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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
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/*
* 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.ast
import static nextflow.Const.*
import static nextflow.ast.ASTHelpers.*
import static org.codehaus.groovy.ast.tools.GeneralUtils.*
import groovy.transform.CompileStatic
import groovy.util.logging.Slf4j
import nextflow.NF
import nextflow.script.BaseScript
import nextflow.script.BodyDef
import nextflow.script.IncludeDef
import nextflow.script.TaskClosure
import nextflow.script.TokenEvalCall
import nextflow.script.TokenEnvCall
import nextflow.script.TokenFileCall
import nextflow.script.TokenPathCall
import nextflow.script.TokenStdinCall
import nextflow.script.TokenStdoutCall
import nextflow.script.TokenValCall
import nextflow.script.TokenValRef
import nextflow.script.TokenVar
import org.codehaus.groovy.ast.ASTNode
import org.codehaus.groovy.ast.ClassCodeVisitorSupport
import org.codehaus.groovy.ast.ClassNode
import org.codehaus.groovy.ast.MethodNode
import org.codehaus.groovy.ast.Parameter
import org.codehaus.groovy.ast.VariableScope
import org.codehaus.groovy.ast.expr.ArgumentListExpression
import org.codehaus.groovy.ast.expr.BinaryExpression
import org.codehaus.groovy.ast.expr.CastExpression
import org.codehaus.groovy.ast.expr.ClosureExpression
import org.codehaus.groovy.ast.expr.ConstantExpression
import org.codehaus.groovy.ast.expr.Expression
import org.codehaus.groovy.ast.expr.GStringExpression
import org.codehaus.groovy.ast.expr.ListExpression
import org.codehaus.groovy.ast.expr.MapEntryExpression
import org.codehaus.groovy.ast.expr.MapExpression
import org.codehaus.groovy.ast.expr.MethodCallExpression
import org.codehaus.groovy.ast.expr.PropertyExpression
import org.codehaus.groovy.ast.expr.TupleExpression
import org.codehaus.groovy.ast.expr.UnaryMinusExpression
import org.codehaus.groovy.ast.expr.VariableExpression
import org.codehaus.groovy.ast.stmt.BlockStatement
import org.codehaus.groovy.ast.stmt.ExpressionStatement
import org.codehaus.groovy.ast.stmt.ReturnStatement
import org.codehaus.groovy.ast.stmt.Statement
import org.codehaus.groovy.control.CompilePhase
import org.codehaus.groovy.control.SourceUnit
import org.codehaus.groovy.syntax.SyntaxException
import org.codehaus.groovy.syntax.Token
import org.codehaus.groovy.syntax.Types
import org.codehaus.groovy.transform.ASTTransformation
import org.codehaus.groovy.transform.GroovyASTTransformation
/**
* Implement some syntax sugars of Nextflow DSL scripting.
*
* @author Paolo Di Tommaso
*/
@Slf4j
@CompileStatic
@GroovyASTTransformation(phase = CompilePhase.CONVERSION)
class NextflowDSLImpl implements ASTTransformation {
final static private String WORKFLOW_TAKE = 'take'
final static private String WORKFLOW_EMIT = 'emit'
final static private String WORKFLOW_MAIN = 'main'
final static private String WORKFLOW_PUBLISH = 'publish'
final static private List SCOPES = [WORKFLOW_TAKE, WORKFLOW_EMIT, WORKFLOW_MAIN, WORKFLOW_PUBLISH]
final static public String PROCESS_WHEN = 'when'
final static public String PROCESS_STUB = 'stub'
static public String OUT_PREFIX = '$out'
static private Set RESERVED_NAMES
static {
// method names implicitly defined by the groovy script SHELL
RESERVED_NAMES = ['main','run','runScript'] as Set
// existing method cannot be used for custom script definition
for( def method : BaseScript.getMethods() ) {
RESERVED_NAMES.add(method.name)
}
}
@Override
void visit(ASTNode[] astNodes, SourceUnit unit) {
createVisitor(unit).visitClass((ClassNode)astNodes[1])
}
/*
* create the code visitor
*/
protected ClassCodeVisitorSupport createVisitor( SourceUnit unit ) {
new DslCodeVisitor(unit)
}
@CompileStatic
static class DslCodeVisitor extends ClassCodeVisitorSupport {
final private SourceUnit unit
private String currentTaskName
private String currentLabel
private String bodyLabel
private Set processNames = []
private Set workflowNames = []
private Set functionNames = []
private int anonymousWorkflow
protected SourceUnit getSourceUnit() { unit }
DslCodeVisitor(SourceUnit unit) {
this.unit = unit
}
@Override
void visitMethod(MethodNode node) {
if( node.public && !node.static && !node.synthetic && !node.metaDataMap?.'org.codehaus.groovy.ast.MethodNode.isScriptBody') {
if( !isIllegalName(node.name, node))
functionNames.add(node.name)
}
super.visitMethod(node)
}
@Override
void visitMethodCallExpression(MethodCallExpression methodCall) {
// pre-condition to be verified to apply the transformation
final preCondition = methodCall.objectExpression?.getText() == 'this'
final methodName = methodCall.getMethodAsString()
/*
* intercept the *process* method in order to transform the script closure
*/
if( methodName == 'process' && preCondition ) {
// clear block label
bodyLabel = null
currentLabel = null
currentTaskName = methodName
try {
convertProcessDef(methodCall,sourceUnit)
super.visitMethodCallExpression(methodCall)
}
finally {
currentTaskName = null
}
}
else if( methodName == 'workflow' && preCondition ) {
convertWorkflowDef(methodCall,sourceUnit)
super.visitMethodCallExpression(methodCall)
}
else if( methodName == 'output' && preCondition ) {
convertOutputDef(methodCall,sourceUnit)
super.visitMethodCallExpression(methodCall)
}
// just apply the default behavior
else {
super.visitMethodCallExpression(methodCall)
}
}
@Override
void visitExpressionStatement(ExpressionStatement stm) {
if( stm.text.startsWith('this.include(') && stm.getExpression() instanceof MethodCallExpression ) {
final methodCall = (MethodCallExpression)stm.getExpression()
convertIncludeDef(methodCall)
// this is necessary to invoke the `load` method on the include definition
final loadCall = new MethodCallExpression(methodCall, 'load0', new ArgumentListExpression(new VariableExpression('params')))
stm.setExpression(loadCall)
}
super.visitExpressionStatement(stm)
}
protected void convertIncludeDef(MethodCallExpression call) {
if( call.methodAsString=='include' && call.arguments instanceof ArgumentListExpression ) {
final allArgs = (ArgumentListExpression)call.arguments
if( allArgs.size() != 1 ) {
syntaxError(call, "Not a valid include definition -- it must specify the module path")
return
}
final arg = allArgs[0]
final newArgs = new ArgumentListExpression()
if( arg instanceof ConstantExpression ) {
newArgs.addExpression( createX(IncludeDef, arg) )
}
else if( arg instanceof VariableExpression ) {
// the name of the component i.e. process, workflow, etc to import
final component = arg.getName()
// wrap the name in a `TokenVar` type
final token = createX(TokenVar, new ConstantExpression(component))
// create a new `IncludeDef` object
newArgs.addExpression(createX(IncludeDef, token))
}
else if( arg instanceof CastExpression && arg.getExpression() instanceof VariableExpression) {
def cast = (CastExpression)arg
// the name of the component i.e. process, workflow, etc to import
final component = (cast.expression as VariableExpression).getName()
// wrap the name in a `TokenVar` type
final token = createX(TokenVar, new ConstantExpression(component))
// the alias to give it
final alias = constX(cast.type.name)
newArgs.addExpression( createX(IncludeDef, token, alias) )
}
else if( arg instanceof ClosureExpression ) {
// multiple modules inclusion
final block = (BlockStatement)arg.getCode()
final modulesList = new ListExpression()
for( Statement stm : block.statements ) {
if( stm instanceof ExpressionStatement ) {
CastExpression castX
VariableExpression varX
Expression moduleX
if( (varX=isVariableX(stm.expression)) ) {
def name = constX(varX.name)
moduleX = createX(IncludeDef.Module, name)
}
else if( (castX=isCastX(stm.expression)) && (varX=isVariableX(castX.expression)) ) {
def name = constX(varX.name)
final alias = constX(castX.type.name)
moduleX = createX(IncludeDef.Module, name, alias)
}
else {
syntaxError(call, "Not a valid include module name")
return
}
modulesList.addExpression(moduleX)
}
else {
syntaxError(call, "Not a valid include module name")
return
}
}
newArgs.addExpression( createX(IncludeDef, modulesList) )
}
else {
syntaxError(call, "Not a valid include definition -- it must specify the module path as a string")
return
}
call.setArguments(newArgs)
}
else if( call.objectExpression instanceof MethodCallExpression ) {
convertIncludeDef((MethodCallExpression)call.objectExpression)
}
}
/*
* this method transforms the DSL definition
*
* workflow foo {
* code
* }
*
* into a method invocation as
*
* workflow('foo', { -> code })
*
*/
protected void convertWorkflowDef(MethodCallExpression methodCall, SourceUnit unit) {
log.trace "Convert 'workflow' ${methodCall.arguments}"
assert methodCall.arguments instanceof ArgumentListExpression
def args = (ArgumentListExpression)methodCall.arguments
def len = args.size()
// anonymous workflow definition
if( len == 1 && args[0] instanceof ClosureExpression ) {
if( anonymousWorkflow++ > 0 ) {
unit.addError( new SyntaxException("Duplicate entry workflow definition", methodCall.lineNumber, methodCall.columnNumber+8))
return
}
def newArgs = new ArgumentListExpression()
def body = (ClosureExpression)args[0]
newArgs.addExpression( makeWorkflowDefWrapper(body,true) )
methodCall.setArguments( newArgs )
return
}
// extract the first argument which has to be a method-call expression
// the name of this method represent the *workflow* name
if( len != 1 || !args[0].class.isAssignableFrom(MethodCallExpression) ) {
log.debug "Missing name in workflow definition at line: ${methodCall.lineNumber}"
unit.addError( new SyntaxException("Workflow definition syntax error -- A string identifier must be provided after the `workflow` keyword", methodCall.lineNumber, methodCall.columnNumber+8))
return
}
final nested = args[0] as MethodCallExpression
final name = nested.getMethodAsString()
// check the process name is not defined yet
if( isIllegalName(name, methodCall) ) {
return
}
workflowNames.add(name)
// the nested method arguments are the arguments to be passed
// to the process definition, plus adding the process *name*
// as an extra item in the arguments list
args = (ArgumentListExpression)nested.getArguments()
len = args.size()
log.trace "Workflow name: $name with args: $args"
// make sure to add the 'name' after the map item
// (which represent the named parameter attributes)
def newArgs = new ArgumentListExpression()
// add the workflow body def
if( len != 1 || !(args[0] instanceof ClosureExpression)) {
syntaxError(methodCall, "Invalid workflow definition")
return
}
final body = (ClosureExpression)args[0]
newArgs.addExpression( constX(name) )
newArgs.addExpression( makeWorkflowDefWrapper(body,false) )
// set the new list as the new arguments
methodCall.setArguments( newArgs )
}
protected Statement normWorkflowParam(ExpressionStatement stat, String type, Set uniqueNames, List body) {
MethodCallExpression callx
VariableExpression varx
if( (callx=isMethodCallX(stat.expression)) && isThisX(callx.objectExpression) ) {
final name = "_${type}_${callx.methodAsString}"
return stmt( callThisX(name, callx.arguments) )
}
if( (varx=isVariableX(stat.expression)) ) {
final name = "_${type}_${varx.name}"
return stmt( callThisX(name) )
}
if( type == WORKFLOW_EMIT ) {
return createAssignX(stat, body, type, uniqueNames)
}
syntaxError(stat, "Workflow malformed parameter definition")
return stat
}
protected Statement createAssignX(ExpressionStatement stat, List body, String type, Set uniqueNames) {
BinaryExpression binx
MethodCallExpression callx
Expression args=null
if( (binx=isAssignX(stat.expression)) ) {
// keep the statement in body to allow it to be evaluated
body.add(stat)
// and create method call expr to capture the var name in the emission
final left = (VariableExpression)binx.leftExpression
final name = "_${type}_${left.name}"
return stmt( callThisX(name) )
}
if( (callx=isMethodCallX(stat.expression)) && callx.objectExpression.text!='this' && hasTo(callx)) {
// keep the args
args = callx.arguments
// replace the method call expression with a property
stat.expression = new PropertyExpression(callx.objectExpression, callx.method)
// then, fallback to default case
}
// wrap the expression into a assignment expression
final var = getNextName(uniqueNames)
final left = new VariableExpression(var)
final right = stat.expression
final token = new Token(Types.ASSIGN, '=', -1, -1)
final assign = new BinaryExpression(left, token, right)
body.add(stmt(assign))
// the call method statement for the emit declaration
final name="_${type}_${var}"
callx = args ? callThisX(name, args) : callThisX(name)
return stmt(callx)
}
protected boolean hasTo(MethodCallExpression callX) {
def tupleX = isTupleX(callX.arguments)
if( !tupleX ) return false
if( !tupleX.expressions ) return false
def mapX = isMapX(tupleX.expressions[0])
if( !mapX ) return false
def entry = mapX.getMapEntryExpressions().find { isConstX(it.keyExpression).text=='to' }
return entry != null
}
protected String getNextName(Set allNames) {
String result
while( true ) {
result = OUT_PREFIX + allNames.size()
if( allNames.add(result) )
break
}
return result
}
protected Statement normWorkflowPublish(ExpressionStatement stm) {
if( stm.expression !instanceof BinaryExpression ) {
syntaxError(stm, "Invalid workflow publish statement")
return stm
}
final binaryX = (BinaryExpression)stm.expression
if( binaryX.operation.type != Types.RIGHT_SHIFT ) {
syntaxError(stm, "Invalid workflow publish statement")
return stm
}
return stmt( callThisX('_publish_target', args(binaryX.leftExpression, binaryX.rightExpression)) )
}
protected Expression makeWorkflowDefWrapper( ClosureExpression closure, boolean anonymous ) {
final codeBlock = (BlockStatement) closure.code
final codeStms = codeBlock.statements
final scope = codeBlock.variableScope
final visited = new HashMap(5);
final emitNames = new LinkedHashSet(codeStms.size())
final wrap = new ArrayList(codeStms.size())
final body = new ArrayList(codeStms.size())
final source = new StringBuilder()
String context = null
String previous = null
for( Statement stm : codeStms ) {
previous = context
context = stm.statementLabel ?: context
// check for changing context
if( context && context != previous ) {
if( visited[context] && visited[previous] ) {
syntaxError(stm, "Unexpected workflow `${context}` context here")
break
}
}
visited[context] = true
switch (context) {
case WORKFLOW_TAKE:
case WORKFLOW_EMIT:
if( !(stm instanceof ExpressionStatement) ) {
syntaxError(stm, "Workflow malformed parameter definition")
break
}
wrap.add(normWorkflowParam(stm as ExpressionStatement, context, emitNames, body))
break
case WORKFLOW_MAIN:
body.add(stm)
break
case WORKFLOW_PUBLISH:
if( !(stm instanceof ExpressionStatement) ) {
syntaxError(stm, "Invalid workflow publish statement")
break
}
body.add(normWorkflowPublish(stm as ExpressionStatement))
break
default:
if( context ) {
def opts = SCOPES.closest(context)
def msg = "Unknown execution scope '$context:'"
if( opts ) msg += " -- Did you mean ${opts.collect{"'$it'"}.join(', ')}"
syntaxError(stm, msg)
}
body.add(stm)
}
}
// read the closure source
readSource(closure, source, unit)
final bodyClosure = closureX(null, block(scope, body))
final invokeBody = makeScriptWrapper(bodyClosure, source.toString(), 'workflow', unit)
wrap.add( stmt(invokeBody) )
closureX(null, block(scope, wrap))
}
protected void syntaxError(ASTNode node, String message) {
int line = node.lineNumber
int coln = node.columnNumber
unit.addError( new SyntaxException(message,line,coln))
}
/**
* Transform targets in the workflow output definition:
*
* output {
* 'foo' { ... }
* }
*
* becomes:
*
* output {
* target('foo') { ... }
* }
*
* @param methodCall
* @param unit
*/
protected void convertOutputDef(MethodCallExpression methodCall, SourceUnit unit) {
log.trace "Convert 'output' ${methodCall.arguments}"
assert methodCall.arguments instanceof ArgumentListExpression
final arguments = (ArgumentListExpression)methodCall.arguments
if( arguments.size() != 1 || arguments[0] !instanceof ClosureExpression ) {
syntaxError(methodCall, "Invalid output definition")
return
}
final closure = (ClosureExpression)arguments[0]
final block = (BlockStatement)closure.code
for( Statement stmt : block.statements ) {
if( stmt !instanceof ExpressionStatement ) {
syntaxError(stmt, "Invalid publish target definition")
return
}
final stmtExpr = (ExpressionStatement)stmt
if( stmtExpr.expression !instanceof MethodCallExpression ) {
syntaxError(stmt, "Invalid publish target definition")
return
}
final call = (MethodCallExpression)stmtExpr.expression
assert call.arguments instanceof ArgumentListExpression
final targetArgs = (ArgumentListExpression)call.arguments
if( targetArgs.size() != 1 || targetArgs[0] !instanceof ClosureExpression ) {
syntaxError(stmt, "Invalid publish target definition")
return
}
final targetName = call.method
final targetBody = (ClosureExpression)targetArgs[0]
stmtExpr.expression = callThisX('target', args(targetName, targetBody))
}
}
/**
* Transform a DSL `process` definition into a proper method invocation
*
* @param methodCall
* @param unit
*/
protected void convertProcessBlock( MethodCallExpression methodCall, SourceUnit unit ) {
log.trace "Apply task closure transformation to method call: $methodCall"
final args = methodCall.arguments as ArgumentListExpression
final lastArg = args.expressions.size()>0 ? args.getExpression(args.expressions.size()-1) : null
final isClosure = lastArg instanceof ClosureExpression
if( isClosure ) {
// the block holding all the statements defined in the process (closure) definition
final block = (lastArg as ClosureExpression).code as BlockStatement
/*
* iterate over the list of statements to:
* - converts the method after the 'input:' label as input parameters
* - converts the method after the 'output:' label as output parameters
* - collect all the statement after the 'exec:' label
*/
def source = new StringBuilder()
List execStatements = []
List whenStatements = []
def whenSource = new StringBuilder()
List stubStatements = []
def stubSource = new StringBuilder()
def iterator = block.getStatements().iterator()
while( iterator.hasNext() ) {
// get next statement
Statement stm = iterator.next()
// keep track of current block label
currentLabel = stm.statementLabel ?: currentLabel
switch(currentLabel) {
case 'input':
if( stm instanceof ExpressionStatement ) {
fixLazyGString( stm )
fixStdinStdout( stm )
convertInputMethod( stm.getExpression() )
}
break
case 'output':
if( stm instanceof ExpressionStatement ) {
fixLazyGString( stm )
fixStdinStdout( stm )
convertOutputMethod( stm.getExpression() )
}
break
case 'exec':
bodyLabel = currentLabel
iterator.remove()
execStatements << stm
readSource(stm,source,unit)
break
case 'script':
case 'shell':
bodyLabel = currentLabel
iterator.remove()
execStatements << stm
readSource(stm,source,unit)
break
case PROCESS_STUB:
iterator.remove()
stubStatements << stm
readSource(stm,stubSource,unit)
break
// capture the statements in a when guard and remove from the current block
case PROCESS_WHEN:
if( iterator.hasNext() ) {
iterator.remove()
whenStatements << stm
readSource(stm,whenSource,unit)
break
}
// when entering in this branch means that this is the last statement,
// which is supposed to be the task command
// hence if no previous `when` statement has been processed, a syntax error is returned
else if( !whenStatements ) {
int line = methodCall.lineNumber
int coln = methodCall.columnNumber
unit.addError(new SyntaxException("Invalid process definition -- Empty `when` or missing `script` statement", line, coln))
return
}
else
break
default:
if(currentLabel) {
def line = stm.getLineNumber()
def coln = stm.getColumnNumber()
unit.addError(new SyntaxException("Invalid process definition -- Unknown keyword `$currentLabel`",line,coln))
return
}
fixLazyGString(stm)
fixDirectiveWithNegativeValue(stm) // Fixes #180
}
}
/*
* add the `when` block if found
*/
if( whenStatements ) {
addWhenGuardCall(whenStatements, whenSource, block)
}
/*
* add try `stub` block if found
*/
if( stubStatements ) {
final newBLock = addStubCall(stubStatements, stubSource, block)
newBLock.visit(new TaskCmdXformVisitor(unit))
}
/*
* wrap all the statements after the 'exec:' label by a new closure containing them (in a new block)
*/
final len = block.statements.size()
boolean done = false
if( execStatements ) {
// create a new Closure
def execBlock = new BlockStatement(execStatements, new VariableScope(block.variableScope))
def execClosure = new ClosureExpression( Parameter.EMPTY_ARRAY, execBlock )
// append the new block to the
// set the 'script' flag parameter
def wrap = makeScriptWrapper(execClosure, source, bodyLabel, unit)
block.addStatement( new ExpressionStatement(wrap) )
if( bodyLabel == 'script' )
block.visit(new TaskCmdXformVisitor(unit))
done = true
}
// when only the `stub` block is defined add an empty command
else if ( !bodyLabel && stubStatements ) {
final cmd = 'true'
final list = new ArrayList(1);
list.add( new ExpressionStatement(constX(cmd)) )
final dummyBlock = new BlockStatement( list, new VariableScope(block.variableScope))
final dummyClosure = new ClosureExpression( Parameter.EMPTY_ARRAY, dummyBlock )
// append the new block to the
// set the 'script' flag parameter
final wrap = makeScriptWrapper(dummyClosure, cmd, 'script', unit)
block.addStatement( new ExpressionStatement(wrap) )
done = true
}
/*
* when the last statement is a string script, the 'script:' label can be omitted
*/
else if( len ) {
def stm = block.getStatements().get(len-1)
readSource(stm,source,unit)
if ( stm instanceof ReturnStatement ){
done = wrapExpressionWithClosure(block, stm.getExpression(), len, source, unit)
}
else if ( stm instanceof ExpressionStatement ) {
done = wrapExpressionWithClosure(block, stm.getExpression(), len, source, unit)
}
// apply command variables escape
stm.visit(new TaskCmdXformVisitor(unit))
}
if (!done) {
log.trace "Invalid 'process' definition -- Process must terminate with string expression"
int line = methodCall.lineNumber
int coln = methodCall.columnNumber
unit.addError( new SyntaxException("Invalid process definition -- Make sure the process ends with a script wrapped by quote characters",line,coln))
}
}
}
/**
* Converts a `when` block into a when method call expression. The when code is converted into a
* closure expression and set a `when` directive in the process configuration properties.
*
* See {@link nextflow.script.ProcessConfig#configProperties}
* See {@link nextflow.processor.TaskConfig#getGuard(java.lang.String)}
*/
protected BlockStatement addWhenGuardCall( List statements, StringBuilder source, BlockStatement parent ) {
createBlock0(PROCESS_WHEN, statements, source, parent)
}
protected BlockStatement addStubCall(List statements, StringBuilder source, BlockStatement parent ) {
createBlock0(PROCESS_STUB, statements, source, parent)
}
protected BlockStatement createBlock0( String blockName, List statements, StringBuilder source, BlockStatement parent ) {
// wrap the code block into a closure expression
def block = new BlockStatement(statements, new VariableScope(parent.variableScope))
def closure = new ClosureExpression( Parameter.EMPTY_ARRAY, block )
// the closure expression is wrapped itself into a TaskClosure object
// in order to capture the closure source other than the closure code
List newArgs = []
newArgs << closure
newArgs << new ConstantExpression(source.toString())
def whenObj = createX( TaskClosure, newArgs )
// creates a method call expression for the method `when`
def method = new MethodCallExpression(VariableExpression.THIS_EXPRESSION, blockName, whenObj)
parent.getStatements().add(0, new ExpressionStatement(method))
return block
}
/**
* Wrap the user provided piece of code, either a script or a closure with a {@code BodyDef} object
*
* @param closure
* @param source
* @param scriptOrNative
* @param unit
* @return a {@code BodyDef} object
*/
private Expression makeScriptWrapper( ClosureExpression closure, CharSequence source, String section, SourceUnit unit ) {
final List newArgs = []
newArgs << (closure)
newArgs << ( new ConstantExpression(source.toString()) )
newArgs << ( new ConstantExpression(section) )
// collect all variable tokens and pass them as single list argument
final variables = fetchVariables(closure,unit)
final listArg = new ArrayList(variables.size())
for( TokenValRef var: variables ) {
def pName = new ConstantExpression(var.name)
def pLine = new ConstantExpression(var.lineNum)
def pCol = new ConstantExpression(var.colNum)
listArg << createX( TokenValRef, pName, pLine, pCol )
}
newArgs << ( new ListExpression(listArg) )
// invokes the BodyDef constructor
createX( BodyDef, newArgs )
}
/**
* Read the user provided script source string
*
* @param node
* @param buffer
* @param unit
*/
private void readSource( Statement node, StringBuilder buffer, SourceUnit unit ) {
final colx = node.getColumnNumber()
final colz = node.getLastColumnNumber()
final first = node.getLineNumber()
final last = node.getLastLineNumber()
for( int i = first; i <= last; i++ ) {
final line = unit.source.getLine(i, null)
// prepend first-line indent
if( i == first ) {
int k = 0
while( k < line.size() && line[k] == ' ' )
k++
buffer.append( line.substring(0, k) )
}
final begin = (i == first) ? colx - 1 : 0
final end = (i == last) ? colz - 1 : line.size()
buffer.append( line.substring(begin, end) ).append('\n')
}
}
private void readSource( ClosureExpression node, StringBuilder buffer, SourceUnit unit ) {
final colx = node.getColumnNumber()
final colz = node.getLastColumnNumber()
final first = node.getLineNumber()
final last = node.getLastLineNumber()
for( int i=first; i<=last; i++ ) {
def line = unit.source.getLine(i, null)
if( i==last ) {
line = line.substring(0,colz-1).replaceFirst(/}.*$/,'')
if( !line.trim() ) continue
}
if( i==first ) {
line = line.substring(colx-1).replaceFirst(/^.*\{/,'').trim()
if( !line ) continue
}
buffer.append(line) .append('\n')
}
}
protected void fixLazyGString( Statement stm ) {
if( stm instanceof ExpressionStatement && stm.getExpression() instanceof MethodCallExpression ) {
new GStringToLazyVisitor(unit).visitExpressionStatement(stm)
}
}
protected void fixDirectiveWithNegativeValue( Statement stm ) {
if( stm instanceof ExpressionStatement && stm.getExpression() instanceof BinaryExpression ) {
def binary = (BinaryExpression)stm.getExpression()
if(!(binary.leftExpression instanceof VariableExpression))
return
if( binary.operation.type != Types.MINUS )
return
// -- transform the binary expression into a method call expression
// where the left expression represents the method name to invoke
def methodName = ((VariableExpression)binary.leftExpression).name
// -- wrap the value into a minus operator
def value = (Expression)new UnaryMinusExpression( binary.rightExpression )
def args = new ArgumentListExpression( [value] )
// -- create the method call expression and replace it to the binary expression
def call = new MethodCallExpression(new VariableExpression('this'), methodName, args)
stm.setExpression(call)
}
}
protected void fixStdinStdout( ExpressionStatement stm ) {
// transform the following syntax:
// `stdin from x` --> stdin() from (x)
// `stdout into x` --> `stdout() into (x)`
VariableExpression varX
if( stm.expression instanceof PropertyExpression ) {
def expr = (PropertyExpression)stm.expression
def obj = expr.objectExpression
def prop = expr.property as ConstantExpression
def target = new VariableExpression(prop.text)
if( obj instanceof MethodCallExpression ) {
def methodCall = obj as MethodCallExpression
if( 'stdout' == methodCall.getMethodAsString() ) {
def stdout = new MethodCallExpression( new VariableExpression('this'), 'stdout', new ArgumentListExpression() )
def into = new MethodCallExpression(stdout, 'into', new ArgumentListExpression(target))
// remove replace the old one with the new one
stm.setExpression( into )
}
else if( 'stdin' == methodCall.getMethodAsString() ) {
def stdin = new MethodCallExpression( new VariableExpression('this'), 'stdin', new ArgumentListExpression() )
def from = new MethodCallExpression(stdin, 'from', new ArgumentListExpression(target))
// remove replace the old one with the new one
stm.setExpression( from )
}
}
}
// transform the following syntax:
// `stdout into (x,y,..)` --> `stdout() into (x,y,..)`
else if( stm.expression instanceof MethodCallExpression ) {
def methodCall = (MethodCallExpression)stm.expression
if( 'stdout' == methodCall.getMethodAsString() ) {
def args = methodCall.getArguments()
if( args instanceof ArgumentListExpression && args.getExpressions() && args.getExpression(0) instanceof MethodCallExpression ) {
def methodCall2 = (MethodCallExpression)args.getExpression(0)
def args2 = methodCall2.getArguments()
if( args2 instanceof ArgumentListExpression && methodCall2.methodAsString == 'into') {
def vars = args2.getExpressions()
def stdout = new MethodCallExpression( new VariableExpression('this'), 'stdout', new ArgumentListExpression() )
def into = new MethodCallExpression(stdout, 'into', new ArgumentListExpression(vars))
// remove replace the old one with the new one
stm.setExpression( into )
}
}
}
}
else if( (varX=isVariableX(stm.expression)) && (varX.name=='stdin' || varX.name=='stdout') && NF.isDsl2() ) {
final name = varX.name=='stdin' ? '_in_stdin' : '_out_stdout'
final call = new MethodCallExpression( new VariableExpression('this'), name, new ArgumentListExpression() )
// remove replace the old one with the new one
stm.setExpression(call)
}
}
/*
* handle *input* parameters
*/
protected void convertInputMethod( Expression expression ) {
log.trace "convert > input expression: $expression"
if( expression instanceof MethodCallExpression ) {
def methodCall = expression as MethodCallExpression
def methodName = methodCall.getMethodAsString()
def nested = methodCall.objectExpression instanceof MethodCallExpression
log.trace "convert > input method: $methodName"
if( methodName in ['val','env','file','each','set','stdin','path','tuple'] ) {
//this methods require a special prefix
if( !nested )
methodCall.setMethod( new ConstantExpression('_in_' + methodName) )
fixMethodCall(methodCall)
}
/*
* Handles a GString a file name, like this:
*
* input:
* file x name "$var_name" from q
*
*/
else if( methodName == 'name' && isWithinMethod(expression, 'file') ) {
varToConstX(methodCall.getArguments())
}
// invoke on the next method call
if( expression.objectExpression instanceof MethodCallExpression ) {
convertInputMethod(methodCall.objectExpression)
}
}
else if( expression instanceof PropertyExpression ) {
// invoke on the next method call
if( expression.objectExpression instanceof MethodCallExpression ) {
convertInputMethod(expression.objectExpression)
}
}
}
protected boolean isWithinMethod(MethodCallExpression method, String name) {
if( method.objectExpression instanceof MethodCallExpression ) {
return isWithinMethod(method.objectExpression as MethodCallExpression, name)
}
return method.getMethodAsString() == name
}
/**
* Transform a map entry `emit: something` into `emit: 'something'
* and `topic: something` into `topic: 'something'
* (ie. as a constant) in a map expression passed as argument to
* a method call. This allow the syntax
*
* output:
* path 'foo', emit: bar, topic: baz
*
* @param call
*/
protected void fixOutEmitAndTopicOptions(MethodCallExpression call) {
List args = isTupleX(call.arguments)?.expressions
if( !args ) return
if( args.size()<2 && (args.size()!=1 || call.methodAsString!='_out_stdout')) return
MapExpression map = isMapX(args[0])
if( !map ) return
for( int i=0; i output expression: $expression"
if( !(expression instanceof MethodCallExpression) ) {
return
}
def methodCall = expression as MethodCallExpression
def methodName = methodCall.getMethodAsString()
def nested = methodCall.objectExpression instanceof MethodCallExpression
log.trace "convert > output method: $methodName"
if( methodName in ['val','env','eval','file','set','stdout','path','tuple'] && !nested ) {
// prefix the method name with the string '_out_'
methodCall.setMethod( new ConstantExpression('_out_' + methodName) )
fixMethodCall(methodCall)
fixOutEmitAndTopicOptions(methodCall)
}
else if( methodName in ['into','mode'] ) {
fixMethodCall(methodCall)
}
// continue to traverse
if( methodCall.objectExpression instanceof MethodCallExpression ) {
convertOutputMethod(methodCall.objectExpression)
}
}
private boolean withinTupleMethod
private boolean withinEachMethod
/**
* This method converts the a method call argument from a Variable to a Constant value
* so that it is possible to reference variable that not yet exist
*
* @param methodCall The method object for which it is required to change args definition
* @param flagVariable Whenever append a flag specified if the variable replacement has been applied
* @param index The index of the argument to modify
* @return
*/
protected void fixMethodCall( MethodCallExpression methodCall ) {
final name = methodCall.methodAsString
withinTupleMethod = name == '_in_set' || name == '_out_set' || name == '_in_tuple' || name == '_out_tuple'
withinEachMethod = name == '_in_each'
try {
if( isOutputWithPropertyExpression(methodCall) ) {
// transform an output value declaration such
// output: val( obj.foo )
// to
// output: val({ obj.foo })
wrapPropertyToClosure((ArgumentListExpression)methodCall.getArguments())
}
else
varToConstX(methodCall.getArguments())
} finally {
withinTupleMethod = false
withinEachMethod = false
}
}
static final private List OUT_PROPERTY_VALID_TYPES = ['_out_val', '_out_env', '_out_file', '_out_path']
protected boolean isOutputWithPropertyExpression(MethodCallExpression methodCall) {
if( methodCall.methodAsString !in OUT_PROPERTY_VALID_TYPES )
return false
if( methodCall.getArguments() instanceof ArgumentListExpression ) {
def args = (ArgumentListExpression)methodCall.getArguments()
if( args.size()==0 || args.size()>2 )
return false
return args.last() instanceof PropertyExpression
}
return false
}
protected void wrapPropertyToClosure(ArgumentListExpression expr) {
final args = expr as ArgumentListExpression
final property = (PropertyExpression) args.last()
final closure = wrapPropertyToClosure(property)
args.getExpressions().set(args.size()-1, closure)
}
protected ClosureExpression wrapPropertyToClosure(PropertyExpression property) {
def block = new BlockStatement()
block.addStatement( new ExpressionStatement(property) )
def closure = new ClosureExpression( Parameter.EMPTY_ARRAY, block )
closure.variableScope = new VariableScope(block.variableScope)
return closure
}
protected Expression varToStrX( Expression expr ) {
if( expr instanceof VariableExpression ) {
def name = ((VariableExpression) expr).getName()
return createX( TokenVar, new ConstantExpression(name) )
}
else if( expr instanceof PropertyExpression ) {
// transform an output declaration such
// output: tuple val( obj.foo )
// to
// output: tuple val({ obj.foo })
return wrapPropertyToClosure(expr)
}
if( expr instanceof TupleExpression ) {
def i = 0
def list = expr.getExpressions()
for( Expression item : list ) {
list[i++] = varToStrX(item)
}
return expr
}
return expr
}
protected Expression varToConstX( Expression expr ) {
if( expr instanceof VariableExpression ) {
// when it is a variable expression, replace it with a constant representing
// the variable name
def name = ((VariableExpression) expr).getName()
/*
* the 'stdin' is used as placeholder for the standard input in the tuple definition. For example:
*
* input:
* tuple( stdin, .. ) from q
*/
if( name == 'stdin' && withinTupleMethod )
return createX( TokenStdinCall )
/*
* input:
* tuple( stdout, .. )
*/
else if ( name == 'stdout' && withinTupleMethod )
return createX( TokenStdoutCall )
else
return createX( TokenVar, new ConstantExpression(name) )
}
if( expr instanceof MethodCallExpression ) {
def methodCall = expr as MethodCallExpression
/*
* replace 'file' method call in the tuple definition, for example:
*
* input:
* tuple( file(fasta:'*.fa'), .. ) from q
*/
if( methodCall.methodAsString == 'file' && (withinTupleMethod || withinEachMethod) ) {
def args = (TupleExpression) varToConstX(methodCall.arguments)
return createX( TokenFileCall, args )
}
else if( methodCall.methodAsString == 'path' && (withinTupleMethod || withinEachMethod) ) {
def args = (TupleExpression) varToConstX(methodCall.arguments)
return createX( TokenPathCall, args )
}
/*
* input:
* tuple( env(VAR_NAME) ) from q
*/
if( methodCall.methodAsString == 'env' && withinTupleMethod ) {
def args = (TupleExpression) varToStrX(methodCall.arguments)
return createX( TokenEnvCall, args )
}
if( methodCall.methodAsString == 'eval' && withinTupleMethod ) {
def args = (TupleExpression) varToStrX(methodCall.arguments)
return createX( TokenEvalCall, args )
}
/*
* input:
* tuple val(x), .. from q
*/
if( methodCall.methodAsString == 'val' && withinTupleMethod ) {
def args = (TupleExpression) varToStrX(methodCall.arguments)
return createX( TokenValCall, args )
}
}
// -- TupleExpression or ArgumentListExpression
if( expr instanceof TupleExpression ) {
def i = 0
def list = expr.getExpressions()
for( Expression item : list ) {
list[i++] = varToConstX(item)
}
return expr
}
return expr
}
/**
* Wrap a generic expression with in a closure expression
*
* @param block The block to which the resulting closure has to be appended
* @param expr The expression to the wrapped in a closure
* @param len
* @return A tuple in which:
* 1st item: {@code true} if successful or {@code false} otherwise
* 2nd item: on error condition the line containing the error in the source script, zero otherwise
* 3rd item: on error condition the column containing the error in the source script, zero otherwise
*
*/
protected boolean wrapExpressionWithClosure( BlockStatement block, Expression expr, int len, CharSequence source, SourceUnit unit ) {
if( expr instanceof GStringExpression || expr instanceof ConstantExpression ) {
// remove the last expression
block.statements.remove(len-1)
// and replace it by a wrapping closure
def closureExp = new ClosureExpression( Parameter.EMPTY_ARRAY, new ExpressionStatement(expr) )
closureExp.variableScope = new VariableScope(block.variableScope)
// append to the list of statement
//def wrap = newObj(BodyDef, closureExp, new ConstantExpression(source.toString()), ConstantExpression.TRUE)
def wrap = makeScriptWrapper(closureExp, source, 'script', unit )
block.statements.add( new ExpressionStatement(wrap) )
return true
}
else if( expr instanceof ClosureExpression ) {
// do not touch it
return true
}
else {
log.trace "Invalid process result expression: ${expr} -- Only constant or string expression can be used"
}
return false
}
protected boolean isIllegalName(String name, ASTNode node) {
if( name in RESERVED_NAMES ) {
unit.addError( new SyntaxException("Identifier `$name` is reserved for internal use", node.lineNumber, node.columnNumber+8) )
return true
}
if( name in workflowNames || name in processNames ) {
unit.addError( new SyntaxException("Identifier `$name` is already used by another definition", node.lineNumber, node.columnNumber+8) )
return true
}
if( name.contains(SCOPE_SEP) ) {
def offset = 8+2+ name.indexOf(SCOPE_SEP)
unit.addError( new SyntaxException("Process and workflow names cannot contain colon character", node.lineNumber, node.columnNumber+offset) )
return true
}
return false
}
/**
* This method handle the process definition, so that it transform the user entered syntax
* process myName ( named: args, .. ) { code .. }
*
* into
* process ( [named:args,..], String myName ) { }
*
* @param methodCall
* @param unit
*/
protected void convertProcessDef( MethodCallExpression methodCall, SourceUnit unit ) {
log.trace "Converts 'process' ${methodCall.arguments}"
assert methodCall.arguments instanceof ArgumentListExpression
def list = (methodCall.arguments as ArgumentListExpression).getExpressions()
// extract the first argument which has to be a method-call expression
// the name of this method represent the *process* name
if( list.size() != 1 || !list[0].class.isAssignableFrom(MethodCallExpression) ) {
log.debug "Missing name in process definition at line: ${methodCall.lineNumber}"
unit.addError( new SyntaxException("Process definition syntax error -- A string identifier must be provided after the `process` keyword", methodCall.lineNumber, methodCall.columnNumber+7))
return
}
def nested = list[0] as MethodCallExpression
def name = nested.getMethodAsString()
// check the process name is not defined yet
if( isIllegalName(name, methodCall) ) {
return
}
processNames.add(name)
// the nested method arguments are the arguments to be passed
// to the process definition, plus adding the process *name*
// as an extra item in the arguments list
def args = nested.getArguments() as ArgumentListExpression
log.trace "Process name: $name with args: $args"
// make sure to add the 'name' after the map item
// (which represent the named parameter attributes)
list = args.getExpressions()
if( list.size()>0 && list[0] instanceof MapExpression ) {
list.add(1, new ConstantExpression(name))
}
else {
list.add(0, new ConstantExpression(name))
}
// set the new list as the new arguments
methodCall.setArguments( args )
// now continue as before !
convertProcessBlock(methodCall, unit)
}
/**
* Fetch all the variable references in a closure expression.
*
* @param closure
* @param unit
* @return The set of variable names referenced in the script. NOTE: it includes properties in the form {@code object.propertyName}
*/
protected Set fetchVariables( ClosureExpression closure, SourceUnit unit ) {
def visitor = new VariableVisitor(unit)
visitor.visitClosureExpression(closure)
return visitor.allVariables
}
}
}
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