@nfdi4plants/arctrl 2.5.1 → 3.0.0-alpha.2

package/dist/ts/cjs/ts/Spreadsheet/ArcAssay.js

@@ -0,0 +1,218 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ArcAssay_fromRows = ArcAssay_fromRows;
+exports.ArcAssay_toRows = ArcAssay_toRows;
+exports.ArcAssay_toMetadataSheet = ArcAssay_toMetadataSheet;
+exports.ArcAssay_fromMetadataSheet = ArcAssay_fromMetadataSheet;
+exports.ArcAssay_toMetadataCollection = ArcAssay_toMetadataCollection;
+exports.ArcAssay_fromMetadataCollection = ArcAssay_fromMetadataCollection;
+exports.ArcAssay_isMetadataSheetName = ArcAssay_isMetadataSheetName;
+exports.ArcAssay_isMetadataSheet = ArcAssay_isMetadataSheet;
+exports.ArcAssay_tryGetMetadataSheet = ArcAssay_tryGetMetadataSheet;
+exports.ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D = ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D;
+exports.ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F = ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F;
+exports.ARCtrl_ArcAssay__ArcAssay_ToFsWorkbook_6FCE9E49 = ARCtrl_ArcAssay__ArcAssay_ToFsWorkbook_6FCE9E49;
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+const Assays_js_1 = require("./Metadata/Assays.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const ArcTypes_js_1 = require("../Core/ArcTypes.js");
+const Contacts_js_1 = require("./Metadata/Contacts.js");
+const Identifier_js_1 = require("../Core/Helper/Identifier.js");
+const SparseTable_js_1 = require("./Metadata/SparseTable.js");
+const FsWorksheet_fs_js_1 = require("../fable_modules/FsSpreadsheet.6.3.1/FsWorksheet.fs.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const FsWorkbook_fs_js_1 = require("../fable_modules/FsSpreadsheet.6.3.1/FsWorkbook.fs.js");
+const ArcTable_js_1 = require("./AnnotationTable/ArcTable.js");
+const DataMapTable_js_1 = require("./DataMapTable/DataMapTable.js");
+function ArcAssay_fromRows(rows) {
+    const patternInput = (0, Seq_js_1.exists)((row) => {
+        const s = (0, Seq_js_1.head)(row)[1];
+        return s.startsWith("Assay");
+    }, rows) ? ["Assay", "Assay Person"] : [undefined, undefined];
+    const en = (0, Util_js_1.getEnumerator)(rows);
+    const loop = (lastRow_mut, assays_mut, contacts_mut, rowNumber_mut) => {
+        let prefix;
+        loop: while (true) {
+            const lastRow = lastRow_mut, assays = assays_mut, contacts = contacts_mut, rowNumber = rowNumber_mut;
+            let matchResult, prefix_2, prefix_3;
+            if (lastRow != null) {
+                if ((prefix = (0, Option_js_1.value)(lastRow), (prefix === "ASSAY") ? true : (prefix === "ASSAY METADATA"))) {
+                    matchResult = 0;
+                    prefix_2 = (0, Option_js_1.value)(lastRow);
+                }
+                else if ((0, Option_js_1.value)(lastRow) === "ASSAY PERFORMERS") {
+                    matchResult = 1;
+                    prefix_3 = (0, Option_js_1.value)(lastRow);
+                }
+                else {
+                    matchResult = 2;
+                }
+            }
+            else {
+                matchResult = 2;
+            }
+            switch (matchResult) {
+                case 0: {
+                    const patternInput_1 = (0, Assays_js_1.fromRows)(patternInput[0], rowNumber + 1, en);
+                    lastRow_mut = patternInput_1[0];
+                    assays_mut = patternInput_1[3];
+                    contacts_mut = contacts;
+                    rowNumber_mut = patternInput_1[1];
+                    continue loop;
+                }
+                case 1: {
+                    const patternInput_2 = (0, Contacts_js_1.fromRows)(patternInput[1], rowNumber + 1, en);
+                    lastRow_mut = patternInput_2[0];
+                    assays_mut = assays;
+                    contacts_mut = patternInput_2[3];
+                    rowNumber_mut = patternInput_2[1];
+                    continue loop;
+                }
+                default: {
+                    let matchResult_1, assays_2, contacts_2;
+                    if ((0, List_js_1.isEmpty)(assays)) {
+                        if ((0, List_js_1.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;
+                    }
+                    switch (matchResult_1) {
+                        case 0:
+                            return ArcTypes_js_1.ArcAssay.create((0, Identifier_js_1.createMissingIdentifier)());
+                        default: {
+                            const performers = Array.from(contacts_2);
+                            const assay = (0, Option_js_1.defaultArg)((0, Seq_js_1.tryHead)(assays_2), ArcTypes_js_1.ArcAssay.create((0, Identifier_js_1.createMissingIdentifier)()));
+                            return ArcTypes_js_1.ArcAssay.setPerformers(performers, assay);
+                        }
+                    }
+                }
+            }
+            break;
+        }
+    };
+    if (en["System.Collections.IEnumerator.MoveNext"]()) {
+        return loop((0, SparseTable_js_1.SparseRowModule_tryGetValueAt)(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), (0, List_js_1.empty)(), (0, List_js_1.empty)(), 1);
+    }
+    else {
+        throw new Error("empty assay metadata sheet");
+    }
+}
+function ArcAssay_toRows(assay) {
+    return (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, SparseTable_js_1.SparseRowModule_fromValues)(["ASSAY"])), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Assays_js_1.toRows)("Assay", (0, List_js_1.singleton)(assay)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, SparseTable_js_1.SparseRowModule_fromValues)(["ASSAY PERFORMERS"])), (0, Seq_js_1.delay)(() => (0, Contacts_js_1.toRows)("Assay Person", (0, List_js_1.ofSeq)(assay.Performers)))))))));
+}
+function ArcAssay_toMetadataSheet(assay) {
+    const sheet = new FsWorksheet_fs_js_1.FsWorksheet("isa_assay");
+    (0, Seq_js_1.iterateIndexed)((rowI, r) => {
+        (0, SparseTable_js_1.SparseRowModule_writeToSheet)(rowI + 1, r, sheet);
+    }, ArcAssay_toRows(assay));
+    return sheet;
+}
+function ArcAssay_fromMetadataSheet(sheet) {
+    try {
+        const rows = (0, Seq_js_1.map)(SparseTable_js_1.SparseRowModule_fromFsRow, sheet.Rows);
+        const hasPrefix = (0, Seq_js_1.exists)((row) => {
+            const s = (0, Seq_js_1.head)(row)[1];
+            return s.startsWith("Assay");
+        }, rows);
+        return ArcAssay_fromRows(rows);
+    }
+    catch (err) {
+        const arg = err.message;
+        return (0, String_js_1.toFail)((0, String_js_1.printf)("Failed while parsing metadatasheet: %s"))(arg);
+    }
+}
+function ArcAssay_toMetadataCollection(assay) {
+    return (0, Seq_js_1.map)(SparseTable_js_1.SparseRowModule_getAllValues, ArcAssay_toRows(assay));
+}
+function ArcAssay_fromMetadataCollection(collection) {
+    try {
+        return ArcAssay_fromRows((0, Seq_js_1.map)(SparseTable_js_1.SparseRowModule_fromAllValues, collection));
+    }
+    catch (err) {
+        const arg = err.message;
+        return (0, String_js_1.toFail)((0, String_js_1.printf)("Failed while parsing metadatasheet: %s"))(arg);
+    }
+}
+function ArcAssay_isMetadataSheetName(name) {
+    if (name === "isa_assay") {
+        return true;
+    }
+    else {
+        return name === "Assay";
+    }
+}
+function ArcAssay_isMetadataSheet(sheet) {
+    return ArcAssay_isMetadataSheetName(sheet.Name);
+}
+function ArcAssay_tryGetMetadataSheet(doc) {
+    return (0, Seq_js_1.tryFind)(ArcAssay_isMetadataSheet, doc.GetWorksheets());
+}
+/**
+ * Reads an assay from a spreadsheet
+ */
+function ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D(doc) {
+    try {
+        let assayMetadata;
+        const matchValue = ArcAssay_tryGetMetadataSheet(doc);
+        if (matchValue == null) {
+            (0, String_js_1.toConsole)((0, String_js_1.printf)("Cannot retrieve metadata: Assay file does not contain \"%s\" or \"%s\" sheet."))("isa_assay")("Assay");
+            assayMetadata = ArcTypes_js_1.ArcAssay.create((0, Identifier_js_1.createMissingIdentifier)());
+        }
+        else {
+            assayMetadata = ArcAssay_fromMetadataSheet((0, Option_js_1.value)(matchValue));
+        }
+        const sheets = doc.GetWorksheets();
+        const annotationTables = (0, Seq_js_1.choose)(ArcTable_js_1.tryFromFsWorksheet, sheets);
+        const datamapSheet = (0, Seq_js_1.tryPick)(DataMapTable_js_1.tryFromFsWorksheet, sheets);
+        if (!(0, Seq_js_1.isEmpty)(annotationTables)) {
+            assayMetadata.Tables = Array.from(annotationTables);
+        }
+        assayMetadata.DataMap = datamapSheet;
+        return assayMetadata;
+    }
+    catch (err) {
+        const arg_2 = err.message;
+        return (0, String_js_1.toFail)((0, String_js_1.printf)("Could not parse assay: \n%s"))(arg_2);
+    }
+}
+/**
+ * Write an assay to a spreadsheet
+ *
+ * If datamapSheet is true, the datamap will be written to a worksheet inside assay workbook.
+ */
+function ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(assay, datamapSheet) {
+    const datamapSheet_1 = (0, Option_js_1.defaultArg)(datamapSheet, true);
+    const doc = new FsWorkbook_fs_js_1.FsWorkbook();
+    const metadataSheet = ArcAssay_toMetadataSheet(assay);
+    doc.AddWorksheet(metadataSheet);
+    if (datamapSheet_1) {
+        (0, Seq_js_1.iterate)((arg) => {
+            const sheet = (0, DataMapTable_js_1.toFsWorksheet)(arg);
+            doc.AddWorksheet(sheet);
+        }, (0, Option_js_1.toArray)(assay.DataMap));
+    }
+    (0, Seq_js_1.iterateIndexed)((i, arg_1) => {
+        const sheet_1 = (0, ArcTable_js_1.toFsWorksheet)(i, arg_1);
+        doc.AddWorksheet(sheet_1);
+    }, assay.Tables);
+    return doc;
+}
+/**
+ * Write an assay to a spreadsheet
+ *
+ * If datamapSheet is true, the datamap will be written to a worksheet inside assay workbook.
+ */
+function ARCtrl_ArcAssay__ArcAssay_ToFsWorkbook_6FCE9E49(this$, datamapSheet) {
+    return ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(this$, (0, Option_js_1.unwrap)(datamapSheet));
+}

package/dist/ts/cjs/ts/Spreadsheet/ArcInvestigation.js

@@ -0,0 +1,340 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ArcInvestigation_InvestigationInfo = void 0;
+exports.ArcInvestigation_InvestigationInfo_$reflection = ArcInvestigation_InvestigationInfo_$reflection;
+exports.ArcInvestigation_InvestigationInfo_create = ArcInvestigation_InvestigationInfo_create;
+exports.ArcInvestigation_InvestigationInfo_get_Labels = ArcInvestigation_InvestigationInfo_get_Labels;
+exports.ArcInvestigation_InvestigationInfo_FromSparseTable_3ECCA699 = ArcInvestigation_InvestigationInfo_FromSparseTable_3ECCA699;
+exports.ArcInvestigation_InvestigationInfo_ToSparseTable_Z720BD3FF = ArcInvestigation_InvestigationInfo_ToSparseTable_Z720BD3FF;
+exports.ArcInvestigation_InvestigationInfo_fromRows = ArcInvestigation_InvestigationInfo_fromRows;
+exports.ArcInvestigation_InvestigationInfo_toRows_Z720BD3FF = ArcInvestigation_InvestigationInfo_toRows_Z720BD3FF;
+exports.ArcInvestigation_fromParts = ArcInvestigation_fromParts;
+exports.ArcInvestigation_fromRows = ArcInvestigation_fromRows;
+exports.ArcInvestigation_toRows = ArcInvestigation_toRows;
+exports.ArcInvestigation_toMetadataCollection = ArcInvestigation_toMetadataCollection;
+exports.ArcInvestigation_fromMetadataCollection = ArcInvestigation_fromMetadataCollection;
+exports.ArcInvestigation_isMetadataSheetName = ArcInvestigation_isMetadataSheetName;
+exports.ArcInvestigation_isMetadataSheet = ArcInvestigation_isMetadataSheet;
+exports.ArcInvestigation_tryGetMetadataSheet = ArcInvestigation_tryGetMetadataSheet;
+exports.ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D = ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D;
+exports.ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF = ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF;
+exports.ARCtrl_ArcInvestigation__ArcInvestigation_ToFsWorkbook = ARCtrl_ArcInvestigation__ArcInvestigation_ToFsWorkbook;
+const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Comment_js_1 = require("../Core/Comment.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+const Reflection_js_1 = require("@fable-org/fable-library-js/Reflection.js");
+const Comment_js_2 = require("./Metadata/Comment.js");
+const SparseTable_js_1 = require("./Metadata/SparseTable.js");
+const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Collections_js_1 = require("../Core/Helper/Collections.js");
+const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
+const ArcTypes_js_1 = require("../Core/ArcTypes.js");
+const OntologySourceReference_js_1 = require("./Metadata/OntologySourceReference.js");
+const Publication_js_1 = require("./Metadata/Publication.js");
+const Contacts_js_1 = require("./Metadata/Contacts.js");
+const Study_js_1 = require("./Metadata/Study.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Map_js_1 = require("@fable-org/fable-library-js/Map.js");
+const FsWorksheet_fs_js_1 = require("../fable_modules/FsSpreadsheet.6.3.1/FsWorksheet.fs.js");
+const FsWorkbook_fs_js_1 = require("../fable_modules/FsSpreadsheet.6.3.1/FsWorkbook.fs.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+class ArcInvestigation_InvestigationInfo extends Types_js_1.Record {
+    constructor(Identifier, Title, Description, SubmissionDate, PublicReleaseDate, Comments) {
+        super();
+        this.Identifier = Identifier;
+        this.Title = Title;
+        this.Description = Description;
+        this.SubmissionDate = SubmissionDate;
+        this.PublicReleaseDate = PublicReleaseDate;
+        this.Comments = Comments;
+    }
+}
+exports.ArcInvestigation_InvestigationInfo = ArcInvestigation_InvestigationInfo;
+function ArcInvestigation_InvestigationInfo_$reflection() {
+    return (0, Reflection_js_1.record_type)("ARCtrl.Spreadsheet.ArcInvestigation.InvestigationInfo", [], ArcInvestigation_InvestigationInfo, () => [["Identifier", Reflection_js_1.string_type], ["Title", Reflection_js_1.string_type], ["Description", Reflection_js_1.string_type], ["SubmissionDate", Reflection_js_1.string_type], ["PublicReleaseDate", Reflection_js_1.string_type], ["Comments", (0, Reflection_js_1.list_type)((0, Comment_js_1.Comment$_$reflection)())]]);
+}
+function ArcInvestigation_InvestigationInfo_create(identifier, title, description, submissionDate, publicReleaseDate, comments) {
+    return new ArcInvestigation_InvestigationInfo(identifier, title, description, submissionDate, publicReleaseDate, comments);
+}
+function ArcInvestigation_InvestigationInfo_get_Labels() {
+    return (0, List_js_1.ofArray)(["Investigation Identifier", "Investigation Title", "Investigation Description", "Investigation Submission Date", "Investigation Public Release Date"]);
+}
+function ArcInvestigation_InvestigationInfo_FromSparseTable_3ECCA699(matrix) {
+    const comments = (0, List_js_1.map)((k) => (0, Comment_js_2.Comment_fromString)(k, (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [k, 0])), matrix.CommentKeys);
+    return ArcInvestigation_InvestigationInfo_create((0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", ["Investigation Identifier", 0]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", ["Investigation Title", 0]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", ["Investigation Description", 0]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", ["Investigation Submission Date", 0]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", ["Investigation Public Release Date", 0]), comments);
+}
+function ArcInvestigation_InvestigationInfo_ToSparseTable_Z720BD3FF(investigation) {
+    const matrix = (0, SparseTable_js_1.SparseTable_Create_Z2192E64B)(undefined, ArcInvestigation_InvestigationInfo_get_Labels(), undefined, 2);
+    let commentKeys = (0, List_js_1.empty)();
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Investigation Identifier", 1], investigation.Identifier);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Investigation Title", 1], (0, Option_js_1.defaultArg)(investigation.Title, ""));
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Investigation Description", 1], (0, Option_js_1.defaultArg)(investigation.Description, ""));
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Investigation Submission Date", 1], (0, Option_js_1.defaultArg)(investigation.SubmissionDate, ""));
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Investigation Public Release Date", 1], (0, Option_js_1.defaultArg)(investigation.PublicReleaseDate, ""));
+    (0, Collections_js_1.ResizeArray_iter)((comment) => {
+        const patternInput = (0, Comment_js_2.Comment_toString)(comment);
+        const n = patternInput[0];
+        commentKeys = (0, List_js_1.cons)(n, commentKeys);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [n, 1], patternInput[1]);
+    }, investigation.Comments);
+    return new SparseTable_js_1.SparseTable(matrix.Matrix, matrix.Keys, (0, List_js_1.reverse)((0, Seq2_js_1.List_distinct)(commentKeys, {
+        Equals: (x, y) => (x === y),
+        GetHashCode: Util_js_1.stringHash,
+    })), matrix.ColumnCount);
+}
+function ArcInvestigation_InvestigationInfo_fromRows(lineNumber, rows) {
+    const tupledArg = (0, SparseTable_js_1.SparseTable_FromRows_Z5579EC29)(rows, ArcInvestigation_InvestigationInfo_get_Labels(), lineNumber);
+    return [tupledArg[0], tupledArg[1], tupledArg[2], ArcInvestigation_InvestigationInfo_FromSparseTable_3ECCA699(tupledArg[3])];
+}
+function ArcInvestigation_InvestigationInfo_toRows_Z720BD3FF(investigation) {
+    return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(ArcInvestigation_InvestigationInfo_ToSparseTable_Z720BD3FF(investigation));
+}
+function ArcInvestigation_fromParts(investigationInfo, ontologySourceReference, publications, contacts, studies, assays, remarks) {
+    const studyIdentifiers = (0, List_js_1.map)((s) => s.Identifier, studies);
+    const title = (0, Collections_js_1.Option_fromValueWithDefault)("", investigationInfo.Title);
+    const description = (0, Collections_js_1.Option_fromValueWithDefault)("", investigationInfo.Description);
+    const submissionDate = (0, Collections_js_1.Option_fromValueWithDefault)("", investigationInfo.SubmissionDate);
+    const publicReleaseDate = (0, Collections_js_1.Option_fromValueWithDefault)("", investigationInfo.PublicReleaseDate);
+    const ontologySourceReferences = Array.from(ontologySourceReference);
+    const publications_1 = Array.from(publications);
+    const contacts_1 = Array.from(contacts);
+    const assays_1 = Array.from(assays);
+    const studies_1 = Array.from(studies);
+    const registeredStudyIdentifiers = Array.from(studyIdentifiers);
+    const comments = Array.from(investigationInfo.Comments);
+    const remarks_1 = Array.from(remarks);
+    return ArcTypes_js_1.ArcInvestigation.make(investigationInfo.Identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications_1, contacts_1, assays_1, studies_1, [], [], registeredStudyIdentifiers, comments, remarks_1);
+}
+function ArcInvestigation_fromRows(rows) {
+    const en = (0, Util_js_1.getEnumerator)(rows);
+    const emptyInvestigationInfo = ArcInvestigation_InvestigationInfo_create("", "", "", "", "", (0, List_js_1.empty)());
+    const loop = (lastLine_mut, ontologySourceReferences_mut, investigationInfo_mut, publications_mut, contacts_mut, studies_mut, remarks_mut, lineNumber_mut) => {
+        loop: while (true) {
+            const lastLine = lastLine_mut, ontologySourceReferences = ontologySourceReferences_mut, investigationInfo = investigationInfo_mut, publications = publications_mut, contacts = contacts_mut, studies = studies_mut, remarks = remarks_mut, lineNumber = lineNumber_mut;
+            let matchResult, k_5, k_6, k_7, k_8, k_9;
+            if (lastLine != null) {
+                switch ((0, Option_js_1.value)(lastLine)) {
+                    case "ONTOLOGY SOURCE REFERENCE": {
+                        matchResult = 0;
+                        k_5 = (0, Option_js_1.value)(lastLine);
+                        break;
+                    }
+                    case "INVESTIGATION": {
+                        matchResult = 1;
+                        k_6 = (0, Option_js_1.value)(lastLine);
+                        break;
+                    }
+                    case "INVESTIGATION PUBLICATIONS": {
+                        matchResult = 2;
+                        k_7 = (0, Option_js_1.value)(lastLine);
+                        break;
+                    }
+                    case "INVESTIGATION CONTACTS": {
+                        matchResult = 3;
+                        k_8 = (0, Option_js_1.value)(lastLine);
+                        break;
+                    }
+                    case "STUDY": {
+                        matchResult = 4;
+                        k_9 = (0, Option_js_1.value)(lastLine);
+                        break;
+                    }
+                    default:
+                        matchResult = 5;
+                }
+            }
+            else {
+                matchResult = 5;
+            }
+            switch (matchResult) {
+                case 0: {
+                    const patternInput = (0, OntologySourceReference_js_1.fromRows)(lineNumber + 1, en);
+                    lastLine_mut = patternInput[0];
+                    ontologySourceReferences_mut = patternInput[3];
+                    investigationInfo_mut = investigationInfo;
+                    publications_mut = publications;
+                    contacts_mut = contacts;
+                    studies_mut = studies;
+                    remarks_mut = (0, List_js_1.append)(remarks, patternInput[2]);
+                    lineNumber_mut = patternInput[1];
+                    continue loop;
+                }
+                case 1: {
+                    const patternInput_1 = ArcInvestigation_InvestigationInfo_fromRows(lineNumber + 1, en);
+                    lastLine_mut = patternInput_1[0];
+                    ontologySourceReferences_mut = ontologySourceReferences;
+                    investigationInfo_mut = patternInput_1[3];
+                    publications_mut = publications;
+                    contacts_mut = contacts;
+                    studies_mut = studies;
+                    remarks_mut = (0, List_js_1.append)(remarks, patternInput_1[2]);
+                    lineNumber_mut = patternInput_1[1];
+                    continue loop;
+                }
+                case 2: {
+                    const patternInput_2 = (0, Publication_js_1.fromRows)("Investigation Publication", lineNumber + 1, en);
+                    lastLine_mut = patternInput_2[0];
+                    ontologySourceReferences_mut = ontologySourceReferences;
+                    investigationInfo_mut = investigationInfo;
+                    publications_mut = patternInput_2[3];
+                    contacts_mut = contacts;
+                    studies_mut = studies;
+                    remarks_mut = (0, List_js_1.append)(remarks, patternInput_2[2]);
+                    lineNumber_mut = patternInput_2[1];
+                    continue loop;
+                }
+                case 3: {
+                    const patternInput_3 = (0, Contacts_js_1.fromRows)("Investigation Person", lineNumber + 1, en);
+                    lastLine_mut = patternInput_3[0];
+                    ontologySourceReferences_mut = ontologySourceReferences;
+                    investigationInfo_mut = investigationInfo;
+                    publications_mut = publications;
+                    contacts_mut = patternInput_3[3];
+                    studies_mut = studies;
+                    remarks_mut = (0, List_js_1.append)(remarks, patternInput_3[2]);
+                    lineNumber_mut = patternInput_3[1];
+                    continue loop;
+                }
+                case 4: {
+                    const patternInput_4 = (0, Study_js_1.fromRows)(lineNumber + 1, en);
+                    const study = patternInput_4[3];
+                    const newRemarks_4 = patternInput_4[2];
+                    const lineNumber_6 = patternInput_4[1] | 0;
+                    const currentLine_4 = patternInput_4[0];
+                    if (study != null) {
+                        lastLine_mut = currentLine_4;
+                        ontologySourceReferences_mut = ontologySourceReferences;
+                        investigationInfo_mut = investigationInfo;
+                        publications_mut = publications;
+                        contacts_mut = contacts;
+                        studies_mut = (0, List_js_1.cons)((0, Option_js_1.value)(study), studies);
+                        remarks_mut = (0, List_js_1.append)(remarks, newRemarks_4);
+                        lineNumber_mut = lineNumber_6;
+                        continue loop;
+                    }
+                    else {
+                        lastLine_mut = currentLine_4;
+                        ontologySourceReferences_mut = ontologySourceReferences;
+                        investigationInfo_mut = investigationInfo;
+                        publications_mut = publications;
+                        contacts_mut = contacts;
+                        studies_mut = studies;
+                        remarks_mut = (0, List_js_1.append)(remarks, newRemarks_4);
+                        lineNumber_mut = lineNumber_6;
+                        continue loop;
+                    }
+                }
+                default: {
+                    let patternInput_5;
+                    const tupledArg = (0, List_js_1.unzip)(studies);
+                    patternInput_5 = [(0, List_js_1.reverse)(tupledArg[0]), (0, Seq2_js_1.List_distinctBy)((a_1) => a_1.Identifier, (0, List_js_1.concat)(tupledArg[1]), {
+                            Equals: (x, y) => (x === y),
+                            GetHashCode: Util_js_1.stringHash,
+                        })];
+                    return ArcInvestigation_fromParts(investigationInfo, ontologySourceReferences, publications, contacts, patternInput_5[0], patternInput_5[1], remarks);
+                }
+            }
+            break;
+        }
+    };
+    if (en["System.Collections.IEnumerator.MoveNext"]()) {
+        return loop((0, SparseTable_js_1.SparseRowModule_tryGetValueAt)(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), (0, List_js_1.empty)(), emptyInvestigationInfo, (0, List_js_1.empty)(), (0, List_js_1.empty)(), (0, List_js_1.empty)(), (0, List_js_1.empty)(), 1);
+    }
+    else {
+        throw new Error("emptyInvestigationFile");
+    }
+}
+function ArcInvestigation_toRows(investigation) {
+    let remarks, rows;
+    return (remarks = (0, List_js_1.ofSeq)(investigation.Remarks), (rows = (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, SparseTable_js_1.SparseRowModule_fromValues)(["ONTOLOGY SOURCE REFERENCE"])), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, OntologySourceReference_js_1.toRows)((0, List_js_1.ofSeq)(investigation.OntologySourceReferences)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, SparseTable_js_1.SparseRowModule_fromValues)(["INVESTIGATION"])), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)(ArcInvestigation_InvestigationInfo_toRows_Z720BD3FF(investigation), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, SparseTable_js_1.SparseRowModule_fromValues)(["INVESTIGATION PUBLICATIONS"])), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Publication_js_1.toRows)("Investigation Publication", (0, List_js_1.ofSeq)(investigation.Publications)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, SparseTable_js_1.SparseRowModule_fromValues)(["INVESTIGATION CONTACTS"])), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Contacts_js_1.toRows)("Investigation Person", (0, List_js_1.ofSeq)(investigation.Contacts)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.collect)((studyIdentifier) => {
+        const study = (0, Option_js_1.defaultArg)(investigation.TryGetStudy(studyIdentifier), new ArcTypes_js_1.ArcStudy(studyIdentifier));
+        return (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, SparseTable_js_1.SparseRowModule_fromValues)(["STUDY"])), (0, Seq_js_1.delay)(() => (0, Study_js_1.toRows)(study, undefined)));
+    }, investigation.RegisteredStudyIdentifiers)))))))))))))))))), (() => {
+        try {
+            const rm = (0, Map_js_1.ofList)((0, List_js_1.map)((remark) => Comment_js_1.Remark.toTuple(remark), remarks), {
+                Compare: Util_js_1.comparePrimitives,
+            });
+            const loop = (i_mut, l_mut, nl_mut) => {
+                loop: while (true) {
+                    const i = i_mut, l = l_mut, nl = nl_mut;
+                    const matchValue = (0, Map_js_1.tryFind)(i, rm);
+                    if (matchValue == null) {
+                        if (!(0, List_js_1.isEmpty)(l)) {
+                            i_mut = (i + 1);
+                            l_mut = (0, List_js_1.tail)(l);
+                            nl_mut = (0, List_js_1.cons)((0, List_js_1.head)(l), nl);
+                            continue loop;
+                        }
+                        else {
+                            return nl;
+                        }
+                    }
+                    else {
+                        const remark_1 = (0, Option_js_1.value)(matchValue);
+                        i_mut = (i + 1);
+                        l_mut = l;
+                        nl_mut = (0, List_js_1.cons)((0, SparseTable_js_1.SparseRowModule_fromValues)([(0, Comment_js_2.Remark_wrapRemark)(remark_1)]), nl);
+                        continue loop;
+                    }
+                    break;
+                }
+            };
+            return (0, List_js_1.reverse)(loop(1, (0, List_js_1.ofSeq)(rows), (0, List_js_1.empty)()));
+        }
+        catch (matchValue_1) {
+            return (0, Seq_js_1.toList)(rows);
+        }
+    })()));
+}
+function ArcInvestigation_toMetadataCollection(investigation) {
+    return (0, Seq_js_1.map)(SparseTable_js_1.SparseRowModule_getAllValues, ArcInvestigation_toRows(investigation));
+}
+function ArcInvestigation_fromMetadataCollection(collection) {
+    return ArcInvestigation_fromRows((0, Seq_js_1.map)(SparseTable_js_1.SparseRowModule_fromAllValues, collection));
+}
+function ArcInvestigation_isMetadataSheetName(name) {
+    if (name === "isa_investigation") {
+        return true;
+    }
+    else {
+        return name === "Investigation";
+    }
+}
+function ArcInvestigation_isMetadataSheet(sheet) {
+    return ArcInvestigation_isMetadataSheetName(sheet.Name);
+}
+function ArcInvestigation_tryGetMetadataSheet(doc) {
+    return (0, Seq_js_1.tryFind)(ArcInvestigation_isMetadataSheet, doc.GetWorksheets());
+}
+function ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D(doc) {
+    let sheet_1, matchValue;
+    try {
+        return ArcInvestigation_fromRows((0, Seq_js_1.map)(SparseTable_js_1.SparseRowModule_fromFsRow, (sheet_1 = ((matchValue = ArcInvestigation_tryGetMetadataSheet(doc), (matchValue == null) ? (() => {
+            throw new Error("Could not find metadata sheet with sheetname \"isa_investigation\" or deprecated sheetname \"Investigation\"");
+        })() : (0, Option_js_1.value)(matchValue))), FsWorksheet_fs_js_1.FsWorksheet.getRows(sheet_1))));
+    }
+    catch (err) {
+        const arg = err.message;
+        return (0, String_js_1.toFail)((0, String_js_1.printf)("Could not read investigation from spreadsheet: %s"))(arg);
+    }
+}
+function ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(investigation) {
+    try {
+        const wb = new FsWorkbook_fs_js_1.FsWorkbook();
+        const sheet = new FsWorksheet_fs_js_1.FsWorksheet("isa_investigation");
+        (0, Seq_js_1.iterateIndexed)((rowI, r) => {
+            (0, SparseTable_js_1.SparseRowModule_writeToSheet)(rowI + 1, r, sheet);
+        }, ArcInvestigation_toRows(investigation));
+        wb.AddWorksheet(sheet);
+        return wb;
+    }
+    catch (err) {
+        const arg = err.message;
+        return (0, String_js_1.toFail)((0, String_js_1.printf)("Could not write investigation to spreadsheet: %s"))(arg);
+    }
+}
+function ARCtrl_ArcInvestigation__ArcInvestigation_ToFsWorkbook(this$) {
+    return ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(this$);
+}