@nfdi4plants/arctrl 1.0.0-beta.1 → 1.0.0-beta.2

package/ARC.js

@@ -1,27 +1,27 @@
-import { concat, fold, exactlyOne, choose, map } from "./fable_modules/fable-library.4.1.4/Array.js";
+import { concat, fold, exactlyOne, choose, map } from "./fable_modules/fable-library.4.4.1/Array.js";
 import { toFsWorkbook as toFsWorkbook_1, fromFsWorkbook } from "./ISA/ISA.Spreadsheet/ArcAssay.js";
 import { tryFromContract } from "./Contracts/Contracts.ArcAssay.js";
 import { ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9, ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D } from "./ISA/ISA.Spreadsheet/ArcStudy.js";
 import { tryFromContract as tryFromContract_1 } from "./Contracts/Contracts.ArcStudy.js";
 import { toFsWorkbook, fromFsWorkbook as fromFsWorkbook_1 } from "./ISA/ISA.Spreadsheet/ArcInvestigation.js";
 import { tryFromContract as tryFromContract_2 } from "./Contracts/Contracts.ArcInvestigation.js";
-import { collect, toList, empty, singleton, append, delay, iterate, find, tryFind, toArray } from "./fable_modules/fable-library.4.1.4/Seq.js";
+import { collect, toList, empty, singleton, append, delay, iterate, find, tryFind, toArray } from "./fable_modules/fable-library.4.4.1/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_1, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library.4.1.4/Option.js";
+import { bind, map as map_1, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library.4.4.1/Option.js";
 import { tryISAReadContractFromPath } from "./Contracts/Contracts.ARCtrl.js";
 import { ArcTables } from "./ISA/ISA/ArcTypes/ArcTables.js";
-import { addToDict } from "./fable_modules/fable-library.4.1.4/MapUtil.js";
+import { addToDict } from "./fable_modules/fable-library.4.4.1/MapUtil.js";
 import { ArcInvestigation } from "./ISA/ISA/ArcTypes/ArcTypes.js";
 import { Assay_fileNameFromIdentifier, Study_fileNameFromIdentifier } from "./ISA/ISA/Identifier.js";
-import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.5.0.0/Cells/FsCellsCollection.fs.js";
+import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.5.0.1/Cells/FsCellsCollection.fs.js";
 import { Contract } from "./Contract/Contract.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.4.1.4/Set.js";
-import { comparePrimitives } from "./fable_modules/fable-library.4.1.4/Util.js";
-import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library.4.1.4/Map.js";
-import { class_type } from "./fable_modules/fable-library.4.1.4/Reflection.js";
+import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library.4.4.1/Set.js";
+import { comparePrimitives } from "./fable_modules/fable-library.4.4.1/Util.js";
+import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library.4.4.1/Map.js";
+import { class_type } from "./fable_modules/fable-library.4.4.1/Reflection.js";
 
 export function ARCAux_getArcAssaysFromContracts(contracts) {
     return map(fromFsWorkbook, choose(tryFromContract, contracts));
@@ -47,23 +47,23 @@ export function ARCAux_updateFSByISA(isa, fs) {
     const assays = createAssaysFolder(map(createAssayFolder, patternInput[1]));
     const studies = createStudiesFolder(map(createStudyFolder, patternInput[0]));
     const investigation = createInvestigationFile();
-    let tree;
-    const arg = FileSystemTree.createRootFolder([investigation, assays, studies]);
-    tree = FileSystem.create({
-        tree: arg,
+    let tree_1;
+    const tree = FileSystemTree.createRootFolder([investigation, assays, studies]);
+    tree_1 = FileSystem.create({
+        tree: tree,
     });
-    return fs.Union(tree);
+    return fs.Union(tree_1);
 }
 
 export function ARCAux_updateFSByCWL(cwl, fs) {
     const workflows = createWorkflowsFolder([]);
     const runs = createRunsFolder([]);
-    let tree;
-    const arg = FileSystemTree.createRootFolder([workflows, runs]);
-    tree = FileSystem.create({
-        tree: arg,
+    let tree_1;
+    const tree = FileSystemTree.createRootFolder([workflows, runs]);
+    tree_1 = FileSystem.create({
+        tree: tree,
     });
-    return fs.Union(tree);
+    return fs.Union(tree_1);
 }
 
 export class ARC {
@@ -181,7 +181,7 @@ export class ARC {
         return new ARC(unwrap(isaCopy), this$._cwl, fsCopy);
     }
     GetRegisteredPayload(IgnoreHidden) {
-        let tree, arg, array_3;
+        let tree, paths, array_3;
         const this$ = this;
         const registeredStudies = defaultArg(map_1((isa) => isa.Studies.slice(), map_1((i) => i.Copy(), this$._isa)), []);
         const registeredAssays = concat(map((s) => s.RegisteredAssays.slice(), registeredStudies));
@@ -219,17 +219,17 @@ export class ARC {
             else {
                 return tree_1;
             }
-        }, (tree = ((arg = ((array_3 = FileSystemTree.toFilePaths()(fsCopy.Tree), array_3.filter((p) => {
+        }, (tree = ((paths = ((array_3 = FileSystemTree.toFilePaths()(fsCopy.Tree), array_3.filter((p) => {
             if ((p.indexOf("workflows") === 0) ? true : (p.indexOf("runs") === 0)) {
                 return true;
             }
             else {
                 return FSharpSet__Contains(includeFiles, p);
             }
-        }))), FileSystemTree.fromFilePaths(arg))), ignoreHidden ? FileSystemTree.filterFiles((n) => !(n.indexOf(".") === 0))(tree) : tree)), FileSystemTree.fromFilePaths([]));
+        }))), FileSystemTree.fromFilePaths(paths))), ignoreHidden ? FileSystemTree.filterFiles((n) => !(n.indexOf(".") === 0))(tree) : tree)), FileSystemTree.fromFilePaths([]));
     }
     GetAdditionalPayload(IgnoreHidden) {
-        let tree, arg, array;
+        let tree, paths, array;
         const this$ = this;
         const ignoreHidden = defaultArg(IgnoreHidden, true);
         const registeredPayload = ofSeq(FileSystemTree.toFilePaths()(this$.GetRegisteredPayload()), {
@@ -242,7 +242,7 @@ export class ARC {
             else {
                 return tree_1;
             }
-        }, (tree = ((arg = ((array = FileSystemTree.toFilePaths()(this$._fs.Copy().Tree), array.filter((p) => !FSharpSet__Contains(registeredPayload, p)))), FileSystemTree.fromFilePaths(arg))), ignoreHidden ? FileSystemTree.filterFiles((n) => !(n.indexOf(".") === 0))(tree) : tree)), FileSystemTree.fromFilePaths([]));
+        }, (tree = ((paths = ((array = FileSystemTree.toFilePaths()(this$._fs.Copy().Tree), array.filter((p) => !FSharpSet__Contains(registeredPayload, p)))), FileSystemTree.fromFilePaths(paths))), ignoreHidden ? FileSystemTree.filterFiles((n) => !(n.indexOf(".") === 0))(tree) : tree)), FileSystemTree.fromFilePaths([]));
     }
     static get DefaultContracts() {
         return ofSeq_1([[".gitignore", gitignoreContract]], {

package/Contract/Contract.js

@@ -1,6 +1,6 @@
-import { Record } from "../fable_modules/fable-library.4.1.4/Types.js";
-import { class_type, option_type, record_type, array_type, string_type } from "../fable_modules/fable-library.4.1.4/Reflection.js";
-import { defaultArg } from "../fable_modules/fable-library.4.1.4/Option.js";
+import { Record } from "../fable_modules/fable-library.4.4.1/Types.js";
+import { class_type, option_type, record_type, array_type, string_type } from "../fable_modules/fable-library.4.4.1/Reflection.js";
+import { defaultArg } from "../fable_modules/fable-library.4.4.1/Option.js";
 
 export class CLITool extends Record {
     constructor(Name, Arguments) {

package/Contracts/Contracts.ArcAssay.js

@@ -1,7 +1,7 @@
-import { some } from "../fable_modules/fable-library.4.1.4/Option.js";
+import { some } from "../fable_modules/fable-library.4.4.1/Option.js";
 import { combineMany } from "../FileSystem/Path.js";
-import { equalsWith } from "../fable_modules/fable-library.4.1.4/Array.js";
-import { defaultOf } from "../fable_modules/fable-library.4.1.4/Util.js";
+import { equalsWith } from "../fable_modules/fable-library.4.4.1/Array.js";
+import { defaultOf } from "../fable_modules/fable-library.4.4.1/Util.js";
 
 export function tryFromContract(c) {
     let matchResult, fsworkbook;

package/Contracts/Contracts.ArcInvestigation.js

@@ -1,7 +1,7 @@
-import { some } from "../fable_modules/fable-library.4.1.4/Option.js";
+import { some } from "../fable_modules/fable-library.4.4.1/Option.js";
 import { combineMany } from "../FileSystem/Path.js";
-import { equalsWith } from "../fable_modules/fable-library.4.1.4/Array.js";
-import { defaultOf } from "../fable_modules/fable-library.4.1.4/Util.js";
+import { equalsWith } from "../fable_modules/fable-library.4.4.1/Array.js";
+import { defaultOf } from "../fable_modules/fable-library.4.4.1/Util.js";
 
 export function tryFromContract(c) {
     let matchResult, fsworkbook;

package/Contracts/Contracts.ArcStudy.js

@@ -1,7 +1,7 @@
-import { some } from "../fable_modules/fable-library.4.1.4/Option.js";
+import { some } from "../fable_modules/fable-library.4.4.1/Option.js";
 import { combineMany } from "../FileSystem/Path.js";
-import { equalsWith } from "../fable_modules/fable-library.4.1.4/Array.js";
-import { defaultOf } from "../fable_modules/fable-library.4.1.4/Util.js";
+import { equalsWith } from "../fable_modules/fable-library.4.4.1/Array.js";
+import { defaultOf } from "../fable_modules/fable-library.4.4.1/Util.js";
 
 export function tryFromContract(c) {
     let matchResult, fsworkbook;

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.4.1.4/Reflection.js";
-import { value, defaultArg } from "../fable_modules/fable-library.4.1.4/Option.js";
-import { replace } from "../fable_modules/fable-library.4.1.4/String.js";
-import { empty, singleton, append, delay, toArray } from "../fable_modules/fable-library.4.1.4/Seq.js";
+import { class_type } from "../fable_modules/fable-library.4.4.1/Reflection.js";
+import { value, defaultArg } from "../fable_modules/fable-library.4.4.1/Option.js";
+import { replace } from "../fable_modules/fable-library.4.4.1/String.js";
+import { empty, singleton, append, delay, toArray } from "../fable_modules/fable-library.4.4.1/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.4.1.4/Types.js";
-import { record_type, class_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, class_type, string_type } from "../fable_modules/fable-library.4.4.1/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.4.1.4/Option.js";
+import { defaultArg } from "../fable_modules/fable-library.4.4.1/Option.js";
 import { FileSystemTree_$reflection, FileSystemTree } from "./FileSystemTree.js";
-import { map, append } from "../fable_modules/fable-library.4.1.4/Array.js";
-import { Record } from "../fable_modules/fable-library.4.1.4/Types.js";
+import { map, append } from "../fable_modules/fable-library.4.4.1/Array.js";
+import { Record } from "../fable_modules/fable-library.4.4.1/Types.js";
 import { Commit_$reflection } from "./Commit.js";
-import { record_type, array_type } from "../fable_modules/fable-library.4.1.4/Reflection.js";
+import { record_type, array_type } from "../fable_modules/fable-library.4.4.1/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.4.1.4/Option.js";
-import { append as append_1, choose, equalsWith, tail, head, map, tryFind } from "../fable_modules/fable-library.4.1.4/Array.js";
-import { singleton, append, delay, toArray } from "../fable_modules/fable-library.4.1.4/Seq.js";
-import { Array_distinct, Array_groupBy } from "../fable_modules/fable-library.4.1.4/Seq2.js";
-import { curry2, arrayHash, 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 { append as append_1, choose, equalsWith, tail, head, map, tryFind } from "../fable_modules/fable-library.4.4.1/Array.js";
+import { singleton, append, delay, toArray } from "../fable_modules/fable-library.4.4.1/Seq.js";
+import { Array_distinct, Array_groupBy } from "../fable_modules/fable-library.4.4.1/Seq2.js";
+import { curry2, arrayHash, stringHash } from "../fable_modules/fable-library.4.4.1/Util.js";
 import { combineMany, split } from "./Path.js";
-import { empty, reverse, toArray as toArray_1, cons } from "../fable_modules/fable-library.4.1.4/List.js";
-import { Union } from "../fable_modules/fable-library.4.1.4/Types.js";
-import { union_type, array_type, string_type } from "../fable_modules/fable-library.4.1.4/Reflection.js";
+import { empty, reverse, toArray as toArray_1, cons } from "../fable_modules/fable-library.4.4.1/List.js";
+import { Union } from "../fable_modules/fable-library.4.4.1/Types.js";
+import { union_type, array_type, string_type } from "../fable_modules/fable-library.4.4.1/Reflection.js";
 
 export class FileSystemTree extends Union {
     constructor(tag, fields) {
@@ -73,9 +73,9 @@ export class FileSystemTree extends Union {
     }
     static fromFilePaths(paths) {
         const loop = (paths_1, parent) => {
-            const files = map((arg_1) => {
-                const arg = head(arg_1);
-                return FileSystemTree.createFile(arg);
+            const files = map((arg) => {
+                const name = head(arg);
+                return FileSystemTree.createFile(name);
             }, paths_1.filter((p) => (p.length === 1)));
             const folders = map((tupledArg) => {
                 const parent_1 = FileSystemTree.createFolder(tupledArg[0], []);
@@ -106,8 +106,8 @@ export class FileSystemTree extends Union {
                 });
             }
             else {
-                const arg = combineMany(toArray_1(reverse(cons(parent.fields[0], output))));
-                void (res.push(arg));
+                const item = combineMany(toArray_1(reverse(cons(parent.fields[0], output))));
+                void (res.push(item));
             }
         };
         if (defaultArg(removeRoot, true)) {
@@ -205,11 +205,11 @@ export class FileSystemTree extends Union {
     Union(otherFST) {
         let array_1;
         const this$ = this;
-        const arg = Array_distinct((array_1 = this$.ToFilePaths(), append_1(otherFST.ToFilePaths(), array_1)), {
+        const paths = Array_distinct((array_1 = this$.ToFilePaths(), append_1(otherFST.ToFilePaths(), array_1)), {
             Equals: (x, y) => (x === y),
             GetHashCode: stringHash,
         });
-        return FileSystemTree.fromFilePaths(arg);
+        return FileSystemTree.fromFilePaths(paths);
     }
     Copy() {
         const this$ = this;

package/FileSystem/Path.js

@@ -1,5 +1,5 @@
-import { trim, join, trimStart, trimEnd, split as split_1 } from "../fable_modules/fable-library.4.1.4/String.js";
-import { last, mapIndexed } from "../fable_modules/fable-library.4.1.4/Array.js";
+import { trim, join, trimStart, trimEnd, split as split_1 } from "../fable_modules/fable-library.4.4.1/String.js";
+import { last, mapIndexed } from "../fable_modules/fable-library.4.4.1/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.4.1.4/Array.js";
+import { append } from "./fable_modules/fable-library.4.4.1/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.4.1.4/MutableMap.js";
-import { compareArrays, safeHash, disposeSafe, getEnumerator, equals, comparePrimitives, arrayHash, equalArrays } from "../../../fable_modules/fable-library.4.1.4/Util.js";
-import { value as value_9, map as map_2, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { Dictionary } from "../../../fable_modules/fable-library.4.4.1/MutableMap.js";
+import { compareArrays, safeHash, disposeSafe, getEnumerator, equals, comparePrimitives, arrayHash, equalArrays } from "../../../fable_modules/fable-library.4.4.1/Util.js";
+import { value as value_9, map as map_2, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.4.1/Option.js";
 import { Unchecked_extendToRowCount, ProcessParsing_processToRows, ProcessParsing_alignByHeaders, ProcessParsing_mergeIdenticalProcesses, ProcessParsing_getProcessGetter, Unchecked_removeRowCells_withIndexChange, 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.4.1.4/Seq.js";
-import { rangeDouble } from "../../../fable_modules/fable-library.4.1.4/Range.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.4.4.1/Seq.js";
+import { rangeDouble } from "../../../fable_modules/fable-library.4.4.1/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.4.1.4/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.4.1.4/List.js";
-import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../../fable_modules/fable-library.4.1.4/System.Text.js";
-import { toString } from "../../../fable_modules/fable-library.4.1.4/Types.js";
-import { join, printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
+import { sortBy, indexed, mapIndexed, singleton as singleton_1, initialize, sortDescending, iterateIndexed, map as map_1 } from "../../../fable_modules/fable-library.4.4.1/Array.js";
+import { append, collect as collect_1, initialize as initialize_1, singleton as singleton_2, empty as empty_1, iterate, isEmpty } from "../../../fable_modules/fable-library.4.4.1/List.js";
+import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../../fable_modules/fable-library.4.4.1/System.Text.js";
+import { toString } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+import { join, printf, toFail } from "../../../fable_modules/fable-library.4.4.1/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_create_Z6C54B221 } from "../JsonTypes/ProtocolParameter.js";
 import { Component_create_61502994 } from "../JsonTypes/Component.js";
-import { Array_groupBy, List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
+import { Array_groupBy, List_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
 import { toProtocol } from "./CompositeRow.js";
 import { Process_create_Z42860F3E } from "../JsonTypes/Process.js";
-import { getItemFromDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
+import { getItemFromDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
 import { HashCodes_boxHashArray } from "../Helper.js";
-import { class_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { class_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
 
 export class ArcTable {
     constructor(name, headers, values) {
@@ -587,27 +587,27 @@ export class ArcTable {
     }
     AddProtocolTypeColumn(types, index) {
         const this$ = this;
-        const cells = map_2((array) => map_1((arg) => (new CompositeCell(0, [arg])), array), types);
+        const cells = map_2((array) => map_1((Item) => (new CompositeCell(0, [Item])), array), types);
         this$.AddColumn(new CompositeHeader(4, []), cells, index);
     }
     AddProtocolVersionColumn(versions, index) {
         const this$ = this;
-        const cells = map_2((array) => map_1((arg) => (new CompositeCell(1, [arg])), array), versions);
+        const cells = map_2((array) => map_1((Item) => (new CompositeCell(1, [Item])), array), versions);
         this$.AddColumn(new CompositeHeader(7, []), cells, index);
     }
     AddProtocolUriColumn(uris, index) {
         const this$ = this;
-        const cells = map_2((array) => map_1((arg) => (new CompositeCell(1, [arg])), array), uris);
+        const cells = map_2((array) => map_1((Item) => (new CompositeCell(1, [Item])), array), uris);
         this$.AddColumn(new CompositeHeader(6, []), cells, index);
     }
     AddProtocolDescriptionColumn(descriptions, index) {
         const this$ = this;
-        const cells = map_2((array) => map_1((arg) => (new CompositeCell(1, [arg])), array), descriptions);
+        const cells = map_2((array) => map_1((Item) => (new CompositeCell(1, [Item])), array), descriptions);
         this$.AddColumn(new CompositeHeader(5, []), cells, index);
     }
     AddProtocolNameColumn(names, index) {
         const this$ = this;
-        const cells = map_2((array) => map_1((arg) => (new CompositeCell(1, [arg])), array), names);
+        const cells = map_2((array) => map_1((Item) => (new CompositeCell(1, [Item])), array), names);
         this$.AddColumn(new CompositeHeader(8, []), cells, index);
     }
     GetProtocolTypeColumn() {
@@ -732,8 +732,8 @@ export class ArcTable {
     static SplitByColumnValues(columnIndex) {
         return (table) => mapIndexed((i, indexGroup) => {
             let headers;
-            const arg = table.Headers;
-            headers = Array.from(arg);
+            const collection = table.Headers;
+            headers = Array.from(collection);
             const rows = map_1((i_1) => table.GetRow(i_1), indexGroup);
             return ArcTable.createFromRows(table.Name, headers, rows);
         }, map_1((tupledArg) => map_1((tuple_1) => tuple_1[0], tupledArg[1], Int32Array), Array_groupBy((tuple) => tuple[1], indexed(table.GetColumn(columnIndex).Cells), {

package/ISA/ISA/ArcTypes/ArcTableAux.js

@@ -1,23 +1,23 @@
-import { getItemFromDict, addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { map as map_1, defaultArg, unwrap, value as value_9, some } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { empty as empty_2, singleton as singleton_1, append, delay, map, tryPick, toList, indexed, initialize, filter, tryFindIndex, maxBy } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
-import { arrayHash, equalArrays, stringHash, int32ToString, compareArrays, disposeSafe, getEnumerator, compare, equals, comparePrimitives } from "../../../fable_modules/fable-library.4.1.4/Util.js";
-import { pick, exists, zip, append as append_1, sortBy, tryPick as tryPick_1, collect, mapIndexed, item, length, map as map_2, ofArray, singleton, choose, ofSeq, empty as empty_1, head, tail as tail_1, isEmpty, cons } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { getItemFromDict, addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { map as map_1, defaultArg, unwrap, value as value_9, some } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { empty as empty_2, singleton as singleton_1, append, delay, map, tryPick, toList, indexed, initialize, filter, tryFindIndex, maxBy } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
+import { arrayHash, equalArrays, stringHash, int32ToString, compareArrays, disposeSafe, getEnumerator, compare, equals, comparePrimitives } from "../../../fable_modules/fable-library.4.4.1/Util.js";
+import { pick, exists, zip, append as append_1, sortBy, tryPick as tryPick_1, collect, mapIndexed, item, length, map as map_2, ofArray, singleton, choose, ofSeq, empty as empty_1, head, tail as tail_1, isEmpty, cons } from "../../../fable_modules/fable-library.4.4.1/List.js";
 import { CompositeCell } from "./CompositeCell.js";
-import { max } from "../../../fable_modules/fable-library.4.1.4/Double.js";
-import { iterateIndexed } from "../../../fable_modules/fable-library.4.1.4/Array.js";
-import { FSharpSet__get_MinimumElement, FSharpSet__get_IsEmpty, difference, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.1.4/Set.js";
-import { Value_fromString_Z721C83C5, Value } from "../JsonTypes/Value.js";
+import { max } from "../../../fable_modules/fable-library.4.4.1/Double.js";
+import { iterateIndexed } from "../../../fable_modules/fable-library.4.4.1/Array.js";
+import { FSharpSet__get_MinimumElement, FSharpSet__get_IsEmpty, difference, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.4.1/Set.js";
+import { Value_fromString_Z721C83C5, Value as Value_1 } from "../JsonTypes/Value.js";
 import { Component_fromOptions } from "../JsonTypes/Component.js";
 import { ProcessParameterValue_create_569825F3 } from "../JsonTypes/ProcessParameterValue.js";
 import { ProtocolParameter_create_Z6C54B221 } from "../JsonTypes/ProtocolParameter.js";
 import { FactorValue_create_18335379 } from "../JsonTypes/FactorValue.js";
 import { Factor } from "../JsonTypes/Factor.js";
-import { toString } from "../../../fable_modules/fable-library.4.1.4/Types.js";
+import { toString } from "../../../fable_modules/fable-library.4.4.1/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.4.1.4/String.js";
+import { remove, printf, toFail } from "../../../fable_modules/fable-library.4.4.1/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";
@@ -26,9 +26,9 @@ import { Sample_create_E50ED22 } from "../JsonTypes/Sample.js";
 import { Process_create_Z42860F3E, Process_decomposeName_Z721C83C5, Process_make, Process_composeName } from "../JsonTypes/Process.js";
 import { List_tryPickAndRemove, Option_fromValueWithDefault } from "../Helper.js";
 import { Protocol_make } from "../JsonTypes/Protocol.js";
-import { List_groupBy } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
+import { List_groupBy } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
 import { createMissingIdentifier } from "../Identifier.js";
-import { Dictionary } from "../../../fable_modules/fable-library.4.1.4/MutableMap.js";
+import { Dictionary } from "../../../fable_modules/fable-library.4.4.1/MutableMap.js";
 
 /**
  * Returns the dictionary with the binding added to the given dictionary.
@@ -418,7 +418,7 @@ export function Unchecked_addRow(index, newCells, headers, values) {
 export function JsonTypes_valueOfCell(value) {
     switch (value.tag) {
         case 0:
-            return [new Value(0, [value.fields[0]]), void 0];
+            return [new Value_1(0, [value.fields[0]]), void 0];
         case 2:
             return [Value_fromString_Z721C83C5(value.fields[0]), value.fields[1]];
         default:
@@ -568,7 +568,7 @@ export function JsonTypes_composeProcessOutput(header, value) {
  * Convert an ISA Value and Unit tuple to a CompositeCell
  */
 export function JsonTypes_cellOfValue(value, unit) {
-    const value_2 = defaultArg(value, new Value(3, [""]));
+    const value_2 = defaultArg(value, new Value_1(3, [""]));
     switch (value_2.tag) {
         case 3:
             if (unit != null) {
@@ -1017,7 +1017,7 @@ export function ProcessParsing_processToRows(p) {
                 return void 0;
             }
         }, ios), head(ios)[1]);
-        const vals = map_2((tuple_5) => tuple_5[0], sortBy((arg_2) => defaultArg(arg_2[1], 10000), append_1(chars, append_1(components, append_1(pvs, map_2((fv) => [JsonTypes_decomposeFactorValue(fv), tryGetFactorColumnIndex(fv)], ProcessOutput_getFactorValues_11830B70(outputForFactors))))), {
+        const vals = map_2((tuple_5) => tuple_5[0], sortBy((arg) => defaultArg(arg[1], 10000), append_1(chars, append_1(components, append_1(pvs, map_2((fv) => [JsonTypes_decomposeFactorValue(fv), tryGetFactorColumnIndex(fv)], ProcessOutput_getFactorValues_11830B70(outputForFactors))))), {
             Compare: comparePrimitives,
         }));
         return toList(delay(() => append(singleton_1(JsonTypes_decomposeProcessInput(inputForType)), delay(() => append(protVals, delay(() => append(vals, delay(() => singleton_1(JsonTypes_decomposeProcessOutput(outputForType))))))))));
@@ -1053,7 +1053,7 @@ export function ProcessParsing_alignByHeaders(keepOrder, rows) {
         loop:
         while (true) {
             const colI = colI_mut, rows_2 = rows_2_mut;
-            if (!exists((arg_1) => !isEmpty(arg_1), rows_2)) {
+            if (!exists((arg) => !isEmpty(arg), rows_2)) {
                 return [headers, values];
             }
             else {

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.4.1.4/Seq.js";
+import { append, toArray, reduce, choose, map as map_1, delay, toList, length, findIndex, tryFindIndex } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
 import { Dict_tryFind } from "../Helper.js";
-import { addToSet, addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { toIterator, equals, comparePrimitives, stringHash, compare, disposeSafe, getEnumerator } from "../../../fable_modules/fable-library.4.1.4/Util.js";
-import { bind, map as map_3, unwrap, defaultArg, value as value_2 } from "../../../fable_modules/fable-library.4.1.4/Option.js";
-import { collect as collect_1, map as map_4, insertRangeInPlace, fold } from "../../../fable_modules/fable-library.4.1.4/Array.js";
+import { addToSet, addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { toIterator, equals, comparePrimitives, stringHash, compare, disposeSafe, getEnumerator } from "../../../fable_modules/fable-library.4.4.1/Util.js";
+import { bind, map as map_3, unwrap, defaultArg, value as value_2 } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { collect as collect_1, map as map_4, insertRangeInPlace, fold } from "../../../fable_modules/fable-library.4.4.1/Array.js";
 import { CompositeHeader } from "./CompositeHeader.js";
-import { Array_groupBy, distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
-import { FSharpSet__get_IsEmpty, ofSeq, intersect } from "../../../fable_modules/fable-library.4.1.4/Set.js";
+import { Array_groupBy, distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { FSharpSet__get_IsEmpty, ofSeq, intersect } from "../../../fable_modules/fable-library.4.4.1/Set.js";
 import { ArcTable } from "./ArcTable.js";
-import { map as map_2, collect } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { map as map_2, collect } from "../../../fable_modules/fable-library.4.4.1/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.4.1.4/Map.js";
-import { class_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { tryFind, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.4.1/Map.js";
+import { class_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
 
 /**
  * If a table with the given name exists in the TableList, returns it, else returns None.
@@ -256,8 +256,8 @@ export class ArcTables {
     }
     GetTable(name) {
         const this$ = this;
-        const arg = ArcTablesAux_findIndexByTableName(name, this$.Tables) | 0;
-        return this$.GetTableAt(arg);
+        const index = ArcTablesAux_findIndexByTableName(name, this$.Tables) | 0;
+        return this$.GetTableAt(index);
     }
     UpdateTableAt(index, table) {
         const this$ = this;
@@ -294,8 +294,8 @@ export class ArcTables {
     }
     RemoveTable(name) {
         const this$ = this;
-        const arg = ArcTablesAux_findIndexByTableName(name, this$.Tables) | 0;
-        this$.RemoveTableAt(arg);
+        const index = ArcTablesAux_findIndexByTableName(name, this$.Tables) | 0;
+        this$.RemoveTableAt(index);
     }
     MapTableAt(index, updateFun) {
         const this$ = this;
@@ -413,23 +413,23 @@ export class ArcTables {
         return new ArcTables(Array.from(tables));
     }
     static fromProcesses(ps) {
-        let arg;
-        return new ArcTables((arg = map_2((tupledArg) => {
+        let collection;
+        return new ArcTables((collection = map_2((tupledArg) => {
             const tupledArg_1 = ProcessParsing_alignByHeaders(true, collect(ProcessParsing_processToRows, tupledArg[1]));
             return ArcTable.create(tupledArg[0], tupledArg_1[0], tupledArg_1[1]);
-        }, ProcessParsing_groupProcesses(ps)), Array.from(arg)));
+        }, ProcessParsing_groupProcesses(ps)), Array.from(collection)));
     }
     static updateReferenceTablesBySheets(referenceTables, sheetTables, keepUnusedRefTables) {
-        let arg_4, s, array;
+        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), {
             Compare: comparePrimitives,
         });
-        return new ArcTables((arg_4 = ((s = map_4((t_3) => {
+        return new ArcTables((collection = ((s = map_4((t_3) => {
             Unchecked_fillMissingCells(t_3.Headers, t_3.Values);
             return t_3;
-        }, map_4((tupledArg) => reduce((arg_2, arg_3) => ArcTable.append(arg_2, arg_3), tupledArg[1]), Array_groupBy((t_2) => t_2.Name, map_4((t_1) => {
+        }, map_4((tupledArg) => reduce((table, table_1) => ArcTable.append(table, table_1), tupledArg[1]), Array_groupBy((t_2) => t_2.Name, map_4((t_1) => {
             const k = defaultArg(bind((c_1) => {
                 if (c_1.AsFreeText === "") {
                     return void 0;
@@ -458,7 +458,7 @@ export class ArcTables {
             else {
                 return kv[1];
             }
-        }, referenceTableMap), s) : s)), Array.from(arg_4)));
+        }, referenceTableMap), s) : s)), Array.from(collection)));
     }
     GetEnumerator() {
         const this$ = this;