@nfdi4plants/arctrl 2.5.0 → 3.0.0-alpha.1

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

@@ -0,0 +1,68 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.labels = exports.descriptionLabel = exports.versionLabel = exports.fileLabel = 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 OntologySourceReference_js_1 = require("../../Core/OntologySourceReference.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.nameLabel = "Term Source Name";
+exports.fileLabel = "Term Source File";
+exports.versionLabel = "Term Source Version";
+exports.descriptionLabel = "Term Source Description";
+exports.labels = (0, List_js_1.ofArray)([exports.nameLabel, exports.fileLabel, exports.versionLabel, exports.descriptionLabel]);
+function fromString(description, file, name, version, comments) {
+    return OntologySourceReference_js_1.OntologySourceReference.make(description, file, name, version, 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 = OntologySourceReference_js_1.OntologySourceReference.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.descriptionLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.fileLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.nameLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.versionLabel, i]), comments_1);
+        });
+    }
+}
+function toSparseTable(ontologySources) {
+    const matrix = (0, SparseTable_js_1.SparseTable_Create_Z2192E64B)(undefined, exports.labels, undefined, (0, List_js_1.length)(ontologySources) + 1);
+    let commentKeys = (0, List_js_1.empty)();
+    (0, List_js_1.iterateIndexed)((i, o) => {
+        const i_1 = (i + 1) | 0;
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.nameLabel, i_1], (0, Option_js_1.defaultArg)(o.Name, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.fileLabel, i_1], (0, Option_js_1.defaultArg)(o.File, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.versionLabel, i_1], (0, Option_js_1.defaultArg)(o.Version, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.descriptionLabel, i_1], (0, Option_js_1.defaultArg)(o.Description, ""));
+        (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]);
+        }, o.Comments);
+    }, ontologySources);
+    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(lineNumber, rows) {
+    const tupledArg = (0, SparseTable_js_1.SparseTable_FromRows_Z5579EC29)(rows, exports.labels, lineNumber);
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(termSources) {
+    return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(toSparseTable(termSources));
+}

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

@@ -0,0 +1,103 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.labels = exports.componentsTypeTermSourceREFLabel = exports.componentsTypeTermAccessionNumberLabel = exports.componentsTypeLabel = exports.componentsNameLabel = exports.parametersTermSourceREFLabel = exports.parametersTermAccessionNumberLabel = exports.parametersNameLabel = exports.versionLabel = exports.uriLabel = exports.descriptionLabel = exports.typeTermSourceREFLabel = exports.typeTermAccessionNumberLabel = exports.protocolTypeLabel = 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 Conversions_js_1 = require("./Conversions.js");
+const Protocol_js_1 = require("../../Core/Process/Protocol.js");
+const URI_js_1 = require("../../Core/URI.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.protocolTypeLabel = "Type";
+exports.typeTermAccessionNumberLabel = "Type Term Accession Number";
+exports.typeTermSourceREFLabel = "Type Term Source REF";
+exports.descriptionLabel = "Description";
+exports.uriLabel = "URI";
+exports.versionLabel = "Version";
+exports.parametersNameLabel = "Parameters Name";
+exports.parametersTermAccessionNumberLabel = "Parameters Term Accession Number";
+exports.parametersTermSourceREFLabel = "Parameters Term Source REF";
+exports.componentsNameLabel = "Components Name";
+exports.componentsTypeLabel = "Components Type";
+exports.componentsTypeTermAccessionNumberLabel = "Components Type Term Accession Number";
+exports.componentsTypeTermSourceREFLabel = "Components Type Term Source REF";
+exports.labels = (0, List_js_1.ofArray)([exports.nameLabel, exports.protocolTypeLabel, exports.typeTermAccessionNumberLabel, exports.typeTermSourceREFLabel, exports.descriptionLabel, exports.uriLabel, exports.versionLabel, exports.parametersNameLabel, exports.parametersTermAccessionNumberLabel, exports.parametersTermSourceREFLabel, exports.componentsNameLabel, exports.componentsTypeLabel, exports.componentsTypeTermAccessionNumberLabel, exports.componentsTypeTermSourceREFLabel]);
+function fromString(name, protocolType, typeTermAccessionNumber, typeTermSourceREF, description, uri, version, parametersName, parametersTermAccessionNumber, parametersTermSourceREF, componentsName, componentsType, componentsTypeTermAccessionNumber, componentsTypeTermSourceREF, comments) {
+    const protocolType_1 = OntologyAnnotation_js_1.OntologyAnnotation.create((0, Option_js_1.unwrap)(protocolType), (0, Option_js_1.unwrap)(typeTermSourceREF), (0, Option_js_1.unwrap)(typeTermAccessionNumber));
+    const parameters = (0, List_js_1.ofSeq)((0, Conversions_js_1.ProtocolParameter_fromAggregatedStrings)(";", parametersName, parametersTermSourceREF, parametersTermAccessionNumber));
+    const components = (0, Conversions_js_1.Component_fromAggregatedStrings)(";", componentsName, componentsType, componentsTypeTermSourceREF, componentsTypeTermAccessionNumber);
+    return (0, Protocol_js_1.Protocol_make)(undefined, (0, Option_js_1.map)(URI_js_1.URIModule_fromString, name), (0, Conversions_js_1.Option_fromValueWithDefault)(new OntologyAnnotation_js_1.OntologyAnnotation(), protocolType_1), description, (0, Option_js_1.map)(URI_js_1.URIModule_fromString, uri), version, (0, Conversions_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), parameters), (0, Conversions_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), components), (0, Conversions_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), comments));
+}
+function fromSparseTable(matrix) {
+    if ((matrix.ColumnCount === 0) && ((0, List_js_1.length)(matrix.CommentKeys) !== 0)) {
+        return (0, List_js_1.singleton)((0, Protocol_js_1.Protocol_create_Z414665E7)(undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, (0, List_js_1.ofSeq)((0, SparseTable_js_1.SparseTable_GetEmptyComments_3ECCA699)(matrix))));
+    }
+    else {
+        return (0, List_js_1.initialize)(matrix.ColumnCount, (i) => {
+            const comments_1 = (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);
+            return fromString((0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.nameLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.protocolTypeLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.typeTermAccessionNumberLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.typeTermSourceREFLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.descriptionLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.uriLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.versionLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.parametersNameLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.parametersTermAccessionNumberLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.parametersTermSourceREFLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.componentsNameLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.componentsTypeLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.componentsTypeTermAccessionNumberLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [exports.componentsTypeTermSourceREFLabel, i]), comments_1);
+        });
+    }
+}
+function toSparseTable(protocols) {
+    const matrix = (0, SparseTable_js_1.SparseTable_Create_Z2192E64B)(undefined, exports.labels, undefined, (0, List_js_1.length)(protocols) + 1);
+    let commentKeys = (0, List_js_1.empty)();
+    (0, List_js_1.iterateIndexed)((i, p) => {
+        const i_1 = (i + 1) | 0;
+        let pt_1;
+        const pt = (0, Option_js_1.defaultArg)(p.ProtocolType, new OntologyAnnotation_js_1.OntologyAnnotation());
+        pt_1 = OntologyAnnotation_js_1.OntologyAnnotation.toStringObject(pt, true);
+        const pAgg = (0, Conversions_js_1.ProtocolParameter_toAggregatedStrings)(";", (0, Option_js_1.defaultArg)(p.Parameters, (0, List_js_1.empty)()));
+        const cAgg = (0, Conversions_js_1.Component_toAggregatedStrings)(";", (0, Option_js_1.defaultArg)(p.Components, (0, List_js_1.empty)()));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.nameLabel, i_1], (0, Option_js_1.defaultArg)(p.Name, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.protocolTypeLabel, i_1], pt_1.TermName);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.typeTermAccessionNumberLabel, i_1], pt_1.TermAccessionNumber);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.typeTermSourceREFLabel, i_1], pt_1.TermSourceREF);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.descriptionLabel, i_1], (0, Option_js_1.defaultArg)(p.Description, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.uriLabel, i_1], (0, Option_js_1.defaultArg)(p.Uri, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.versionLabel, i_1], (0, Option_js_1.defaultArg)(p.Version, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.parametersNameLabel, i_1], pAgg.TermNameAgg);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.parametersTermAccessionNumberLabel, i_1], pAgg.TermAccessionNumberAgg);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.parametersTermSourceREFLabel, i_1], pAgg.TermSourceREFAgg);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.componentsNameLabel, i_1], cAgg.NameAgg);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.componentsTypeLabel, i_1], cAgg.TermNameAgg);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.componentsTypeTermAccessionNumberLabel, i_1], cAgg.TermAccessionNumberAgg);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.componentsTypeTermSourceREFLabel, i_1], cAgg.TermSourceREFAgg);
+        const matchValue = p.Comments;
+        if (matchValue != null) {
+            (0, List_js_1.iterate)((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));
+        }
+    }, protocols);
+    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, protocols) {
+    const m = toSparseTable(protocols);
+    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/Publication.js

@@ -0,0 +1,88 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.labels = exports.statusTermSourceREFLabel = exports.statusTermAccessionNumberLabel = exports.statusLabel = exports.titleLabel = exports.authorListLabel = exports.doiLabel = exports.pubMedIDLabel = 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 URI_js_1 = require("../../Core/URI.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
+const Publication_js_1 = require("../../Core/Publication.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.pubMedIDLabel = "PubMed ID";
+exports.doiLabel = "DOI";
+exports.authorListLabel = "Author List";
+exports.titleLabel = "Title";
+exports.statusLabel = "Status";
+exports.statusTermAccessionNumberLabel = "Status Term Accession Number";
+exports.statusTermSourceREFLabel = "Status Term Source REF";
+exports.labels = (0, List_js_1.ofArray)([exports.pubMedIDLabel, exports.doiLabel, exports.authorListLabel, exports.titleLabel, exports.statusLabel, exports.statusTermAccessionNumberLabel, exports.statusTermSourceREFLabel]);
+function fromString(pubMedID, doi, author, title, status, statusTermSourceREF, statusTermAccessionNumber, comments) {
+    const status_1 = new OntologyAnnotation_js_1.OntologyAnnotation((0, Option_js_1.unwrap)(status), (0, Option_js_1.unwrap)(statusTermSourceREF), (0, Option_js_1.unwrap)(statusTermAccessionNumber));
+    const pubMedID_1 = (0, Option_js_1.map)(URI_js_1.URIModule_fromString, pubMedID);
+    const status_2 = (0, Collections_js_1.Option_fromValueWithDefault)(new OntologyAnnotation_js_1.OntologyAnnotation(), status_1);
+    return Publication_js_1.Publication.make(pubMedID_1, doi, author, title, status_2, 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 = Publication_js_1.Publication.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.pubMedIDLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.doiLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.authorListLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.titleLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.statusLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.statusTermSourceREFLabel, i]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, [exports.statusTermAccessionNumberLabel, i]), comments_1);
+        });
+    }
+}
+function toSparseTable(publications) {
+    const matrix = (0, SparseTable_js_1.SparseTable_Create_Z2192E64B)(undefined, exports.labels, undefined, (0, List_js_1.length)(publications) + 1);
+    let commentKeys = (0, List_js_1.empty)();
+    (0, List_js_1.iterateIndexed)((i, p) => {
+        const i_1 = (i + 1) | 0;
+        let s_1;
+        const s = (0, Option_js_1.defaultArg)(p.Status, new OntologyAnnotation_js_1.OntologyAnnotation());
+        s_1 = OntologyAnnotation_js_1.OntologyAnnotation.toStringObject(s, true);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.pubMedIDLabel, i_1], (0, Option_js_1.defaultArg)(p.PubMedID, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.doiLabel, i_1], (0, Option_js_1.defaultArg)(p.DOI, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.authorListLabel, i_1], (0, Option_js_1.defaultArg)(p.Authors, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.titleLabel, i_1], (0, Option_js_1.defaultArg)(p.Title, ""));
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.statusLabel, i_1], s_1.TermName);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.statusTermAccessionNumberLabel, i_1], s_1.TermAccessionNumber);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [exports.statusTermSourceREFLabel, i_1], s_1.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]);
+        }, p.Comments);
+    }, publications);
+    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, publications) {
+    const m = toSparseTable(publications);
+    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/Run.js

@@ -0,0 +1,99 @@
+"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 Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const OntologyAnnotation_js_1 = require("../../Core/OntologyAnnotation.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 Comment_js_1 = require("./Comment.js");
+const SparseTable_js_1 = require("./SparseTable.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.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", "Workflow Identifiers", "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, workflowIdentifiers, measurementType, measurementTypeTermSourceREF, measurementTypeTermAccessionNumber, technologyType, technologyTypeTermSourceREF, technologyTypeTermAccessionNumber, technologyPlatform, fileName, comments) {
+    let workflowIdentifiers_1;
+    if (workflowIdentifiers == null) {
+        workflowIdentifiers_1 = [];
+    }
+    else {
+        const wi = (0, Option_js_1.value)(workflowIdentifiers);
+        const collection = wi.split(";");
+        workflowIdentifiers_1 = Array.from(collection);
+    }
+    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.ArcRun.make(identifier_4, title, description, measurementType_2, technologyType_2, technologyPlatform_1, workflowIdentifiers_1, [], undefined, [], comments);
+}
+function fromSparseTable(matrix) {
+    let comments;
+    const collection = (0, List_js_1.map)((k) => (0, Comment_js_1.Comment_fromString)(k, (0, SparseTable_js_1.SparseTable__TryGetValueDefault_5BAE6133)(matrix, "", [k, 0])), matrix.CommentKeys);
+    comments = Array.from(collection);
+    return fromString((0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Identifier", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Title", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Description", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Workflow Identifiers", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Measurement Type", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Measurement Type Term Source REF", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Measurement Type Term Accession Number", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Technology Type", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Technology Type Term Source REF", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Technology Type Term Accession Number", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["Technology Platform", 0]), (0, SparseTable_js_1.SparseTable__TryGetValue_11FD62A8)(matrix, ["File Name", 0]), comments);
+}
+function toSparseTable(run) {
+    const matrix = (0, SparseTable_js_1.SparseTable_Create_Z2192E64B)(undefined, exports.labels, undefined, 2);
+    let commentKeys = (0, List_js_1.empty)();
+    const patternInput = run.Identifier.startsWith("MISSING_IDENTIFIER_") ? ["", ""] : [run.Identifier, (0, Identifier_js_1.Run_fileNameFromIdentifier)(run.Identifier)];
+    const workflowIdentifiers = (0, String_js_1.join)(";", run.WorkflowIdentifiers);
+    let mt_1;
+    const mt = (0, Option_js_1.defaultArg)(run.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)(run.TechnologyType, new OntologyAnnotation_js_1.OntologyAnnotation());
+    tt_1 = OntologyAnnotation_js_1.OntologyAnnotation.toStringObject(tt, true);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Identifier", 1], patternInput[0]);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Title", 1], (0, Option_js_1.defaultArg)(run.Title, ""));
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Description", 1], (0, Option_js_1.defaultArg)(run.Description, ""));
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Workflow Identifiers", 1], workflowIdentifiers);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Measurement Type", 1], mt_1.TermName);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Measurement Type Term Accession Number", 1], mt_1.TermAccessionNumber);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Measurement Type Term Source REF", 1], mt_1.TermSourceREF);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Technology Type", 1], tt_1.TermName);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Technology Type Term Accession Number", 1], tt_1.TermAccessionNumber);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Technology Type Term Source REF", 1], tt_1.TermSourceREF);
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["Technology Platform", 1], (0, Option_js_1.defaultArg)((0, Option_js_1.map)(Conversion_js_1.JsonTypes_composeTechnologyPlatform, run.TechnologyPlatform), ""));
+    (0, MapUtil_js_1.addToDict)(matrix.Matrix, ["File Name", 1], patternInput[1]);
+    (0, Collections_js_1.ResizeArray_iter)((comment) => {
+        const patternInput_1 = (0, Comment_js_1.Comment_toString)(comment);
+        const n = patternInput_1[0];
+        commentKeys = (0, List_js_1.cons)(n, commentKeys);
+        (0, MapUtil_js_1.addToDict)(matrix.Matrix, [n, 1], patternInput_1[1]);
+    }, run.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 fromRows(lineNumber, rows) {
+    const tupledArg = (0, SparseTable_js_1.SparseTable_FromRows_Z5579EC29)(rows, exports.labels, lineNumber, "Run");
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(run) {
+    return (0, SparseTable_js_1.SparseTable_ToRows_759CAFC1)(toSparseTable(run), "Run");
+}