@nfdi4plants/arctrl 1.0.0-alpha9 → 1.0.0-beta.2

package/ISA/ISA.Json/Protocol.js

@@ -1,17 +1,17 @@
-import { value as value_19 } from "../../fable_modules/fable-library.4.1.4/Option.js";
+import { value as value_19 } from "../../fable_modules/fable-library.4.4.1/Option.js";
 import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
 import { toString, nil, object as object_18 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { choose } from "../../fable_modules/fable-library.4.1.4/List.js";
-import { uncurry2, equals } from "../../fable_modules/fable-library.4.1.4/Util.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.1.4/Seq.js";
+import { choose } from "../../fable_modules/fable-library.4.4.1/List.js";
+import { uncurry2, equals } from "../../fable_modules/fable-library.4.4.1/Util.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.4.1/Seq.js";
 import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
 import { tryInclude } from "./GEncode.js";
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
 import { list as list_1, string, object as object_19 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
 import { fromJsonString, uri } from "./Decode.js";
 import { ProtocolParameter } from "../ISA/JsonTypes/ProtocolParameter.js";
-import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
-import { Result_Map } from "../../fable_modules/fable-library.4.1.4/Choice.js";
+import { replace } from "../../fable_modules/fable-library.4.4.1/String.js";
+import { Result_Map } from "../../fable_modules/fable-library.4.4.1/Choice.js";
 import { Component, Component_decomposeName_Z721C83C5 } from "../ISA/JsonTypes/Component.js";
 import { decoder as decoder_3, encoder } from "./Comment.js";
 import { Protocol } from "../ISA/JsonTypes/Protocol.js";

package/ISA/ISA.Json/Publication.js

@@ -1,8 +1,8 @@
-import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { replace } from "../../fable_modules/fable-library.4.4.1/String.js";
 import { toString, nil, object as object_12 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { choose } from "../../fable_modules/fable-library.4.1.4/List.js";
-import { uncurry2, equals } from "../../fable_modules/fable-library.4.1.4/Util.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.1.4/Seq.js";
+import { choose } from "../../fable_modules/fable-library.4.4.1/List.js";
+import { uncurry2, equals } from "../../fable_modules/fable-library.4.4.1/Util.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.4.1/Seq.js";
 import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
 import { tryInclude } from "./GEncode.js";
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";

package/ISA/ISA.Json/Study.js

@@ -1,14 +1,14 @@
 import { toString, nil, object as object_36 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { ofArray, choose } from "../../fable_modules/fable-library.4.1.4/List.js";
-import { uncurry2, equals } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { ofArray, choose } from "../../fable_modules/fable-library.4.4.1/List.js";
+import { uncurry2, equals } from "../../fable_modules/fable-library.4.4.1/Util.js";
 import { tryInclude } from "./GEncode.js";
 import { Sample_decoder, Source_decoder, Sample_encoder, Source_encoder } from "./Data.js";
 import { MaterialAttribute_decoder, MaterialAttribute_encoder, Material_decoder, Material_encoder } from "./Material.js";
 import { string, list as list_1, object as object_37 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
 import { StudyMaterials } from "../ISA/JsonTypes/StudyMaterials.js";
-import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { replace } from "../../fable_modules/fable-library.4.4.1/String.js";
 import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.1.4/Seq.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.4.1/Seq.js";
 import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
 import { decoder as decoder_10, encoder } from "./Publication.js";
 import { decoder as decoder_11, encoder as encoder_1 } from "./Person.js";
@@ -212,8 +212,8 @@ export function Study_toStringLD(s) {
 }
 
 export function ArcStudy_fromJsonString(s) {
-    const arg = fromJsonString(uncurry2(Study_decoder(ConverterOptions_$ctor())), s);
-    return ArcStudy.fromStudy(arg);
+    const s_1 = fromJsonString(uncurry2(Study_decoder(ConverterOptions_$ctor())), s);
+    return ArcStudy.fromStudy(s_1);
 }
 
 export function ArcStudy_toJsonString(a, assays) {

package/ISA/ISA.Json/Validation/Fable.js

@@ -1,10 +1,10 @@
-import { Record } from "../../../fable_modules/fable-library.4.1.4/Types.js";
-import { bool_type, option_type, array_type, record_type, string_type, obj_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
-import { map } from "../../../fable_modules/fable-library.4.1.4/Array.js";
-import { singleton } from "../../../fable_modules/fable-library.4.1.4/AsyncBuilder.js";
-import { awaitPromise } from "../../../fable_modules/fable-library.4.1.4/Async.js";
+import { Record } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+import { bool_type, option_type, array_type, record_type, string_type, obj_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
+import { map } from "../../../fable_modules/fable-library.4.4.1/Array.js";
+import { singleton } from "../../../fable_modules/fable-library.4.4.1/AsyncBuilder.js";
+import { awaitPromise } from "../../../fable_modules/fable-library.4.4.1/Async.js";
 import * as JsonValidation from "../../../../../src/ISA/ISA.Json/Validation/JsonValidation.js";
-import { value } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { value } from "../../../fable_modules/fable-library.4.4.1/Option.js";
 
 export class ValidationError extends Record {
     constructor(path, property, message, schema, instance, name, argument, stack) {

package/ISA/ISA.Json/Validation/JsonSchemaValidation.js

@@ -1,4 +1,4 @@
-import { singleton } from "../../../fable_modules/fable-library.4.1.4/AsyncBuilder.js";
+import { singleton } from "../../../fable_modules/fable-library.4.4.1/AsyncBuilder.js";
 import { validate } from "./Fable.js";
 import { ValidationResult, ValidationResult_OfJSchemaOutput_Z6EC48F6B } from "./ValidationResult.js";
 

package/ISA/ISA.Json/Validation/ValidationResult.js

@@ -1,5 +1,5 @@
-import { Union } from "../../../fable_modules/fable-library.4.1.4/Types.js";
-import { union_type, array_type, string_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { Union } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+import { union_type, array_type, string_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
 
 export class ValidationResult extends Union {
     constructor(tag, fields) {

package/ISA/ISA.Spreadsheet/AnnotationTable/ArcTable.js

@@ -1,15 +1,15 @@
-import { iterateIndexed, length, ofArray, sortBy, collect, toArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { iterateIndexed, length, ofArray, sortBy, collect, toArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { tryParseReferenceColumnHeader } from "../../ISA/Regex.js";
-import { map as map_1, toList, tryFind } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
+import { map as map_1, toList, tryFind } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
 import { toFsColumns, fixDeprecatedIOHeader, fromFsColumns } from "./CompositeColumn.js";
 import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
-import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.4.1.0/FsWorksheet.fs.js";
-import { comparePrimitives } from "../../../fable_modules/fable-library.4.1.4/Util.js";
-import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.4.1.0/Ranges/FsRangeAddress.fs.js";
-import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.4.1.0/FsAddress.fs.js";
-import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.4.1.0/Cells/FsCellsCollection.fs.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.4.1.0/Ranges/FsRangeBase.fs.js";
+import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.5.0.1/FsWorksheet.fs.js";
+import { comparePrimitives } from "../../../fable_modules/fable-library.4.4.1/Util.js";
+import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.0.1/Ranges/FsRangeAddress.fs.js";
+import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.0.1/FsAddress.fs.js";
+import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.5.0.1/Cells/FsCellsCollection.fs.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.5.0.1/Ranges/FsRangeBase.fs.js";
 
 /**
  * Iterates over elements of the input list and groups adjacent elements.
@@ -63,8 +63,9 @@ export function classifyColumnOrder(column) {
 
 export function groupColumnsByHeader(columns) {
     return Aux_List_groupWhen((c) => {
-        if (tryParseReferenceColumnHeader(c.Item(1).Value) == null) {
-            return !(c.Item(1).Value.indexOf("Unit") === 0);
+        const v = c.Item(1).ValueAsString();
+        if (tryParseReferenceColumnHeader(v) == null) {
+            return !(v.indexOf("Unit") === 0);
         }
         else {
             return false;
@@ -113,20 +114,21 @@ export function toFsWorksheet(table) {
     iterateIndexed((colI, col) => {
         iterateIndexed((rowI, cell) => {
             let value;
+            const v = cell.ValueAsString();
             if (rowI === 0) {
-                const matchValue = Dictionary_tryGet(cell.Value, stringCount);
+                const matchValue = Dictionary_tryGet(v, stringCount);
                 if (matchValue == null) {
-                    addToDict(stringCount, cell.Value, "");
-                    value = cell.Value;
+                    addToDict(stringCount, cell.ValueAsString(), "");
+                    value = v;
                 }
                 else {
                     const spaces = matchValue;
-                    stringCount.set(cell.Value, spaces + " ");
-                    value = ((cell.Value + " ") + spaces);
+                    stringCount.set(v, spaces + " ");
+                    value = ((v + " ") + spaces);
                 }
             }
             else {
-                value = cell.Value;
+                value = v;
             }
             const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
             FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeCell.js

@@ -1,10 +1,10 @@
-import { singleton, ofArray, head, tail, isEmpty, map } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { singleton, ofArray, head, tail, isEmpty, map } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { CompositeCell } from "../../ISA/ArcTypes/CompositeCell.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
-import { FsCell } from "../../../fable_modules/FsSpreadsheet.4.1.0/Cells/FsCell.fs.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.4.1/String.js";
+import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.0.1/Cells/FsCell.fs.js";
 
 export function fromFsCells(cells) {
-    const cellValues = map((c) => c.Value, cells);
+    const cellValues = map((c) => c.ValueAsString(), cells);
     let matchResult, v, v1, v2, v3, v1_1, v2_1, v3_1, v4;
     if (!isEmpty(cellValues)) {
         if (!isEmpty(tail(cellValues))) {

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeColumn.js

@@ -1,15 +1,15 @@
 import { CompositeHeader, IOType } from "../../ISA/ArcTypes/CompositeHeader.js";
-import { toString } from "../../../fable_modules/fable-library.4.1.4/Types.js";
+import { toString } from "../../../fable_modules/fable-library.4.4.1/Types.js";
 import { toFsCells, fromFsCells } from "./CompositeHeader.js";
-import { singleton as singleton_1, ofArray, item, map } from "../../../fable_modules/fable-library.4.1.4/List.js";
-import { FsAddress__get_RowNumber } from "../../../fable_modules/FsSpreadsheet.4.1.0/FsAddress.fs.js";
-import { FsRangeAddress__get_LastAddress } from "../../../fable_modules/FsSpreadsheet.4.1.0/Ranges/FsRangeAddress.fs.js";
-import { FsRangeBase__get_RangeAddress } from "../../../fable_modules/FsSpreadsheet.4.1.0/Ranges/FsRangeBase.fs.js";
-import { singleton, append, toList, exists, map as map_1, delay, toArray } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
+import { singleton as singleton_1, ofArray, item, map } from "../../../fable_modules/fable-library.4.4.1/List.js";
+import { FsAddress__get_RowNumber } from "../../../fable_modules/FsSpreadsheet.5.0.1/FsAddress.fs.js";
+import { FsRangeAddress__get_LastAddress } from "../../../fable_modules/FsSpreadsheet.5.0.1/Ranges/FsRangeAddress.fs.js";
+import { FsRangeBase__get_RangeAddress } from "../../../fable_modules/FsSpreadsheet.5.0.1/Ranges/FsRangeBase.fs.js";
+import { singleton, append, toList, exists, map as map_1, delay, toArray } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
 import { toFsCells as toFsCells_1, fromFsCells as fromFsCells_1 } from "./CompositeCell.js";
-import { rangeDouble } from "../../../fable_modules/fable-library.4.1.4/Range.js";
+import { rangeDouble } from "../../../fable_modules/fable-library.4.4.1/Range.js";
 import { CompositeColumn } from "../../ISA/ArcTypes/CompositeColumn.js";
-import { map as map_2 } from "../../../fable_modules/fable-library.4.1.4/Array.js";
+import { map as map_2 } from "../../../fable_modules/fable-library.4.4.1/Array.js";
 
 /**
  * Checks if the column header is a deprecated IO Header. If so, fixes it.
@@ -19,7 +19,7 @@ import { map as map_2 } from "../../../fable_modules/fable-library.4.1.4/Array.j
  * A "Source Name" column will now be mapped to the propper "Input [Source Name]", and all other IO types will be mapped to "Output [<IO Type>]".
  */
 export function fixDeprecatedIOHeader(col) {
-    const matchValue = IOType.ofString(col.Item(1).Value);
+    const matchValue = IOType.ofString(col.Item(1).ValueAsString());
     switch (matchValue.tag) {
         case 6:
             return col;

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeHeader.js

@@ -1,11 +1,11 @@
-import { printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
-import { singleton, tail, head, isEmpty, map } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.4.1/String.js";
+import { singleton, tail, head, isEmpty, map } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
 import { ActivePatterns_$007COutputColumnHeader$007C_$007C, ActivePatterns_$007CInputColumnHeader$007C_$007C, tryParseComponentColumnHeader, tryParseCharacteristicColumnHeader, tryParseFactorColumnHeader, tryParseParameterColumnHeader, ActivePatterns_$007CUnitColumnHeader$007C_$007C, ActivePatterns_$007CTANColumnHeader$007C_$007C, ActivePatterns_$007CTSRColumnHeader$007C_$007C } from "../../ISA/Regex.js";
 import { IOType, CompositeHeader } from "../../ISA/ArcTypes/CompositeHeader.js";
-import { FsCell } from "../../../fable_modules/FsSpreadsheet.4.1.0/Cells/FsCell.fs.js";
-import { toString } from "../../../fable_modules/fable-library.4.1.4/Types.js";
-import { empty, singleton as singleton_1, append, delay, toList } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
+import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.0.1/Cells/FsCell.fs.js";
+import { toString } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+import { empty, singleton as singleton_1, append, delay, toList } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
 
 export function ActivePattern_mergeIDInfo(idSpace1, localID1, idSpace2, localID2) {
     if (idSpace1 !== idSpace2) {
@@ -22,7 +22,7 @@ export function ActivePattern_mergeIDInfo(idSpace1, localID1, idSpace2, localID2
 
 export function ActivePattern_$007CTerm$007C_$007C(categoryParser, f, cells) {
     const $007CAC$007C_$007C = categoryParser;
-    const cellValues = map((c) => c.Value, cells);
+    const cellValues = map((c) => c.ValueAsString(), cells);
     let matchResult, name;
     if (!isEmpty(cellValues)) {
         const activePatternResult = $007CAC$007C_$007C(head(cellValues));
@@ -190,7 +190,7 @@ export function ActivePattern_$007CTerm$007C_$007C(categoryParser, f, cells) {
 }
 
 export function ActivePattern_$007CParameter$007C_$007C(cells) {
-    const activePatternResult = ActivePattern_$007CTerm$007C_$007C(tryParseParameterColumnHeader, (arg) => (new CompositeHeader(3, [arg])), cells);
+    const activePatternResult = ActivePattern_$007CTerm$007C_$007C(tryParseParameterColumnHeader, (Item) => (new CompositeHeader(3, [Item])), cells);
     if (activePatternResult != null) {
         const r = activePatternResult;
         return r;
@@ -201,7 +201,7 @@ export function ActivePattern_$007CParameter$007C_$007C(cells) {
 }
 
 export function ActivePattern_$007CFactor$007C_$007C(cells) {
-    const activePatternResult = ActivePattern_$007CTerm$007C_$007C(tryParseFactorColumnHeader, (arg) => (new CompositeHeader(2, [arg])), cells);
+    const activePatternResult = ActivePattern_$007CTerm$007C_$007C(tryParseFactorColumnHeader, (Item) => (new CompositeHeader(2, [Item])), cells);
     if (activePatternResult != null) {
         const r = activePatternResult;
         return r;
@@ -212,7 +212,7 @@ export function ActivePattern_$007CFactor$007C_$007C(cells) {
 }
 
 export function ActivePattern_$007CCharacteristic$007C_$007C(cells) {
-    const activePatternResult = ActivePattern_$007CTerm$007C_$007C(tryParseCharacteristicColumnHeader, (arg) => (new CompositeHeader(1, [arg])), cells);
+    const activePatternResult = ActivePattern_$007CTerm$007C_$007C(tryParseCharacteristicColumnHeader, (Item) => (new CompositeHeader(1, [Item])), cells);
     if (activePatternResult != null) {
         const r = activePatternResult;
         return r;
@@ -223,7 +223,7 @@ export function ActivePattern_$007CCharacteristic$007C_$007C(cells) {
 }
 
 export function ActivePattern_$007CComponent$007C_$007C(cells) {
-    const activePatternResult = ActivePattern_$007CTerm$007C_$007C(tryParseComponentColumnHeader, (arg) => (new CompositeHeader(0, [arg])), cells);
+    const activePatternResult = ActivePattern_$007CTerm$007C_$007C(tryParseComponentColumnHeader, (Item) => (new CompositeHeader(0, [Item])), cells);
     if (activePatternResult != null) {
         const r = activePatternResult;
         return r;
@@ -234,7 +234,7 @@ export function ActivePattern_$007CComponent$007C_$007C(cells) {
 }
 
 export function ActivePattern_$007CInput$007C_$007C(cells) {
-    const cellValues = map((c) => c.Value, cells);
+    const cellValues = map((c) => c.ValueAsString(), cells);
     let matchResult, ioType;
     if (!isEmpty(cellValues)) {
         const activePatternResult = ActivePatterns_$007CInputColumnHeader$007C_$007C(head(cellValues));
@@ -263,7 +263,7 @@ export function ActivePattern_$007CInput$007C_$007C(cells) {
 }
 
 export function ActivePattern_$007COutput$007C_$007C(cells) {
-    const cellValues = map((c) => c.Value, cells);
+    const cellValues = map((c) => c.ValueAsString(), cells);
     let matchResult, ioType;
     if (!isEmpty(cellValues)) {
         const activePatternResult = ActivePatterns_$007COutputColumnHeader$007C_$007C(head(cellValues));
@@ -292,7 +292,7 @@ export function ActivePattern_$007COutput$007C_$007C(cells) {
 }
 
 export function ActivePattern_$007CProtocolHeader$007C_$007C(cells) {
-    const cellValues = map((c) => c.Value, cells);
+    const cellValues = map((c) => c.ValueAsString(), cells);
     let matchResult;
     if (!isEmpty(cellValues)) {
         switch (head(cellValues)) {
@@ -382,7 +382,7 @@ export function ActivePattern_$007CProtocolHeader$007C_$007C(cells) {
 }
 
 export function ActivePattern_$007CFreeText$007C_$007C(cells) {
-    const cellValues = map((c) => c.Value, cells);
+    const cellValues = map((c) => c.ValueAsString(), cells);
     let matchResult, text;
     if (!isEmpty(cellValues)) {
         if (isEmpty(tail(cellValues))) {

package/ISA/ISA.Spreadsheet/ArcAssay.js

@@ -1,16 +1,16 @@
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.4.1.0/FsWorksheet.fs.js";
-import { iterate, isEmpty as isEmpty_1, choose, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../../fable_modules/fable-library.4.1.4/Seq.js";
+import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.0.1/FsWorksheet.fs.js";
+import { iterate, isEmpty as isEmpty_1, choose, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../../fable_modules/fable-library.4.4.1/Seq.js";
 import { SparseRowModule_tryGetValueAt, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_writeToSheet } from "./Metadata/SparseTable.js";
 import { fromRows as fromRows_1, toRows as toRows_1 } from "./Metadata/Assays.js";
-import { empty, isEmpty, toArray, ofArray, singleton as singleton_1 } from "../../fable_modules/fable-library.4.1.4/List.js";
+import { empty, isEmpty, toArray, ofArray, singleton as singleton_1 } from "../../fable_modules/fable-library.4.4.1/List.js";
 import { fromRows as fromRows_2, toRows as toRows_2 } from "./Metadata/Contacts.js";
-import { getEnumerator } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { getEnumerator } from "../../fable_modules/fable-library.4.4.1/Util.js";
 import { ArcAssay } from "../ISA/ArcTypes/ArcTypes.js";
 import { createMissingIdentifier } from "../ISA/Identifier.js";
-import { defaultArg } from "../../fable_modules/fable-library.4.1.4/Option.js";
-import { printf, toConsole } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { defaultArg } from "../../fable_modules/fable-library.4.4.1/Option.js";
+import { printf, toConsole } from "../../fable_modules/fable-library.4.4.1/String.js";
 import { toFsWorksheet, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
-import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.4.1.0/FsWorkbook.fs.js";
+import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.0.1/FsWorkbook.fs.js";
 
 export function toMetadataSheet(assay) {
     let assay_1;
@@ -90,9 +90,9 @@ export function fromMetadataSheet(sheet) {
                         case 0:
                             return ArcAssay.create(createMissingIdentifier());
                         default: {
-                            const arg = toArray(contacts_2);
-                            const arg_1 = defaultArg(tryHead(assays_2), ArcAssay.create(createMissingIdentifier()));
-                            return ArcAssay.setPerformers(arg, arg_1);
+                            const performers = toArray(contacts_2);
+                            const assay = defaultArg(tryHead(assays_2), ArcAssay.create(createMissingIdentifier()));
+                            return ArcAssay.setPerformers(performers, assay);
                         }
                     }
                 }
@@ -127,23 +127,20 @@ export function fromFsWorkbook(doc) {
     else {
         assayMetaData = fromMetadataSheet(matchValue);
     }
-    const sheets = choose(tryFromFsWorksheet, doc.GetWorksheets());
-    if (isEmpty_1(sheets)) {
-        return assayMetaData;
-    }
-    else {
-        assayMetaData.Tables = Array.from(sheets);
-        return assayMetaData;
+    const tables = choose(tryFromFsWorksheet, doc.GetWorksheets());
+    if (!isEmpty_1(tables)) {
+        assayMetaData.Tables = Array.from(tables);
     }
+    return assayMetaData;
 }
 
 export function toFsWorkbook(assay) {
     const doc = new FsWorkbook();
     const metaDataSheet = toMetadataSheet(assay);
     doc.AddWorksheet(metaDataSheet);
-    iterate((arg_1) => {
-        const arg = toFsWorksheet(arg_1);
-        doc.AddWorksheet(arg);
+    iterate((arg) => {
+        const sheet = toFsWorksheet(arg);
+        doc.AddWorksheet(sheet);
     }, assay.Tables);
     return doc;
 }

package/ISA/ISA.Spreadsheet/ArcInvestigation.js

@@ -1,24 +1,24 @@
-import { Record } from "../../fable_modules/fable-library.4.1.4/Types.js";
-import { record_type, list_type, string_type } from "../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { Record } from "../../fable_modules/fable-library.4.4.1/Types.js";
+import { record_type, list_type, string_type } from "../../fable_modules/fable-library.4.4.1/Reflection.js";
 import { Remark, Comment$_$reflection } from "../ISA/JsonTypes/Comment.js";
-import { head, tail, isEmpty, ofSeq, concat, unzip, append, toArray, reverse, cons, empty, map, ofArray } from "../../fable_modules/fable-library.4.1.4/List.js";
+import { ofSeq, head, tail, isEmpty, concat, unzip, append, toArray, reverse, cons, empty, map, ofArray } from "../../fable_modules/fable-library.4.4.1/List.js";
 import { Remark_wrapRemark, Comment_toString, Comment_fromString } from "./Metadata/Comment.js";
 import { SparseRowModule_writeToSheet, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt, SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "./Metadata/SparseTable.js";
-import { addToDict } from "../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { value as value_1, defaultArg } from "../../fable_modules/fable-library.4.1.4/Option.js";
-import { List_distinctBy, List_distinct } from "../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { comparePrimitives, getEnumerator, stringHash } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { addToDict } from "../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { value as value_1, defaultArg } from "../../fable_modules/fable-library.4.4.1/Option.js";
+import { List_distinctBy, List_distinct } from "../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { comparePrimitives, getEnumerator, stringHash } from "../../fable_modules/fable-library.4.4.1/Util.js";
 import { Option_fromValueWithDefault } from "./Metadata/Conversions.js";
 import { ArcInvestigation } from "../ISA/ArcTypes/ArcTypes.js";
 import { toRows as toRows_1, fromRows as fromRows_1 } from "./Metadata/OntologySourceReference.js";
 import { toRows as toRows_2, fromRows as fromRows_2 } from "./Metadata/Publication.js";
 import { toRows as toRows_3, fromRows as fromRows_3 } from "./Metadata/Contacts.js";
 import { toRows as toRows_4, fromRows as fromRows_4 } from "./Metadata/Study.js";
-import { iterateIndexed, map as map_1, toList, collect, singleton, append as append_1, delay } from "../../fable_modules/fable-library.4.1.4/Seq.js";
-import { tryFind, ofList } from "../../fable_modules/fable-library.4.1.4/Map.js";
-import { printf, toFail } from "../../fable_modules/fable-library.4.1.4/String.js";
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.4.1.0/FsWorksheet.fs.js";
-import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.4.1.0/FsWorkbook.fs.js";
+import { iterateIndexed, map as map_1, toList, collect, singleton, append as append_1, delay } from "../../fable_modules/fable-library.4.4.1/Seq.js";
+import { tryFind, ofList } from "../../fable_modules/fable-library.4.4.1/Map.js";
+import { printf, toFail } from "../../fable_modules/fable-library.4.4.1/String.js";
+import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.0.1/FsWorksheet.fs.js";
+import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.0.1/FsWorkbook.fs.js";
 
 export class InvestigationInfo extends Record {
     constructor(Identifier, Title, Description, SubmissionDate, PublicReleaseDate, Comments) {
@@ -83,19 +83,19 @@ export function InvestigationInfo_toRows_Z4D87C88C(investigation) {
 
 export function fromParts(investigationInfo, ontologySourceReference, publications, contacts, studies, assays, remarks) {
     const studyIdentifiers = map((s) => s.Identifier, studies);
-    const arg_1 = Option_fromValueWithDefault("", investigationInfo.Title);
-    const arg_2 = Option_fromValueWithDefault("", investigationInfo.Description);
-    const arg_3 = Option_fromValueWithDefault("", investigationInfo.SubmissionDate);
-    const arg_4 = Option_fromValueWithDefault("", investigationInfo.PublicReleaseDate);
-    const arg_5 = toArray(ontologySourceReference);
-    const arg_6 = toArray(publications);
-    const arg_7 = toArray(contacts);
-    const arg_8 = Array.from(assays);
-    const arg_9 = Array.from(studies);
-    const arg_10 = Array.from(studyIdentifiers);
-    const arg_11 = toArray(investigationInfo.Comments);
-    const arg_12 = toArray(remarks);
-    return ArcInvestigation.make(investigationInfo.Identifier, arg_1, arg_2, arg_3, arg_4, arg_5, arg_6, arg_7, arg_8, arg_9, arg_10, arg_11, arg_12);
+    const title = Option_fromValueWithDefault("", investigationInfo.Title);
+    const description = Option_fromValueWithDefault("", investigationInfo.Description);
+    const submissionDate = Option_fromValueWithDefault("", investigationInfo.SubmissionDate);
+    const publicReleaseDate = Option_fromValueWithDefault("", investigationInfo.PublicReleaseDate);
+    const ontologySourceReferences = toArray(ontologySourceReference);
+    const publications_1 = toArray(publications);
+    const contacts_1 = toArray(contacts);
+    const assays_1 = Array.from(assays);
+    const studies_1 = Array.from(studies);
+    const registeredStudyIdentifiers = Array.from(studyIdentifiers);
+    const comments = toArray(investigationInfo.Comments);
+    const remarks_1 = toArray(remarks);
+    return ArcInvestigation.make(investigationInfo.Identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications_1, contacts_1, assays_1, studies_1, registeredStudyIdentifiers, comments, remarks_1);
 }
 
 export function fromRows(rows) {
@@ -196,7 +196,7 @@ export function fromRows(rows) {
                     const patternInput_4 = fromRows_4(lineNumber + 1, en);
                     const study = patternInput_4[3];
                     const newRemarks_4 = patternInput_4[2];
-                    const lineNumber_5 = patternInput_4[1] | 0;
+                    const lineNumber_6 = patternInput_4[1] | 0;
                     const currentLine_4 = patternInput_4[0];
                     if (study != null) {
                         lastLine_mut = currentLine_4;
@@ -206,7 +206,7 @@ export function fromRows(rows) {
                         contacts_mut = contacts;
                         studies_mut = cons(value_1(study), studies);
                         remarks_mut = append(remarks, newRemarks_4);
-                        lineNumber_mut = lineNumber_5;
+                        lineNumber_mut = lineNumber_6;
                         continue loop;
                     }
                     else {
@@ -217,7 +217,7 @@ export function fromRows(rows) {
                         contacts_mut = contacts;
                         studies_mut = studies;
                         remarks_mut = append(remarks, newRemarks_4);
-                        lineNumber_mut = lineNumber_5;
+                        lineNumber_mut = lineNumber_6;
                         continue loop;
                     }
                 }
@@ -244,9 +244,9 @@ export function fromRows(rows) {
 
 export function toRows(investigation) {
     let remarks, rows;
-    return (remarks = ofArray(investigation.Remarks), (rows = delay(() => append_1(singleton(SparseRowModule_fromValues(["ONTOLOGY SOURCE REFERENCE"])), delay(() => append_1(toRows_1(ofArray(investigation.OntologySourceReferences)), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION"])), delay(() => append_1(InvestigationInfo_toRows_Z4D87C88C(investigation), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION PUBLICATIONS"])), delay(() => append_1(toRows_2("Investigation Publication", ofArray(investigation.Publications)), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION CONTACTS"])), delay(() => append_1(toRows_3("Investigation Person", ofArray(investigation.Contacts)), delay(() => collect((study) => append_1(singleton(SparseRowModule_fromValues(["STUDY"])), delay(() => toRows_4(study, void 0))), ofSeq(investigation.Studies))))))))))))))))))), (() => {
+    return (remarks = ofArray(investigation.Remarks), (rows = delay(() => append_1(singleton(SparseRowModule_fromValues(["ONTOLOGY SOURCE REFERENCE"])), delay(() => append_1(toRows_1(ofArray(investigation.OntologySourceReferences)), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION"])), delay(() => append_1(InvestigationInfo_toRows_Z4D87C88C(investigation), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION PUBLICATIONS"])), delay(() => append_1(toRows_2("Investigation Publication", ofArray(investigation.Publications)), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION CONTACTS"])), delay(() => append_1(toRows_3("Investigation Person", ofArray(investigation.Contacts)), delay(() => collect((study) => append_1(singleton(SparseRowModule_fromValues(["STUDY"])), delay(() => toRows_4(study, void 0))), investigation.RegisteredStudies)))))))))))))))))), (() => {
         try {
-            const rm = ofList(map((arg) => Remark.toTuple(arg), remarks), {
+            const rm = ofList(map((remark) => Remark.toTuple(remark), remarks), {
                 Compare: comparePrimitives,
             });
             const loop = (i_mut, l_mut, nl_mut) => {
@@ -266,10 +266,10 @@ export function toRows(investigation) {
                         }
                     }
                     else {
-                        const remark = matchValue;
+                        const remark_1 = matchValue;
                         i_mut = (i + 1);
                         l_mut = l;
-                        nl_mut = cons(SparseRowModule_fromValues([Remark_wrapRemark(remark)]), nl);
+                        nl_mut = cons(SparseRowModule_fromValues([Remark_wrapRemark(remark_1)]), nl);
                         continue loop;
                     }
                     break;
@@ -284,15 +284,15 @@ export function toRows(investigation) {
 }
 
 export function fromFsWorkbook(doc) {
-    let arg, matchValue, matchValue_1;
+    let sheet_2, matchValue, matchValue_1;
     try {
-        return fromRows(map_1(SparseRowModule_fromFsRow, (arg = ((matchValue = doc.TryGetWorksheetByName("isa_investigation"), (matchValue == null) ? ((matchValue_1 = doc.TryGetWorksheetByName("Investigation"), (matchValue_1 == null) ? (() => {
+        return fromRows(map_1(SparseRowModule_fromFsRow, (sheet_2 = ((matchValue = doc.TryGetWorksheetByName("isa_investigation"), (matchValue == null) ? ((matchValue_1 = doc.TryGetWorksheetByName("Investigation"), (matchValue_1 == null) ? (() => {
             throw new Error("Could not find metadata sheet with sheetname \"isa_investigation\" or deprecated sheetname \"Investigation\"");
-        })() : matchValue_1)) : matchValue)), FsWorksheet.getRows(arg))));
+        })() : matchValue_1)) : matchValue)), FsWorksheet.getRows(sheet_2))));
     }
     catch (err) {
-        const arg_1 = err.message;
-        return toFail(printf("Could not read investigation from spreadsheet: %s"))(arg_1);
+        const arg = err.message;
+        return toFail(printf("Could not read investigation from spreadsheet: %s"))(arg);
     }
 }
 

package/ISA/ISA.Spreadsheet/ArcStudy.js

@@ -1,16 +1,16 @@
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.4.1.0/FsWorksheet.fs.js";
-import { iterate, isEmpty, choose, map, append, iterateIndexed } from "../../fable_modules/fable-library.4.1.4/Seq.js";
+import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.0.1/FsWorksheet.fs.js";
+import { iterate, isEmpty, choose, map, append, iterateIndexed } from "../../fable_modules/fable-library.4.4.1/Seq.js";
 import { SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_writeToSheet } from "./Metadata/SparseTable.js";
 import { fromRows as fromRows_1, toRows } from "./Metadata/Study.js";
-import { defaultArg } from "../../fable_modules/fable-library.4.1.4/Option.js";
-import { getEnumerator } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { defaultArg } from "../../fable_modules/fable-library.4.4.1/Option.js";
+import { getEnumerator } from "../../fable_modules/fable-library.4.4.1/Util.js";
 import { ArcStudy } from "../ISA/ArcTypes/ArcTypes.js";
 import { createMissingIdentifier } from "../ISA/Identifier.js";
-import { empty } from "../../fable_modules/fable-library.4.1.4/List.js";
-import { printf, toConsole } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { empty } from "../../fable_modules/fable-library.4.4.1/List.js";
+import { printf, toConsole } from "../../fable_modules/fable-library.4.4.1/String.js";
 import { toFsWorksheet, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
-import { ArcTables__get_Tables, ArcTables_$ctor_Z18C2F36D, ArcTables_updateReferenceTablesBySheets_Z2EE88E97 } from "../ISA/ArcTypes/ArcTables.js";
-import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.4.1.0/FsWorkbook.fs.js";
+import { ArcTables } from "../ISA/ArcTypes/ArcTables.js";
+import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.0.1/FsWorkbook.fs.js";
 
 export function ArcStudy_toMetadataSheet(study, assays) {
     let source_1;
@@ -48,8 +48,8 @@ export function ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(doc
     const studyMetadata = patternInput[0];
     const sheets = choose(tryFromFsWorksheet, doc.GetWorksheets());
     if (!isEmpty(sheets)) {
-        const updatedTables = ArcTables_updateReferenceTablesBySheets_Z2EE88E97(ArcTables_$ctor_Z18C2F36D(studyMetadata.Tables), ArcTables_$ctor_Z18C2F36D(Array.from(sheets)), true);
-        studyMetadata.Tables = ArcTables__get_Tables(updatedTables);
+        const updatedTables = ArcTables.updateReferenceTablesBySheets(new ArcTables(studyMetadata.Tables), new ArcTables(Array.from(sheets)), true);
+        studyMetadata.Tables = updatedTables.Tables;
     }
     return [studyMetadata, patternInput[1]];
 }
@@ -58,9 +58,9 @@ export function ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9(stud
     const doc = new FsWorkbook();
     const metaDataSheet = ArcStudy_toMetadataSheet(study, assays);
     doc.AddWorksheet(metaDataSheet);
-    iterate((arg_1) => {
-        const arg = toFsWorksheet(arg_1);
-        doc.AddWorksheet(arg);
+    iterate((arg) => {
+        const sheet = toFsWorksheet(arg);
+        doc.AddWorksheet(sheet);
     }, study.Tables);
     return doc;
 }

package/ISA/ISA.Spreadsheet/CollectionAux.js

@@ -1,10 +1,10 @@
-import { tryFind, maxBy, skip } from "../../fable_modules/fable-library.4.1.4/Seq.js";
-import { tryItem, skip as skip_1, initialize } from "../../fable_modules/fable-library.4.1.4/Array.js";
-import { defaultOf, comparePrimitives } from "../../fable_modules/fable-library.4.1.4/Util.js";
-import { some, value } from "../../fable_modules/fable-library.4.1.4/Option.js";
-import { empty, tail, cons, head, reverse, isEmpty, tryPick } from "../../fable_modules/fable-library.4.1.4/List.js";
-import { tryGetValue } from "../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { FSharpRef } from "../../fable_modules/fable-library.4.1.4/Types.js";
+import { tryFind, maxBy, skip } from "../../fable_modules/fable-library.4.4.1/Seq.js";
+import { tryItem, skip as skip_1, initialize } from "../../fable_modules/fable-library.4.4.1/Array.js";
+import { defaultOf, comparePrimitives } from "../../fable_modules/fable-library.4.4.1/Util.js";
+import { some, value } from "../../fable_modules/fable-library.4.4.1/Option.js";
+import { empty, tail, cons, head, reverse, isEmpty, tryPick } from "../../fable_modules/fable-library.4.4.1/List.js";
+import { tryGetValue } from "../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { FSharpRef } from "../../fable_modules/fable-library.4.4.1/Types.js";
 
 /**
  * If at least i values exist in seq a, builds a new array that contains the elements of the given seq, exluding the first i elements