@nfdi4plants/arctrl 2.5.1 → 3.0.0-alpha.2

package/dist/ts/cjs/ts/Spreadsheet/Metadata/Assays.js

@@ -0,0 +1,98 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.labels = void 0;
+exports.fromString = fromString;
+exports.fromSparseTable = fromSparseTable;
+exports.toSparseTable = toSparseTable;
+exports.fromRows = fromRows;
+exports.toRows = toRows;
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const OntologyAnnotation_js_1 = require("../../Core/OntologyAnnotation.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Identifier_js_1 = require("../../Core/Helper/Identifier.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
+const Conversion_js_1 = require("../../Core/Conversion.js");
+const ArcTypes_js_1 = require("../../Core/ArcTypes.js");
+const SparseTable_js_1 = require("./SparseTable.js");
+const Comment_js_1 = require("./Comment.js");
+const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+exports.labels = (0, List_js_1.ofArray)(["Identifier", "Title", "Description", "Measurement Type", "Measurement Type Term Accession Number", "Measurement Type Term Source REF", "Technology Type", "Technology Type Term Accession Number", "Technology Type Term Source REF", "Technology Platform", "File Name"]);
+function fromString(identifier, title, description, measurementType, measurementTypeTermSourceREF, measurementTypeTermAccessionNumber, technologyType, technologyTypeTermSourceREF, technologyTypeTermAccessionNumber, technologyPlatform, fileName, comments) {
+    const measurementType_1 = OntologyAnnotation_js_1.OntologyAnnotation.create((0, Option_js_1.unwrap)(measurementType), (0, Option_js_1.unwrap)(measurementTypeTermSourceREF), (0, Option_js_1.unwrap)(measurementTypeTermAccessionNumber));
+    const technologyType_1 = OntologyAnnotation_js_1.OntologyAnnotation.create((0, Option_js_1.unwrap)(technologyType), (0, Option_js_1.unwrap)(technologyTypeTermSourceREF), (0, Option_js_1.unwrap)(technologyTypeTermAccessionNumber));
+    let identifier_4;
+    if (identifier == null) {
+        if (fileName == null) {
+            identifier_4 = (0, Identifier_js_1.createMissingIdentifier)();
+        }
+        else {
+            const matchValue = (0, Identifier_js_1.Assay_tryIdentifierFromFileName)((0, Option_js_1.value)(fileName));
+            identifier_4 = ((matchValue != null) ? (0, Option_js_1.value)(matchValue) : (0, Identifier_js_1.createMissingIdentifier)());
+        }
+    }
+    else {
+        identifier_4 = (0, Option_js_1.value)(identifier);
+    }
+    const measurementType_2 = (0, Collections_js_1.Option_fromValueWithDefault)(new OntologyAnnotation_js_1.OntologyAnnotation(), measurementType_1);
+    const technologyType_2 = (0, Collections_js_1.Option_fromValueWithDefault)(new OntologyAnnotation_js_1.OntologyAnnotation(), technologyType_1);
+    const technologyPlatform_1 = (0, Option_js_1.map)(Conversion_js_1.JsonTypes_decomposeTechnologyPlatform, technologyPlatform);
+    return ArcTypes_js_1.ArcAssay.make(identifier_4, title, description, measurementType_2, technologyType_2, technologyPlatform_1, [], undefined, [], comments);
+}
+function fromSparseTable(matrix) {
+    if ((matrix.ColumnCount === 0) && ((0, List_js_1.length)(matrix.CommentKeys) !== 0)) {
+        const comments = (0, SparseTable_js_1.SparseTable_GetEmptyComments_3ECCA699)(matrix);
+        return (0, List_js_1.singleton)(ArcTypes_js_1.ArcAssay.create((0, Identifier_js_1.createMissingIdentifier)(), undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, comments));
+    }
+    else {
+        return (0, List_js_1.initialize)(matrix.ColumnCount, (i) => {
+            let comments_1;
+            const collection = (0, List_js_1.map)((k) => (0, Comment_js_1.Comment_fromString)(k, (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
+            return fromString((0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Identifier", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Title", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Description", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Measurement Type", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Measurement Type Term Source REF", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Measurement Type Term Accession Number", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Technology Type", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Technology Type Term Source REF", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Technology Type Term Accession Number", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Technology Platform", i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["File Name", i]), comments_1);
+        });
+    }
+}
+function toSparseTable(assays) {
+    const matrix = (0, SparseTable_js_1.SparseTable_Create_Z2192E64B)(undefined, exports.labels, undefined, (0, List_js_1.length)(assays) + 1);
+    let commentKeys = (0, List_js_1.empty)();
+    (0, List_js_1.iterateIndexed)((i, a) => {
+        const processedFileName = a.Identifier.startsWith("MISSING_IDENTIFIER_") ? (0, Identifier_js_1.removeMissingIdentifier)(a.Identifier) : (0, Identifier_js_1.Assay_fileNameFromIdentifier)(a.Identifier);
+        const i_1 = (i + 1) | 0;
+        let mt_1;
+        const mt = (0, Option_js_1.defaultArg)(a.MeasurementType, new OntologyAnnotation_js_1.OntologyAnnotation());
+        mt_1 = OntologyAnnotation_js_1.OntologyAnnotation.toStringObject(mt, true);
+        let tt_1;
+        const tt = (0, Option_js_1.defaultArg)(a.TechnologyType, new OntologyAnnotation_js_1.OntologyAnnotation());
+        tt_1 = OntologyAnnotation_js_1.OntologyAnnotation.toStringObject(tt, true);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Identifier", i_1], (0, Identifier_js_1.removeMissingIdentifier)(a.Identifier));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Title", i_1], (0, Option_js_1.defaultArg)(a.Title, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Description", i_1], (0, Option_js_1.defaultArg)(a.Description, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Measurement Type", i_1], mt_1.TermName);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Measurement Type Term Accession Number", i_1], mt_1.TermAccessionNumber);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Measurement Type Term Source REF", i_1], mt_1.TermSourceREF);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Technology Type", i_1], tt_1.TermName);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Technology Type Term Accession Number", i_1], tt_1.TermAccessionNumber);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Technology Type Term Source REF", i_1], tt_1.TermSourceREF);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Technology Platform", i_1], (0, Option_js_1.defaultArg)((0, Option_js_1.map)(Conversion_js_1.JsonTypes_composeTechnologyPlatform, a.TechnologyPlatform), ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["File Name", i_1], processedFileName);
+        (0, Collections_js_1.ResizeArray_iter)((comment) => {
+            const patternInput = (0, Comment_js_1.Comment_toString)(comment);
+            const n = patternInput[0];
+            commentKeys = (0, List_js_1.cons)(n, commentKeys);
+            (0, MapUtil_js_1.addToDict)(matrix.Matrix, [n, i_1], patternInput[1]);
+        }, a.Comments);
+    }, assays);
+    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 fromRows(prefix, lineNumber, rows) {
+    const tupledArg = (0, SparseTable_js_1.SparseTable_FromRows_Z5579EC29)(rows, exports.labels, lineNumber, (0, Option_js_1.unwrap)(prefix));
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(prefix, assays) {
+    return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(toSparseTable(assays), (0, Option_js_1.unwrap)(prefix));
+}

package/dist/ts/cjs/ts/Spreadsheet/Metadata/Comment.js

@@ -0,0 +1,68 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Remark_remarkPattern = exports.Remark_remarkValueKey = exports.Comment_commentPatternNoAngleBrackets = exports.Comment_commentPattern = exports.Comment_commentValueKey = void 0;
+exports.Comment_$007CComment$007C_$007C = Comment_$007CComment$007C_$007C;
+exports.Comment_wrapCommentKey = Comment_wrapCommentKey;
+exports.Comment_fromString = Comment_fromString;
+exports.Comment_toString = Comment_toString;
+exports.Remark_$007CRemark$007C_$007C = Remark_$007CRemark$007C_$007C;
+exports.Remark_wrapRemark = Remark_wrapRemark;
+const Regex_js_1 = require("../../Core/Helper/Regex.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const Conversions_js_1 = require("./Conversions.js");
+const Comment_js_1 = require("../../Core/Comment.js");
+exports.Comment_commentValueKey = "commentValue";
+exports.Comment_commentPattern = `Comment\\s*\\[<(?<${exports.Comment_commentValueKey}>.+)>\\]`;
+exports.Comment_commentPatternNoAngleBrackets = `Comment\\s*\\[(?<${exports.Comment_commentValueKey}>.+)\\]`;
+function Comment_$007CComment$007C_$007C(key) {
+    const activePatternResult = (0, Regex_js_1.ActivePatterns_$007CRegex$007C_$007C)(exports.Comment_commentPattern, key);
+    if (activePatternResult != null) {
+        const r = (0, Option_js_1.value)(activePatternResult);
+        return (r.groups && r.groups[exports.Comment_commentValueKey]) || "";
+    }
+    else {
+        const activePatternResult_1 = (0, Regex_js_1.ActivePatterns_$007CRegex$007C_$007C)(exports.Comment_commentPatternNoAngleBrackets, key);
+        if (activePatternResult_1 != null) {
+            const r_1 = (0, Option_js_1.value)(activePatternResult_1);
+            const v = (r_1.groups && r_1.groups[exports.Comment_commentValueKey]) || "";
+            if (v === "<>") {
+                return undefined;
+            }
+            else {
+                return v;
+            }
+        }
+        else {
+            return undefined;
+        }
+    }
+}
+function Comment_wrapCommentKey(k) {
+    return (0, String_js_1.toText)((0, String_js_1.printf)("Comment[%s]"))(k);
+}
+function Comment_fromString(k, v) {
+    const name = (0, Conversions_js_1.Option_fromValueWithDefault)("", k);
+    const value = (0, Conversions_js_1.Option_fromValueWithDefault)("", v);
+    return Comment_js_1.Comment$.make(name, value);
+}
+function Comment_toString(c) {
+    return [(0, Option_js_1.defaultArg)(c.Name, ""), (0, Option_js_1.defaultArg)(c.Value, "")];
+}
+exports.Remark_remarkValueKey = "remarkValue";
+exports.Remark_remarkPattern = `#(?<${exports.Remark_remarkValueKey}>.+)`;
+function Remark_$007CRemark$007C_$007C(key) {
+    return (0, Option_js_1.bind)((k) => {
+        const activePatternResult = (0, Regex_js_1.ActivePatterns_$007CRegex$007C_$007C)(exports.Remark_remarkPattern, k);
+        if (activePatternResult != null) {
+            const r = (0, Option_js_1.value)(activePatternResult);
+            return (r.groups && r.groups[exports.Remark_remarkValueKey]) || "";
+        }
+        else {
+            return undefined;
+        }
+    }, key);
+}
+function Remark_wrapRemark(r) {
+    return (0, String_js_1.toText)((0, String_js_1.printf)("#%s"))(r);
+}

package/dist/ts/cjs/ts/Spreadsheet/Metadata/Contacts.js

@@ -0,0 +1,92 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.labels = exports.rolesTermSourceREFLabel = exports.rolesTermAccessionNumberLabel = exports.rolesLabel = exports.affiliationLabel = exports.addressLabel = exports.faxLabel = exports.phoneLabel = exports.emailLabel = exports.midInitialsLabel = exports.firstNameLabel = exports.lastNameLabel = void 0;
+exports.fromString = fromString;
+exports.fromSparseTable = fromSparseTable;
+exports.toSparseTable = toSparseTable;
+exports.fromRows = fromRows;
+exports.toRows = toRows;
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Conversion_js_1 = require("../../Core/Conversion.js");
+const Conversions_js_1 = require("./Conversions.js");
+const Person_js_1 = require("../../Core/Person.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const SparseTable_js_1 = require("./SparseTable.js");
+const Comment_js_1 = require("./Comment.js");
+const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
+const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+exports.lastNameLabel = "Last Name";
+exports.firstNameLabel = "First Name";
+exports.midInitialsLabel = "Mid Initials";
+exports.emailLabel = "Email";
+exports.phoneLabel = "Phone";
+exports.faxLabel = "Fax";
+exports.addressLabel = "Address";
+exports.affiliationLabel = "Affiliation";
+exports.rolesLabel = "Roles";
+exports.rolesTermAccessionNumberLabel = "Roles Term Accession Number";
+exports.rolesTermSourceREFLabel = "Roles Term Source REF";
+exports.labels = (0, List_js_1.ofArray)([exports.lastNameLabel, exports.firstNameLabel, exports.midInitialsLabel, exports.emailLabel, exports.phoneLabel, exports.faxLabel, exports.addressLabel, exports.affiliationLabel, exports.rolesLabel, exports.rolesTermAccessionNumberLabel, exports.rolesTermSourceREFLabel]);
+function fromString(lastName, firstName, midInitials, email, phone, fax, address, affiliation, role, rolesTermAccessionNumber, rolesTermSourceREF, comments) {
+    let roles_1;
+    return (0, Conversion_js_1.Person_setOrcidFromComments)((roles_1 = (0, Conversions_js_1.OntologyAnnotation_fromAggregatedStrings)(";", role, rolesTermSourceREF, rolesTermAccessionNumber), Person_js_1.Person.make(undefined, lastName, firstName, midInitials, email, phone, fax, address, affiliation, roles_1, comments)));
+}
+function fromSparseTable(matrix) {
+    let returnVal;
+    if ((matrix.ColumnCount === 0) && ((0, List_js_1.length)(matrix.CommentKeys) !== 0)) {
+        const comments = (0, SparseTable_js_1.SparseTable_GetEmptyComments_3ECCA699)(matrix);
+        return (0, List_js_1.singleton)((returnVal = Person_js_1.Person.create(), (returnVal.Comments = comments, returnVal)));
+    }
+    else {
+        return (0, List_js_1.initialize)(matrix.ColumnCount, (i) => {
+            let comments_1;
+            const collection = (0, List_js_1.map)((k) => (0, Comment_js_1.Comment_fromString)(k, (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
+            return fromString((0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.lastNameLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.firstNameLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.midInitialsLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.emailLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.phoneLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.faxLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.addressLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.affiliationLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.rolesLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.rolesTermAccessionNumberLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.rolesTermSourceREFLabel, i]), comments_1);
+        });
+    }
+}
+function toSparseTable(persons) {
+    const matrix = (0, SparseTable_js_1.SparseTable_Create_Z2192E64B)(undefined, exports.labels, undefined, (0, List_js_1.length)(persons) + 1);
+    let commentKeys = (0, List_js_1.empty)();
+    (0, List_js_1.iterateIndexed)((i, p) => {
+        const i_1 = (i + 1) | 0;
+        const rAgg = (0, Conversions_js_1.OntologyAnnotation_toAggregatedStrings)(";", Array.from(p.Roles));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.lastNameLabel, i_1], (0, Option_js_1.defaultArg)(p.LastName, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.firstNameLabel, i_1], (0, Option_js_1.defaultArg)(p.FirstName, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.midInitialsLabel, i_1], (0, Option_js_1.defaultArg)(p.MidInitials, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.emailLabel, i_1], (0, Option_js_1.defaultArg)(p.EMail, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.phoneLabel, i_1], (0, Option_js_1.defaultArg)(p.Phone, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.faxLabel, i_1], (0, Option_js_1.defaultArg)(p.Fax, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.addressLabel, i_1], (0, Option_js_1.defaultArg)(p.Address, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.affiliationLabel, i_1], (0, Option_js_1.defaultArg)(p.Affiliation, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.rolesLabel, i_1], rAgg.TermNameAgg);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.rolesTermAccessionNumberLabel, i_1], rAgg.TermAccessionNumberAgg);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.rolesTermSourceREFLabel, i_1], rAgg.TermSourceREFAgg);
+        (0, Collections_js_1.ResizeArray_iter)((comment) => {
+            const patternInput = (0, Comment_js_1.Comment_toString)(comment);
+            const n = patternInput[0];
+            commentKeys = (0, List_js_1.cons)(n, commentKeys);
+            (0, MapUtil_js_1.addToDict)(matrix.Matrix, [n, i_1], patternInput[1]);
+        }, p.Comments);
+    }, (0, List_js_1.map)(Conversion_js_1.Person_setCommentFromORCID, persons));
+    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 fromRows(prefix, lineNumber, rows) {
+    const tupledArg = (0, SparseTable_js_1.SparseTable_FromRows_Z5579EC29)(rows, exports.labels, lineNumber, (0, Option_js_1.unwrap)(prefix));
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(prefix, persons) {
+    const m = toSparseTable(persons);
+    if (prefix == null) {
+        return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(m);
+    }
+    else {
+        return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(m, (0, Option_js_1.value)(prefix));
+    }
+}

package/dist/ts/cjs/ts/Spreadsheet/Metadata/Conversions.js

@@ -0,0 +1,187 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Option_fromValueWithDefault = Option_fromValueWithDefault;
+exports.Option_mapDefault = Option_mapDefault;
+exports.OntologyAnnotation_getLengthOfAggregatedStrings = OntologyAnnotation_getLengthOfAggregatedStrings;
+exports.OntologyAnnotation_fromAggregatedStrings = OntologyAnnotation_fromAggregatedStrings;
+exports.OntologyAnnotation_toAggregatedStrings = OntologyAnnotation_toAggregatedStrings;
+exports.Component_fromAggregatedStrings = Component_fromAggregatedStrings;
+exports.Component_toAggregatedStrings = Component_toAggregatedStrings;
+exports.ProtocolParameter_fromAggregatedStrings = ProtocolParameter_fromAggregatedStrings;
+exports.ProtocolParameter_toAggregatedStrings = ProtocolParameter_toAggregatedStrings;
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const OntologyAnnotation_js_1 = require("../../Core/OntologyAnnotation.js");
+const Component_js_1 = require("../../Core/Process/Component.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const CollectionAux_js_1 = require("../CollectionAux.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
+const ProtocolParameter_js_1 = require("../../Core/Process/ProtocolParameter.js");
+/**
+ * If the value matches the default, a None is returned, else a Some is returned
+ */
+function Option_fromValueWithDefault(d, v) {
+    if ((0, Util_js_1.equals)(d, v)) {
+        return undefined;
+    }
+    else {
+        return (0, Option_js_1.some)(v);
+    }
+}
+/**
+ * Applies the function f on the value of the option if it exists, else applies it on the default value. If the result value matches the default, a None is returned
+ */
+function Option_mapDefault(d, f, o) {
+    return Option_fromValueWithDefault(d, (o == null) ? f(d) : f((0, Option_js_1.value)(o)));
+}
+/**
+ * Returns the length of a subpropertylist from the aggregated strings
+ *
+ * In ISATab format, some subproperties which are stored as lists in ISAJson are stored as semicolon delimited tables
+ *
+ * These strings should either contain the same number of semicolon delimited elements or be empty.
+ */
+function OntologyAnnotation_getLengthOfAggregatedStrings(separator, strings) {
+    return (0, Array_js_1.fold)((l, s) => {
+        if (s === "") {
+            return l | 0;
+        }
+        else if (l === 0) {
+            return s.split(separator).length | 0;
+        }
+        else if (l === s.split(separator).length) {
+            return l | 0;
+        }
+        else {
+            return (0, String_js_1.toFail)((0, String_js_1.printf)("The length of the aggregated string %s does not match the length of the others"))(s) | 0;
+        }
+    }, 0, strings);
+}
+/**
+ * Returns a list of ISAJson OntologyAnnotation objects from ISATab aggregated strings
+ */
+function OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions) {
+    const l = OntologyAnnotation_getLengthOfAggregatedStrings(separator, [terms, source, accessions]) | 0;
+    if (l === 0) {
+        return [];
+    }
+    else {
+        const collection = (0, Array_js_1.map3)((a, b, c) => OntologyAnnotation_js_1.OntologyAnnotation.create(a, b, c), (terms === "") ? (0, Array_js_1.fill)(new Array(l), 0, l, "") : terms.split(separator), (source === "") ? (0, Array_js_1.fill)(new Array(l), 0, l, "") : source.split(separator), (accessions === "") ? (0, Array_js_1.fill)(new Array(l), 0, l, "") : accessions.split(separator));
+        return Array.from(collection);
+    }
+}
+/**
+ * Returns the aggregated ISATab OntologyAnnotation Name, ontology source and Accession number from a list of ISAJson OntologyAnnotation objects
+ */
+function OntologyAnnotation_toAggregatedStrings(separator, oas) {
+    let first = true;
+    if ((0, Array_js_1.equalsWith)(Util_js_1.equals, oas, [])) {
+        return {
+            TermAccessionNumberAgg: "",
+            TermNameAgg: "",
+            TermSourceREFAgg: "",
+        };
+    }
+    else {
+        const tupledArg_1 = (0, Array_js_1.fold)((tupledArg, term) => {
+            const matchValue = (0, Option_js_1.defaultArg)(term.Name, "");
+            const tsr = (0, Option_js_1.defaultArg)(term.TermSourceREF, "");
+            const tan = (0, Option_js_1.defaultArg)(term.TermAccessionNumber, "");
+            const name = matchValue;
+            if (first) {
+                first = false;
+                return [name, tsr, tan];
+            }
+            else {
+                return [(0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[0])(separator)(name), (0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[1])(separator)(tsr), (0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[2])(separator)(tan)];
+            }
+        }, ["", "", ""], oas);
+        return {
+            TermAccessionNumberAgg: tupledArg_1[2],
+            TermNameAgg: tupledArg_1[0],
+            TermSourceREFAgg: tupledArg_1[1],
+        };
+    }
+}
+/**
+ * Returns a list of ISAJson Component objects from ISATab aggregated strings
+ */
+function Component_fromAggregatedStrings(separator, names, terms, source, accessions) {
+    const l = OntologyAnnotation_getLengthOfAggregatedStrings(separator, [names, terms, source, accessions]) | 0;
+    if (l === 0) {
+        return (0, List_js_1.empty)();
+    }
+    else {
+        return (0, List_js_1.ofArray)((0, CollectionAux_js_1.Array_map4)(Component_js_1.Component_fromISAString_7C9A7CF8, (names === "") ? (0, Array_js_1.fill)(new Array(l), 0, l, "") : names.split(separator), (terms === "") ? (0, Array_js_1.fill)(new Array(l), 0, l, "") : terms.split(separator), (source === "") ? (0, Array_js_1.fill)(new Array(l), 0, l, "") : source.split(separator), (accessions === "") ? (0, Array_js_1.fill)(new Array(l), 0, l, "") : accessions.split(separator)));
+    }
+}
+/**
+ * Returns the aggregated ISATAb Component Name, Ontology Annotation value, Accession number and ontology source from a list of ISAJson Component objects
+ */
+function Component_toAggregatedStrings(separator, cs) {
+    let first = true;
+    if ((0, Util_js_1.equals)(cs, (0, List_js_1.empty)())) {
+        return {
+            NameAgg: "",
+            TermAccessionNumberAgg: "",
+            TermNameAgg: "",
+            TermSourceREFAgg: "",
+        };
+    }
+    else {
+        const tupledArg_2 = (0, List_js_1.fold)((tupledArg, tupledArg_1) => {
+            const name = tupledArg_1[0];
+            const term = tupledArg_1[1];
+            if (first) {
+                first = false;
+                return [name, term.TermName, term.TermSourceREF, term.TermAccessionNumber];
+            }
+            else {
+                return [(0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[0])(separator)(name), (0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[1])(separator)(term.TermName), (0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[2])(separator)(term.TermSourceREF), (0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[3])(separator)(term.TermAccessionNumber)];
+            }
+        }, ["", "", "", ""], (0, List_js_1.map)(Component_js_1.Component_toStringObject_Z685B8F25, cs));
+        return {
+            NameAgg: tupledArg_2[0],
+            TermAccessionNumberAgg: tupledArg_2[3],
+            TermNameAgg: tupledArg_2[1],
+            TermSourceREFAgg: tupledArg_2[2],
+        };
+    }
+}
+/**
+ * Returns a list of ISAJson ProtocolParameter objects from ISATab aggregated strings
+ */
+function ProtocolParameter_fromAggregatedStrings(separator, terms, source, accessions) {
+    return (0, Collections_js_1.ResizeArray_map)((arg) => ((parameterName) => ProtocolParameter_js_1.ProtocolParameter.make(undefined, parameterName))(arg), OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions));
+}
+/**
+ * Returns the aggregated ISATAb Ontology Annotation value, Accession number and ontology source from a list of ISAJson ProtocolParameter objects
+ */
+function ProtocolParameter_toAggregatedStrings(separator, oas) {
+    let first = true;
+    if ((0, Util_js_1.equals)(oas, (0, List_js_1.empty)())) {
+        return {
+            TermAccessionNumberAgg: "",
+            TermNameAgg: "",
+            TermSourceREFAgg: "",
+        };
+    }
+    else {
+        const tupledArg_1 = (0, List_js_1.fold)((tupledArg, term) => {
+            if (first) {
+                first = false;
+                return [term.TermName, term.TermSourceREF, term.TermAccessionNumber];
+            }
+            else {
+                return [(0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[0])(separator)(term.TermName), (0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[1])(separator)(term.TermSourceREF), (0, String_js_1.toText)((0, String_js_1.printf)("%s%c%s"))(tupledArg[2])(separator)(term.TermAccessionNumber)];
+            }
+        }, ["", "", ""], (0, List_js_1.map)((pp) => ProtocolParameter_js_1.ProtocolParameter.toStringObject(pp), oas));
+        return {
+            TermAccessionNumberAgg: tupledArg_1[2],
+            TermNameAgg: tupledArg_1[0],
+            TermSourceREFAgg: tupledArg_1[1],
+        };
+    }
+}

package/dist/ts/cjs/ts/Spreadsheet/Metadata/DesignDescriptors.js

@@ -0,0 +1,25 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.labels = exports.designTypeTermSourceREFLabel = exports.designTypeTermAccessionNumberLabel = exports.designTypeLabel = void 0;
+exports.fromSparseTable = fromSparseTable;
+exports.toSparseTable = toSparseTable;
+exports.fromRows = fromRows;
+exports.toRows = toRows;
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const OntologyAnnotation_js_1 = require("./OntologyAnnotation.js");
+exports.designTypeLabel = "Type";
+exports.designTypeTermAccessionNumberLabel = "Type Term Accession Number";
+exports.designTypeTermSourceREFLabel = "Type Term Source REF";
+exports.labels = (0, List_js_1.ofArray)([exports.designTypeLabel, exports.designTypeTermAccessionNumberLabel, exports.designTypeTermSourceREFLabel]);
+function fromSparseTable(matrix) {
+    return (0, OntologyAnnotation_js_1.fromSparseTable)(exports.designTypeLabel, exports.designTypeTermSourceREFLabel, exports.designTypeTermAccessionNumberLabel, matrix);
+}
+function toSparseTable(designs) {
+    return (0, OntologyAnnotation_js_1.toSparseTable)(exports.designTypeLabel, exports.designTypeTermSourceREFLabel, exports.designTypeTermAccessionNumberLabel, designs);
+}
+function fromRows(prefix, lineNumber, rows) {
+    return (0, OntologyAnnotation_js_1.fromRows)(prefix, exports.designTypeLabel, exports.designTypeTermSourceREFLabel, exports.designTypeTermAccessionNumberLabel, lineNumber, rows);
+}
+function toRows(prefix, designs) {
+    return (0, OntologyAnnotation_js_1.toRows)(prefix, exports.designTypeLabel, exports.designTypeTermSourceREFLabel, exports.designTypeTermAccessionNumberLabel, designs);
+}

package/dist/ts/cjs/ts/Spreadsheet/Metadata/Factors.js

@@ -0,0 +1,83 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.labels = exports.typeTermSourceREFLabel = exports.typeTermAccessionNumberLabel = exports.factorTypeLabel = exports.nameLabel = void 0;
+exports.fromString = fromString;
+exports.fromSparseTable = fromSparseTable;
+exports.toSparseTable = toSparseTable;
+exports.fromRows = fromRows;
+exports.toRows = toRows;
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const OntologyAnnotation_js_1 = require("../../Core/OntologyAnnotation.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
+const Factor_js_1 = require("../../Core/Process/Factor.js");
+const SparseTable_js_1 = require("./SparseTable.js");
+const Comment_js_1 = require("./Comment.js");
+const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+exports.nameLabel = "Name";
+exports.factorTypeLabel = "Type";
+exports.typeTermAccessionNumberLabel = "Type Term Accession Number";
+exports.typeTermSourceREFLabel = "Type Term Source REF";
+exports.labels = (0, List_js_1.ofArray)([exports.nameLabel, exports.factorTypeLabel, exports.typeTermAccessionNumberLabel, exports.typeTermSourceREFLabel]);
+function fromString(name, designType, typeTermSourceREF, typeTermAccessionNumber, comments) {
+    const factorType = OntologyAnnotation_js_1.OntologyAnnotation.create((0, Option_js_1.unwrap)(designType), (0, Option_js_1.unwrap)(typeTermSourceREF), (0, Option_js_1.unwrap)(typeTermAccessionNumber));
+    const factorType_1 = (0, Collections_js_1.Option_fromValueWithDefault)(new OntologyAnnotation_js_1.OntologyAnnotation(), factorType);
+    const comments_1 = (0, Collections_js_1.Option_fromValueWithDefault)([], comments);
+    return Factor_js_1.Factor.make(name, factorType_1, comments_1);
+}
+function fromSparseTable(matrix) {
+    if ((matrix.ColumnCount === 0) && ((0, List_js_1.length)(matrix.CommentKeys) !== 0)) {
+        const comments = (0, SparseTable_js_1.SparseTable_GetEmptyComments_3ECCA699)(matrix);
+        return (0, List_js_1.singleton)(Factor_js_1.Factor.create(undefined, undefined, comments));
+    }
+    else {
+        return (0, List_js_1.initialize)(matrix.ColumnCount, (i) => {
+            let comments_1;
+            const collection = (0, List_js_1.map)((k) => (0, Comment_js_1.Comment_fromString)(k, (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
+            return fromString((0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.nameLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.factorTypeLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.typeTermSourceREFLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.typeTermAccessionNumberLabel, i]), comments_1);
+        });
+    }
+}
+function toSparseTable(factors) {
+    const matrix = (0, SparseTable_js_1.SparseTable_Create_Z2192E64B)(undefined, exports.labels, undefined, (0, List_js_1.length)(factors) + 1);
+    let commentKeys = (0, List_js_1.empty)();
+    (0, List_js_1.iterateIndexed)((i, f) => {
+        const i_1 = (i + 1) | 0;
+        let ft;
+        const f_1 = (0, Option_js_1.defaultArg)(f.FactorType, new OntologyAnnotation_js_1.OntologyAnnotation());
+        ft = OntologyAnnotation_js_1.OntologyAnnotation.toStringObject(f_1, true);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.nameLabel, i_1], (0, Option_js_1.defaultArg)(f.Name, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.factorTypeLabel, i_1], ft.TermName);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.typeTermAccessionNumberLabel, i_1], ft.TermAccessionNumber);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.typeTermSourceREFLabel, i_1], ft.TermSourceREF);
+        const matchValue = f.Comments;
+        if (matchValue != null) {
+            (0, Collections_js_1.ResizeArray_iter)((comment) => {
+                const patternInput = (0, Comment_js_1.Comment_toString)(comment);
+                const n = patternInput[0];
+                commentKeys = (0, List_js_1.cons)(n, commentKeys);
+                (0, MapUtil_js_1.addToDict)(matrix.Matrix, [n, i_1], patternInput[1]);
+            }, (0, Option_js_1.value)(matchValue));
+        }
+    }, factors);
+    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 fromRows(prefix, lineNumber, rows) {
+    const tupledArg = (prefix == null) ? (0, SparseTable_js_1.SparseTable_FromRows_Z5579EC29)(rows, exports.labels, lineNumber) : (0, SparseTable_js_1.SparseTable_FromRows_Z5579EC29)(rows, exports.labels, lineNumber, (0, Option_js_1.value)(prefix));
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(prefix, factors) {
+    const m = toSparseTable(factors);
+    if (prefix == null) {
+        return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(m);
+    }
+    else {
+        return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(m, (0, Option_js_1.value)(prefix));
+    }
+}

package/dist/ts/cjs/ts/Spreadsheet/Metadata/OntologyAnnotation.js

@@ -0,0 +1,65 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fromSparseTable = fromSparseTable;
+exports.toSparseTable = toSparseTable;
+exports.fromRows = fromRows;
+exports.toRows = toRows;
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const SparseTable_js_1 = require("./SparseTable.js");
+const OntologyAnnotation_js_1 = require("../../Core/OntologyAnnotation.js");
+const Comment_js_1 = require("./Comment.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
+const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+function fromSparseTable(label, labelTSR, labelTAN, matrix) {
+    let returnVal;
+    if ((matrix.ColumnCount === 0) && ((0, List_js_1.length)(matrix.CommentKeys) !== 0)) {
+        const comments = (0, SparseTable_js_1.SparseTable_GetEmptyComments_3ECCA699)(matrix);
+        return (0, List_js_1.singleton)((returnVal = OntologyAnnotation_js_1.OntologyAnnotation.create(), (returnVal.Comments = comments, returnVal)));
+    }
+    else {
+        return (0, List_js_1.initialize)(matrix.ColumnCount, (i) => {
+            let comments_1;
+            const collection = (0, List_js_1.map)((k) => (0, Comment_js_1.Comment_fromString)(k, (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
+            return new OntologyAnnotation_js_1.OntologyAnnotation((0, Option_js_1.unwrap)((0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [label, i])), (0, Option_js_1.unwrap)((0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [labelTSR, i])), (0, Option_js_1.unwrap)((0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [labelTAN, i])), comments_1);
+        });
+    }
+}
+function toSparseTable(label, labelTSR, labelTAN, designs) {
+    const matrix = (0, SparseTable_js_1.SparseTable_Create_Z2192E64B)(undefined, (0, List_js_1.ofArray)([label, labelTAN, labelTSR]), undefined, (0, List_js_1.length)(designs) + 1);
+    let commentKeys = (0, List_js_1.empty)();
+    (0, List_js_1.iterateIndexed)((i, d) => {
+        const i_1 = (i + 1) | 0;
+        const oa = OntologyAnnotation_js_1.OntologyAnnotation.toStringObject(d, true);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [label, i_1], oa.TermName);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [labelTAN, i_1], oa.TermAccessionNumber);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [labelTSR, i_1], oa.TermSourceREF);
+        (0, Collections_js_1.ResizeArray_iter)((comment) => {
+            const patternInput = (0, Comment_js_1.Comment_toString)(comment);
+            const n = patternInput[0];
+            commentKeys = (0, List_js_1.cons)(n, commentKeys);
+            (0, MapUtil_js_1.addToDict)(matrix.Matrix, [n, i_1], patternInput[1]);
+        }, d.Comments);
+    }, designs);
+    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 fromRows(prefix, label, labelTSR, labelTAN, lineNumber, rows) {
+    const labels = (0, List_js_1.ofArray)([label, labelTAN, labelTSR]);
+    const tupledArg = (prefix == null) ? (0, SparseTable_js_1.SparseTable_FromRows_Z5579EC29)(rows, labels, lineNumber) : (0, SparseTable_js_1.SparseTable_FromRows_Z5579EC29)(rows, labels, lineNumber, (0, Option_js_1.value)(prefix));
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(label, labelTSR, labelTAN, tupledArg[3])];
+}
+function toRows(prefix, label, labelTSR, labelTAN, designs) {
+    const m = toSparseTable(label, labelTSR, labelTAN, designs);
+    if (prefix == null) {
+        return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(m);
+    }
+    else {
+        return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(m, (0, Option_js_1.value)(prefix));
+    }
+}