npm - @nfdi4plants/arctrl - Versions diffs - 3.0.0-beta.15 → 3.0.0-beta.16 - Mend

@nfdi4plants/arctrl 3.0.0-beta.15 → 3.0.0-beta.16

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (63) hide show

package/dist/ts/ts/CWL/ToolDescription.d.ts CHANGED Viewed

@@ -12,7 +12,9 @@ export declare class CWLToolDescription extends DynamicObj {
     _hints: Option<Requirement_$union[]>;
     _inputs: Option<CWLInput[]>;
     _metadata: Option<DynamicObj>;
-    constructor(outputs: CWLOutput[], cwlVersion?: string, baseCommand?: string[], requirements?: Requirement_$union[], hints?: Requirement_$union[], inputs?: CWLInput[], metadata?: DynamicObj);
+    _label: Option<string>;
+    _doc: Option<string>;
+    constructor(outputs: CWLOutput[], cwlVersion?: string, baseCommand?: string[], requirements?: Requirement_$union[], hints?: Requirement_$union[], inputs?: CWLInput[], metadata?: DynamicObj, label?: string, doc?: string);
     get CWLVersion(): string;
     set CWLVersion(version: string);
     get Outputs(): CWLOutput[];
@@ -27,7 +29,11 @@ export declare class CWLToolDescription extends DynamicObj {
     set Inputs(inputs: Option<CWLInput[]>);
     get Metadata(): DynamicObj | undefined;
     set Metadata(metadata: Option<DynamicObj>);
+    get Label(): string | undefined;
+    set Label(label: Option<string>);
+    get Doc(): string | undefined;
+    set Doc(doc: Option<string>);
 }
 export declare function CWLToolDescription_$reflection(): TypeInfo;
-export declare function CWLToolDescription_$ctor_Z3224DB85(outputs: CWLOutput[], cwlVersion?: string, baseCommand?: string[], requirements?: Requirement_$union[], hints?: Requirement_$union[], inputs?: CWLInput[], metadata?: DynamicObj): CWLToolDescription;
+export declare function CWLToolDescription_$ctor_10F2CC7B(outputs: CWLOutput[], cwlVersion?: string, baseCommand?: string[], requirements?: Requirement_$union[], hints?: Requirement_$union[], inputs?: CWLInput[], metadata?: DynamicObj, label?: string, doc?: string): CWLToolDescription;
 //# sourceMappingURL=ToolDescription.d.ts.map

package/dist/ts/ts/CWL/ToolDescription.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"ToolDescription.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/CWL/ToolDescription.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAC;AACzC,OAAO,EAAc,MAAM,EAAU,MAAM,uCAAuC,CAAC;AACnF,OAAO,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AACvD,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AACvC,OAAO,EAA0B,UAAU,EAAE,MAAM,oDAAoD,CAAC;AACxG,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAEjF,qBAAa,kBAAmB,SAAQ,UAAU;IAC9C,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,SAAS,EAAE,CAAC;IACtB,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;IAC/B,aAAa,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC;IAC5C,MAAM,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC;IACrC,OAAO,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC5B,SAAS,EAAE,MAAM,CAAC,UAAU,CAAC,CAAC;IAC9B,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC;IACvB,IAAI,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC;gBACT,OAAO,EAAE,SAAS,EAAE,EAAE,UAAU,CAAC,EAAE,MAAM,EAAE,WAAW,CAAC,EAAE,MAAM,EAAE,EAAE,YAAY,CAAC,EAAE,kBAAkB,EAAE,EAAE,KAAK,CAAC,EAAE,kBAAkB,EAAE,EAAE,MAAM,CAAC,EAAE,QAAQ,EAAE,EAAE,QAAQ,CAAC,EAAE,UAAU,EAAE,KAAK,CAAC,EAAE,MAAM,EAAE,GAAG,CAAC,EAAE,MAAM;IAY1N,IAAI,UAAU,IAAI,MAAM,CAGvB;IACD,IAAI,UAAU,CAAC,OAAO,EAAE,MAAM,EAG7B;IACD,IAAI,OAAO,IAAI,SAAS,EAAE,CAGzB;IACD,IAAI,OAAO,CAAC,OAAO,EAAE,SAAS,EAAE,EAG/B;IACD,IAAI,WAAW,IAAI,MAAM,EAAE,GAAG,SAAS,CAGtC;IACD,IAAI,WAAW,CAAC,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,EAG5C;IACD,IAAI,YAAY,IAAI,kBAAkB,EAAE,GAAG,SAAS,CAGnD;IACD,IAAI,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,EAG1D;IACD,IAAI,KAAK,IAAI,kBAAkB,EAAE,GAAG,SAAS,CAG5C;IACD,IAAI,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,EAG5C;IACD,IAAI,MAAM,IAAI,QAAQ,EAAE,GAAG,SAAS,CAGnC;IACD,IAAI,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC,EAGpC;IACD,IAAI,QAAQ,IAAI,UAAU,GAAG,SAAS,CAGrC;IACD,IAAI,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC,UAAU,CAAC,EAGxC;IACD,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAG9B;IACD,IAAI,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,EAG9B;IACD,IAAI,GAAG,IAAI,MAAM,GAAG,SAAS,CAG5B;IACD,IAAI,GAAG,CAAC,GAAG,EAAE,MAAM,CAAC,MAAM,CAAC,EAG1B;CACJ;AAED,wBAAgB,8BAA8B,IAAI,QAAQ,CAEzD;AAED,wBAAgB,iCAAiC,CAAC,OAAO,EAAE,SAAS,EAAE,EAAE,UAAU,CAAC,EAAE,MAAM,EAAE,WAAW,CAAC,EAAE,MAAM,EAAE,EAAE,YAAY,CAAC,EAAE,kBAAkB,EAAE,EAAE,KAAK,CAAC,EAAE,kBAAkB,EAAE,EAAE,MAAM,CAAC,EAAE,QAAQ,EAAE,EAAE,QAAQ,CAAC,EAAE,UAAU,EAAE,KAAK,CAAC,EAAE,MAAM,EAAE,GAAG,CAAC,EAAE,MAAM,GAAG,kBAAkB,CAEpR"}

package/dist/ts/ts/CWL/ToolDescription.js CHANGED Viewed

@@ -3,7 +3,7 @@ import { DynamicObj, DynamicObj_$reflection } from '../fable_modules/DynamicObj.
 import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
 class CWLToolDescription extends DynamicObj {
-  constructor(outputs, cwlVersion, baseCommand, requirements, hints, inputs, metadata) {
+  constructor(outputs, cwlVersion, baseCommand, requirements, hints, inputs, metadata, label, doc) {
     super();
     this._cwlVersion = defaultArg(cwlVersion, "v1.2");
     this._outputs = outputs;
@@ -12,6 +12,8 @@ class CWLToolDescription extends DynamicObj {
     this._hints = hints;
     this._inputs = inputs;
     this._metadata = metadata;
+    this._label = label;
+    this._doc = doc;
   }
   get CWLVersion() {
     const this$ = this;
@@ -69,12 +71,28 @@ class CWLToolDescription extends DynamicObj {
     const this$ = this;
     this$._metadata = metadata;
   }
+  get Label() {
+    const this$ = this;
+    return unwrap(this$._label);
+  }
+  set Label(label) {
+    const this$ = this;
+    this$._label = label;
+  }
+  get Doc() {
+    const this$ = this;
+    return unwrap(this$._doc);
+  }
+  set Doc(doc) {
+    const this$ = this;
+    this$._doc = doc;
+  }
 }
 function CWLToolDescription_$reflection() {
   return class_type("ARCtrl.CWL.CWLToolDescription", void 0, CWLToolDescription, DynamicObj_$reflection());
 }
-function CWLToolDescription_$ctor_Z3224DB85(outputs, cwlVersion, baseCommand, requirements, hints, inputs, metadata) {
-  return new CWLToolDescription(outputs, cwlVersion, baseCommand, requirements, hints, inputs, metadata);
+function CWLToolDescription_$ctor_10F2CC7B(outputs, cwlVersion, baseCommand, requirements, hints, inputs, metadata, label, doc) {
+  return new CWLToolDescription(outputs, cwlVersion, baseCommand, requirements, hints, inputs, metadata, label, doc);
 }
-export { CWLToolDescription, CWLToolDescription_$ctor_Z3224DB85, CWLToolDescription_$reflection };
+export { CWLToolDescription, CWLToolDescription_$ctor_10F2CC7B, CWLToolDescription_$reflection };

package/dist/ts/ts/CWL/WorkflowDescription.d.ts CHANGED Viewed

@@ -13,7 +13,9 @@ export declare class CWLWorkflowDescription extends DynamicObj {
     _requirements: Option<Requirement_$union[]>;
     _hints: Option<Requirement_$union[]>;
     _metadata: Option<DynamicObj>;
-    constructor(steps: WorkflowStep[], inputs: CWLInput[], outputs: CWLOutput[], cwlVersion?: string, requirements?: Requirement_$union[], hints?: Requirement_$union[], metadata?: DynamicObj);
+    _label: Option<string>;
+    _doc: Option<string>;
+    constructor(steps: WorkflowStep[], inputs: CWLInput[], outputs: CWLOutput[], cwlVersion?: string, requirements?: Requirement_$union[], hints?: Requirement_$union[], metadata?: DynamicObj, label?: string, doc?: string);
     get CWLVersion(): string;
     set CWLVersion(version: string);
     get Steps(): WorkflowStep[];
@@ -28,7 +30,11 @@ export declare class CWLWorkflowDescription extends DynamicObj {
     set Hints(hints: Option<Requirement_$union[]>);
     get Metadata(): DynamicObj | undefined;
     set Metadata(metadata: Option<DynamicObj>);
+    get Label(): string | undefined;
+    set Label(label: Option<string>);
+    get Doc(): string | undefined;
+    set Doc(doc: Option<string>);
 }
 export declare function CWLWorkflowDescription_$reflection(): TypeInfo;
-export declare function CWLWorkflowDescription_$ctor_704BBD06(steps: WorkflowStep[], inputs: CWLInput[], outputs: CWLOutput[], cwlVersion?: string, requirements?: Requirement_$union[], hints?: Requirement_$union[], metadata?: DynamicObj): CWLWorkflowDescription;
+export declare function CWLWorkflowDescription_$ctor_ZE122AFA(steps: WorkflowStep[], inputs: CWLInput[], outputs: CWLOutput[], cwlVersion?: string, requirements?: Requirement_$union[], hints?: Requirement_$union[], metadata?: DynamicObj, label?: string, doc?: string): CWLWorkflowDescription;
 //# sourceMappingURL=WorkflowDescription.d.ts.map

package/dist/ts/ts/CWL/WorkflowDescription.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"WorkflowDescription.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/CWL/WorkflowDescription.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AACvC,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAC;AACzC,OAAO,EAAc,MAAM,EAAU,MAAM,uCAAuC,CAAC;AACnF,OAAO,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AACvD,OAAO,EAA0B,UAAU,EAAE,MAAM,oDAAoD,CAAC;AACxG,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAEjF,qBAAa,sBAAuB,SAAQ,UAAU;IAClD,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,YAAY,EAAE,CAAC;IACvB,OAAO,EAAE,QAAQ,EAAE,CAAC;IACpB,QAAQ,EAAE,SAAS,EAAE,CAAC;IACtB,aAAa,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC;IAC5C,MAAM,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC;IACrC,SAAS,EAAE,MAAM,CAAC,UAAU,CAAC,CAAC;~~gBAClB~~,KAAK,EAAE,YAAY,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE,OAAO,EAAE,SAAS,EAAE,EAAE,UAAU,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,kBAAkB,EAAE,EAAE,KAAK,CAAC,EAAE,kBAAkB,EAAE,EAAE,QAAQ,CAAC,EAAE,UAAU;~~IAU1L~~,IAAI,UAAU,IAAI,MAAM,CAGvB;IACD,IAAI,UAAU,CAAC,OAAO,EAAE,MAAM,EAG7B;IACD,IAAI,KAAK,IAAI,YAAY,EAAE,CAG1B;IACD,IAAI,KAAK,CAAC,KAAK,EAAE,YAAY,EAAE,EAG9B;IACD,IAAI,MAAM,IAAI,QAAQ,EAAE,CAGvB;IACD,IAAI,MAAM,CAAC,MAAM,EAAE,QAAQ,EAAE,EAG5B;IACD,IAAI,OAAO,IAAI,SAAS,EAAE,CAGzB;IACD,IAAI,OAAO,CAAC,OAAO,EAAE,SAAS,EAAE,EAG/B;IACD,IAAI,YAAY,IAAI,kBAAkB,EAAE,GAAG,SAAS,CAGnD;IACD,IAAI,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,EAG1D;IACD,IAAI,KAAK,IAAI,kBAAkB,EAAE,GAAG,SAAS,CAG5C;IACD,IAAI,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,EAG5C;IACD,IAAI,QAAQ,IAAI,UAAU,GAAG,SAAS,CAGrC;IACD,IAAI,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC,UAAU,CAAC,EAGxC;CACJ;AAED,wBAAgB,kCAAkC,IAAI,QAAQ,CAE7D;AAED,wBAAgB,qCAAqC,CAAC,KAAK,EAAE,YAAY,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE,OAAO,EAAE,SAAS,EAAE,EAAE,UAAU,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,kBAAkB,EAAE,EAAE,KAAK,CAAC,EAAE,kBAAkB,EAAE,EAAE,QAAQ,CAAC,EAAE,UAAU,GAAG,sBAAsB,~~CAE5P~~"}
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package/dist/ts/ts/CWL/WorkflowDescription.js CHANGED Viewed

@@ -3,7 +3,7 @@ import { DynamicObj, DynamicObj_$reflection } from '../fable_modules/DynamicObj.
 import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
 class CWLWorkflowDescription extends DynamicObj {
-  constructor(steps, inputs, outputs, cwlVersion, requirements, hints, metadata) {
+  constructor(steps, inputs, outputs, cwlVersion, requirements, hints, metadata, label, doc) {
     super();
     this._cwlVersion = defaultArg(cwlVersion, "v1.2");
     this._steps = steps;
@@ -12,6 +12,8 @@ class CWLWorkflowDescription extends DynamicObj {
     this._requirements = requirements;
     this._hints = hints;
     this._metadata = metadata;
+    this._label = label;
+    this._doc = doc;
   }
   get CWLVersion() {
     const this$ = this;
@@ -69,12 +71,28 @@ class CWLWorkflowDescription extends DynamicObj {
     const this$ = this;
     this$._metadata = metadata;
   }
+  get Label() {
+    const this$ = this;
+    return unwrap(this$._label);
+  }
+  set Label(label) {
+    const this$ = this;
+    this$._label = label;
+  }
+  get Doc() {
+    const this$ = this;
+    return unwrap(this$._doc);
+  }
+  set Doc(doc) {
+    const this$ = this;
+    this$._doc = doc;
+  }
 }
 function CWLWorkflowDescription_$reflection() {
   return class_type("ARCtrl.CWL.CWLWorkflowDescription", void 0, CWLWorkflowDescription, DynamicObj_$reflection());
 }
-function CWLWorkflowDescription_$ctor_704BBD06(steps, inputs, outputs, cwlVersion, requirements, hints, metadata) {
-  return new CWLWorkflowDescription(steps, inputs, outputs, cwlVersion, requirements, hints, metadata);
+function CWLWorkflowDescription_$ctor_ZE122AFA(steps, inputs, outputs, cwlVersion, requirements, hints, metadata, label, doc) {
+  return new CWLWorkflowDescription(steps, inputs, outputs, cwlVersion, requirements, hints, metadata, label, doc);
 }
-export { CWLWorkflowDescription, CWLWorkflowDescription_$ctor_704BBD06, CWLWorkflowDescription_$reflection };
+export { CWLWorkflowDescription, CWLWorkflowDescription_$ctor_ZE122AFA, CWLWorkflowDescription_$reflection };

package/dist/ts/ts/CWL/WorkflowSteps.d.ts CHANGED Viewed

@@ -1,16 +1,17 @@
 import { Record } from '@fable-org/fable-library-js/Types.js';
 import { Option } from '@fable-org/fable-library-js/Option.js';
-import { IComparable, IEquatable } from '@fable-org/fable-library-js/Util.js';
+import { IEquatable } from '@fable-org/fable-library-js/Util.js';
 import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
 import { Requirement_$union } from './Requirements.js';
 import { DynamicObj } from '../fable_modules/DynamicObj.7.1.0/DynamicObj.fs.js';
-export declare class StepInput extends Record implements IEquatable<StepInput>, IComparable<StepInput> {
+export declare class StepInput extends Record implements IEquatable<StepInput> {
     readonly Id: string;
-    readonly Source: Option<string>;
+    readonly Source: Option<string[]>;
     readonly DefaultValue: Option<string>;
     readonly ValueFrom: Option<string>;
-    constructor(Id: string, Source: Option<string>, DefaultValue: Option<string>, ValueFrom: Option<string>);
-    static create(id: string, source?: string, defaultValue?: string, valueFrom?: string): StepInput;
+    readonly LinkMerge: Option<string>;
+    constructor(Id: string, Source: Option<string[]>, DefaultValue: Option<string>, ValueFrom: Option<string>, LinkMerge: Option<string>);
+    static create(id: string, source?: string[], defaultValue?: string, valueFrom?: string, linkMerge?: string): StepInput;
 }
 export declare function StepInput_$reflection(): TypeInfo;
 export declare class StepOutput extends Record implements IEquatable<StepOutput> {

package/dist/ts/ts/CWL/WorkflowSteps.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"WorkflowSteps.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/CWL/WorkflowSteps.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,sCAAsC,CAAC;AAC9D,OAAO,EAAU,MAAM,EAAE,MAAM,uCAAuC,CAAC;AACvE,OAAO,EAAE,UAAU,EAAE,MAAM,qCAAqC,CAAC;AACjE,OAAO,EAAiE,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AACpI,OAAO,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AACvD,OAAO,EAA0B,UAAU,EAAE,MAAM,oDAAoD,CAAC;AAExG,qBAAa,SAAU,SAAQ,MAAO,YAAW,UAAU,CAAC,SAAS,CAAC;IAClE,QAAQ,CAAC,EAAE,EAAE,MAAM,CAAC;IACpB,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;IAClC,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC;IACtC,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC;IACnC,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC;gBACvB,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,YAAY,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,MAAM,CAAC;IAQpI,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,EAAE,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS;CAGzH;AAED,wBAAgB,qBAAqB,IAAI,QAAQ,CAEhD;AAED,qBAAa,UAAW,SAAQ,MAAO,YAAW,UAAU,CAAC,UAAU,CAAC;IACpE,QAAQ,CAAC,EAAE,EAAE,MAAM,EAAE,CAAC;gBACV,EAAE,EAAE,MAAM,EAAE;IAIxB,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,MAAM,EAAE,GAAG,UAAU;CAG1C;AAED,wBAAgB,sBAAsB,IAAI,QAAQ,CAEjD;AAED,qBAAa,YAAa,SAAQ,UAAU;IACxC,GAAG,EAAE,MAAM,CAAC;IACZ,GAAG,EAAE,SAAS,EAAE,CAAC;IACjB,IAAI,EAAE,UAAU,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,aAAa,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC;IAC5C,MAAM,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC;gBACzB,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,SAAS,EAAE,EAAE,IAAI,EAAE,UAAU,EAAE,GAAG,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,kBAAkB,EAAE,EAAE,KAAK,CAAC,EAAE,kBAAkB,EAAE;IAS1I,IAAI,EAAE,IAAI,MAAM,CAGf;IACD,IAAI,EAAE,CAAC,EAAE,EAAE,MAAM,EAGhB;IACD,IAAI,EAAE,IAAI,SAAS,EAAE,CAGpB;IACD,IAAI,EAAE,CAAC,GAAG,EAAE,SAAS,EAAE,EAGtB;IACD,IAAI,GAAG,IAAI,UAAU,CAGpB;IACD,IAAI,GAAG,CAAC,IAAI,EAAE,UAAU,EAGvB;IACD,IAAI,GAAG,IAAI,MAAM,CAGhB;IACD,IAAI,GAAG,CAAC,GAAG,EAAE,MAAM,EAGlB;IACD,IAAI,YAAY,IAAI,kBAAkB,EAAE,GAAG,SAAS,CAGnD;IACD,IAAI,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,EAG1D;IACD,IAAI,KAAK,IAAI,kBAAkB,EAAE,GAAG,SAAS,CAG5C;IACD,IAAI,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,kBAAkB,EAAE,CAAC,EAG5C;CACJ;AAED,wBAAgB,wBAAwB,IAAI,QAAQ,CAEnD;AAED,wBAAgB,2BAA2B,CAAC,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,SAAS,EAAE,EAAE,IAAI,EAAE,UAAU,EAAE,GAAG,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,kBAAkB,EAAE,EAAE,KAAK,CAAC,EAAE,kBAAkB,EAAE,GAAG,YAAY,CAExL"}

package/dist/ts/ts/CWL/WorkflowSteps.js CHANGED Viewed

@@ -4,19 +4,20 @@ import { record_type, string_type, option_type, array_type, class_type } from '.
 import { DynamicObj, DynamicObj_$reflection } from '../fable_modules/DynamicObj.7.1.0/DynamicObj.fs.js';
 class StepInput extends Record {
-  constructor(Id, Source, DefaultValue, ValueFrom) {
+  constructor(Id, Source, DefaultValue, ValueFrom, LinkMerge) {
     super();
     this.Id = Id;
     this.Source = Source;
     this.DefaultValue = DefaultValue;
     this.ValueFrom = ValueFrom;
+    this.LinkMerge = LinkMerge;
   }
-  static create(id, source, defaultValue, valueFrom) {
-    return new StepInput(id, source, defaultValue, valueFrom);
+  static create(id, source, defaultValue, valueFrom, linkMerge) {
+    return new StepInput(id, source, defaultValue, valueFrom, linkMerge);
   }
 }
 function StepInput_$reflection() {
-  return record_type("ARCtrl.CWL.StepInput", [], StepInput, () => [["Id", string_type], ["Source", option_type(string_type)], ["DefaultValue", option_type(string_type)], ["ValueFrom", option_type(string_type)]]);
+  return record_type("ARCtrl.CWL.StepInput", [], StepInput, () => [["Id", string_type], ["Source", option_type(array_type(string_type))], ["DefaultValue", option_type(string_type)], ["ValueFrom", option_type(string_type)], ["LinkMerge", option_type(string_type)]]);
 }
 class StepOutput extends Record {
   constructor(Id) {

package/dist/ts/ts/Conversion/Investigation.d.ts CHANGED Viewed

@@ -7,6 +7,6 @@ export declare class InvestigationConversion {
     constructor();
 }
 export declare function InvestigationConversion_$reflection(): TypeInfo;
-export declare function InvestigationConversion_composeInvestigation_5AEC717D(investigation: ArcInvestigation, fs?: FileSystem): LDNode;
+export declare function InvestigationConversion_composeInvestigation_Z284BC0AC(investigation: ArcInvestigation, fs?: FileSystem, ignoreBrokenWR?: boolean): LDNode;
 export declare function InvestigationConversion_decomposeInvestigation_Z6839B9E8(investigation: LDNode, graph?: LDGraph, context?: LDContext): ArcInvestigation;
 //# sourceMappingURL=Investigation.d.ts.map

package/dist/ts/ts/Conversion/Investigation.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"Investigation.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Investigation.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAOjF,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAOzD,OAAO,EAAE,gBAAgB,EAA2C,MAAM,qBAAqB,CAAC;AAKhG,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,qBAAa,uBAAuB;;CAGnC;AAED,wBAAgB,mCAAmC,IAAI,QAAQ,CAE9D;AAED,wBAAgB,~~qDAAqD~~,CAAC,aAAa,EAAE,gBAAgB,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,~~CAkB9H~~;AAED,wBAAgB,wDAAwD,CAAC,aAAa,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,gBAAgB,CAetJ"}
1	+ {"version":3,"file":"Investigation.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Investigation.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAOjF,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAOzD,OAAO,EAAE,gBAAgB,EAA2C,MAAM,qBAAqB,CAAC;AAKhG,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,qBAAa,uBAAuB;;CAGnC;AAED,wBAAgB,mCAAmC,IAAI,QAAQ,CAE9D;AAED,wBAAgB,sDAAsD,CAAC,aAAa,EAAE,gBAAgB,EAAE,EAAE,CAAC,EAAE,UAAU,EAAE,cAAc,CAAC,EAAE,OAAO,GAAG,MAAM,CA0CzJ;AAED,wBAAgB,wDAAwD,CAAC,aAAa,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,gBAAgB,CAetJ"}

package/dist/ts/ts/Conversion/Investigation.js CHANGED Viewed

@@ -2,7 +2,7 @@ import { class_type } from '../../node_modules/@fable-org/fable-library-js/Refle
 import { value, bind, defaultArg, unwrap, map } from '../../node_modules/@fable-org/fable-library-js/Option.js';
 import { tryFromString, toString } from './DateTime.js';
 import { now } from '../../node_modules/@fable-org/fable-library-js/Date.js';
-import { Option_fromSeq, ResizeArray_map, ResizeArray_filter } from '../Core/Helper/Collections.js';
+import { Option_fromSeq, ResizeArray_map, ResizeArray_choose, ResizeArray_filter } from '../Core/Helper/Collections.js';
 import { ScholarlyArticleConversion_composeScholarlyArticle_D324A6D, ScholarlyArticleConversion_decomposeScholarlyArticle_Z6839B9E8 } from './ScholarlyArticle.js';
 import { PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
 import { BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
@@ -21,7 +21,7 @@ class InvestigationConversion {
 function InvestigationConversion_$reflection() {
   return class_type("ARCtrl.Conversion.InvestigationConversion", void 0, InvestigationConversion);
 }
-function InvestigationConversion_composeInvestigation_5AEC717D(investigation, fs) {
+function InvestigationConversion_composeInvestigation_Z284BC0AC(investigation, fs, ignoreBrokenWR) {
   let collection;
   let name;
   const matchValue = investigation.Title;
@@ -35,7 +35,27 @@ function InvestigationConversion_composeInvestigation_5AEC717D(investigation, fs
   const publications = Option_fromSeq(ResizeArray_map(ScholarlyArticleConversion_composeScholarlyArticle_D324A6D, investigation.Publications));
   const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, investigation.Contacts));
   const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, investigation.Comments));
-  const hasParts = Option_fromSeq((collection = toList(delay(() => append(ResizeArray_map((a_3) => AssayConversion_composeAssay_Z5C53FD5C(a_3, unwrap(fs)), investigation.Assays), delay(() => append(ResizeArray_map((s_2) => StudyConversion_composeStudy_ZFE0E38E(s_2, unwrap(fs)), investigation.Studies), delay(() => append(ResizeArray_map((w) => WorkflowConversion_composeWorkflow_42450E6E(w, unwrap(fs)), investigation.Workflows), delay(() => ResizeArray_map((r) => RunConversion_composeRun_Z8CC08AC(r, unwrap(fs)), investigation.Runs))))))))), Array.from(collection)));
+  const hasParts = Option_fromSeq((collection = toList(delay(() => append(ResizeArray_map((a_3) => AssayConversion_composeAssay_Z5C53FD5C(a_3, unwrap(fs)), investigation.Assays), delay(() => append(ResizeArray_map((s_2) => StudyConversion_composeStudy_ZFE0E38E(s_2, unwrap(fs)), investigation.Studies), delay(() => append(ResizeArray_choose((w) => {
+    try {
+      return WorkflowConversion_composeWorkflow_42450E6E(w, unwrap(fs));
+    } catch (matchValue_1) {
+      if (ignoreBrokenWR != null && value(ignoreBrokenWR)) {
+        return void 0;
+      } else {
+        throw matchValue_1;
+      }
+    }
+  }, investigation.Workflows), delay(() => ResizeArray_choose((r) => {
+    try {
+      return RunConversion_composeRun_Z8CC08AC(r, unwrap(fs));
+    } catch (matchValue_2) {
+      if (ignoreBrokenWR != null && value(ignoreBrokenWR)) {
+        return void 0;
+      } else {
+        throw matchValue_2;
+      }
+    }
+  }, investigation.Runs))))))))), Array.from(collection)));
   const mentions = Option_fromSeq([]);
   return LDDataset.createInvestigation(investigation.Identifier, name, void 0, unwrap(creators), unwrap(dateCreated), datePublished, void 0, unwrap(investigation.Description), unwrap(hasParts), unwrap(publications), unwrap(comments), unwrap(mentions));
 }
@@ -56,4 +76,4 @@ function InvestigationConversion_decomposeInvestigation_Z6839B9E8(investigation,
   return ArcInvestigation.create(LDDataset.getIdentifierAsString(investigation, unwrap(context)), unwrap(title), unwrap(LDDataset.tryGetDescriptionAsString(investigation, unwrap(context))), unwrap(dateCreated), unwrap(datePublished), void 0, publications, creators, assays, studies, workflows, runs, void 0, comments);
 }
-export { InvestigationConversion, InvestigationConversion_$reflection, InvestigationConversion_composeInvestigation_5AEC717D, InvestigationConversion_decomposeInvestigation_Z6839B9E8 };
+export { InvestigationConversion, InvestigationConversion_$reflection, InvestigationConversion_composeInvestigation_Z284BC0AC, InvestigationConversion_decomposeInvestigation_Z6839B9E8 };

package/dist/ts/ts/Conversion/Run.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"Run.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Run.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AASjF,OAAO,EAAE,QAAQ,EAAgB,MAAM,kBAAkB,CAAC;AAI1D,OAAO,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AACrE,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,OAAO,EAAE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AAQvE,OAAO,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAC7C,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAczD,qBAAa,aAAa;;CAGzB;AAED,wBAAgB,yBAAyB,IAAI,QAAQ,CAEpD;AAyBD;;;;GAIG;AACH,wBAAgB,+CAA+C,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAOrG;AAED,wBAAgB,iDAAiD,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAQvG;AAED,wBAAgB,2CAA2C,CAAC,UAAU,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAwCnK;AAED,wBAAgB,8CAA8C,CAAC,UAAU,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,qBAAqB,CAqB/J;AAED,wBAAgB,0DAA0D,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,EAAE,CAkDjH;AAED,wBAAgB,uDAAuD,CAAC,kBAAkB,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,CAAC,wBAAwB,EAAE,qBAAqB,EAAE,CAAC,CAK9M;AAED,wBAAgB,iCAAiC,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CA8BtF;AAED,wBAAgB,oCAAoC,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAoC9G"}

package/dist/ts/ts/Conversion/Run.js CHANGED Viewed

@@ -1,10 +1,11 @@
 import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+import { writeYaml, encodeCWLType } from '../CWL/Encode.js';
+import { CWLType_file } from '../CWL/CWLTypes.js';
+import { exists, tryPick, find } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
 import { replace, trimStart, join, toFail, printf } from '../../node_modules/@fable-org/fable-library-js/String.js';
 import { combineMany, combine } from '../FileSystem/Path.js';
 import { value, defaultArg, bind, unwrap, map } from '../../node_modules/@fable-org/fable-library-js/Option.js';
-import { CWLType_file } from '../CWL/CWLTypes.js';
 import { equals } from '../../node_modules/@fable-org/fable-library-js/Util.js';
-import { toString } from '../../node_modules/@fable-org/fable-library-js/Types.js';
 import { LDFile } from '../ROCrate/LDTypes/File.js';
 import { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
 import { ResizeArray_singleton, ResizeArray_map, ResizeArray_zip, ResizeArray_appendSingleton, Option_fromSeq, Option_fromValueWithDefault, ResizeArray_filter } from '../Core/Helper/Collections.js';
@@ -12,7 +13,6 @@ import { CWLParameterReference } from '../CWL/ParameterReference.js';
 import { LDFormalParameter } from '../ROCrate/LDTypes/FormalParameter.js';
 import { Run_cwlFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
 import { WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7, WorkflowConversion_getInputParametersFromProcessingUnit_30922B92, WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_2664C4B8 } from './Workflow.js';
-import { tryPick, find } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
 import { LDComputationalWorkflow } from '../ROCrate/LDTypes/ComputationalWorkflow.js';
 import { ARCtrl_ArcTables__ArcTables_GetProcesses_5E660E5C, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586 } from './Table.js';
 import { ArcTables } from '../Core/Table/ArcTables.js';
@@ -22,6 +22,8 @@ import { LDLabProcess } from '../ROCrate/LDTypes/LabProcess.js';
 import { ArcRun } from '../Core/ArcTypes.js';
 import { BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composePropertyValueFromOA_ZDED3A0F, BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_decomposePropertyValueToOA_Z2F770004, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
 import { PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
+import { LDOrganization } from '../ROCrate/LDTypes/Organization.js';
+import { utcNow } from '../../node_modules/@fable-org/fable-library-js/Date.js';
 import { DatamapConversion_composeFragmentDescriptors_Z892BFC3, DatamapConversion_decomposeFragmentDescriptors_Z6E59645F } from './Datamap.js';
 import { Datamap } from '../Core/Datamap.js';
 import { AssayConversion_getDataFilesFromProcesses_6BABD1B0 } from './Assay.js';
@@ -35,6 +37,29 @@ class RunConversion {
 function RunConversion_$reflection() {
   return class_type("ARCtrl.Conversion.RunConversion", void 0, RunConversion);
 }
+function RunConversion_formatCWLType_Z5C31A0F9(type_) {
+  const s = writeYaml(encodeCWLType(type_));
+  return s.trim();
+}
+function RunConversion_isArrayType_Z5C31A0F9(type_) {
+  switch (type_.tag) {
+    case /* Array */
+    11:
+      return true;
+    case /* Union */
+    14:
+      return exists((_arg) => {
+        if (_arg.tag === /* Array */
+        11) {
+          return true;
+        } else {
+          return false;
+        }
+      }, type_.fields[0]);
+    default:
+      return false;
+  }
+}
 function RunConversion_composeCWLInputFilePath_Z384F8060(path, runName) {
   if (path.startsWith("../..")) {
     return replace(replace(path, "../../", ""), "../..", "");
@@ -57,7 +82,7 @@ function RunConversion_composeCWLInputValue_70DD9184(inputValue, exampleOfWork,
   const type_ = value(inputParam.Type_);
   if (inputValue.Type != null) {
     if (!equals(value(inputValue.Type), type_)) {
-      throw new Error(`Type (${toString(value(inputValue.Type))}) of yml input value "${inputValue.Key}" does not match type of workflow input parameter (${toString(type_)}).`);
+      throw new Error(`Type (${RunConversion_formatCWLType_Z5C31A0F9(value(inputValue.Type))}) of yml input value "${inputValue.Key}" does not match type of workflow input parameter (${RunConversion_formatCWLType_Z5C31A0F9(type_)}).`);
     }
   }
   let matchResult;
@@ -65,12 +90,12 @@ function RunConversion_composeCWLInputValue_70DD9184(inputValue, exampleOfWork,
   0) {
     if (inputValue.Values.length === 1) {
       matchResult = 0;
-    } else if (toString(type_).toLocaleLowerCase().indexOf("array") >= 0) {
+    } else if (RunConversion_isArrayType_Z5C31A0F9(type_)) {
       matchResult = 1;
     } else {
       matchResult = 2;
     }
-  } else if (toString(type_).toLocaleLowerCase().indexOf("array") >= 0) {
+  } else if (RunConversion_isArrayType_Z5C31A0F9(type_)) {
     matchResult = 1;
   } else {
     matchResult = 2;
@@ -162,18 +187,36 @@ function RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(workflowInvocat
 }
 function RunConversion_composeRun_Z8CC08AC(run, fs) {
   let fds_1, vm_1, fds, vm;
+  let workflowProtocol;
+  const workflowFilePath = Run_cwlFileNameFromIdentifier(run.Identifier);
+  const matchValue = run.CWLDescription;
+  if (matchValue == null) {
+    const arg = run.Identifier;
+    workflowProtocol = toFail(printf("Run %s must have a CWL description"))(arg);
+  } else {
+    workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, value(matchValue), void 0, run.Identifier);
+  }
   const workflowInvocations = Option_fromSeq(RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run, unwrap(fs)));
   const measurementMethod = map(BaseTypes_composeDefinedTerm_ZDED3A0F, run.TechnologyType);
   const measurementTechnique = map(BaseTypes_composeDefinedTerm_ZDED3A0F, run.TechnologyPlatform);
   const variableMeasured = map(BaseTypes_composePropertyValueFromOA_ZDED3A0F, run.MeasurementType);
   const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, run.Performers));
+  const publisher = LDOrganization.create("DataPLANT");
+  const dateCreated = utcNow();
+  if (creators != null) {
+    LDComputationalWorkflow.setCreators(workflowProtocol, value(creators));
+  }
+  LDComputationalWorkflow.setSdPublisher(workflowProtocol, publisher);
+  LDComputationalWorkflow.setDateCreatedAsDateTime(workflowProtocol, dateCreated);
   const fragmentDescriptors = map(DatamapConversion_composeFragmentDescriptors_Z892BFC3, run.Datamap);
   const dataFiles = map((ps) => AssayConversion_getDataFilesFromProcesses_6BABD1B0(ps, unwrap(fragmentDescriptors)), workflowInvocations);
+  const hasParts = dataFiles == null ? ResizeArray_singleton(workflowProtocol) : ResizeArray_appendSingleton(workflowProtocol, value(dataFiles));
   const variableMeasureds = variableMeasured == null ? fragmentDescriptors == null ? void 0 : (fds_1 = value(fragmentDescriptors), fds_1) : fragmentDescriptors == null ? (vm_1 = value(variableMeasured), ResizeArray_singleton(vm_1)) : (fds = value(fragmentDescriptors), vm = value(variableMeasured), ResizeArray_appendSingleton(vm, fds));
   const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, run.Comments));
-  return LDDataset.createARCRun(run.Identifier, void 0, unwrap(run.Title), unwrap(run.Description), unwrap(creators), unwrap(dataFiles), unwrap(measurementMethod), unwrap(measurementTechnique), unwrap(variableMeasureds), unwrap(workflowInvocations), unwrap(workflowInvocations), unwrap(comments));
+  return LDDataset.createARCRun(run.Identifier, ResizeArray_singleton(workflowProtocol), void 0, unwrap(run.Title), unwrap(run.Description), unwrap(creators), unwrap(hasParts), unwrap(measurementMethod), unwrap(measurementTechnique), unwrap(variableMeasureds), unwrap(workflowInvocations), unwrap(workflowInvocations), unwrap(comments));
 }
 function RunConversion_decomposeRun_Z6839B9E8(run, graph, context) {
+  const workflowProtocol = LDDataset.tryGetMainEntityAsWorkflowProtocol(run, unwrap(graph), unwrap(context));
   const mainWorkflowInvocation = find((wi) => {
     let lp;
     const matchValue = LDLabProcess.tryGetExecutesLabProtocol(wi, unwrap(graph), unwrap(context));
@@ -195,7 +238,7 @@ function RunConversion_decomposeRun_Z6839B9E8(run, graph, context) {
         return false;
     }
   }, LDDataset.getAboutsAsWorkflowInvocation(run, unwrap(graph), unwrap(context)));
-  const patternInput = RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(mainWorkflowInvocation, LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(context), unwrap(graph));
+  const patternInput = workflowProtocol == null ? RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(mainWorkflowInvocation, LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(context), unwrap(graph)) : [WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_2664C4B8(value(workflowProtocol), unwrap(context), unwrap(graph)), ResizeArray_map((iv) => RunConversion_decomposeCWLInputValue_Z1346FE9D(iv, LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(context), unwrap(graph)), LDLabProcess.getObjects(mainWorkflowInvocation, unwrap(graph), unwrap(context)))];
   const measurementMethod = map((m) => BaseTypes_decomposeDefinedTerm_Z2F770004(m, unwrap(context)), LDDataset.tryGetMeasurementMethodAsDefinedTerm(run, unwrap(graph), unwrap(context)));
   const measurementTechnique = map((m_1) => BaseTypes_decomposeDefinedTerm_Z2F770004(m_1, unwrap(context)), LDDataset.tryGetMeasurementTechniqueAsDefinedTerm(run, unwrap(graph), unwrap(context)));
   const variableMeasured = map((v) => BaseTypes_decomposePropertyValueToOA_Z2F770004(v, unwrap(context)), LDDataset.tryGetVariableMeasuredAsMeasurementType(run, unwrap(graph), unwrap(context)));

package/dist/ts/ts/Conversion/Workflow.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"Workflow.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Workflow.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAEjF,OAAO,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAIpD,OAAO,EAAiC,MAAM,EAAoB,MAAM,uCAAuC,CAAC;AAChH,OAAO,EAAW,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAEtE,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,EAAgC,QAAQ,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAExF,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AACpD,OAAO,EAAiC,SAAS,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAI5F,OAAO,EAA8B,SAAS,EAAE,MAAM,8BAA8B,CAAC;AAErF,OAAO,EAAE,sBAAsB,EAAE,MAAM,+BAA+B,CAAC;AAEvE,OAAO,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAiE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AAKtI,OAAO,EAAc,YAAY,EAAE,MAAM,yBAAyB,CAAC;AAWnE,OAAO,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAClD,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,qBAAa,kBAAkB;;CAG9B;AAED,wBAAgB,8BAA8B,IAAI,QAAQ,CAEzD;AAED,wBAAgB,kDAAkD,CAAC,CAAC,EAAE,cAAc,GAAG,MAAM,CAG5F;AAED,wBAAgB,oDAAoD,CAAC,CAAC,EAAE,MAAM,GAAG,cAAc,CAE9F;AAED,wBAAgB,qDAAqD,CAAC,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,KAAK,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,CAmBvI;AAED,wBAAgB,4DAA4D,CAAC,GAAG,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAa3I;AAED,wBAAgB,kDAAkD,CAAC,WAAW,EAAE,MAAM,EAAE,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAAC,YAAY,CAAC,CAqBnI;AAED,wBAAgB,6DAA6D,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,QAAQ,CA0BzI;AAED,wBAAgB,mEAAmE,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,CAQ1H;AAED,wBAAgB,6DAA6D,CAAC,GAAG,EAAE,SAAS,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAY7I;AAED,wBAAgB,mDAAmD,CAAC,WAAW,EAAE,MAAM,EAAE,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,aAAa,CAE7H;AAED,wBAAgB,8DAA8D,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAK3I;AAED,wBAAgB,qDAAqD,CAAC,IAAI,EAAE,SAAS,GAAG,MAAM,CAsC7F;AAED,wBAAgB,uDAAuD,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,SAAS,CAGrI;AAED,wBAAgB,gEAAgE,CAAC,EAAE,EAAE,wBAAwB,GAAG,QAAQ,EAAE,CAezH;AAED,wBAAgB,8CAA8C,IAAI,MAAM,CAEvE;AAED,wBAAgB,kDAAkD,IAAI,MAAM,CAE3E;AAED,wBAAgB,sEAAsE,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,kBAAkB,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAItL;AAED,wBAAgB,sEAAsE,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,kBAAkB,CAGjK;AAED,wBAAgB,gDAAgD,CAAC,EAAE,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,EAAE,GAAG,MAAM,CAK/G;AAED,wBAAgB,gEAAgE,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,sBAAsB,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAKpL;AAED,wBAAgB,iDAAiD,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,YAAY,CAIlI;AAED,wBAAgB,+DAA+D,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,sBAAsB,CAI9J;AAED,wBAAgB,sEAAsE,CAAC,QAAQ,EAAE,MAAM,EAAE,EAAE,EAAE,wBAAwB,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAOtL;AAED,wBAAgB,qEAAqE,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,wBAAwB,CAOtK;AAED,wBAAgB,2CAA2C,CAAC,QAAQ,EAAE,WAAW,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CAqC1G;AAED,wBAAgB,8CAA8C,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,WAAW,CAalI"}

package/dist/ts/ts/Conversion/Workflow.js CHANGED Viewed

@@ -1,8 +1,8 @@
 import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
 import { writeYaml, encodeCWLType } from '../CWL/Encode.js';
-import { object } from '../fable_modules/YAMLicious.0.0.3/Decode.fs.js';
+import { object } from '../fable_modules/YAMLicious.1.0.0-alpha.2/Decode.fs.js';
 import { Decode_cwlTypeStringMatcher } from '../CWL/Decode.js';
-import { YAMLElement_Comment } from '../fable_modules/YAMLicious.0.0.3/YAMLiciousTypes.fs.js';
+import { YAMLElement_Comment } from '../fable_modules/YAMLicious.1.0.0-alpha.2/YAMLiciousTypes.fs.js';
 import { value, defaultArg, unwrap, bind, map } from '../../node_modules/@fable-org/fable-library-js/Option.js';
 import { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
 import { LDFormalParameter } from '../ROCrate/LDTypes/FormalParameter.js';
@@ -13,7 +13,7 @@ import { int32ToString } from '../../node_modules/@fable-org/fable-library-js/Ut
 import { Component_create_Z2F0B38C7 } from '../Core/Process/Component.js';
 import { BaseTypes_decomposePropertyValue_Z2F770004, BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
 import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.js';
-import { ResizeArray_map, ResizeArray_singleton, ResizeArray_choose, Option_fromSeq, Option_fromValueWithDefault } from '../Core/Helper/Collections.js';
+import { ResizeArray_map, ResizeArray_singleton, Option_fromSeq, ResizeArray_choose, ResizeArray_appendSingleton, Option_fromValueWithDefault } from '../Core/Helper/Collections.js';
 import { CWLToolDescription } from '../CWL/ToolDescription.js';
 import { CWLProcessingUnit_Workflow, CWLProcessingUnit_CommandLineTool } from '../CWL/CWLProcessingUnit.js';
 import { LDWorkflowProtocol } from '../ROCrate/LDTypes/WorkflowProtocol.js';
@@ -23,10 +23,12 @@ import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
 import { WorkflowStep, StepOutput } from '../CWL/WorkflowSteps.js';
 import { Workflow_cwlFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
 import { toFail, printf } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { LDOrganization } from '../ROCrate/LDTypes/Organization.js';
+import { PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
+import { utcNow } from '../../node_modules/@fable-org/fable-library-js/Date.js';
 import { LDLabProtocol } from '../ROCrate/LDTypes/LabProtocol.js';
 import { DatamapConversion_composeFragmentDescriptors_Z892BFC3, DatamapConversion_decomposeFragmentDescriptors_Z6E59645F } from './Datamap.js';
 import { Datamap } from '../Core/Datamap.js';
-import { PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
 import { ArcWorkflow } from '../Core/ArcTypes.js';
 class WorkflowConversion {
@@ -214,7 +216,7 @@ function WorkflowConversion_get_workflowDescriptionTypeName() {
 function WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA(filePath, workflow, workflowName, runName) {
   const inputs = map((a) => ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), a), workflow.Inputs);
   const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), workflow.Outputs);
-  return LDWorkflowProtocol.create(filePath, unwrap(inputs), outputs, void 0, void 0, void 0, void 0, ResizeArray_singleton(LDComputerLanguage.createCWL()), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, [WorkflowConversion_get_toolDescriptionTypeName()]);
+  return LDWorkflowProtocol.create(filePath, unwrap(inputs), outputs, void 0, void 0, void 0, filePath, ResizeArray_singleton(LDComputerLanguage.createCWL()), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, [WorkflowConversion_get_toolDescriptionTypeName()]);
 }
 function WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8(protocol, context, graph) {
   const inputs = ResizeArray_map((i) => WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(i, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getInputsAsFormalParameters(protocol, unwrap(graph), unwrap(context)));
@@ -230,7 +232,7 @@ function WorkflowConversion_composeWorkflowProtocolFromWorkflow_Z6FBB852F(filePa
   const inputs = ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), workflow.Inputs);
   const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), workflow.Outputs);
   const steps = ResizeArray_map((s) => WorkflowConversion_composeWorkflowStep_Z35AB9E5D(s, filePath), workflow.Steps);
-  return LDWorkflowProtocol.create(filePath, inputs, outputs, void 0, void 0, void 0, void 0, ResizeArray_singleton(LDComputerLanguage.createCWL()), void 0, void 0, void 0, void 0, steps, void 0, void 0, void 0, [WorkflowConversion_get_workflowDescriptionTypeName()]);
+  return LDWorkflowProtocol.create(filePath, inputs, outputs, void 0, void 0, void 0, filePath, ResizeArray_singleton(LDComputerLanguage.createCWL()), void 0, void 0, void 0, void 0, steps, void 0, void 0, void 0, [WorkflowConversion_get_workflowDescriptionTypeName()]);
 }
 function WorkflowConversion_decomposeWorkflowStep_2664C4B8(step, context, graph) {
   const name = LDComputationalWorkflow.getNameAsString(step, unwrap(context));
@@ -267,6 +269,14 @@ function WorkflowConversion_composeWorkflow_42450E6E(workflow, fs) {
   } else {
     workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, value(matchValue), workflow.Identifier);
   }
+  const publisher = LDOrganization.create("DataPLANT");
+  const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, workflow.Contacts));
+  const dateCreated = utcNow();
+  if (creators != null) {
+    LDComputationalWorkflow.setCreators(workflowProtocol, value(creators));
+  }
+  LDComputationalWorkflow.setSdPublisher(workflowProtocol, publisher);
+  LDComputationalWorkflow.setDateCreatedAsDateTime(workflowProtocol, dateCreated);
   if (workflow.Version != null) {
     LDLabProtocol.setVersionAsString(workflowProtocol, value(workflow.Version));
   }
@@ -282,8 +292,7 @@ function WorkflowConversion_composeWorkflow_42450E6E(workflow, fs) {
     const softwareTools = ResizeArray_map(WorkflowConversion_composeComputationalTool_Z685B8F25, workflow.Components);
     LDLabProtocol.setComputationalTools(workflowProtocol, softwareTools);
   }
-  const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, workflow.Contacts));
-  const hasParts = Option_fromSeq(dataFiles);
+  const hasParts = dataFiles.length === 0 ? ResizeArray_singleton(workflowProtocol) : ResizeArray_appendSingleton(workflowProtocol, dataFiles);
   const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, workflow.Comments));
   return LDDataset.createARCWorkflow(workflow.Identifier, ResizeArray_singleton(workflowProtocol), void 0, unwrap(workflow.Title), unwrap(workflow.Description), unwrap(creators), unwrap(hasParts), unwrap(comments));
 }

package/dist/ts/ts/Conversion.d.ts CHANGED Viewed

@@ -12,7 +12,7 @@ export declare function ARCtrl_ArcWorkflow__ArcWorkflow_ToROCrateWorkflow_1695DD
 export declare function ARCtrl_ArcWorkflow__ArcWorkflow_fromROCrateWorkflow_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcWorkflow;
 export declare function ARCtrl_ArcRun__ArcRun_ToROCrateRun_1695DD5C(this$: ArcRun, fs: Option<FileSystem>): LDNode;
 export declare function ARCtrl_ArcRun__ArcRun_fromROCrateRun_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcRun;
-export declare function ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_1695DD5C(this$: ArcInvestigation, fs: Option<FileSystem>): LDNode;
+export declare function ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_Z7960E96B(this$: ArcInvestigation, fs: Option<FileSystem>, ignoreBrokenWR: Option<boolean>): LDNode;
 export declare function ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcInvestigation;
 export declare function ARCtrl_ROCrate_Dataset__Dataset_toArcAssay_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcAssay;
 export declare function ARCtrl_ROCrate_Dataset__Dataset_fromArcAssay_Static_1501C0F8(a: ArcAssay): LDNode;
@@ -34,7 +34,7 @@ export declare class Conversion {
     static datasetToArcWorkflow(a: LDNode, graph?: LDGraph, context?: LDContext): ArcWorkflow;
     static arcRunToDataset(a: ArcRun, fs?: FileSystem): LDNode;
     static datasetToArcRun(a: LDNode, graph?: LDGraph, context?: LDContext): ArcRun;
-    static arcInvestigationToDataset(a: ArcInvestigation, fs?: FileSystem): LDNode;
+    static arcInvestigationToDataset(a: ArcInvestigation, fs?: FileSystem, ignoreBrokenWR?: boolean): LDNode;
     static datasetToArcInvestigation(a: LDNode, graph?: LDGraph, context?: LDContext): ArcInvestigation;
 }
 export declare function Conversion_$reflection(): TypeInfo;

package/dist/ts/ts/Conversion.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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