@nfdi4plants/arctrl 1.2.0 → 2.0.0-alpha.2

package/{ISA/ISA.Spreadsheet → Spreadsheet}/ArcInvestigation.js

@@ -1,24 +1,24 @@
-import { Record } from "../../fable_modules/fable-library-js.4.13.0/Types.js";
-import { record_type, list_type, string_type } from "../../fable_modules/fable-library-js.4.13.0/Reflection.js";
-import { Remark, Comment$_$reflection } from "../ISA/JsonTypes/Comment.js";
-import { ofSeq, head, tail, isEmpty, concat, unzip, append, toArray, reverse, cons, empty, map, ofArray } from "../../fable_modules/fable-library-js.4.13.0/List.js";
+import { Record } from "../fable_modules/fable-library-js.4.16.0/Types.js";
+import { record_type, list_type, string_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
+import { Remark, Comment$_$reflection } from "../Core/Comment.js";
+import { head, tail, isEmpty, ofSeq, concat, unzip, append, reverse, cons, empty, map, ofArray } from "../fable_modules/fable-library-js.4.16.0/List.js";
 import { Remark_wrapRemark, Comment_toString, Comment_fromString } from "./Metadata/Comment.js";
-import { SparseRowModule_writeToSheet, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt, SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "./Metadata/SparseTable.js";
-import { addToDict } from "../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { value as value_1, defaultArg } from "../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { List_distinctBy, List_distinct } from "../../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { comparePrimitives, getEnumerator, stringHash } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { Option_fromValueWithDefault } from "./Metadata/Conversions.js";
-import { ArcStudy, ArcInvestigation } from "../ISA/ArcTypes/ArcTypes.js";
+import { SparseRowModule_writeToSheet, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt, SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "./Metadata/SparseTable.js";
+import { addToDict } from "../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { value as value_1, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { Option_fromValueWithDefault, ResizeArray_iter } from "../Core/Helper/Collections.js";
+import { List_distinctBy, List_distinct } from "../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { comparePrimitives, getEnumerator, stringHash } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { ArcStudy, ArcInvestigation } from "../Core/ArcTypes.js";
 import { toRows as toRows_1, fromRows as fromRows_1 } from "./Metadata/OntologySourceReference.js";
 import { toRows as toRows_2, fromRows as fromRows_2 } from "./Metadata/Publication.js";
 import { toRows as toRows_3, fromRows as fromRows_3 } from "./Metadata/Contacts.js";
 import { toRows as toRows_4, fromRows as fromRows_4 } from "./Metadata/Study.js";
-import { iterateIndexed, map as map_1, toList, empty as empty_1, collect, singleton, append as append_1, delay } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { tryFind, ofList } from "../../fable_modules/fable-library-js.4.13.0/Map.js";
-import { printf, toFail } from "../../fable_modules/fable-library-js.4.13.0/String.js";
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
-import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
+import { iterateIndexed, map as map_1, toList, empty as empty_1, collect, singleton, append as append_1, delay } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { tryFind, ofList } from "../fable_modules/fable-library-js.4.16.0/Map.js";
+import { printf, toFail } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { FsWorksheet } from "../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
+import { FsWorkbook } from "../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
 
 export class InvestigationInfo extends Record {
     constructor(Identifier, Title, Description, SubmissionDate, PublicReleaseDate, Comments) {
@@ -33,7 +33,7 @@ export class InvestigationInfo extends Record {
 }
 
 export function InvestigationInfo_$reflection() {
-    return record_type("ARCtrl.ISA.Spreadsheet.ArcInvestigation.InvestigationInfo", [], InvestigationInfo, () => [["Identifier", string_type], ["Title", string_type], ["Description", string_type], ["SubmissionDate", string_type], ["PublicReleaseDate", string_type], ["Comments", list_type(Comment$_$reflection())]]);
+    return record_type("ARCtrl.Spreadsheet.ArcInvestigation.InvestigationInfo", [], InvestigationInfo, () => [["Identifier", string_type], ["Title", string_type], ["Description", string_type], ["SubmissionDate", string_type], ["PublicReleaseDate", string_type], ["Comments", list_type(Comment$_$reflection())]]);
 }
 
 export function InvestigationInfo_create(identifier, title, description, submissionDate, publicReleaseDate, comments) {
@@ -44,12 +44,12 @@ export function InvestigationInfo_get_Labels() {
     return ofArray(["Investigation Identifier", "Investigation Title", "Investigation Description", "Investigation Submission Date", "Investigation Public Release Date"]);
 }
 
-export function InvestigationInfo_FromSparseTable_651559CC(matrix) {
+export function InvestigationInfo_FromSparseTable_3ECCA699(matrix) {
     const comments = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, 0])), matrix.CommentKeys);
     return InvestigationInfo_create(SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Identifier", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Title", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Description", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Submission Date", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Public Release Date", 0]), comments);
 }
 
-export function InvestigationInfo_ToSparseTable_Z4D87C88C(investigation) {
+export function InvestigationInfo_ToSparseTable_Z720BD3FF(investigation) {
     const matrix = SparseTable_Create_Z2192E64B(void 0, InvestigationInfo_get_Labels(), void 0, 2);
     let commentKeys = empty();
     addToDict(matrix.Matrix, ["Investigation Identifier", 1], investigation.Identifier);
@@ -57,15 +57,12 @@ export function InvestigationInfo_ToSparseTable_Z4D87C88C(investigation) {
     addToDict(matrix.Matrix, ["Investigation Description", 1], defaultArg(investigation.Description, ""));
     addToDict(matrix.Matrix, ["Investigation Submission Date", 1], defaultArg(investigation.SubmissionDate, ""));
     addToDict(matrix.Matrix, ["Investigation Public Release Date", 1], defaultArg(investigation.PublicReleaseDate, ""));
-    if (!(investigation.Comments.length === 0)) {
-        const array = investigation.Comments;
-        array.forEach((comment) => {
-            const patternInput = Comment_toString(comment);
-            const n = patternInput[0];
-            commentKeys = cons(n, commentKeys);
-            addToDict(matrix.Matrix, [n, 1], patternInput[1]);
-        });
-    }
+    ResizeArray_iter((comment) => {
+        const patternInput = Comment_toString(comment);
+        const n = patternInput[0];
+        commentKeys = cons(n, commentKeys);
+        addToDict(matrix.Matrix, [n, 1], patternInput[1]);
+    }, investigation.Comments);
     return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
         Equals: (x, y) => (x === y),
         GetHashCode: stringHash,
@@ -74,11 +71,11 @@ export function InvestigationInfo_ToSparseTable_Z4D87C88C(investigation) {
 
 export function InvestigationInfo_fromRows(lineNumber, rows) {
     const tupledArg = SparseTable_FromRows_Z5579EC29(rows, InvestigationInfo_get_Labels(), lineNumber);
-    return [tupledArg[0], tupledArg[1], tupledArg[2], InvestigationInfo_FromSparseTable_651559CC(tupledArg[3])];
+    return [tupledArg[0], tupledArg[1], tupledArg[2], InvestigationInfo_FromSparseTable_3ECCA699(tupledArg[3])];
 }
 
-export function InvestigationInfo_toRows_Z4D87C88C(investigation) {
-    return SparseTable_ToRows_6A3D4534(InvestigationInfo_ToSparseTable_Z4D87C88C(investigation));
+export function InvestigationInfo_toRows_Z720BD3FF(investigation) {
+    return SparseTable_ToRows_759CAFC1(InvestigationInfo_ToSparseTable_Z720BD3FF(investigation));
 }
 
 export function fromParts(investigationInfo, ontologySourceReference, publications, contacts, studies, assays, remarks) {
@@ -87,14 +84,14 @@ export function fromParts(investigationInfo, ontologySourceReference, publicatio
     const description = Option_fromValueWithDefault("", investigationInfo.Description);
     const submissionDate = Option_fromValueWithDefault("", investigationInfo.SubmissionDate);
     const publicReleaseDate = Option_fromValueWithDefault("", investigationInfo.PublicReleaseDate);
-    const ontologySourceReferences = toArray(ontologySourceReference);
-    const publications_1 = toArray(publications);
-    const contacts_1 = toArray(contacts);
+    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 = toArray(investigationInfo.Comments);
-    const remarks_1 = toArray(remarks);
+    const comments = Array.from(investigationInfo.Comments);
+    const remarks_1 = Array.from(remarks);
     return ArcInvestigation.make(investigationInfo.Identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications_1, contacts_1, assays_1, studies_1, registeredStudyIdentifiers, comments, remarks_1);
 }
 
@@ -244,7 +241,7 @@ export function fromRows(rows) {
 
 export function toRows(isLight, investigation) {
     let remarks, rows;
-    return (remarks = ofArray(investigation.Remarks), (rows = delay(() => append_1(singleton(SparseRowModule_fromValues(["ONTOLOGY SOURCE REFERENCE"])), delay(() => append_1(toRows_1(ofArray(investigation.OntologySourceReferences)), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION"])), delay(() => append_1(InvestigationInfo_toRows_Z4D87C88C(investigation), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION PUBLICATIONS"])), delay(() => append_1(toRows_2("Investigation Publication", ofArray(investigation.Publications)), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION CONTACTS"])), delay(() => append_1(toRows_3("Investigation Person", ofArray(investigation.Contacts)), delay(() => (!isLight ? collect((studyIdentifier) => {
+    return (remarks = ofSeq(investigation.Remarks), (rows = delay(() => append_1(singleton(SparseRowModule_fromValues(["ONTOLOGY SOURCE REFERENCE"])), delay(() => append_1(toRows_1(ofSeq(investigation.OntologySourceReferences)), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION"])), delay(() => append_1(InvestigationInfo_toRows_Z720BD3FF(investigation), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION PUBLICATIONS"])), delay(() => append_1(toRows_2("Investigation Publication", ofSeq(investigation.Publications)), delay(() => append_1(singleton(SparseRowModule_fromValues(["INVESTIGATION CONTACTS"])), delay(() => append_1(toRows_3("Investigation Person", ofSeq(investigation.Contacts)), delay(() => (!isLight ? collect((studyIdentifier) => {
         const study = defaultArg(investigation.TryGetStudy(studyIdentifier), new ArcStudy(studyIdentifier));
         return append_1(singleton(SparseRowModule_fromValues(["STUDY"])), delay(() => toRows_4(study, void 0)));
     }, investigation.RegisteredStudyIdentifiers) : empty_1())))))))))))))))))), (() => {

package/{ISA/ISA.Spreadsheet → Spreadsheet}/ArcStudy.js

@@ -1,16 +1,16 @@
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
-import { map, append, iterateIndexed } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { FsWorksheet } from "../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
+import { map, append, iterateIndexed } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_writeToSheet } from "./Metadata/SparseTable.js";
 import { fromRows as fromRows_1, toRows } from "./Metadata/Study.js";
-import { toConsole, printf, toFail } from "../../fable_modules/fable-library-js.4.13.0/String.js";
-import { defaultArg } from "../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { getEnumerator } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { ArcStudy } from "../ISA/ArcTypes/ArcTypes.js";
-import { createMissingIdentifier } from "../ISA/Identifier.js";
-import { empty } from "../../fable_modules/fable-library-js.4.13.0/List.js";
-import { ResizeArray_iter, ResizeArray_isEmpty, ResizeArray_choose } from "../ISA/Helper.js";
+import { toConsole, printf, toFail } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { getEnumerator } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { ArcStudy } from "../Core/ArcTypes.js";
+import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
+import { empty } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { ResizeArray_iter, ResizeArray_isEmpty, ResizeArray_choose } from "../Core/Helper/Collections.js";
 import { toFsWorksheet, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
-import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
+import { FsWorkbook } from "../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
 
 export function ArcStudy_toMetadataSheet(study, assays) {
     let source_1;
@@ -35,7 +35,7 @@ export function ArcStudy_fromMetadataSheet(sheet) {
 /**
  * Reads an assay from a spreadsheet
  */
-export function ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(doc) {
+export function ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(doc) {
     try {
         let patternInput;
         const matchValue = doc.TryGetWorksheetByName("isa_study");
@@ -65,7 +65,7 @@ export function ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(doc
     }
 }
 
-export function ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9(study, assays) {
+export function ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_353D0DB7(study, assays) {
     const doc = new FsWorkbook();
     const metaDataSheet = ArcStudy_toMetadataSheet(study, assays);
     doc.AddWorksheet(metaDataSheet);

package/{ISA/ISA.Spreadsheet → Spreadsheet}/CollectionAux.js

@@ -1,10 +1,10 @@
-import { tryFind, maxBy, skip } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { item, tryItem, skip as skip_1, initialize } from "../../fable_modules/fable-library-js.4.13.0/Array.js";
-import { defaultOf, comparePrimitives } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { some, value } from "../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { empty, tail, cons, head, reverse, isEmpty, tryPick } from "../../fable_modules/fable-library-js.4.13.0/List.js";
-import { tryGetValue } from "../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { FSharpRef } from "../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { tryFind, maxBy, skip } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { item, tryItem, skip as skip_1, initialize } from "../fable_modules/fable-library-js.4.16.0/Array.js";
+import { defaultOf, comparePrimitives } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { some, value } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { empty, tail, cons, head, reverse, isEmpty, tryPick } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { tryGetValue } from "../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { FSharpRef } from "../fable_modules/fable-library-js.4.16.0/Types.js";
 
 /**
  * If at least i values exist in seq a, builds a new array that contains the elements of the given seq, exluding the first i elements

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/Assays.js

@@ -1,34 +1,37 @@
-import { reverse, cons, iterateIndexed, empty, map as map_1, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
-import { Option_fromValueWithDefault } from "./Conversions.js";
-import { unwrap, defaultArg, map } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { ArcAssay } from "../../ISA/ArcTypes/ArcTypes.js";
-import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
-import { Assay_fileNameFromIdentifier, removeMissingIdentifier, Assay_identifierFromFileName, createMissingIdentifier } from "../../ISA/Identifier.js";
+import { reverse, cons, iterateIndexed, empty, map as map_1, initialize, singleton, length, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { ResizeArray_iter, Option_fromValueWithDefault } from "../../Core/Helper/Collections.js";
+import { unwrap, defaultArg, map } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { JsonTypes_composeTechnologyPlatform, JsonTypes_decomposeTechnologyPlatform } from "../../Core/Conversion.js";
+import { ArcAssay } from "../../Core/ArcTypes.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
+import { Assay_fileNameFromIdentifier, removeMissingIdentifier, Assay_identifierFromFileName, createMissingIdentifier } from "../../Core/Helper/Identifier.js";
 import { Comment_toString, Comment_fromString } from "./Comment.js";
-import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { List_distinct } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { stringHash } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 
 export const labels = ofArray(["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"]);
 
 export function fromString(measurementType, measurementTypeTermSourceREF, measurementTypeTermAccessionNumber, technologyType, technologyTypeTermSourceREF, technologyTypeTermAccessionNumber, technologyPlatform, fileName, comments) {
-    const measurementType_1 = OntologyAnnotation.fromString(measurementType, measurementTypeTermSourceREF, measurementTypeTermAccessionNumber);
-    const technologyType_1 = OntologyAnnotation.fromString(technologyType, technologyTypeTermSourceREF, technologyTypeTermAccessionNumber);
-    const measurementType_2 = Option_fromValueWithDefault(OntologyAnnotation.empty, measurementType_1);
-    const technologyType_2 = Option_fromValueWithDefault(OntologyAnnotation.empty, technologyType_1);
-    const technologyPlatform_1 = map((name) => ArcAssay.decomposeTechnologyPlatform(name), technologyPlatform);
+    const measurementType_1 = OntologyAnnotation.create(measurementType, measurementTypeTermSourceREF, measurementTypeTermAccessionNumber);
+    const technologyType_1 = OntologyAnnotation.create(technologyType, technologyTypeTermSourceREF, technologyTypeTermAccessionNumber);
+    const measurementType_2 = Option_fromValueWithDefault(new OntologyAnnotation(), measurementType_1);
+    const technologyType_2 = Option_fromValueWithDefault(new OntologyAnnotation(), technologyType_1);
+    const technologyPlatform_1 = map(JsonTypes_decomposeTechnologyPlatform, technologyPlatform);
     return ArcAssay.make(fileName, measurementType_2, technologyType_2, technologyPlatform_1, [], [], comments);
 }
 
 export function fromSparseTable(matrix) {
     if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
-        const comments = SparseTable_GetEmptyComments_651559CC(matrix);
+        const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
         return singleton(ArcAssay.create(createMissingIdentifier(), void 0, void 0, void 0, void 0, void 0, comments));
     }
     else {
         return initialize(matrix.ColumnCount, (i) => {
-            const comments_1 = toArray(map_1((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys));
+            let comments_1;
+            const collection = map_1((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
             return fromString(SparseTable__TryGetValue_11FD62A8(matrix, ["Measurement Type", i]), SparseTable__TryGetValue_11FD62A8(matrix, ["Measurement Type Term Source REF", i]), SparseTable__TryGetValue_11FD62A8(matrix, ["Measurement Type Term Accession Number", i]), SparseTable__TryGetValue_11FD62A8(matrix, ["Technology Type", i]), SparseTable__TryGetValue_11FD62A8(matrix, ["Technology Type Term Source REF", i]), SparseTable__TryGetValue_11FD62A8(matrix, ["Technology Type Term Accession Number", i]), SparseTable__TryGetValue_11FD62A8(matrix, ["Technology Platform", i]), Assay_identifierFromFileName(SparseTable__TryGetValueDefault_5BAE6133(matrix, createMissingIdentifier(), ["File Name", i])), comments_1);
         });
     }
@@ -41,28 +44,25 @@ export function toSparseTable(assays) {
         const processedFileName = (a.Identifier.indexOf("MISSING_IDENTIFIER_") === 0) ? removeMissingIdentifier(a.Identifier) : Assay_fileNameFromIdentifier(a.Identifier);
         const i_1 = (i + 1) | 0;
         let mt_1;
-        const mt = defaultArg(a.MeasurementType, OntologyAnnotation.empty);
-        mt_1 = OntologyAnnotation.toString(mt, true);
+        const mt = defaultArg(a.MeasurementType, new OntologyAnnotation());
+        mt_1 = OntologyAnnotation.toStringObject(mt, true);
         let tt_1;
-        const tt = defaultArg(a.TechnologyType, OntologyAnnotation.empty);
-        tt_1 = OntologyAnnotation.toString(tt, true);
+        const tt = defaultArg(a.TechnologyType, new OntologyAnnotation());
+        tt_1 = OntologyAnnotation.toStringObject(tt, true);
         addToDict(matrix.Matrix, ["Measurement Type", i_1], mt_1.TermName);
         addToDict(matrix.Matrix, ["Measurement Type Term Accession Number", i_1], mt_1.TermAccessionNumber);
         addToDict(matrix.Matrix, ["Measurement Type Term Source REF", i_1], mt_1.TermSourceREF);
         addToDict(matrix.Matrix, ["Technology Type", i_1], tt_1.TermName);
         addToDict(matrix.Matrix, ["Technology Type Term Accession Number", i_1], tt_1.TermAccessionNumber);
         addToDict(matrix.Matrix, ["Technology Type Term Source REF", i_1], tt_1.TermSourceREF);
-        addToDict(matrix.Matrix, ["Technology Platform", i_1], defaultArg(map((tp) => ArcAssay.composeTechnologyPlatform(tp), a.TechnologyPlatform), ""));
+        addToDict(matrix.Matrix, ["Technology Platform", i_1], defaultArg(map(JsonTypes_composeTechnologyPlatform, a.TechnologyPlatform), ""));
         addToDict(matrix.Matrix, ["File Name", i_1], processedFileName);
-        if (!(a.Comments.length === 0)) {
-            const array = a.Comments;
-            array.forEach((comment) => {
-                const patternInput = Comment_toString(comment);
-                const n = patternInput[0];
-                commentKeys = cons(n, commentKeys);
-                addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
-            });
-        }
+        ResizeArray_iter((comment) => {
+            const patternInput = Comment_toString(comment);
+            const n = patternInput[0];
+            commentKeys = cons(n, commentKeys);
+            addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+        }, a.Comments);
     }, assays);
     return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
         Equals: (x, y) => (x === y),
@@ -76,6 +76,6 @@ export function fromRows(prefix, lineNumber, rows) {
 }
 
 export function toRows(prefix, assays) {
-    return SparseTable_ToRows_6A3D4534(toSparseTable(assays), unwrap(prefix));
+    return SparseTable_ToRows_759CAFC1(toSparseTable(assays), unwrap(prefix));
 }
 

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/Comment.js

@@ -1,8 +1,8 @@
-import { ActivePatterns_$007CRegex$007C_$007C } from "../../ISA/Regex.js";
-import { printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
+import { ActivePatterns_$007CRegex$007C_$007C } from "../../Core/Helper/Regex.js";
+import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
 import { Option_fromValueWithDefault } from "./Conversions.js";
-import { Comment$ } from "../../ISA/JsonTypes/Comment.js";
-import { bind, defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
+import { Comment$ } from "../../Core/Comment.js";
+import { bind, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 
 export const Comment_commentValueKey = "commentValue";
 
@@ -41,7 +41,7 @@ export function Comment_wrapCommentKey(k) {
 export function Comment_fromString(k, v) {
     const name = Option_fromValueWithDefault("", k);
     const value = Option_fromValueWithDefault("", v);
-    return Comment$.make(void 0, name, value);
+    return Comment$.make(name, value);
 }
 
 export function Comment_toString(c) {

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/Contacts.js

@@ -1,12 +1,14 @@
-import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { OntologyAnnotation_toAggregatedStrings, OntologyAnnotation_fromAggregatedStrings, Option_fromValueWithDefault } from "./Conversions.js";
-import { Person } from "../../ISA/JsonTypes/Person.js";
-import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { reverse, cons, iterateIndexed, empty, map, initialize, singleton, length, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { Person_setCommentFromORCID, Person_setOrcidFromComments } from "../../Core/Conversion.js";
+import { OntologyAnnotation_toAggregatedStrings, OntologyAnnotation_fromAggregatedStrings } from "./Conversions.js";
+import { Person } from "../../Core/Person.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
 import { Comment_toString, Comment_fromString } from "./Comment.js";
-import { unwrap, defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { ResizeArray_iter } from "../../Core/Helper/Collections.js";
+import { List_distinct } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { stringHash } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 
 export const lastNameLabel = "Last Name";
 
@@ -33,21 +35,21 @@ export const rolesTermSourceREFLabel = "Roles Term Source REF";
 export const labels = ofArray([lastNameLabel, firstNameLabel, midInitialsLabel, emailLabel, phoneLabel, faxLabel, addressLabel, affiliationLabel, rolesLabel, rolesTermAccessionNumberLabel, rolesTermSourceREFLabel]);
 
 export function fromString(lastName, firstName, midInitials, email, phone, fax, address, affiliation, role, rolesTermAccessionNumber, rolesTermSourceREF, comments) {
-    let person;
-    const roles_1 = Option_fromValueWithDefault([], OntologyAnnotation_fromAggregatedStrings(";", role, rolesTermSourceREF, rolesTermAccessionNumber));
-    const comments_1 = Option_fromValueWithDefault([], comments);
-    person = Person.make(void 0, void 0, lastName, firstName, midInitials, email, phone, fax, address, affiliation, roles_1, comments_1);
-    return Person.setOrcidFromComments(person);
+    let roles_1;
+    return Person_setOrcidFromComments((roles_1 = OntologyAnnotation_fromAggregatedStrings(";", role, rolesTermSourceREF, rolesTermAccessionNumber), Person.make(void 0, lastName, firstName, midInitials, email, phone, fax, address, affiliation, roles_1, comments)));
 }
 
 export function fromSparseTable(matrix) {
+    let returnVal;
     if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
-        const comments = SparseTable_GetEmptyComments_651559CC(matrix);
-        return singleton(Person.create(void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, comments));
+        const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+        return singleton((returnVal = Person.create(), (returnVal.Comments = comments, returnVal)));
     }
     else {
         return initialize(matrix.ColumnCount, (i) => {
-            const comments_1 = toArray(map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys));
+            let comments_1;
+            const collection = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
             return fromString(SparseTable__TryGetValue_11FD62A8(matrix, [lastNameLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [firstNameLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [midInitialsLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [emailLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [phoneLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [faxLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [addressLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [affiliationLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [rolesLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [rolesTermAccessionNumberLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [rolesTermSourceREFLabel, i]), comments_1);
         });
     }
@@ -58,7 +60,7 @@ export function toSparseTable(persons) {
     let commentKeys = empty();
     iterateIndexed((i, p) => {
         const i_1 = (i + 1) | 0;
-        const rAgg = OntologyAnnotation_toAggregatedStrings(";", defaultArg(p.Roles, []));
+        const rAgg = OntologyAnnotation_toAggregatedStrings(";", Array.from(p.Roles));
         addToDict(matrix.Matrix, [lastNameLabel, i_1], defaultArg(p.LastName, ""));
         addToDict(matrix.Matrix, [firstNameLabel, i_1], defaultArg(p.FirstName, ""));
         addToDict(matrix.Matrix, [midInitialsLabel, i_1], defaultArg(p.MidInitials, ""));
@@ -70,17 +72,13 @@ export function toSparseTable(persons) {
         addToDict(matrix.Matrix, [rolesLabel, i_1], rAgg.TermNameAgg);
         addToDict(matrix.Matrix, [rolesTermAccessionNumberLabel, i_1], rAgg.TermAccessionNumberAgg);
         addToDict(matrix.Matrix, [rolesTermSourceREFLabel, i_1], rAgg.TermSourceREFAgg);
-        const matchValue = p.Comments;
-        if (matchValue != null) {
-            const array = matchValue;
-            array.forEach((comment) => {
-                const patternInput = Comment_toString(comment);
-                const n = patternInput[0];
-                commentKeys = cons(n, commentKeys);
-                addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
-            });
-        }
-    }, map((person) => Person.setCommentFromORCID(person), persons));
+        ResizeArray_iter((comment) => {
+            const patternInput = Comment_toString(comment);
+            const n = patternInput[0];
+            commentKeys = cons(n, commentKeys);
+            addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+        }, p.Comments);
+    }, map(Person_setCommentFromORCID, persons));
     return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
         Equals: (x, y) => (x === y),
         GetHashCode: stringHash,
@@ -95,10 +93,10 @@ export function fromRows(prefix, lineNumber, rows) {
 export function toRows(prefix, persons) {
     const m = toSparseTable(persons);
     if (prefix == null) {
-        return SparseTable_ToRows_6A3D4534(m);
+        return SparseTable_ToRows_759CAFC1(m);
     }
     else {
-        return SparseTable_ToRows_6A3D4534(m, prefix);
+        return SparseTable_ToRows_759CAFC1(m, prefix);
     }
 }
 

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/Conversions.js

@@ -1,12 +1,13 @@
-import { equals } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { value, some } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { map, equalsWith, fill, map3, fold } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
-import { toText, printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
-import { map as map_1, fold as fold_1, ofArray, empty } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
+import { equals } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+import { defaultArg, value, some } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { equalsWith, fill, map3, fold } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+import { toText, printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { map, fold as fold_1, ofArray, empty } from "../../fable_modules/fable-library-js.4.16.0/List.js";
 import { Array_map4 } from "../CollectionAux.js";
-import { Component_toString_Z609B8895, Component_fromString_Z61E08C1 } from "../../ISA/JsonTypes/Component.js";
-import { ProtocolParameter } from "../../ISA/JsonTypes/ProtocolParameter.js";
+import { Component_toStringObject_Z685B8F25, Component_fromISAString_7C9A7CF8 } from "../../Core/Process/Component.js";
+import { ResizeArray_map } from "../../Core/Helper/Collections.js";
+import { ProtocolParameter } from "../../Core/Process/ProtocolParameter.js";
 
 /**
  * If the value matches the default, a None is returned, else a Some is returned
@@ -60,7 +61,8 @@ export function OntologyAnnotation_fromAggregatedStrings(separator, terms, sourc
         return [];
     }
     else {
-        return map3((a, b, c) => OntologyAnnotation.fromString(a, b, c), (terms === "") ? fill(new Array(l), 0, l, "") : terms.split(separator), (source === "") ? fill(new Array(l), 0, l, "") : source.split(separator), (accessions === "") ? fill(new Array(l), 0, l, "") : accessions.split(separator));
+        const collection = map3((a, b, c) => OntologyAnnotation.create(a, b, c), (terms === "") ? fill(new Array(l), 0, l, "") : terms.split(separator), (source === "") ? fill(new Array(l), 0, l, "") : source.split(separator), (accessions === "") ? fill(new Array(l), 0, l, "") : accessions.split(separator));
+        return Array.from(collection);
     }
 }
 
@@ -78,14 +80,18 @@ export function OntologyAnnotation_toAggregatedStrings(separator, oas) {
     }
     else {
         const tupledArg_1 = fold((tupledArg, term) => {
+            const matchValue = defaultArg(term.Name, "");
+            const tsr = defaultArg(term.TermSourceREF, "");
+            const tan = defaultArg(term.TermAccessionNumber, "");
+            const name = matchValue;
             if (first) {
                 first = false;
-                return [term.TermName, term.TermSourceREF, term.TermAccessionNumber];
+                return [name, tsr, tan];
             }
             else {
-                return [toText(printf("%s%c%s"))(tupledArg[0])(separator)(term.TermName), toText(printf("%s%c%s"))(tupledArg[1])(separator)(term.TermSourceREF), toText(printf("%s%c%s"))(tupledArg[2])(separator)(term.TermAccessionNumber)];
+                return [toText(printf("%s%c%s"))(tupledArg[0])(separator)(name), toText(printf("%s%c%s"))(tupledArg[1])(separator)(tsr), toText(printf("%s%c%s"))(tupledArg[2])(separator)(tan)];
             }
-        }, ["", "", ""], map((oa) => OntologyAnnotation.toString(oa), oas));
+        }, ["", "", ""], oas);
         return {
             TermAccessionNumberAgg: tupledArg_1[2],
             TermNameAgg: tupledArg_1[0],
@@ -103,7 +109,7 @@ export function Component_fromAggregatedStrings(separator, names, terms, source,
         return empty();
     }
     else {
-        return ofArray(Array_map4(Component_fromString_Z61E08C1, (names === "") ? fill(new Array(l), 0, l, "") : names.split(separator), (terms === "") ? fill(new Array(l), 0, l, "") : terms.split(separator), (source === "") ? fill(new Array(l), 0, l, "") : source.split(separator), (accessions === "") ? fill(new Array(l), 0, l, "") : accessions.split(separator)));
+        return ofArray(Array_map4(Component_fromISAString_7C9A7CF8, (names === "") ? fill(new Array(l), 0, l, "") : names.split(separator), (terms === "") ? fill(new Array(l), 0, l, "") : terms.split(separator), (source === "") ? fill(new Array(l), 0, l, "") : source.split(separator), (accessions === "") ? fill(new Array(l), 0, l, "") : accessions.split(separator)));
     }
 }
 
@@ -131,7 +137,7 @@ export function Component_toAggregatedStrings(separator, cs) {
             else {
                 return [toText(printf("%s%c%s"))(tupledArg[0])(separator)(name), toText(printf("%s%c%s"))(tupledArg[1])(separator)(term.TermName), toText(printf("%s%c%s"))(tupledArg[2])(separator)(term.TermSourceREF), toText(printf("%s%c%s"))(tupledArg[3])(separator)(term.TermAccessionNumber)];
             }
-        }, ["", "", "", ""], map_1(Component_toString_Z609B8895, cs));
+        }, ["", "", "", ""], map(Component_toStringObject_Z685B8F25, cs));
         return {
             NameAgg: tupledArg_2[0],
             TermAccessionNumberAgg: tupledArg_2[3],
@@ -145,7 +151,7 @@ export function Component_toAggregatedStrings(separator, cs) {
  * Returns a list of ISAJson ProtocolParameter objects from ISATab aggregated strings
  */
 export function ProtocolParameter_fromAggregatedStrings(separator, terms, source, accessions) {
-    return map((arg) => ((parameterName) => ProtocolParameter.make(void 0, parameterName))(arg), OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions));
+    return ResizeArray_map((arg) => ((parameterName) => ProtocolParameter.make(void 0, parameterName))(arg), OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions));
 }
 
 /**
@@ -169,7 +175,7 @@ export function ProtocolParameter_toAggregatedStrings(separator, oas) {
             else {
                 return [toText(printf("%s%c%s"))(tupledArg[0])(separator)(term.TermName), toText(printf("%s%c%s"))(tupledArg[1])(separator)(term.TermSourceREF), toText(printf("%s%c%s"))(tupledArg[2])(separator)(term.TermAccessionNumber)];
             }
-        }, ["", "", ""], map_1((pp) => ProtocolParameter.toString(pp), oas));
+        }, ["", "", ""], map((pp) => ProtocolParameter.toStringObject(pp), oas));
         return {
             TermAccessionNumberAgg: tupledArg_1[2],
             TermNameAgg: tupledArg_1[0],

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/DesignDescriptors.js

@@ -1,4 +1,4 @@
-import { ofArray } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
+import { ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
 import { toRows as toRows_1, fromRows as fromRows_1, toSparseTable as toSparseTable_1, fromSparseTable as fromSparseTable_1 } from "./OntologyAnnotation.js";
 
 export const designTypeLabel = "Type";