@nfdi4plants/arctrl 1.0.1 → 1.0.2

package/ISA/ISA/ArcTypes/ArcTable.js

@@ -1,5 +1,5 @@
 import { Dictionary } from "../../../fable_modules/fable-library.4.5.0/MutableMap.js";
-import { compareArrays, safeHash, disposeSafe, getEnumerator, equals, comparePrimitives, arrayHash, equalArrays } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { compareArrays, safeHash, disposeSafe, getEnumerator, comparePrimitives, equals, arrayHash, equalArrays } from "../../../fable_modules/fable-library.4.5.0/Util.js";
 import { value as value_9, map as map_2, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.5.0/Option.js";
 import { Unchecked_extendToRowCount, ProcessParsing_processToRows, ProcessParsing_alignByHeaders, ProcessParsing_mergeIdenticalProcesses, ProcessParsing_getProcessGetter, Unchecked_removeRowCells_withIndexChange, Unchecked_addRow, Unchecked_getEmptyCellForHeader, Unchecked_removeColumnCells_withIndexChange, tryFindDuplicateUniqueInArray, Unchecked_removeColumnCells, Unchecked_removeHeader, Unchecked_fillMissingCells, Unchecked_addColumn, tryFindDuplicateUnique, Unchecked_setCellAt, SanityChecks_validateColumn, SanityChecks_validateRowIndex, SanityChecks_validateColumnIndex, Unchecked_tryGetCellAt, getRowCount, getColumnCount } from "./ArcTableAux.js";
 import { item, append as append_1, indexed as indexed_1, choose, toList, zip, fold, filter, length, tryFindIndex, empty, singleton, collect, removeAt, map, delay, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
@@ -189,7 +189,7 @@ export class ArcTable {
             return newTable;
         };
     }
-    AddColumn(header, cells, index, forceReplace) {
+    AddColumn(header, cells, index, forceReplace, SkipFillMissing) {
         const this$ = this;
         const index_1 = defaultArg(index, this$.ColumnCount) | 0;
         const cells_1 = defaultArg(cells, []);
@@ -197,16 +197,18 @@ export class ArcTable {
         SanityChecks_validateColumnIndex(index_1, this$.ColumnCount, true);
         SanityChecks_validateColumn(CompositeColumn.create(header, cells_1));
         Unchecked_addColumn(header, cells_1, index_1, forceReplace_1, false, this$.Headers, this$.Values);
-        Unchecked_fillMissingCells(this$.Headers, this$.Values);
+        if (!equals(SkipFillMissing, true)) {
+            Unchecked_fillMissingCells(this$.Headers, this$.Values);
+        }
     }
     static addColumn(header, cells, index, forceReplace) {
         return (table) => {
             const newTable = table.Copy();
-            newTable.AddColumn(header, unwrap(cells), unwrap(index), unwrap(forceReplace));
+            newTable.AddColumn(header, cells, index, forceReplace);
             return newTable;
         };
     }
-    UpdateColumn(columnIndex, header, cells) {
+    UpdateColumn(columnIndex, header, cells, SkipFillMissing) {
         const this$ = this;
         SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);
         const column = CompositeColumn.create(header, unwrap(cells));
@@ -222,18 +224,20 @@ export class ArcTable {
         iterateIndexed((rowIndex, v) => {
             Unchecked_setCellAt(columnIndex, rowIndex, v, this$.Values);
         }, column.Cells);
-        Unchecked_fillMissingCells(this$.Headers, this$.Values);
+        if (!equals(SkipFillMissing, true)) {
+            Unchecked_fillMissingCells(this$.Headers, this$.Values);
+        }
     }
     static updateColumn(columnIndex, header, cells) {
         return (table) => {
             const newTable = table.Copy();
-            newTable.UpdateColumn(columnIndex, header, unwrap(cells));
+            newTable.UpdateColumn(columnIndex, header, cells);
             return newTable;
         };
     }
     InsertColumn(index, header, cells) {
         const this$ = this;
-        this$.AddColumn(header, unwrap(cells), index, false);
+        this$.AddColumn(header, cells, index, false);
     }
     static insertColumn(index, header, cells) {
         return (table) => {
@@ -244,7 +248,7 @@ export class ArcTable {
     }
     AppendColumn(header, cells) {
         const this$ = this;
-        this$.AddColumn(header, unwrap(cells), this$.ColumnCount, false);
+        this$.AddColumn(header, cells, this$.ColumnCount, false);
     }
     static appendColumn(header, cells) {
         return (table) => {
@@ -253,7 +257,7 @@ export class ArcTable {
             return newTable;
         };
     }
-    AddColumns(columns, index, forceReplace) {
+    AddColumns(columns, index, forceReplace, SkipFillMissing) {
         const this$ = this;
         let index_1 = defaultArg(index, this$.ColumnCount);
         const forceReplace_1 = defaultArg(forceReplace, false);
@@ -277,12 +281,14 @@ export class ArcTable {
                 index_1 = ((index_1 + 1) | 0);
             }
         });
-        Unchecked_fillMissingCells(this$.Headers, this$.Values);
+        if (!equals(SkipFillMissing, true)) {
+            Unchecked_fillMissingCells(this$.Headers, this$.Values);
+        }
     }
-    static addColumns(columns, index) {
+    static addColumns(columns, index, SkipFillMissing) {
         return (table) => {
             const newTable = table.Copy();
-            newTable.AddColumns(columns, index);
+            newTable.AddColumns(columns, unwrap(index), void 0, unwrap(SkipFillMissing));
             return newTable;
         };
     }
@@ -552,15 +558,17 @@ export class ArcTable {
             return newTable;
         };
     }
-    GetRow(rowIndex) {
+    GetRow(rowIndex, SkipValidation) {
         const this$ = this;
-        SanityChecks_validateRowIndex(rowIndex, this$.RowCount, false);
+        if (!equals(SkipValidation, true)) {
+            SanityChecks_validateRowIndex(rowIndex, this$.RowCount, false);
+        }
         return toArray(delay(() => map((columnIndex) => value_9(this$.TryGetCellAt(columnIndex, rowIndex)), rangeDouble(0, 1, this$.ColumnCount - 1))));
     }
     static getRow(index) {
         return (table) => table.GetRow(index);
     }
-    Join(table, joinOptions, forceReplace) {
+    Join(table, joinOptions, forceReplace, SkipFillMissing) {
         const this$ = this;
         const joinOptions_1 = defaultArg(joinOptions, "headers");
         const forceReplace_1 = defaultArg(forceReplace, false);
@@ -596,12 +604,14 @@ export class ArcTable {
                 index = ((index + 1) | 0);
             }
         });
-        Unchecked_fillMissingCells(this$.Headers, this$.Values);
+        if (!equals(SkipFillMissing, true)) {
+            Unchecked_fillMissingCells(this$.Headers, this$.Values);
+        }
     }
     static join(table, joinOptions, forceReplace) {
         return (this$) => {
             const copy = this$.Copy();
-            copy.Join(table, unwrap(joinOptions), unwrap(forceReplace));
+            copy.Join(table, joinOptions, forceReplace);
             return copy;
         };
     }
@@ -728,7 +738,7 @@ export class ArcTable {
             }
         }, Protocol_create_Z7DFD6E67(void 0, this$.Name), source))) : List_distinct(initialize_1(this$.RowCount, (i) => {
             let row;
-            const source_2 = this$.GetRow(i);
+            const source_2 = this$.GetRow(i, true);
             row = zip(this$.Headers, source_2);
             return toProtocol(this$.Name, row);
         }), {

package/ISA/ISA/ArcTypes/ArcTableAux.js

@@ -345,8 +345,13 @@ export function Unchecked_addColumn(newHeader, newCells, index, forceReplace, on
         if (hasDuplicateUnique != null) {
             Unchecked_removeColumnCells(index_1, values);
         }
-        iterateIndexed((rowIndex_1, cell) => {
-            Unchecked_setCellAt(index_1, rowIndex_1, cell, values);
+        const f = (index_1 >= startColCount) ? ((tupledArg) => ((values_1) => {
+            const value = addToDict(values_1, [tupledArg[0], tupledArg[1]], tupledArg[2]);
+        })) : ((tupledArg_1) => ((cells) => {
+            Unchecked_setCellAt(tupledArg_1[0], tupledArg_1[1], tupledArg_1[2], cells);
+        }));
+        iterateIndexed((rowIndex_3, cell_1) => {
+            f([index_1, rowIndex_3, cell_1])(values);
         }, newCells);
     }
 }

package/ISA/ISA/ArcTypes/ArcTables.js

@@ -326,7 +326,7 @@ export class ArcTables {
     AddColumnAt(tableIndex, header, cells, columnIndex, forceReplace) {
         const this$ = this;
         this$.MapTableAt(tableIndex, (table) => {
-            table.AddColumn(header, unwrap(cells), unwrap(columnIndex), unwrap(forceReplace));
+            table.AddColumn(header, cells, columnIndex, forceReplace);
         });
     }
     AddColumn(tableName, header, cells, columnIndex, forceReplace) {
@@ -348,7 +348,7 @@ export class ArcTables {
     UpdateColumnAt(tableIndex, columnIndex, header, cells) {
         const this$ = this;
         this$.MapTableAt(tableIndex, (table) => {
-            table.UpdateColumn(columnIndex, header, unwrap(cells));
+            table.UpdateColumn(columnIndex, header, cells);
         });
     }
     UpdateColumn(tableName, columnIndex, header, cells) {

package/ISA/ISA/ArcTypes/ArcTypes.js

@@ -7,7 +7,6 @@ import { printf, toText } from "../../../fable_modules/fable-library.4.5.0/Strin
 import { ActivePatterns_$007CRegex$007C_$007C } from "../Regex.js";
 import { OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { Value } from "../JsonTypes/Value.js";
-import { AnnotationValue } from "../JsonTypes/AnnotationValue.js";
 import { ArcTablesAux_applyIOMap, ArcTablesAux_getIOMap, ArcTables_$reflection, ArcTables } from "./ArcTables.js";
 import { AssayMaterials_get_empty, AssayMaterials_create_Z253F0553 } from "../JsonTypes/AssayMaterials.js";
 import { ResizeArray_choose, ResizeArray_filter, ResizeArray_map, HashCodes_boxHashOption, HashCodes_boxHashArray, Option_fromValueWithDefault } from "../Helper.js";
@@ -450,7 +449,7 @@ export class ArcAssay extends ArcTables {
             let v;
             const value = (r.groups && r.groups.value) || "";
             v = Value.fromString(value);
-            return new OntologyAnnotation(oa.ID, new AnnotationValue(0, [v.Text]), oa.TermSourceREF, oa.TermAccessionNumber, oa.Comments);
+            return new OntologyAnnotation(oa.ID, v.Text, oa.TermSourceREF, oa.TermAccessionNumber, oa.Comments);
         }
         else {
             return OntologyAnnotation.fromString(name);

package/ISA/ISA/ArcTypes/CompositeCell.js

@@ -1,7 +1,6 @@
 import { int32ToString } from "../../../fable_modules/fable-library.4.5.0/Util.js";
 import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
 import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
-import { AnnotationValue } from "../JsonTypes/AnnotationValue.js";
 import { Union } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { union_type, string_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
 
@@ -110,11 +109,11 @@ export class CompositeCell extends Union {
     }
     ToUnitizedCell() {
         const this$ = this;
-        return (this$.tag === 1) ? (new CompositeCell(2, ["", OntologyAnnotation.create(void 0, new AnnotationValue(0, [this$.fields[0]]))])) : ((this$.tag === 0) ? (new CompositeCell(2, ["", this$.fields[0]])) : this$);
+        return (this$.tag === 1) ? (new CompositeCell(2, ["", OntologyAnnotation.create(void 0, this$.fields[0])])) : ((this$.tag === 0) ? (new CompositeCell(2, ["", this$.fields[0]])) : this$);
     }
     ToTermCell() {
         const this$ = this;
-        return (this$.tag === 2) ? (new CompositeCell(0, [this$.fields[1]])) : ((this$.tag === 1) ? (new CompositeCell(0, [OntologyAnnotation.create(void 0, new AnnotationValue(0, [this$.fields[0]]))])) : this$);
+        return (this$.tag === 2) ? (new CompositeCell(0, [this$.fields[1]])) : ((this$.tag === 1) ? (new CompositeCell(0, [OntologyAnnotation.create(void 0, this$.fields[0])])) : this$);
     }
     ToFreeTextCell() {
         const this$ = this;

package/ISA/ISA/Helper.js

@@ -163,6 +163,10 @@ export function ResizeArray_distinct(a) {
     return b;
 }
 
+export function ResizeArray_isEmpty(a) {
+    return a.length === 0;
+}
+
 export function HashCodes_boxHashOption(a) {
     let copyOfStruct, copyOfStruct_1;
     return (a != null) ? ((copyOfStruct = value_1(a), identityHash(copyOfStruct))) : ((copyOfStruct_1 = 0, numberHash(copyOfStruct_1)));

package/ISA/ISA/JsonTypes/AnnotationValue.js

@@ -1,7 +1,5 @@
 import { Union } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { union_type, int32_type, float64_type, string_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
-import { parse } from "../../../fable_modules/fable-library.4.5.0/Double.js";
-import { parse as parse_1 } from "../../../fable_modules/fable-library.4.5.0/Int32.js";
 import { int32ToString } from "../../../fable_modules/fable-library.4.5.0/Util.js";
 
 export class AnnotationValue extends Union {
@@ -27,17 +25,7 @@ export function AnnotationValue_get_empty() {
  * Create a ISAJson Annotation value from a ISATab string entry
  */
 export function AnnotationValue_fromString_Z721C83C5(s) {
-    try {
-        return new AnnotationValue(2, [parse_1(s, 511, false, 32)]);
-    }
-    catch (matchValue) {
-        try {
-            return new AnnotationValue(1, [parse(s)]);
-        }
-        catch (matchValue_1) {
-            return new AnnotationValue(0, [s]);
-        }
-    }
+    return new AnnotationValue(0, [s]);
 }
 
 /**

package/ISA/ISA/JsonTypes/Component.js

@@ -3,7 +3,6 @@ import { record_type, option_type, string_type } from "../../../fable_modules/fa
 import { Value as Value_1, Value_$reflection } from "./Value.js";
 import { OntologyAnnotation, OntologyAnnotation_$reflection } from "./OntologyAnnotation.js";
 import { ActivePatterns_$007CRegex$007C_$007C } from "../Regex.js";
-import { AnnotationValue } from "./AnnotationValue.js";
 import { map, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.5.0/Option.js";
 import { Option_fromValueWithDefault } from "../Helper.js";
 import { printf, toText } from "../../../fable_modules/fable-library.4.5.0/String.js";
@@ -75,7 +74,7 @@ export function Component_decomposeName_Z721C83C5(name) {
         let oa;
         const termAnnotation = (unitr.groups && unitr.groups.ontology) || "";
         oa = OntologyAnnotation.fromTermAnnotation(termAnnotation);
-        return [(value = ((unitr.groups && unitr.groups.value) || ""), Value_1.fromString(value)), new OntologyAnnotation(oa.ID, new AnnotationValue(0, [(unitr.groups && unitr.groups.unit) || ""]), oa.TermSourceREF, oa.TermAccessionNumber, oa.Comments)];
+        return [(value = ((unitr.groups && unitr.groups.value) || ""), Value_1.fromString(value)), new OntologyAnnotation(oa.ID, (unitr.groups && unitr.groups.unit) || "", oa.TermSourceREF, oa.TermAccessionNumber, oa.Comments)];
     }
     else {
         const activePatternResult_1 = ActivePatterns_$007CRegex$007C_$007C("(?<value>[^\\(]+) \\((?<ontology>[^(]*:[^)]*)\\)", name);
@@ -87,7 +86,7 @@ export function Component_decomposeName_Z721C83C5(name) {
             let v_1;
             const value_1 = (r.groups && r.groups.value) || "";
             v_1 = Value_1.fromString(value_1);
-            return [new Value_1(0, [new OntologyAnnotation(oa_1.ID, new AnnotationValue(0, [v_1.Text]), oa_1.TermSourceREF, oa_1.TermAccessionNumber, oa_1.Comments)]), void 0];
+            return [new Value_1(0, [new OntologyAnnotation(oa_1.ID, v_1.Text, oa_1.TermSourceREF, oa_1.TermAccessionNumber, oa_1.Comments)]), void 0];
         }
         else {
             return [new Value_1(3, [name]), void 0];

package/ISA/ISA/JsonTypes/MaterialAttribute.js

@@ -67,7 +67,7 @@ export function MaterialAttribute__get_NameText(this$) {
  * Returns the name of the characteristic as string
  */
 export function MaterialAttribute__get_TryNameText(this$) {
-    return bind((oa) => oa.TryNameText, this$.CharacteristicType);
+    return bind((oa) => oa.Name, this$.CharacteristicType);
 }
 
 export function MaterialAttribute__MapCategory_Z69DD836A(this$, f) {

package/ISA/ISA/JsonTypes/OntologyAnnotation.js

@@ -1,8 +1,7 @@
-import { value as value_4, map, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { map as map_1, value as value_4, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.5.0/Option.js";
 import { Pattern_TermAnnotationShortPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseTermAnnotation } from "../Regex.js";
-import { equals, stringHash, int32ToString } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { AnnotationValue_$reflection, AnnotationValue_toString_Z6FAD7738, AnnotationValue_fromString_Z721C83C5 } from "./AnnotationValue.js";
-import { filter, map as map_1, singleton, append, exists, tryFind } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { equals, stringHash } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { filter, map, singleton, append, exists, tryFind } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { record_type, array_type, option_type, string_type, getRecordFields, makeRecord } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
 import { map as map_2, map2 } from "../../../fable_modules/fable-library.4.5.0/Array.js";
 import { Update_updateOnlyByExistingAppend, Update_updateOnlyByExisting, Update_updateAppend } from "../Helper.js";
@@ -35,29 +34,7 @@ export class OntologyAnnotation extends Record {
     }
     get NameText() {
         const this$ = this;
-        return defaultArg(map((av) => {
-            switch (av.tag) {
-                case 1:
-                    return av.fields[0].toString();
-                case 2:
-                    return int32ToString(av.fields[0]);
-                default:
-                    return av.fields[0];
-            }
-        }, this$.Name), "");
-    }
-    get TryNameText() {
-        const this$ = this;
-        return unwrap(map((av) => {
-            switch (av.tag) {
-                case 1:
-                    return av.fields[0].toString();
-                case 2:
-                    return int32ToString(av.fields[0]);
-                default:
-                    return av.fields[0];
-            }
-        }, this$.Name));
+        return defaultArg(this$.Name, "");
     }
     get TermSourceREFString() {
         const this$ = this;
@@ -71,8 +48,7 @@ export class OntologyAnnotation extends Record {
         return `${"http://purl.obolibrary.org/obo/"}${termSourceRef}_${localTAN}`;
     }
     static fromString(termName, tsr, tan, comments) {
-        const name = map(AnnotationValue_fromString_Z721C83C5, termName);
-        return OntologyAnnotation.make(void 0, name, tsr, tan, comments);
+        return OntologyAnnotation.make(void 0, termName, tsr, tan, comments);
     }
     static fromTermAnnotation(termAnnotation) {
         const r = value_4(tryParseTermAnnotation(termAnnotation));
@@ -115,7 +91,7 @@ export class OntologyAnnotation extends Record {
     static toString(oa, asOntobeePurlUrlIfShort) {
         let url;
         const asOntobeePurlUrlIfShort_1 = defaultArg(asOntobeePurlUrlIfShort, false);
-        const TermName = defaultArg(map(AnnotationValue_toString_Z6FAD7738, oa.Name), "");
+        const TermName = defaultArg(oa.Name, "");
         const TermSourceREF = defaultArg(oa.TermSourceREF, "");
         return {
             TermAccessionNumber: asOntobeePurlUrlIfShort_1 ? ((url = oa.TermAccessionAndOntobeeUrlIfShort, (url === "") ? defaultArg(oa.TermAccessionNumber, "") : url)) : defaultArg(oa.TermAccessionNumber, ""),
@@ -140,8 +116,8 @@ export class OntologyAnnotation extends Record {
         const this$ = this;
         return stringHash(this$.NameText + this$.TermAccessionShort) | 0;
     }
-    static tryGetNameText(oa) {
-        return oa.TryNameText;
+    static tryGetName(oa) {
+        return oa.Name;
     }
     static getNameText(oa) {
         return oa.NameText;
@@ -159,7 +135,7 @@ export class OntologyAnnotation extends Record {
         return append(onotolgyAnnotations, singleton(onotolgyAnnotation));
     }
     static updateBy(predicate, updateOption, design, annotations) {
-        return exists(predicate, annotations) ? map_1((d) => {
+        return exists(predicate, annotations) ? map((d) => {
             if (predicate(d)) {
                 const this$ = updateOption;
                 const recordType_1 = d;
@@ -197,7 +173,7 @@ export class OntologyAnnotation extends Record {
     }
     Copy() {
         const this$ = this;
-        const comments = map((array) => map_2((c) => c.Copy(), array), this$.Comments);
+        const comments = map_1((array) => map_2((c) => c.Copy(), array), this$.Comments);
         return OntologyAnnotation.make(this$.ID, this$.Name, this$.TermSourceREF, this$.TermAccessionNumber, comments);
     }
     Print() {
@@ -215,6 +191,6 @@ export class OntologyAnnotation extends Record {
 }
 
 export function OntologyAnnotation_$reflection() {
-    return record_type("ARCtrl.ISA.OntologyAnnotation", [], OntologyAnnotation, () => [["ID", option_type(string_type)], ["Name", option_type(AnnotationValue_$reflection())], ["TermSourceREF", option_type(string_type)], ["TermAccessionNumber", option_type(string_type)], ["Comments", option_type(array_type(Comment$_$reflection()))]]);
+    return record_type("ARCtrl.ISA.OntologyAnnotation", [], OntologyAnnotation, () => [["ID", option_type(string_type)], ["Name", option_type(string_type)], ["TermSourceREF", option_type(string_type)], ["TermAccessionNumber", option_type(string_type)], ["Comments", option_type(array_type(Comment$_$reflection()))]]);
 }
 

package/ISA/ISA/JsonTypes/ProtocolParameter.js

@@ -38,7 +38,7 @@ export class ProtocolParameter extends Record {
     }
     get TryNameText() {
         const this$ = this;
-        return unwrap(bind((oa) => oa.TryNameText, this$.ParameterName));
+        return unwrap(bind((oa) => oa.Name, this$.ParameterName));
     }
     MapCategory(f) {
         const this$ = this;

package/ISA/ISA/JsonTypes/Value.js

@@ -1,9 +1,8 @@
 import { parse } from "../../../fable_modules/fable-library.4.5.0/Double.js";
 import { parse as parse_1 } from "../../../fable_modules/fable-library.4.5.0/Int32.js";
 import { OntologyAnnotation_$reflection, OntologyAnnotation } from "./OntologyAnnotation.js";
-import { map, defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
 import { int32ToString } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { AnnotationValue_toString_Z6FAD7738 } from "./AnnotationValue.js";
 import { Union, toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { printf, toText } from "../../../fable_modules/fable-library.4.5.0/String.js";
 import { union_type, string_type, float64_type, int32_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
@@ -56,7 +55,7 @@ export class Value extends Union {
                 return [value.fields[0], void 0, void 0];
             default: {
                 const oa = value.fields[0];
-                return [map(AnnotationValue_toString_Z6FAD7738, oa.Name), oa.TermAccessionNumber, oa.TermSourceREF];
+                return [oa.Name, oa.TermAccessionNumber, oa.TermSourceREF];
             }
         }
     }

package/ISA/ISA.Json/Ontology.js

@@ -166,24 +166,28 @@ export function OntologyAnnotation_encoder(options, oa) {
             return (typeof value_3 === "string") ? ((s_1 = value_3, s_1)) : nil;
         }, oa["ID"])), delay(() => {
             let value_5, s_2;
-            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "OntologyAnnotation", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("annotationValue", (value_7) => AnnotationValue_encoder(options, value_7), oa["Name"])), delay(() => append(singleton(tryInclude("termSource", (value_8) => {
+            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "OntologyAnnotation", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("annotationValue", (value_7) => {
                 let s_3;
-                const value_9 = value_8;
-                return (typeof value_9 === "string") ? ((s_3 = value_9, s_3)) : nil;
-            }, oa["TermSourceREF"])), delay(() => append(singleton(tryInclude("termAccession", (value_11) => {
+                const value_8 = value_7;
+                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
+            }, oa["Name"])), delay(() => append(singleton(tryInclude("termSource", (value_10) => {
                 let s_4;
-                const value_12 = value_11;
-                return (typeof value_12 === "string") ? ((s_4 = value_12, s_4)) : nil;
+                const value_11 = value_10;
+                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
+            }, oa["TermSourceREF"])), delay(() => append(singleton(tryInclude("termAccession", (value_13) => {
+                let s_5;
+                const value_14 = value_13;
+                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
             }, oa["TermAccessionNumber"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), oa["Comments"]))))))))));
         }));
     }))));
 }
 
 export function OntologyAnnotation_decoder(options) {
-    return (path_3) => ((v) => object_11((get$) => {
+    return (path_4) => ((v) => object_11((get$) => {
         let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, decoder, objectArg_4;
-        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("annotationValue", (s_1, json_1) => AnnotationValue_decoder(options, s_1, json_1)))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termSource", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("termAccession", string))), unwrap((arg_9 = ((decoder = decoder_1(options), (path_2) => ((value_2) => array(uncurry2(decoder), path_2, value_2)))), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", uncurry2(arg_9))))));
-    }, path_3, v));
+        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("annotationValue", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termSource", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("termAccession", string))), unwrap((arg_9 = ((decoder = decoder_1(options), (path_3) => ((value_3) => array(uncurry2(decoder), path_3, value_3)))), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", uncurry2(arg_9))))));
+    }, path_4, v));
 }
 
 export function OntologyAnnotation_fromJsonString(s) {

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

@@ -98,7 +98,7 @@ export function tryFromFsWorksheet(sheet) {
     else {
         const t = matchValue;
         const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
-        return ArcTable.addColumns(compositeColumns)(ArcTable.init(sheet.Name));
+        return ArcTable.addColumns(compositeColumns, void 0, true)(ArcTable.init(sheet.Name));
     }
 }
 

package/ISA/ISA.Spreadsheet/ArcStudy.js

@@ -1,5 +1,5 @@
 import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.0.1/FsWorksheet.fs.js";
-import { iterate, isEmpty, choose, map, append, iterateIndexed } from "../../fable_modules/fable-library.4.5.0/Seq.js";
+import { map, append, iterateIndexed } from "../../fable_modules/fable-library.4.5.0/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.4.5.0/Option.js";
@@ -8,6 +8,7 @@ import { ArcStudy } from "../ISA/ArcTypes/ArcTypes.js";
 import { createMissingIdentifier } from "../ISA/Identifier.js";
 import { empty } from "../../fable_modules/fable-library.4.5.0/List.js";
 import { printf, toConsole } from "../../fable_modules/fable-library.4.5.0/String.js";
+import { ResizeArray_iter, ResizeArray_isEmpty, ResizeArray_choose } from "../ISA/Helper.js";
 import { toFsWorksheet, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
 import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.0.1/FsWorkbook.fs.js";
 
@@ -45,9 +46,9 @@ export function ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(doc
         patternInput = ArcStudy_fromMetadataSheet(matchValue);
     }
     const studyMetadata = patternInput[0];
-    const annotationTables = choose(tryFromFsWorksheet, doc.GetWorksheets());
-    if (!isEmpty(annotationTables)) {
-        studyMetadata.Tables = Array.from(annotationTables);
+    const annotationTables = ResizeArray_choose(tryFromFsWorksheet, doc.GetWorksheets());
+    if (!ResizeArray_isEmpty(annotationTables)) {
+        studyMetadata.Tables = annotationTables;
     }
     return [studyMetadata, patternInput[1]];
 }
@@ -56,7 +57,7 @@ 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) => {
+    ResizeArray_iter((arg) => {
         const sheet = toFsWorksheet(arg);
         doc.AddWorksheet(sheet);
     }, study.Tables);

package/fable_modules/project_cracked.json

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nfdi4plants/arctrl",
-  "version": "1.0.1+5576d43",
+  "version": "1.0.2+488e332",
   "description": "Top level ARC DataModel and API function descriptions.",
   "type": "module",
   "main": "index.js",