@nfdi4plants/arctrl 1.0.0-beta.3 → 1.0.0-beta.5

package/ARC.js

@@ -1,27 +1,27 @@
-import { concat, fold, exactlyOne, choose, map } from "./fable_modules/fable-library.4.4.1/Array.js";
+import { concat, fold, exactlyOne, choose, map } from "./fable_modules/fable-library.4.5.0/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.4.4.1/Seq.js";
+import { collect, toList, empty, singleton, append, delay, iterate, find, tryFind, toArray } from "./fable_modules/fable-library.4.5.0/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_1, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library.4.4.1/Option.js";
+import { bind, map as map_1, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library.4.5.0/Option.js";
 import { tryISAReadContractFromPath } from "./Contracts/Contracts.ARCtrl.js";
 import { ArcTables } from "./ISA/ISA/ArcTypes/ArcTables.js";
-import { addToDict } from "./fable_modules/fable-library.4.4.1/MapUtil.js";
+import { addToDict } from "./fable_modules/fable-library.4.5.0/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.5.0.1/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.4.4.1/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";
+import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library.4.5.0/Set.js";
+import { comparePrimitives } from "./fable_modules/fable-library.4.5.0/Util.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";
 
 export function ARCAux_getArcAssaysFromContracts(contracts) {
     return map(fromFsWorkbook, choose(tryFromContract, contracts));

package/Contract/Contract.js

@@ -1,6 +1,6 @@
-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";
+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";
 
 export class CLITool extends Record {
     constructor(Name, Arguments) {

package/Contracts/Contracts.ArcAssay.js

@@ -1,7 +1,7 @@
-import { some } from "../fable_modules/fable-library.4.4.1/Option.js";
+import { some } from "../fable_modules/fable-library.4.5.0/Option.js";
 import { combineMany } from "../FileSystem/Path.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";
+import { equalsWith } from "../fable_modules/fable-library.4.5.0/Array.js";
+import { defaultOf } from "../fable_modules/fable-library.4.5.0/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.4.4.1/Option.js";
+import { some } from "../fable_modules/fable-library.4.5.0/Option.js";
 import { combineMany } from "../FileSystem/Path.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";
+import { equalsWith } from "../fable_modules/fable-library.4.5.0/Array.js";
+import { defaultOf } from "../fable_modules/fable-library.4.5.0/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.4.4.1/Option.js";
+import { some } from "../fable_modules/fable-library.4.5.0/Option.js";
 import { combineMany } from "../FileSystem/Path.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";
+import { equalsWith } from "../fable_modules/fable-library.4.5.0/Array.js";
+import { defaultOf } from "../fable_modules/fable-library.4.5.0/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.4.4.1/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";
+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";
 
 export function gitWithArgs(arguments$) {
     return CLITool.create("git", arguments$);

package/FileSystem/Commit.js

@@ -1,5 +1,5 @@
-import { Record } from "../fable_modules/fable-library.4.4.1/Types.js";
-import { record_type, class_type, string_type } from "../fable_modules/fable-library.4.4.1/Reflection.js";
+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";
 
 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.4.4.1/Option.js";
+import { defaultArg } from "../fable_modules/fable-library.4.5.0/Option.js";
 import { FileSystemTree_$reflection, FileSystemTree } from "./FileSystemTree.js";
-import { map, append } from "../fable_modules/fable-library.4.4.1/Array.js";
-import { Record } from "../fable_modules/fable-library.4.4.1/Types.js";
+import { map, append } from "../fable_modules/fable-library.4.5.0/Array.js";
+import { Record } from "../fable_modules/fable-library.4.5.0/Types.js";
 import { Commit_$reflection } from "./Commit.js";
-import { record_type, array_type } from "../fable_modules/fable-library.4.4.1/Reflection.js";
+import { record_type, array_type } from "../fable_modules/fable-library.4.5.0/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.4.4.1/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 { 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 { combineMany, split } from "./Path.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";
+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";
 
 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.4.4.1/String.js";
-import { last, mapIndexed } from "../fable_modules/fable-library.4.4.1/Array.js";
+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";
 
 export const seperators = ["/", "\\"];
 

package/FileSystemTree.js

@@ -1,5 +1,5 @@
 import { FileSystemTree } from "./FileSystem/FileSystemTree.js";
-import { append } from "./fable_modules/fable-library.4.4.1/Array.js";
+import { append } from "./fable_modules/fable-library.4.5.0/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.4.4.1/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 { Dictionary } from "../../../fable_modules/fable-library.4.5.0/MutableMap.js";
+import { compareArrays, safeHash, disposeSafe, getEnumerator, equals, comparePrimitives, 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 { 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.4.4.1/Seq.js";
-import { rangeDouble } from "../../../fable_modules/fable-library.4.4.1/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.4.5.0/Seq.js";
+import { rangeDouble } from "../../../fable_modules/fable-library.4.5.0/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.4.4.1/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_$ctor } from "../../../fable_modules/fable-library.4.4.1/System.Text.js";
-import { toString } from "../../../fable_modules/fable-library.4.4.1/Types.js";
-import { join, printf, toFail } from "../../../fable_modules/fable-library.4.4.1/String.js";
+import { sortBy, indexed, mapIndexed, singleton as singleton_1, initialize, sortDescending, iterateIndexed, map as map_1 } from "../../../fable_modules/fable-library.4.5.0/Array.js";
+import { append, collect as collect_1, initialize as initialize_1, singleton as singleton_2, empty as empty_1, iterate, isEmpty } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$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 { 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.4.4.1/Seq2.js";
+import { Array_groupBy, List_distinct } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
 import { toProtocol } from "./CompositeRow.js";
 import { Process_create_Z42860F3E } from "../JsonTypes/Process.js";
-import { getItemFromDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
+import { getItemFromDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
 import { HashCodes_boxHashArray } from "../Helper.js";
-import { class_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
+import { class_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
 
 export class ArcTable {
     constructor(name, headers, values) {
@@ -113,6 +113,32 @@ export class ArcTable {
     static tryGetCellAt(column, row) {
         return (table) => table.TryGetCellAt(column, row);
     }
+    IterColumns(action) {
+        const this$ = this;
+        for (let columnIndex = 0; columnIndex <= (this$.ColumnCount - 1); columnIndex++) {
+            action(this$.GetColumn(columnIndex));
+        }
+    }
+    static iterColumns(action) {
+        return (table) => {
+            const copy = table.Copy();
+            copy.IterColumns(action);
+            return copy;
+        };
+    }
+    IteriColumns(action) {
+        const this$ = this;
+        for (let columnIndex = 0; columnIndex <= (this$.ColumnCount - 1); columnIndex++) {
+            action(columnIndex, this$.GetColumn(columnIndex));
+        }
+    }
+    static iteriColumns(action) {
+        return (table) => {
+            const copy = table.Copy();
+            copy.IteriColumns(action);
+            return copy;
+        };
+    }
     UpdateCellAt(columnIndex, rowIndex, c) {
         const this$ = this;
         SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);

package/ISA/ISA/ArcTypes/ArcTableAux.js

@@ -1,23 +1,23 @@
-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 { getItemFromDict, addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
+import { map as map_1, defaultArg, unwrap, value as value_9, some } from "../../../fable_modules/fable-library.4.5.0/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.4.5.0/Seq.js";
+import { arrayHash, equalArrays, stringHash, int32ToString, compareArrays, disposeSafe, getEnumerator, compare, equals, 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_2, ofArray, singleton, choose, ofSeq, empty as empty_1, head, tail as tail_1, isEmpty, cons } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { CompositeCell } from "./CompositeCell.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 { max } from "../../../fable_modules/fable-library.4.5.0/Double.js";
+import { iterateIndexed } from "../../../fable_modules/fable-library.4.5.0/Array.js";
+import { FSharpSet__get_MinimumElement, FSharpSet__get_IsEmpty, difference, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.5.0/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.4.4.1/Types.js";
+import { toString } from "../../../fable_modules/fable-library.4.5.0/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.4.4.1/String.js";
+import { remove, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/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";
@@ -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.4.4.1/Seq2.js";
+import { List_groupBy } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
 import { createMissingIdentifier } from "../Identifier.js";
-import { Dictionary } from "../../../fable_modules/fable-library.4.4.1/MutableMap.js";
+import { Dictionary } from "../../../fable_modules/fable-library.4.5.0/MutableMap.js";
 
 /**
  * Returns the dictionary with the binding added to the given dictionary.

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.4.4.1/Seq.js";
+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 { Dict_tryFind } from "../Helper.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 { 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 { CompositeHeader } from "./CompositeHeader.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 { 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 { ArcTable } from "./ArcTable.js";
-import { map as map_2, collect } from "../../../fable_modules/fable-library.4.4.1/List.js";
+import { map as map_2, collect } from "../../../fable_modules/fable-library.4.5.0/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.4.4.1/Map.js";
-import { class_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.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";
 
 /**
  * If a table with the given name exists in the TableList, returns it, else returns None.
@@ -60,7 +60,7 @@ export function ArcTablesAux_getIOMap(tables) {
             }
             else {
                 const ic = matchValue_1;
-                const ioType_1 = value_2(ic.Header.tryInput());
+                const ioType_1 = value_2(ic.Header.TryInput());
                 ic.Cells.forEach((c) => {
                     includeInMap(c.ToFreeTextCell().AsFreeText, ioType_1);
                 });
@@ -70,7 +70,7 @@ export function ArcTablesAux_getIOMap(tables) {
             }
             else {
                 const oc = matchValue_2;
-                const ioType_2 = value_2(oc.Header.tryOutput());
+                const ioType_2 = value_2(oc.Header.TryOutput());
                 oc.Cells.forEach((c_1) => {
                     includeInMap(c_1.ToFreeTextCell().AsFreeText, ioType_2);
                 });
@@ -103,7 +103,7 @@ export function ArcTablesAux_applyIOMap(map, tables) {
                         const newIO = matchValue_1;
                         return io.Merge(newIO);
                     }
-                }, value_2(ic.Header.tryInput()), ic.Cells);
+                }, value_2(ic.Header.TryInput()), ic.Cells);
                 table.UpdateHeader(index, new CompositeHeader(11, [newIOType]));
             }
             const matchValue_2 = table.TryGetOutputColumn();
@@ -121,7 +121,7 @@ export function ArcTablesAux_applyIOMap(map, tables) {
                         const newIO_1 = matchValue_3;
                         return io_1.Merge(newIO_1);
                     }
-                }, value_2(oc.Header.tryOutput()), oc.Cells);
+                }, value_2(oc.Header.TryOutput()), oc.Cells);
                 table.UpdateHeader(index_1, new CompositeHeader(12, [newIOType_1]));
             }
         }
@@ -210,6 +210,10 @@ export class ArcTables {
         const __ = this;
         __["Tables@"] = v;
     }
+    get_Item(index) {
+        const this$ = this;
+        return this$.Tables[index];
+    }
     get TableNames() {
         const this$ = this;
         return toList(delay(() => map_1((s) => s.Name, this$.Tables)));
@@ -412,6 +416,12 @@ export class ArcTables {
     static ofSeq(tables) {
         return new ArcTables(Array.from(tables));
     }
+    MoveTable(oldIndex, newIndex) {
+        const this$ = this;
+        const table = this$.GetTableAt(oldIndex);
+        this$.Tables.splice(oldIndex, 1);
+        this$.Tables.splice(newIndex, 0, table);
+    }
     static fromProcesses(ps) {
         let collection;
         return new ArcTables((collection = map_2((tupledArg) => {

package/ISA/ISA/ArcTypes/ArcTypes.js

@@ -1,26 +1,26 @@
-import { map as map_1, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.4.1/Option.js";
-import { concat, collect, append as append_4, tryFind, removeAt, tryFindIndex, item as item_1, map as map_2, delay, toList, fold, length, forAll, contains, filter, toArray } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
-import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../../../fable_modules/fable-library.4.4.1/Util.js";
-import { addRangeInPlace, tryFind as tryFind_1, removeInPlace, equalsWith, append as append_3, contains as contains_1, map } from "../../../fable_modules/fable-library.4.4.1/Array.js";
-import { distinctBy, Array_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
-import { printf, toText } from "../../../fable_modules/fable-library.4.4.1/String.js";
-import { create, match } from "../../../fable_modules/fable-library.4.4.1/RegExp.js";
+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, item as item_1, 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, tryFind as tryFind_1, 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 { create, match } from "../../../fable_modules/fable-library.4.5.0/RegExp.js";
 import { OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { Value_fromString_Z721C83C5, Value__get_Text } from "../JsonTypes/Value.js";
 import { AnnotationValue } from "../JsonTypes/AnnotationValue.js";
 import { ArcTablesAux_applyIOMap, ArcTablesAux_getIOMap, ArcTables_$reflection, ArcTables } from "./ArcTables.js";
 import { AssayMaterials_get_empty, AssayMaterials_create_Z253F0553 } from "../JsonTypes/AssayMaterials.js";
 import { 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.4.4.1/List.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 { 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.4.4.1/Range.js";
-import { class_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.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 { 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.4.4.1/Types.js";
+import { FSharpRef } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 
 export class ArcAssay extends ArcTables {
     constructor(identifier, measurementType, technologyType, technologyPlatform, tables, performers, comments) {

package/ISA/ISA/ArcTypes/CompositeCell.js

@@ -1,9 +1,9 @@
-import { int32ToString } from "../../../fable_modules/fable-library.4.4.1/Util.js";
-import { defaultArg } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+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 { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { AnnotationValue } from "../JsonTypes/AnnotationValue.js";
-import { Union } from "../../../fable_modules/fable-library.4.4.1/Types.js";
-import { union_type, string_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.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";
 
 export class CompositeCell extends Union {
     constructor(tag, fields) {
@@ -89,6 +89,10 @@ export class CompositeCell extends Union {
         const this$ = this;
         return this$.tag === 1;
     }
+    GetEmptyCell() {
+        const this$ = this;
+        return (this$.tag === 2) ? CompositeCell.emptyUnitized : ((this$.tag === 1) ? CompositeCell.emptyFreeText : CompositeCell.emptyTerm);
+    }
     GetContent() {
         const this$ = this;
         switch (this$.tag) {

package/ISA/ISA/ArcTypes/CompositeColumn.js

@@ -1,9 +1,9 @@
-import { defaultArg } from "../../../fable_modules/fable-library.4.4.1/Option.js";
-import { empty, singleton, collect, delay, toArray } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
-import { Record } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+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 { CompositeCell_$reflection, CompositeCell } from "./CompositeCell.js";
+import { Record } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { CompositeHeader_$reflection } from "./CompositeHeader.js";
-import { CompositeCell_$reflection } from "./CompositeCell.js";
-import { record_type, array_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
+import { record_type, array_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
 
 export class CompositeColumn extends Record {
     constructor(Header, Cells) {
@@ -40,6 +40,27 @@ export class CompositeColumn extends Record {
         const arr = toArray(delay(() => collect((cell) => (cell.isUnitized ? singleton(cell.AsUnitized[1]) : empty()), this$.Cells)));
         return (arr.length === 0) ? void 0 : arr;
     }
+    GetDefaultEmptyCell() {
+        const this$ = this;
+        if (!this$.Header.IsTermColumn) {
+            return CompositeCell.emptyFreeText;
+        }
+        else {
+            let patternInput;
+            const arg = [0, 0];
+            patternInput = fold((tupledArg, cell) => {
+                const units = tupledArg[0] | 0;
+                const terms = tupledArg[1] | 0;
+                if (cell.isUnitized) {
+                    return [units + 1, terms];
+                }
+                else {
+                    return [units, terms + 1];
+                }
+            }, [arg[0], arg[1]], this$.Cells);
+            return (patternInput[1] >= patternInput[0]) ? CompositeCell.emptyTerm : CompositeCell.emptyUnitized;
+        }
+    }
 }
 
 export function CompositeColumn_$reflection() {

package/ISA/ISA/ArcTypes/CompositeHeader.js

@@ -1,9 +1,9 @@
-import { map } from "../../../fable_modules/fable-library.4.4.1/Array.js";
-import { union_type, string_type, getUnionCases, name } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
-import { Union, toString } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+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 { ActivePatterns_$007CTermColumn$007C_$007C, Pattern_OutputPattern, Pattern_InputPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseIOTypeHeader } from "../Regex.js";
-import { equals } from "../../../fable_modules/fable-library.4.4.1/Util.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.4.1/String.js";
+import { equals } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
 import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { ProtocolParameter_create_Z6C54B221 } from "../JsonTypes/ProtocolParameter.js";
 import { Factor } from "../JsonTypes/Factor.js";
@@ -242,7 +242,7 @@ export class CompositeHeader extends Union {
     }
     ToTerm() {
         const this$ = this;
-        return (this$.tag === 2) ? this$.fields[0] : ((this$.tag === 1) ? this$.fields[0] : ((this$.tag === 0) ? this$.fields[0] : ((this$.tag === 4) ? OntologyAnnotation.fromString("Protocol Type") : ((this$.tag === 8) ? OntologyAnnotation.fromString("Protocol REF") : ((this$.tag === 5) ? OntologyAnnotation.fromString("Protocol Description") : ((this$.tag === 6) ? OntologyAnnotation.fromString("Protocol Uri") : ((this$.tag === 7) ? OntologyAnnotation.fromString("Protocol Version") : ((this$.tag === 9) ? OntologyAnnotation.fromString("Performer") : ((this$.tag === 10) ? OntologyAnnotation.fromString("Date") : ((this$.tag === 11) ? OntologyAnnotation.fromString(this$.fields[0].asInput) : ((this$.tag === 12) ? OntologyAnnotation.fromString(this$.fields[0].asOutput) : ((this$.tag === 13) ? OntologyAnnotation.fromString(this$.fields[0]) : this$.fields[0]))))))))))));
+        return (this$.tag === 2) ? this$.fields[0] : ((this$.tag === 1) ? this$.fields[0] : ((this$.tag === 0) ? this$.fields[0] : ((this$.tag === 4) ? OntologyAnnotation.fromString(toString(this$), void 0, this$.GetFeaturedColumnAccession) : ((this$.tag === 8) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 5) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 6) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 7) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 9) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 10) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 11) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 12) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 13) ? OntologyAnnotation.fromString(toString(this$)) : this$.fields[0]))))))))))));
     }
     static OfHeaderString(str) {
         const matchValue = str.trim();
@@ -492,14 +492,38 @@ export class CompositeHeader extends Union {
         const this$ = this;
         return this$.tag === 13;
     }
-    tryInput() {
+    TryInput() {
         const this$ = this;
         return (this$.tag === 11) ? this$.fields[0] : void 0;
     }
-    tryOutput() {
+    TryOutput() {
         const this$ = this;
         return (this$.tag === 12) ? this$.fields[0] : void 0;
     }
+    TryIOType() {
+        const this$ = this;
+        let matchResult, io;
+        switch (this$.tag) {
+            case 12: {
+                matchResult = 0;
+                io = this$.fields[0];
+                break;
+            }
+            case 11: {
+                matchResult = 0;
+                io = this$.fields[0];
+                break;
+            }
+            default:
+                matchResult = 1;
+        }
+        switch (matchResult) {
+            case 0:
+                return io;
+            default:
+                return void 0;
+        }
+    }
     TryParameter() {
         const this$ = this;
         return (this$.tag === 3) ? ProtocolParameter_create_Z6C54B221(void 0, this$.fields[0]) : void 0;

package/ISA/ISA/ArcTypes/CompositeRow.js

@@ -1,4 +1,4 @@
-import { fold } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
+import { fold } from "../../../fable_modules/fable-library.4.5.0/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_create_Z6C54B221 } 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.4.4.1/Types.js";
-import { list_type, union_type, string_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
+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 { 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.4.4.1/List.js";
-import { map, value as value_4, defaultArg } from "../../../fable_modules/fable-library.4.4.1/Option.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 { 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.4.4.1/String.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
 import { Study } from "../JsonTypes/Study.js";
 
 export class ProtocolTransformation extends Union {