@nfdi4plants/arctrl 1.0.7 → 1.1.0

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

@@ -2,14 +2,15 @@ import { iterateIndexed, length, ofArray, sortBy, collect, toArray, empty, tail,
 import { tryParseReferenceColumnHeader } from "../../ISA/Regex.js";
 import { map as map_1, toList, tryFind } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
 import { toFsColumns, fixDeprecatedIOHeader, fromFsColumns } from "./CompositeColumn.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
 import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
-import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.5.1.2/FsWorksheet.fs.js";
+import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
 import { comparePrimitives } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.2/Ranges/FsRangeAddress.fs.js";
-import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.2/FsAddress.fs.js";
-import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.5.1.2/Cells/FsCellsCollection.fs.js";
+import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
+import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCellsCollection.fs.js";
 import { addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
-import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.5.1.2/Ranges/FsRangeBase.fs.js";
+import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeBase.fs.js";
 
 /**
  * Iterates over elements of the input list and groups adjacent elements.
@@ -91,49 +92,61 @@ export function composeColumns(columns) {
  * Returns the protocol described by the headers and a function for parsing the values of the matrix to the processes of this protocol
  */
 export function tryFromFsWorksheet(sheet) {
-    const matchValue = tryAnnotationTable(sheet);
-    if (matchValue == null) {
-        return void 0;
+    try {
+        const matchValue = tryAnnotationTable(sheet);
+        if (matchValue == null) {
+            return void 0;
+        }
+        else {
+            const t = matchValue;
+            const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
+            return ArcTable.addColumns(compositeColumns, void 0, true)(ArcTable.init(sheet.Name));
+        }
     }
-    else {
-        const t = matchValue;
-        const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
-        return ArcTable.addColumns(compositeColumns, void 0, true)(ArcTable.init(sheet.Name));
+    catch (err) {
+        const arg = sheet.Name;
+        const arg_1 = err.message;
+        return toFail(printf("Could not parse table with name \"%s\":\n%s"))(arg)(arg_1);
     }
 }
 
 export function toFsWorksheet(table) {
     const stringCount = new Map([]);
     const ws = new FsWorksheet(table.Name);
-    const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
-        Compare: comparePrimitives,
-    }));
-    const maxRow = length(head(columns)) | 0;
-    const maxCol = length(columns) | 0;
-    const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
-    iterateIndexed((colI, col) => {
-        iterateIndexed((rowI, cell) => {
-            let value;
-            const v = cell.ValueAsString();
-            if (rowI === 0) {
-                const matchValue = Dictionary_tryGet(v, stringCount);
-                if (matchValue == null) {
-                    addToDict(stringCount, cell.ValueAsString(), "");
-                    value = v;
+    if (table.Columns.length === 0) {
+        return ws;
+    }
+    else {
+        const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
+            Compare: comparePrimitives,
+        }));
+        const maxRow = length(head(columns)) | 0;
+        const maxCol = length(columns) | 0;
+        const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
+        iterateIndexed((colI, col) => {
+            iterateIndexed((rowI, cell) => {
+                let value;
+                const v = cell.ValueAsString();
+                if (rowI === 0) {
+                    const matchValue = Dictionary_tryGet(v, stringCount);
+                    if (matchValue == null) {
+                        addToDict(stringCount, cell.ValueAsString(), "");
+                        value = v;
+                    }
+                    else {
+                        const spaces = matchValue;
+                        stringCount.set(v, spaces + " ");
+                        value = ((v + " ") + spaces);
+                    }
                 }
                 else {
-                    const spaces = matchValue;
-                    stringCount.set(v, spaces + " ");
-                    value = ((v + " ") + spaces);
+                    value = v;
                 }
-            }
-            else {
-                value = v;
-            }
-            const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
-            FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);
-        }, col);
-    }, columns);
-    return ws;
+                const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
+                FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);
+            }, col);
+        }, columns);
+        return ws;
+    }
 }
 

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

@@ -1,7 +1,7 @@
 import { singleton, ofArray, head, tail, isEmpty, map } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { CompositeCell } from "../../ISA/ArcTypes/CompositeCell.js";
 import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
-import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.2/Cells/FsCell.fs.js";
+import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
 
 export function fromFsCells(cells) {
     const cellValues = map((c) => c.ValueAsString(), cells);

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.4.5.0/Types.js";
 import { toFsCells, fromFsCells } from "./CompositeHeader.js";
 import { singleton as singleton_1, ofArray, item, map } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { FsAddress__get_RowNumber } from "../../../fable_modules/FsSpreadsheet.5.1.2/FsAddress.fs.js";
-import { FsRangeAddress__get_LastAddress } from "../../../fable_modules/FsSpreadsheet.5.1.2/Ranges/FsRangeAddress.fs.js";
-import { FsRangeBase__get_RangeAddress } from "../../../fable_modules/FsSpreadsheet.5.1.2/Ranges/FsRangeBase.fs.js";
+import { FsAddress__get_RowNumber } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
+import { FsRangeAddress__get_LastAddress } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsRangeBase__get_RangeAddress } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeBase.fs.js";
 import { singleton, append, toList, exists, map as map_1, delay, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
 import { toFsCells as toFsCells_1, fromFsCells as fromFsCells_1 } from "./CompositeCell.js";
 import { rangeDouble } from "../../../fable_modules/fable-library.4.5.0/Range.js";

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.5.1.2/Cells/FsCell.fs.js";
+import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
 import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { empty, singleton as singleton_1, append, delay, toList } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
 

package/ISA/ISA.Spreadsheet/ArcAssay.js

@@ -1,16 +1,16 @@
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.2/FsWorksheet.fs.js";
+import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
 import { iterate, isEmpty as isEmpty_1, choose, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../../fable_modules/fable-library.4.5.0/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.4.5.0/List.js";
 import { fromRows as fromRows_2, toRows as toRows_2 } from "./Metadata/Contacts.js";
+import { toConsole, printf, toFail } from "../../fable_modules/fable-library.4.5.0/String.js";
 import { getEnumerator } from "../../fable_modules/fable-library.4.5.0/Util.js";
 import { ArcAssay } from "../ISA/ArcTypes/ArcTypes.js";
 import { createMissingIdentifier } from "../ISA/Identifier.js";
 import { defaultArg } from "../../fable_modules/fable-library.4.5.0/Option.js";
-import { printf, toConsole } from "../../fable_modules/fable-library.4.5.0/String.js";
 import { toFsWorksheet, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
-import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.1.2/FsWorkbook.fs.js";
+import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
 
 export function toMetadataSheet(assay) {
     let assay_1;
@@ -22,89 +22,95 @@ export function toMetadataSheet(assay) {
 }
 
 export function fromMetadataSheet(sheet) {
-    const rows_1 = map(SparseRowModule_fromFsRow, sheet.Rows);
-    const patternInput = exists((row) => {
-        const s = head(row)[1];
-        return s.indexOf("Assay") === 0;
-    }, rows_1) ? ["Assay", "Assay Person"] : [void 0, void 0];
-    const en = getEnumerator(rows_1);
-    const loop = (lastLine_mut, assays_mut, contacts_mut, lineNumber_mut) => {
-        let k;
-        loop:
-        while (true) {
-            const lastLine = lastLine_mut, assays = assays_mut, contacts = contacts_mut, lineNumber = lineNumber_mut;
-            let matchResult, k_2, k_3, k_4;
-            if (lastLine != null) {
-                if ((k = lastLine, (k === "ASSAY") ? true : (k === "ASSAY METADATA"))) {
-                    matchResult = 0;
-                    k_2 = lastLine;
-                }
-                else if (lastLine === "ASSAY PERFORMERS") {
-                    matchResult = 1;
-                    k_3 = lastLine;
+    try {
+        const rows_1 = map(SparseRowModule_fromFsRow, sheet.Rows);
+        const patternInput = exists((row) => {
+            const s = head(row)[1];
+            return s.indexOf("Assay") === 0;
+        }, rows_1) ? ["Assay", "Assay Person"] : [void 0, void 0];
+        const en = getEnumerator(rows_1);
+        const loop = (lastLine_mut, assays_mut, contacts_mut, lineNumber_mut) => {
+            let k;
+            loop:
+            while (true) {
+                const lastLine = lastLine_mut, assays = assays_mut, contacts = contacts_mut, lineNumber = lineNumber_mut;
+                let matchResult, k_2, k_3, k_4;
+                if (lastLine != null) {
+                    if ((k = lastLine, (k === "ASSAY") ? true : (k === "ASSAY METADATA"))) {
+                        matchResult = 0;
+                        k_2 = lastLine;
+                    }
+                    else if (lastLine === "ASSAY PERFORMERS") {
+                        matchResult = 1;
+                        k_3 = lastLine;
+                    }
+                    else {
+                        matchResult = 2;
+                        k_4 = lastLine;
+                    }
                 }
                 else {
                     matchResult = 2;
                     k_4 = lastLine;
                 }
-            }
-            else {
-                matchResult = 2;
-                k_4 = lastLine;
-            }
-            switch (matchResult) {
-                case 0: {
-                    const patternInput_1 = fromRows_1(patternInput[0], lineNumber + 1, en);
-                    lastLine_mut = patternInput_1[0];
-                    assays_mut = patternInput_1[3];
-                    contacts_mut = contacts;
-                    lineNumber_mut = patternInput_1[1];
-                    continue loop;
-                }
-                case 1: {
-                    const patternInput_2 = fromRows_2(patternInput[1], lineNumber + 1, en);
-                    lastLine_mut = patternInput_2[0];
-                    assays_mut = assays;
-                    contacts_mut = patternInput_2[3];
-                    lineNumber_mut = patternInput_2[1];
-                    continue loop;
-                }
-                default: {
-                    let matchResult_1, assays_2, contacts_2;
-                    if (isEmpty(assays)) {
-                        if (isEmpty(contacts)) {
-                            matchResult_1 = 0;
+                switch (matchResult) {
+                    case 0: {
+                        const patternInput_1 = fromRows_1(patternInput[0], lineNumber + 1, en);
+                        lastLine_mut = patternInput_1[0];
+                        assays_mut = patternInput_1[3];
+                        contacts_mut = contacts;
+                        lineNumber_mut = patternInput_1[1];
+                        continue loop;
+                    }
+                    case 1: {
+                        const patternInput_2 = fromRows_2(patternInput[1], lineNumber + 1, en);
+                        lastLine_mut = patternInput_2[0];
+                        assays_mut = assays;
+                        contacts_mut = patternInput_2[3];
+                        lineNumber_mut = patternInput_2[1];
+                        continue loop;
+                    }
+                    default: {
+                        let matchResult_1, assays_2, contacts_2;
+                        if (isEmpty(assays)) {
+                            if (isEmpty(contacts)) {
+                                matchResult_1 = 0;
+                            }
+                            else {
+                                matchResult_1 = 1;
+                                assays_2 = assays;
+                                contacts_2 = contacts;
+                            }
                         }
                         else {
                             matchResult_1 = 1;
                             assays_2 = assays;
                             contacts_2 = contacts;
                         }
-                    }
-                    else {
-                        matchResult_1 = 1;
-                        assays_2 = assays;
-                        contacts_2 = contacts;
-                    }
-                    switch (matchResult_1) {
-                        case 0:
-                            return ArcAssay.create(createMissingIdentifier());
-                        default: {
-                            const performers = toArray(contacts_2);
-                            const assay = defaultArg(tryHead(assays_2), ArcAssay.create(createMissingIdentifier()));
-                            return ArcAssay.setPerformers(performers, assay);
+                        switch (matchResult_1) {
+                            case 0:
+                                return ArcAssay.create(createMissingIdentifier());
+                            default: {
+                                const performers = toArray(contacts_2);
+                                const assay = defaultArg(tryHead(assays_2), ArcAssay.create(createMissingIdentifier()));
+                                return ArcAssay.setPerformers(performers, assay);
+                            }
                         }
                     }
                 }
+                break;
             }
-            break;
+        };
+        if (en["System.Collections.IEnumerator.MoveNext"]()) {
+            return loop(SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), empty(), empty(), 1);
+        }
+        else {
+            throw new Error("empty assay metadata sheet");
         }
-    };
-    if (en["System.Collections.IEnumerator.MoveNext"]()) {
-        return loop(SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), empty(), empty(), 1);
     }
-    else {
-        throw new Error("empty assay metadata sheet");
+    catch (err) {
+        const arg = err.message;
+        return toFail(printf("Failed while parsing metadatasheet: %s"))(arg);
     }
 }
 
@@ -112,26 +118,32 @@ export function fromMetadataSheet(sheet) {
  * Reads an assay from a spreadsheet
  */
 export function fromFsWorkbook(doc) {
-    let assayMetaData;
-    const matchValue = doc.TryGetWorksheetByName("isa_assay");
-    if (matchValue == null) {
-        const matchValue_1 = doc.TryGetWorksheetByName("Assay");
-        if (matchValue_1 == null) {
-            toConsole(printf("Cannot retrieve metadata: Assay file does not contain \"%s\" or \"%s\" sheet."))("isa_assay")("Assay");
-            assayMetaData = ArcAssay.create(createMissingIdentifier());
+    try {
+        let assayMetaData;
+        const matchValue = doc.TryGetWorksheetByName("isa_assay");
+        if (matchValue == null) {
+            const matchValue_1 = doc.TryGetWorksheetByName("Assay");
+            if (matchValue_1 == null) {
+                toConsole(printf("Cannot retrieve metadata: Assay file does not contain \"%s\" or \"%s\" sheet."))("isa_assay")("Assay");
+                assayMetaData = ArcAssay.create(createMissingIdentifier());
+            }
+            else {
+                assayMetaData = fromMetadataSheet(matchValue_1);
+            }
         }
         else {
-            assayMetaData = fromMetadataSheet(matchValue_1);
+            assayMetaData = fromMetadataSheet(matchValue);
         }
+        const annotationTables = choose(tryFromFsWorksheet, doc.GetWorksheets());
+        if (!isEmpty_1(annotationTables)) {
+            assayMetaData.Tables = Array.from(annotationTables);
+        }
+        return assayMetaData;
     }
-    else {
-        assayMetaData = fromMetadataSheet(matchValue);
-    }
-    const annotationTables = choose(tryFromFsWorksheet, doc.GetWorksheets());
-    if (!isEmpty_1(annotationTables)) {
-        assayMetaData.Tables = Array.from(annotationTables);
+    catch (err) {
+        const arg_2 = err.message;
+        return toFail(printf("Could not parse assay: \n%s"))(arg_2);
     }
-    return assayMetaData;
 }
 
 export function toFsWorkbook(assay) {

package/ISA/ISA.Spreadsheet/ArcInvestigation.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, empty as empty_1, collect, singleton, append as append_1, delay } from "../../fable_modules/fable-library.4.5.0/Seq.js";
 import { tryFind, ofList } from "../../fable_modules/fable-library.4.5.0/Map.js";
 import { printf, toFail } from "../../fable_modules/fable-library.4.5.0/String.js";
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.2/FsWorksheet.fs.js";
-import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.1.2/FsWorkbook.fs.js";
+import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
+import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
 
 export class InvestigationInfo extends Record {
     constructor(Identifier, Title, Description, SubmissionDate, PublicReleaseDate, Comments) {

package/ISA/ISA.Spreadsheet/ArcStudy.js

@@ -1,16 +1,16 @@
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.2/FsWorksheet.fs.js";
+import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.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 { toConsole, printf, toFail } from "../../fable_modules/fable-library.4.5.0/String.js";
 import { defaultArg } from "../../fable_modules/fable-library.4.5.0/Option.js";
 import { getEnumerator } from "../../fable_modules/fable-library.4.5.0/Util.js";
 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.5.1.2/FsWorkbook.fs.js";
+import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
 
 export function ArcStudy_toMetadataSheet(study, assays) {
     let source_1;
@@ -23,34 +23,46 @@ export function ArcStudy_toMetadataSheet(study, assays) {
 
 export function ArcStudy_fromMetadataSheet(sheet) {
     let en;
-    return defaultArg((en = getEnumerator(map(SparseRowModule_fromFsRow, sheet.Rows)), (void en["System.Collections.IEnumerator.MoveNext"](), fromRows_1(2, en)[3])), [ArcStudy.create(createMissingIdentifier()), empty()]);
+    try {
+        return defaultArg((en = getEnumerator(map(SparseRowModule_fromFsRow, sheet.Rows)), (void en["System.Collections.IEnumerator.MoveNext"](), fromRows_1(2, en)[3])), [ArcStudy.create(createMissingIdentifier()), empty()]);
+    }
+    catch (err) {
+        const arg = err.message;
+        return toFail(printf("Failed while parsing metadatasheet: %s"))(arg);
+    }
 }
 
 /**
  * Reads an assay from a spreadsheet
  */
 export function ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(doc) {
-    let patternInput;
-    const matchValue = doc.TryGetWorksheetByName("isa_study");
-    if (matchValue == null) {
-        const matchValue_1 = doc.TryGetWorksheetByName("Study");
-        if (matchValue_1 == null) {
-            toConsole(printf("Cannot retrieve metadata: Study file does not contain \"%s\" or \"%s\" sheet."))("isa_study")("Study");
-            patternInput = [ArcStudy.create(createMissingIdentifier()), empty()];
+    try {
+        let patternInput;
+        const matchValue = doc.TryGetWorksheetByName("isa_study");
+        if (matchValue == null) {
+            const matchValue_1 = doc.TryGetWorksheetByName("Study");
+            if (matchValue_1 == null) {
+                toConsole(printf("Cannot retrieve metadata: Study file does not contain \"%s\" or \"%s\" sheet."))("isa_study")("Study");
+                patternInput = [ArcStudy.create(createMissingIdentifier()), empty()];
+            }
+            else {
+                patternInput = ArcStudy_fromMetadataSheet(matchValue_1);
+            }
         }
         else {
-            patternInput = ArcStudy_fromMetadataSheet(matchValue_1);
+            patternInput = ArcStudy_fromMetadataSheet(matchValue);
         }
+        const studyMetadata = patternInput[0];
+        const annotationTables = ResizeArray_choose(tryFromFsWorksheet, doc.GetWorksheets());
+        if (!ResizeArray_isEmpty(annotationTables)) {
+            studyMetadata.Tables = annotationTables;
+        }
+        return [studyMetadata, patternInput[1]];
     }
-    else {
-        patternInput = ArcStudy_fromMetadataSheet(matchValue);
-    }
-    const studyMetadata = patternInput[0];
-    const annotationTables = ResizeArray_choose(tryFromFsWorksheet, doc.GetWorksheets());
-    if (!ResizeArray_isEmpty(annotationTables)) {
-        studyMetadata.Tables = annotationTables;
+    catch (err) {
+        const arg_2 = err.message;
+        return toFail(printf("Could not parse study: \n%s"))(arg_2);
     }
-    return [studyMetadata, patternInput[1]];
 }
 
 export function ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9(study, assays) {

package/ISA/ISA.Spreadsheet/Metadata/SparseTable.js

@@ -2,14 +2,14 @@ import { append as append_1, delay, tryItem, length as length_1, isEmpty, iterat
 import { defaultArg, map as map_1 } from "../../../fable_modules/fable-library.4.5.0/Option.js";
 import { tryFind, ofSeq } from "../../../fable_modules/fable-library.4.5.0/Map.js";
 import { arrayHash, equalArrays, equals, comparePrimitives } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { RowBuilder_get_Empty, RowBuilder__Combine_19F30600, RowBuilder_$ctor } from "../../../fable_modules/FsSpreadsheet.5.1.2/DSL/RowBuilder.fs.js";
-import { CellBuilder_$ctor, CellBuilder__AsCellElement_6F87C2ED } from "../../../fable_modules/FsSpreadsheet.5.1.2/DSL/CellBuilder.fs.js";
-import { Messages_format, SheetEntity$1_some_2B595 } from "../../../fable_modules/FsSpreadsheet.5.1.2/DSL/Types.fs.js";
-import { DataType } from "../../../fable_modules/FsSpreadsheet.5.1.2/Cells/FsCell.fs.js";
+import { RowBuilder_get_Empty, RowBuilder__Combine_19F30600, RowBuilder_$ctor } from "../../../fable_modules/FsSpreadsheet.5.1.3/DSL/RowBuilder.fs.js";
+import { CellBuilder_$ctor, CellBuilder__AsCellElement_6F87C2ED } from "../../../fable_modules/FsSpreadsheet.5.1.3/DSL/CellBuilder.fs.js";
+import { Messages_format, SheetEntity$1_some_2B595 } from "../../../fable_modules/FsSpreadsheet.5.1.3/DSL/Types.fs.js";
+import { DataType } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
 import { map as map_2, toArray, initialize as initialize_1, exists, find, cons, append, empty, singleton } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { ColumnIndex, RowElement } from "../../../fable_modules/FsSpreadsheet.5.1.2/DSL/Types.fs.js";
-import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.2/Ranges/FsRangeAddress.fs.js";
-import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.2/FsAddress.fs.js";
+import { ColumnIndex, RowElement } from "../../../fable_modules/FsSpreadsheet.5.1.3/DSL/Types.fs.js";
+import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
 import { Record } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { record_type, list_type, class_type, tuple_type, int32_type, string_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
 import { Seq_trySkip, Dictionary_tryGetValue } from "../CollectionAux.js";

package/Templates/Template.Spreadsheet.js

@@ -15,10 +15,10 @@ import { toArray } from "../fable_modules/fable-library.4.5.0/Option.js";
 import { toRows as toRows_1, fromRows as fromRows_1 } from "../ISA/ISA.Spreadsheet/Metadata/Contacts.js";
 import { parse } from "../fable_modules/fable-library.4.5.0/Guid.js";
 import { Template, Organisation } from "./Template.js";
-import { FsWorksheet } from "../fable_modules/FsSpreadsheet.5.1.2/FsWorksheet.fs.js";
+import { FsWorksheet } from "../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
 import { toFsWorksheet, tryFromFsWorksheet } from "../ISA/ISA.Spreadsheet/AnnotationTable/ArcTable.js";
 import { now } from "../fable_modules/fable-library.4.5.0/Date.js";
-import { FsWorkbook } from "../fable_modules/FsSpreadsheet.5.1.2/FsWorkbook.fs.js";
+import { FsWorkbook } from "../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
 
 export class TemplateReadError extends FSharpException {
     constructor(Data0) {

package/fable_modules/{FsSpreadsheet.5.1.2 → FsSpreadsheet.5.1.3}/FsAddress.fs

@@ -4,6 +4,13 @@
 /// Module containing functions to work with "A1" style excel cell references.
 module CellReference =
     
+    [<Literal>]
+    let indexPattern = 
+        "([A-Z]*)(\d*)"
+
+    let indexRegex = 
+        System.Text.RegularExpressions.Regex(indexPattern)
+
     /// Transforms excel column string indices (e.g. A, B, Z, AA, CD) to index number (starting with A = 1).
     let colAdressToIndex (columnAdress : string) =
         let length = columnAdress.Length
@@ -30,17 +37,24 @@ module CellReference =
     let ofIndices column (row : uint32) = 
         sprintf "%s%i" (indexToColAdress column) row
 
+    
+
     /// Maps a "A1" style excel cell reference to a column * row index tuple (1 Based indices).
     let toIndices (reference : string) = 
-        let inp = reference.ToUpper()
-        let pattern = "([A-Z]*)(\d*)"
-        let regex = System.Text.RegularExpressions.Regex.Match(inp,pattern)
+        let charPart = System.Text.StringBuilder()
+        let numPart = System.Text.StringBuilder()
         
-        if regex.Success then
-            regex.Groups
-            |> fun a -> colAdressToIndex a.[1].Value, uint32 a.[2].Value
-        else 
-            failwithf "Reference %s does not match Excel A1-style" reference
+        reference
+        |> Seq.iter (fun c -> 
+            if System.Char.IsLetter c then
+                charPart.Append c |> ignore
+            elif System.Char.IsDigit c then
+                numPart.Append c |> ignore
+            else
+                failwithf "Reference %s does not match Excel A1-style" reference
+        )
+        colAdressToIndex (charPart.ToString()), uint32 (numPart.ToString())
+
 
     /// Maps a "A1" style excel cell reference to a column (1 Based indices).
     let toColIndex (reference : string) = 

package/fable_modules/{FsSpreadsheet.5.1.2 → FsSpreadsheet.5.1.3}/FsAddress.fs.js

@@ -1,9 +1,14 @@
 import { toFail, printf, toText } from "../fable-library.4.5.0/String.js";
-import { create, match } from "../fable-library.4.5.0/RegExp.js";
+import { StringBuilder__Append_244C7CD6, StringBuilder_$ctor } from "../fable-library.4.5.0/System.Text.js";
+import { iterate } from "../fable-library.4.5.0/Seq.js";
+import { isDigit, isLetter } from "../fable-library.4.5.0/Char.js";
+import { toString } from "../fable-library.4.5.0/Types.js";
 import { parse } from "../fable-library.4.5.0/Int32.js";
 import { toUInt32, fromInt32, fromUInt32, op_Addition, toInt64 } from "../fable-library.4.5.0/BigInt.js";
 import { class_type } from "../fable-library.4.5.0/Reflection.js";
 
+export const CellReference_indexRegex = /([A-Z]*)(\d*)/gu;
+
 /**
  * Transforms excel column string indices (e.g. A, B, Z, AA, CD) to index number (starting with A = 1).
  */
@@ -57,15 +62,20 @@ export function CellReference_ofIndices(column, row) {
  * Maps a "A1" style excel cell reference to a column * row index tuple (1 Based indices).
  */
 export function CellReference_toIndices(reference) {
-    const inp = reference.toLocaleUpperCase();
-    const regex = match(create("([A-Z]*)(\\d*)"), inp);
-    if (regex != null) {
-        const a = regex;
-        return [CellReference_colAdressToIndex(a[1] || ""), parse(a[2] || "", 511, true, 32)];
-    }
-    else {
-        return toFail(printf("Reference %s does not match Excel A1-style"))(reference);
-    }
+    const charPart = StringBuilder_$ctor();
+    const numPart = StringBuilder_$ctor();
+    iterate((c) => {
+        if (isLetter(c)) {
+            StringBuilder__Append_244C7CD6(charPart, c);
+        }
+        else if (isDigit(c)) {
+            StringBuilder__Append_244C7CD6(numPart, c);
+        }
+        else {
+            toFail(printf("Reference %s does not match Excel A1-style"))(reference);
+        }
+    }, reference.split(""));
+    return [CellReference_colAdressToIndex(toString(charPart)), parse(toString(numPart), 511, true, 32)];
 }
 
 /**