Merge pull request #129 from rabix/maint/march-2021

Maint/march 2021

package.json

@@ -1,6 +1,6 @@
 {
   "name": "cwlts",
-  "version": "1.20.1",
+  "version": "1.21.0",
   "description": "TypeScript data model for Common Workflow Language",
   "scripts": {
     "tsc": "npx tsc",

src/models/d2sb/SBDraft2CommandLineToolModel.ts

@@ -320,18 +320,7 @@ export class SBDraft2CommandLineToolModel extends CommandLineToolModel implement
 
         this.baseCommand = [];
 
-        (<Array<string | Expression>> tool.baseCommand).reduce((acc, curr) => {
-            if (typeof curr === "string") {
-                if (typeof acc[acc.length - 1] === "string") {
-                    acc[acc.length - 1] += ` ${curr}`;
-                    return acc;
-                } else {
-                    return acc.concat([curr]);
-                }
-            } else {
-                return acc.concat([curr]);
-            }
-        }, []).forEach((cmd) => {
+        tool.baseCommand.forEach((cmd) => {
             this.addBaseCommand(cmd);
         });
 

src/models/d2sb/SBDraft2CommandOutputBindingModel.ts

@@ -22,7 +22,7 @@ export class SBDraft2CommandOutputBindingModel extends CommandOutputBindingModel
     }
 
     set glob(value: SBDraft2ExpressionModel) {
-        this.setGlob(value, SBDraft2ExpressionModel);
+        this.setGlobExpression(value, SBDraft2ExpressionModel);
     }
 
     protected _outputEval: SBDraft2ExpressionModel;
@@ -152,4 +152,4 @@ export class SBDraft2CommandOutputBindingModel extends CommandOutputBindingModel
             });
         }
     }
-}
+}

src/models/generic/CommandOutputBindingModel.ts

@@ -14,9 +14,9 @@ export abstract class CommandOutputBindingModel extends ValidationBase implement
 
     secondaryFiles: ExpressionModel[];
 
-    glob: ExpressionModel;
+    glob: ExpressionModel | Array<string>;
 
-    protected _glob: ExpressionModel;
+    protected _glob: ExpressionModel | Array<string>;
 
     loadContents: boolean;
 
@@ -36,27 +36,21 @@ export abstract class CommandOutputBindingModel extends ValidationBase implement
 
     abstract deserialize(attr: any): void;
 
-    protected setGlob(value: ExpressionModel, exprConstructor: new (...args: any[]) => ExpressionModel) {
-        let val = value.serialize();
-        this._glob.clearIssue(ErrorCode.ALL);
-        this._glob = new exprConstructor(val, `${this.loc}.glob`, this.eventHub);
-        this._glob.setValidationCallback(err => this.updateValidity(err));
-        this.validateGlob();
-    }
-
     protected validateGlob() {
         if (!this._glob) return;
 
-        if (this._glob.serialize() === undefined) {
-            this._glob.setIssue({
-                [`${this.loc}.glob`]: {
-                    message: "Glob should be specified",
-                    type: "warning",
-                    code: ErrorCode.OUTPUT_GLOB_MISSING
-                }
-            }, true);
-        } else {
-            this._glob.clearIssue(ErrorCode.OUTPUT_GLOB_MISSING);
+        if (this._glob instanceof ExpressionModel) {
+            if (this._glob.serialize() === undefined) {
+                this._glob.setIssue({
+                    [`${this.loc}.glob`]: {
+                        message: "Glob should be specified",
+                        type: "warning",
+                        code: ErrorCode.OUTPUT_GLOB_MISSING
+                    }
+                }, true);
+            } else {
+                this._glob.clearIssue(ErrorCode.OUTPUT_GLOB_MISSING);
+            }
         }
     }
 
@@ -67,4 +61,15 @@ export abstract class CommandOutputBindingModel extends ValidationBase implement
         this._outputEval = new exprConstructor(value.serialize(), `${this.loc}.outputEval`, this.eventHub);
         this._outputEval.setValidationCallback(err => this.updateValidity(err));
     }
-}
+
+    protected setGlobExpression(expression: ExpressionModel, exprConstructor: new (...args: any[]) => ExpressionModel) {
+        if (this._glob instanceof ExpressionModel) {
+            this._glob.clearIssue(ErrorCode.ALL);
+        }
+
+        this._glob = new exprConstructor(expression.serialize(), `${this.loc}.glob`, this.eventHub);
+        this._glob.setValidationCallback(err => this.updateValidity(err));
+        this.validateGlob();
+    }
+
+}

src/models/helpers/Glob.ts

@@ -0,0 +1,15 @@
+import {V1ExpressionModel} from "../v1.0";
+
+export function toExpression(array: Array<string>): V1ExpressionModel {
+    return array.length === 1 ? new V1ExpressionModel(array[0]) : new V1ExpressionModel();
+}
+
+export function toArray(expression: V1ExpressionModel): Array<string> {
+    const strExpression = expression.serialize();
+
+    if (expression.isExpression) {
+        return [];
+    }
+
+    return strExpression ? [strExpression] : [];
+}

src/models/helpers/utils.ts

@@ -1,8 +1,11 @@
 import {
     CommandInputParameterModel,
     CommandOutputParameterModel,
+    ExpressionModel,
     ParameterTypeModel,
-    WorkflowOutputParameterModel
+    StepModel,
+    WorkflowInputParameterModel,
+    WorkflowOutputParameterModel,
 } from "../generic";
 import {InputParameterModel} from "../generic/InputParameterModel";
 import {ErrorCode, Issue, ValidityError} from "./validation";
@@ -288,6 +291,36 @@ export const checkIfConnectionIsValid = (pointA, pointB, ltr = true) => {
         }
     };
 
+    const stepHasScatterInput = (step: StepModel, scatter: string) => {
+        return ensureArray(step.scatter).some(s => s == scatter);
+    };
+
+    const checkBothPointsForSameScatter = () => {
+        if (pointA instanceof WorkflowInputParameterModel ||
+            pointA instanceof WorkflowOutputParameterModel ||
+            pointB instanceof WorkflowInputParameterModel ||
+            pointB instanceof WorkflowOutputParameterModel) {
+            return true;
+        }
+
+        if (pointB.parentStep && pointA.parentStep) {
+            const stepBHasDefinedScatter = stepHasScatterInput(pointB.parentStep, pointB.id);
+            const stepAHasDefinedScatter = stepHasScatterInput(pointA.parentStep, pointB.id);
+
+            if ((!stepAHasDefinedScatter && stepBHasDefinedScatter) ||
+                (stepAHasDefinedScatter && !stepBHasDefinedScatter)) {
+                throw new ValidityError(
+                    `Invalid connection. Scatter '${pointB.id}' is making a mismatch in connection`,
+                    ErrorCode.CONNECTION_SCATTER_TYPE
+                );
+            }
+
+            return true;
+        }
+
+        return true;
+    }
+
     // fetch type
     const pointAType  = pointA.type.type;
     const pointBType  = pointB.type.type;
@@ -334,10 +367,50 @@ export const checkIfConnectionIsValid = (pointA, pointB, ltr = true) => {
             }
         }
 
+        if (pointAType === pointBType) {
+            checkBothPointsForSameScatter();
+        }
+
+        if (pointB.secondaryFiles.length) {
+
+            if (pointB.secondaryFiles.length > pointA.secondaryFiles.length) {
+                throw new ValidityError(`Input connection is missing required secondary files`, ErrorCode.CONNECTION_SEC_FILES);
+            }
+
+            const isRequired = (secondaryFile): boolean => secondaryFile.required !== undefined ? secondaryFile.required : true;
+            const getPattern = (secondaryFile): ExpressionModel => secondaryFile.pattern ? secondaryFile.pattern : secondaryFile;
+
+            const requiredSecondaryFiles = pointB.secondaryFiles
+                .filter(isRequired)
+                .map(getPattern);
+
+            const outputSecondaryFiles = pointA.secondaryFiles.map(getPattern);
+
+            requiredSecondaryFiles.forEach(secondaryFile => {
+                if (secondaryFile.isExpression) {
+                    return;
+                }
+
+                const secondaryFilePattern = `${secondaryFile}`;
+                const foundSamePattern = outputSecondaryFiles.find(sf => sf.toString().toUpperCase() === secondaryFilePattern.toUpperCase());
+
+                if (!foundSamePattern) {
+                    throw new ValidityError(`Input connection is missing required secondary files with a pattern: ${secondaryFilePattern}`, ErrorCode.CONNECTION_SEC_FILES);
+                }
+            });
+
+            return true;
+        }
+
         // if not file or fileTypes not defined
         return true;
     }
 
+    // mark connection as valid if pointB has scatter and pointA[]
+    if ((pointAItems === pointBType) && stepHasScatterInput(pointB.parentStep, pointB.id)) {
+        return true;
+    }
+
     // if types are both defined and do not match
     const pointATypeOutput = pointAItems ? `"${pointAItems}[]"` : `"${pointAType}"`;
     const pointBTypeOutput = pointBItems ? `"${pointBItems}[]"` : `"${pointBType}"`;

src/models/helpers/validation/ErrorCode.ts

@@ -17,6 +17,8 @@ export enum ErrorCode {
     CONNECTION_TYPE         = 301,
     CONNECTION_FILE_TYPE    = 302,
     CONNECTION_SAME_STEP    = 303,
+    CONNECTION_SCATTER_TYPE = 304,
+    CONNECTION_SEC_FILES    = 305,
 
     OUTPUT_ALL              = 400,
     OUTPUT_GLOB_MISSING     = 401,

src/models/v1.0/V1CommandOutputBindingModel.ts

@@ -13,14 +13,18 @@ export class V1CommandOutputBindingModel extends CommandOutputBindingModel {
     static INHERIT_REGEX = /.*(?:\s*)inheritMetadata\((?:\s*)self(?:\s*),(?:\s*)inputs.(.*?)(?:\s*)\)(?:\s*).*/g;
     public inheritMetadataFrom: string;
 
-    protected _glob: V1ExpressionModel;
+    protected _glob: V1ExpressionModel | Array<string>;
 
-    get glob(): V1ExpressionModel {
+    get glob(): V1ExpressionModel | Array<string> {
         return this._glob;
     }
 
-    set glob(value: V1ExpressionModel) {
-        this.setGlob(value, V1ExpressionModel);
+    set glob(value: V1ExpressionModel | Array<string>) {
+        if (value instanceof V1ExpressionModel) {
+            this.setGlobExpression(value, V1ExpressionModel);
+        } else {
+            this._glob = value;
+        }
     }
 
     protected _outputEval: V1ExpressionModel;
@@ -81,15 +85,14 @@ export class V1CommandOutputBindingModel extends CommandOutputBindingModel {
     }
 
     public deserialize(binding: CommandOutputBinding) {
-        let glob = binding.glob;
-
         if (Array.isArray(binding.glob)) {
-            glob = binding.glob[0];
+            this._glob = binding.glob;
+            return;
         }
 
         this.loadContents = binding.loadContents === true;
 
-        this._glob = new V1ExpressionModel(<string> glob, `${this.loc}.glob`, this.eventHub);
+        this._glob = new V1ExpressionModel(<string> binding.glob, `${this.loc}.glob`, this.eventHub);
         this._glob.setValidationCallback(err => this.updateValidity(err));
         this.validateGlob();
 
@@ -108,10 +111,23 @@ export class V1CommandOutputBindingModel extends CommandOutputBindingModel {
     public serialize(): CommandOutputBinding {
         let base: CommandOutputBinding = <CommandOutputBinding> {};
 
-        if (this.loadContents) base.loadContents = true;
+        if (this.loadContents) {
+            base.loadContents = true;
+        }
+
+        if (this._glob) {
+            const globSerialized = this._glob instanceof V1ExpressionModel
+                ? this._glob.serialize()
+                : this._glob;
 
-        if (this._glob && this._glob.serialize() !== undefined) base.glob = this._glob.serialize();
-        if (this._outputEval && this._outputEval.serialize() !== undefined) base.outputEval = this._outputEval.serialize();
+            if (globSerialized) {
+                base.glob = globSerialized;
+            }
+        }
+
+        if (this._outputEval && this._outputEval.serialize() !== undefined) {
+            base.outputEval = this._outputEval.serialize();
+        }
 
         return base;
     }