Session (nextflow 19.11.0-edge API)

nextflow.Session

All Implemented Interfaces and Traits:

nextflow.ISession
```
@groovy.util.logging.Slf4j
@groovy.transform.CompileStatic
class Session
extends java.lang.Object
```
Holds the information on the current execution
Authors:
Paolo Di Tommaso

Properties Summary

Properties
Type	Name and description
`java.util.Collection<groovyx.gpars.dataflow.operator.DataflowProcessor>`	`allOperators` Keep a list of all processor created
`boolean`	`ansiLog`
`AnsiLogObserver`	`ansiLogObserver`
`java.nio.file.Path`	`baseDir` The folder where the main script is contained
`ScriptBinding`	`binding` Script binding
`ScriptBinding`	`binding`
`java.nio.file.Path`	`bucketDir` Bucket work directory for cloud based executors
`boolean`	`cacheable` Enable / disable tasks result caching
`java.lang.String`	`commandLine`
`java.util.Map`	`config` Holds the configuration object
`java.util.List<java.nio.file.Path>`	`configFiles` List files that concurrent on the session configuration
`ExecutorFactory`	`executorFactory` Creates process executors
`java.util.List<groovy.lang.Closure>`	`igniters`
`java.util.List<java.nio.file.Path>`	`libDir` Folder(s) containing libs and classes to be added to the classpath
`java.lang.String`	`libDir`
`java.lang.String`	`profile`
`java.lang.String`	`resolvedConfig`
`boolean`	`resumeMode` whenever it has been launched in resume mode
`java.lang.String`	`runName` Mnemonic name of this run instance
`BaseScript`	`script` The main script object
`java.lang.String`	`scriptName` The pipeline script name (without parent path)
`java.nio.file.Path`	`workDir` The folder where tasks temporary files are stored

Constructor Summary

Constructors
Constructor and description
`Session ()` Creates a new session with an 'empty' (default) configuration
`Session (java.util.Map obj)` Create a new session given the configuration specified

Methods Summary

Methods
Type Params	Return Type	Name and description
	`void`	`abort(java.lang.Throwable cause = null)` Terminate the pipeline execution killing all running tasks
	`void`	`addIgniter(groovy.lang.Closure action)`
	`void`	`await()` Await the termination of all processors
	`protected boolean`	`checkValidProcessName(java.util.Collection<java.lang.String> processNames, java.lang.String selector, java.util.List<java.lang.String> errorMessage)` Check that the specified name belongs to the list of existing process names
	`void`	`cleanup()` Delete the workflow work directory from tasks temporary files
	`void`	`destroy()`
	`java.lang.String`	`dumpNetworkStatus()` Dump the current dataflow network listing the status of active processes and operators for debugging purpose
	`void`	`fault(TaskFault fault, TaskHandler handler = null)` Halt the pipeline execution choosing exiting immediately or completing current pending task depending the chosen ErrorStrategy
	`java.lang.Object`	`fetchContainers()`
	`protected java.util.Map<java.lang.String, java.nio.file.Path>`	`findBinEntries(java.nio.file.Path path)`
	`void`	`fireDataflowNetwork()`
	`Barrier`	`getBarrier()`
	`java.nio.file.Path`	`getBinDir()` The folder where script binaries file are located, by default the folder 'bin' in the script base directory
	`java.util.Map<java.lang.String, java.nio.file.Path>`	`getBinEntries()`
	`ScriptBinding`	`getBinding()`
	`CacheDB`	`getCache()`
	`java.lang.ClassLoader`	`getClassLoader()`
	`java.nio.file.Path`	`getClassesDir()`
	`java.lang.Object`	`getConfigAttribute(java.lang.String name, java.lang.Object defValue)`
	`java.util.Map`	`getConfigEnv()`
	`ContainerConfig`	`getContainerConfig()` @return A ContainerConfig object representing the container engine configuration defined in config object
	`DAG`	`getDag()`
	`java.util.List<java.lang.String>`	`getDumpChannels()`
	`boolean`	`getDumpHashes()`
	`java.lang.Throwable`	`getError()`
	`java.lang.Object`	`getExecConfigProp(java.lang.String execName, java.lang.String name, java.lang.Object defValue, java.util.Map env = null )`
	`java.util.concurrent.ExecutorService`	`getExecService()`
	`nextflow.util.Duration`	`getExitReadTimeout(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('90sec')` Determines how long the executors waits before return an error status when a process is terminated but the exit file does not exist or it is empty.
	`TaskFault`	`getFault()`
	`FilePorter`	`getFilePorter()`
	`java.util.concurrent.ExecutorService`	`getFileTransferThreadPool()`
	`java.util.List<java.nio.file.Path>`	`getLibDir()`
	`Manifest`	`getManifest()`
	`nextflow.util.Duration`	`getMonitorDumpInterval(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('5min')` Determines how often the executor status is written in the application log file
	`ParamsMap`	`getParams()`
	`nextflow.util.Duration`	`getPollInterval(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('1sec')` Determines how often a poll occurs to check for a process termination
	`int`	`getPoolSize()` @return The session max number of thread allowed
	`int`	`getQueueSize(java.lang.String execName, int defValue)` Defines the number of tasks the executor will handle in a parallel manner
	`nextflow.util.Duration`	`getQueueStatInterval(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('1min')` Determines how often the queue status is fetched from the cluster system.
	`boolean`	`getStatsEnabled()`
	`protected java.util.Map<java.lang.String, java.lang.String>`	`getSystemEnv()`
	`java.util.UUID`	`getUniqueId()` @return The current session java.util.UUID
	`WorkflowMetadata`	`getWorkflowMetadata()`
	`WorkflowStats`	`getWorkflowStats()`
	`Session`	`init(ScriptFile scriptFile, java.util.List<java.lang.String> args = null )` Initialize the session workDir, libDir, baseDir and scriptName variables
	`boolean`	`isAborted()`
	`boolean`	`isCancelled()`
	`boolean`	`isSuccess()`
	`boolean`	`isTerminated()`
	`ProcessFactory`	`newProcessFactory(BaseScript script)`
	`void`	`notifyAfterWorkflowExecution()`
	`void`	`notifyBeforeWorkflowExecution()`
	`void`	`notifyError(TaskHandler handler)` Notify a task failure
	`void`	`notifyFlowBegin()`
	`void`	`notifyFlowComplete()`
	`void`	`notifyFlowInit()`
	`void`	`notifyProcessCreate(TaskProcessor process)`
	`void`	`notifyProcessTerminate(TaskProcessor process)`
	`void`	`notifyTaskCached(TaskHandler handler)`
	`void`	`notifyTaskComplete(TaskHandler handler)` Notifies task termination event
	`void`	`notifyTaskPending(TaskHandler handler)`
	`void`	`notifyTaskStart(TaskHandler handler)` Notifies task start event
	`void`	`notifyTaskSubmit(TaskHandler handler)` Notifies that a task has been submitted
	`void`	`onError(groovy.lang.Closure action)` Define the error event handler
	`void`	`onShutdown(groovy.lang.Closure shutdown)` Register a shutdown hook to close services when the session terminates
	`void`	`printConsole(java.lang.String str, boolean newLine = false)`
	`void`	`printConsole(java.nio.file.Path file)`
	`void`	`processDeregister(TaskProcessor process)`
	`void`	`processRegister(TaskProcessor process)`
	`protected java.lang.String`	`resolveClosure(java.lang.Object val)` Resolve dynamically defined attributes to the actual value
	`void`	`setBaseDir(java.nio.file.Path baseDir)`
	`Session`	`setBinding(ScriptBinding binding)`
	`void`	`setLibDir(java.lang.String str)`
	`protected void`	`shutdown0()`
	`Session`	`start()`
	`protected void`	`validate()` Check preconditions before run the main script
	`void`	`validateConfig(java.util.Collection<java.lang.String> processNames)` Validate the config file
	`protected java.util.List<java.lang.String>`	`validateConfig0(java.util.Collection<java.lang.String> processNames)`

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#wait(long, int), java.lang.Object#wait(long), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll()`

- Property Detail
  - final java.util.Collection<groovyx.gpars.dataflow.operator.DataflowProcessor> allOperators
    
    Keep a list of all processor created
  - boolean ansiLog
  - AnsiLogObserver ansiLogObserver
  - java.nio.file.Path baseDir
    
    The folder where the main script is contained
  - ScriptBinding binding
    
    Script binding
  - ScriptBinding binding
  - java.nio.file.Path bucketDir
    
    Bucket work directory for cloud based executors
  - boolean cacheable
    
    Enable / disable tasks result caching
  - java.lang.String commandLine
  - java.util.Map config
    
    Holds the configuration object
  - java.util.List<java.nio.file.Path> configFiles
    
    List files that concurrent on the session configuration
  - ExecutorFactory executorFactory
    
    Creates process executors
  - final java.util.List<groovy.lang.Closure> igniters
  - java.util.List<java.nio.file.Path> libDir
    
    Folder(s) containing libs and classes to be added to the classpath
  - java.lang.String libDir
  - java.lang.String profile
  - java.lang.String resolvedConfig
  - boolean resumeMode
    
    whenever it has been launched in resume mode
  - java.lang.String runName
    
    Mnemonic name of this run instance
  - BaseScript script
    
    The main script object
  - java.lang.String scriptName
    
    The pipeline script name (without parent path)
  - java.nio.file.Path workDir
    
    The folder where tasks temporary files are stored
- Constructor Detail
  - Session()
    
    Creates a new session with an 'empty' (default) configuration
  - Session(java.util.Map obj)
    
    Create a new session given the configuration specified
    Parameters:
    config
- Method Detail
  - void abort(java.lang.Throwable cause = null)
    
    Terminate the pipeline execution killing all running tasks
    Parameters:
    cause - A java.lang.Throwable instance representing the execution that caused the pipeline execution to abort
  - void addIgniter(groovy.lang.Closure action)
  - void await()
    
    Await the termination of all processors
  - protected boolean checkValidProcessName(java.util.Collection<java.lang.String> processNames, java.lang.String selector, java.util.List<java.lang.String> errorMessage)
    
    Check that the specified name belongs to the list of existing process names
    Parameters:
    selector - The process name to check
    processNames - The list of processes declared in the workflow script
    errorMessage - A list of strings used to return the error message to the caller
    Returns:
    true if the name specified belongs to the list of process names or false otherwise
  - void cleanup()
    
    Delete the workflow work directory from tasks temporary files
  - void destroy()
  - java.lang.String dumpNetworkStatus()
    
    Dump the current dataflow network listing the status of active processes and operators for debugging purpose
  - void fault(TaskFault fault, TaskHandler handler = null)
    
    Halt the pipeline execution choosing exiting immediately or completing current pending task depending the chosen ErrorStrategy
    Parameters:
    fault - A TaskFault instance representing the error that caused the pipeline to stop
  - @groovy.transform.CompileDynamic java.lang.Object fetchContainers()
  - protected java.util.Map<java.lang.String, java.nio.file.Path> findBinEntries(java.nio.file.Path path)
  - void fireDataflowNetwork()
  - Barrier getBarrier()
  - java.nio.file.Path getBinDir()
    
    The folder where script binaries file are located, by default the folder 'bin' in the script base directory
  - java.util.Map<java.lang.String, java.nio.file.Path> getBinEntries()
  - ScriptBinding getBinding()
  - CacheDB getCache()
  - @groovy.transform.Memoized java.lang.ClassLoader getClassLoader()
  - java.nio.file.Path getClassesDir()
  - @groovy.transform.Memoized java.lang.Object getConfigAttribute(java.lang.String name, java.lang.Object defValue)
  - java.util.Map getConfigEnv()
  - @groovy.transform.Memoized ContainerConfig getContainerConfig()
    
    Returns:
    A ContainerConfig object representing the container engine configuration defined in config object
  - DAG getDag()
  - java.util.List<java.lang.String> getDumpChannels()
  - boolean getDumpHashes()
  - java.lang.Throwable getError()
  - @groovy.transform.Memoized java.lang.Object getExecConfigProp(java.lang.String execName, java.lang.String name, java.lang.Object defValue, java.util.Map env = null )
  - java.util.concurrent.ExecutorService getExecService()
  - @groovy.transform.Memoized nextflow.util.Duration getExitReadTimeout(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('90sec')
    
    Determines how long the executors waits before return an error status when a process is terminated but the exit file does not exist or it is empty. This setting is used only by grid executors
    Parameters:
    execName - The executor name
    defValue - The default value if setting is not defined in the configuration file
    Returns:
    A Duration object. Default '90 second'
  - TaskFault getFault()
  - FilePorter getFilePorter()
  - @groovy.transform.Memoized // <-- this guarantees that the same executor is used across different publish dir in the same session @groovy.transform.CompileStatic java.util.concurrent.ExecutorService getFileTransferThreadPool()
  - java.util.List<java.nio.file.Path> getLibDir()
  - @groovy.transform.Memoized Manifest getManifest()
  - @groovy.transform.Memoized nextflow.util.Duration getMonitorDumpInterval(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('5min')
    
    Determines how often the executor status is written in the application log file
    Parameters:
    execName - The executor name
    defValue - The default value if setting is not defined in the configuration file
    Returns:
    A Duration object. Default '5 minutes'
  - ParamsMap getParams()
  - @groovy.transform.Memoized nextflow.util.Duration getPollInterval(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('1sec')
    
    Determines how often a poll occurs to check for a process termination
    Parameters:
    execName - The executor name
    defValue - The default value if setting is not defined in the configuration file
    Returns:
    A Duration object. Default '1 second'
  - int getPoolSize()
    
    Returns:
    The session max number of thread allowed
  - @groovy.transform.Memoized int getQueueSize(java.lang.String execName, int defValue)
    
    Defines the number of tasks the executor will handle in a parallel manner
    Parameters:
    execName - The executor name
    defValue - The default value if setting is not defined in the configuration file
    Returns:
    The value of tasks to handle in parallel
  - @groovy.transform.Memoized nextflow.util.Duration getQueueStatInterval(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('1min')
    
    Determines how often the queue status is fetched from the cluster system. This setting is used only by grid executors
    Parameters:
    execName - The executor name
    defValue - The default value if setting is not defined in the configuration file
    Returns:
    A Duration object. Default '1 minute'
  - boolean getStatsEnabled()
  - @groovy.transform.Memoized protected java.util.Map<java.lang.String, java.lang.String> getSystemEnv()
  - java.util.UUID getUniqueId()
    
    Returns:
    The current session java.util.UUID
  - WorkflowMetadata getWorkflowMetadata()
  - WorkflowStats getWorkflowStats()
  - Session init(ScriptFile scriptFile, java.util.List<java.lang.String> args = null )
    
    Initialize the session workDir, libDir, baseDir and scriptName variables
  - boolean isAborted()
  - boolean isCancelled()
  - boolean isSuccess()
  - boolean isTerminated()
  - ProcessFactory newProcessFactory(BaseScript script)
  - void notifyAfterWorkflowExecution()
  - void notifyBeforeWorkflowExecution()
  - void notifyError(TaskHandler handler)
    
    Notify a task failure
    Parameters:
    handler
    e
  - void notifyFlowBegin()
  - void notifyFlowComplete()
  - void notifyFlowInit()
  - void notifyProcessCreate(TaskProcessor process)
  - void notifyProcessTerminate(TaskProcessor process)
  - void notifyTaskCached(TaskHandler handler)
  - void notifyTaskComplete(TaskHandler handler)
    
    Notifies task termination event
    Parameters:
    handler
  - void notifyTaskPending(TaskHandler handler)
  - void notifyTaskStart(TaskHandler handler)
    
    Notifies task start event
  - void notifyTaskSubmit(TaskHandler handler)
    
    Notifies that a task has been submitted
  - void onError(groovy.lang.Closure action)
    
    Define the error event handler
    Parameters:
    action
  - void onShutdown(groovy.lang.Closure shutdown)
    
    Register a shutdown hook to close services when the session terminates
    Parameters:
    Closure
  - void printConsole(java.lang.String str, boolean newLine = false)
  - void printConsole(java.nio.file.Path file)
  - void processDeregister(TaskProcessor process)
  - void processRegister(TaskProcessor process)
  - protected java.lang.String resolveClosure(java.lang.Object val)
    
    Resolve dynamically defined attributes to the actual value
    Parameters:
    val - A process container definition either a plain string or a closure
    Returns:
    The actual container value
  - void setBaseDir(java.nio.file.Path baseDir)
  - Session setBinding(ScriptBinding binding)
  - void setLibDir(java.lang.String str)
  - protected final void shutdown0()
  - Session start()
  - protected void validate()
    
    Check preconditions before run the main script
  - void validateConfig(java.util.Collection<java.lang.String> processNames)
    
    Validate the config file
    Parameters:
    processNames - The list of process names defined in the pipeline script
  - protected java.util.List<java.lang.String> validateConfig0(java.util.Collection<java.lang.String> processNames)

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation

[Groovy] Class Session

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Property Detail

final java.util.Collection<groovyx.gpars.dataflow.operator.DataflowProcessor> allOperators

boolean ansiLog

AnsiLogObserver ansiLogObserver

java.nio.file.Path baseDir

ScriptBinding binding

ScriptBinding binding

java.nio.file.Path bucketDir

boolean cacheable

java.lang.String commandLine

java.util.Map config

java.util.List<java.nio.file.Path> configFiles

ExecutorFactory executorFactory

final java.util.List<groovy.lang.Closure> igniters

java.util.List<java.nio.file.Path> libDir

java.lang.String libDir

java.lang.String profile

java.lang.String resolvedConfig

boolean resumeMode

java.lang.String runName

BaseScript script

java.lang.String scriptName

java.nio.file.Path workDir

Constructor Detail

Session()

Session(java.util.Map obj)

Method Detail

void abort(java.lang.Throwable cause = null)

void addIgniter(groovy.lang.Closure action)

void await()

protected boolean checkValidProcessName(java.util.Collection<java.lang.String> processNames, java.lang.String selector, java.util.List<java.lang.String> errorMessage)

void cleanup()

void destroy()

java.lang.String dumpNetworkStatus()

void fault(TaskFault fault, TaskHandler handler = null)

@groovy.transform.CompileDynamic java.lang.Object fetchContainers()

protected java.util.Map<java.lang.String, java.nio.file.Path> findBinEntries(java.nio.file.Path path)

void fireDataflowNetwork()

Barrier getBarrier()

java.nio.file.Path getBinDir()

java.util.Map<java.lang.String, java.nio.file.Path> getBinEntries()

ScriptBinding getBinding()

CacheDB getCache()

@groovy.transform.Memoized java.lang.ClassLoader getClassLoader()

java.nio.file.Path getClassesDir()

@groovy.transform.Memoized java.lang.Object getConfigAttribute(java.lang.String name, java.lang.Object defValue)

java.util.Map getConfigEnv()

@groovy.transform.Memoized ContainerConfig getContainerConfig()

DAG getDag()

java.util.List<java.lang.String> getDumpChannels()

boolean getDumpHashes()

java.lang.Throwable getError()

@groovy.transform.Memoized java.lang.Object getExecConfigProp(java.lang.String execName, java.lang.String name, java.lang.Object defValue, java.util.Map env = null )

java.util.concurrent.ExecutorService getExecService()

@groovy.transform.Memoized nextflow.util.Duration getExitReadTimeout(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('90sec')

TaskFault getFault()

FilePorter getFilePorter()

@groovy.transform.Memoized // <-- this guarantees that the same executor is used across different publish dir in the same session @groovy.transform.CompileStatic java.util.concurrent.ExecutorService getFileTransferThreadPool()

java.util.List<java.nio.file.Path> getLibDir()

@groovy.transform.Memoized Manifest getManifest()

@groovy.transform.Memoized nextflow.util.Duration getMonitorDumpInterval(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('5min')

ParamsMap getParams()

@groovy.transform.Memoized nextflow.util.Duration getPollInterval(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('1sec')

int getPoolSize()

@groovy.transform.Memoized int getQueueSize(java.lang.String execName, int defValue)

@groovy.transform.Memoized nextflow.util.Duration getQueueStatInterval(java.lang.String execName, nextflow.util.Duration defValue = Duration.of('1min')

boolean getStatsEnabled()

@groovy.transform.Memoized protected java.util.Map<java.lang.String, java.lang.String> getSystemEnv()

java.util.UUID getUniqueId()

WorkflowMetadata getWorkflowMetadata()

WorkflowStats getWorkflowStats()

Session init(ScriptFile scriptFile, java.util.List<java.lang.String> args = null )

boolean isAborted()

boolean isCancelled()

boolean isSuccess()