Serialized Form

Package fr.ens.biologie.genomique.eoulsan

Error fr.ens.biologie.genomique.eoulsan.EoulsanError

class EoulsanError extends Error implements Serializable

serialVersionUID:

-8816286109335295387L

Exception fr.ens.biologie.genomique.eoulsan.EoulsanException

class EoulsanException extends Exception implements Serializable

serialVersionUID:

7021095498629981700L

Exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException

class EoulsanITRuntimeException extends EoulsanRuntimeException implements Serializable

serialVersionUID:

-1897738767737351557L

Exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException

class EoulsanRuntimeException extends RuntimeException implements Serializable

serialVersionUID:

4568739390687951448L

Class fr.ens.biologie.genomique.eoulsan.Settings

class Settings extends Object implements Serializable

serialVersionUID:

-7897805708866950402L

Serialized Fields

properties

Properties properties

Package fr.ens.biologie.genomique.eoulsan.checkers

Class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker

class DESeq2DesignChecker extends Object implements Serializable

serialVersionUID:

-7079642248159153890L

Package fr.ens.biologie.genomique.eoulsan.core

Class fr.ens.biologie.genomique.eoulsan.core.AbstractPort

class AbstractPort extends Object implements Serializable

serialVersionUID:

1773398938012180465L

Serialized Fields

format

DataFormat format

list

boolean list

name

String name

Class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts

class AbstractPorts extends Object implements Serializable

serialVersionUID:

-5116830881426447140L

Serialized Fields

ports

Map<String,E extends Port> ports

Exception fr.ens.biologie.genomique.eoulsan.core.FileNamingParsingRuntimeException

class FileNamingParsingRuntimeException extends RuntimeException implements Serializable

serialVersionUID:

7857462649825953398L

Class fr.ens.biologie.genomique.eoulsan.core.Parameter

class Parameter extends Object implements Serializable

serialVersionUID:

-3788321419921821433L

Serialized Fields

name

String name

value

String value

Class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort

class SimpleInputPort extends AbstractPort implements Serializable

serialVersionUID:

4663590179211976634L

Serialized Fields

compressionsAccepted

EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> compressionsAccepted

requiredInWorkingDirectory

boolean requiredInWorkingDirectory

Class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPorts

class SimpleInputPorts extends AbstractPorts<InputPort> implements Serializable

serialVersionUID:

-6661589274392547355L

Class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort

class SimpleOutputPort extends AbstractPort implements Serializable

serialVersionUID:

3565485272173523695L

Serialized Fields

compression

fr.ens.biologie.genomique.kenetre.io.CompressionType compression

Class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPorts

class SimpleOutputPorts extends AbstractPorts<OutputPort> implements Serializable

serialVersionUID:

-1607044916452828888L

Package fr.ens.biologie.genomique.eoulsan.core.workflow

Class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep

class AbstractStep extends Object implements Serializable

serialVersionUID:

2040628014465126384L

Serialized Fields

checker

Checker checker

createLogFiles

boolean createLogFiles

dataProduct

fr.ens.biologie.genomique.eoulsan.core.workflow.DataProduct dataProduct

dataProductConfiguration

String dataProductConfiguration

discardOutput

Step.DiscardOutput discardOutput

id

String id

inputPorts

fr.ens.biologie.genomique.eoulsan.core.workflow.StepInputPorts inputPorts

inputPortsParameter

InputPorts inputPortsParameter

mode

ExecutionMode mode

moduleName

String moduleName

number

int number

outputDir

DataFile outputDir

outputPorts

fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPorts outputPorts

outputPortsParameter

OutputPorts outputPortsParameter

parallelizationMode

ParallelizationMode parallelizationMode

parameters

Set<Parameter> parameters

requiredMemory

int requiredMemory

requiredProcessors

int requiredProcessors

skip

boolean skip

stepStateDependencies

StepStateDependencies stepStateDependencies

terminalStep

boolean terminalStep

type

Step.StepType type

version

String version

workflow

AbstractWorkflow workflow

Class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow

class AbstractWorkflow extends Object implements Serializable

serialVersionUID:

4865597995432347155L

Serialization Methods

writeObject

private void writeObject(ObjectOutputStream s)
                  throws IOException

Throws:

IOException

Serialized Fields

checkerStep

AbstractStep checkerStep

dataDir

DataFile dataDir

deleteOnExitFiles

Set<DataFile> deleteOnExitFiles

design

Design design

designStep

AbstractStep designStep

firstStep

AbstractStep firstStep

hadoopWorkingDir

DataFile hadoopWorkingDir

jobDir

DataFile jobDir

localWorkingDir

DataFile localWorkingDir

outputDir

DataFile outputDir

rootStep

AbstractStep rootStep

shutdownNow

boolean shutdownNow

states

com.google.common.collect.Multimap<Step.StepState,AbstractStep> states

stepIds

Set<String> stepIds

steps

Map<AbstractStep,Step.StepState> steps

stopwatch

SerializableStopwatch stopwatch

taskDir

DataFile taskDir

tmpDir

DataFile tmpDir

workflowContext

WorkflowContext workflowContext

Class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep

class CommandStep extends AbstractStep implements Serializable

serialVersionUID:

-1736197317540226070L

Class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflow

class CommandWorkflow extends AbstractWorkflow implements Serializable

serialVersionUID:

4132064673361068654L

Serialized Fields

steps

List<CommandStep> steps

stepsIds

Set<String> stepsIds

workflowCommand

CommandWorkflowModel workflowCommand

Class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel

class CommandWorkflowModel extends Object implements Serializable

serialVersionUID:

-5182569666862886788L

Serialized Fields

author

String author

description

String description

globalParameters

Set<Parameter> globalParameters

moduleNames

Map<String,String> moduleNames

name

String name

stepDataProduct

Map<String,String> stepDataProduct

stepDiscardOutput

Map<String,Step.DiscardOutput> stepDiscardOutput

stepIdList

List<String> stepIdList

stepInputs

Map<String,Map<String,fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel.StepPort>> stepInputs

stepParameters

Map<String,Set<Parameter>> stepParameters

stepRequiredMemory

Map<String,Integer> stepRequiredMemory

stepRequiredProcessors

Map<String,Integer> stepRequiredProcessors

stepSkipped

Map<String,Boolean> stepSkipped

stepVersions

Map<String,String> stepVersions

Class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList

class DataList extends fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractData implements Serializable

serialVersionUID:

-2933515018143805029L

Serialized Fields

design

Design design

list

List<Data> list

port

fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port

Class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch

class SerializableStopwatch extends Object implements Serializable

serialVersionUID:

75544289032075405L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream s)
                  throws IOException

Throws:

IOException

Serialized Fields

stopWatch

fr.ens.biologie.genomique.eoulsan.core.workflow.Stopwatch stopWatch

Class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies

class StepStateDependencies extends Object implements Serializable

serialVersionUID:

3290646225243643382L

Serialized Fields

dependenciesDone

Map<Integer,Boolean> dependenciesDone

noInput

boolean noInput

requiredSteps

Set<AbstractStep> requiredSteps

step

AbstractStep step

stepState

Step.StepState stepState

Class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl

class TaskContextImpl extends Object implements Serializable

serialVersionUID:

8288158811122533646L

Serialized Fields

contextName

String contextName

id

int id

inputData

Map<String,Data> inputData

outputData

Map<String,fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractData> outputData

step

AbstractStep step

workflowContext

WorkflowContext workflowContext

Class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl

class TaskResultImpl extends Object implements Serializable

serialVersionUID:

-1698693204391020077L

Serialized Fields

context

TaskContextImpl context

counters

Map<String,Long> counters

duration

long duration

endTime

Instant endTime

errorMessage

String errorMessage

exception

Throwable exception

startTime

Instant startTime

success

boolean success

taskCommandLine

String taskCommandLine

taskDescription

String taskDescription

taskDockerImage

String taskDockerImage

taskMessage

String taskMessage

Class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData

class UnmodifiableData extends Object implements Serializable

serialVersionUID:

-7754468478398255288L

Serialized Fields

data

Data data

Class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext

class WorkflowContext extends Object implements Serializable

serialVersionUID:

-260344001954382358L

Serialized Fields

commandAuthor

String commandAuthor

commandDescription

String commandDescription

commandName

String commandName

contextCreationTime

long contextCreationTime

designFile

DataFile designFile

host

String host

jarFile

DataFile jarFile

jobDescription

String jobDescription

jobEnvironment

String jobEnvironment

jobId

String jobId

jobUUID

String jobUUID

workflow

AbstractWorkflow workflow

workflowFile

DataFile workflowFile

Package fr.ens.biologie.genomique.eoulsan.data

Class fr.ens.biologie.genomique.eoulsan.data.DataFile

class DataFile extends Object implements Serializable

serialVersionUID:

-3280343485491150872L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Deserialize the object.

Parameters:

in - the object input stream

Throws:

IOException - if an error occurs while deserializing the object

ClassNotFoundException - if class not found while deserializing the object

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Serialize the object.

Parameters:

out - the object output stream

Throws:

IOException - if an error occurs while serializing the object

Serialized Fields

md

DataFileMetadata md

name

String name

protocol

DataProtocol protocol

protocolPrefixInSource

String protocolPrefixInSource

src

String src

unknownProtocolName

String unknownProtocolName

Class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat

class MapperIndexDataFormat extends fr.ens.biologie.genomique.eoulsan.data.AbstractDataFormat implements Serializable

serialVersionUID:

-943794645213547885L

Serialized Fields

formatName

String formatName

mapperName

String mapperName

prefix

String prefix

Class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat

class XMLDataFormat extends fr.ens.biologie.genomique.eoulsan.data.AbstractDataFormat implements Serializable

serialVersionUID:

-6926659317643003910L

Serialized Fields

alias

String alias

checkerClassName

String checkerClassName

contentType

String contentType

dataFormatFromDesignFile

boolean dataFormatFromDesignFile

description

String description

designMetadataKeyName

String designMetadataKeyName

extensions

List<String> extensions

galaxyFormatNames

List<String> galaxyFormatNames

generatorClassName

String generatorClassName

generatorParameters

Set<Parameter> generatorParameters

maxFilesCount

int maxFilesCount

mergerClassName

String mergerClassName

name

String name

oneFilePerAnalysis

boolean oneFilePerAnalysis

prefix

String prefix

sampleMetadataKeyName

String sampleMetadataKeyName

splitterClassName

String splitterClassName

Package fr.ens.biologie.genomique.eoulsan.design

Class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata

class AbstractMetadata extends Object implements Serializable

serialVersionUID:

5756414666624839231L

Serialized Fields

metadata

Map<String,String> metadata

Class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl

class DesignMetadataImpl extends AbstractMetadata implements Serializable

serialVersionUID:

-2481571646937449716L

Class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl

class ExperimentImpl extends Object implements Serializable

serialVersionUID:

-2644491674956956116L

Serialized Fields

design

Design design

experimentId

String experimentId

experimentName

String experimentName

experimentNumber

int experimentNumber

metadata

fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadataImpl metadata

sampleNames

Set<String> sampleNames

samples

List<ExperimentSample> samples

Class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl

class ExperimentSampleImpl extends Object implements Serializable

serialVersionUID:

-3180171254543892681L

Serialized Fields

metadata

ExperimentSampleMetadataImpl metadata

sample

Sample sample

Class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl

class ExperimentSampleMetadataImpl extends AbstractMetadata implements Serializable

serialVersionUID:

4079804296437126108L

Class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment

class UnmodifiableExperiment extends Object implements Serializable

serialVersionUID:

2564230655661740901L

Serialized Fields

experiment

Experiment experiment

Class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata

class UnmodifiableExperimentMetadata extends Object implements Serializable

serialVersionUID:

-426306838693570333L

Serialized Fields

md

ExperimentMetadata md

Class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata

class UnmodifiableExperimentSampleMetadata extends Object implements Serializable

serialVersionUID:

2441285392336371023L

Serialized Fields

md

ExperimentSampleMetadata md

Package fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop

Exception fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp.DuplicationException

class DuplicationException extends IOException implements Serializable

serialVersionUID:

1L

Package fr.ens.biologie.genomique.eoulsan.util

Class fr.ens.biologie.genomique.eoulsan.util.EnhancedBloomFilter

class EnhancedBloomFilter extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

addedNumberOfElements

int addedNumberOfElements

bf

com.google.common.hash.BloomFilter<String> bf

expectedNumberOfElements

int expectedNumberOfElements

falsePositiveProbability

double falsePositiveProbability

Package fr.ens.biologie.genomique.eoulsan.util.locker

Class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket

class Ticket extends Object implements Serializable

serialVersionUID:

-7934169474677708526L

Serialized Fields

creationTime

long creationTime

description

String description

lastActiveTime

long lastActiveTime

nanoCreationTime

long nanoCreationTime

pid

int pid

threadId

long threadId

working

boolean working