@nfdi4plants/arctrl 3.0.0-alpha.4 → 3.0.0-beta.2

package/dist/ts/esm/ts/Json.js

@@ -5,6 +5,7 @@ import { ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47, ARCtrl_A
 import { ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086, ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1, ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromJsonString_Static_Z721C83C5 } from "./JsonIO/Study.js";
 import { ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_Z3B036AA, ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromJsonString_Static_Z721C83C5 } from "./JsonIO/Investigation.js";
 import { ARC } from "./ARC.js";
+import { ARCtrl_ROCrate_LDNode__LDNode_toROCrateJsonString_Static_71136F3F, ARCtrl_ROCrate_LDNode__LDNode_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ROCrate_LDGraph__LDGraph_toROCrateJsonString_Static_71136F3F, ARCtrl_ROCrate_LDGraph__LDGraph_fromROCrateJsonString_Static_Z721C83C5 } from "./JsonIO/LDObject.js";
 export class JsonHelper_OntologyAnnotationJson {
     constructor() {
     }
@@ -151,6 +152,38 @@ export function JsonHelper_ARCJson_$reflection() {
 export function JsonHelper_ARCJson_$ctor() {
     return new JsonHelper_ARCJson();
 }
+export class JsonHelper_LDGraphJson {
+    constructor() {
+    }
+    fromROCrateJsonString(s) {
+        return ARCtrl_ROCrate_LDGraph__LDGraph_fromROCrateJsonString_Static_Z721C83C5(s);
+    }
+    toROCrateJsonString(spaces) {
+        return ARCtrl_ROCrate_LDGraph__LDGraph_toROCrateJsonString_Static_71136F3F(unwrap(spaces));
+    }
+}
+export function JsonHelper_LDGraphJson_$reflection() {
+    return class_type("ARCtrl.JsonHelper.LDGraphJson", undefined, JsonHelper_LDGraphJson);
+}
+export function JsonHelper_LDGraphJson_$ctor() {
+    return new JsonHelper_LDGraphJson();
+}
+export class JsonHelper_LDNodeJson {
+    constructor() {
+    }
+    fromROCrateJsonString(s) {
+        return ARCtrl_ROCrate_LDNode__LDNode_fromROCrateJsonString_Static_Z721C83C5(s);
+    }
+    toROCrateJsonString(spaces) {
+        return ARCtrl_ROCrate_LDNode__LDNode_toROCrateJsonString_Static_71136F3F(unwrap(spaces));
+    }
+}
+export function JsonHelper_LDNodeJson_$reflection() {
+    return class_type("ARCtrl.JsonHelper.LDNodeJson", undefined, JsonHelper_LDNodeJson);
+}
+export function JsonHelper_LDNodeJson_$ctor() {
+    return new JsonHelper_LDNodeJson();
+}
 export class JsonController {
     constructor() {
     }
@@ -169,6 +202,12 @@ export class JsonController {
     static get ARC() {
         return new JsonHelper_ARCJson();
     }
+    static get LDGraph() {
+        return new JsonHelper_LDGraphJson();
+    }
+    static get LDNode() {
+        return new JsonHelper_LDNodeJson();
+    }
 }
 export function JsonController_$reflection() {
     return class_type("ARCtrl.JsonController", undefined, JsonController);

package/dist/ts/esm/ts/ROCrateIO.js

@@ -1,6 +1,6 @@
 import { class_type } from "@fable-org/fable-library-js/Reflection.js";
 import { LDRef, LDNode } from "./ROCrate/LDObject.js";
-import { unwrap, value } from "@fable-org/fable-library-js/Option.js";
+import { unwrap, value as value_1 } from "@fable-org/fable-library-js/Option.js";
 import { ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8, ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation } from "./Conversion.js";
 import { LDDataset } from "./ROCrate/Generic/Dataset.js";
 import { now } from "@fable-org/fable-library-js/Date.js";
@@ -8,6 +8,8 @@ import { LDContext } from "./ROCrate/LDContext.js";
 import { initBioschemasContext, initV1_1 } from "./ROCrate/ROCrateContext.js";
 import { decoder, encoder } from "./Json/ROCrate/LDGraph.js";
 import { map } from "./fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
+import { ResizeArray_choose } from "./Core/Helper/Collections.js";
+import { LDFile } from "./ROCrate/Generic/File.js";
 import { exactlyOne } from "@fable-org/fable-library-js/Seq.js";
 import { decoder as decoder_1 } from "./Json/ROCrate/LDNode.js";
 export class ROCrate {
@@ -27,7 +29,7 @@ export function ROCrate_get_metadataFileDescriptor() {
     return node;
 }
 export function ROCrate_encoder_8A8D439(isa, license) {
-    const license_2 = (license == null) ? ROCrate_getDefaultLicense() : value(license);
+    const license_2 = (license == null) ? ROCrate_getDefaultLicense() : value_1(license);
     const isa_1 = ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation(isa);
     LDDataset.setSDDatePublishedAsDateTime(isa_1, now());
     LDDataset.setLicenseAsCreativeWork(isa_1, license_2);
@@ -45,7 +47,16 @@ export function ROCrate_get_decoder() {
             throw new Error("RO-Crate graph did not contain root data Entity");
         }
         else {
-            return ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(value(matchValue), graph, unwrap(graph.TryGetContext()));
+            const node = value_1(matchValue);
+            const files = ResizeArray_choose((n) => {
+                if (LDFile.validate(n, unwrap(graph.TryGetContext())) && !(n.Id.indexOf("#") >= 0)) {
+                    return n.Id;
+                }
+                else {
+                    return undefined;
+                }
+            }, graph.Nodes);
+            return [ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(node, graph, unwrap(graph.TryGetContext())), files];
         }
     }, decoder);
 }

package/dist/ts/esm/ts/Spreadsheet/AnnotationTable/ArcTable.js

@@ -1,9 +1,11 @@
-import { iterateIndexed, length, sortBy, collect as collect_1, exists, toArray, ofArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "@fable-org/fable-library-js/List.js";
-import { item, map as map_1 } from "@fable-org/fable-library-js/Array.js";
+import { iterateIndexed, length, ofSeq, sortBy, collect as collect_1, exists, toArray, ofArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "@fable-org/fable-library-js/List.js";
+import { unzip, item, map as map_1 } from "@fable-org/fable-library-js/Array.js";
 import { fold as fold_1, singleton as singleton_1, collect, map as map_2, delay, toArray as toArray_1, tryFind } from "@fable-org/fable-library-js/Seq.js";
 import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.6.3.1/FsWorksheet.fs.js";
 import { value as value_1 } from "@fable-org/fable-library-js/Option.js";
-import { toStringCellColumns, fixDeprecatedIOHeader, fromStringCellColumns } from "./CompositeColumn.js";
+import { toStringCellColumns, fixDeprecatedIOHeader, ColumnValueRefs_fromStringCellColumns, fromStringCellColumns } from "./CompositeColumn.js";
+import { comparePrimitives } from "@fable-org/fable-library-js/Util.js";
+import { ArcTableValues } from "../../Core/Table/ArcTableAux.js";
 import { printf, toFail } from "@fable-org/fable-library-js/String.js";
 import { Dictionary_tryGet, FsCellsCollection__TryGetCell_Z37302880 } from "../../fable_modules/FsSpreadsheet.6.3.1/Cells/FsCellsCollection.fs.js";
 import { rangeDouble } from "@fable-org/fable-library-js/Range.js";
@@ -11,7 +13,6 @@ import { FsAddress_$ctor_Z37302880, FsAddress__get_ColumnNumber, FsAddress__get_
 import { FsRangeAddress_$ctor_7E77A4A0, FsRangeAddress__get_LastAddress } from "../../fable_modules/FsSpreadsheet.6.3.1/Ranges/FsRangeAddress.fs.js";
 import { FsRangeBase__Cell_Z3407A44B, FsRangeBase__get_RangeAddress } from "../../fable_modules/FsSpreadsheet.6.3.1/Ranges/FsRangeBase.fs.js";
 import { ArcTable } from "../../Core/Table/ArcTable.js";
-import { comparePrimitives } from "@fable-org/fable-library-js/Util.js";
 import { max } from "@fable-org/fable-library-js/Double.js";
 import { addToDict } from "@fable-org/fable-library-js/MapUtil.js";
 /**
@@ -81,6 +82,15 @@ export function tryAnnotationTable(sheet) {
 export function composeColumns(stringCellColumns) {
     return map_1(fromStringCellColumns, groupColumnsByHeader(stringCellColumns));
 }
+/**
+ * Groups and parses a collection of single columns into the according ISA composite columns
+ */
+export function composeArcTableValues(stringCellColumns) {
+    const valueMap = new Map([]);
+    const rowCount = (item(0, stringCellColumns).length - 1) | 0;
+    const patternInput = unzip(map_1((columns) => ColumnValueRefs_fromStringCellColumns(valueMap, columns), groupColumnsByHeader(stringCellColumns)));
+    return [patternInput[0], ArcTableValues.fromRefColumns(patternInput[1], valueMap, rowCount)];
+}
 /**
  * Returns the protocol described by the headers and a function for parsing the values of the matrix to the processes of this protocol
  */
@@ -92,7 +102,7 @@ export function tryFromFsWorksheet(sheet) {
         }
         else {
             const t = value_1(matchValue);
-            const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, toArray_1(delay(() => map_2((c) => toArray_1(delay(() => collect((r) => {
+            const patternInput = composeArcTableValues(map_1(fixDeprecatedIOHeader, toArray_1(delay(() => map_2((c) => toArray_1(delay(() => collect((r) => {
                 const matchValue_1 = FsCellsCollection__TryGetCell_Z37302880(sheet.CellCollection, r, c);
                 if (matchValue_1 == null) {
                     return singleton_1("");
@@ -102,7 +112,7 @@ export function tryFromFsWorksheet(sheet) {
                     return singleton_1(cell.ValueAsString());
                 }
             }, rangeDouble(1, 1, FsAddress__get_RowNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(t))))))), rangeDouble(1, 1, FsAddress__get_ColumnNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(t)))))))));
-            return ArcTable.addColumns(compositeColumns, undefined, true)(ArcTable.init(sheet.Name));
+            return ArcTable.fromArcTableValues(sheet.Name, Array.from(patternInput[0]), patternInput[1]);
         }
     }
     catch (err) {
@@ -118,7 +128,7 @@ export function toFsWorksheet(index, table) {
         return ws;
     }
     else {
-        const columns = collect_1(toStringCellColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
+        const columns = collect_1(toStringCellColumns, sortBy(classifyColumnOrder, ofSeq(table.Columns), {
             Compare: comparePrimitives,
         }));
         let tableRowCount;

package/dist/ts/esm/ts/Spreadsheet/AnnotationTable/CompositeColumn.js

@@ -1,14 +1,18 @@
 import { tryItem, map, setItem, item, skip } from "@fable-org/fable-library-js/Array.js";
 import { CompositeHeader_Output, CompositeHeader_Input, IOType_Source, IOType } from "../../Core/Table/CompositeHeader.js";
-import { toString } from "@fable-org/fable-library-js/Types.js";
+import { FSharpRef, toString } from "@fable-org/fable-library-js/Types.js";
 import { toStringCells, fromStringCells } from "./CompositeHeader.js";
-import { singleton, append, toList, exists, map as map_1, delay, toArray } from "@fable-org/fable-library-js/Seq.js";
+import { reduce, singleton, append, toList, exists, map as map_1, delay, toArray } from "@fable-org/fable-library-js/Seq.js";
 import { rangeDouble } from "@fable-org/fable-library-js/Range.js";
 import { CompositeColumn } from "../../Core/Table/CompositeColumn.js";
 import { FsCell } from "../../fable_modules/FsSpreadsheet.6.3.1/Cells/FsCell.fs.js";
 import { toStringCells as toStringCells_1 } from "./CompositeCell.js";
-import { defaultArg } from "@fable-org/fable-library-js/Option.js";
+import { value as value_1, defaultArg } from "@fable-org/fable-library-js/Option.js";
 import { map as map_2, singleton as singleton_1, ofArray } from "@fable-org/fable-library-js/List.js";
+import { defaultOf, stringHash } from "@fable-org/fable-library-js/Util.js";
+import { ColumnValueRefs_Constant, ensureCellHashInValueMap, ColumnValueRefs_Sparse } from "../../Core/Table/ArcTableAux.js";
+import { mergeHashes } from "../../Core/Helper/HashCodes.js";
+import { getItemFromDict, tryGetValue } from "@fable-org/fable-library-js/MapUtil.js";
 /**
  * Checks if the column header is a deprecated IO Header. If so, fixes it.
  *
@@ -38,9 +42,15 @@ export function fixDeprecatedIOHeader(stringCellCol) {
 export function fromStringCellColumns(columns) {
     const patternInput = fromStringCells(map((c) => item(0, c), columns));
     const l = item(0, columns).length | 0;
-    const cells = toArray(delay(() => map_1((i) => patternInput[1](map((c_1) => item(i, c_1), columns)), rangeDouble(1, 1, l - 1))));
+    const cells = Array.from(toArray(delay(() => map_1((i) => patternInput[1](map((c_1) => item(i, c_1), columns)), rangeDouble(1, 1, l - 1)))));
     return CompositeColumn.create(patternInput[0], cells);
 }
+export function stringCellColumnsOfFsColumns(columns) {
+    return map((c) => {
+        c.ToDenseColumn();
+        return map((cell) => cell.ValueAsString(), toArray(c.Cells));
+    }, columns);
+}
 export function fromFsColumns(columns) {
     return fromStringCellColumns(map((c) => {
         c.ToDenseColumn();
@@ -52,21 +62,80 @@ export function toStringCellColumns(column) {
     const isTerm = column.Header.IsTermColumn;
     const isData = column.Header.IsDataColumn && exists((c_1) => c_1.isData, column.Cells);
     const header = toStringCells(hasUnit, column.Header);
-    const cells = map((cell) => toStringCells_1(isTerm, hasUnit, cell), column.Cells);
+    const compositeCells = toArray(column.Cells);
+    const cells = map((cell) => toStringCells_1(isTerm, hasUnit, cell), toArray(column.Cells));
     const getCellOrDefault = (ri, ci, cells_1) => defaultArg(tryItem(ci, item(ri, cells_1)), "");
     if (hasUnit) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i) => getCellOrDefault(i, 0, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_1) => getCellOrDefault(i_1, 1, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_2) => getCellOrDefault(i_2, 2, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(3, header)), delay(() => map_1((i_3) => getCellOrDefault(i_3, 3, cells), rangeDouble(0, 1, column.Cells.length - 1))))))]);
+        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i) => getCellOrDefault(i, 0, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_1) => getCellOrDefault(i_1, 1, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_2) => getCellOrDefault(i_2, 2, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(3, header)), delay(() => map_1((i_3) => getCellOrDefault(i_3, 3, cells), rangeDouble(0, 1, compositeCells.length - 1))))))]);
     }
     else if (isTerm) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_4) => getCellOrDefault(i_4, 0, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_5) => getCellOrDefault(i_5, 1, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_6) => getCellOrDefault(i_6, 2, cells), rangeDouble(0, 1, column.Cells.length - 1))))))]);
+        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_4) => getCellOrDefault(i_4, 0, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_5) => getCellOrDefault(i_5, 1, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_6) => getCellOrDefault(i_6, 2, cells), rangeDouble(0, 1, compositeCells.length - 1))))))]);
     }
     else if (isData) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_7) => getCellOrDefault(i_7, 0, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_8) => getCellOrDefault(i_8, 1, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_9) => getCellOrDefault(i_9, 2, cells), rangeDouble(0, 1, column.Cells.length - 1))))))]);
+        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_7) => getCellOrDefault(i_7, 0, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_8) => getCellOrDefault(i_8, 1, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_9) => getCellOrDefault(i_9, 2, cells), rangeDouble(0, 1, compositeCells.length - 1))))))]);
     }
     else {
-        return singleton_1(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_10) => item(0, item(i_10, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))));
+        return singleton_1(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_10) => item(0, item(i_10, cells)), rangeDouble(0, 1, compositeCells.length - 1)))))));
     }
 }
 export function toFsColumns(column) {
     return map_2((c) => map_2((s) => (new FsCell(s)), c), toStringCellColumns(column));
 }
+export function ColumnValueRefs_fromStringCellColumns(valueMap, columns) {
+    let cellHash;
+    const hashMap = new Map([]);
+    const cells = new Map([]);
+    let constant = true;
+    const patternInput = fromStringCells(map((c) => item(0, c), columns));
+    const header = patternInput[0];
+    const cellParser = patternInput[1];
+    const l = item(0, columns).length | 0;
+    if (l === 1) {
+        return [header, ColumnValueRefs_Sparse(cells)];
+    }
+    else {
+        for (let i = 1; i <= (l - 1); i++) {
+            const strings = map((c_1) => item(i, c_1), columns);
+            const hash_2 = reduce(mergeHashes, map_1(stringHash, strings)) | 0;
+            let matchValue;
+            let patternInput_1;
+            let outArg = defaultOf();
+            patternInput_1 = [tryGetValue(hashMap, hash_2, new FSharpRef(() => outArg, (v) => {
+                    outArg = (v | 0);
+                })), outArg];
+            matchValue = (patternInput_1[0] ? patternInput_1[1] : undefined);
+            if (matchValue == null) {
+                if (i === 1) {
+                    const cellHash_3 = ensureCellHashInValueMap(cellParser(strings), valueMap) | 0;
+                    hashMap.set(hash_2, cellHash_3);
+                    cells.set(i - 1, cellHash_3);
+                }
+                else {
+                    if (constant) {
+                        constant = false;
+                        for (let j = 0; j <= (i - 1); j++) {
+                            const cellHash_4 = getItemFromDict(cells, 0) | 0;
+                            cells.set(j, cellHash_4);
+                        }
+                    }
+                    const cellHash_5 = ensureCellHashInValueMap(cellParser(strings), valueMap) | 0;
+                    hashMap.set(hash_2, cellHash_5);
+                    cells.set(i - 1, cellHash_5);
+                }
+            }
+            else if ((cellHash = (value_1(matchValue) | 0), constant)) {
+                const cellHash_1 = value_1(matchValue) | 0;
+            }
+            else {
+                const cellHash_2 = value_1(matchValue) | 0;
+                cells.set(i - 1, cellHash_2);
+            }
+        }
+        if (constant) {
+            return [header, ColumnValueRefs_Constant(getItemFromDict(cells, 0))];
+        }
+        else {
+            return [header, ColumnValueRefs_Sparse(cells)];
+        }
+    }
+}

package/dist/ts/esm/ts/Spreadsheet/ArcInvestigation.js

@@ -1,5 +1,5 @@
 import { Record } from "@fable-org/fable-library-js/Types.js";
-import { head, tail, isEmpty, ofSeq, concat, unzip, append, reverse, cons, empty, map, ofArray } from "@fable-org/fable-library-js/List.js";
+import { head, tail, isEmpty as isEmpty_1, ofSeq, concat, unzip, append, reverse, cons, empty, map, ofArray } from "@fable-org/fable-library-js/List.js";
 import { Remark, Comment$_$reflection } from "../Core/Comment.js";
 import { comparePrimitives, getEnumerator, stringHash } from "@fable-org/fable-library-js/Util.js";
 import { record_type, list_type, string_type } from "@fable-org/fable-library-js/Reflection.js";
@@ -10,11 +10,11 @@ import { value as value_1, defaultArg } from "@fable-org/fable-library-js/Option
 import { Option_fromValueWithDefault, ResizeArray_iter } from "../Core/Helper/Collections.js";
 import { List_distinctBy, List_distinct } from "@fable-org/fable-library-js/Seq2.js";
 import { ArcStudy, ArcInvestigation } from "../Core/ArcTypes.js";
+import { iterateIndexed, tryFind as tryFind_1, map as map_1, toList, collect, singleton, append as append_1, delay, isEmpty } from "@fable-org/fable-library-js/Seq.js";
 import { toRows, fromRows } from "./Metadata/OntologySourceReference.js";
 import { toRows as toRows_1, fromRows as fromRows_1 } from "./Metadata/Publication.js";
 import { toRows as toRows_2, fromRows as fromRows_2 } from "./Metadata/Contacts.js";
 import { toRows as toRows_3, fromRows as fromRows_3 } from "./Metadata/Study.js";
-import { iterateIndexed, tryFind as tryFind_1, map as map_1, toList, collect, singleton, append as append_1, delay } from "@fable-org/fable-library-js/Seq.js";
 import { tryFind, ofList } from "@fable-org/fable-library-js/Map.js";
 import { FsWorksheet } from "../fable_modules/FsSpreadsheet.6.3.1/FsWorksheet.fs.js";
 import { FsWorkbook } from "../fable_modules/FsSpreadsheet.6.3.1/FsWorkbook.fs.js";
@@ -86,6 +86,9 @@ export function ArcInvestigation_fromParts(investigationInfo, ontologySourceRefe
     return ArcInvestigation.make(investigationInfo.Identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications_1, contacts_1, assays_1, studies_1, [], [], registeredStudyIdentifiers, comments, remarks_1);
 }
 export function ArcInvestigation_fromRows(rows) {
+    if (isEmpty(rows)) {
+        throw new Error("isa_investigation sheet in Investigation file is empty");
+    }
     const en = getEnumerator(rows);
     const emptyInvestigationInfo = ArcInvestigation_InvestigationInfo_create("", "", "", "", "", empty());
     const loop = (lastLine_mut, ontologySourceReferences_mut, investigationInfo_mut, publications_mut, contacts_mut, studies_mut, remarks_mut, lineNumber_mut) => {
@@ -204,25 +207,38 @@ export function ArcInvestigation_fromRows(rows) {
                         continue loop;
                     }
                 }
-                default: {
-                    let patternInput_5;
-                    const tupledArg = unzip(studies);
-                    patternInput_5 = [reverse(tupledArg[0]), List_distinctBy((a_1) => a_1.Identifier, concat(tupledArg[1]), {
-                            Equals: (x, y) => (x === y),
-                            GetHashCode: stringHash,
-                        })];
-                    return ArcInvestigation_fromParts(investigationInfo, ontologySourceReferences, publications, contacts, patternInput_5[0], patternInput_5[1], remarks);
-                }
+                default:
+                    if (en["System.Collections.IEnumerator.MoveNext"]()) {
+                        lastLine_mut = SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]());
+                        ontologySourceReferences_mut = ontologySourceReferences;
+                        investigationInfo_mut = investigationInfo;
+                        publications_mut = publications;
+                        contacts_mut = contacts;
+                        studies_mut = studies;
+                        remarks_mut = remarks;
+                        lineNumber_mut = lineNumber;
+                        continue loop;
+                    }
+                    else {
+                        let patternInput_5;
+                        const tupledArg = unzip(studies);
+                        patternInput_5 = [reverse(tupledArg[0]), List_distinctBy((a_1) => a_1.Identifier, concat(tupledArg[1]), {
+                                Equals: (x, y) => (x === y),
+                                GetHashCode: stringHash,
+                            })];
+                        return ArcInvestigation_fromParts(investigationInfo, ontologySourceReferences, publications, contacts, patternInput_5[0], patternInput_5[1], remarks);
+                    }
             }
             break;
         }
     };
-    if (en["System.Collections.IEnumerator.MoveNext"]()) {
-        return loop(SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), empty(), emptyInvestigationInfo, empty(), empty(), empty(), empty(), 1);
-    }
-    else {
-        throw new Error("emptyInvestigationFile");
+    let arcInvestigation;
+    en["System.Collections.IEnumerator.MoveNext"]();
+    arcInvestigation = loop(SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), empty(), emptyInvestigationInfo, empty(), empty(), empty(), empty(), 1);
+    if (arcInvestigation.Identifier === "") {
+        throw new Error("Mandatory Investigation identifier is not present");
     }
+    return arcInvestigation;
 }
 export function ArcInvestigation_toRows(investigation) {
     let remarks, rows;
@@ -239,7 +255,7 @@ export function ArcInvestigation_toRows(investigation) {
                     const i = i_mut, l = l_mut, nl = nl_mut;
                     const matchValue = tryFind(i, rm);
                     if (matchValue == null) {
-                        if (!isEmpty(l)) {
+                        if (!isEmpty_1(l)) {
                             i_mut = (i + 1);
                             l_mut = tail(l);
                             nl_mut = cons(head(l), nl);

package/dist/ts/esm/ts/Spreadsheet/DataMapTable/DataMapHeader.js

@@ -459,5 +459,5 @@ export function fromFsCells(cells) {
     }
 }
 export function toFsCells(commentKeys) {
-    return toList(delay(() => append([new FsCell("Data"), new FsCell("Data Format"), new FsCell("Data Selector Format")], delay(() => append([new FsCell("Explication"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")], delay(() => append([new FsCell("Unit"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")], delay(() => append([new FsCell("Object Type"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")], delay(() => append([new FsCell("Description")], delay(() => append([new FsCell("Generated By")], delay(() => append([new FsCell("Label")], delay(() => map_2((ck) => (new FsCell(ck)), commentKeys)))))))))))))))));
+    return toList(delay(() => append([new FsCell("Data"), new FsCell("Data Format"), new FsCell("Data Selector Format")], delay(() => append([new FsCell("Explication"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")], delay(() => append([new FsCell("Unit"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")], delay(() => append([new FsCell("Object Type"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")], delay(() => append([new FsCell("Description")], delay(() => append([new FsCell("Generated By")], delay(() => append([new FsCell("Label")], delay(() => map_2((ck) => (new FsCell(`Comment [${ck}]`)), commentKeys)))))))))))))))));
 }

package/dist/ts/esm/ts/Spreadsheet/Metadata/SparseTable.js

@@ -1,7 +1,7 @@
 import { append as append_1, delay, tryItem, length as length_1, isEmpty, iterate, fold, tryPick, maxBy, initialize, choose, map, indexed } from "@fable-org/fable-library-js/Seq.js";
 import { defaultArg, value as value_1, map as map_1 } from "@fable-org/fable-library-js/Option.js";
 import { tryFind, ofSeq } from "@fable-org/fable-library-js/Map.js";
-import { arrayHash, equalArrays, equals, comparePrimitives } from "@fable-org/fable-library-js/Util.js";
+import { equals, comparePrimitives } from "@fable-org/fable-library-js/Util.js";
 import { DataType_String } from "../../fable_modules/FsSpreadsheet.6.3.1/Cells/FsCell.fs.js";
 import { RowBuilder_get_Empty, RowBuilder__Combine_19F30600, RowBuilder_$ctor } from "../../fable_modules/FsSpreadsheet.6.3.1/DSL/RowBuilder.fs.js";
 import { RowElement_IndexedCell, ColumnIndex, RowElement_UnindexedCell } from "../../fable_modules/FsSpreadsheet.6.3.1/DSL/Types.fs.js";
@@ -14,7 +14,7 @@ import { Record } from "@fable-org/fable-library-js/Types.js";
 import { record_type, list_type, class_type, tuple_type, int32_type, string_type } from "@fable-org/fable-library-js/Reflection.js";
 import { Seq_trySkip, Dictionary_tryGetValue } from "../CollectionAux.js";
 import { addToDict, getItemFromDict } from "@fable-org/fable-library-js/MapUtil.js";
-import { Dictionary } from "@fable-org/fable-library-js/MutableMap.js";
+import { Dictionary_init } from "../../Core/Helper/Collections.js";
 import { printf, toFail } from "@fable-org/fable-library-js/String.js";
 import { Comment$, Remark } from "../../Core/Comment.js";
 import { Comment_wrapCommentKey, Comment_$007CComment$007C_$007C, Remark_$007CRemark$007C_$007C } from "./Comment.js";
@@ -296,10 +296,7 @@ export function SparseTable__TryGetValueDefault_5BAE6133(this$, defaultValue, ke
     }
 }
 export function SparseTable_Create_Z2192E64B(matrix, keys, commentKeys, length) {
-    return new SparseTable(defaultArg(matrix, new Dictionary([], {
-        Equals: equalArrays,
-        GetHashCode: arrayHash,
-    })), defaultArg(keys, empty()), defaultArg(commentKeys, empty()), defaultArg(length, 0));
+    return new SparseTable(defaultArg(matrix, Dictionary_init()), defaultArg(keys, empty()), defaultArg(commentKeys, empty()), defaultArg(length, 0));
 }
 export function SparseTable_AddRow(key, values, matrix) {
     iterate((tupledArg) => {

package/dist/ts/types/ts/ARC.d.ts

@@ -17,7 +17,7 @@ import { TypeInfo } from "@fable-org/fable-library-js/Reflection.js";
 export declare class ARC extends ArcInvestigation {
     _cwl: Option<void>;
     _fs: FileSystem;
-    "init@89": int32;
+    "init@90": int32;
     constructor(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, ontologySourceReferences?: OntologySourceReference[], publications?: Publication[], contacts?: Person[], assays?: ArcAssay[], studies?: ArcStudy[], workflows?: ArcWorkflow[], runs?: ArcRun[], registeredStudyIdentifiers?: string[], comments?: Comment$[], remarks?: Remark[], cwl?: Option<void>, fs?: FileSystem);
     get FileSystem(): FileSystem;
     set FileSystem(fs: FileSystem);
@@ -48,7 +48,7 @@ export declare class ARC extends ArcInvestigation {
     UpdateFileSystem(): void;
     GetWriteContracts(skipUpdateFS?: boolean): Contract[];
     GetUpdateContracts(skipUpdateFS?: boolean): Contract[];
-    GetGitInitContracts(branch?: string, repositoryAddress?: string, defaultGitignore?: boolean): Contract[];
+    GetGitInitContracts(branch?: string, repositoryAddress?: string, defaultGitignore?: boolean, defaultGitattributes?: boolean): Contract[];
     static getCloneContract(remoteUrl: string, merge?: boolean, branch?: string, token?: [string, string], nolfs?: boolean): Contract;
     Copy(): ARC;
     GetRegisteredPayload(IgnoreHidden?: boolean): FileSystemTree_$union;

package/dist/ts/types/ts/ARC.d.ts.map

@@ -1 +1 @@
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package/dist/ts/types/ts/Conversion.d.ts

@@ -1,7 +1,6 @@
 import { Option } from "@fable-org/fable-library-js/Option.js";
 import { int32 } from "@fable-org/fable-library-js/Int32.js";
 import { LDGraph, LDNode } from "./ROCrate/LDObject.js";
-import { IMap } from "@fable-org/fable-library-js/Util.js";
 import { TypeInfo } from "@fable-org/fable-library-js/Reflection.js";
 import { Comment$ } from "./Core/Comment.js";
 import { LDContext } from "./ROCrate/LDContext.js";
@@ -10,8 +9,8 @@ import { Data } from "./Core/Data.js";
 import { CompositeCell_$union } from "./Core/Table/CompositeCell.js";
 import { CompositeHeader_$union } from "./Core/Table/CompositeHeader.js";
 import { DataContext } from "./Core/DataContext.js";
-import { FSharpList } from "@fable-org/fable-library-js/List.js";
 import { ArcTable } from "./Core/Table/ArcTable.js";
+import { FSharpList } from "@fable-org/fable-library-js/List.js";
 import { ArcTables } from "./Core/Table/ArcTables.js";
 import { DataMap } from "./Core/DataMap.js";
 import { Person } from "./Core/Person.js";
@@ -123,56 +122,56 @@ export declare function ProcessConversion_decomposeProcessName_Z721C83C5(name: s
 /**
  * If the given headers depict a component, returns a function for parsing the values of the matrix to the values of this component
  */
-export declare function ProcessConversion_tryComponentGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => LDNode))>;
+export declare function ProcessConversion_tryComponentGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
 /**
  * If the given headers depict a parameter, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryParameterGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => LDNode))>;
+export declare function ProcessConversion_tryParameterGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
 /**
  * If the given headers depict a factor, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryFactorGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => LDNode))>;
+export declare function ProcessConversion_tryFactorGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
 /**
  * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryCharacteristicGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => LDNode))>;
+export declare function ProcessConversion_tryCharacteristicGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
 /**
  * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryGetProtocolTypeGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => LDNode))>;
+export declare function ProcessConversion_tryGetProtocolTypeGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
 /**
  * If the given headers depict a protocolREF, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryGetProtocolREFGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => string))>;
+export declare function ProcessConversion_tryGetProtocolREFGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
 /**
  * If the given headers depict a protocolDescription, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryGetProtocolDescriptionGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => string))>;
+export declare function ProcessConversion_tryGetProtocolDescriptionGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
 /**
  * If the given headers depict a protocolURI, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryGetProtocolURIGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => string))>;
+export declare function ProcessConversion_tryGetProtocolURIGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
 /**
  * If the given headers depict a protocolVersion, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryGetProtocolVersionGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => string))>;
+export declare function ProcessConversion_tryGetProtocolVersionGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
 /**
  * If the given headers depict an input, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryGetInputGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => LDNode))>;
+export declare function ProcessConversion_tryGetInputGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
 /**
  * If the given headers depict an output, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryGetOutputGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => LDNode))>;
+export declare function ProcessConversion_tryGetOutputGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
 /**
  * If the given headers depict a comment, returns a function for parsing the values of the matrix to the values of this type
  */
-export declare function ProcessConversion_tryGetCommentGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => string))>;
-export declare function ProcessConversion_tryGetPerformerGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => LDNode))>;
+export declare function ProcessConversion_tryGetCommentGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+export declare function ProcessConversion_tryGetPerformerGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
 /**
  * Given the header sequence of an ArcTable, returns a function for parsing each row of the table to a process
  */
-export declare function ProcessConversion_getProcessGetter(assayName: Option<string>, studyName: Option<string>, processNameRoot: string, headers: Iterable<CompositeHeader_$union>): ((arg0: IMap<[int32, int32], CompositeCell_$union>) => ((arg0: int32) => LDNode));
+export declare function ProcessConversion_getProcessGetter(assayName: Option<string>, studyName: Option<string>, processNameRoot: string, headers: Iterable<CompositeHeader_$union>): ((arg0: ArcTable) => ((arg0: int32) => LDNode));
 /**
  * Groups processes by their name, or by the name of the protocol they execute
  *