@nfdi4plants/arctrl 1.0.0-alpha9 → 1.0.0-beta.2

package/ISA/ISA.Spreadsheet/Metadata/Assays.js

@@ -1,24 +1,24 @@
-import { reverse, cons, iterateIndexed, empty, map as map_1, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { reverse, cons, iterateIndexed, empty, map as map_1, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
 import { Option_fromValueWithDefault } from "./Conversions.js";
-import { unwrap, defaultArg, map } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { unwrap, defaultArg, map } from "../../../fable_modules/fable-library.4.4.1/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 { Comment_toString, Comment_fromString } from "./Comment.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.4.1/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 arg_1 = Option_fromValueWithDefault(OntologyAnnotation.empty, measurementType_1);
-    const arg_2 = Option_fromValueWithDefault(OntologyAnnotation.empty, technologyType_1);
-    const arg_3 = map((arg_7) => ArcAssay.decomposeTechnologyPlatform(arg_7), technologyPlatform);
-    return ArcAssay.make(fileName, arg_1, arg_2, arg_3, [], [], comments);
+    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);
+    return ArcAssay.make(fileName, measurementType_2, technologyType_2, technologyPlatform_1, [], [], comments);
 }
 
 export function fromSparseTable(matrix) {
@@ -52,7 +52,7 @@ export function toSparseTable(assays) {
         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((arg) => ArcAssay.composeTechnologyPlatform(arg), a.TechnologyPlatform), ""));
+        addToDict(matrix.Matrix, ["Technology Platform", i_1], defaultArg(map((tp) => ArcAssay.composeTechnologyPlatform(tp), a.TechnologyPlatform), ""));
         addToDict(matrix.Matrix, ["File Name", i_1], processedFileName);
         if (!(a.Comments.length === 0)) {
             const array = a.Comments;

package/ISA/ISA.Spreadsheet/Metadata/Comment.js

@@ -1,6 +1,6 @@
-import { defaultArg, bind } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { match } from "../../../fable_modules/fable-library.4.1.4/RegExp.js";
-import { printf, toText } from "../../../fable_modules/fable-library.4.1.4/String.js";
+import { defaultArg, bind } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { match } from "../../../fable_modules/fable-library.4.4.1/RegExp.js";
+import { printf, toText } from "../../../fable_modules/fable-library.4.4.1/String.js";
 import { Option_fromValueWithDefault } from "./Conversions.js";
 import { Comment$ } from "../../ISA/JsonTypes/Comment.js";
 
@@ -31,9 +31,9 @@ export function Comment_wrapCommentKey(k) {
 }
 
 export function Comment_fromString(k, v) {
-    const arg_1 = Option_fromValueWithDefault("", k);
-    const arg_2 = Option_fromValueWithDefault("", v);
-    return Comment$.make(void 0, arg_1, arg_2);
+    const name = Option_fromValueWithDefault("", k);
+    const value = Option_fromValueWithDefault("", v);
+    return Comment$.make(void 0, name, value);
 }
 
 export function Comment_toString(c) {

package/ISA/ISA.Spreadsheet/Metadata/Contacts.js

@@ -1,12 +1,12 @@
-import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.4.1/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 { Comment_toString, Comment_fromString } from "./Comment.js";
-import { unwrap, defaultArg } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { unwrap, defaultArg } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.4.1/Util.js";
 
 export const lastNameLabel = "Last Name";
 
@@ -33,11 +33,11 @@ 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 arg_12;
-    const arg_10 = Option_fromValueWithDefault([], OntologyAnnotation_fromAggregatedStrings(";", role, rolesTermSourceREF, rolesTermAccessionNumber));
-    const arg_11 = Option_fromValueWithDefault([], comments);
-    arg_12 = Person.make(void 0, void 0, lastName, firstName, midInitials, email, phone, fax, address, affiliation, arg_10, arg_11);
-    return Person.setOrcidFromComments(arg_12);
+    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);
 }
 
 export function fromSparseTable(matrix) {
@@ -80,7 +80,7 @@ export function toSparseTable(persons) {
                 addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
             });
         }
-    }, map((arg) => Person.setCommentFromORCID(arg), persons));
+    }, map((person) => Person.setCommentFromORCID(person), persons));
     return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
         Equals: (x, y) => (x === y),
         GetHashCode: stringHash,

package/ISA/ISA.Spreadsheet/Metadata/Conversions.js

@@ -1,9 +1,9 @@
-import { equals } from "../../../fable_modules/fable-library.4.1.4/Util.js";
-import { value, some } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { map, equalsWith, fill, map3, fold } from "../../../fable_modules/fable-library.4.1.4/Array.js";
-import { toText, printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
+import { equals } from "../../../fable_modules/fable-library.4.4.1/Util.js";
+import { value, some } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { map, equalsWith, fill, map3, fold } from "../../../fable_modules/fable-library.4.4.1/Array.js";
+import { toText, printf, toFail } from "../../../fable_modules/fable-library.4.4.1/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.4.1.4/List.js";
+import { map as map_1, fold as fold_1, ofArray, empty } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { Array_map4 } from "../CollectionAux.js";
 import { Component_toString_Z609B8895, Component_fromString_Z61E08C1 } from "../../ISA/JsonTypes/Component.js";
 import { ProtocolParameter_toString_Z3A4310A5, ProtocolParameter_make } from "../../ISA/JsonTypes/ProtocolParameter.js";
@@ -85,7 +85,7 @@ export function OntologyAnnotation_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((arg) => OntologyAnnotation.toString(arg), oas));
+        }, ["", "", ""], map((oa) => OntologyAnnotation.toString(oa), oas));
         return {
             TermAccessionNumberAgg: tupledArg_1[2],
             TermNameAgg: tupledArg_1[0],
@@ -145,7 +145,7 @@ 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_3) => ((arg_2) => ProtocolParameter_make(void 0, arg_2))(arg_3), OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions));
+    return map((arg) => ((parameterName) => ProtocolParameter_make(void 0, parameterName))(arg), OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions));
 }
 
 /**

package/ISA/ISA.Spreadsheet/Metadata/DesignDescriptors.js

@@ -1,4 +1,4 @@
-import { ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { ofArray } from "../../../fable_modules/fable-library.4.4.1/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";

package/ISA/ISA.Spreadsheet/Metadata/Factors.js

@@ -1,13 +1,13 @@
-import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
 import { Option_fromValueWithDefault } from "./Conversions.js";
 import { Factor } from "../../ISA/JsonTypes/Factor.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 { Comment_toString, Comment_fromString } from "./Comment.js";
-import { defaultArg } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.4.1/Util.js";
 
 export const nameLabel = "Name";
 
@@ -21,9 +21,9 @@ export const labels = ofArray([nameLabel, factorTypeLabel, typeTermAccessionNumb
 
 export function fromString(name, designType, typeTermSourceREF, typeTermAccessionNumber, comments) {
     const factorType = OntologyAnnotation.fromString(designType, typeTermSourceREF, typeTermAccessionNumber);
-    const arg_2 = Option_fromValueWithDefault(OntologyAnnotation.empty, factorType);
-    const arg_3 = Option_fromValueWithDefault([], comments);
-    return Factor.make(void 0, name, arg_2, arg_3);
+    const factorType_1 = Option_fromValueWithDefault(OntologyAnnotation.empty, factorType);
+    const comments_1 = Option_fromValueWithDefault([], comments);
+    return Factor.make(void 0, name, factorType_1, comments_1);
 }
 
 export function fromSparseTable(matrix) {

package/ISA/ISA.Spreadsheet/Metadata/OntologyAnnotation.js

@@ -1,12 +1,12 @@
-import { reverse, cons, iterateIndexed, empty, ofArray, map, toArray, initialize, singleton, length } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { reverse, cons, iterateIndexed, empty, ofArray, map, toArray, initialize, singleton, length } from "../../../fable_modules/fable-library.4.4.1/List.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 { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
 import { Option_fromValueWithDefault } from "./Conversions.js";
 import { Comment_toString, Comment_fromString } from "./Comment.js";
-import { unwrap } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { unwrap } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.4.1/Util.js";
 
 export function fromSparseTable(label, labelTSR, labelTAN, matrix) {
     if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {

package/ISA/ISA.Spreadsheet/Metadata/OntologySourceReference.js

@@ -1,12 +1,12 @@
-import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { Option_fromValueWithDefault } from "./Conversions.js";
 import { OntologySourceReference } from "../../ISA/JsonTypes/OntologySourceReference.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 { Comment_toString, Comment_fromString } from "./Comment.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { defaultArg } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.4.1/Util.js";
 
 export const nameLabel = "Term Source Name";
 
@@ -19,8 +19,8 @@ export const descriptionLabel = "Term Source Description";
 export const labels = ofArray([nameLabel, fileLabel, versionLabel, descriptionLabel]);
 
 export function fromString(description, file, name, version, comments) {
-    const arg_4 = Option_fromValueWithDefault([], comments);
-    return OntologySourceReference.make(description, file, name, version, arg_4);
+    const comments_1 = Option_fromValueWithDefault([], comments);
+    return OntologySourceReference.make(description, file, name, version, comments_1);
 }
 
 export function fromSparseTable(matrix) {

package/ISA/ISA.Spreadsheet/Metadata/Protocols.js

@@ -1,14 +1,14 @@
-import { reverse, cons, iterate, iterateIndexed, map as map_1, initialize, singleton, length, empty, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { reverse, cons, iterate, iterateIndexed, map as map_1, initialize, singleton, length, empty, ofArray } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
 import { Component_toAggregatedStrings, ProtocolParameter_toAggregatedStrings, Option_fromValueWithDefault, Component_fromAggregatedStrings, ProtocolParameter_fromAggregatedStrings } from "./Conversions.js";
 import { Protocol_create_Z7DFD6E67, Protocol_make } from "../../ISA/JsonTypes/Protocol.js";
-import { defaultArg, map } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { defaultArg, map } from "../../../fable_modules/fable-library.4.4.1/Option.js";
 import { URIModule_fromString } from "../../ISA/JsonTypes/URI.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 { Comment_toString, Comment_fromString } from "./Comment.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.4.1/Util.js";
 
 export const nameLabel = "Name";
 

package/ISA/ISA.Spreadsheet/Metadata/Publication.js

@@ -1,14 +1,14 @@
-import { reverse, cons, iterateIndexed, empty, map as map_1, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { reverse, cons, iterateIndexed, empty, map as map_1, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
-import { defaultArg, map } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { defaultArg, map } from "../../../fable_modules/fable-library.4.4.1/Option.js";
 import { URIModule_fromString } from "../../ISA/JsonTypes/URI.js";
 import { Option_fromValueWithDefault } from "./Conversions.js";
 import { Publication } from "../../ISA/JsonTypes/Publication.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 { Comment_toString, Comment_fromString } from "./Comment.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.4.1/Util.js";
 
 export const pubMedIDLabel = "PubMed ID";
 
@@ -28,10 +28,10 @@ export const labels = ofArray([pubMedIDLabel, doiLabel, authorListLabel, titleLa
 
 export function fromString(pubMedID, doi, author, title, status, statusTermSourceREF, statusTermAccessionNumber, comments) {
     const status_1 = OntologyAnnotation.fromString(status, statusTermSourceREF, statusTermAccessionNumber);
-    const arg = map(URIModule_fromString, pubMedID);
-    const arg_4 = Option_fromValueWithDefault(OntologyAnnotation.empty, status_1);
-    const arg_5 = Option_fromValueWithDefault([], comments);
-    return Publication.make(arg, doi, author, title, arg_4, arg_5);
+    const pubMedID_1 = map(URIModule_fromString, pubMedID);
+    const status_2 = Option_fromValueWithDefault(OntologyAnnotation.empty, status_1);
+    const comments_1 = Option_fromValueWithDefault([], comments);
+    return Publication.make(pubMedID_1, doi, author, title, status_2, comments_1);
 }
 
 export function fromSparseTable(matrix) {

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

@@ -1,19 +1,19 @@
-import { append as append_1, delay, tryItem, length as length_1, isEmpty, iterate, fold, tryPick, maxBy, initialize, choose, map, indexed } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
-import { defaultArg, map as map_1 } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { tryFind, ofSeq } from "../../../fable_modules/fable-library.4.1.4/Map.js";
-import { arrayHash, equalArrays, equals, comparePrimitives } from "../../../fable_modules/fable-library.4.1.4/Util.js";
-import { RowBuilder_get_Empty, RowBuilder__Combine_19F30600, RowBuilder_$ctor } from "../../../fable_modules/FsSpreadsheet.4.1.0/DSL/RowBuilder.fs.js";
-import { CellBuilder_$ctor, CellBuilder__AsCellElement_825BA8D } from "../../../fable_modules/FsSpreadsheet.4.1.0/DSL/CellBuilder.fs.js";
-import { Messages_format, SheetEntity$1_some_2B595 } from "../../../fable_modules/FsSpreadsheet.4.1.0/DSL/Types.fs.js";
-import { DataType } from "../../../fable_modules/FsSpreadsheet.4.1.0/Cells/FsCell.fs.js";
-import { map as map_2, toArray, initialize as initialize_1, exists, find, cons, append, empty, singleton } from "../../../fable_modules/fable-library.4.1.4/List.js";
-import { ColumnIndex, RowElement } from "../../../fable_modules/FsSpreadsheet.4.1.0/DSL/Types.fs.js";
-import { Record } from "../../../fable_modules/fable-library.4.1.4/Types.js";
-import { record_type, list_type, class_type, tuple_type, int32_type, string_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { append as append_1, delay, tryItem, length as length_1, isEmpty, iterate, fold, tryPick, maxBy, initialize, choose, map, indexed } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
+import { defaultArg, map as map_1 } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { tryFind, ofSeq } from "../../../fable_modules/fable-library.4.4.1/Map.js";
+import { arrayHash, equalArrays, equals, comparePrimitives } from "../../../fable_modules/fable-library.4.4.1/Util.js";
+import { RowBuilder_get_Empty, RowBuilder__Combine_19F30600, RowBuilder_$ctor } from "../../../fable_modules/FsSpreadsheet.5.0.1/DSL/RowBuilder.fs.js";
+import { CellBuilder_$ctor, CellBuilder__AsCellElement_6F87C2ED } from "../../../fable_modules/FsSpreadsheet.5.0.1/DSL/CellBuilder.fs.js";
+import { Messages_format, SheetEntity$1_some_2B595 } from "../../../fable_modules/FsSpreadsheet.5.0.1/DSL/Types.fs.js";
+import { DataType } from "../../../fable_modules/FsSpreadsheet.5.0.1/Cells/FsCell.fs.js";
+import { map as map_2, toArray, initialize as initialize_1, exists, find, cons, append, empty, singleton } from "../../../fable_modules/fable-library.4.4.1/List.js";
+import { ColumnIndex, RowElement } from "../../../fable_modules/FsSpreadsheet.5.0.1/DSL/Types.fs.js";
+import { Record } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+import { record_type, list_type, class_type, tuple_type, int32_type, string_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
 import { Seq_trySkip, Dictionary_tryGetValue } from "../CollectionAux.js";
-import { addToDict, getItemFromDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { Dictionary } from "../../../fable_modules/fable-library.4.1.4/MutableMap.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
+import { addToDict, getItemFromDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { Dictionary } from "../../../fable_modules/fable-library.4.4.1/MutableMap.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.4.1/String.js";
 import { Comment$, Remark } from "../../ISA/JsonTypes/Comment.js";
 import { Comment_wrapCommentKey, Comment_$007CComment$007C_$007C, Remark_$007CRemark$007C_$007C } from "./Comment.js";
 
@@ -40,11 +40,11 @@ export function SparseRowModule_getAllValues(i) {
 
 export function SparseRowModule_fromFsRow(r) {
     return choose((c) => {
-        if (c.Value === "") {
+        if (equals(c.Value, "")) {
             return void 0;
         }
         else {
-            return [c.ColumnNumber - 1, c.Value];
+            return [c.ColumnNumber - 1, c.ValueAsString()];
         }
     }, r.Cells);
 }
@@ -63,11 +63,11 @@ export function SparseRowModule_tryGetValueAt(i, vs) {
 export function SparseRowModule_toDSLRow(vs) {
     const builder$0040 = RowBuilder_$ctor();
     let this$_9;
-    const arg = map((_arg) => {
+    const ns = map((_arg) => {
         const v = _arg;
         if (v == null) {
             let c_1;
-            const this$_5 = CellBuilder__AsCellElement_825BA8D(CellBuilder_$ctor(), SheetEntity$1_some_2B595(singleton([new DataType(0, []), ""])));
+            const this$_5 = CellBuilder__AsCellElement_6F87C2ED(CellBuilder_$ctor(), SheetEntity$1_some_2B595(singleton([new DataType(0, []), ""])));
             let matchResult, errs_1, f_1, ms_2_1;
             switch (this$_5.tag) {
                 case 1: {
@@ -137,7 +137,7 @@ export function SparseRowModule_toDSLRow(vs) {
         else {
             const v_1 = v;
             let c;
-            const this$_2 = CellBuilder__AsCellElement_825BA8D(CellBuilder_$ctor(), SheetEntity$1_some_2B595(singleton([new DataType(0, []), v_1])));
+            const this$_2 = CellBuilder__AsCellElement_6F87C2ED(CellBuilder_$ctor(), SheetEntity$1_some_2B595(singleton([new DataType(0, []), v_1])));
             let matchResult_2, errs, f, ms_2;
             switch (this$_2.tag) {
                 case 1: {
@@ -205,7 +205,7 @@ export function SparseRowModule_toDSLRow(vs) {
             return SheetEntity$1_some_2B595(singleton((c[1] == null) ? (new RowElement(1, [c[0]])) : (new RowElement(0, [new ColumnIndex(c[1]), c[0]]))));
         }
     }, SparseRowModule_getAllValues(vs));
-    this$_9 = fold((state, we) => RowBuilder__Combine_19F30600(builder$0040, state, we), RowBuilder_get_Empty(), arg);
+    this$_9 = fold((state, we) => RowBuilder__Combine_19F30600(builder$0040, state, we), RowBuilder_get_Empty(), ns);
     let matchResult_4, errs_2, f_3, ms_2_2;
     switch (this$_9.tag) {
         case 1: {
@@ -435,8 +435,8 @@ export function SparseTable_FromRows_Z5579EC29(en, labels, lineNumber, prefix) {
         return loop(SparseTable_Create_Z2192E64B(), empty(), lineNumber);
     }
     catch (err) {
-        const arg_9 = err.message;
-        return toFail(printf("Error parsing block in investigation file starting from line number %i: %s"))(lineNumber)(arg_9);
+        const arg_1 = err.message;
+        return toFail(printf("Error parsing block in investigation file starting from line number %i: %s"))(lineNumber)(arg_1);
     }
 }
 

package/ISA/ISA.Spreadsheet/Metadata/Study.js

@@ -1,14 +1,14 @@
-import { Record } from "../../../fable_modules/fable-library.4.1.4/Types.js";
-import { record_type, list_type, string_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { Record } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+import { record_type, list_type, string_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
 import { Comment$_$reflection } from "../../ISA/JsonTypes/Comment.js";
-import { ofSeq, append, toArray, reverse, cons, empty, map, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { ofSeq, append, toArray, reverse, cons, empty, map, ofArray } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { Comment_toString, Comment_fromString } from "./Comment.js";
 import { SparseRowModule_fromValues, SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "./SparseTable.js";
 import { Study_fileNameFromIdentifier, createMissingIdentifier } from "../../ISA/Identifier.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { defaultArg } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.4.1/Util.js";
 import { Option_fromValueWithDefault } from "./Conversions.js";
 import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
 import { ArcStudy } from "../../ISA/ArcTypes/ArcTypes.js";
@@ -18,7 +18,7 @@ import { toRows as toRows_3, fromRows as fromRows_3 } from "./Factors.js";
 import { toRows as toRows_4, fromRows as fromRows_4 } from "./Assays.js";
 import { toRows as toRows_5, fromRows as fromRows_5 } from "./Protocols.js";
 import { toRows as toRows_6, fromRows as fromRows_6 } from "./Contacts.js";
-import { singleton, append as append_1, delay, collect } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
+import { singleton, append as append_1, delay, collect } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
 
 export class StudyInfo extends Record {
     constructor(Identifier, Title, Description, SubmissionDate, PublicReleaseDate, FileName, Comments) {
@@ -87,20 +87,20 @@ export function StudyInfo_toRows_1B3D5E9B(study) {
 export function fromParts(studyInfo, designDescriptors, publications, factors, assays, protocols, contacts) {
     const assayIdentifiers = map((assay) => assay.Identifier, assays);
     let arcstudy;
-    const arg_1 = Option_fromValueWithDefault("", studyInfo.Title);
-    const arg_2 = Option_fromValueWithDefault("", studyInfo.Description);
-    const arg_3 = Option_fromValueWithDefault("", studyInfo.SubmissionDate);
-    const arg_4 = Option_fromValueWithDefault("", studyInfo.PublicReleaseDate);
-    const arg_5 = toArray(publications);
-    const arg_6 = toArray(contacts);
-    const arg_7 = toArray(designDescriptors);
-    let arg_8;
-    const arg_13 = map((arg_12) => ArcTable.fromProtocol(arg_12), protocols);
-    arg_8 = Array.from(arg_13);
-    const arg_9 = Array.from(assayIdentifiers);
-    const arg_10 = toArray(factors);
-    const arg_11 = toArray(studyInfo.Comments);
-    arcstudy = ArcStudy.make(studyInfo.Identifier, arg_1, arg_2, arg_3, arg_4, arg_5, arg_6, arg_7, arg_8, arg_9, arg_10, arg_11);
+    const title = Option_fromValueWithDefault("", studyInfo.Title);
+    const description = Option_fromValueWithDefault("", studyInfo.Description);
+    const submissionDate = Option_fromValueWithDefault("", studyInfo.SubmissionDate);
+    const publicReleaseDate = Option_fromValueWithDefault("", studyInfo.PublicReleaseDate);
+    const publications_1 = toArray(publications);
+    const contacts_1 = toArray(contacts);
+    const studyDesignDescriptors = toArray(designDescriptors);
+    let tables;
+    const collection = map((p) => ArcTable.fromProtocol(p), protocols);
+    tables = Array.from(collection);
+    const registeredAssayIdentifiers = Array.from(assayIdentifiers);
+    const factors_1 = toArray(factors);
+    const comments = toArray(studyInfo.Comments);
+    arcstudy = ArcStudy.make(studyInfo.Identifier, title, description, submissionDate, publicReleaseDate, publications_1, contacts_1, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors_1, comments);
     if (arcstudy.isEmpty && (arcstudy.Identifier === "")) {
         return void 0;
     }