@nfdi4plants/arctrl 3.0.0-beta.8 → 3.0.0

package/dist/ts/ts/Core/Datamap.d.ts

@@ -0,0 +1,53 @@
+import { CompositeHeader_$union } from './Table/CompositeHeader.js';
+import { OntologyAnnotation } from './OntologyAnnotation.js';
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { CompositeCell_$union } from './Table/CompositeCell.js';
+import { DataContext } from './DataContext.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+export declare const DatamapAux_dataHeader: CompositeHeader_$union;
+export declare const DatamapAux_explication: OntologyAnnotation;
+export declare const DatamapAux_explicationHeader: CompositeHeader_$union;
+export declare const DatamapAux_unit: OntologyAnnotation;
+export declare const DatamapAux_unitHeader: CompositeHeader_$union;
+export declare const DatamapAux_objectType: OntologyAnnotation;
+export declare const DatamapAux_objectTypeHeader: CompositeHeader_$union;
+export declare const DatamapAux_labelHeader: CompositeHeader_$union;
+export declare const DatamapAux_descriptionHeader: CompositeHeader_$union;
+export declare const DatamapAux_generatedByHeader: CompositeHeader_$union;
+export declare const DatamapAux_allowedHeaders: FSharpList<CompositeHeader_$union>;
+export declare function DatamapAux_getOntologyColumn(f: ((arg0: DataContext) => Option<OntologyAnnotation>), dataContexts: DataContext[]): CompositeCell_$union[];
+export declare function DatamapAux_getStringColumn(f: ((arg0: DataContext) => Option<string>), dataContexts: DataContext[]): CompositeCell_$union[];
+export declare function DatamapAux_setOntologyColumn(f: ((arg0: DataContext, arg1: Option<OntologyAnnotation>) => void), column: CompositeCell_$union[], dataContexts: DataContext[]): void;
+export declare function DatamapAux_setStringColumn(f: ((arg0: DataContext, arg1: Option<string>) => void), column: CompositeCell_$union[], dataContexts: DataContext[]): void;
+export declare function DatamapAux_SanityChecks_rowIndexInBoundaries(row: int32, dataContexts: DataContext[]): void;
+export declare function DatamapAux_SanityChecks_lengthOfNewColumn(newColumn: CompositeCell_$union[], dataContexts: DataContext[]): void;
+export declare class Datamap {
+    staticHash: int32;
+    "dataContexts@108": DataContext[];
+    constructor(dataContexts: DataContext[]);
+    get StaticHash(): int32;
+    set StaticHash(value: int32);
+    get DataContexts(): DataContext[];
+    static init(): Datamap;
+    GetExplicationColumn(): CompositeCell_$union[];
+    SetExplicationColumn(cells: CompositeCell_$union[]): void;
+    GetUnitColumn(): CompositeCell_$union[];
+    SetUnitColumn(cells: CompositeCell_$union[]): void;
+    GetObjectTypeColumn(): CompositeCell_$union[];
+    SetDataTypeColumn(cells: CompositeCell_$union[]): void;
+    GetLabelColumn(): CompositeCell_$union[];
+    SetLabelColumn(cells: CompositeCell_$union[]): void;
+    GetDescriptionColumn(): CompositeCell_$union[];
+    SetDescriptionColumn(cells: CompositeCell_$union[]): void;
+    GetDataContext<$b>(row: int32, SkipValidation?: Option<$b>): DataContext;
+    static getDataContext<$a>(row: int32, SkipValidation?: Option<$a>): ((arg0: Datamap) => DataContext);
+    Copy(): Datamap;
+    Equals(obj: any): boolean;
+    GetHashCode(): int32;
+    static get FileName(): string;
+}
+export declare function Datamap_$reflection(): TypeInfo;
+export declare function Datamap_$ctor_4E3220A7(dataContexts: DataContext[]): Datamap;
+//# sourceMappingURL=Datamap.d.ts.map

package/dist/ts/ts/Core/{DataMap.d.ts.map → Datamap.d.ts.map}

@@ -1 +1 @@
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package/dist/ts/ts/Core/Datamap.js

@@ -0,0 +1,177 @@
+import { CompositeHeader_Input, IOType_Data, CompositeHeader_Parameter, CompositeHeader_FreeText } from './Table/CompositeHeader.js';
+import { OntologyAnnotation } from './OntologyAnnotation.js';
+import { ofArray } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { map, iterateIndexed } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { value } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { CompositeCell, CompositeCell_Term, CompositeCell_FreeText } from './Table/CompositeCell.js';
+import { DataContext__get_Explication, DataContext__set_Explication_279AAFF2, DataContext__get_Unit, DataContext__set_Unit_279AAFF2, DataContext__get_ObjectType, DataContext__set_ObjectType_279AAFF2, DataContext__get_Description, DataContext__set_Description_6DFDD678, DataContext__Copy } from './DataContext.js';
+import { hash, boxHashSeq } from './Helper/HashCodes.js';
+import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+
+const DatamapAux_dataHeader = CompositeHeader_Input(IOType_Data());
+const DatamapAux_explication = new OntologyAnnotation("Clarification", "NCIT", "http://purl.obolibrary.org/obo/NCIT_C94778");
+const DatamapAux_explicationHeader = CompositeHeader_Parameter(DatamapAux_explication);
+const DatamapAux_unit = new OntologyAnnotation("Unit", "UO", "http://purl.obolibrary.org/obo/UO_0000000");
+const DatamapAux_unitHeader = CompositeHeader_Parameter(DatamapAux_unit);
+const DatamapAux_objectType = new OntologyAnnotation("Data Type", "NCIT", "http://purl.obolibrary.org/obo/NCIT_C42645");
+const DatamapAux_objectTypeHeader = CompositeHeader_Parameter(DatamapAux_objectType);
+const DatamapAux_labelHeader = CompositeHeader_FreeText("Label");
+const DatamapAux_descriptionHeader = CompositeHeader_FreeText("Description");
+const DatamapAux_generatedByHeader = CompositeHeader_FreeText("Generated By");
+const DatamapAux_allowedHeaders = ofArray([DatamapAux_dataHeader, DatamapAux_explicationHeader, DatamapAux_unitHeader, DatamapAux_objectTypeHeader, DatamapAux_descriptionHeader, DatamapAux_generatedByHeader]);
+function DatamapAux_getOntologyColumn(f, dataContexts) {
+  const collection = map((dc) => {
+    const matchValue = f(dc);
+    if (matchValue == null) {
+      return CompositeCell.emptyTerm;
+    } else {
+      return CompositeCell_Term(value(matchValue));
+    }
+  }, dataContexts);
+  return Array.from(collection);
+}
+function DatamapAux_getStringColumn(f, dataContexts) {
+  const collection = map((dc) => {
+    const matchValue = f(dc);
+    if (matchValue == null) {
+      return CompositeCell.emptyFreeText;
+    } else {
+      return CompositeCell_FreeText(value(matchValue));
+    }
+  }, dataContexts);
+  return Array.from(collection);
+}
+function DatamapAux_setOntologyColumn(f, column, dataContexts) {
+  iterateIndexed((i, cell) => {
+    if (cell.tag === /* Term */
+    0) {
+      const s = cell.fields[0];
+      f(dataContexts[i], s);
+    }
+  }, column);
+}
+function DatamapAux_setStringColumn(f, column, dataContexts) {
+  iterateIndexed((i, cell) => {
+    if (cell.tag === /* FreeText */
+    1) {
+      const s = cell.fields[0];
+      f(dataContexts[i], s);
+    }
+  }, column);
+}
+function DatamapAux_SanityChecks_rowIndexInBoundaries(row, dataContexts) {
+  if (row < 0) {
+    throw new Error("Row index must be greater or equal to 0.");
+  }
+  if (row >= dataContexts.length) {
+    throw new Error("Row index must be less than the number of rows.");
+  }
+}
+function DatamapAux_SanityChecks_lengthOfNewColumn(newColumn, dataContexts) {
+  if (newColumn.length !== dataContexts.length) {
+    throw new Error("Length of new column does not match length of data contexts.");
+  }
+}
+class Datamap {
+  constructor(dataContexts) {
+    this.staticHash = 0;
+    this["dataContexts@108"] = dataContexts;
+  }
+  get StaticHash() {
+    const this$ = this;
+    return this$.staticHash | 0;
+  }
+  set StaticHash(value) {
+    const this$ = this;
+    this$.staticHash = value | 0;
+  }
+  get DataContexts() {
+    const this$ = this;
+    return this$["dataContexts@108"];
+  }
+  static init() {
+    return new Datamap([]);
+  }
+  GetExplicationColumn() {
+    const this$ = this;
+    return DatamapAux_getOntologyColumn(DataContext__get_Explication, this$["dataContexts@108"]);
+  }
+  SetExplicationColumn(cells) {
+    const this$ = this;
+    DatamapAux_setOntologyColumn((dc, oa) => {
+      DataContext__set_Explication_279AAFF2(dc, oa);
+    }, cells, this$["dataContexts@108"]);
+  }
+  GetUnitColumn() {
+    const this$ = this;
+    return DatamapAux_getOntologyColumn(DataContext__get_Unit, this$["dataContexts@108"]);
+  }
+  SetUnitColumn(cells) {
+    const this$ = this;
+    DatamapAux_setOntologyColumn((dc, oa) => {
+      DataContext__set_Unit_279AAFF2(dc, oa);
+    }, cells, this$["dataContexts@108"]);
+  }
+  GetObjectTypeColumn() {
+    const this$ = this;
+    return DatamapAux_getOntologyColumn(DataContext__get_ObjectType, this$["dataContexts@108"]);
+  }
+  SetDataTypeColumn(cells) {
+    const this$ = this;
+    DatamapAux_setOntologyColumn((dc, oa) => {
+      DataContext__set_ObjectType_279AAFF2(dc, oa);
+    }, cells, this$["dataContexts@108"]);
+  }
+  GetLabelColumn() {
+    const this$ = this;
+    return DatamapAux_getStringColumn((dc) => dc.Name, this$["dataContexts@108"]);
+  }
+  SetLabelColumn(cells) {
+    const this$ = this;
+    DatamapAux_setStringColumn((dc, s) => {
+      dc.Name = s;
+    }, cells, this$["dataContexts@108"]);
+  }
+  GetDescriptionColumn() {
+    const this$ = this;
+    return DatamapAux_getStringColumn(DataContext__get_Description, this$["dataContexts@108"]);
+  }
+  SetDescriptionColumn(cells) {
+    const this$ = this;
+    DatamapAux_setStringColumn((dc, s) => {
+      DataContext__set_Description_6DFDD678(dc, s);
+    }, cells, this$["dataContexts@108"]);
+  }
+  GetDataContext(row, SkipValidation) {
+    const this$ = this;
+    DatamapAux_SanityChecks_rowIndexInBoundaries(row, this$["dataContexts@108"]);
+    return this$["dataContexts@108"][row];
+  }
+  static getDataContext(row, SkipValidation) {
+    return (dm) => dm.GetDataContext(row, SkipValidation);
+  }
+  Copy() {
+    let collection;
+    const this$ = this;
+    return new Datamap((collection = map(DataContext__Copy, this$["dataContexts@108"]), Array.from(collection)));
+  }
+  Equals(obj) {
+    const this$ = this;
+    return hash(this$) === hash(obj);
+  }
+  GetHashCode() {
+    const this$ = this;
+    return boxHashSeq(this$["dataContexts@108"]) | 0;
+  }
+  static get FileName() {
+    return "isa.datamap.xlsx";
+  }
+}
+function Datamap_$reflection() {
+  return class_type("ARCtrl.Datamap", void 0, Datamap);
+}
+function Datamap_$ctor_4E3220A7(dataContexts) {
+  return new Datamap(dataContexts);
+}
+
+export { Datamap, DatamapAux_SanityChecks_lengthOfNewColumn, DatamapAux_SanityChecks_rowIndexInBoundaries, DatamapAux_allowedHeaders, DatamapAux_dataHeader, DatamapAux_descriptionHeader, DatamapAux_explication, DatamapAux_explicationHeader, DatamapAux_generatedByHeader, DatamapAux_getOntologyColumn, DatamapAux_getStringColumn, DatamapAux_labelHeader, DatamapAux_objectType, DatamapAux_objectTypeHeader, DatamapAux_setOntologyColumn, DatamapAux_setStringColumn, DatamapAux_unit, DatamapAux_unitHeader, Datamap_$ctor_4E3220A7, Datamap_$reflection };

package/dist/ts/ts/Core/Helper/Identifier.d.ts

@@ -80,6 +80,14 @@ export declare function Workflow_fileNameFromIdentifier(identifier: string): str
  * On writing a xlsx file we unify our output to a relative path to ARC root. So: `workflows/workflowIdentifier/isa.workflow.xlsx`.
  */
 export declare function Workflow_tryFileNameFromIdentifier(identifier: string): Option<string>;
+/**
+ * On writing a cwl file we unify our output to a relative path to ARC root. So: `workflows/workflowIdentifier/workflow.cwl`.
+ */
+export declare function Workflow_cwlFileNameFromIdentifier(identifier: string): string;
+/**
+ * On writing a cwl file we unify our output to a relative path to ARC root. So: `workflows/workflowIdentifier/workflow.cwl`.
+ */
+export declare function Workflow_tryCwlFileNameFromIdentifier(identifier: string): Option<string>;
 /**
  * On writing a xlsx file we unify our output to a relative path to ARC root. So: `workflows/workflowIdentifier/isa.datamap.xlsx`.
  */
@@ -108,6 +116,22 @@ export declare function Run_fileNameFromIdentifier(identifier: string): string;
  * On writing a xlsx file we unify our output to a relative path to ARC root. So: `runs/runIdentifier/isa.run.xlsx`.
  */
 export declare function Run_tryFileNameFromIdentifier(identifier: string): Option<string>;
+/**
+ * On writing a cwl file we unify our output to a relative path to ARC root. So: `runs/runIdentifier/run.cwl`.
+ */
+export declare function Run_cwlFileNameFromIdentifier(identifier: string): string;
+/**
+ * On writing a cwl file we unify our output to a relative path to ARC root. So: `runs/runIdentifier/run.cwl`.
+ */
+export declare function Run_tryCwlFileNameFromIdentifier(identifier: string): Option<string>;
+/**
+ * On writing a yml file we unify our output to a relative path to ARC root. So: `runs/runIdentifier/run.yml`.
+ */
+export declare function Run_ymlFileNameFromIdentifier(identifier: string): string;
+/**
+ * On writing a yml file we unify our output to a relative path to ARC root. So: `runs/runIdentifier/run.yml`.
+ */
+export declare function Run_tryYmlFileNameFromIdentifier(identifier: string): Option<string>;
 /**
  * On writing a xlsx file we unify our output to a relative path to ARC root. So: `runs/runIdentifier/isa.datamap.xlsx`.
  */

package/dist/ts/ts/Core/Helper/Identifier.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"Identifier.d.ts","sourceRoot":"","sources":["../../../../../src/ARCtrl/ts/Core/Helper/Identifier.ts"],"names":[],"mappings":"AAEA,OAAO,EAAS,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAGtE,wBAAgB,uBAAuB,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO,CAOnE;AAED,wBAAgB,oBAAoB,CAAC,UAAU,EAAE,MAAM,GAAG,IAAI,CAM7D;AAED,wBAAgB,uBAAuB,IAAI,MAAM,CAGhD;AAED,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAExD;AAED,wBAAgB,uBAAuB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAO3D;AAED;;;;GAIG;AACH,wBAAgB,4BAA4B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CASrE;AAED;;;;GAIG;AACH,wBAAgB,+BAA+B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAShF;AAED;;GAEG;AACH,wBAAgB,4BAA4B,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGvE;AAED;;GAEG;AACH,wBAAgB,+BAA+B,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOlF;AAED;;GAEG;AACH,wBAAgB,mCAAmC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAG9E;AAED;;GAEG;AACH,wBAAgB,sCAAsC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOzF;AAED;;;;GAIG;AACH,wBAAgB,4BAA4B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CASrE;AAED;;;;GAIG;AACH,wBAAgB,+BAA+B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAShF;AAED;;GAEG;AACH,wBAAgB,4BAA4B,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGvE;AAED;;GAEG;AACH,wBAAgB,+BAA+B,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOlF;AAED;;GAEG;AACH,wBAAgB,mCAAmC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAG9E;AAED;;GAEG;AACH,wBAAgB,sCAAsC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOzF;AAED;;;;GAIG;AACH,wBAAgB,+BAA+B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CASxE;AAED;;;;GAIG;AACH,wBAAgB,kCAAkC,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CASnF;AAED;;GAEG;AACH,wBAAgB,+BAA+B,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAG1E;AAED;;GAEG;AACH,wBAAgB,kCAAkC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOrF;AAED;;GAEG;AACH,wBAAgB,kCAAkC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAG7E;AAED;;GAEG;AACH,wBAAgB,qCAAqC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOxF;AAED;;GAEG;AACH,wBAAgB,sCAAsC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGjF;AAED;;GAEG;AACH,wBAAgB,yCAAyC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAO5F;AAED;;;;GAIG;AACH,wBAAgB,0BAA0B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CASnE;AAED;;;;GAIG;AACH,wBAAgB,6BAA6B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAS9E;AAED;;GAEG;AACH,wBAAgB,0BAA0B,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGrE;AAED;;GAEG;AACH,wBAAgB,6BAA6B,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOhF;AAED;;GAEG;AACH,wBAAgB,6BAA6B,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGxE;AAED;;GAEG;AACH,wBAAgB,gCAAgC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOnF;AAED;;GAEG;AACH,wBAAgB,6BAA6B,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGxE;AAED;;GAEG;AACH,wBAAgB,gCAAgC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOnF;AAED;;GAEG;AACH,wBAAgB,iCAAiC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAG5E;AAED;;GAEG;AACH,wBAAgB,oCAAoC,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAOvF"}

package/dist/ts/ts/Core/Helper/Identifier.js

@@ -13,7 +13,7 @@ function tryCheckValidCharacters(identifier) {
 function checkValidCharacters(identifier) {
   if (tryCheckValidCharacters(identifier)) {
   } else {
-    throw new Error(`New identifier "${identifier}"contains forbidden characters! Allowed characters are: letters, digits, underscore (_), dash (-) and whitespace ( ).`);
+    throw new Error(`New identifier "${identifier}" contains forbidden characters! Allowed characters are: letters, digits, underscore (_), dash (-) and whitespace ( ).`);
   }
 }
 function createMissingIdentifier() {
@@ -139,6 +139,17 @@ function Workflow_tryFileNameFromIdentifier(identifier) {
     return void 0;
   }
 }
+function Workflow_cwlFileNameFromIdentifier(identifier) {
+  checkValidCharacters(identifier);
+  return combineMany(["workflows", identifier, "workflow.cwl"]);
+}
+function Workflow_tryCwlFileNameFromIdentifier(identifier) {
+  if (tryCheckValidCharacters(identifier)) {
+    return combineMany(["workflows", identifier, "workflow.cwl"]);
+  } else {
+    return void 0;
+  }
+}
 function Workflow_datamapFileNameFromIdentifier(identifier) {
   checkValidCharacters(identifier);
   return combineMany(["workflows", identifier, "isa.datamap.xlsx"]);
@@ -179,6 +190,28 @@ function Run_tryFileNameFromIdentifier(identifier) {
     return void 0;
   }
 }
+function Run_cwlFileNameFromIdentifier(identifier) {
+  checkValidCharacters(identifier);
+  return combineMany(["runs", identifier, "run.cwl"]);
+}
+function Run_tryCwlFileNameFromIdentifier(identifier) {
+  if (tryCheckValidCharacters(identifier)) {
+    return combineMany(["runs", identifier, "run.cwl"]);
+  } else {
+    return void 0;
+  }
+}
+function Run_ymlFileNameFromIdentifier(identifier) {
+  checkValidCharacters(identifier);
+  return combineMany(["runs", identifier, "run.yml"]);
+}
+function Run_tryYmlFileNameFromIdentifier(identifier) {
+  if (tryCheckValidCharacters(identifier)) {
+    return combineMany(["runs", identifier, "run.yml"]);
+  } else {
+    return void 0;
+  }
+}
 function Run_datamapFileNameFromIdentifier(identifier) {
   checkValidCharacters(identifier);
   return combineMany(["runs", identifier, "isa.datamap.xlsx"]);
@@ -191,4 +224,4 @@ function Run_tryDatamapFileNameFromIdentifier(identifier) {
   }
 }
 
-export { Assay_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Assay_identifierFromFileName, Assay_tryDatamapFileNameFromIdentifier, Assay_tryFileNameFromIdentifier, Assay_tryIdentifierFromFileName, Run_datamapFileNameFromIdentifier, Run_fileNameFromIdentifier, Run_identifierFromFileName, Run_tryDatamapFileNameFromIdentifier, Run_tryFileNameFromIdentifier, Run_tryIdentifierFromFileName, Study_datamapFileNameFromIdentifier, Study_fileNameFromIdentifier, Study_identifierFromFileName, Study_tryDatamapFileNameFromIdentifier, Study_tryFileNameFromIdentifier, Study_tryIdentifierFromFileName, Workflow_datamapFileNameFromIdentifier, Workflow_fileNameFromIdentifier, Workflow_identifierFromFileName, Workflow_tryDatamapFileNameFromIdentifier, Workflow_tryFileNameFromIdentifier, Workflow_tryIdentifierFromFileName, checkValidCharacters, createMissingIdentifier, isMissingIdentifier, removeMissingIdentifier, tryCheckValidCharacters };
+export { Assay_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Assay_identifierFromFileName, Assay_tryDatamapFileNameFromIdentifier, Assay_tryFileNameFromIdentifier, Assay_tryIdentifierFromFileName, Run_cwlFileNameFromIdentifier, Run_datamapFileNameFromIdentifier, Run_fileNameFromIdentifier, Run_identifierFromFileName, Run_tryCwlFileNameFromIdentifier, Run_tryDatamapFileNameFromIdentifier, Run_tryFileNameFromIdentifier, Run_tryIdentifierFromFileName, Run_tryYmlFileNameFromIdentifier, Run_ymlFileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Study_fileNameFromIdentifier, Study_identifierFromFileName, Study_tryDatamapFileNameFromIdentifier, Study_tryFileNameFromIdentifier, Study_tryIdentifierFromFileName, Workflow_cwlFileNameFromIdentifier, Workflow_datamapFileNameFromIdentifier, Workflow_fileNameFromIdentifier, Workflow_identifierFromFileName, Workflow_tryCwlFileNameFromIdentifier, Workflow_tryDatamapFileNameFromIdentifier, Workflow_tryFileNameFromIdentifier, Workflow_tryIdentifierFromFileName, checkValidCharacters, createMissingIdentifier, isMissingIdentifier, removeMissingIdentifier, tryCheckValidCharacters };

package/dist/ts/ts/Core/Table/ArcTable.d.ts

@@ -70,14 +70,14 @@ export declare class ArcTable {
     static removeColumn(index: int32): ((arg0: ArcTable) => ArcTable);
     RemoveColumns(indexArr: int32[]): void;
     static removeColumns(indexArr: int32[]): ((arg0: ArcTable) => ArcTable);
-    GetColumn(columnIndex: int32, fillDefault?: boolean): CompositeColumn;
-    static getColumn(index: int32, fillDefault?: boolean): ((arg0: ArcTable) => CompositeColumn);
-    TryGetColumnByHeader(header: CompositeHeader_$union, fillDefault?: boolean): Option<CompositeColumn>;
-    static tryGetColumnByHeader(header: CompositeHeader_$union, fillDefault?: boolean): ((arg0: ArcTable) => Option<CompositeColumn>);
-    TryGetColumnByHeaderBy(headerPredicate: ((arg0: CompositeHeader_$union) => boolean), fillDefault?: boolean): Option<CompositeColumn>;
-    static tryGetColumnByHeaderBy(headerPredicate: ((arg0: CompositeHeader_$union) => boolean), fillDefault?: boolean): ((arg0: ArcTable) => Option<CompositeColumn>);
-    GetColumnByHeader(header: CompositeHeader_$union, fillDefault?: boolean): CompositeColumn;
-    static getColumnByHeader(header: CompositeHeader_$union, fillDefault?: boolean): ((arg0: ArcTable) => CompositeColumn);
+    GetColumn(columnIndex: int32, failOnMissingCell?: boolean): CompositeColumn;
+    static getColumn(index: int32, failOnMissingCell?: boolean): ((arg0: ArcTable) => CompositeColumn);
+    TryGetColumnByHeader(header: CompositeHeader_$union, failOnMissingCell?: boolean): Option<CompositeColumn>;
+    static tryGetColumnByHeader(header: CompositeHeader_$union, failOnMissingCell?: boolean): ((arg0: ArcTable) => Option<CompositeColumn>);
+    TryGetColumnByHeaderBy(headerPredicate: ((arg0: CompositeHeader_$union) => boolean), failOnMissingCell?: boolean): Option<CompositeColumn>;
+    static tryGetColumnByHeaderBy(headerPredicate: ((arg0: CompositeHeader_$union) => boolean), failOnMissingCell?: boolean): ((arg0: ArcTable) => Option<CompositeColumn>);
+    GetColumnByHeader(header: CompositeHeader_$union, failOnMissingCell?: boolean): CompositeColumn;
+    static getColumnByHeader(header: CompositeHeader_$union, failOnMissingCell?: boolean): ((arg0: ArcTable) => CompositeColumn);
     TryGetInputColumn(): Option<CompositeColumn>;
     static tryGetInputColumn(): ((arg0: ArcTable) => Option<CompositeColumn>);
     GetInputColumn(): CompositeColumn;

package/dist/ts/ts/Core/Table/ArcTable.d.ts.map

@@ -1 +1 @@
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package/dist/ts/ts/Core/Table/ArcTable.js

@@ -417,9 +417,9 @@ class ArcTable {
       return newTable;
     };
   }
-  GetColumn(columnIndex, fillDefault) {
+  GetColumn(columnIndex, failOnMissingCell) {
     const this$ = this;
-    const fillDefault_1 = defaultArg(fillDefault, false);
+    const failOnMissingCell_1 = defaultArg(failOnMissingCell, false);
     SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);
     const h = this$.Headers[columnIndex];
     const cells = [];
@@ -432,10 +432,10 @@ class ArcTable {
         for (let rowIndex = 0; rowIndex <= this$.RowCount - 1; rowIndex++) {
           if (vals.has(rowIndex)) {
             void cells.push(getItemFromDict(this$._values.ValueMap, getItemFromDict(vals, rowIndex)));
-          } else if (fillDefault_1) {
-            void cells.push(emptyCell);
-          } else {
+          } else if (failOnMissingCell_1) {
             toFail(printf("Could not return column: Unable to find cell for index: (%i, %i)"))(columnIndex)(rowIndex);
+          } else {
+            void cells.push(emptyCell);
           }
         }
       } else {
@@ -448,26 +448,26 @@ class ArcTable {
     }
     return CompositeColumn.create(h, cells);
   }
-  static getColumn(index, fillDefault) {
-    return (table) => table.GetColumn(index, unwrap(fillDefault));
+  static getColumn(index, failOnMissingCell) {
+    return (table) => table.GetColumn(index, unwrap(failOnMissingCell));
   }
-  TryGetColumnByHeader(header, fillDefault) {
+  TryGetColumnByHeader(header, failOnMissingCell) {
     const this$ = this;
-    return map$1((i) => this$.GetColumn(i, unwrap(fillDefault)), tryFindIndex((x) => equals(x, header), this$.Headers));
+    return map$1((i) => this$.GetColumn(i, unwrap(failOnMissingCell)), tryFindIndex((x) => equals(x, header), this$.Headers));
   }
-  static tryGetColumnByHeader(header, fillDefault) {
-    return (table) => table.TryGetColumnByHeader(header, unwrap(fillDefault));
+  static tryGetColumnByHeader(header, failOnMissingCell) {
+    return (table) => table.TryGetColumnByHeader(header, unwrap(failOnMissingCell));
   }
-  TryGetColumnByHeaderBy(headerPredicate, fillDefault) {
+  TryGetColumnByHeaderBy(headerPredicate, failOnMissingCell) {
     const this$ = this;
-    return map$1((i) => this$.GetColumn(i, unwrap(fillDefault)), tryFindIndex(headerPredicate, this$.Headers));
+    return map$1((i) => this$.GetColumn(i, unwrap(failOnMissingCell)), tryFindIndex(headerPredicate, this$.Headers));
   }
-  static tryGetColumnByHeaderBy(headerPredicate, fillDefault) {
-    return (table) => table.TryGetColumnByHeaderBy(headerPredicate, unwrap(fillDefault));
+  static tryGetColumnByHeaderBy(headerPredicate, failOnMissingCell) {
+    return (table) => table.TryGetColumnByHeaderBy(headerPredicate, unwrap(failOnMissingCell));
   }
-  GetColumnByHeader(header, fillDefault) {
+  GetColumnByHeader(header, failOnMissingCell) {
     const this$ = this;
-    const matchValue = this$.TryGetColumnByHeader(header, unwrap(fillDefault));
+    const matchValue = this$.TryGetColumnByHeader(header, unwrap(failOnMissingCell));
     if (matchValue == null) {
       const arg = this$.Name;
       return toFail(printf("Unable to find column with header in table %s: %O"))(arg)(header);
@@ -475,8 +475,8 @@ class ArcTable {
       return value(matchValue);
     }
   }
-  static getColumnByHeader(header, fillDefault) {
-    return (table) => table.GetColumnByHeader(header, unwrap(fillDefault));
+  static getColumnByHeader(header, failOnMissingCell) {
+    return (table) => table.GetColumnByHeader(header, unwrap(failOnMissingCell));
   }
   TryGetInputColumn() {
     const this$ = this;
@@ -820,7 +820,7 @@ class ArcTable {
       const headers = table.Headers;
       const rows = ResizeArray_map((i_1) => table.GetRow(i_1, true), indexGroup);
       return ArcTable.createFromRows(table.Name, headers, rows);
-    }, ResizeArray_map((tupledArg) => ResizeArray_map((tuple_1) => tuple_1[0], tupledArg[1]), ResizeArray_groupBy((tuple) => tuple[1], ResizeArray_indexed(table.GetColumn(columnIndex, true).Cells))));
+    }, ResizeArray_map((tupledArg) => ResizeArray_map((tuple_1) => tuple_1[0], tupledArg[1]), ResizeArray_groupBy((tuple) => tuple[1], ResizeArray_indexed(table.GetColumn(columnIndex).Cells))));
   }
   static SplitByColumnValuesByHeader(header) {
     return (table) => {

package/dist/ts/ts/FileSystem/FileSystemTree.d.ts

@@ -41,10 +41,10 @@ export declare class FileSystemTree<Tag extends keyof FileSystemTree_$cases> ext
     static createGitKeepFile(): FileSystemTree_$union;
     static createReadmeFile(): FileSystemTree_$union;
     static createEmptyFolder(name: string): FileSystemTree_$union;
-    static createAssayFolder(assayName: string, hasDataMap?: boolean): FileSystemTree_$union;
-    static createStudyFolder(studyName: string, hasDataMap?: boolean): FileSystemTree_$union;
-    static createWorkflowFolder(workflowName: string, hasDataMap?: boolean): FileSystemTree_$union;
-    static createRunFolder(runName: string, hasDataMap?: boolean): FileSystemTree_$union;
+    static createAssayFolder(assayName: string, hasDatamap?: boolean): FileSystemTree_$union;
+    static createStudyFolder(studyName: string, hasDatamap?: boolean): FileSystemTree_$union;
+    static createWorkflowFolder(workflowName: string, hasCWL?: boolean, hasDatamap?: boolean): FileSystemTree_$union;
+    static createRunFolder(runName: string, hasCWL?: boolean, hasYML?: boolean, hasDatamap?: boolean): FileSystemTree_$union;
     static createInvestigationFile(): FileSystemTree_$union;
     static createLicenseFile(): FileSystemTree_$union;
     static createAssaysFolder(assays: FileSystemTree_$union[]): FileSystemTree_$union;

package/dist/ts/ts/FileSystem/FileSystemTree.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"FileSystemTree.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/FileSystem/FileSystemTree.ts"],"names":[],"mappings":"AAAA,OAAO,EAAU,MAAM,EAAc,MAAM,uCAAuC,CAAC;AAQnF,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAC7D,OAAO,EAAuC,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAE1G,MAAM,MAAM,qBAAqB,GAC3B,cAAc,CAAC,CAAC,CAAC,GACjB,cAAc,CAAC,CAAC,CAAC,CAAA;AAEvB,MAAM,MAAM,qBAAqB,GAAG;IAChC,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC;IACtB,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,MAAM,EAAE,qBAAqB,EAAE,CAAC,CAAC,CAAA;CACnD,CAAA;AAED,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,qBAE/C;AAED,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,qBAAqB,EAAE,qBAEpF;AAED,qBAAa,cAAc,CAAC,GAAG,SAAS,MAAM,qBAAqB,CAAE,SAAQ,KAAK,CAAC,GAAG,EAAE,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;IACtG,QAAQ,CAAC,GAAG,EAAE,GAAG;IAAE,QAAQ,CAAC,MAAM,EAAE,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;gBAAxD,GAAG,EAAE,GAAG,EAAW,MAAM,EAAE,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;IAG7E,KAAK;IAGL,IAAI,IAAI,IAAI,MAAM,CAUjB;IACD,IAAI,QAAQ,IAAI,OAAO,CAGtB;IACD,IAAI,MAAM,IAAI,OAAO,CAGpB;IACD,MAAM,KAAK,SAAS,IAAI,MAAM,CAE7B;IACD,MAAM,CAAC,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,qBAAqB;IAGtD,MAAM,CAAC,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,qBAAqB,EAAE,GAAG,qBAAqB;IAG5F,MAAM,CAAC,gBAAgB,CAAC,QAAQ,EAAE,qBAAqB,EAAE,GAAG,qBAAqB;IAGjF,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAAC,qBAAqB,CAAC;IAI9D,MAAM,CAAC,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,qBAAqB,KAAK,MAAM,CAAC,qBAAqB,CAAC,CAAC;IAGxG,qBAAqB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO;IAU5C,MAAM,CAAC,qBAAqB,CAAC,IAAI,EAAE,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,qBAAqB,KAAK,OAAO,CAAC;IAGtF,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAAC,qBAAqB,CAAC;IAmCvD,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,qBAAqB;IAM5C,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,qBAAqB,KAAK,qBAAqB,CAAC;IAGtF,MAAM,CAAC,aAAa,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,qBAAqB;IA0B5D,WAAW,CAAC,UAAU,CAAC,EAAE,OAAO,GAAG,MAAM,EAAE;IAgC3C,MAAM,CAAC,WAAW,CAAC,UAAU,CAAC,EAAE,OAAO,GAAG,CAAC,CAAC,IAAI,EAAE,qBAAqB,KAAK,MAAM,EAAE,CAAC;IAGrF,WAAW,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,GAAG,MAAM,CAAC,qBAAqB,CAAC;IAkBlF,MAAM,CAAC,WAAW,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,qBAAqB,KAAK,MAAM,CAAC,qBAAqB,CAAC,CAAC;IAG5H,aAAa,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,GAAG,MAAM,CAAC,qBAAqB,CAAC;IAmBpF,MAAM,CAAC,aAAa,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,qBAAqB,KAAK,MAAM,CAAC,qBAAqB,CAAC,CAAC;IAG9H,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,GAAG,MAAM,CAAC,qBAAqB,CAAC;IA+B7E,MAAM,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,qBAAqB,KAAK,MAAM,CAAC,qBAAqB,CAAC,CAAC;IAGvH,KAAK,CAAC,QAAQ,EAAE,qBAAqB,GAAG,qBAAqB;IAS7D,IAAI,IAAI,qBAAqB;IAI7B,MAAM,CAAC,iBAAiB,IAAI,qBAAqB;IAGjD,MAAM,CAAC,gBAAgB,IAAI,qBAAqB;IAGhD,MAAM,CAAC,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,qBAAqB;IAG7D,MAAM,CAAC,iBAAiB,CAAC,SAAS,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,OAAO,GAAG,qBAAqB;IAcxF,MAAM,CAAC,iBAAiB,CAAC,SAAS,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,OAAO,GAAG,qBAAqB;IAcxF,MAAM,CAAC,oBAAoB,CAAC,YAAY,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,OAAO,EAAE,UAAU,CAAC,EAAE,OAAO,GAAG,qBAAqB;IAOhH,MAAM,CAAC,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,OAAO,EAAE,MAAM,CAAC,EAAE,OAAO,EAAE,UAAU,CAAC,EAAE,OAAO,GAAG,qBAAqB;IAQxH,MAAM,CAAC,uBAAuB,IAAI,qBAAqB;IAGvD,MAAM,CAAC,iBAAiB,IAAI,qBAAqB;IAGjD,MAAM,CAAC,kBAAkB,CAAC,MAAM,EAAE,qBAAqB,EAAE,GAAG,qBAAqB;IAGjF,MAAM,CAAC,mBAAmB,CAAC,OAAO,EAAE,qBAAqB,EAAE,GAAG,qBAAqB;IAGnF,MAAM,CAAC,qBAAqB,CAAC,SAAS,EAAE,qBAAqB,EAAE,GAAG,qBAAqB;IAGvF,MAAM,CAAC,gBAAgB,CAAC,IAAI,EAAE,qBAAqB,EAAE,GAAG,qBAAqB;CAGhF;AAED,wBAAgB,0BAA0B,IAAI,QAAQ,CAErD"}