This is an automated email from the ASF dual-hosted git repository. sunlan pushed a commit to branch nextflow-perf-issue in repository https://gitbox.apache.org/repos/asf/groovy.git
commit 017ef6da4f4147095272fcb89b857cfb0a0f69ec Author: Daniel Sun <[email protected]> AuthorDate: Sun Jan 19 17:59:06 2020 +0800 Add a test to reproduce the performance issue. If we could work out why generating stubs with antlr2 parser is much faster than parsing source file with antlr2 parser, we should be able to address what compilation steps are skipped, thus we can apply the strategy for generating stubs with Parrot parser too. antlr2-parse: 4.883s elapsed <--- antlr4-parse: 1.497s elapsed antlr2-gen: 0.551s elapsed <--- much less than the time cost by antlr2-parse antlr4-gen: 1.636s elapsed --- .../nextflow/ast/NextflowDSLImpl.groovy | 1190 ++++++++++++++++++++ src/test/groovy/bugs/StubGenTest.groovy | 90 ++ 2 files changed, 1280 insertions(+) diff --git a/src/test-resources/stubgenerator/nextflow/ast/NextflowDSLImpl.groovy b/src/test-resources/stubgenerator/nextflow/ast/NextflowDSLImpl.groovy new file mode 100644 index 0000000..1dbef5e --- /dev/null +++ b/src/test-resources/stubgenerator/nextflow/ast/NextflowDSLImpl.groovy @@ -0,0 +1,1190 @@ +/* + * Copyright 2013-2019, Centre for Genomic Regulation (CRG) + * + * 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 groovy.transform.CompileStatic +import groovy.util.logging.Slf4j +import nextflow.script.BaseScript +import nextflow.script.BodyDef +import nextflow.script.IncludeDef +import nextflow.script.TaskClosure +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.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 +import static nextflow.Const.SCOPE_SEP +import static nextflow.ast.ASTHelpers.createX +import static nextflow.ast.ASTHelpers.isAssignX +import static nextflow.ast.ASTHelpers.isConstX +import static nextflow.ast.ASTHelpers.isMapX +import static nextflow.ast.ASTHelpers.isMethodCallX +import static nextflow.ast.ASTHelpers.isThisX +import static nextflow.ast.ASTHelpers.isTupleX +import static nextflow.ast.ASTHelpers.isVariableX +import static org.codehaus.groovy.ast.tools.GeneralUtils.block +import static org.codehaus.groovy.ast.tools.GeneralUtils.callThisX +import static org.codehaus.groovy.ast.tools.GeneralUtils.closureX +import static org.codehaus.groovy.ast.tools.GeneralUtils.constX +import static org.codehaus.groovy.ast.tools.GeneralUtils.stmt +/** + * Implement some syntax sugars of Nextflow DSL scripting. + * + * @author Paolo Di Tommaso <[email protected]> + */ + +@Slf4j +@CompileStatic +@GroovyASTTransformation(phase = CompilePhase.CONVERSION) +class NextflowDSLImpl implements ASTTransformation { + + static public String OUT_PREFIX = '$out' + + static private Set<String> 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 { + + @Deprecated final static String WORKFLOW_GET = 'get' + final static String WORKFLOW_TAKE = 'take' + final static String WORKFLOW_EMIT = 'emit' + final static String WORKFLOW_MAIN = 'main' + final static String WORKFLOW_PUBLISH = 'publish' + + final static Random RND = new Random() + + final private SourceUnit unit + + private String currentTaskName + + private String currentLabel + + private Set<String> processNames = [] + + private Set<String> workflowNames = [] + + private Set<String> 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 + 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) + } + + // 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, 'load', new ArgumentListExpression()) + 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 { + 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: $args" + + // make sure to add the 'name' after the map item + // (which represent the named parameter attributes) + def newArgs = new ArgumentListExpression() + + // add the workflow body def + if( len != 1 || !(args[0] instanceof ClosureExpression)) { + syntaxError(methodCall, "Invalid workflow definition") + return + } + + final body = (ClosureExpression)args[0] + newArgs.addExpression( constX(name) ) + newArgs.addExpression( makeWorkflowDefWrapper(body,false) ) + + // set the new list as the new arguments + methodCall.setArguments( newArgs ) + } + + + protected Statement normWorkflowParam(ExpressionStatement stat, String type, Set<String> uniqueNames, List<Statement> body) { + MethodCallExpression callx + VariableExpression varx + + if( (callx=isMethodCallX(stat.expression)) && isThisX(callx.objectExpression) ) { + final name = "_${type}_${callx.methodAsString}" + return stmt( callThisX(name, callx.arguments) ) + } + + if( (varx=isVariableX(stat.expression)) ) { + final name = "_${type}_${varx.name}" + return stmt( callThisX(name) ) + } + + if( type == WORKFLOW_EMIT ) { + return createAssignX(stat, body, type, uniqueNames) + } + + if( type == WORKFLOW_PUBLISH ) { + return createAssignX(stat, body, type, uniqueNames) + } + + syntaxError(stat, "Workflow malformed parameter definition") + return stat + } + + protected Statement createAssignX(ExpressionStatement stat, List<Statement> body, String type, Set<String> uniqueNames) { + BinaryExpression binx + MethodCallExpression callx + Expression args=null + + if( (binx=isAssignX(stat.expression)) ) { + // keep the statement in body to allow it to be evaluated + body.add(stat) + // and create method call expr to capture the var name in the emission + final left = (VariableExpression)binx.leftExpression + final name = "_${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}_${var}" + callx = args ? callThisX(name, args) : callThisX(name) + return stmt(callx) + } + + protected boolean hasTo(MethodCallExpression callX) { + def tupleX = isTupleX(callX.arguments) + if( !tupleX ) return false + if( !tupleX.expressions ) return false + def mapX = isMapX(tupleX.expressions[0]) + if( !mapX ) return false + def entry = mapX.getMapEntryExpressions().find { isConstX(it.keyExpression).text=='to' } + return entry != null + } + + protected String getNextName(Set<String> allNames) { + String result + while( true ) { + result = OUT_PREFIX + allNames.size() + if( allNames.add(result) ) + break + } + return result + } + + protected Expression makeWorkflowDefWrapper( ClosureExpression closure, boolean anonymous ) { + + final codeBlock = (BlockStatement) closure.code + final codeStms = codeBlock.statements + final scope = codeBlock.variableScope + + final visited = new HashMap<String,Boolean>(5); + final emitNames = new LinkedHashSet<String>(codeStms.size()) + final wrap = new ArrayList<Statement>(codeStms.size()) + final body = new ArrayList<Statement>(codeStms.size()) + final source = new StringBuilder() + String context = null + String previous = null + for( Statement stm : codeStms ) { + previous = context + context = stm.statementLabel ?: context + // check for changing context + if( context && context != previous ) { + if( visited[context] && visited[previous] ) { + syntaxError(stm, "Unexpected workflow `${context}` context here") + break + } + } + visited[context] = true + + switch (context) { + case WORKFLOW_PUBLISH: + if( !anonymous ) { + syntaxError(stm, "Publish declaration is only allowed in main workflow definition") + } + + case WORKFLOW_GET: + 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 + + default: + body.add(stm) + } + } + // read the closure source + readSource(closure, source, unit, true) + + 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 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<Statement> execStatements = [] + + List<Statement> whenStatements = [] + def whenSource = 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': + iterator.remove() + execStatements << stm + readSource(stm,source,unit) + break + + case 'script': + case 'shell': + iterator.remove() + execStatements << stm + readSource(stm,source,unit) + break + + // capture the statements in a when guard and remove from the current block + case '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) + } + + /* + * 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, currentLabel, 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) + } + + // set the 'script' flag + currentLabel = 'script' + } + + 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 void addWhenGuardCall( List<Statement> 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<Expression> 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, 'when', whenObj) + parent.getStatements().add(0, new ExpressionStatement(method)) + + } + /** + * 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<Expression> newArgs = [] + newArgs << (closure) + newArgs << ( new ConstantExpression(source.toString()) ) + newArgs << ( new ConstantExpression(section) ) + + final variables = fetchVariables(closure,unit) + for( TokenValRef var: variables ) { + def pName = new ConstantExpression(var.name) + def pLine = new ConstantExpression(var.lineNum) + def pCol = new ConstantExpression(var.colNum) + newArgs << createX( TokenValRef, pName, pLine, pCol ) + } + + // invokes the BodyDef constructor + createX( BodyDef, newArgs ) + } + + /** + * Read the user provided script source string + * + * @param node + * @param buffer + * @param unit + */ + private void readSource( ASTNode node, StringBuilder buffer, SourceUnit unit, stripBrackets=false ) { + 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) + if( stripBrackets ) { + line = line.replaceFirst(/}.*$/,'') + if( !line.trim() ) continue + } + } + if( i==first ) { + line = line.substring(colx-1) + if( stripBrackets ) { + line = line.replaceFirst(/^.*\{/,'').trim() + if( !line.trim() ) 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)` + 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 ) + } + } + } + } + } + + /* + * 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' + * (ie. as a constant) in a map expression passed as argument to + * a method call. This allow the syntax + * + * output: + * path 'foo', emit: bar + * + * @param call + */ + protected void fixOutEmitOption(MethodCallExpression call) { + List<Expression> 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<map.mapEntryExpressions.size(); i++ ) { + final entry = map.mapEntryExpressions[i] + final key = isConstX(entry.keyExpression) + final val = isVariableX(entry.valueExpression) + if( key?.text == 'emit' && val ) { + map.mapEntryExpressions[i] = new MapEntryExpression(key, constX(val.text)) + } + } + } + + protected void convertOutputMethod( Expression expression ) { + log.trace "convert > 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','file','set','stdout','path','tuple'] && !nested ) { + // prefix the method name with the string '_out_' + methodCall.setMethod( new ConstantExpression('_out_' + methodName) ) + fixMethodCall(methodCall) + fixOutEmitOption(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( isOutputValWithPropertyExpression(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 + } + } + + protected boolean isOutputValWithPropertyExpression(MethodCallExpression methodCall) { + if( methodCall.methodAsString != '_out_val' ) + 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 ) + } + + /* + * 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: + * <li>1st item: {@code true} if successful or {@code false} otherwise + * <li>2nd item: on error condition the line containing the error in the source script, zero otherwise + * <li>3nd 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 functionNames || 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<TokenValRef> fetchVariables( ClosureExpression closure, SourceUnit unit ) { + def visitor = new VariableVisitor(unit) + visitor.visitClosureExpression(closure) + return visitor.allVariables + } + + } + +} diff --git a/src/test/groovy/bugs/StubGenTest.groovy b/src/test/groovy/bugs/StubGenTest.groovy new file mode 100644 index 0000000..7a76511 --- /dev/null +++ b/src/test/groovy/bugs/StubGenTest.groovy @@ -0,0 +1,90 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you 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 groovy.bugs + +import groovy.transform.CompileStatic +import org.apache.groovy.parser.AbstractParser +import org.apache.groovy.parser.Antlr2Parser +import org.apache.groovy.parser.Antlr4Parser +import org.codehaus.groovy.control.CompilerConfiguration +import org.codehaus.groovy.control.ParserPluginFactory +import org.codehaus.groovy.control.Phases +import org.codehaus.groovy.tools.javac.JavaStubCompilationUnit +import org.junit.Test + +@CompileStatic +final class StubGenTest { + @Test + @CompileStatic + void testStubGenWithAntlr4() { + File destdir = File.createTempDir() + CompilerConfiguration compilerConfiguration = new CompilerConfiguration(CompilerConfiguration.DEFAULT) + compilerConfiguration.setPluginFactory(ParserPluginFactory.antlr4(compilerConfiguration)) + JavaStubCompilationUnit cu = new JavaStubCompilationUnit(compilerConfiguration, new GroovyClassLoader(), destdir) + cu.addSource(StubGenTest.getResource('/stubgenerator/nextflow/ast/NextflowDSLImpl.groovy')) + + def b = System.currentTimeMillis() + cu.compile(Phases.CONVERSION) + def e = System.currentTimeMillis() + + println "antlr4-gen: ${(e - b) / 1000}s elapsed" + } + + @Test + @CompileStatic + void testStubGenWithAntlr2() { + File destdir = File.createTempDir() + CompilerConfiguration compilerConfiguration = new CompilerConfiguration(CompilerConfiguration.DEFAULT) + compilerConfiguration.setPluginFactory(ParserPluginFactory.antlr2()) + JavaStubCompilationUnit cu = new JavaStubCompilationUnit(compilerConfiguration, new GroovyClassLoader(), destdir) + cu.addSource(StubGenTest.getResource('/stubgenerator/nextflow/ast/NextflowDSLImpl.groovy')) + + def b = System.currentTimeMillis() + cu.compile(Phases.CONVERSION) + def e = System.currentTimeMillis() + + println "antlr2-gen: ${(e - b) / 1000}s elapsed" + } + + @Test + @CompileStatic + void testParseWithAntlr4() { + AbstractParser parser = new Antlr4Parser() + File file = new File(StubGenTest.getResource('/stubgenerator/nextflow/ast/NextflowDSLImpl.groovy').toURI()) + + def b = System.currentTimeMillis() + parser.parse(file) + def e = System.currentTimeMillis() + + println "antlr4-parse: ${(e - b) / 1000}s elapsed" + } + + @Test + @CompileStatic + void testParseWithAntlr2() { + AbstractParser parser = new Antlr2Parser() + File file = new File(StubGenTest.getResource('/stubgenerator/nextflow/ast/NextflowDSLImpl.groovy').toURI()) + + def b = System.currentTimeMillis() + parser.parse(file) + def e = System.currentTimeMillis() + + println "antlr2-parse: ${(e - b) / 1000}s elapsed" + } +}
