@nfdi4plants/arctrl 3.1.1 → 3.2.0

package/dist/ts/ts/Conversion/Process.d.ts

@@ -1,14 +1,17 @@
-import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
-import { Option } from '@fable-org/fable-library-js/Option.js';
-import { LDGraph, LDNode } from '../ROCrate/LDObject.js';
-import { OntologyAnnotation } from '../Core/OntologyAnnotation.js';
-import { LDContext } from '../ROCrate/LDContext.js';
-import { int32 } from '@fable-org/fable-library-js/Int32.js';
-import { CompositeCell_$union } from '../Core/Table/CompositeCell.js';
-import { ArcTable } from '../Core/Table/ArcTable.js';
-import { CompositeHeader_$union } from '../Core/Table/CompositeHeader.js';
-import { FileSystem } from '../FileSystem/FileSystem.js';
-import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { TypeInfo } from '@fable-org/fable-library-ts/Reflection.ts';
+import { Option } from '@fable-org/fable-library-ts/Option.ts';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.ts';
+import { OntologyAnnotation } from '../Core/OntologyAnnotation.ts';
+import { LDContext } from '../ROCrate/LDContext.ts';
+import { int32 } from '@fable-org/fable-library-ts/Int32.ts';
+import { CompositeCell_$union } from '../Core/Table/CompositeCell.ts';
+import { ArcTable } from '../Core/Table/ArcTable.ts';
+import { CompositeHeader_$union } from '../Core/Table/CompositeHeader.ts';
+import { FileSystem } from '../FileSystem/FileSystem.ts';
+import { FSharpList } from '@fable-org/fable-library-ts/List.ts';
+/**
+ * Functions for parsing ArcTables to ISA json Processes and vice versa
+ */
 export declare class ProcessConversion {
     constructor();
 }

package/dist/ts/ts/Conversion/Process.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"Process.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Process.ts"],"names":[],"mappings":"AACA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAEjF,OAAO,EAAgC,MAAM,EAAU,MAAM,uCAAuC,CAAC;AACrG,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AACzD,OAAO,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AAEnE,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AACpD,OAAO,EAAS,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAIpE,OAAO,EAA8C,oBAAoB,EAAE,MAAM,gCAAgC,CAAC;AAClH,OAAO,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAC;AACrD,OAAO,EAA4D,sBAAsB,EAAE,MAAM,kCAAkC,CAAC;AACpI,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAKzD,OAAO,EAA+C,UAAU,EAAE,MAAM,qCAAqC,CAAC;AAQ9G;;GAEG;AACH,qBAAa,iBAAiB;;CAG7B;AAED,wBAAgB,6BAA6B,IAAI,QAAQ,CAExD;AAED,wBAAgB,8CAA8C,CAAC,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAAC,kBAAkB,CAAC,CAe3I;AAED,wBAAgB,oCAAoC,CAAC,eAAe,EAAE,MAAM,EAAE,CAAC,EAAE,KAAK,GAAG,MAAM,CAE9F;AAED,wBAAgB,gDAAgD,CAAC,IAAI,EAAE,MAAM,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC,CAStG;AAED;;GAEG;AACH,wBAAgB,oCAAoC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAajL;AAED;;GAEG;AACH,wBAAgB,oCAAoC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAajL;AAED;;GAEG;AACH,wBAAgB,iCAAiC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAa9K;AAED;;GAEG;AACH,wBAAgB,yCAAyC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAatL;AAED;;GAEG;AACH,wBAAgB,0CAA0C,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAUnK;AAED;;GAEG;AACH,wBAAgB,yCAAyC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAgBlK;AAED;;GAEG;AACH,wBAAgB,iDAAiD,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAgB1K;AAED;;GAEG;AACH,wBAAgB,yCAAyC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAgBlK;AAED;;GAEG;AACH,wBAAgB,6CAA6C,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAgBtK;AAED;;GAEG;AACH,wBAAgB,mCAAmC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,sBAAsB,EAAE,EAAE,EAAE,MAAM,CAAC,UAAU,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAWpL;AAED;;GAEG;AACH,wBAAgB,oCAAoC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,sBAAsB,EAAE,EAAE,EAAE,MAAM,CAAC,UAAU,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAWrL;AAED;;GAEG;AACH,wBAAgB,qCAAqC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAW9J;AAED,wBAAgB,uCAAuC,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,EAAE,sBAAsB,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,CAkBhK;AAED;;GAEG;AACH,wBAAgB,kCAAkC,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,eAAe,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,CAAC,sBAAsB,CAAC,EAAE,EAAE,EAAE,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,QAAQ,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,MAAM,CAAC,CAAC,CAkGpP;AAED;;;;;;GAMG;AACH,wBAAgB,0CAA0C,CAAC,SAAS,EAAE,UAAU,CAAC,MAAM,CAAC,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,UAAU,CAAC,CAAC,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAuDxK;AAED;;GAEG;AACH,wBAAgB,yCAAyC,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,UAAU,CAAC,CAAC,sBAAsB,EAAE,oBAAoB,CAAC,CAAC,EAAE,CAiFvK"}

package/dist/ts/ts/Conversion/Process.js

@@ -1,25 +1,25 @@
-import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+import { class_type } from '../../node_modules/@fable-org/fable-library-ts/Reflection.js';
 import { LDLabProtocol } from '../ROCrate/LDTypes/LabProtocol.js';
-import { unwrap, value, map as map$1, defaultArg } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { unwrap, value, defaultArg } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
 import { OntologyAnnotation } from '../Core/OntologyAnnotation.js';
 import { BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_composeComponent, BaseTypes_composeParameterValue, BaseTypes_composeFactorValue, BaseTypes_composeCharacteristicValue, BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composeProcessInput, BaseTypes_composeProcessOutput, BaseTypes_decomposeParameterValue_Z2F770004, BaseTypes_decomposeComponent_Z2F770004, BaseTypes_decomposeCharacteristicValue_Z2F770004, BaseTypes_decomposeFactorValue_Z2F770004, BaseTypes_decomposeProcessInput_Z2F770004, BaseTypes_decomposeProcessOutput_Z2F770004 } from './Basic.js';
-import { parse } from '../../node_modules/@fable-org/fable-library-js/Int32.js';
+import { parse } from '../../node_modules/@fable-org/fable-library-ts/Int32.js';
 import { ActivePatterns_$007CRegex$007C_$007C } from '../Core/Helper/Regex.js';
 import { Unchecked_tryGetCellAt, getEmptyCellForHeader } from '../Core/Table/ArcTableAux.js';
 import { ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4, tryGetIndex } from './ColumnIndex.js';
 import { CompositeCell_FreeText, CompositeCell_Term } from '../Core/Table/CompositeCell.js';
-import { CompositeHeader_ProtocolREF, CompositeHeader_ProtocolDescription, CompositeHeader_ProtocolUri, CompositeHeader_ProtocolVersion, CompositeHeader_ProtocolType, CompositeHeader_Comment } from '../Core/Table/CompositeHeader.js';
-import { toString } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+import { CompositeHeader, CompositeHeader_Comment$ } from '../Core/Table/CompositeHeader.js';
+import { toString } from '../../node_modules/@fable-org/fable-library-ts/Types.js';
 import { Comment$ } from '../Core/Comment.js';
 import { LDPerson } from '../ROCrate/LDTypes/Person.js';
-import { indexed, toList, filter, tryPick, choose as choose$1, map, delay, append, empty as empty$1, singleton } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
-import { choose, length, empty, map as map$2, sortBy } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { indexed, toList, filter, tryPick, choose as choose$1, map, delay, append, empty as empty$1, singleton } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
+import { choose, length, empty, map as map$1, sortBy } from '../../node_modules/@fable-org/fable-library-ts/List.js';
 import { ResizeArray_singleton, Option_fromValueWithDefault, ResizeArray_map, ResizeArray_create, ResizeArray_zip } from '../Core/Helper/Collections.js';
 import { LDSample } from '../ROCrate/LDTypes/Sample.js';
 import { LDLabProcess } from '../ROCrate/LDTypes/LabProcess.js';
-import { List_groupBy } from '../../node_modules/@fable-org/fable-library-js/Seq2.js';
+import { List_groupBy } from '../../node_modules/@fable-org/fable-library-ts/Seq2.js';
 import { createMissingIdentifier } from '../Core/Helper/Identifier.js';
-import { stringHash, comparePrimitives } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { stringHash, comparePrimitives } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 
 class ProcessConversion {
   constructor() {
@@ -57,9 +57,9 @@ function ProcessConversion_decomposeProcessName_Z721C83C5(name) {
 function ProcessConversion_tryComponentGetter(generalI, valueI, valueHeader) {
   if (valueHeader.tag === /* Component */
   0) {
-    const oa = valueHeader.fields[0];
+    valueHeader.fields[0];
     return (table) => (i) => {
-      let matchValue;
+      let matchValue = void 0;
       const c = BaseTypes_composeComponent(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : value(matchValue)));
       ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(c, valueI);
       return c;
@@ -71,9 +71,9 @@ function ProcessConversion_tryComponentGetter(generalI, valueI, valueHeader) {
 function ProcessConversion_tryParameterGetter(generalI, valueI, valueHeader) {
   if (valueHeader.tag === /* Parameter */
   3) {
-    const oa = valueHeader.fields[0];
+    valueHeader.fields[0];
     return (table) => (i) => {
-      let matchValue;
+      let matchValue = void 0;
       const p = BaseTypes_composeParameterValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : value(matchValue)));
       ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(p, valueI);
       return p;
@@ -85,9 +85,9 @@ function ProcessConversion_tryParameterGetter(generalI, valueI, valueHeader) {
 function ProcessConversion_tryFactorGetter(generalI, valueI, valueHeader) {
   if (valueHeader.tag === /* Factor */
   2) {
-    const oa = valueHeader.fields[0];
+    valueHeader.fields[0];
     return (table) => (i) => {
-      let matchValue;
+      let matchValue = void 0;
       const f = BaseTypes_composeFactorValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : value(matchValue)));
       ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(f, valueI);
       return f;
@@ -99,9 +99,9 @@ function ProcessConversion_tryFactorGetter(generalI, valueI, valueHeader) {
 function ProcessConversion_tryCharacteristicGetter(generalI, valueI, valueHeader) {
   if (valueHeader.tag === /* Characteristic */
   1) {
-    const oa = valueHeader.fields[0];
+    valueHeader.fields[0];
     return (table) => (i) => {
-      let matchValue;
+      let matchValue = void 0;
       const c = BaseTypes_composeCharacteristicValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : value(matchValue)));
       ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(c, valueI);
       return c;
@@ -114,7 +114,7 @@ function ProcessConversion_tryGetProtocolTypeGetter(generalI, header) {
   if (header.tag === /* ProtocolType */
   4) {
     return (table) => (i) => {
-      let matchValue, cell;
+      let matchValue = void 0, cell = void 0;
       return BaseTypes_composeDefinedTerm_ZDED3A0F((matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? new OntologyAnnotation() : (cell = value(matchValue), cell.AsTerm)));
     };
   } else {
@@ -188,9 +188,9 @@ function ProcessConversion_tryGetProtocolVersionGetter(generalI, header) {
 function ProcessConversion_tryGetInputGetter(generalI, header, fs) {
   if (header.tag === /* Input */
   11) {
-    const io = header.fields[0];
+    header.fields[0];
     return (table) => (i) => {
-      let matchValue;
+      let matchValue = void 0;
       return BaseTypes_composeProcessInput(header, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(header, void 0) : value(matchValue)), fs);
     };
   } else {
@@ -200,9 +200,9 @@ function ProcessConversion_tryGetInputGetter(generalI, header, fs) {
 function ProcessConversion_tryGetOutputGetter(generalI, header, fs) {
   if (header.tag === /* Output */
   12) {
-    const io = header.fields[0];
+    header.fields[0];
     return (table) => (i) => {
-      let matchValue;
+      let matchValue = void 0;
       return BaseTypes_composeProcessOutput(header, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(header, void 0) : value(matchValue)), fs);
     };
   } else {
@@ -214,7 +214,7 @@ function ProcessConversion_tryGetCommentGetter(generalI, header) {
   14) {
     const c = header.fields[0];
     return (table) => (i) => {
-      let matchValue, cell;
+      let matchValue = void 0, cell = void 0;
       return toString((matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? new Comment$(c) : (cell = value(matchValue), new Comment$(c, cell.AsFreeText))));
     };
   } else {
@@ -310,27 +310,38 @@ function ProcessConversion_getProcessGetter(assayName, studyName, processNameRoo
     };
   }
   return (table_6) => (i_6) => {
+    let collection_4 = void 0, collection_5 = void 0, collection_6 = void 0, option_9 = void 0, option_11 = void 0, option_13 = void 0, option_15 = void 0;
     const pn = table_6.RowCount === 1 ? processNameRoot : ProcessConversion_composeProcessName(processNameRoot, i_6);
-    const paramvalues = map$1((collection_4) => Array.from(collection_4), Option_fromValueWithDefault(empty(), map$2((f_4) => f_4(table_6)(i_6), parameterValueGetters)));
-    const comments = map$1((collection_5) => Array.from(collection_5), Option_fromValueWithDefault(empty(), map$2((f_5) => f_5(table_6)(i_6), commentGetters)));
-    const components = map$1((collection_6) => Array.from(collection_6), Option_fromValueWithDefault(empty(), map$2((f_6) => f_6(table_6)(i_6), componentGetters)));
+    let paramvalues;
+    const option_1 = Option_fromValueWithDefault(empty(), map$1((f_4) => f_4(table_6)(i_6), parameterValueGetters));
+    paramvalues = option_1 != null ? (collection_4 = value(option_1), Array.from(collection_4)) : void 0;
+    let comments;
+    const option_3 = Option_fromValueWithDefault(empty(), map$1((f_5) => f_5(table_6)(i_6), commentGetters));
+    comments = option_3 != null ? (collection_5 = value(option_3), Array.from(collection_5)) : void 0;
+    let components;
+    const option_5 = Option_fromValueWithDefault(empty(), map$1((f_6) => f_6(table_6)(i_6), componentGetters));
+    components = option_5 != null ? (collection_6 = value(option_5), Array.from(collection_6)) : void 0;
     const id = LDLabProcess.genId(processNameRoot, unwrap(assayName), unwrap(studyName)) + `_${i_6}`;
     let protocol;
-    const name = map$1((f_7) => f_7(table_6)(i_6), protocolREFGetter);
+    let name;
+    const option_7 = protocolREFGetter;
+    name = option_7 != null ? value(option_7)(table_6)(i_6) : void 0;
     const protocolId = LDLabProtocol.genId(unwrap(name), processNameRoot);
-    protocol = LDLabProtocol.create(protocolId, unwrap(name), unwrap(map$1((f_8) => f_8(table_6)(i_6), protocolDescriptionGetter)), unwrap(map$1((f_9) => f_9(table_6)(i_6), protocolTypeGetter)), void 0, void 0, unwrap(components), void 0, unwrap(map$1((f_10) => f_10(table_6)(i_6), protocolURIGetter)), unwrap(map$1((f_11) => f_11(table_6)(i_6), protocolVersionGetter)));
+    protocol = LDLabProtocol.create(protocolId, unwrap(name), unwrap((option_9 = protocolDescriptionGetter, option_9 != null ? value(option_9)(table_6)(i_6) : void 0)), unwrap((option_11 = protocolTypeGetter, option_11 != null ? value(option_11)(table_6)(i_6) : void 0)), void 0, void 0, unwrap(components), void 0, unwrap((option_13 = protocolURIGetter, option_13 != null ? value(option_13)(table_6)(i_6) : void 0)), unwrap((option_15 = protocolVersionGetter, option_15 != null ? value(option_15)(table_6)(i_6) : void 0)));
     const matchValue_2 = inputGetter_1(table_6)(i_6);
     const matchValue_3 = outputGetter_1(table_6)(i_6);
-    const agent = map$1((f_12) => f_12(table_6)(i_6), performerGetter);
+    let agent;
+    const option_17 = performerGetter;
+    agent = option_17 != null ? value(option_17)(table_6)(i_6) : void 0;
     return LDLabProcess.create(pn, matchValue_2, matchValue_3, id, unwrap(agent), unwrap(protocol), unwrap(paramvalues), void 0, unwrap(comments));
   };
 }
 function ProcessConversion_groupProcesses_Z27F0B586(processes, graph, context) {
   return List_groupBy((p) => {
-    let protocol, protocol_1;
+    let protocol = void 0, protocol_1 = void 0;
     const matchValue = LDLabProcess.tryGetNameAsString(p, unwrap(context));
     const matchValue_1 = LDLabProcess.tryGetExecutesLabProtocol(p, unwrap(graph), unwrap(context));
-    let matchResult, name_1, protocol_2, name_2, protocol_3;
+    let matchResult = void 0, name_1 = void 0, protocol_2 = void 0, name_2 = void 0, protocol_3 = void 0;
     if (matchValue != null) {
       if (ProcessConversion_decomposeProcessName_Z721C83C5(value(matchValue))[1] != null) {
         matchResult = 0;
@@ -372,7 +383,7 @@ function ProcessConversion_groupProcesses_Z27F0B586(processes, graph, context) {
     }
   }, processes, {
     Equals: (x, y) => x === y,
-    GetHashCode: stringHash
+    GetHashCode: (x) => stringHash(x) | 0
   });
 }
 function ProcessConversion_processToRows_Z6839B9E8(p, graph, context) {
@@ -392,19 +403,19 @@ function ProcessConversion_processToRows_Z6839B9E8(p, graph, context) {
   } else {
     const prot_1 = value(matchValue_1);
     protVals = toList(delay(() => {
-      let matchValue_2;
-      return append((matchValue_2 = LDLabProtocol.tryGetNameAsString(prot_1, unwrap(context)), matchValue_2 == null ? empty$1() : singleton([CompositeHeader_ProtocolREF(), CompositeCell_FreeText(value(matchValue_2))])), delay(() => {
-        let matchValue_3;
-        return append((matchValue_3 = LDLabProtocol.tryGetDescriptionAsString(prot_1, unwrap(context)), matchValue_3 == null ? empty$1() : singleton([CompositeHeader_ProtocolDescription(), CompositeCell_FreeText(value(matchValue_3))])), delay(() => {
-          let matchValue_4;
-          return append((matchValue_4 = LDLabProtocol.tryGetUrl(prot_1, unwrap(context)), matchValue_4 == null ? empty$1() : singleton([CompositeHeader_ProtocolUri(), CompositeCell_FreeText(value(matchValue_4))])), delay(() => {
-            let matchValue_5;
-            return append((matchValue_5 = LDLabProtocol.tryGetVersionAsString(prot_1, unwrap(context)), matchValue_5 == null ? empty$1() : singleton([CompositeHeader_ProtocolVersion(), CompositeCell_FreeText(value(matchValue_5))])), delay(() => {
+      let matchValue_2 = void 0;
+      return append((matchValue_2 = LDLabProtocol.tryGetNameAsString(prot_1, unwrap(context)), matchValue_2 == null ? empty$1() : singleton([CompositeHeader.ProtocolREF, CompositeCell_FreeText(value(matchValue_2))])), delay(() => {
+        let matchValue_3 = void 0;
+        return append((matchValue_3 = LDLabProtocol.tryGetDescriptionAsString(prot_1, unwrap(context)), matchValue_3 == null ? empty$1() : singleton([CompositeHeader.ProtocolDescription, CompositeCell_FreeText(value(matchValue_3))])), delay(() => {
+          let matchValue_4 = void 0;
+          return append((matchValue_4 = LDLabProtocol.tryGetUrl(prot_1, unwrap(context)), matchValue_4 == null ? empty$1() : singleton([CompositeHeader.ProtocolUri, CompositeCell_FreeText(value(matchValue_4))])), delay(() => {
+            let matchValue_5 = void 0;
+            return append((matchValue_5 = LDLabProtocol.tryGetVersionAsString(prot_1, unwrap(context)), matchValue_5 == null ? empty$1() : singleton([CompositeHeader.ProtocolVersion, CompositeCell_FreeText(value(matchValue_5))])), delay(() => {
               const matchValue_6 = ProcessConversion_tryGetProtocolType_Z6839B9E8(prot_1, unwrap(graph), unwrap(context));
               if (matchValue_6 == null) {
                 return empty$1();
               } else {
-                return singleton([CompositeHeader_ProtocolType(), CompositeCell_Term(value(matchValue_6))]);
+                return singleton([CompositeHeader.ProtocolType, CompositeCell_Term(value(matchValue_6))]);
               }
             }));
           }));
@@ -414,7 +425,7 @@ function ProcessConversion_processToRows_Z6839B9E8(p, graph, context) {
   }
   const comments = ResizeArray_map((c) => {
     const c_1 = Comment$.fromString(c);
-    return [CompositeHeader_Comment(defaultArg(c_1.Name, "")), CompositeCell_FreeText(defaultArg(c_1.Value, ""))];
+    return [CompositeHeader_Comment$(defaultArg(c_1.Name, "")), CompositeCell_FreeText(defaultArg(c_1.Value, ""))];
   }, LDLabProcess.getDisambiguatingDescriptionsAsString(p, unwrap(context)));
   const inputs = LDLabProcess.getObjects(p, unwrap(graph), unwrap(context));
   const outputs = LDLabProcess.getResults(p, unwrap(graph), unwrap(context));
@@ -422,8 +433,8 @@ function ProcessConversion_processToRows_Z6839B9E8(p, graph, context) {
   const outputs_1 = patternInput[1];
   const inputs_1 = patternInput[0];
   if (inputs_1.length === 0 && outputs_1.length === 0) {
-    const vals = map$2((tuple_1) => tuple_1[0], sortBy((arg) => defaultArg(arg[1], 1e4), toList(delay(() => append(components, delay(() => pvs)))), {
-      Compare: comparePrimitives
+    const vals = map$1((tuple_1) => tuple_1[0], sortBy((arg) => defaultArg(arg[1], 1e4) | 0, toList(delay(() => append(components, delay(() => pvs)))), {
+      Compare: (x, y) => comparePrimitives(x, y) | 0
     }));
     return ResizeArray_singleton(toList(delay(() => append(protVals, delay(() => append(vals, delay(() => comments)))))));
   } else {
@@ -444,8 +455,8 @@ function ProcessConversion_processToRows_Z6839B9E8(p, graph, context) {
         const o_1 = value(o);
         factors = ResizeArray_map((fv) => [BaseTypes_decomposeFactorValue_Z2F770004(fv, unwrap(context)), tryGetIndex(fv)], LDSample.getFactors(o_1, unwrap(graph), unwrap(context)));
       }
-      const vals_1 = map$2((tuple_3) => tuple_3[0], sortBy((arg_1) => defaultArg(arg_1[1], 1e4), toList(delay(() => append(chars, delay(() => append(components, delay(() => append(pvs, delay(() => factors)))))))), {
-        Compare: comparePrimitives
+      const vals_1 = map$1((tuple_3) => tuple_3[0], sortBy((arg_1) => defaultArg(arg_1[1], 1e4) | 0, toList(delay(() => append(chars, delay(() => append(components, delay(() => append(pvs, delay(() => factors)))))))), {
+        Compare: (x_1, y_1) => comparePrimitives(x_1, y_1) | 0
       }));
       return toList(delay(() => append(i != null ? singleton(BaseTypes_decomposeProcessInput_Z2F770004(value(i), unwrap(context))) : empty$1(), delay(() => append(protVals, delay(() => append(vals_1, delay(() => append(comments, delay(() => o != null ? singleton(BaseTypes_decomposeProcessOutput_Z2F770004(value(o), unwrap(context))) : empty$1()))))))))));
     }, ResizeArray_zip(inputs_1, outputs_1));

package/dist/ts/ts/Conversion/Run.d.ts

@@ -1,24 +1,17 @@
-import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
-import { CWLType_$union } from '../CWL/CWLTypes.js';
-import { CWLInput } from '../CWL/Inputs.js';
-import { CWLParameterReference } from '../CWL/ParameterReference.js';
-import { LDGraph, LDNode } from '../ROCrate/LDObject.js';
-import { LDContext } from '../ROCrate/LDContext.js';
-import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.js';
-import { ArcRun } from '../Core/ArcTypes.js';
-import { FileSystem } from '../FileSystem/FileSystem.js';
+import { TypeInfo } from '@fable-org/fable-library-ts/Reflection.ts';
+import { CWLType_$union } from '../CWL/CWLTypes.ts';
+import { CWLParameterValue_$union } from '../CWL/ParameterValue.ts';
+import { LDContext } from '../ROCrate/LDContext.ts';
+import { CWLParameterReference } from '../CWL/ParameterReference.ts';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.ts';
+import { CWLInput } from '../CWL/Inputs.ts';
+import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.ts';
+import { ArcRun } from '../Core/ArcTypes.ts';
+import { FileSystem } from '../FileSystem/FileSystem.ts';
 export declare class RunConversion {
     constructor();
 }
 export declare function RunConversion_$reflection(): TypeInfo;
-/**
- * Helper function to format CWLType for display in error messages
- */
-export declare function RunConversion_formatCWLType_Z5C31A0F9(type_: CWLType_$union): string;
-/**
- * Helper function to check if a CWLType is or contains an Array type
- */
-export declare function RunConversion_isArrayType_Z5C31A0F9(type_: CWLType_$union): boolean;
 /**
  * File paths in CWL files are relative to the file itself. In RO-Crate, we use relative paths from the root of the crate.
  *
@@ -26,7 +19,9 @@ export declare function RunConversion_isArrayType_Z5C31A0F9(type_: CWLType_$unio
  */
 export declare function RunConversion_composeCWLInputFilePath_Z384F8060(path: string, runName: string): string;
 export declare function RunConversion_decomposeCWLInputFilePath_Z384F8060(path: string, runName: string): string;
+export declare function RunConversion_composeCWLParameterValue_6CF93391(value: CWLParameterValue_$union, runName: string, context?: LDContext): any;
 export declare function RunConversion_composeCWLInputValue_70DD9184(inputValue: CWLParameterReference, exampleOfWork: LDNode, inputParam: CWLInput, runName: string): LDNode;
+export declare function RunConversion_decomposeCWLParameterValue_Z3524B680(value: any, runName: string, expectedType?: CWLType_$union, graph?: LDGraph): CWLParameterValue_$union;
 export declare function RunConversion_decomposeCWLInputValue_Z1346FE9D(inputValue: LDNode, runName: string, context?: LDContext, graph?: LDGraph): CWLParameterReference;
 export declare function RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run: ArcRun, fs?: FileSystem): LDNode[];
 export declare function RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(workflowInvocation: LDNode, runName: string, context?: LDContext, graph?: LDGraph): [CWLProcessingUnit_$union, CWLParameterReference[]];

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

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+{"version":3,"file":"Run.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Run.ts"],"names":[],"mappings":"AACA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAIjF,OAAO,EAAkM,cAAc,EAA8G,MAAM,oBAAoB,CAAC;AAIhW,OAAO,EAA4U,wBAAwB,EAAE,MAAM,0BAA0B,CAAC;AAM9Y,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AACpD,OAAO,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAGrE,OAAO,EAAE,OAAO,EAAS,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAEhE,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAQ5C,OAAO,EAAE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AAOvE,OAAO,EAAoB,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAC/D,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAczD,qBAAa,aAAa;;CAGzB;AAED,wBAAgB,yBAAyB,IAAI,QAAQ,CAEpD;AAED;;;;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,+CAA+C,CAAC,KAAK,EAAE,wBAAwB,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,GAAG,CAiC1I;AAaD,wBAAgB,2CAA2C,CAAC,UAAU,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAwEnK;AAyBD,wBAAgB,kDAAkD,CAAC,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,cAAc,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,wBAAwB,CA4RxK;AAYD,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,CAoDjH;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,CA2CtF;AAED,wBAAgB,oCAAoC,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CA0C9G"}