@nfdi4plants/arctrl 1.1.0 → 1.2.0

package/ARC.js

@@ -1,17 +1,17 @@
-import { concat, fold, map, exactlyOne, choose } from "./fable_modules/fable-library.4.5.0/Array.js";
+import { concat, fold, map, exactlyOne, choose } from "./fable_modules/fable-library-js.4.13.0/Array.js";
 import { ARCtrl_ISA_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ISA_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ISA_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ISA_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49, ARCtrl_ISA_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ISA_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, ARCtrl_ISA_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, ARCtrl_ISA_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from "./Contracts/Contracts.ArcTypes.js";
-import { collect, empty, iterate, find, tryFind, map as map_1, singleton, append, delay, toList, toArray } from "./fable_modules/fable-library.4.5.0/Seq.js";
+import { collect, empty, iterate, find, tryFind, map as map_1, singleton, append, delay, toList, toArray } from "./fable_modules/fable-library-js.4.13.0/Seq.js";
 import { createRunsFolder, createWorkflowsFolder, createInvestigationFile, createStudyFolder, createStudiesFolder, createAssayFolder, createAssaysFolder } from "./FileSystemTree.js";
 import { FileSystemTree } from "./FileSystem/FileSystemTree.js";
 import { FileSystem } from "./FileSystem/FileSystem.js";
-import { bind, map as map_2, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library.4.5.0/Option.js";
+import { bind, map as map_2, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library-js.4.13.0/Option.js";
 import { getStudyFolderPath, getAssayFolderPath } from "./Path.js";
 import { Contract } from "./Contract/Contract.js";
-import { ofArray } from "./fable_modules/fable-library.4.5.0/List.js";
+import { ofArray } from "./fable_modules/fable-library-js.4.13.0/List.js";
 import { tryISAReadContractFromPath } from "./Contracts/Contracts.ARCtrl.js";
 import { ArcTables } from "./ISA/ISA/ArcTypes/ArcTables.js";
-import { comparePrimitives, safeHash } from "./fable_modules/fable-library.4.5.0/Util.js";
-import { addToDict } from "./fable_modules/fable-library.4.5.0/MapUtil.js";
+import { comparePrimitives, safeHash } from "./fable_modules/fable-library-js.4.13.0/Util.js";
+import { addToDict } from "./fable_modules/fable-library-js.4.13.0/MapUtil.js";
 import { toFsWorkbook, toLightFsWorkbook } from "./ISA/ISA.Spreadsheet/ArcInvestigation.js";
 import { ArcInvestigation } from "./ISA/ISA/ArcTypes/ArcTypes.js";
 import { Assay_fileNameFromIdentifier, Study_fileNameFromIdentifier } from "./ISA/ISA/Identifier.js";
@@ -19,9 +19,9 @@ import { ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9 } from "./I
 import { toFsWorkbook as toFsWorkbook_1 } from "./ISA/ISA.Spreadsheet/ArcAssay.js";
 import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.5.1.3/Cells/FsCellsCollection.fs.js";
 import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, Init_createInitContract_6DFDD678 } from "./Contracts/Contracts.Git.js";
-import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library.4.5.0/Set.js";
-import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library.4.5.0/Map.js";
-import { class_type } from "./fable_modules/fable-library.4.5.0/Reflection.js";
+import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library-js.4.13.0/Set.js";
+import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library-js.4.13.0/Map.js";
+import { class_type } from "./fable_modules/fable-library-js.4.13.0/Reflection.js";
 
 export function ARCAux_getArcAssaysFromContracts(contracts) {
     return choose(ARCtrl_ISA_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, contracts);

package/Contract/Contract.js

@@ -1,6 +1,6 @@
-import { Record } from "../fable_modules/fable-library.4.5.0/Types.js";
-import { class_type, option_type, record_type, array_type, string_type } from "../fable_modules/fable-library.4.5.0/Reflection.js";
-import { defaultArg } from "../fable_modules/fable-library.4.5.0/Option.js";
+import { Record } from "../fable_modules/fable-library-js.4.13.0/Types.js";
+import { class_type, option_type, record_type, array_type, string_type } from "../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { defaultArg } from "../fable_modules/fable-library-js.4.13.0/Option.js";
 
 export class CLITool extends Record {
     constructor(Name, Arguments) {

package/Contracts/Contracts.ArcTypes.js

@@ -1,12 +1,12 @@
+import { equalsWith, item } from "../fable_modules/fable-library-js.4.13.0/Array.js";
 import { combineMany } from "../FileSystem/Path.js";
-import { equalsWith } from "../fable_modules/fable-library.4.5.0/Array.js";
-import { defaultOf } from "../fable_modules/fable-library.4.5.0/Util.js";
-import { unwrap, defaultArg } from "../fable_modules/fable-library.4.5.0/Option.js";
+import { defaultOf } from "../fable_modules/fable-library-js.4.13.0/Util.js";
+import { unwrap, defaultArg } from "../fable_modules/fable-library-js.4.13.0/Option.js";
 import { fromFsWorkbook, toFsWorkbook, toLightFsWorkbook } from "../ISA/ISA.Spreadsheet/ArcInvestigation.js";
 import { Contract } from "../Contract/Contract.js";
 import { Assay_fileNameFromIdentifier, Study_fileNameFromIdentifier } from "../ISA/ISA/Identifier.js";
 import { ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D, ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9 } from "../ISA/ISA.Spreadsheet/ArcStudy.js";
-import { empty, singleton, collect, append, delay, toArray } from "../fable_modules/fable-library.4.5.0/Seq.js";
+import { empty, singleton, collect, append, delay, toArray } from "../fable_modules/fable-library-js.4.13.0/Seq.js";
 import { createAssayFolder, createStudyFolder, createStudiesFolder } from "../FileSystemTree.js";
 import { getAssayFolderPath, getStudyFolderPath } from "../Path.js";
 import { fromFsWorkbook as fromFsWorkbook_1, toFsWorkbook as toFsWorkbook_1 } from "../ISA/ISA.Spreadsheet/ArcAssay.js";
@@ -14,8 +14,8 @@ import { fromFsWorkbook as fromFsWorkbook_1, toFsWorkbook as toFsWorkbook_1 } fr
 export function $007CStudyPath$007C_$007C(input) {
     let matchResult;
     if (!equalsWith((x, y) => (x === y), input, defaultOf()) && (input.length === 3)) {
-        if (input[0] === "studies") {
-            if (input[2] === "isa.study.xlsx") {
+        if (item(0, input) === "studies") {
+            if (item(2, input) === "isa.study.xlsx") {
                 matchResult = 0;
             }
             else {
@@ -31,7 +31,7 @@ export function $007CStudyPath$007C_$007C(input) {
     }
     switch (matchResult) {
         case 0: {
-            const anyStudyName = input[1];
+            const anyStudyName = item(1, input);
             return combineMany(input);
         }
         default:
@@ -42,8 +42,8 @@ export function $007CStudyPath$007C_$007C(input) {
 export function $007CAssayPath$007C_$007C(input) {
     let matchResult;
     if (!equalsWith((x, y) => (x === y), input, defaultOf()) && (input.length === 3)) {
-        if (input[0] === "assays") {
-            if (input[2] === "isa.assay.xlsx") {
+        if (item(0, input) === "assays") {
+            if (item(2, input) === "isa.assay.xlsx") {
                 matchResult = 0;
             }
             else {
@@ -59,7 +59,7 @@ export function $007CAssayPath$007C_$007C(input) {
     }
     switch (matchResult) {
         case 0: {
-            const anyAssayName = input[1];
+            const anyAssayName = item(1, input);
             return combineMany(input);
         }
         default:
@@ -70,7 +70,7 @@ export function $007CAssayPath$007C_$007C(input) {
 export function $007CInvestigationPath$007C_$007C(input) {
     let matchResult;
     if (!equalsWith((x, y) => (x === y), input, defaultOf()) && (input.length === 1)) {
-        if (input[0] === "isa.investigation.xlsx") {
+        if (item(0, input) === "isa.investigation.xlsx") {
             matchResult = 0;
         }
         else {

package/Contracts/Contracts.Git.js

@@ -1,9 +1,9 @@
 import { Contract, CLITool } from "../Contract/Contract.js";
 import { dgi } from "../FileSystem/DefaultGitignore.js";
-import { class_type } from "../fable_modules/fable-library.4.5.0/Reflection.js";
-import { value, defaultArg } from "../fable_modules/fable-library.4.5.0/Option.js";
-import { replace } from "../fable_modules/fable-library.4.5.0/String.js";
-import { empty, singleton, append, delay, toArray } from "../fable_modules/fable-library.4.5.0/Seq.js";
+import { class_type } from "../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { value, defaultArg } from "../fable_modules/fable-library-js.4.13.0/Option.js";
+import { replace } from "../fable_modules/fable-library-js.4.13.0/String.js";
+import { empty, singleton, append, delay, toArray } from "../fable_modules/fable-library-js.4.13.0/Seq.js";
 
 export function gitWithArgs(arguments$) {
     return CLITool.create("git", arguments$);

package/FileSystem/Commit.js

@@ -1,5 +1,5 @@
-import { Record } from "../fable_modules/fable-library.4.5.0/Types.js";
-import { record_type, class_type, string_type } from "../fable_modules/fable-library.4.5.0/Reflection.js";
+import { Record } from "../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, class_type, string_type } from "../fable_modules/fable-library-js.4.13.0/Reflection.js";
 
 export class Commit extends Record {
     constructor(Hash, UserName, UserEmail, Date$, Message) {

package/FileSystem/FileSystem.js

@@ -1,9 +1,9 @@
-import { defaultArg } from "../fable_modules/fable-library.4.5.0/Option.js";
+import { defaultArg } from "../fable_modules/fable-library-js.4.13.0/Option.js";
 import { FileSystemTree_$reflection, FileSystemTree } from "./FileSystemTree.js";
-import { map, append } from "../fable_modules/fable-library.4.5.0/Array.js";
-import { Record } from "../fable_modules/fable-library.4.5.0/Types.js";
+import { map, append } from "../fable_modules/fable-library-js.4.13.0/Array.js";
+import { Record } from "../fable_modules/fable-library-js.4.13.0/Types.js";
 import { Commit_$reflection } from "./Commit.js";
-import { record_type, array_type } from "../fable_modules/fable-library.4.5.0/Reflection.js";
+import { record_type, array_type } from "../fable_modules/fable-library-js.4.13.0/Reflection.js";
 
 export class FileSystem extends Record {
     constructor(Tree, History) {

package/FileSystem/FileSystemTree.js

@@ -1,12 +1,12 @@
-import { unwrap, defaultArg } from "../fable_modules/fable-library.4.5.0/Option.js";
-import { append as append_1, choose, equalsWith, tail, head, map, tryFind } from "../fable_modules/fable-library.4.5.0/Array.js";
-import { singleton, append, delay, toArray } from "../fable_modules/fable-library.4.5.0/Seq.js";
-import { Array_distinct, Array_groupBy } from "../fable_modules/fable-library.4.5.0/Seq2.js";
-import { curry2, arrayHash, stringHash } from "../fable_modules/fable-library.4.5.0/Util.js";
+import { unwrap, defaultArg } from "../fable_modules/fable-library-js.4.13.0/Option.js";
+import { append as append_1, choose, equalsWith, tail, head, map, tryFind } from "../fable_modules/fable-library-js.4.13.0/Array.js";
+import { singleton, append, delay, toArray } from "../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { Array_distinct, Array_groupBy } from "../fable_modules/fable-library-js.4.13.0/Seq2.js";
+import { curry2, arrayHash, stringHash } from "../fable_modules/fable-library-js.4.13.0/Util.js";
 import { combineMany, split } from "./Path.js";
-import { empty, reverse, toArray as toArray_1, cons } from "../fable_modules/fable-library.4.5.0/List.js";
-import { Union } from "../fable_modules/fable-library.4.5.0/Types.js";
-import { union_type, array_type, string_type } from "../fable_modules/fable-library.4.5.0/Reflection.js";
+import { empty, reverse, toArray as toArray_1, cons } from "../fable_modules/fable-library-js.4.13.0/List.js";
+import { Union } from "../fable_modules/fable-library-js.4.13.0/Types.js";
+import { union_type, array_type, string_type } from "../fable_modules/fable-library-js.4.13.0/Reflection.js";
 
 export class FileSystemTree extends Union {
     constructor(tag, fields) {

package/FileSystem/Path.js

@@ -1,5 +1,5 @@
-import { trim, join, trimStart, trimEnd, split as split_1 } from "../fable_modules/fable-library.4.5.0/String.js";
-import { last, mapIndexed } from "../fable_modules/fable-library.4.5.0/Array.js";
+import { trim, join, trimStart, trimEnd, split as split_1 } from "../fable_modules/fable-library-js.4.13.0/String.js";
+import { last, mapIndexed } from "../fable_modules/fable-library-js.4.13.0/Array.js";
 
 export const seperators = ["/", "\\"];
 

package/FileSystemTree.js

@@ -1,5 +1,5 @@
 import { FileSystemTree } from "./FileSystem/FileSystemTree.js";
-import { append } from "./fable_modules/fable-library.4.5.0/Array.js";
+import { append } from "./fable_modules/fable-library-js.4.13.0/Array.js";
 
 export function createGitKeepFile() {
     return FileSystemTree.createFile(".gitkeep");

package/ISA/ISA/ArcTypes/ArcTable.js

@@ -1,15 +1,15 @@
-import { Dictionary } from "../../../fable_modules/fable-library.4.5.0/MutableMap.js";
-import { compareArrays, safeHash, disposeSafe, getEnumerator, comparePrimitives, equals, arrayHash, equalArrays } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { value as value_9, map as map_2, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { Dictionary } from "../../../fable_modules/fable-library-js.4.13.0/MutableMap.js";
+import { compareArrays, safeHash, disposeSafe, getEnumerator, comparePrimitives, equals, arrayHash, equalArrays } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { value as value_9, map as map_2, defaultArg, unwrap } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
 import { boxHashValues, Unchecked_extendToRowCount, ProcessParsing_processToRows, ProcessParsing_alignByHeaders, ProcessParsing_mergeIdenticalProcesses, ProcessParsing_getProcessGetter, Unchecked_removeRowCells_withIndexChange, Unchecked_addRows, Unchecked_addRow, Unchecked_getEmptyCellForHeader, Unchecked_removeColumnCells_withIndexChange, tryFindDuplicateUniqueInArray, Unchecked_removeColumnCells, Unchecked_removeHeader, Unchecked_fillMissingCells, Unchecked_addColumn, tryFindDuplicateUnique, Unchecked_setCellAt, SanityChecks_validateColumn, SanityChecks_validateRowIndex, SanityChecks_validateColumnIndex, Unchecked_tryGetCellAt, getRowCount, getColumnCount } from "./ArcTableAux.js";
-import { item, append as append_1, indexed as indexed_1, choose, toList, zip, fold, filter, length, tryFindIndex, empty, singleton, collect, removeAt, map, delay, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
-import { rangeDouble } from "../../../fable_modules/fable-library.4.5.0/Range.js";
+import { item as item_1, append as append_1, indexed as indexed_1, choose, toList, zip, fold, filter, length, tryFindIndex, empty, singleton, collect, removeAt, map, delay, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { rangeDouble } from "../../../fable_modules/fable-library-js.4.13.0/Range.js";
 import { CompositeColumn } from "./CompositeColumn.js";
-import { sortBy, indexed, mapIndexed, singleton as singleton_1, initialize, sortDescending, iterateIndexed, map as map_1 } from "../../../fable_modules/fable-library.4.5.0/Array.js";
-import { append, collect as collect_1, initialize as initialize_1, singleton as singleton_2, empty as empty_1, iterate, isEmpty } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../../fable_modules/fable-library.4.5.0/System.Text.js";
-import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
-import { join, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { sortBy, indexed, mapIndexed, singleton as singleton_1, initialize, item, sortDescending, iterateIndexed, map as map_1 } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
+import { append, collect as collect_1, initialize as initialize_1, singleton as singleton_2, empty as empty_1, iterate, isEmpty } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
+import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../../fable_modules/fable-library-js.4.13.0/System.Text.js";
+import { toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { join, printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
 import { CompositeCell } from "./CompositeCell.js";
 import { CompositeHeader } from "./CompositeHeader.js";
 import { createMissingIdentifier } from "../Identifier.js";
@@ -18,12 +18,12 @@ import { Protocol_create_Z7DFD6E67, Protocol_addComponent, Protocol_addParameter
 import { OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { ProtocolParameter } from "../JsonTypes/ProtocolParameter.js";
 import { Component_create_61502994 } from "../JsonTypes/Component.js";
-import { Array_groupBy, List_distinct } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
+import { Array_groupBy, List_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
 import { toProtocol } from "./CompositeRow.js";
 import { Process_create_Z42860F3E } from "../JsonTypes/Process.js";
-import { getItemFromDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
+import { getItemFromDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
 import { HashCodes_boxHashSeq, HashCodes_boxHashArray } from "../Helper.js";
-import { class_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
+import { class_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
 
 export class ArcTable {
     constructor(name, headers, values) {
@@ -422,7 +422,7 @@ export class ArcTable {
         }
         for (let columnIndex_1 = 0; columnIndex_1 <= (this$.ColumnCount - 1); columnIndex_1++) {
             const h_1 = this$.Headers[columnIndex_1];
-            SanityChecks_validateColumn(CompositeColumn.create(h_1, [cells_1[columnIndex_1]]));
+            SanityChecks_validateColumn(CompositeColumn.create(h_1, [item(columnIndex_1, cells_1)]));
         }
         Unchecked_addRow(index_1, cells_1, this$.Headers, this$.Values);
     }
@@ -496,10 +496,10 @@ export class ArcTable {
             }
         });
         for (let idx = 0; idx <= (rows.length - 1); idx++) {
-            const row_1 = rows[idx];
+            const row_1 = item(idx, rows);
             for (let columnIndex = 0; columnIndex <= (this$.ColumnCount - 1); columnIndex++) {
                 const h = this$.Headers[columnIndex];
-                SanityChecks_validateColumn(CompositeColumn.create(h, [row_1[columnIndex]]));
+                SanityChecks_validateColumn(CompositeColumn.create(h, [item(columnIndex, row_1)]));
             }
         }
         Unchecked_addRows(index_1, rows, this$.Headers, this$.Values);
@@ -807,7 +807,7 @@ export class ArcTable {
         Unchecked_extendToRowCount(annotationTable_1.RowCount, refTable_1.Headers, refTable_1.Values);
         const arr = annotationTable_1.Columns;
         for (let idx = 0; idx <= (arr.length - 1); idx++) {
-            const c = arr[idx];
+            const c = item(idx, arr);
             refTable_1.AddColumn(c.Header, c.Cells, void 0, true);
         }
         return refTable_1;
@@ -834,7 +834,7 @@ export class ArcTable {
             else {
                 return false;
             }
-        }, true, toList(delay(() => map((i) => equals(item(i, a), item(i, b)), rangeDouble(0, 1, length(a) - 1))))))))) {
+        }, true, toList(delay(() => map((i) => equals(item_1(i, a), item_1(i, b)), rangeDouble(0, 1, length(a) - 1))))))))) {
             const a_1 = sort(this$.Values);
             const b_1 = sort(other.Values);
             return (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
@@ -844,7 +844,7 @@ export class ArcTable {
                 else {
                     return false;
                 }
-            }, true, toList(delay(() => map((i_1) => equals(item(i_1, a_1), item(i_1, b_1)), rangeDouble(0, 1, length(a_1) - 1)))));
+            }, true, toList(delay(() => map((i_1) => equals(item_1(i_1, a_1), item_1(i_1, b_1)), rangeDouble(0, 1, length(a_1) - 1)))));
         }
         else {
             return false;

package/ISA/ISA/ArcTypes/ArcTableAux.js

@@ -1,25 +1,25 @@
-import { addToDict, getItemFromDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
-import { map as map_2, defaultArg, unwrap, value as value_9, some } from "../../../fable_modules/fable-library.4.5.0/Option.js";
-import { empty as empty_1, singleton as singleton_1, append, delay, map as map_1, tryPick, toList, indexed, head as head_1, toArray, filter, tryFindIndex, maxBy } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
-import { arrayHash, equalArrays, stringHash, int32ToString, numberHash, disposeSafe, getEnumerator, compare, equals, safeHash, comparePrimitives } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { pick, exists, zip, append as append_1, sortBy, tryPick as tryPick_1, collect, mapIndexed, item, length, map as map_3, ofArray as ofArray_2, singleton, choose, ofSeq, empty, head, tail as tail_1, isEmpty, cons } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { addToDict, getItemFromDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
+import { map as map_2, defaultArg, unwrap, value as value_9, some } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
+import { empty as empty_1, singleton as singleton_1, append, delay, map as map_1, tryPick, toList, indexed, head as head_1, toArray, filter, tryFindIndex, maxBy } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { arrayHash, equalArrays, stringHash, int32ToString, numberHash, disposeSafe, getEnumerator, compare, equals, safeHash, comparePrimitives } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { pick, exists, zip, append as append_1, sortBy, tryPick as tryPick_1, collect, mapIndexed, item as item_1, length, map as map_3, ofArray as ofArray_2, singleton, choose, ofSeq, empty, head, tail as tail_1, isEmpty, cons } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
 import { CompositeCell } from "./CompositeCell.js";
-import { max } from "../../../fable_modules/fable-library.4.5.0/Double.js";
-import { map, iterateIndexed } from "../../../fable_modules/fable-library.4.5.0/Array.js";
-import { tryFind, ofArray } from "../../../fable_modules/fable-library.4.5.0/Map.js";
-import { List_groupBy, Array_groupBy } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
-import { FSharpSet__Contains, ofArray as ofArray_1 } from "../../../fable_modules/fable-library.4.5.0/Set.js";
+import { max } from "../../../fable_modules/fable-library-js.4.13.0/Double.js";
+import { item, map, iterateIndexed } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
+import { tryFind, ofArray } from "../../../fable_modules/fable-library-js.4.13.0/Map.js";
+import { List_groupBy, Array_groupBy } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
+import { FSharpSet__Contains, ofArray as ofArray_1 } from "../../../fable_modules/fable-library-js.4.13.0/Set.js";
 import { Value as Value_1 } from "../JsonTypes/Value.js";
 import { Component_fromOptions } from "../JsonTypes/Component.js";
 import { ProtocolParameter } from "../JsonTypes/ProtocolParameter.js";
 import { ProcessParameterValue } from "../JsonTypes/ProcessParameterValue.js";
 import { FactorValue_create_18335379 } from "../JsonTypes/FactorValue.js";
 import { Factor } from "../JsonTypes/Factor.js";
-import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
+import { toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
 import { MaterialAttributeValue_create_7F714043 } from "../JsonTypes/MaterialAttributeValue.js";
 import { MaterialAttribute_create_Z6C54B221 } from "../JsonTypes/MaterialAttribute.js";
 import { ProcessInput_getCharacteristicValues_102B6859, ProcessInput__isMaterial, ProcessInput__isData, ProcessInput_setCharacteristicValues, ProcessInput__get_Name, ProcessInput__isSource, ProcessInput__isSample, ProcessInput, ProcessInput_createDerivedData_Z721C83C5, ProcessInput_createRawData_Z721C83C5, ProcessInput_createImageFile_Z721C83C5, ProcessInput_createMaterial_2363974C, ProcessInput_createSample_Z6DF16D07, ProcessInput_createSource_7888CE42 } from "../JsonTypes/ProcessInput.js";
-import { remove, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { remove, printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
 import { ProcessOutput_getFactorValues_11830B70, ProcessOutput__isMaterial, ProcessOutput__isData, ProcessOutput_setFactorValues, ProcessOutput__get_Name, ProcessOutput__isSample, ProcessOutput, ProcessOutput_createDerivedData_Z721C83C5, ProcessOutput_createRawData_Z721C83C5, ProcessOutput_createImageFile_Z721C83C5, ProcessOutput_createMaterial_2363974C, ProcessOutput_createSample_Z6DF16D07 } from "../JsonTypes/ProcessOutput.js";
 import { IOType, CompositeHeader } from "./CompositeHeader.js";
 import { tryGetFactorColumnIndex, tryGetCharacteristicColumnIndex, tryGetComponentIndex, tryGetParameterColumnIndex, ARCtrl_ISA_OntologyAnnotation__OntologyAnnotation_SetColumnIndex_Z524259A4 } from "../JsonTypes/ColumnIndex.js";
@@ -29,7 +29,7 @@ import { Process_create_Z42860F3E, Process_decomposeName_Z721C83C5, Process_make
 import { List_tryPickAndRemove, HashCodes_boxHashSeq, Option_fromValueWithDefault } from "../Helper.js";
 import { Protocol_make } from "../JsonTypes/Protocol.js";
 import { createMissingIdentifier } from "../Identifier.js";
-import { Dictionary } from "../../../fable_modules/fable-library.4.5.0/MutableMap.js";
+import { Dictionary } from "../../../fable_modules/fable-library-js.4.13.0/MutableMap.js";
 
 /**
  * Lookup an element in the dictionary, returning a <c>Some</c> value if the element is in the domain
@@ -455,7 +455,7 @@ export function Unchecked_addRows(index, newRows, headers, values) {
     for (let idx = 0; idx <= (newRows.length - 1); idx++) {
         const setNewCells = iterateIndexed((columnIndex_1, cell) => {
             Unchecked_setCellAt(columnIndex_1, currentRowIndex, cell, values);
-        }, newRows[idx]);
+        }, item(idx, newRows));
         currentRowIndex = ((currentRowIndex + 1) | 0);
     }
 }
@@ -945,7 +945,7 @@ export function ProcessParsing_getProcessGetter(processNameRoot, headers) {
         let patternInput;
         const inputs = inputGetter_1(matrix_4)(i_4);
         const outputs = outputGetter_1(matrix_4)(i_4);
-        patternInput = (((length(inputs) === 1) && (length(outputs) === 2)) ? [ofArray_2([item(0, inputs), item(0, inputs)]), outputs] : (((length(inputs) === 2) && (length(outputs) === 1)) ? [inputs, ofArray_2([item(0, outputs), item(0, outputs)])] : [inputs, outputs]));
+        patternInput = (((length(inputs) === 1) && (length(outputs) === 2)) ? [ofArray_2([item_1(0, inputs), item_1(0, inputs)]), outputs] : (((length(inputs) === 2) && (length(outputs) === 1)) ? [inputs, ofArray_2([item_1(0, outputs), item_1(0, outputs)])] : [inputs, outputs]));
         return Process_make(void 0, pn, protocol, paramvalues, void 0, void 0, void 0, void 0, patternInput[0], patternInput[1], void 0);
     });
 }
@@ -1006,7 +1006,7 @@ export function ProcessParsing_mergeIdenticalProcesses(processes) {
         const _arg = tupledArg[0];
         const processes_1 = tupledArg[1];
         const n = _arg[0];
-        const pVs = item(0, processes_1).ParameterValues;
+        const pVs = item_1(0, processes_1).ParameterValues;
         const inputs = Option_fromValueWithDefault(empty(), collect((p) => defaultArg(p.Inputs, empty()), processes_1));
         const outputs = Option_fromValueWithDefault(empty(), collect((p_1) => defaultArg(p_1.Outputs, empty()), processes_1));
         return Process_create_Z42860F3E(void 0, (length(l) > 1) ? Process_composeName(n, i) : n, _arg[1], pVs, void 0, void 0, void 0, void 0, inputs, outputs);

package/ISA/ISA/ArcTypes/ArcTables.js

@@ -1,17 +1,17 @@
-import { append, toArray, reduce, choose, map as map_1, delay, toList, length, findIndex, tryFindIndex } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { append, toArray, reduce, choose, map as map_1, delay, toList, length, findIndex, tryFindIndex } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
 import { Dict_tryFind } from "../Helper.js";
-import { addToSet, addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
-import { toIterator, equals, comparePrimitives, stringHash, compare, disposeSafe, getEnumerator } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { bind, map as map_3, unwrap, defaultArg, value as value_2 } from "../../../fable_modules/fable-library.4.5.0/Option.js";
-import { collect as collect_1, map as map_4, insertRangeInPlace, fold } from "../../../fable_modules/fable-library.4.5.0/Array.js";
+import { addToSet, addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
+import { toIterator, equals, comparePrimitives, stringHash, compare, disposeSafe, getEnumerator } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { bind, map as map_3, unwrap, defaultArg, value as value_2 } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
+import { collect as collect_1, map as map_4, item, insertRangeInPlace, fold } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
 import { CompositeHeader } from "./CompositeHeader.js";
-import { Array_groupBy, distinct } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
-import { FSharpSet__get_IsEmpty, ofSeq, intersect } from "../../../fable_modules/fable-library.4.5.0/Set.js";
+import { Array_groupBy, distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
+import { FSharpSet__get_IsEmpty, ofSeq, intersect } from "../../../fable_modules/fable-library-js.4.13.0/Set.js";
 import { ArcTable } from "./ArcTable.js";
-import { map as map_2, collect } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { map as map_2, collect } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
 import { Unchecked_fillMissingCells, ProcessParsing_groupProcesses, ProcessParsing_processToRows, ProcessParsing_alignByHeaders } from "./ArcTableAux.js";
-import { tryFind, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.5.0/Map.js";
-import { class_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
+import { tryFind, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library-js.4.13.0/Map.js";
+import { class_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
 
 /**
  * If a table with the given name exists in the TableList, returns it, else returns None.
@@ -433,7 +433,7 @@ export class ArcTables {
         let collection, s, array;
         const keepUnusedRefTables_1 = defaultArg(keepUnusedRefTables, false);
         const usedTables = new Set([]);
-        const referenceTableMap = ofSeq_1(choose((t) => map_3((c) => [c.Cells[0].AsFreeText, t], t.TryGetProtocolNameColumn()), referenceTables.Tables), {
+        const referenceTableMap = ofSeq_1(choose((t) => map_3((c) => [item(0, c.Cells).AsFreeText, t], t.TryGetProtocolNameColumn()), referenceTables.Tables), {
             Compare: comparePrimitives,
         });
         return new ArcTables((collection = ((s = map_4((t_3) => {

package/ISA/ISA/ArcTypes/ArcTypes.js

@@ -1,25 +1,25 @@
-import { map as map_1, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.5.0/Option.js";
-import { concat, collect, append as append_4, tryFind, removeAt, tryFindIndex, exists, choose, item, map as map_2, delay, toList, fold, length, forAll, contains, filter, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
-import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { addRangeInPlace, removeInPlace, equalsWith, append as append_3, contains as contains_1, map } from "../../../fable_modules/fable-library.4.5.0/Array.js";
-import { distinctBy, Array_distinct } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
-import { printf, toText } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { map as map_1, defaultArg, unwrap } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
+import { concat, collect, append as append_4, tryFind, removeAt, tryFindIndex, exists, choose, item, map as map_2, delay, toList, fold, length, forAll, contains, filter, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { addRangeInPlace, removeInPlace, equalsWith, append as append_3, contains as contains_1, map } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
+import { distinctBy, Array_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
+import { printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
 import { ActivePatterns_$007CRegex$007C_$007C } from "../Regex.js";
 import { OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { Value } from "../JsonTypes/Value.js";
 import { ArcTablesAux_applyIOMap, ArcTablesAux_getIOMap, ArcTables_$reflection, ArcTables } from "./ArcTables.js";
 import { AssayMaterials_get_empty, AssayMaterials_create_Z253F0553 } from "../JsonTypes/AssayMaterials.js";
 import { ResizeArray_choose, ResizeArray_filter, ResizeArray_map, HashCodes_boxHashOption, HashCodes_boxHashArray, Option_fromValueWithDefault } from "../Helper.js";
-import { unzip, ofSeq, map as map_3, toArray as toArray_1, ofArray, empty } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { unzip, ofSeq, map as map_3, toArray as toArray_1, ofArray, empty } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
 import { getSources, getProtocols, getUnits, getCharacteristics, getData, getMaterials, getSamples } from "../JsonTypes/ProcessSequence.js";
 import { Assay_create_3D372A24 } from "../JsonTypes/Assay.js";
 import { Study_identifierFromFileName, Study_fileNameFromIdentifier, Assay_identifierFromFileName, createMissingIdentifier, Assay_fileNameFromIdentifier, isMissingIdentifier } from "../Identifier.js";
-import { rangeDouble } from "../../../fable_modules/fable-library.4.5.0/Range.js";
-import { class_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
+import { rangeDouble } from "../../../fable_modules/fable-library-js.4.13.0/Range.js";
+import { class_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
 import { StudyMaterials_get_empty, StudyMaterials_create_1BE9FA55 } from "../JsonTypes/StudyMaterials.js";
 import { Study_create_Z2D28E954 } from "../JsonTypes/Study.js";
 import { Investigation_create_4AD66BBE } from "../JsonTypes/Investigation.js";
-import { FSharpRef } from "../../../fable_modules/fable-library.4.5.0/Types.js";
+import { FSharpRef } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
 
 export class ArcAssay extends ArcTables {
     constructor(identifier, measurementType, technologyType, technologyPlatform, tables, performers, comments) {

package/ISA/ISA/ArcTypes/CompositeCell.js

@@ -1,8 +1,8 @@
-import { int32ToString } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { int32ToString } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
 import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
-import { Union } from "../../../fable_modules/fable-library.4.5.0/Types.js";
-import { union_type, string_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
+import { Union } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { union_type, string_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
 
 export class CompositeCell extends Union {
     constructor(tag, fields) {

package/ISA/ISA/ArcTypes/CompositeColumn.js

@@ -1,9 +1,10 @@
-import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
-import { fold, empty, singleton, collect, delay, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
+import { item } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
+import { fold, empty, singleton, collect, delay, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
 import { CompositeCell_$reflection, CompositeCell } from "./CompositeCell.js";
-import { Record } from "../../../fable_modules/fable-library.4.5.0/Types.js";
+import { Record } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
 import { CompositeHeader_$reflection } from "./CompositeHeader.js";
-import { record_type, array_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
+import { record_type, array_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
 
 export class CompositeColumn extends Record {
     constructor(Header, Cells) {
@@ -22,15 +23,15 @@ export class CompositeColumn extends Record {
         if (cells.length === 0) {
             return true;
         }
-        else if (header.IsTermColumn && (cells[0].isTerm ? true : cells[0].isUnitized)) {
+        else if (header.IsTermColumn && (item(0, cells).isTerm ? true : item(0, cells).isUnitized)) {
             return true;
         }
-        else if (!header.IsTermColumn && cells[0].isFreeText) {
+        else if (!header.IsTermColumn && item(0, cells).isFreeText) {
             return true;
         }
         else {
             if (raiseExeption) {
-                throw new Error(`Invalid combination of header \`${header}\` and cells \`${cells[0]}\``);
+                throw new Error(`Invalid combination of header \`${header}\` and cells \`${item(0, cells)}\``);
             }
             return false;
         }

package/ISA/ISA/ArcTypes/CompositeHeader.js

@@ -1,9 +1,9 @@
-import { map } from "../../../fable_modules/fable-library.4.5.0/Array.js";
-import { union_type, string_type, getUnionCases, name } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
-import { Union, toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
+import { map } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
+import { union_type, string_type, getUnionCases, name } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Union, toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
 import { ActivePatterns_$007CTermColumn$007C_$007C, Pattern_OutputPattern, Pattern_InputPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseIOTypeHeader } from "../Regex.js";
-import { equals } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { equals } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
 import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { ProtocolParameter } from "../JsonTypes/ProtocolParameter.js";
 import { Factor } from "../JsonTypes/Factor.js";

package/ISA/ISA/ArcTypes/CompositeRow.js

@@ -1,4 +1,4 @@
-import { fold } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { fold } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
 import { Protocol_create_Z7DFD6E67, Protocol_addComponent, Protocol_addParameter, Protocol_setName, Protocol_setDescription, Protocol_setUri, Protocol_setVersion, Protocol_setProtocolType } from "../JsonTypes/Protocol.js";
 import { ProtocolParameter } from "../JsonTypes/ProtocolParameter.js";
 import { Component_create_61502994 } from "../JsonTypes/Component.js";

package/ISA/ISA/Builder/Types.js

@@ -1,15 +1,15 @@
-import { Union } from "../../../fable_modules/fable-library.4.5.0/Types.js";
-import { list_type, union_type, string_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
+import { Union } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { list_type, union_type, string_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
 import { OntologyAnnotation_$reflection } from "../JsonTypes/OntologyAnnotation.js";
 import { Protocol_get_empty, Protocol } from "../JsonTypes/Protocol.js";
 import { ProcessParameterValue_$reflection } from "../JsonTypes/ProcessParameterValue.js";
 import { MaterialAttributeValue_$reflection } from "../JsonTypes/MaterialAttributeValue.js";
 import { FactorValue_$reflection } from "../JsonTypes/FactorValue.js";
-import { map as map_1, exists, fold, singleton, empty, append } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { map, value as value_4, defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { map as map_1, exists, fold, singleton, empty, append } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
+import { map, value as value_4, defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
 import { Process_get_empty, Process } from "../JsonTypes/Process.js";
 import { Assay_get_empty, Assay } from "../JsonTypes/Assay.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
 import { Study } from "../JsonTypes/Study.js";
 
 export class ProtocolTransformation extends Union {

package/ISA/ISA/Fable.js

@@ -1,9 +1,9 @@
-import { toString } from "../../fable_modules/fable-library.4.5.0/Types.js";
-import { map, reduce, append } from "../../fable_modules/fable-library.4.5.0/Seq.js";
-import { append as append_1 } from "../../fable_modules/fable-library.4.5.0/List.js";
-import { append as append_2 } from "../../fable_modules/fable-library.4.5.0/Array.js";
-import { Array_distinct, List_distinct, distinct } from "../../fable_modules/fable-library.4.5.0/Seq2.js";
-import { identityHash, structuralHash, equals } from "../../fable_modules/fable-library.4.5.0/Util.js";
+import { toString } from "../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { map, reduce, append } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { append as append_1 } from "../../fable_modules/fable-library-js.4.13.0/List.js";
+import { append as append_2 } from "../../fable_modules/fable-library-js.4.13.0/Array.js";
+import { Array_distinct, List_distinct, distinct } from "../../fable_modules/fable-library-js.4.13.0/Seq2.js";
+import { identityHash, structuralHash, equals } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
 
 export function isList_python(l1) {
     return (to_string(type(l1))).indexOf("FSharpList") >= 0;