3po.adaptor.rules.CreateElementIdentifierRule

createFormatVersion(String, String, String, String) - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

Creates the format version property.

createIdentity(String, String) - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

Reads the FITS identity information and creates the format and mimetype out of it.

createPuid(String, String, String) - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

Creates a pronom identifier record.

createValue(String, String, String, String, String) - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

Creates a value out of the given value and information if the processing rules do not skip it.

CSVGenerator - Class in com.petpet.c3po.analysis

A CSV generator that creates a sparse matrix view of the data, where each column is a property and each row is an element identifier and each cell has the corresponding value.

CSVGenerator(PersistenceLayer) - Constructor for class com.petpet.c3po.analysis.CSVGenerator

Creates the generator with the given persistence layer.

D

DataHelper - Class in com.petpet.c3po.utils

The data helper class offers some data manipulation methods.

DATE_HISTOGRAM_MAP - Static variable in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

A javascript Map function for building a histogram over a specific date property.

DBCache - Class in com.petpet.c3po.dao

Implements the Cache interface.

DBCache() - Constructor for class com.petpet.c3po.dao.DBCache

Creates a new cache with synchronized empty maps.

DefaultPersistenceLayer - Class in com.petpet.c3po.dao

This default persistence layer just wraps a real implementation and is used by the Configurator if no persistence is specified.

DefaultPersistenceLayer() - Constructor for class com.petpet.c3po.dao.DefaultPersistenceLayer

The default constructor initialised the default persistence layer.

deserialize(Object) - Method in class com.petpet.c3po.dao.mongo.MongoActionLogDeserializer

Deserializes the DBObject to an ActionLog.

deserialize(Object) - Method in class com.petpet.c3po.dao.mongo.MongoElementDeserialzer

Deserializes DBObjects to elements.

deserialize(Object) - Method in interface com.petpet.c3po.dao.mongo.MongoModelDeserializer

Deserializes the given object into the correct Java object.

deserialize(Object) - Method in class com.petpet.c3po.dao.mongo.MongoPropertyDeserialzer

Deserializes the given DBObject into a property.

deserialize(Object) - Method in class com.petpet.c3po.dao.mongo.MongoSourceDeserializer

Deserializes a DBObject into a Source object.

DigesterContext - Class in com.petpet.c3po.adaptor.fits

The digester context is a simple helper object that is pushed onto the Apache Digester stack and its methods are used during SAX parsing.

DigesterContext(ReadOnlyCache, List<PreProcessingRule>) - Constructor for class com.petpet.c3po.adaptor.fits.DigesterContext

Creates the digester context object.

distinct(Class<T>, String, Filter) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Returns the distinct values for the given property (in string form).

distinct(Class<T>, String, Filter) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Returns the distinct values for the given property (in string form).

distinct(Class<T>, String, Filter) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Returns the distinct values for the given property (in string form).

DistributionRepresentativeGenerator - Class in com.petpet.c3po.analysis

This class generates a sample set based on a distribution coverage strategy.

DistributionRepresentativeGenerator() - Constructor for class com.petpet.c3po.analysis.DistributionRepresentativeGenerator

E

Element - Class in com.petpet.c3po.api.model

A domain object class that encapsulates a digital object and its meta data.

Element(String, String) - Constructor for class com.petpet.c3po.api.model.Element

Creates an element with the given uid and name.

Element(String, String, String) - Constructor for class com.petpet.c3po.api.model.Element

Creates an element with the given uid, name and collection.

EmptyStringValidator - Class in com.petpet.c3po.parameters.validation

A empty string validator for the passed command line parameters.

EmptyStringValidator() - Constructor for class com.petpet.c3po.parameters.validation.EmptyStringValidator

EmptyValueProcessingRule - Class in com.petpet.c3po.adaptor.rules

A PreProcessingRule that skips the meta data records if their value is null or an empty string.

EmptyValueProcessingRule() - Constructor for class com.petpet.c3po.adaptor.rules.EmptyValueProcessingRule

equals(Object) - Method in class com.petpet.c3po.api.model.helper.Filter

equals(Object) - Method in class com.petpet.c3po.api.model.helper.FilterCondition

equals(Object) - Method in class com.petpet.c3po.api.model.Property

establishConnection(Map<String, String>) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

This method will be called upon initialisation of the application.

establishConnection(Map<String, String>) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

This method will be called upon initialisation of the application.

establishConnection(Map<String, String>) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Establishes the connection to mongo database.

execute() - Method in class com.petpet.c3po.analysis.DistributionRepresentativeGenerator

Executes with the default sample size of 10.

execute(int) - Method in class com.petpet.c3po.analysis.DistributionRepresentativeGenerator

Executes with the given sample size and returns a list of size up to the given limit.

execute() - Method in class com.petpet.c3po.analysis.RepresentativeGenerator

Retrieves a list of identifiers for the representative sample objects.

execute(int) - Method in class com.petpet.c3po.analysis.RepresentativeGenerator

Retrieves a list of identifiers for the representative sample objects with a predefined number of objects.

execute() - Method in class com.petpet.c3po.analysis.SizeRepresentativeGenerator

Selects 10 samples per default.

execute(int) - Method in class com.petpet.c3po.analysis.SizeRepresentativeGenerator

execute() - Method in class com.petpet.c3po.analysis.SystematicSamplingRepresentativeGenerator

Selects 10 samples per default.

execute(int) - Method in class com.petpet.c3po.analysis.SystematicSamplingRepresentativeGenerator

execute() - Method in interface com.petpet.c3po.command.Command

Called if everything was ok and should execute the current command.

execute() - Method in class com.petpet.c3po.command.ExportCommand

Creates a controller and submits an export request.

execute() - Method in class com.petpet.c3po.command.GatherCommand

Creates a controller and submits a process meta data request.

execute() - Method in class com.petpet.c3po.command.HelpCommand

Prints the help.

execute() - Method in class com.petpet.c3po.command.ProfileCommand

Submits a profile request to the controller.

execute() - Method in class com.petpet.c3po.command.RemoveCommand

Prompts for confirmation and submits a remove request to the controller.

execute() - Method in class com.petpet.c3po.command.SamplesCommand

Submits a find samples request to the controller with the passed parameters.

execute() - Method in class com.petpet.c3po.command.VersionCommand

export(String, List<Property>, String) - Method in class com.petpet.c3po.analysis.CSVGenerator

Exports all the given properties for the given mimetype to a sparse matrix view where each column is a property and each row is an element with the values for the corresponding property.

export(Filter, String) - Method in class com.petpet.c3po.analysis.CSVGenerator

Exports all the data matching the given filter to the given output file.

export(Filter, List<Property>, String) - Method in class com.petpet.c3po.analysis.CSVGenerator

Exports all the given properties and data that matches the given filter to the given output file.

export(Map<String, Object>) - Method in class com.petpet.c3po.controller.Controller

Exports the data in a CSV format.

exportAll(String, String) - Method in class com.petpet.c3po.analysis.CSVGenerator

Exports all the data from the given collection to a sparse matrix view where each column is a property and each row is an element with the values for the corresponding property.

ExportCommand - Class in com.petpet.c3po.command

Submits an export to csv request to the controller based on the passed parameters.

ExportCommand() - Constructor for class com.petpet.c3po.command.ExportCommand

ExportParams - Class in com.petpet.c3po.parameters

The supported parameters for the ExportCommand

ExportParams() - Constructor for class com.petpet.c3po.parameters.ExportParams

F

FileMetadataStream - Class in com.petpet.c3po.gatherer

A simple wrapper around an input stream that holds the fileName (or some human readable identifier) of the stream.

FileMetadataStream(String) - Constructor for class com.petpet.c3po.gatherer.FileMetadataStream

Sets the passed variables.

Filter - Class in com.petpet.c3po.api.model.helper

This class is used to define a filter for a c3po data model class.

Filter() - Constructor for class com.petpet.c3po.api.model.helper.Filter

Create a new empty filter with an initialized empty list of FilterConditions.

Filter(FilterCondition) - Constructor for class com.petpet.c3po.api.model.helper.Filter

Creates a new filter and adds the given conditions to the filter.

Filter(List<FilterCondition>) - Constructor for class com.petpet.c3po.api.model.helper.Filter

Creates a new filter and sets the FilterConditions to the passed list.

Filter(Filter) - Constructor for class com.petpet.c3po.api.model.helper.Filter

Copies the given filter to this filter.

FILTER_AGGREGATE_MAP - Static variable in class com.petpet.c3po.common.Constants

Deprecated.

FilterCondition - Class in com.petpet.c3po.api.model.helper

Encapsulates a single filter condition of a filter.

FilterCondition() - Constructor for class com.petpet.c3po.api.model.helper.FilterCondition

Default empty constructor.

FilterCondition(String, Object) - Constructor for class com.petpet.c3po.api.model.helper.FilterCondition

Sets the fields of this object.

find(Class<T>, Filter) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Finds objects corresponding to the supplied filter and type.

find(Class<T>, Filter) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Finds objects corresponding to the supplied filter and type.

find(Class<T>, Filter) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Finds objects corresponding to the supplied filter and type.

findSamples(Map<String, Object>) - Method in class com.petpet.c3po.controller.Controller

Finds sample records that are representative.

FITSAdaptor - Class in com.petpet.c3po.adaptor.fits

An adaptor for FITS https://github.com/harvard-lts/fits meta data.

FITSAdaptor() - Constructor for class com.petpet.c3po.adaptor.fits.FITSAdaptor

A default constructor that initialises the digester and sets up the parsing rules.

FITSHelper - Class in com.petpet.c3po.adaptor.fits

A simple helper that reads a file of fits to c3po property mappings.

FITSHelper() - Constructor for class com.petpet.c3po.adaptor.fits.FITSHelper

FormatVersionResolutionRule - Class in com.petpet.c3po.adaptor.rules

A post processing rule to correct a FITS reported conflict in the format version that was marked as ok.

FormatVersionResolutionRule() - Constructor for class com.petpet.c3po.adaptor.rules.FormatVersionResolutionRule

G

GatherCommand - Class in com.petpet.c3po.command

Submits a gather meta data request to the controller based on the passed parameters.

GatherCommand() - Constructor for class com.petpet.c3po.command.GatherCommand

GatherParams - Class in com.petpet.c3po.parameters

The supported parameters for the GatherCommand

GatherParams() - Constructor for class com.petpet.c3po.parameters.GatherParams

generateProfile(Filter) - Method in class com.petpet.c3po.analysis.ProfileGenerator

Generates a profile for the given filter with a default sample size set of 5 and without including the element identifiers.

generateProfile(Filter, int, boolean) - Method in class com.petpet.c3po.analysis.ProfileGenerator

Generates a profile matching the given filter with the given sample set size and including the elements if set to true.

getAction() - Method in class com.petpet.c3po.api.model.ActionLog

getAdaptorPrefix() - Method in class com.petpet.c3po.adaptor.fits.FITSAdaptor

Returns the prefix of this adaptor ('fits').

getAdaptorPrefix() - Method in class com.petpet.c3po.adaptor.tika.TIKAAdaptor

getAdaptorPrefix() - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

The prefix that this adaptor should be associated with.

getAlgorithm(String) - Method in class com.petpet.c3po.analysis.RepresentativeAlgorithmFactory

The factory method.

getAlgorithm() - Method in class com.petpet.c3po.parameters.ProfileParams

getAlgorithm() - Method in class com.petpet.c3po.parameters.SamplesParams

getAverage() - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

getBooleanConfig(String, boolean) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Gets a boolean config for the given key.

getBooleanProperty(String) - Method in class com.petpet.c3po.utils.Configurator

Returns a boolean value for the specified property key or false if none was found.

getCache() - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Gets a read only instance of the application cache.

getCache() - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Gets a cache object.

getCache() - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Gets a cache object.

getCache() - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Gets a cache object.

getCollection() - Method in class com.petpet.c3po.api.model.ActionLog

getCollection() - Method in class com.petpet.c3po.api.model.Element

getCollection() - Method in class com.petpet.c3po.parameters.ExportParams

getCollection() - Method in class com.petpet.c3po.parameters.GatherParams

getCollection() - Method in class com.petpet.c3po.parameters.ProfileParams

getCollection() - Method in class com.petpet.c3po.parameters.RemoveParams

getCollection() - Method in class com.petpet.c3po.parameters.SamplesParams

getConditions() - Method in class com.petpet.c3po.api.model.helper.Filter

getConfig(String) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Gets a string config for the given key.

getCount() - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

getData() - Method in interface com.petpet.c3po.api.model.helper.MetadataStream

The data that has to be parsed.

getData() - Method in class com.petpet.c3po.gatherer.FileMetadataStream

getDate() - Method in class com.petpet.c3po.api.model.ActionLog

getDefaultConfigurator() - Static method in class com.petpet.c3po.utils.Configurator

Obtains the singleton instance of this class.

getElement() - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

getField() - Method in class com.petpet.c3po.api.model.helper.FilterCondition

getFilter() - Method in class com.petpet.c3po.analysis.RepresentativeGenerator

getHOperator() - Method in class com.petpet.c3po.api.model.helper.BetweenFilterCondition

getHValue() - Method in class com.petpet.c3po.api.model.helper.BetweenFilterCondition

getId() - Method in class com.petpet.c3po.api.model.Element

getId() - Method in class com.petpet.c3po.api.model.Property

getId() - Method in class com.petpet.c3po.api.model.Source

getIntegerConfig(String, int) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Gets a integer config for the given key.

getIntProperty(String) - Method in class com.petpet.c3po.utils.Configurator

Returns an integer value for the specified property key or -1.

getIntProperty(String, int) - Method in class com.petpet.c3po.utils.Configurator

Returns an integer for the specified property or the default value if the key is not defined in the configs.

getKey() - Method in class com.petpet.c3po.api.model.Property

getKeyValueMap(String) - Static method in class com.petpet.c3po.adaptor.tika.TIKAResultParser

Reads a file line by line and assumes it is a raw TIKA output.

getLastAction(String) - Method in class com.petpet.c3po.utils.ActionLogHelper

Obtains the last action for the given collection.

getLocation() - Method in class com.petpet.c3po.parameters.ExportParams

getLocation() - Method in class com.petpet.c3po.parameters.GatherParams

getLocation() - Method in class com.petpet.c3po.parameters.ProfileParams

getLocation() - Method in class com.petpet.c3po.parameters.SamplesParams

getLOperator() - Method in class com.petpet.c3po.api.model.helper.BetweenFilterCondition

getLValue() - Method in class com.petpet.c3po.api.model.helper.BetweenFilterCondition

getMax() - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

getMetadata() - Method in class com.petpet.c3po.api.model.Element

getMin() - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

getName() - Method in class com.petpet.c3po.api.model.Element

getName() - Method in interface com.petpet.c3po.api.model.helper.MetadataStream

The name of the resource (e.g.

getName() - Method in class com.petpet.c3po.api.model.Source

getName() - Method in class com.petpet.c3po.gatherer.FileMetadataStream

getNext() - Method in interface com.petpet.c3po.api.gatherer.MetaDataGatherer

Gets the next MetadataStream object.

getNext() - Method in class com.petpet.c3po.gatherer.LocalFileGatherer

Gets the next MetadataStream object.

getNumericStatistics(Property, Filter) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Returns statistics for the given numeric property for all elements according to the given filter.

getNumericStatistics(Property, Filter) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Returns statistics for the given numeric property for all elements according to the given filter.

getNumericStatistics(Property, Filter) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Gets the numeric statistics for the given property and the given filter.

getObject(Object) - Method in interface com.petpet.c3po.api.dao.ReadOnlyCache

Any other non-persistence layer object that can be cached.

getObject(Object) - Method in class com.petpet.c3po.dao.DBCache

Any other non-persistence layer object that can be cached.

getOptions() - Method in class com.petpet.c3po.analysis.RepresentativeGenerator

getPersistence() - Method in class com.petpet.c3po.utils.Configurator

Retrieves the current persistence layer.

getPreProcessingRules() - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Gets a unmodifiable list of PreProcessingRule objects.

getPriority() - Method in class com.petpet.c3po.adaptor.rules.AssignCollectionToElementRule

Has a very high priority.

getPriority() - Method in class com.petpet.c3po.adaptor.rules.CreateElementIdentifierRule

This rule has a low priority.

getPriority() - Method in class com.petpet.c3po.adaptor.rules.EmptyValueProcessingRule

Has a high priority.

getPriority() - Method in class com.petpet.c3po.adaptor.rules.FormatVersionResolutionRule

Has a high priotity.

getPriority() - Method in class com.petpet.c3po.adaptor.rules.HtmlInfoProcessingRule

Has the lowest possible priority.

getPriority() - Method in class com.petpet.c3po.adaptor.rules.InferDateFromFileNameRule

Has a low priority.

getPriority() - Method in interface com.petpet.c3po.api.adaptor.ProcessingRule

A priority between 0 and 1000 in the case of more rules, where 0 is the least important and 1000 is the most important rule.

getProperties() - Method in class com.petpet.c3po.parameters.ProfileParams

getProperties() - Method in class com.petpet.c3po.parameters.SamplesParams

getProperty(String) - Method in interface com.petpet.c3po.api.dao.ReadOnlyCache

Retrieves the property designated by the given key.

getProperty() - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

getProperty(String) - Method in class com.petpet.c3po.dao.DBCache

Looks in the cache for a property with the given key.

getPropertyKeyByFitsName(String) - Static method in class com.petpet.c3po.adaptor.fits.FITSHelper

Returns the mapping for the given fits property name or the same name if no mapping was defined.

getPropertyKeyByTikaName(String) - Static method in class com.petpet.c3po.adaptor.tika.TIKAHelper

For now we support only the specified properties within the file as the TIKA adaptor is still experimental

getPropertyType(String) - Static method in class com.petpet.c3po.utils.DataHelper

Gets the type of the property defined by the given key.

getSize() - Method in class com.petpet.c3po.parameters.ProfileParams

getSize() - Method in class com.petpet.c3po.parameters.SamplesParams

getSource(String, String) - Method in interface com.petpet.c3po.api.dao.ReadOnlyCache

Retrieves the source designated by the given name and version.

getSource(String, String) - Method in class com.petpet.c3po.dao.DBCache

Looks in the cache for a source with the given name and version.

getSources() - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

getStandardDeviation() - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

getStatus() - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

getStringConfig(String, String) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Gets a string config for the given key.

getStringProperty(String) - Method in class com.petpet.c3po.utils.Configurator

Gets a String representation for the property key or an empty string if no property was found.

getStringProperty(String, String) - Method in class com.petpet.c3po.utils.Configurator

Returns the string property for the given key, or returns the default value if nothing is defined under the given key.

getSum() - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

getTime() - Method in class com.petpet.c3po.command.AbstractCLICommand

Retrieves the time needed for the execution of this command in milliseconds.

getTime() - Method in interface com.petpet.c3po.command.Command

Retrieves the time needed for the execution of this command in milliseconds.

getTime() - Method in class com.petpet.c3po.command.HelpCommand

getTime() - Method in class com.petpet.c3po.command.VersionCommand

getType() - Method in class com.petpet.c3po.analysis.DistributionRepresentativeGenerator

getType() - Method in class com.petpet.c3po.analysis.RepresentativeGenerator

Retrieves the type/name of the algorithm used to identify the sample objects.

getType() - Method in class com.petpet.c3po.analysis.SizeRepresentativeGenerator

getType() - Method in class com.petpet.c3po.analysis.SystematicSamplingRepresentativeGenerator

getType() - Method in class com.petpet.c3po.api.model.Property

getType() - Method in class com.petpet.c3po.parameters.GatherParams

getTypedValue(String, String) - Static method in class com.petpet.c3po.utils.DataHelper

Tries to infer the type of the value based on the property type and converts the value.

getUid() - Method in class com.petpet.c3po.api.model.Element

getValue() - Method in class com.petpet.c3po.api.model.helper.FilterCondition

getValue() - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

getValueHistogramFor(Property, Filter) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Returns a property value histogram for the given property and type and respecting the given filter.

getValueHistogramFor(Property, Filter) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Returns a property value histogram for the given property and type and respecting the given filter.

getValueHistogramFor(Property, Filter) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Gets a value histogram for the given property and the given filter.

getValues() - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

getValues() - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

getVariance() - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

getVersion() - Method in class com.petpet.c3po.api.model.Source

H

hashCode() - Method in class com.petpet.c3po.api.model.helper.Filter

hashCode() - Method in class com.petpet.c3po.api.model.helper.FilterCondition

hashCode() - Method in class com.petpet.c3po.api.model.Property

hasNext() - Method in interface com.petpet.c3po.api.gatherer.MetaDataGatherer

Whether or not the gatherer has a next element at the moment of the call.

hasNext() - Method in class com.petpet.c3po.dao.mongo.MongoIterator

hasNext() - Method in class com.petpet.c3po.gatherer.LocalFileGatherer

Whether or not the gatherer has a next element at the moment of the call.

HelpCommand - Class in com.petpet.c3po.command

Prints help messages for all supported modes of C3PO.

HelpCommand(Map<String, Params>) - Constructor for class com.petpet.c3po.command.HelpCommand

Creates the help command.

HISTOGRAM_MAP - Static variable in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

A javascript Map function for building a histogram of a specific property.

HISTOGRAM_REDUCE - Static variable in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

The reduce function for the Constants#HISTOGRAM_MAP.

HtmlInfoProcessingRule - Class in com.petpet.c3po.adaptor.rules

A PreProcessingRule that cleans up values provided by a special tool bundled in FITS by TU Wien.

HtmlInfoProcessingRule() - Constructor for class com.petpet.c3po.adaptor.rules.HtmlInfoProcessingRule

I

InferDateFromFileNameRule - Class in com.petpet.c3po.adaptor.rules

A post processing rule that tries to infer the creation date of an object out of its name.

InferDateFromFileNameRule() - Constructor for class com.petpet.c3po.adaptor.rules.InferDateFromFileNameRule

Creates the rule.

InferDateFromFileNameRule(ReadOnlyCache) - Constructor for class com.petpet.c3po.adaptor.rules.InferDateFromFileNameRule

Creates the rule with the given cache.

init() - Static method in class com.petpet.c3po.adaptor.fits.FITSHelper

Reads the mappings into the Properties object.

init() - Static method in class com.petpet.c3po.adaptor.tika.TIKAHelper

Loads the property mappings to the Properties object.

init() - Static method in class com.petpet.c3po.utils.DataHelper

Loads the types of known properties into the TYPES Properties object.

init() - Static method in class com.petpet.c3po.utils.XMLUtils

InputTypeValidator - Class in com.petpet.c3po.parameters.validation

Checks that the passed meta data input type is supported.

InputTypeValidator() - Constructor for class com.petpet.c3po.parameters.validation.InputTypeValidator

insert(T) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Inserts the given object to the underlying data store.

insert(T) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Inserts the given object to the underlying data store.

insert(T) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Inserts the given object to the underlying data store.

isConnected() - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Whether or not there is an established connection to the database.

isConnected() - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Whether or not there is an established connection to the database.

isConnected() - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Whether or not the persistence layer is connected.

isIncludeElements() - Method in class com.petpet.c3po.parameters.ProfileParams

isLastActionUpdated(String) - Method in class com.petpet.c3po.utils.ActionLogHelper

Checks if the last action for the given collection was ActionLog.UPDATED_ACTION.

isReady() - Method in interface com.petpet.c3po.api.gatherer.MetaDataGatherer

Whether or not the gatherer has finished its work.

isReady() - Method in class com.petpet.c3po.gatherer.LocalFileGatherer

Whether or not the gatherer has finished its work.

isRecursive() - Method in class com.petpet.c3po.parameters.GatherParams

isRunning() - Method in class com.petpet.c3po.controller.Consolidator

isValidAlgorithm(String) - Static method in class com.petpet.c3po.analysis.RepresentativeAlgorithmFactory

Checks if the given algorithm is supported and returns true if yes, false otherwise.

J

join(String[], String) - Static method in class com.petpet.c3po.adaptor.tika.TIKAResultParser

L

LocalFileGatherer - Class in com.petpet.c3po.gatherer

A gatherer of a local file system.

LocalFileGatherer() - Constructor for class com.petpet.c3po.gatherer.LocalFileGatherer

Creates a new gatherer.

LocalFileGatherer(Map<String, String>) - Constructor for class com.petpet.c3po.gatherer.LocalFileGatherer

Creates a new gatherer with the given config.

LocalFileGatherer(Object) - Constructor for class com.petpet.c3po.gatherer.LocalFileGatherer

Creates a new gatherer with the given object lock.

M

main(String[]) - Static method in class com.petpet.c3po.C3PO

The entry point for this command line interfaces.

mapFieldToProperty(String, Object) - Method in class com.petpet.c3po.dao.mongo.MongoFilterSerializer

Wraps the field within a metadata.[field].value if necessary, so that it corresponds to the current element structure.

mergeMetadataRecord(Element, MetadataRecord) - Static method in class com.petpet.c3po.utils.DataHelper

Merges the given metadata record within the given element.

MetaDataGatherer - Interface in com.petpet.c3po.api.gatherer

An interface for a meta data gatherer.

MetadataRecord - Class in com.petpet.c3po.api.model.helper

A single metadata record of an element.

MetadataRecord() - Constructor for class com.petpet.c3po.api.model.helper.MetadataRecord

Creates an empty record with a status ok.

MetadataRecord(Property, String) - Constructor for class com.petpet.c3po.api.model.helper.MetadataRecord

Creates an record for the given property with the given value and a status SINGLE_RESULT.

MetadataRecord(Property, String, MetadataRecord.Status) - Constructor for class com.petpet.c3po.api.model.helper.MetadataRecord

Creates a record for the given property with the given value and the given status.

MetadataRecord.Status - Enum in com.petpet.c3po.api.model.helper

The status of the element shows the certainty with which the value for the given property is correct.

MetadataStream - Interface in com.petpet.c3po.api.model.helper

This interface abstracts a gathered resource that is passed for parsing to the adaptors.

Model - Interface in com.petpet.c3po.api.model

An empty interface that designates the classes that have to be supported by a PersistenceLayer provider.

MongoActionLogDeserializer - Class in com.petpet.c3po.dao.mongo

Deserializes DBObjects to ActionLog objects.

MongoActionLogDeserializer() - Constructor for class com.petpet.c3po.dao.mongo.MongoActionLogDeserializer

MongoActionLogSerializer - Class in com.petpet.c3po.dao.mongo

Serializes an ActionLog object to a mongo DBObject.

MongoActionLogSerializer() - Constructor for class com.petpet.c3po.dao.mongo.MongoActionLogSerializer

MongoElementDeserialzer - Class in com.petpet.c3po.dao.mongo

Deserializes DBObjects into Element objects.

MongoElementDeserialzer(PersistenceLayer) - Constructor for class com.petpet.c3po.dao.mongo.MongoElementDeserialzer

MongoElementSerializer - Class in com.petpet.c3po.dao.mongo

Serializes Elements into DBObjects.

MongoElementSerializer() - Constructor for class com.petpet.c3po.dao.mongo.MongoElementSerializer

MongoFilterSerializer - Class in com.petpet.c3po.dao.mongo

The MongoFilterSerializer translates a filter object to a DBObject query, so that the dataset is first filtered and then the persistence layer function is applied.

MongoFilterSerializer() - Constructor for class com.petpet.c3po.dao.mongo.MongoFilterSerializer

MongoIterator<E extends Model> - Class in com.petpet.c3po.dao.mongo

Wraps a Mongo DBCursor into an iterator.

MongoIterator(MongoModelDeserializer, DBCursor) - Constructor for class com.petpet.c3po.dao.mongo.MongoIterator

Creates an iterator.

MongoModelDeserializer - Interface in com.petpet.c3po.dao.mongo

Deserializes the given object into a model object.

MongoModelSerializer - Interface in com.petpet.c3po.dao.mongo

A simple interface for serializing objects into Mongo DBObjects.

MongoPersistenceLayer - Class in com.petpet.c3po.dao.mongo

A MongoDB (http://www.mongodb.org) specific back-end persistence layer implementation.

MongoPersistenceLayer() - Constructor for class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

The constructor initializes all needed objects, such as the serializers and deserializers.

MongoPropertyDeserialzer - Class in com.petpet.c3po.dao.mongo

Deserializes the mongo DBObject into a Property object.

MongoPropertyDeserialzer() - Constructor for class com.petpet.c3po.dao.mongo.MongoPropertyDeserialzer

MongoPropertySerializer - Class in com.petpet.c3po.dao.mongo

Serializes a Property object to a mongo DBObject.

MongoPropertySerializer() - Constructor for class com.petpet.c3po.dao.mongo.MongoPropertySerializer

MongoSourceDeserializer - Class in com.petpet.c3po.dao.mongo

MongoSourceDeserializer() - Constructor for class com.petpet.c3po.dao.mongo.MongoSourceDeserializer

MongoSourceSerializer - Class in com.petpet.c3po.dao.mongo

Serializes Source objects to a Mongo DBObject.

MongoSourceSerializer() - Constructor for class com.petpet.c3po.dao.mongo.MongoSourceSerializer

N

next() - Method in class com.petpet.c3po.dao.mongo.MongoIterator

Returns the next element (after deserialization) if the iterator has a next element.

NUMERIC_HISTOGRAM_MAP - Static variable in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

A javascript Map function for building a histogram with fixed bin size.

NumericStatistics - Class in com.petpet.c3po.api.model.helper

A simple object that encapsulates the results of some simple statistical calculations over the values of a numeric property.

NumericStatistics() - Constructor for class com.petpet.c3po.api.model.helper.NumericStatistics

A default empty constructor.

NumericStatistics(long, double, double, double, double, double, double) - Constructor for class com.petpet.c3po.api.model.helper.NumericStatistics

Sets the passed values correspondigly.

O

OPT_COLLECTION_LOCATION - Static variable in class com.petpet.c3po.common.Constants

A c3po configuration for the location where the metadata is.

OPT_COLLECTION_NAME - Static variable in class com.petpet.c3po.common.Constants

A c3po configuration for the collection on which to operate.

OPT_INCLUDE_ELEMENTS - Static variable in class com.petpet.c3po.common.Constants

A configuration option for including the element identifiers.

OPT_INPUT_TYPE - Static variable in class com.petpet.c3po.common.Constants

A c3po configuration for the type of the input files.

OPT_OUTPUT_LOCATION - Static variable in class com.petpet.c3po.common.Constants

A configuration option for the output location of a CLI command.

OPT_RECURSIVE - Static variable in class com.petpet.c3po.common.Constants

A configuartion for recursive processing.

OPT_SAMPLING_ALGORITHM - Static variable in class com.petpet.c3po.common.Constants

A configuration option for the sampling algorithm to use.

OPT_SAMPLING_PROPERTIES - Static variable in class com.petpet.c3po.common.Constants

A configuration option for the properties over which some sample algorithms should work.

OPT_SAMPLING_SIZE - Static variable in class com.petpet.c3po.common.Constants

A configuration option for the size of the sample set.

P

Params - Interface in com.petpet.c3po.parameters

An empty Parameters interface to denote classes that are annotated with JCommander parameter annotations.

parseElement(String, String) - Method in class com.petpet.c3po.adaptor.fits.FITSAdaptor

Parses the meta data and retrieves it.

parseElement(String, String) - Method in class com.petpet.c3po.adaptor.tika.TIKAAdaptor

Parses the TIKA data.

parseElement(String, String) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

This element is responsible for adapting the data in the object to a Element.

PersistenceLayer - Interface in com.petpet.c3po.api.dao

The persistence layer interface offers some common methods for interacting with the underlying database.

PostProcessingRule - Interface in com.petpet.c3po.api.adaptor

A post processing rule gets a parsed element and does some processing on the given element.

PreProcessingRule - Interface in com.petpet.c3po.api.adaptor

A pre processing rule is a special processing rule that should be applied before (or during ) meta data processing in an adaptor.

process(Element) - Method in class com.petpet.c3po.adaptor.rules.AssignCollectionToElementRule

Sets the collection of the given element to the colleciton name and returns it.

process(Element) - Method in class com.petpet.c3po.adaptor.rules.CreateElementIdentifierRule

Sets a random uuid if the element has no uid defined.

process(Element) - Method in class com.petpet.c3po.adaptor.rules.FormatVersionResolutionRule

Make sure that all format_version have the correct status.

process(Element) - Method in class com.petpet.c3po.adaptor.rules.InferDateFromFileNameRule

Tries to extract the meta data for the created property and sets it if successful, otherwise it returns the unmodified element.

process(Element) - Method in interface com.petpet.c3po.api.adaptor.PostProcessingRule

This method does some processing over the passed element and returns it.

ProcessingRule - Interface in com.petpet.c3po.api.adaptor

A processing rule is a rule that has a priority.

processMetaData(Map<String, String>) - Method in class com.petpet.c3po.controller.Controller

This starts a gather-adapt-persist workflow, where all the needed components are configured and run.

profile(Map<String, Object>) - Method in class com.petpet.c3po.controller.Controller

Generates a profile.

ProfileCommand - Class in com.petpet.c3po.command

Submits a profile request to the controller based on the passed parameters.

ProfileCommand() - Constructor for class com.petpet.c3po.command.ProfileCommand

ProfileGenerator - Class in com.petpet.c3po.analysis

Generates a c3po content profile in an xml format according to the c3po/format/c3po.xsd schema.

ProfileGenerator(PersistenceLayer, RepresentativeGenerator) - Constructor for class com.petpet.c3po.analysis.ProfileGenerator

Creates this generator.

ProfileParams - Class in com.petpet.c3po.parameters

The paremters supported by the ProfileCommand

ProfileParams() - Constructor for class com.petpet.c3po.parameters.ProfileParams

PROPERTIES_IN_COLLECTION_MAP - Static variable in class com.petpet.c3po.common.Constants

Deprecated.

PROPERTIES_IN_COLLECTION_REDUCE - Static variable in class com.petpet.c3po.common.Constants

Deprecated.

Property - Class in com.petpet.c3po.api.model

A domain object encapsulating a property document.

Property() - Constructor for class com.petpet.c3po.api.model.Property

A default constructor.

Property(String) - Constructor for class com.petpet.c3po.api.model.Property

Creates a property with the given key as key and id and sets the type to a string.

Property(String, PropertyType) - Constructor for class com.petpet.c3po.api.model.Property

Creates a property with the given key as key and id and sets the type to the given type.

PropertyType - Enum in com.petpet.c3po.api.model.helper

An enumeration of the property types.

put(Object, Object) - Method in interface com.petpet.c3po.api.dao.Cache

Puts the given value to the given key.

put(Object, Object) - Method in class com.petpet.c3po.dao.DBCache

Puts the given value to the given key.

R

ReadOnlyCache - Interface in com.petpet.c3po.api.dao

A simple Read Only cache for Property, Source and any kind of other objects.

recordAction(ActionLog) - Method in class com.petpet.c3po.utils.ActionLogHelper

Records the action.

remove(Class<T>, Filter) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Removes the objects of the given type that match the filter from the underlying data store.

remove(T) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Removes the given object from the underlying data store.

remove(T) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Removes the given object from the underlying data store.

remove(Class<T>, Filter) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Removes the objects of the given type that match the filter from the underlying data store.

remove() - Method in class com.petpet.c3po.dao.mongo.MongoIterator

remove(T) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Removes the given object from the underlying data store.

remove(Class<T>, Filter) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Removes the objects of the given type that match the filter from the underlying data store.

removeCollection(Map<String, Object>) - Method in class com.petpet.c3po.controller.Controller

Removes all elements for a given collection.

RemoveCommand - Class in com.petpet.c3po.command

Submits a remove request to the controller based on the passed parameters.

RemoveCommand() - Constructor for class com.petpet.c3po.command.RemoveCommand

removeMetadata(String) - Method in class com.petpet.c3po.api.model.Element

Removes all records for the given property id and returns a list of all removed meta data records.

RemoveParams - Class in com.petpet.c3po.parameters

The supported paremters for the RemoveCommand.

RemoveParams() - Constructor for class com.petpet.c3po.parameters.RemoveParams

removeTrailingZero(String) - Static method in class com.petpet.c3po.utils.DataHelper

Removes a trailing zero (.0) from a string.

RepresentativeAlgorithmFactory - Class in com.petpet.c3po.analysis

A simple factory that chooses the representative sample selection algorithm based on the specified id.

RepresentativeAlgorithmFactory() - Constructor for class com.petpet.c3po.analysis.RepresentativeAlgorithmFactory

RepresentativeGenerator - Class in com.petpet.c3po.analysis

A representative generator is a class that can select a set of sample objects that are somehow representative to a collection or a super set of elements.

RepresentativeGenerator() - Constructor for class com.petpet.c3po.analysis.RepresentativeGenerator

RULE_KEYS - Static variable in class com.petpet.c3po.common.Constants

An array of the configurable processing rule keys.

run() - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Starts a loop that runs this thread.

run() - Method in class com.petpet.c3po.controller.Consolidator

Runs as long as the queue is not empty or the running flag is true.

run() - Method in class com.petpet.c3po.gatherer.LocalFileGatherer

Runs this gatherer and traverses the file system (optionally in a recursive fashion) .

S

SampleAlgorithmValidator - Class in com.petpet.c3po.parameters.validation

Checks wheter the passed value is a supported representative selection algorithm.

SampleAlgorithmValidator() - Constructor for class com.petpet.c3po.parameters.validation.SampleAlgorithmValidator

SamplesCommand - Class in com.petpet.c3po.command

Submits a samples generation request to the controller based on the passed parameters.

SamplesCommand() - Constructor for class com.petpet.c3po.command.SamplesCommand

SampleSizeValidator - Class in com.petpet.c3po.parameters.validation

Checks that the size value is > 0.

SampleSizeValidator() - Constructor for class com.petpet.c3po.parameters.validation.SampleSizeValidator

SamplesParams - Class in com.petpet.c3po.parameters

The supported paremters for the SamplesCommand.

SamplesParams() - Constructor for class com.petpet.c3po.parameters.SamplesParams

serialize(Object) - Method in class com.petpet.c3po.dao.mongo.MongoActionLogSerializer

Maps the given ActionLog to a mongo document.

serialize(Object) - Method in class com.petpet.c3po.dao.mongo.MongoElementSerializer

Maps the given element object to a mongo NoSQL schema, where every element is represented as a single document wrapping all its meta data records.

serialize(Filter) - Method in class com.petpet.c3po.dao.mongo.MongoFilterSerializer

Serializes the given filter according to the strategy proposed here: Filter.

serialize(Object) - Method in interface com.petpet.c3po.dao.mongo.MongoModelSerializer

Serializes the given object to a DBObject.

serialize(Object) - Method in class com.petpet.c3po.dao.mongo.MongoPropertySerializer

Serializes the given Property object to a mongo NoSQL document.

serialize(Object) - Method in class com.petpet.c3po.dao.mongo.MongoSourceSerializer

Maps the given Source object to a mongo DBObject.

setAction(String) - Method in class com.petpet.c3po.api.model.ActionLog

setAlgorithm(String) - Method in class com.petpet.c3po.parameters.ProfileParams

setAlgorithm(String) - Method in class com.petpet.c3po.parameters.SamplesParams

setAverage(double) - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

setCache(ReadOnlyCache) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Sets the cache to the passed ReadOnlyCache iff it is not null and the current cache is not set yet.

setCache(Cache) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Sets the cache to the passed cache.

setCache(Cache) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Sets the cache to the passed cache.

setCache(Cache) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Sets the cache to the passed cache.

setCollection(String) - Method in class com.petpet.c3po.api.model.ActionLog

setCollection(String) - Method in class com.petpet.c3po.api.model.Element

setCollection(String) - Method in class com.petpet.c3po.parameters.ExportParams

setCollection(String) - Method in class com.petpet.c3po.parameters.GatherParams

setCollection(String) - Method in class com.petpet.c3po.parameters.ProfileParams

setCollection(String) - Method in class com.petpet.c3po.parameters.RemoveParams

setCollection(String) - Method in class com.petpet.c3po.parameters.SamplesParams

setConditions(List<FilterCondition>) - Method in class com.petpet.c3po.api.model.helper.Filter

setConfig(Map<String, String>) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Sets the configuration of this adaptor iff the given config is not null and the current config is not set yet..

setConfig(Map<String, String>) - Method in interface com.petpet.c3po.api.gatherer.MetaDataGatherer

Some gatherer specific configuration.

setConfig(Map<String, String>) - Method in class com.petpet.c3po.gatherer.LocalFileGatherer

Some gatherer specific configuration.

setCount(long) - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

setDate(Date) - Method in class com.petpet.c3po.api.model.ActionLog

setFilter(Filter) - Method in class com.petpet.c3po.analysis.RepresentativeGenerator

setGatherer(MetaDataGatherer) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Sets the gatherer to the passed MetaDataGatherer iff it is not null.

setGatherLock(Object) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Sets the object on which to synchronize with the gatherer.

setHOperator(BetweenFilterCondition.Operator) - Method in class com.petpet.c3po.api.model.helper.BetweenFilterCondition

setHValue(Object) - Method in class com.petpet.c3po.api.model.helper.BetweenFilterCondition

setId(String) - Method in class com.petpet.c3po.api.model.Element

setId(String) - Method in class com.petpet.c3po.api.model.Property

setId(String) - Method in class com.petpet.c3po.api.model.Source

setIdentityStatus(String) - Method in class com.petpet.c3po.adaptor.fits.DigesterContext

Sets the status of the identity to the given status, if it is not null.

setIncludeElements(boolean) - Method in class com.petpet.c3po.parameters.ProfileParams

setKey(String) - Method in class com.petpet.c3po.api.model.Property

setLocation(String) - Method in class com.petpet.c3po.parameters.ExportParams

setLocation(String) - Method in class com.petpet.c3po.parameters.GatherParams

setLocation(String) - Method in class com.petpet.c3po.parameters.ProfileParams

setLocation(String) - Method in class com.petpet.c3po.parameters.SamplesParams

setLOperator(BetweenFilterCondition.Operator) - Method in class com.petpet.c3po.api.model.helper.BetweenFilterCondition

setLValue(Object) - Method in class com.petpet.c3po.api.model.helper.BetweenFilterCondition

setMax(double) - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

setMetadata(List<MetadataRecord>) - Method in class com.petpet.c3po.api.model.Element

setMin(double) - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

setName(String) - Method in class com.petpet.c3po.api.model.Element

setName(String) - Method in class com.petpet.c3po.api.model.Source

setOptions(Map<String, Object>) - Method in class com.petpet.c3po.analysis.RepresentativeGenerator

setParams(Params) - Method in interface com.petpet.c3po.command.Command

Sets the parameter for the command (that were passed on the command line).

setParams(Params) - Method in class com.petpet.c3po.command.ExportCommand

setParams(Params) - Method in class com.petpet.c3po.command.GatherCommand

setParams(Params) - Method in class com.petpet.c3po.command.HelpCommand

setParams(Params) - Method in class com.petpet.c3po.command.ProfileCommand

setParams(Params) - Method in class com.petpet.c3po.command.RemoveCommand

setParams(Params) - Method in class com.petpet.c3po.command.SamplesCommand

setParams(Params) - Method in class com.petpet.c3po.command.VersionCommand

setPersistence(PersistenceLayer) - Method in class com.petpet.c3po.dao.DBCache

Sets the persistence layer

setProperties(List<String>) - Method in class com.petpet.c3po.parameters.ProfileParams

setProperties(List<String>) - Method in class com.petpet.c3po.parameters.SamplesParams

setProperty(String) - Method in class com.petpet.c3po.api.model.helper.FilterCondition

setProperty(Property) - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

setQueue(Queue<Element>) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Sets the elements queue to the given queue, iff it is not null and the current queue is not set yet.

setReadOnlyCache(ReadOnlyCache) - Method in class com.petpet.c3po.adaptor.rules.InferDateFromFileNameRule

setRecursive(boolean) - Method in class com.petpet.c3po.parameters.GatherParams

setRules(List<ProcessingRule>) - Method in class com.petpet.c3po.api.adaptor.AbstractAdaptor

Sets the processing rules to the given rules iff they are not null and the current list is not set yet.

setRunning(boolean) - Method in class com.petpet.c3po.controller.Consolidator

setSize(int) - Method in class com.petpet.c3po.parameters.ProfileParams

setSize(int) - Method in class com.petpet.c3po.parameters.SamplesParams

setSources(List<String>) - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

setStandardDeviation(double) - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

setStatus(String) - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

setSum(double) - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

setTime(long) - Method in class com.petpet.c3po.command.AbstractCLICommand

setType(String) - Method in class com.petpet.c3po.api.model.Property

setType(String) - Method in class com.petpet.c3po.parameters.GatherParams

setUid(String) - Method in class com.petpet.c3po.api.model.Element

setValue(Object) - Method in class com.petpet.c3po.api.model.helper.FilterCondition

setValue(String) - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

setValues(List<String>) - Method in class com.petpet.c3po.api.model.helper.MetadataRecord

setVariance(double) - Method in class com.petpet.c3po.api.model.helper.NumericStatistics

setVersion(String) - Method in class com.petpet.c3po.api.model.Source

shouldSkip(String, String, String, String, String) - Method in class com.petpet.c3po.adaptor.rules.EmptyValueProcessingRule

Skips the empty values.

shouldSkip(String, String, String, String, String) - Method in class com.petpet.c3po.adaptor.rules.HtmlInfoProcessingRule

Skips the value if the property is not a valid html tag.

shouldSkip(String, String, String, String, String) - Method in interface com.petpet.c3po.api.adaptor.PreProcessingRule

Returns true if the property and value should be skipped for some reason.

SizeRepresentativeGenerator - Class in com.petpet.c3po.analysis

The size representative generator is a strategy for selecting samples based on size.

SizeRepresentativeGenerator() - Constructor for class com.petpet.c3po.analysis.SizeRepresentativeGenerator

Creates the generator.

Source - Class in com.petpet.c3po.api.model

The source represents a tool that has extracted specific measurements of elements.

Source() - Constructor for class com.petpet.c3po.api.model.Source

A default constructor.

Source(String, String) - Constructor for class com.petpet.c3po.api.model.Source

Creates a new source with the name and the version and auto generates an id.

subFilter(String...) - Method in class com.petpet.c3po.api.model.helper.Filter

Create a new filter that contains only the FilterCondition objects that are part of the fields array.

SystematicSamplingRepresentativeGenerator - Class in com.petpet.c3po.analysis

Systematic sampling generator selects samples on random in a fair fashion.

SystematicSamplingRepresentativeGenerator() - Constructor for class com.petpet.c3po.analysis.SystematicSamplingRepresentativeGenerator

Creates the generator.

T

tail(String[]) - Static method in class com.petpet.c3po.adaptor.tika.TIKAResultParser

TIKAAdaptor - Class in com.petpet.c3po.adaptor.tika

A C3PO adaptor for RAW Apache TIKA output.

TIKAAdaptor() - Constructor for class com.petpet.c3po.adaptor.tika.TIKAAdaptor

TIKAHelper - Class in com.petpet.c3po.adaptor.tika

A simple TIKA helper that maps the tika properties to c3po properties.

TIKAHelper() - Constructor for class com.petpet.c3po.adaptor.tika.TIKAHelper

TIKAResultParser - Class in com.petpet.c3po.adaptor.tika

A TIKA Result parser.

TIKAResultParser() - Constructor for class com.petpet.c3po.adaptor.tika.TIKAResultParser

U

update(T, Filter) - Method in interface com.petpet.c3po.api.dao.PersistenceLayer

Inserts or updates the given object to the underlying data store.

update(T, Filter) - Method in class com.petpet.c3po.dao.DefaultPersistenceLayer

Inserts or updates the given object to the underlying data store.

update(T, Filter) - Method in class com.petpet.c3po.dao.mongo.MongoPersistenceLayer

Inserts or updates all objects that correspond to the given filter.

UPDATED_ACTION - Static variable in class com.petpet.c3po.api.model.ActionLog

A constant denoting that the last action over a collection has changed the collection and might have changed the results of any cached data for this collection.

USER_PROPERTIES - Static variable in class com.petpet.c3po.utils.Configurator

The user specified configuration file path.

V

validate(String, String) - Method in class com.petpet.c3po.parameters.validation.EmptyStringValidator

validate(String, String) - Method in class com.petpet.c3po.parameters.validation.InputTypeValidator

validate(String, String) - Method in class com.petpet.c3po.parameters.validation.SampleAlgorithmValidator

validate(String, Integer) - Method in class com.petpet.c3po.parameters.validation.SampleSizeValidator

validate(File) - Static method in class com.petpet.c3po.utils.XMLUtils

valueOf(String) - Static method in enum com.petpet.c3po.api.model.helper.BetweenFilterCondition.Operator

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.petpet.c3po.api.model.helper.MetadataRecord.Status

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.petpet.c3po.api.model.helper.PropertyType

Returns the enum constant of this type with the specified name.

values() - Static method in enum com.petpet.c3po.api.model.helper.BetweenFilterCondition.Operator

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.petpet.c3po.api.model.helper.MetadataRecord.Status

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.petpet.c3po.api.model.helper.PropertyType

Returns an array containing the constants of this enum type, in the order they are declared.

VERSION - Static variable in class com.petpet.c3po.C3PO

The version of the command line interface.

VersionCommand - Class in com.petpet.c3po.command

Prints the version information of c3po.

VersionCommand() - Constructor for class com.petpet.c3po.command.VersionCommand

W

write(String) - Method in class com.petpet.c3po.analysis.ProfileGenerator

writes the xml string to a local folder 'profiles' in a file called output.xml.

write(Document) - Method in class com.petpet.c3po.analysis.ProfileGenerator

Writes the xml document to a local 'profiles' folder.

write(Document, String) - Method in class com.petpet.c3po.analysis.ProfileGenerator

Writes the given document to the given path.

X

XML_SCHEMA_LANGUAGE - Static variable in class com.petpet.c3po.common.Constants

The url for the xml schema language used by the sax parser while validating xml files against their schemata.

XML_SCHEMA_PROPERTY - Static variable in class com.petpet.c3po.common.Constants

The url for the xml schema property used by the sax parser while validating xml files against their schemata.

XMLUtils - Class in com.petpet.c3po.utils

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