@nfdi4plants/arctrl 1.0.0-alpha8 → 1.0.0-beta.1

package/ISA/ISA/ArcTypes/CompositeColumn.js

@@ -1,4 +1,5 @@
 import { defaultArg } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { empty, singleton, collect, delay, toArray } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
 import { Record } from "../../../fable_modules/fable-library.4.1.4/Types.js";
 import { CompositeHeader_$reflection } from "./CompositeHeader.js";
 import { CompositeCell_$reflection } from "./CompositeCell.js";
@@ -13,7 +14,7 @@ export class CompositeColumn extends Record {
     static create(header, cells) {
         return new CompositeColumn(header, defaultArg(cells, []));
     }
-    validate(raiseException) {
+    Validate(raiseException) {
         const this$ = this;
         const raiseExeption = defaultArg(raiseException, false);
         const header = this$.Header;
@@ -34,6 +35,11 @@ export class CompositeColumn extends Record {
             return false;
         }
     }
+    TryGetColumnUnits() {
+        const this$ = this;
+        const arr = toArray(delay(() => collect((cell) => (cell.isUnitized ? singleton(cell.AsUnitized[1]) : empty()), this$.Cells)));
+        return (arr.length === 0) ? void 0 : arr;
+    }
 }
 
 export function CompositeColumn_$reflection() {

package/ISA/ISA/ArcTypes/CompositeHeader.js

@@ -2,6 +2,7 @@ import { map } from "../../../fable_modules/fable-library.4.1.4/Array.js";
 import { union_type, string_type, getUnionCases, name } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
 import { Union, toString } from "../../../fable_modules/fable-library.4.1.4/Types.js";
 import { ActivePatterns_$007CTermColumn$007C_$007C, Pattern_OutputPattern, Pattern_InputPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseIOTypeHeader } from "../Regex.js";
+import { equals } from "../../../fable_modules/fable-library.4.1.4/Util.js";
 import { printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
 import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { ProtocolParameter_create_Z6C54B221 } from "../JsonTypes/ProtocolParameter.js";
@@ -40,6 +41,82 @@ export class IOType extends Union {
         };
         return (this$.tag === 6) ? stringCreate(this$.fields[0]) : stringCreate(this$);
     }
+    Merge(other) {
+        const this$ = this;
+        switch (this$.tag) {
+            case 4:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(4, []);
+                    case 2:
+                        return new IOType(4, []);
+                    case 3:
+                        return new IOType(4, []);
+                    case 4:
+                        return new IOType(4, []);
+                    default:
+                        throw new Error(`ImageFile IO column and ${other} can not be merged`);
+                }
+            case 3:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(3, []);
+                    case 2:
+                        return new IOType(3, []);
+                    case 3:
+                        return new IOType(3, []);
+                    case 4:
+                        return new IOType(4, []);
+                    default:
+                        throw new Error(`DerivedDataFile IO column and ${other} can not be merged`);
+                }
+            case 2:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(2, []);
+                    case 2:
+                        return new IOType(2, []);
+                    case 3:
+                        return new IOType(3, []);
+                    case 4:
+                        return new IOType(4, []);
+                    default:
+                        throw new Error(`RawDataFile IO column and ${other} can not be merged`);
+                }
+            case 1:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(1, []);
+                    case 1:
+                        return new IOType(1, []);
+                    default:
+                        throw new Error(`Sample IO column and ${other} can not be merged`);
+                }
+            case 0:
+                return (other.tag === 0) ? (new IOType(0, [])) : other;
+            case 5:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(5, []);
+                    case 5:
+                        return new IOType(5, []);
+                    default:
+                        throw new Error(`Material IO column and ${other} can not be merged`);
+                }
+            default:
+                if (other.tag === 6) {
+                    if (this$.fields[0] === other.fields[0]) {
+                        return new IOType(6, [this$.fields[0]]);
+                    }
+                    else {
+                        throw new Error(`FreeText IO column names ${this$.fields[0]} and ${other.fields[0]} do differ`);
+                    }
+                }
+                else {
+                    throw new Error(`FreeText IO column and ${other} can not be merged`);
+                }
+        }
+    }
     toString() {
         const this$ = this;
         return (this$.tag === 1) ? "Sample Name" : ((this$.tag === 2) ? "Raw Data File" : ((this$.tag === 3) ? "Derived Data File" : ((this$.tag === 4) ? "Image File" : ((this$.tag === 5) ? "Material" : ((this$.tag === 6) ? this$.fields[0] : "Source Name")))));
@@ -57,6 +134,87 @@ export class IOType extends Union {
             return IOType.ofString(s);
         }
     }
+    GetUITooltip() {
+        const this$ = this;
+        return IOType.getUITooltip(this$);
+    }
+    static getUITooltip(iotype) {
+        let matchResult;
+        if (typeof iotype === "string") {
+            if (equals(iotype, "Source")) {
+                matchResult = 0;
+            }
+            else if (equals(iotype, "Sample")) {
+                matchResult = 1;
+            }
+            else if (equals(iotype, "RawDataFile")) {
+                matchResult = 2;
+            }
+            else if (equals(iotype, "DerivedDataFile")) {
+                matchResult = 3;
+            }
+            else if (equals(iotype, "ImageFile")) {
+                matchResult = 4;
+            }
+            else if (equals(iotype, "Material")) {
+                matchResult = 5;
+            }
+            else if (equals(iotype, "FreeText")) {
+                matchResult = 6;
+            }
+            else {
+                matchResult = 7;
+            }
+        }
+        else {
+            switch (iotype.tag) {
+                case 1: {
+                    matchResult = 1;
+                    break;
+                }
+                case 2: {
+                    matchResult = 2;
+                    break;
+                }
+                case 3: {
+                    matchResult = 3;
+                    break;
+                }
+                case 4: {
+                    matchResult = 4;
+                    break;
+                }
+                case 5: {
+                    matchResult = 5;
+                    break;
+                }
+                case 6: {
+                    matchResult = 6;
+                    break;
+                }
+                default:
+                    matchResult = 0;
+            }
+        }
+        switch (matchResult) {
+            case 0:
+                return "The source value must be a unique identifier for an organism or a sample.";
+            case 1:
+                return "The Sample Name column describes specifc laboratory samples with a unique identifier.";
+            case 2:
+                return "The Raw Data File column defines untransformed and unprocessed data files.";
+            case 3:
+                return "The Derived Data File column defines transformed and/or processed data files.";
+            case 4:
+                return "Placeholder";
+            case 5:
+                return "Placeholder";
+            case 6:
+                return "Placeholder";
+            default:
+                throw new Error(`Unable to parse combination to existing IOType: \`${iotype}\``);
+        }
+    }
 }
 
 export function IOType_$reflection() {
@@ -271,7 +429,7 @@ export class CompositeHeader extends Union {
     }
     get isOutput() {
         const this$ = this;
-        return this$.tag === 11;
+        return this$.tag === 12;
     }
     get isParameter() {
         const this$ = this;
@@ -334,6 +492,14 @@ export class CompositeHeader extends Union {
         const this$ = this;
         return this$.tag === 13;
     }
+    tryInput() {
+        const this$ = this;
+        return (this$.tag === 11) ? this$.fields[0] : void 0;
+    }
+    tryOutput() {
+        const this$ = this;
+        return (this$.tag === 12) ? this$.fields[0] : void 0;
+    }
     TryParameter() {
         const this$ = this;
         return (this$.tag === 3) ? ProtocolParameter_create_Z6C54B221(void 0, this$.fields[0]) : void 0;
@@ -350,6 +516,150 @@ export class CompositeHeader extends Union {
         const this$ = this;
         return (this$.tag === 0) ? Component_create_61502994(void 0, void 0, void 0, this$.fields[0]) : void 0;
     }
+    GetUITooltip() {
+        const this$ = this;
+        return CompositeHeader.getUITooltip(this$);
+    }
+    static getUITooltip(header) {
+        let matchResult;
+        if (typeof header === "string") {
+            if (equals(header, "Component")) {
+                matchResult = 0;
+            }
+            else if (equals(header, "Characteristic")) {
+                matchResult = 1;
+            }
+            else if (equals(header, "Factor")) {
+                matchResult = 2;
+            }
+            else if (equals(header, "Parameter")) {
+                matchResult = 3;
+            }
+            else if (equals(header, "ProtocolType")) {
+                matchResult = 4;
+            }
+            else if (equals(header, "ProtocolDescription")) {
+                matchResult = 5;
+            }
+            else if (equals(header, "ProtocolUri")) {
+                matchResult = 6;
+            }
+            else if (equals(header, "ProtocolVersion")) {
+                matchResult = 7;
+            }
+            else if (equals(header, "ProtocolREF")) {
+                matchResult = 8;
+            }
+            else if (equals(header, "Performer")) {
+                matchResult = 9;
+            }
+            else if (equals(header, "Date")) {
+                matchResult = 10;
+            }
+            else if (equals(header, "Input")) {
+                matchResult = 11;
+            }
+            else if (equals(header, "Output")) {
+                matchResult = 12;
+            }
+            else if (equals(header, "FreeText")) {
+                matchResult = 13;
+            }
+            else {
+                matchResult = 14;
+            }
+        }
+        else {
+            switch (header.tag) {
+                case 1: {
+                    matchResult = 1;
+                    break;
+                }
+                case 2: {
+                    matchResult = 2;
+                    break;
+                }
+                case 3: {
+                    matchResult = 3;
+                    break;
+                }
+                case 4: {
+                    matchResult = 4;
+                    break;
+                }
+                case 5: {
+                    matchResult = 5;
+                    break;
+                }
+                case 6: {
+                    matchResult = 6;
+                    break;
+                }
+                case 7: {
+                    matchResult = 7;
+                    break;
+                }
+                case 8: {
+                    matchResult = 8;
+                    break;
+                }
+                case 9: {
+                    matchResult = 9;
+                    break;
+                }
+                case 10: {
+                    matchResult = 10;
+                    break;
+                }
+                case 11: {
+                    matchResult = 11;
+                    break;
+                }
+                case 12: {
+                    matchResult = 12;
+                    break;
+                }
+                case 13: {
+                    matchResult = 13;
+                    break;
+                }
+                default:
+                    matchResult = 0;
+            }
+        }
+        switch (matchResult) {
+            case 0:
+                return "Component columns are used to describe physical components of a experiment, e.g. instrument names, software names, and reagents names.";
+            case 1:
+                return "Characteristic columns are used for study descriptions and describe inherent properties of the source material, e.g. a certain strain or organism part.";
+            case 2:
+                return "Use Factor columns to describe independent variables that result in a specific output of your experiment, e.g. the light intensity under which an organism was grown.";
+            case 3:
+                return "Parameter columns describe steps in your experimental workflow, e.g. the centrifugation time or the temperature used for your assay.";
+            case 4:
+                return "Defines the protocol type according to your preferred endpoint repository.";
+            case 5:
+                return "Describe the protocol in free text.";
+            case 6:
+                return "Web or local address where the in-depth protocol is stored.";
+            case 7:
+                return "Defines the protocol version.";
+            case 8:
+                return "Defines the protocol name.";
+            case 9:
+                return "Defines the protocol performer.";
+            case 10:
+                return "Defines the date the protocol was performed.";
+            case 11:
+                return "Only one input column per table. E.g. experimental samples or files.";
+            case 12:
+                return "Only one output column per table. E.g. experimental samples or files.";
+            case 13:
+                return "Placeholder";
+            default:
+                throw new Error(`Unable to parse combination to existing CompositeHeader: \`${header}\``);
+        }
+    }
 }
 
 export function CompositeHeader_$reflection() {

package/ISA/ISA/Helper.js

@@ -1,5 +1,6 @@
-import { isIterable, defaultOf, structuralHash, equals } from "../../fable_modules/fable-library.4.1.4/Util.js";
-import { value as value_1, some } from "../../fable_modules/fable-library.4.1.4/Option.js";
+import { some, value as value_1 } from "../../fable_modules/fable-library.4.1.4/Option.js";
+import { isIterable, defaultOf, structuralHash, equals, numberHash, identityHash } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { exactlyOne, partition, fold } from "../../fable_modules/fable-library.4.1.4/Array.js";
 import { empty, singleton, append, head, tail, isEmpty } from "../../fable_modules/fable-library.4.1.4/List.js";
 import { Dictionary } from "../../fable_modules/fable-library.4.1.4/MutableMap.js";
 import { isEmpty as isEmpty_1, iterate } from "../../fable_modules/fable-library.4.1.4/Seq.js";
@@ -7,7 +8,18 @@ import { tryGetValue, addToDict } from "../../fable_modules/fable-library.4.1.4/
 import { Union, toString, FSharpRef } from "../../fable_modules/fable-library.4.1.4/Types.js";
 import { append_generic, distinct_generic, isList_generic, isMap_generic } from "./Fable.js";
 import { union_type, makeUnion, option_type, makeGenericType, getUnionCases, name, obj_type } from "../../fable_modules/fable-library.4.1.4/Reflection.js";
-import { exactlyOne, partition } from "../../fable_modules/fable-library.4.1.4/Array.js";
+
+export function HashCodes_boxHashOption(a) {
+    let copyOfStruct, copyOfStruct_1;
+    return (a != null) ? ((copyOfStruct = value_1(a), identityHash(copyOfStruct))) : ((copyOfStruct_1 = 0, numberHash(copyOfStruct_1)));
+}
+
+export function HashCodes_boxHashArray(a) {
+    return fold((acc, o) => {
+        let copyOfStruct;
+        return ((-1640531527 + ((copyOfStruct = o, identityHash(copyOfStruct)))) + (acc << 6)) + (acc >> 2);
+    }, 0, a);
+}
 
 /**
  * If the value matches the default, a None is returned, else a Some is returned

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

@@ -1,15 +1,15 @@
-import { iterateIndexed, length, 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.4.1.4/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 { 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 { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.5.0.0/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 { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.0.0/Ranges/FsRangeAddress.fs.js";
+import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.0.0/FsAddress.fs.js";
+import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.5.0.0/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 { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.5.0.0/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;
@@ -104,7 +105,7 @@ export function tryFromFsWorksheet(sheet) {
 export function toFsWorksheet(table) {
     const stringCount = new Map([]);
     const ws = new FsWorksheet(table.Name);
-    const columns = collect(toFsColumns, sortBy(classifyColumnOrder, table.Columns, {
+    const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
         Compare: comparePrimitives,
     }));
     const maxRow = length(head(columns)) | 0;
@@ -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 { 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 { FsCell } from "../../../fable_modules/FsSpreadsheet.5.0.0/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

@@ -2,9 +2,9 @@ import { CompositeHeader, IOType } from "../../ISA/ArcTypes/CompositeHeader.js";
 import { toString } from "../../../fable_modules/fable-library.4.1.4/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 { FsAddress__get_RowNumber } from "../../../fable_modules/FsSpreadsheet.5.0.0/FsAddress.fs.js";
+import { FsRangeAddress__get_LastAddress } from "../../../fable_modules/FsSpreadsheet.5.0.0/Ranges/FsRangeAddress.fs.js";
+import { FsRangeBase__get_RangeAddress } from "../../../fable_modules/FsSpreadsheet.5.0.0/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 { toFsCells as toFsCells_1, fromFsCells as fromFsCells_1 } from "./CompositeCell.js";
 import { rangeDouble } from "../../../fable_modules/fable-library.4.1.4/Range.js";
@@ -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

@@ -3,7 +3,7 @@ import { singleton, tail, head, isEmpty, map } from "../../../fable_modules/fabl
 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 { FsCell } from "../../../fable_modules/FsSpreadsheet.5.0.0/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";
 
@@ -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));
@@ -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

@@ -1,4 +1,4 @@
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.4.1.0/FsWorksheet.fs.js";
+import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.0.0/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 { 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";
@@ -10,7 +10,7 @@ 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 { toFsWorksheet, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
-import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.4.1.0/FsWorkbook.fs.js";
+import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.0.0/FsWorkbook.fs.js";
 
 export function toMetadataSheet(assay) {
     let assay_1;
@@ -127,14 +127,11 @@ 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) {

package/ISA/ISA.Spreadsheet/ArcInvestigation.js

@@ -1,7 +1,7 @@
 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 { 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.4.1.4/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";
@@ -17,8 +17,8 @@ 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 { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.0.0/FsWorksheet.fs.js";
+import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.0.0/FsWorkbook.fs.js";
 
 export class InvestigationInfo extends Record {
     constructor(Identifier, Title, Description, SubmissionDate, PublicReleaseDate, Comments) {
@@ -244,7 +244,7 @@ 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), {
                 Compare: comparePrimitives,