Declaration generation

src/generator/WDL/entities/TaskGenerator.js

@@ -31,10 +31,10 @@ export default class TaskGenerator {
 
       this.taskBlockString += buildDeclarations(this.declarations, this.settings);
       this.taskBlockString += this.buildCommand(this.command, this.commandStyle);
-      this.taskBlockString += this.buildSegment(constants.OUTPUT, this.outputMappings);
       this.taskBlockString += this.buildSegment(constants.META, this.meta);
       this.taskBlockString += this.buildSegment(constants.PARAMETER_META, this.parameterMeta);
       this.taskBlockString += this.buildSegment(constants.RUNTIME, this.runtime);
+      this.taskBlockString += this.buildSegment(constants.OUTPUT, this.outputMappings);
 
       this.taskBlockString += `${constants.SCOPE_CLOSE}${EOL}${EOL}`;
     }
@@ -82,7 +82,7 @@ export default class TaskGenerator {
 
       _.forEach(data, (val, key) => {
         res += `${DOUBLE_SCOPE_INDENT}${segmentName === constants.OUTPUT ? val.type : ''} `;
-        res += `${key} ${segmentName === constants.OUTPUT ? constants.EQ : constants.COLON} ${buildValue(val)}${EOL}`;
+        res += `${key}${segmentName === constants.OUTPUT ? ` ${constants.EQ}` : constants.COLON} ${buildValue(val)}${EOL}`;
       });
 
       res += `${SCOPE_INDENT}${constants.SCOPE_CLOSE}${EOL}`;

src/generator/WDL/entities/WorkflowGenerator.js

@@ -19,7 +19,7 @@ export default class WorkflowGenerator {
     this.wfStep = wfStep;
 
     const action = wfStep.action;
-    this.declarations = action.i;
+    this.declarations = this.getDeclarations(wfStep);
     this.outputMappings = wfStep.o;
 
     this.children = wfStep.children;
@@ -32,6 +32,21 @@ export default class WorkflowGenerator {
     this.settings = new Settings(settings);
   }
 
+  // eslint-disable-next-line class-methods-use-this
+  getDeclarations(step) {
+    const declarations = {};
+    _.forEach(step.action.i || {}, (input, name) => {
+      declarations[name] = input;
+    });
+    _.forEach(step.ownDeclarations || {}, (declaration, name) => {
+      declarations[name] = {
+        default: declaration.expression.string,
+        type: declaration.desc.type,
+      };
+    });
+    return declarations;
+  }
+
   renderWorkflow() {
     const EOL = this.settings.getValue('style.eol');
 
@@ -50,7 +65,7 @@ export default class WorkflowGenerator {
   }
 
   renderStepMainBody(step, prosessed) {
-    const declarations = step.action.i;
+    const declarations = this.getDeclarations(step);
     const children = step.children;
 
     let res = '';
@@ -68,18 +83,14 @@ export default class WorkflowGenerator {
     return res;
   }
 
+  // eslint-disable-next-line class-methods-use-this
   getNextOrderedChild(children, processed) {
     let res = '';
-    const isSubset = (source, target) => !_.difference(_.flatten(source), _.flatten(target)).length;
 
     _.forEach(children, (child) => {
       if (_.indexOf(processed, child.name) < 0) {
-        const refs = this.findCallReferences(child);
-
-        if (refs.length === 0 || isSubset(refs, processed)) {
-          res = child.name;
-          return false;
-        }
+        res = child.name;
+        return false;
       }
 
       return true;
@@ -91,32 +102,14 @@ export default class WorkflowGenerator {
     return res;
   }
 
-  findCallReferences(child) {
-    const res = [];
-
-    _.forEach(child.i, (value) => {
-      if (value.inputs && _.size(value.inputs) > 0) {
-        if (_.size(value.inputs) > 1) {
-          throw new Error('Multiple links into one input are prohibited');
-        }
-
-        const connection = value.inputs[0];
-        if (connection.from instanceof Port && connection.from.step.name !== this.wfStep.name) {
-          res.push(connection.from.step.name);
-        }
-      }
-    });
-
-    _.forEach(child.children, (item) => {
-      res.concat(this.findCallReferences(item));
-    });
-
-    return res;
-  }
-
   buildPortValue(value) {
     if (value.desc && value.desc.default && !_.isUndefined(value.desc.default)) {
       return `${value.desc.default}`;
+    } else if (value.desc && value.desc.expression && !_.isUndefined(value.desc.expression)) {
+      return `${value.desc.expression}`;
+    } else if (value.expression && value.expression.type.toLowerCase() !== 'identifier'
+      && value.expression.type.toLowerCase() !== 'memberaccess' && !_.isUndefined(value.expression.string)) {
+      return `${value.expression.string}`;
     } else if (value.inputs && _.size(value.inputs) > 0) {
       if (_.size(value.inputs) > 1) {
         throw new Error('Multiple links into one input are prohibited');

src/generator/WDL/generate.js

@@ -16,8 +16,6 @@ export default function generate(objectModel) {
       if (!val.type) {
         const action = val.action;
         actionsToBeRendered[action.name] = action;
-      } else if (val.type.toLowerCase() === 'workflow') {
-        actionsToBeRendered[val.action.name] = val;
       } else {
         actionSelector(val.children);
       }
@@ -27,11 +25,7 @@ export default function generate(objectModel) {
   actionSelector(objectModel.children);
 
   _.forEach(actionsToBeRendered, (action) => {
-    if (!!action.type && action.type.toLowerCase() === 'workflow') {
-      tasks += new WorkflowGenerator(action, {}).renderWorkflow();
-    } else {
-      tasks += new TaskGenerator(action).renderTask();
-    }
+    tasks += new TaskGenerator(action).renderTask();
   });
 
   return wf + tasks;

src/model/Declaration.js

@@ -19,20 +19,24 @@ export default class Declaration extends Port {
     if (!declaration.expression || !declaration.type) {
       throw new Error('Declaration could be created only using declaration object');
     }
-    super(name, step, {});
-
-    delete this.desc;
+    const expression = extractExpression(declaration.expression);
+    const type = extractType(declaration.type);
+    const desc = {
+      default: expression.string || undefined,
+      type,
+    };
+    super(name, step, desc);
 
     /**
      * Declaration expression extracted object.
-     * @type {string}
+     * @type {Object}
      */
-    this.expression = extractExpression(declaration.expression);
+    this.expression = expression;
     /**
      * Declaration type.
      * @type {string}
      */
-    this.type = extractType(declaration.type);
+    this.type = type;
   }
 
 }

src/parser/WDL/entities/WDLWorkflow.js

@@ -140,6 +140,10 @@ export default class WDLWorkflow {
 
     const scatter = WDLWorkflow.findStepInStructureRecursively(parent, item.scatterName);
     scatter.i[itemName].bind(port);
+    if (collection.type.toLowerCase() !== 'memberaccess' && collection.type.toLowerCase() !== 'identifier'
+      && !_.isUndefined(collection.string)) {
+      scatter.i[itemName].desc.expression = collection.string;
+    }
 
     this.parseBodyBindings(item.attributes.body.list, 'scatter', scatter, ['workflowoutputs', 'meta', 'parametermeta']);
   }
@@ -270,14 +274,25 @@ export default class WDLWorkflow {
     if (!step.i[declaration] && step instanceof Workflow && step.ownDeclarations[declaration]) {
       // remove declaration and add it as an input
       const declarationObj = step.removeDeclaration(declaration);
-      const port = new Port(declaration, step, { type: declarationObj.type });
+      const desc = {
+        type: declarationObj.type,
+      };
+      if (expression.string
+        && expression.type.toLowerCase() !== 'memberaccess' && expression.type.toLowerCase() !== 'identifier') {
+        desc.expression = expression.string;
+      }
+      const port = new Port(declaration, step, desc);
       _.forEach(declarationObj.outputs, conn => conn.to.bind(port));
       step.i[declaration] = port;
     }
 
     if (step.i[declaration]) {
       const bindings = WDLWorkflow.getPortsForBinding(this.workflowStep, parentStep, expression);
       _.forEach(bindings, binding => step.i[declaration].bind(binding));
+      if (expression.string
+        && expression.type.toLowerCase() !== 'memberaccess' && expression.type.toLowerCase() !== 'identifier') {
+        step.i[declaration].expression = expression;
+      }
     } else {
       throw new WDLParserError(`Undeclared variable trying to be assigned: call '${step.name}' --> '${declaration}'`);
     }