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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
/*
* Copyright 2013-2024, Seqera Labs
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package nextflow.processor
import nextflow.trace.TraceRecord
import static nextflow.processor.ErrorStrategy.*
import java.lang.reflect.InvocationTargetException
import java.nio.file.FileSystems
import java.nio.file.LinkOption
import java.nio.file.NoSuchFileException
import java.nio.file.Path
import java.nio.file.Paths
import java.util.concurrent.atomic.AtomicBoolean
import java.util.concurrent.atomic.AtomicInteger
import java.util.concurrent.atomic.AtomicIntegerArray
import java.util.concurrent.atomic.LongAdder
import java.util.regex.Matcher
import java.util.regex.Pattern
import ch.artecat.grengine.Grengine
import com.google.common.hash.HashCode
import groovy.json.JsonOutput
import groovy.transform.CompileStatic
import groovy.transform.Memoized
import groovy.transform.PackageScope
import groovy.util.logging.Slf4j
import groovyx.gpars.agent.Agent
import groovyx.gpars.dataflow.Dataflow
import groovyx.gpars.dataflow.DataflowQueue
import groovyx.gpars.dataflow.DataflowReadChannel
import groovyx.gpars.dataflow.DataflowWriteChannel
import groovyx.gpars.dataflow.expression.DataflowExpression
import groovyx.gpars.dataflow.operator.DataflowEventAdapter
import groovyx.gpars.dataflow.operator.DataflowOperator
import groovyx.gpars.dataflow.operator.DataflowProcessor
import groovyx.gpars.dataflow.operator.PoisonPill
import groovyx.gpars.dataflow.stream.DataflowStreamWriteAdapter
import groovyx.gpars.group.PGroup
import nextflow.NF
import nextflow.Nextflow
import nextflow.Session
import nextflow.ast.NextflowDSLImpl
import nextflow.ast.TaskCmdXform
import nextflow.ast.TaskTemplateVarsXform
import nextflow.cloud.CloudSpotTerminationException
import nextflow.dag.NodeMarker
import nextflow.exception.FailedGuardException
import nextflow.exception.IllegalArityException
import nextflow.exception.MissingFileException
import nextflow.exception.MissingValueException
import nextflow.exception.ProcessEvalException
import nextflow.exception.ProcessException
import nextflow.exception.ProcessFailedException
import nextflow.exception.ProcessRetryableException
import nextflow.exception.ProcessSubmitTimeoutException
import nextflow.exception.ProcessUnrecoverableException
import nextflow.exception.ShowOnlyExceptionMessage
import nextflow.exception.UnexpectedException
import nextflow.executor.CachedTaskHandler
import nextflow.executor.Executor
import nextflow.executor.StoredTaskHandler
import nextflow.extension.CH
import nextflow.extension.DataflowHelper
import nextflow.file.FileHelper
import nextflow.file.FileHolder
import nextflow.file.FilePatternSplitter
import nextflow.file.FilePorter
import nextflow.plugin.Plugins
import nextflow.processor.tip.TaskTipProvider
import nextflow.script.BaseScript
import nextflow.script.BodyDef
import nextflow.script.ProcessConfig
import nextflow.script.ScriptMeta
import nextflow.script.ScriptType
import nextflow.script.bundle.ResourcesBundle
import nextflow.script.params.BaseOutParam
import nextflow.script.params.CmdEvalParam
import nextflow.script.params.DefaultOutParam
import nextflow.script.params.EachInParam
import nextflow.script.params.EnvInParam
import nextflow.script.params.EnvOutParam
import nextflow.script.params.FileInParam
import nextflow.script.params.FileOutParam
import nextflow.script.params.InParam
import nextflow.script.params.MissingParam
import nextflow.script.params.OptionalParam
import nextflow.script.params.OutParam
import nextflow.script.params.StdInParam
import nextflow.script.params.StdOutParam
import nextflow.script.params.TupleInParam
import nextflow.script.params.TupleOutParam
import nextflow.script.params.ValueInParam
import nextflow.script.params.ValueOutParam
import nextflow.util.ArrayBag
import nextflow.util.BlankSeparatedList
import nextflow.util.CacheHelper
import nextflow.util.Escape
import nextflow.util.HashBuilder
import nextflow.util.LockManager
import nextflow.util.LoggerHelper
import nextflow.util.TestOnly
import org.codehaus.groovy.control.CompilerConfiguration
import org.codehaus.groovy.control.customizers.ASTTransformationCustomizer
/**
* Implement nextflow process execution logic
*
* @author Paolo Di Tommaso
*/
@Slf4j
class TaskProcessor {
static enum RunType {
SUBMIT('Submitted process'),
RETRY('Re-submitted process')
String message;
RunType(String str) { message=str };
}
static final public String TASK_CONTEXT_PROPERTY_NAME = 'task'
final private static Pattern ENV_VAR_NAME = ~/[a-zA-Z_]+[a-zA-Z0-9_]*/
final private static Pattern QUESTION_MARK = ~/(\?+)/
@TestOnly private static volatile TaskProcessor currentProcessor0
@TestOnly static TaskProcessor currentProcessor() { currentProcessor0 }
/**
* Keeps track of the task instance executed by the current thread
*/
protected final ThreadLocal currentTask = new ThreadLocal<>()
/**
* Unique task index number (run)
*/
final protected AtomicInteger indexCount = new AtomicInteger()
/**
* The current workflow execution session
*/
protected Session session
/**
* The script object which defines this task
*/
protected BaseScript ownerScript
/**
* The processor descriptive name
*/
protected String name
/**
* The piece of code to be execute provided by the user
*/
protected BodyDef taskBody
/**
* The corresponding {@code DataflowProcessor} which will receive and
* manage accordingly the task inputs
*
* note: it must be declared volatile -- issue #41
*/
protected volatile DataflowProcessor operator
/**
* The underlying executor which will run the task
*/
protected Executor executor
/**
* The corresponding task configuration properties, it holds the inputs/outputs
* definition as well as other execution meta-declaration
*/
protected ProcessConfig config
/**
* Count the number of time an error occurred
*/
private volatile int errorCount
/**
* Set to true the very first time the error is shown.
*
* Note: it is declared static because the error must be shown only the
* very first time for all processes
*/
private static final AtomicBoolean errorShown = new AtomicBoolean()
/**
* Flag set {@code true} when the processor termination has been invoked
*
* See {@code #checkProcessTermination}
*/
protected volatile boolean completed
protected boolean allScalarValues
protected boolean hasEachParams
/**
* The state is maintained by using an agent
*/
protected Agent state
/**
* Groovy engine used to evaluate dynamic code
*/
protected Grengine grengine
/**
* Whenever the process is executed only once
*/
protected boolean singleton
/**
* Track the status of input ports. When 1 the port is open (waiting for data),
* when 0 the port is closed (ie. received the STOP signal)
*/
protected AtomicIntegerArray openPorts
/**
* Process ID number. The first is 1, the second 2 and so on ..
*/
private final int id
private LongAdder forksCount
private int maxForks
private static int processCount
private static LockManager lockManager = new LockManager()
private List> fairBuffers = new ArrayList<>()
private int currentEmission
private Boolean isFair0
private TaskArrayCollector arrayCollector
private CompilerConfiguration compilerConfig() {
final config = new CompilerConfiguration()
config.addCompilationCustomizers( new ASTTransformationCustomizer(TaskTemplateVarsXform) )
config.addCompilationCustomizers( new ASTTransformationCustomizer(TaskCmdXform) )
return config
}
@TestOnly
static void reset() {
processCount=0
errorShown.set(false)
currentProcessor0 = null
}
/*
* Initialise the process ID
*
* Note: processes are create in a sequential manner (by the main thread that parse the script)
* so it does not require a synchronized block
*/
{
id = ++processCount
grengine = session && session.classLoader ? new Grengine(session.classLoader, compilerConfig()) : new Grengine(compilerConfig())
currentProcessor0 = this
}
/* for testing purpose - do not remove */
protected TaskProcessor() { }
/**
* Create and initialize the processor object
*
* @param name
* @param executor
* @param session
* @param script
* @param config
* @param taskBody
*/
TaskProcessor(String name, Executor executor, Session session, BaseScript script, ProcessConfig config, BodyDef taskBody ) {
assert executor
assert session
assert script
assert taskBody
this.executor = executor
this.session = session
this.ownerScript = script
this.config = config
this.taskBody = taskBody
this.name = name
this.maxForks = config.maxForks && config.maxForks>0 ? config.maxForks as int : 0
this.forksCount = maxForks ? new LongAdder() : null
this.isFair0 = config.getFair()
final arraySize = config.getArray()
this.arrayCollector = arraySize > 0 ? new TaskArrayCollector(this, executor, arraySize) : null
}
/**
* @return The processor unique id
*/
int getId() { id }
/**
* @return The {@code TaskConfig} object holding the task configuration properties
*/
ProcessConfig getConfig() { config }
/**
* @return The current {@code Session} instance
*/
Session getSession() { session }
/**
* @return The processor name
*/
String getName() { name }
/**
* @return The {@link Executor} associated to this processor
*/
Executor getExecutor() { executor }
/**
* @return The {@code DataflowOperator} underlying this process
*/
DataflowProcessor getOperator() { operator }
/**
* @return The {@code BaseScript} object which represents pipeline script
*/
BaseScript getOwnerScript() { ownerScript }
/**
* Define the type of script hold by the {@code #code} property
*/
protected ScriptType getScriptType() { taskBody.type }
/**
* @return The user provided script block
*/
BodyDef getTaskBody() { taskBody }
Set getDeclaredNames() {
Set result = new HashSet<>(20)
result.addAll(config.getInputs().getNames())
result.addAll(config.getOutputs().getNames())
return result
}
LongAdder getForksCount() { forksCount }
int getMaxForks() { maxForks }
boolean hasErrors() { errorCount>0 }
@Memoized
protected TaskTipProvider getTipProvider() {
final provider = Plugins.getPriorityExtensions(TaskTipProvider).find(it-> it.enabled())
if( !provider )
throw new IllegalStateException("Unable to find any tip provider")
return provider
}
boolean isSingleton() { singleton }
/**
* Create a "preview" for a task run. This method is only meant for the creation of "mock" task run
* to allow the access for the associated {@link TaskConfig} during a pipeline "preview" execution.
*
* Note this returns an "eventually" task configuration object. Also Inputs and output parameters are NOT
* resolved by this method.
*
* @return A {@link TaskRun} object holding a reference to the associated {@link TaskConfig}
*/
TaskRun createTaskPreview() {
final task = new TaskRun(
processor: this,
type: scriptType,
config: config.createTaskConfig(),
context: new TaskContext(this)
)
task.config.context = task.context
task.config.process = task.processor.name
task.config.executor = task.processor.executor.name
return task
}
protected void checkWarn(String msg, Map opts=null) {
if( NF.isStrictMode() )
throw new ProcessUnrecoverableException(msg)
if( opts )
log.warn1(opts, msg)
else
log.warn(msg)
}
/**
* Launch the 'script' define by the code closure as a local bash script
*
* @param code A {@code Closure} returning a bash script e.g.
*
* {
* """
* #!/bin/bash
* do this ${x}
* do that ${y}
* :
* """
* }
*
* @return {@code this} instance
*/
def run() {
// -- check that the task has a body
if ( !taskBody )
throw new IllegalStateException("Missing task body for process `$name`")
// -- check that input tuple defines at least two elements
def invalidInputTuple = config.getInputs().find { it instanceof TupleInParam && it.inner.size()<2 }
if( invalidInputTuple )
checkWarn "Input `tuple` must define at least two elements -- Check process `$name`"
// -- check that output tuple defines at least two elements
def invalidOutputTuple = config.getOutputs().find { it instanceof TupleOutParam && it.inner.size()<2 }
if( invalidOutputTuple )
checkWarn "Output `tuple` must define at least two elements -- Check process `$name`"
/**
* Verify if this process run only one time
*/
allScalarValues = config.getInputs().allScalarInputs()
hasEachParams = config.getInputs().any { it instanceof EachInParam }
/*
* Normalize input channels
*/
config.fakeInput()
/*
* Normalize the output
* - even though the output may be empty, let return the stdout as output by default
*/
if ( config.getOutputs().size() == 0 ) {
config.fakeOutput()
}
// the state agent
state = new Agent<>(new StateObj(name))
state.addListener { StateObj old, StateObj obj ->
try {
log.trace "<$name> Process state changed to: $obj -- finished: ${obj.isFinished()}"
if( !completed && obj.isFinished() ) {
terminateProcess()
completed = true
}
}
catch( Throwable e ) {
session.abort(e)
}
}
// register the processor
// note: register the task *before* creating (and starting the dataflow operator) in order
// a race condition on the processes barrier - this fix issue #43
session.processRegister(this)
// create the underlying dataflow operator
createOperator()
session.notifyProcessCreate(this)
/*
* When there is a single output channel, return let returns that item
* otherwise return the list
*/
def result = config.getOutputs().channels
return result.size() == 1 ? result[0] : result
}
/**
* Template method which extending classes have to override in order to
* create the underlying *dataflow* operator associated with this processor
*
* See {@code DataflowProcessor}
*/
protected void createOperator() {
def opInputs = new ArrayList(config.getInputs().getChannels())
/*
* check if there are some iterators declaration
* the list holds the index in the list of all *inputs* for the {@code each} declaration
*/
List iteratorIndexes = []
config.getInputs().eachWithIndex { param, index ->
if( param instanceof EachInParam ) {
log.trace "Process ${name} > got each param: ${param.name} at index: ${index} -- ${param.dump()}"
iteratorIndexes << index
}
}
/**
* The thread pool used by GPars. The thread pool to be used is set in the static
* initializer of {@link nextflow.cli.CmdRun} class. See also {@link nextflow.util.CustomPoolFactory}
*/
final PGroup group = Dataflow.retrieveCurrentDFPGroup()
/*
* When one (or more) {@code each} are declared as input, it is created an extra
* operator which will receive the inputs from the channel (excepts the values over iterate)
*
* The operator will *expand* the received inputs, iterating over the user provided value and
* forwarding the final values the the second *parallel* processor executing the user specified task
*/
if( iteratorIndexes ) {
log.debug "Creating *combiner* operator for each param(s) at index(es): ${iteratorIndexes}"
// don't care about the last channel, being the control channel it doesn't bring real values
final size = opInputs.size()-1
// the iterator operator needs to executed just one time
// thus add a dataflow queue binding a single value and then a stop signal
def termination = new DataflowQueue<>()
termination << Boolean.TRUE
opInputs[size] = termination
// the channel forwarding the data from the *iterator* process to the target task
final linkingChannels = new ArrayList(size)
size.times { linkingChannels[it] = new DataflowQueue() }
// the script implementing the iterating process
final forwarder = new ForwardClosure(size, iteratorIndexes)
// instantiate the iteration process
def DataflowOperator op1
def stopAfterFirstRun = allScalarValues
def interceptor = new BaseProcessInterceptor(opInputs, stopAfterFirstRun)
def params = [inputs: opInputs, outputs: linkingChannels, maxForks: 1, listeners: [interceptor]]
session.allOperators << (op1 = new DataflowOperator(group, params, forwarder))
// fix issue #41
start(op1)
// set as next inputs the result channels of the iteration process
// adding the 'control' channel removed previously
opInputs = new ArrayList(size+1)
opInputs.addAll( linkingChannels )
opInputs.add( config.getInputs().getChannels().last() )
}
/*
* finally create the operator
*/
// note: do not specify the output channels in the operator declaration
// this allows us to manage them independently from the operator life-cycle
this.singleton = allScalarValues && !hasEachParams
this.openPorts = createPortsArray(opInputs.size())
config.getOutputs().setSingleton(singleton)
def interceptor = new TaskProcessorInterceptor(opInputs, singleton)
def params = [inputs: opInputs, maxForks: session.poolSize, listeners: [interceptor] ]
def invoke = new InvokeTaskAdapter(this, opInputs.size())
session.allOperators << (operator = new DataflowOperator(group, params, invoke))
// notify the creation of a new vertex the execution DAG
NodeMarker.addProcessNode(this, config.getInputs(), config.getOutputs())
// fix issue #41
start(operator)
}
private start(DataflowProcessor op) {
if( !NF.dsl2 ) {
op.start()
return
}
session.addIgniter {
log.debug "Starting process > $name"
op.start()
}
}
private AtomicIntegerArray createPortsArray(int size) {
def result = new AtomicIntegerArray(size)
for( int i=0; i $name with params=$params; values=$values"
// -- create the task run instance
final task = createTaskRun(params)
// -- set the task instance as the current in this thread
currentTask.set(task)
// -- validate input lengths
validateInputTuples(values)
// -- map the inputs to a map and use to delegate closure values interpolation
final secondPass = [:]
int count = makeTaskContextStage1(task, secondPass, values)
makeTaskContextStage2(task, secondPass, count)
// verify that `when` guard, when specified, is satisfied
if( !checkWhenGuard(task) )
return
// -- resolve the task command script
task.resolve(taskBody)
// -- verify if exists a stored result for this case,
// if true skip the execution and return the stored data
if( checkStoredOutput(task) )
return
def hash = createTaskHashKey(task)
checkCachedOrLaunchTask(task, hash, resumable)
}
@Memoized
private List getDeclaredInputTuple() {
getConfig().getInputs().ofType(TupleInParam)
}
protected void validateInputTuples( List values ) {
def declaredSets = getDeclaredInputTuple()
for( int i=0; i{@code TaskRun#id}
* {@code TaskRun#status}
* {@code TaskRun#index}
* {@code TaskRun#name}
* {@code TaskRun#process}
*
* @return The new newly created {@code TaskRun}
*/
final protected TaskRun createTaskRun(TaskStartParams params) {
final task = new TaskRun(
id: params.id,
index: params.index,
processor: this,
type: scriptType,
config: config.createTaskConfig(),
context: new TaskContext(this)
)
// setup config
task.config.index = task.index
task.config.process = task.processor.name
task.config.executor = task.processor.executor.name
/*
* initialize the inputs/outputs for this task instance
*/
config.getInputs().each { InParam param ->
if( param instanceof TupleInParam )
param.inner.each { task.setInput(it) }
else if( param instanceof EachInParam )
task.setInput(param.inner)
else
task.setInput(param)
}
config.getOutputs().each { OutParam param ->
if( param instanceof TupleOutParam ) {
param.inner.each { task.setOutput(it) }
}
else
task.setOutput(param)
}
return task
}
/**
* Try to check if exists a previously executed process result in the a cached folder. If it exists
* use the that result and skip the process execution, otherwise the task is sumitted for execution.
*
* @param task
* The {@code TaskRun} instance to be executed
* @param hash
* The unique {@code HashCode} for the given task inputs
* @param script
* The script to be run (only when it's a merge task)
* @return
* {@code false} when a cached result has been found and the execution has skipped,
* or {@code true} if the task has been submitted for execution
*
*/
@CompileStatic
final protected void checkCachedOrLaunchTask( TaskRun task, HashCode hash, boolean shouldTryCache ) {
int tries = task.failCount +1
while( true ) {
hash = HashBuilder.defaultHasher().putBytes(hash.asBytes()).putInt(tries).hash()
Path resumeDir = null
boolean exists = false
try {
final entry = session.cache.getTaskEntry(hash, this)
resumeDir = entry ? FileHelper.asPath(entry.trace.getWorkDir()) : null
if( resumeDir )
exists = resumeDir.exists()
log.trace "[${safeTaskName(task)}] Cacheable folder=${resumeDir?.toUriString()} -- exists=$exists; try=$tries; shouldTryCache=$shouldTryCache; entry=$entry"
final cached = shouldTryCache && exists && entry.trace.isCompleted() && checkCachedOutput(task.clone(), resumeDir, hash, entry)
if( cached )
break
}
catch (Throwable t) {
log.warn1("[${safeTaskName(task)}] Unable to resume cached task -- See log file for details", causedBy: t)
}
if( exists ) {
tries++
continue
}
final lock = lockManager.acquire(hash)
final workDir = task.getWorkDirFor(hash)
try {
if( resumeDir != workDir )
exists = workDir.exists()
if( !exists && !workDir.mkdirs() )
throw new IOException("Unable to create directory=$workDir -- check file system permissions")
}
finally {
lock.release()
}
// submit task for execution
submitTask( task, hash, workDir )
break
}
}
/**
* Check if exists a *storeDir* for the specified task. When if exists
* and contains the expected result files, the process execution is skipped.
*
* @param task The task for which check the stored output
* @return {@code true} when the folder exists and it contains the expected outputs,
* {@code false} otherwise
*/
final boolean checkStoredOutput( TaskRun task ) {
if( !task.config.storeDir ) {
log.trace "[${safeTaskName(task)}] Store dir not set -- return false"
return false
}
// -- when store path is set, only output params of type 'file' can be specified
final ctx = task.context
def invalid = task.getOutputs().keySet().any {
if( it instanceof ValueOutParam ) {
return !ctx.containsKey(it.name)
}
if( it instanceof FileOutParam ) {
return false
}
return true
}
if( invalid ) {
checkWarn "[${safeTaskName(task)}] StoreDir can only be used when using 'file' outputs"
return false
}
if( !task.config.getStoreDir().exists() ) {
log.trace "[${safeTaskName(task)}] Store dir does not exist > ${task.config.storeDir} -- return false"
// no folder -> no cached result
return false
}
try {
// -- expose task exit status to make accessible as output value
task.config.exitStatus = TaskConfig.EXIT_ZERO
// -- check if all output resources are available
collectOutputs(task)
log.info "[skipping] Stored process > ${safeTaskName(task)}"
// set the exit code in to the task object
task.exitStatus = TaskConfig.EXIT_ZERO
task.cached = true
session.notifyTaskCached(new StoredTaskHandler(task))
// -- now bind the results
finalizeTask0(task)
return true
}
catch( MissingFileException | MissingValueException e ) {
log.trace "[${safeTaskName(task)}] Missed store > ${e.getMessage()} -- folder: ${task.config.storeDir}"
task.exitStatus = Integer.MAX_VALUE
task.workDir = null
return false
}
}
/**
* Check whenever the outputs for the specified task already exist
*
* @param task The task instance
* @param folder The folder where the outputs are stored (eventually)
* @return {@code true} when all outputs are available, {@code false} otherwise
*/
final boolean checkCachedOutput(TaskRun task, Path folder, HashCode hash, TaskEntry entry) {
// check if exists the task exit code file
def exitCode = null
def exitFile = folder.resolve(TaskRun.CMD_EXIT)
if( task.type == ScriptType.SCRIPTLET ) {
def str
try {
str = exitFile.text?.trim()
}
catch( IOException e ) {
log.trace "[${safeTaskName(task)}] Exit file can't be read > $exitFile -- return false -- Cause: ${e.message}"
return false
}
exitCode = str.isInteger() ? str.toInteger() : null
if( !task.isSuccess(exitCode) ) {
log.trace "[${safeTaskName(task)}] Exit code is not valid > $str -- return false"
return false
}
}
/*
* verify cached context map
*/
if( !entry ) {
log.trace "[${safeTaskName(task)}] Missing cache entry -- return false"
return false
}
if( task.hasCacheableValues() && !entry.context ) {
log.trace "[${safeTaskName(task)}] Missing cache context -- return false"
return false
}
/*
* verify stdout file
*/
final stdoutFile = folder.resolve( TaskRun.CMD_OUTFILE )
if( entry.context != null ) {
task.context = entry.context
task.config.context = entry.context
task.code?.delegate = entry.context
}
try {
// -- expose task exit status to make accessible as output value
task.config.exitStatus = exitCode
// -- check if all output resources are available
collectOutputs(task, folder, stdoutFile, task.context)
// set the exit code in to the task object
task.cached = true
task.hash = hash
task.workDir = folder
task.stdout = stdoutFile
if( exitCode != null ) {
task.exitStatus = exitCode
}
log.info "[${task.hashLog}] Cached process > ${task.name}"
// -- notify cached event
if( entry )
session.notifyTaskCached(new CachedTaskHandler(task,entry.trace))
// -- now bind the results
finalizeTask0(task)
return true
}
catch( MissingFileException | MissingValueException e ) {
log.trace "[${safeTaskName(task)}] Missed cache > ${e.getMessage()} -- folder: $folder"
task.exitStatus = Integer.MAX_VALUE
task.workDir = null
return false
}
}
/**
* Handles an error raised during the processor execution
*
* @param error The exception raised during the task execution
* @param task The {@code TaskDef} instance which raised the exception
* @return {@code true} to terminate the processor execution,
* {@code false} ignore the error and continue to process other pending tasks
*/
final protected boolean handleException( Throwable error, TaskRun task = null ) {
log.trace "Handling error: $error -- task: $task"
def fault = resumeOrDie(task, error)
log.trace "Task fault (2): $fault"
if (fault instanceof TaskFault) {
session.fault(fault)
// when a `TaskFault` is returned a `TERMINATE` is implicit, thus return `true`
return true
}
return fault == TERMINATE || fault == FINISH
}
/**
* @param task The {@code TaskRun} instance that raised an error
* @param error The error object
* @return
* Either a value of value of {@link ErrorStrategy} representing the error strategy chosen
* or an instance of {@TaskFault} representing the cause of the error (that implicitly means
* a {@link ErrorStrategy#TERMINATE})
*/
@PackageScope
final synchronized resumeOrDie( TaskRun task, Throwable error, TraceRecord traceRecord = null) {
log.debug "Handling unexpected condition for\n task: name=${safeTaskName(task)}; work-dir=${task?.workDirStr}\n error [${error?.class?.name}]: ${error?.getMessage()?:error}"
ErrorStrategy errorStrategy = TERMINATE
final List message = []
try {
// -- do not recoverable error, just re-throw it
if( error instanceof Error ) throw error
// -- retry without increasing the error counts
if( task && (error.cause instanceof ProcessRetryableException || error.cause instanceof CloudSpotTerminationException) ) {
if( error.cause instanceof ProcessRetryableException )
log.info "[$task.hashLog] NOTE: ${error.message} -- Execution is retried"
else
log.info "[$task.hashLog] NOTE: ${error.message} -- Cause: ${error.cause.message} -- Execution is retried"
task.failCount+=1
final taskCopy = task.makeCopy()
session.getExecService().submit {
try {
taskCopy.runType = RunType.RETRY
checkCachedOrLaunchTask( taskCopy, taskCopy.hash, false )
}
catch( Throwable e ) {
log.error("Unable to re-submit task `${taskCopy.name}`", e)
session.abort(e)
}
}
task.failed = true
task.errorAction = RETRY
return RETRY
}
final submitTimeout = error.cause instanceof ProcessSubmitTimeoutException
final submitErrMsg = submitTimeout ? error.cause.message : null
final int submitRetries = submitTimeout ? ++task.submitRetries : 0
final int taskErrCount = !submitTimeout && task ? ++task.failCount : 0
final int procErrCount = !submitTimeout ? ++errorCount : errorCount
// -- when is a task level error and the user has chosen to ignore error,
// just report and error message and DO NOT stop the execution
if( task && error instanceof ProcessException ) {
// expose current task exit status
task.config.exitStatus = task.exitStatus
task.config.errorCount = procErrCount
task.config.retryCount = taskErrCount
//Add trace of the previous execution in the task context for next execution
if ( traceRecord )
task.config.previousTrace = traceRecord
task.config.previousException = error
errorStrategy = checkErrorStrategy(task, error, taskErrCount, procErrCount, submitRetries)
if( errorStrategy.soft ) {
def msg = "[$task.hashLog] NOTE: ${submitTimeout ? submitErrMsg : error.message}"
if( errorStrategy == IGNORE )
msg += " -- Error is ignored"
else if( errorStrategy == RETRY )
msg += " -- Execution is retried (${submitTimeout ? submitRetries : taskErrCount})"
log.info msg
task.failed = true
task.errorAction = errorStrategy
return errorStrategy
}
}
// -- mark the task as failed
if( task ) {
task.failed = true
task.errorAction = errorStrategy
}
// -- make sure the error is showed only the very first time across all processes
if( errorShown.getAndSet(true) || session.aborted ) {
log.trace "Task errorShown=${errorShown.get()}; aborted=${session.aborted}"
return errorStrategy
}
def dumpStackTrace = log.isTraceEnabled()
message << "Error executing process > '${safeTaskName(task)}'"
switch( error ) {
case ProcessException:
formatTaskError( message, error, task )
break
case ProcessEvalException:
formatCommandError( message, error, task )
break
case FailedGuardException:
formatGuardError( message, error as FailedGuardException, task )
break;
default:
message << formatErrorCause(error)
dumpStackTrace = true
}
if( dumpStackTrace )
log.error(message.join('\n'), error)
else
log.error(message.join('\n'))
}
catch( Throwable e ) {
// no recoverable error
log.error("Execution aborted due to an unexpected error", e )
}
return new TaskFault(error: error, task: task, report: message.join('\n'))
}
protected String safeTaskName(TaskRun task) {
return task!=null
? task.lazyName()
: name
}
protected ErrorStrategy checkErrorStrategy( TaskRun task, ProcessException error, final int taskErrCount, final int procErrCount, final submitRetries ) {
final action = task.config.getErrorStrategy()
// retry is not allowed when the script cannot be compiled or similar errors
if( error instanceof ProcessUnrecoverableException || error.cause instanceof ProcessUnrecoverableException ) {
return !action.soft ? action : TERMINATE
}
// IGNORE strategy -- just continue
if( action == IGNORE ) {
return IGNORE
}
// RETRY strategy -- check that process do not exceed 'maxError' and the task do not exceed 'maxRetries'
if( action == RETRY ) {
final int maxErrors = task.config.getMaxErrors()
final int maxRetries = task.config.getMaxRetries()
if( (procErrCount < maxErrors || maxErrors == -1) && taskErrCount <= maxRetries && submitRetries <= maxRetries ) {
final taskCopy = task.makeCopy()
session.getExecService().submit({
try {
taskCopy.config.attempt = taskErrCount+1
taskCopy.config.submitAttempt = submitRetries+1
taskCopy.runType = RunType.RETRY
taskCopy.resolve(taskBody)
checkCachedOrLaunchTask( taskCopy, taskCopy.hash, false )
}
catch( Throwable e ) {
log.error("Unable to re-submit task `${safeTaskName(taskCopy)}`", e)
session.abort(e)
}
} as Runnable)
return RETRY
}
return TERMINATE
}
return action
}
final protected List formatCommandError(List message, ProcessEvalException error, TaskRun task) {
// compose a readable error message
message << formatErrorCause(error)
// - print the executed command
message << "Command executed:\n"
error.command.stripIndent(true)?.trim()?.eachLine {
message << " ${it}"
}
// - the exit status
message << "\nCommand exit status:\n ${error.status}"
// - the tail of the process stdout
message << "\nCommand output:"
def lines = error.output.readLines()
if( lines.size() == 0 ) {
message << " (empty)"
}
for( String it : lines ) {
message << " ${stripWorkDir(it, task.workDir)}"
}
if( task?.workDir )
message << "\nWork dir:\n ${task.workDirStr}"
return message
}
final protected List formatGuardError( List message, FailedGuardException error, TaskRun task ) {
// compose a readable error message
message << formatErrorCause(error)
if( error.source ) {
message << "\nWhen block:"
error.source.stripIndent(true).eachLine {
message << " $it"
}
}
if( task?.workDir )
message << "\nWork dir:\n ${task.workDirStr}"
return message
}
final protected List formatTaskError( List message, Throwable error, TaskRun task ) {
// compose a readable error message
message << formatErrorCause( error )
/*
* task executing scriptlets
*/
if( task?.script ) {
// - print the executed command
message << "Command executed${task.template ? " [$task.template]": ''}:\n"
task.script?.stripIndent(true)?.trim()?.eachLine {
message << " ${it}"
}
// - the exit status
message << "\nCommand exit status:\n ${task.exitStatus != Integer.MAX_VALUE ? task.exitStatus : '-'}"
// - the tail of the process stdout
message << "\nCommand output:"
final max = 50
def lines = task.dumpStdout(max)
if( lines.size() == 0 ) {
message << " (empty)"
}
for( String it : lines ) {
message << " ${stripWorkDir(it, task.workDir)}"
}
// - the tail of the process stderr
lines = task.dumpStderr(max)
if( lines ) {
message << "\nCommand error:"
for( String it : lines ) {
message << " ${stripWorkDir(it, task.workDir)}"
}
}
// - this is likely a task wrapper issue
else if( task.exitStatus != 0 ) {
lines = task.dumpLogFile(max)
if( lines ) {
message << "\nCommand wrapper:"
for( String it : lines ) {
message << " ${stripWorkDir(it, task.workDir)}"
}
}
}
}
else {
if( task?.source ) {
message << "Source block:"
task.source.stripIndent(true).eachLine {
message << " $it"
}
}
}
if( task?.workDir )
message << "\nWork dir:\n ${task.workDirStr}"
if( task?.isContainerEnabled() )
message << "\nContainer:\n ${task.container}".toString()
message << suggestTip(message)
return message
}
private String suggestTip(List message) {
try {
return "\nTip: ${getTipProvider().suggestTip(message)}"
}
catch (Exception e) {
log.debug "Unable to get tip for task message: $message", e
return ''
}
}
private static String stripWorkDir(String line, Path workDir) {
if( workDir==null ) return line
if( workDir.fileSystem != FileSystems.default ) return line
return workDir ? line.replace(workDir.toString()+'/','') : line
}
/**
* Send a poison pill over all the outputs channel
*/
final protected synchronized void sendPoisonPill() {
log.trace "<$name> Sending a poison pill(s)"
for( DataflowWriteChannel channel : config.getOutputs().getChannels() ){
if( channel instanceof DataflowQueue ) {
channel.bind( PoisonPill.instance )
}
else if( channel instanceof DataflowStreamWriteAdapter ) {
channel.bind( PoisonPill.instance )
}
else if( channel instanceof DataflowExpression && !channel.isBound()) {
channel.bind( PoisonPill.instance )
}
}
}
private String formatErrorCause( Throwable error ) {
def result = new StringBuilder()
result << '\nCaused by:\n'
def message
if( error instanceof ShowOnlyExceptionMessage || !error.cause )
message = err0(error)
else
message = err0(error.cause)
for( String line : message.readLines() ) {
result << ' ' << line << '\n'
}
result
.append('\n')
.toString()
}
static String err0(Throwable e) {
final fail = e instanceof InvocationTargetException ? e.targetException : e
if( fail instanceof NoSuchFileException ) {
return "No such file or directory: $fail.message"
}
if( fail instanceof MissingPropertyException ) {
def name = fail.property ?: LoggerHelper.getDetailMessage(fail)
def result = "No such variable: ${name}"
def details = LoggerHelper.findErrorLine(fail)
if( details )
result += " -- Check script '${details[0]}' at line: ${details[1]}"
return result
}
def result = fail.message ?: fail.toString()
def details = LoggerHelper.findErrorLine(fail)
if( details ){
result += " -- Check script '${details[0]}' at line: ${details[1]}"
}
return result
}
/**
* Publish output files to a specified target folder
*
* @param task The task whose outputs need to be published
* @param overwrite When {@code true} any existing file will be overwritten, otherwise the publishing is ignored
*/
@CompileStatic
protected void publishOutputs( TaskRun task ) {
final publishList = task.config.getPublishDir()
if( !publishList ) {
return
}
for( PublishDir pub : publishList ) {
publishOutputs0(task, pub)
}
}
private void publishOutputs0( TaskRun task, PublishDir publish ) {
if( publish.overwrite == null ) {
publish.overwrite = !task.cached
}
HashSet files = []
def outputs = task.getOutputsByType(FileOutParam)
for( Map.Entry entry : outputs ) {
final value = entry.value
if( value instanceof Path ) {
files.add((Path)value)
}
else if( value instanceof Collection ) {
files.addAll(value)
}
else if( value != null ) {
throw new IllegalArgumentException("Unknown output file object [${value.class.name}]: ${value}")
}
}
publish.apply(files, task)
}
/**
* Bind the expected output files to the corresponding output channels
* @param processor
*/
synchronized protected void bindOutputs( TaskRun task ) {
// -- creates the map of all tuple values to bind
Map tuples = [:]
for( OutParam param : config.getOutputs() ) {
tuples.put(param.index, [])
}
// -- collects the values to bind
for( OutParam param: task.outputs.keySet() ){
def value = task.outputs.get(param)
switch( param ) {
case StdOutParam:
log.trace "Process $name > normalize stdout param: $param"
value = value instanceof Path ? value.text : value?.toString()
case OptionalParam:
if( !value && param instanceof OptionalParam && param.optional ) {
final holder = [] as MissingParam; holder.missing = param
tuples[param.index] = holder
break
}
case EnvOutParam:
case ValueOutParam:
case DefaultOutParam:
log.trace "Process $name > collecting out param: ${param} = $value"
tuples[param.index].add(value)
break
default:
throw new IllegalArgumentException("Illegal output parameter type: $param")
}
}
// bind the output
if( isFair0 ) {
fairBindOutputs0(tuples, task)
}
else {
bindOutputs0(tuples)
}
// -- finally prints out the task output when 'debug' is true
if( task.config.debug ) {
task.echoStdout(session)
}
}
protected void fairBindOutputs0(Map emissions, TaskRun task) {
synchronized (isFair0) {
// decrement -1 because tasks are 1-based
final index = task.index-1
// store the task emission values in a buffer
fairBuffers[index-currentEmission] = emissions
// check if the current task index matches the expected next emission index
if( currentEmission == index ) {
while( emissions!=null ) {
// bind the emission values
bindOutputs0(emissions)
// remove the head and try with the following
fairBuffers.remove(0)
// increase the index of the next emission
currentEmission++
// take the next emissions
emissions = fairBuffers[0]
}
}
}
}
protected void bindOutputs0(Map tuples) {
// -- bind out the collected values
for( OutParam param : config.getOutputs() ) {
final outValue = tuples[param.index]
if( outValue == null )
throw new IllegalStateException()
if( outValue instanceof MissingParam ) {
log.debug "Process $name > Skipping output binding because one or more optional files are missing: $outValue.missing"
continue
}
log.trace "Process $name > Binding out param: ${param} = ${outValue}"
bindOutParam(param, outValue)
}
}
protected void bindOutParam( OutParam param, List values ) {
log.trace "<$name> Binding param $param with $values"
final x = values.size() == 1 ? values[0] : values
final ch = param.getOutChannel()
if( ch != null ) {
// create a copy of the output list of operation made by a downstream task
// can modify the list which is used internally by the task processor
// and result in a potential error. See https://github.com/nextflow-io/nextflow/issues/3768
final copy = x instanceof List && x instanceof Cloneable ? x.clone() : x
// emit the final value
ch.bind(copy)
}
}
protected void collectOutputs( TaskRun task ) {
collectOutputs( task, task.getTargetDir(), task.@stdout, task.context )
}
/**
* Once the task has completed this method is invoked to collected all the task results
*
* @param task
*/
final protected void collectOutputs( TaskRun task, Path workDir, def stdout, Map context ) {
log.trace "<$name> collecting output: ${task.outputs}"
for( OutParam param : task.outputs.keySet() ) {
switch( param ) {
case StdOutParam:
collectStdOut(task, (StdOutParam)param, stdout)
break
case FileOutParam:
collectOutFiles(task, (FileOutParam)param, workDir, context)
break
case ValueOutParam:
collectOutValues(task, (ValueOutParam)param, context)
break
case EnvOutParam:
collectOutEnvParam(task, (EnvOutParam)param, workDir)
break
case CmdEvalParam:
collectOutEnvParam(task, (CmdEvalParam)param, workDir)
break
case DefaultOutParam:
task.setOutput(param, DefaultOutParam.Completion.DONE)
break
default:
throw new IllegalArgumentException("Illegal output parameter: ${param.class.simpleName}")
}
}
// mark ready for output binding
task.canBind = true
}
protected void collectOutEnvParam(TaskRun task, BaseOutParam param, Path workDir) {
// fetch the output value
final outCmds = param instanceof CmdEvalParam ? task.getOutputEvals() : null
final val = collectOutEnvMap(workDir,outCmds).get(param.name)
if( val == null && !param.optional )
throw new MissingValueException("Missing environment variable: $param.name")
// set into the output set
task.setOutput(param,val)
// trace the result
log.trace "Collecting param: ${param.name}; value: ${val}"
}
/**
* Parse the `.command.env` file which holds the value for `env` and `cmd`
* output types
*
* @param workDir
* The task work directory that contains the `.command.env` file
* @param outEvals
* A {@link Map} instance containing key-value pairs
* @return
*/
@CompileStatic
@Memoized(maxCacheSize = 10_000)
protected Map collectOutEnvMap(Path workDir, Map outEvals) {
final env = workDir.resolve(TaskRun.CMD_ENV).text
final result = new HashMap(50)
Matcher matcher
// `current` represent the current capturing env variable name
String current=null
for(String line : env.readLines() ) {
// Opening condition:
// line should match a KEY=VALUE syntax
if( !current && (matcher = (line=~/([a-zA-Z_][a-zA-Z0-9_]*)=(.*)/)) ) {
final k = matcher.group(1)
final v = matcher.group(2)
if (!k) continue
result.put(k,v)
current = k
}
// Closing condition:
// line should match /KEY/ or /KEY/=exit_status
else if( current && (matcher = (line=~/\/${current}\/(?:=exit:(\d+))?/)) ) {
final status = matcher.group(1) as Integer ?: 0
// when exit status is defined and it is a non-zero, it should be interpreted
// as a failure of the execution of the output command; in this case the variable
// holds the std error message
if( outEvals!=null && status ) {
final cmd = outEvals.get(current)
final out = result[current]
throw new ProcessEvalException("Unable to evaluate output", cmd, out, status)
}
// reset current key
current = null
}
else if( current && line!=null) {
result[current] += '\n' + line
}
}
return result
}
/**
* Collects the process 'std output'
*
* @param task The executed process instance
* @param param The declared {@link StdOutParam} object
* @param stdout The object holding the task produced std out object
*/
protected void collectStdOut( TaskRun task, StdOutParam param, def stdout ) {
if( stdout == null && task.type == ScriptType.SCRIPTLET ) {
throw new IllegalArgumentException("Missing 'stdout' for process > ${safeTaskName(task)}")
}
if( stdout instanceof Path && !stdout.exists() ) {
throw new MissingFileException("Missing 'stdout' file: ${stdout.toUriString()} for process > ${safeTaskName(task)}")
}
task.setOutput(param, stdout)
}
protected void collectOutFiles( TaskRun task, FileOutParam param, Path workDir, Map context ) {
final List allFiles = []
// type file parameter can contain a multiple files pattern separating them with a special character
def entries = param.getFilePatterns(context, task.workDir)
boolean inputsRemovedFlag = false
// for each of them collect the produced files
for( String filePattern : entries ) {
List result = null
def splitter = param.glob ? FilePatternSplitter.glob().parse(filePattern) : null
if( splitter?.isPattern() ) {
result = fetchResultFiles(param, filePattern, workDir)
// filter the inputs
if( result && !param.includeInputs ) {
result = filterByRemovingStagedInputs(task, result, workDir)
log.trace "Process ${safeTaskName(task)} > after removing staged inputs: ${result}"
inputsRemovedFlag |= (result.size()==0)
}
}
else {
def path = param.glob ? splitter.strip(filePattern) : filePattern
def file = workDir.resolve(path)
def exists = checkFileExists(file, param.followLinks)
if( exists )
result = List.of(file)
else
log.debug "Process `${safeTaskName(task)}` is unable to find [${file.class.simpleName}]: `$file` (pattern: `$filePattern`)"
}
if( result )
allFiles.addAll(result)
else if( !param.optional && (!param.arity || param.arity.min > 0) ) {
def msg = "Missing output file(s) `$filePattern` expected by process `${safeTaskName(task)}`"
if( inputsRemovedFlag )
msg += " (note: input files are not included in the default matching set)"
throw new MissingFileException(msg)
}
}
if( !param.isValidArity(allFiles.size()) )
throw new IllegalArityException("Incorrect number of output files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${allFiles.size()}")
task.setOutput( param, allFiles.size()==1 && param.isSingle() ? allFiles[0] : allFiles )
}
protected boolean checkFileExists(Path file, boolean followLinks) {
followLinks ? file.exists() : file.exists(LinkOption.NOFOLLOW_LINKS)
}
protected void collectOutValues( TaskRun task, ValueOutParam param, Map ctx ) {
try {
// fetch the output value
final val = param.resolve(ctx)
// set into the output set
task.setOutput(param,val)
// trace the result
log.trace "Collecting param: ${param.name}; value: ${val}"
}
catch( MissingPropertyException e ) {
throw new MissingValueException("Missing value declared as output parameter: ${e.property}")
}
}
/**
* Collect the file(s) with the name specified, produced by the execution
*
* @param workDir The job working path
* @param namePattern The file name, it may include file name wildcards
* @return The list of files matching the specified name in lexicographical order
* @throws MissingFileException when no matching file is found
*/
@PackageScope
List fetchResultFiles( FileOutParam param, String namePattern, Path workDir ) {
assert namePattern
assert workDir
List files = []
def opts = visitOptions(param, namePattern)
// scan to find the file with that name
try {
FileHelper.visitFiles(opts, workDir, namePattern) { Path it -> files.add(it) }
}
catch( NoSuchFileException e ) {
throw new MissingFileException("Cannot access directory: '$workDir'", e)
}
return files.sort()
}
/**
* Given a {@link FileOutParam} object create the option map for the
* {@link FileHelper#visitFiles(java.util.Map, java.nio.file.Path, java.lang.String, groovy.lang.Closure)} method
*
* @param param A task {@link FileOutParam}
* @param namePattern A file glob pattern
* @return A {@link Map} object holding the traverse options for the {@link FileHelper#visitFiles(java.util.Map, java.nio.file.Path, java.lang.String, groovy.lang.Closure)} method
*/
@PackageScope
Map visitOptions( FileOutParam param, String namePattern ) {
final opts = [:]
opts.relative = false
opts.hidden = param.hidden ?: namePattern.startsWith('.')
opts.followLinks = param.followLinks
opts.maxDepth = param.maxDepth
opts.type = param.type ? param.type : ( namePattern.contains('**') ? 'file' : 'any' )
return opts
}
/**
* Given a list of {@code Path} removes all the hidden file i.e. the ones which names starts with a dot char
* @param files A list of {@code Path}
* @return The result list not containing hidden file entries
*/
@PackageScope
List filterByRemovingHiddenFiles( List files ) {
files.findAll { !it.getName().startsWith('.') }
}
/**
* Given a list of {@code Path} removes all the entries which name match the name of
* file used as input for the specified {@code TaskRun}
*
* See TaskRun#getStagedInputs
*
* @param task
* A {@link TaskRun} object representing the task executed
* @param collectedFiles
* Collection of candidate output files
* @return
* List of the actual output files (not including any input matching an output file name pattern)
*/
@PackageScope
List filterByRemovingStagedInputs( TaskRun task, List collectedFiles, Path workDir ) {
// get the list of input files
final List allStaged = task.getStagedInputs()
final List result = new ArrayList<>(collectedFiles.size())
for( int i=0; i getBinDirs() {
final result = new ArrayList(10)
// module bundle bin dir have priority, add before
final bundle = session.enableModuleBinaries() ? getModuleBundle() : null
if( bundle!=null )
result.addAll(bundle.getBinDirs())
// then add project bin dir
if( executor.binDir )
result.add(executor.binDir)
return result
}
@Memoized
boolean isLocalWorkDir() {
return executor.workDir.fileSystem == FileSystems.default
}
/**
* @return The map holding the shell environment variables for the task to be executed
*/
@Memoized
Map getProcessEnvironment() {
def result = new LinkedHashMap(20)
// add the taskConfig environment entries
if( session.config.env instanceof Map ) {
session.config.env.each { name, value ->
result.put( name, value?.toString() )
}
}
else {
log.debug "Invalid 'session.config.env' object: ${session.config.env?.class?.name}"
}
// append the 'bin' folder to the task environment
List paths
if( isLocalWorkDir() && (paths=getBinDirs()) ) {
for( Path it : paths ) {
if( result.containsKey('PATH') ) {
// note: do not escape potential blanks in the bin path because the PATH
// variable is enclosed in `"` when in rendered in the launcher script -- see #630
result['PATH'] = "${result['PATH']}:${it}".toString()
}
else {
// note: append custom bin path *after* the system PATH
// to prevent unnecessary network round-trip for each command
// when the added path is a shared file system directory
result['PATH'] = "\$PATH:${it}".toString()
}
}
}
return Collections.unmodifiableMap(result)
}
/**
* An input file parameter can be provided with any value other than a file.
* This function normalize a generic value to a {@code Path} create a temporary file
* in the for it.
*
* @param input The input value
* @param altName The name to be used when a temporary file is created.
* @return The {@code Path} that will be staged in the task working folder
*/
protected FileHolder normalizeInputToFile( Object input, String altName ) {
/*
* when it is a local file, just return a reference holder to it
*/
if( input instanceof Path ) {
return new FileHolder(input)
}
/*
* default case, convert the input object to a string and save
* to a local file
*/
def source = input?.toString() ?: ''
def result = Nextflow.tempFile(altName)
result.text = source
return new FileHolder(source, result)
}
protected Path normalizeToPath( obj ) {
if( obj instanceof Path )
return obj
if( obj == null )
throw new ProcessUnrecoverableException("Path value cannot be null")
if( !(obj instanceof CharSequence) )
throw new ProcessUnrecoverableException("Not a valid path value type: ${obj.getClass().getName()} ($obj)")
def str = obj.toString().trim()
if( str.contains('\n') )
throw new ProcessUnrecoverableException("Path value cannot contain a new-line character: $str")
if( str.startsWith('/') )
return FileHelper.asPath(str)
if( FileHelper.getUrlProtocol(str) )
return FileHelper.asPath(str)
if( !str )
throw new ProcessUnrecoverableException("Path value cannot be empty")
throw new ProcessUnrecoverableException("Not a valid path value: '$str'")
}
protected List normalizeInputToFiles( Object obj, int count, boolean coerceToPath, FilePorter.Batch batch ) {
Collection allItems = obj instanceof Collection ? obj : [obj]
def len = allItems.size()
// use a bag so that cache hash key is not affected by file entries order
def files = new ArrayBag(len)
for( def item : allItems ) {
if( item instanceof Path || coerceToPath ) {
def path = normalizeToPath(item)
def target = executor.isForeignFile(path) ? batch.addToForeign(path) : path
def holder = new FileHolder(target)
files << holder
}
else {
files << normalizeInputToFile(item, "input.${++count}")
}
}
return files
}
protected singleItemOrList( List items, boolean single, ScriptType type ) {
assert items != null
if( items.size() == 1 && single ) {
return makePath(items[0],type)
}
def result = new ArrayList(items.size())
for( int i=0; i expandWildcards( String name, List files ) {
assert files != null
// use an unordered so that cache hash key is not affected by file entries order
final result = new ArrayBag(files.size())
if( files.size()==0 ) { return result }
if( !name || name == '*' ) {
result.addAll(files)
return result
}
if( !name.contains('*') && !name.contains('?') && files.size()>1 ) {
/*
* When name do not contain any wildcards *BUT* multiple files are provide
* it is managed like having a 'star' at the end of the file name
*/
name += '*'
}
for( int i=0; i environment, boolean escape=false ) {
if( !environment )
return null
final List script = []
for( String name : environment.keySet() ) {
String value = environment.get(name)
if( !ENV_VAR_NAME.matcher(name).matches() )
log.trace "Illegal environment variable name: '${name}' -- This variable definition is ignored"
else if( !value ) {
log.warn "Environment variable `$name` evaluates to an empty value"
script << "export $name=''"
}
else if( !escape ) {
script << /export $name="$value"/
}
else {
// escape both wrapping double quotes and the dollar var placeholder
script << /export $name="${Escape.variable(value)}"/
}
}
script << ''
return script.join('\n')
}
final protected int makeTaskContextStage1( TaskRun task, Map secondPass, List values ) {
final contextMap = task.context
int count = 0
task.inputs.keySet().each { InParam param ->
// add the value to the task instance
def val = param.decodeInputs(values)
switch(param) {
case ValueInParam:
contextMap.put( param.name, val )
break
case FileInParam:
secondPass[param] = val
return // <-- leave it, because we do not want to add this 'val' at this stage
case StdInParam:
case EnvInParam:
// nothing to do
break
default:
throw new IllegalStateException("Unsupported input param type: ${param?.class?.simpleName}")
}
// add the value to the task instance context
task.setInput(param, val)
}
return count
}
final protected void makeTaskContextStage2( TaskRun task, Map secondPass, int count ) {
final ctx = task.context
final allNames = new HashMap()
final FilePorter.Batch batch = session.filePorter.newBatch(executor.getStageDir())
// -- all file parameters are processed in a second pass
// so that we can use resolve the variables that eventually are in the file name
for( Map.Entry entry : secondPass.entrySet() ) {
final param = entry.getKey()
final val = entry.getValue()
final fileParam = param as FileInParam
final normalized = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch)
final resolved = expandWildcards( fileParam.getFilePattern(ctx), normalized )
if( !param.isValidArity(resolved.size()) )
throw new IllegalArityException("Incorrect number of input files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${resolved.size()}")
ctx.put( param.name, singleItemOrList(resolved, param.isSingle(), task.type) )
count += resolved.size()
for( FileHolder item : resolved ) {
Integer num = allNames.getOrCreate(item.stageName, 0) +1
allNames.put(item.stageName,num)
}
// add the value to the task instance context
task.setInput(param, resolved)
}
// -- set the delegate map as context in the task config
// so that lazy directives will be resolved against it
task.config.context = ctx
// check conflicting file names
def conflicts = allNames.findAll { name, num -> num>1 }
if( conflicts ) {
log.debug("Process $name > collision check staging file names: $allNames")
def message = "Process `$name` input file name collision -- There are multiple input files for each of the following file names: ${conflicts.keySet().join(', ')}"
throw new ProcessUnrecoverableException(message)
}
// -- download foreign files
session.filePorter.transfer(batch)
}
final protected void makeTaskContextStage3( TaskRun task, HashCode hash, Path folder ) {
// set hash-code & working directory
task.hash = hash
task.workDir = folder
task.config.workDir = folder
task.config.hash = hash.toString()
task.config.name = task.getName()
}
final protected HashCode createTaskHashKey(TaskRun task) {
List keys = [ session.uniqueId, name, task.source ]
if( task.isContainerEnabled() )
keys << task.getContainerFingerprint()
// add all the input name-value pairs to the key generator
for( Map.Entry it : task.inputs ) {
keys.add( it.key.name )
keys.add( it.value )
}
// add all variable references in the task script but not declared as input/output
def vars = getTaskGlobalVars(task)
if( vars ) {
log.trace "Task: $name > Adding script vars hash code: ${vars}"
keys.add(vars.entrySet())
}
final binEntries = getTaskBinEntries(task.source)
if( binEntries ) {
log.trace "Task: $name > Adding scripts on project bin path: ${-> binEntries.join('; ')}"
keys.addAll(binEntries)
}
final modules = task.getConfig().getModule()
if( modules ) {
keys.addAll(modules)
}
final conda = task.getCondaEnv()
if( conda ) {
keys.add(conda)
}
final spack = task.getSpackEnv()
final arch = task.getConfig().getArchitecture()
if( spack ) {
keys.add(spack)
if( arch ) {
keys.add(arch)
}
}
if( session.stubRun ) {
keys.add('stub-run')
}
final mode = config.getHashMode()
final hash = computeHash(keys, mode)
if( session.dumpHashes ) {
session.dumpHashes=='json'
? traceInputsHashesJson(task, keys, mode, hash)
: traceInputsHashes(task, keys, mode, hash)
}
return hash
}
HashCode computeHash(List keys, CacheHelper.HashMode mode) {
try {
return CacheHelper.hasher(keys, mode).hash()
}
catch (Throwable e) {
final msg = "Something went wrong while creating task '$name' unique id -- Offending keys: ${ keys.collect {"\n - type=${it.getClass().getName()} value=$it"} }"
throw new UnexpectedException(msg,e)
}
}
/**
* This method scans the task command string looking for invocations of scripts
* defined in the project bin folder.
*
* @param script The task command string
* @return The list of paths of scripts in the project bin folder referenced in the task command
*/
@Memoized
protected List getTaskBinEntries(String script) {
List result = []
def tokenizer = new StringTokenizer(script," \t\n\r\f()[]{};&|<>`")
while( tokenizer.hasMoreTokens() ) {
def token = tokenizer.nextToken()
def path = session.binEntries.get(token)
if( path )
result.add(path)
}
return result
}
private void traceInputsHashesJson( TaskRun task, List entries, CacheHelper.HashMode mode, hash ) {
final collector = (item) -> [
hash: CacheHelper.hasher(item, mode).hash().toString(),
type: item?.getClass()?.getName(),
value: item?.toString()
]
final json = JsonOutput.toJson(entries.collect(collector))
log.info "[${safeTaskName(task)}] cache hash: ${hash}; mode: ${mode}; entries: ${JsonOutput.prettyPrint(json)}"
}
private void traceInputsHashes( TaskRun task, List entries, CacheHelper.HashMode mode, hash ) {
def buffer = new StringBuilder()
buffer.append("[${safeTaskName(task)}] cache hash: ${hash}; mode: $mode; entries: \n")
for( Object item : entries ) {
buffer.append( " ${CacheHelper.hasher(item, mode).hash()} [${item?.getClass()?.getName()}] $item \n")
}
log.info(buffer.toString())
}
protected Map getTaskGlobalVars(TaskRun task) {
final result = task.getGlobalVars(ownerScript.binding)
final directives = getTaskExtensionDirectiveVars(task)
result.putAll(directives)
return result
}
protected Map getTaskExtensionDirectiveVars(TaskRun task) {
final variableNames = task.getVariableNames()
final result = new HashMap(variableNames.size())
final taskConfig = task.config
for( String key : variableNames ) {
if( !key.startsWith('task.ext.') ) continue
final value = taskConfig.eval(key.substring(5))
result.put(key, value)
}
return result
}
/**
* Execute the specified task shell script
*
* @param script The script string to be execute, e.g. a BASH script
* @return {@code TaskDef}
*/
final protected void submitTask( TaskRun task, HashCode hash, Path folder ) {
log.trace "[${safeTaskName(task)}] actual run folder: ${folder}"
makeTaskContextStage3(task, hash, folder)
// add the task to the collection of running tasks
if( arrayCollector )
arrayCollector.collect(task)
else
executor.submit(task)
}
protected boolean checkWhenGuard(TaskRun task) {
try {
def pass = task.config.getGuard(NextflowDSLImpl.PROCESS_WHEN)
if( pass ) {
return true
}
log.trace "Task ${safeTaskName(task)} is not executed because `when` condition is not verified"
finalizeTask0(task)
return false
}
catch ( FailedGuardException error ) {
handleException(error, task)
return false
}
}
/**
* Finalize the task execution, checking the exit status
* and binding output values accordingly
*
* @param task The {@code TaskRun} instance to finalize
*/
@PackageScope
final finalizeTask( TaskHandler handler) {
def task = handler.task
log.trace "finalizing process > ${safeTaskName(task)} -- $task"
def fault = null
try {
// -- verify task exit status
if( task.error )
throw new ProcessFailedException("Process `${safeTaskName(task)}` failed", task.error)
if( task.type == ScriptType.SCRIPTLET ) {
if( task.exitStatus == Integer.MAX_VALUE )
throw new ProcessFailedException("Process `${safeTaskName(task)}` terminated for an unknown reason -- Likely it has been terminated by the external system")
if ( !task.isSuccess() )
throw new ProcessFailedException("Process `${safeTaskName(task)}` terminated with an error exit status (${task.exitStatus})")
}
// -- expose task exit status to make accessible as output value
task.config.exitStatus = task.exitStatus
// -- if it's OK collect results and finalize
collectOutputs(task)
}
catch ( Throwable error ) {
fault = resumeOrDie(task, error, handler.getTraceRecord())
log.trace "Task fault (3): $fault"
}
// -- finalize the task
if( fault != ErrorStrategy.RETRY )
finalizeTask0(task)
return fault
}
/**
* Whenever the process can be cached
*/
boolean isCacheable() {
session.cacheable && config.cacheable
}
@PackageScope boolean isResumable() {
isCacheable() && session.resumeMode
}
/**
* Finalize the task execution, checking the exit status
* and binding output values accordingly
*
* @param task The {@code TaskRun} instance to finalize
* @param producedFiles The map of files to be bind the outputs
*/
private void finalizeTask0( TaskRun task ) {
log.trace "Finalize process > ${safeTaskName(task)}"
// -- bind output (files)
if( task.canBind ) {
bindOutputs(task)
publishOutputs(task)
}
// increment the number of processes executed
state.update { StateObj it -> it.incCompleted() }
}
protected void closeProcess() {
arrayCollector?.close()
}
protected void terminateProcess() {
log.trace "<${name}> Sending poison pills and terminating process"
sendPoisonPill()
session.notifyProcessTerminate(this)
session.processDeregister(this)
}
/**
* Dump the current process status listing
* all input *port* statuses for debugging purpose
*
* @return The text description representing the process status
*/
String dumpTerminationStatus() {
def result = new StringBuilder()
def terminated = !DataflowHelper.isProcessorActive(operator)
result << "[process] $name\n"
if( terminated )
return result.toString()
def statusStr = !completed && !terminated ? 'status=ACTIVE' : ( completed && terminated ? 'status=TERMINATED' : "completed=$completed; terminated=$terminated" )
result << " $statusStr\n"
// add extra info about port statuses
for( int i=0; i inputs
final boolean stopAfterFirstRun
final int len
final DataflowQueue control
final int first
BaseProcessInterceptor( List inputs, boolean stop ) {
this.inputs = new ArrayList<>(inputs)
this.stopAfterFirstRun = stop
this.len = inputs.size()
this.control = (DataflowQueue)inputs.get(len-1)
this.first = inputs.findIndexOf { CH.isChannelQueue(it) }
}
@Override
Object messageArrived(final DataflowProcessor processor, final DataflowReadChannel © 2015 - 2025 Weber Informatics LLC | Privacy Policy