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

package/dist/ts/cjs/ts/Json.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.JsonController = exports.JsonHelper_ARCJson = exports.JsonHelper_InvestigationJson = exports.JsonHelper_StudyJson = exports.JsonHelper_AssayJson = exports.JsonHelper_OntologyAnnotationJson = void 0;
+exports.JsonController = exports.JsonHelper_LDNodeJson = exports.JsonHelper_LDGraphJson = exports.JsonHelper_ARCJson = exports.JsonHelper_InvestigationJson = exports.JsonHelper_StudyJson = exports.JsonHelper_AssayJson = exports.JsonHelper_OntologyAnnotationJson = void 0;
 exports.JsonHelper_OntologyAnnotationJson_$reflection = JsonHelper_OntologyAnnotationJson_$reflection;
 exports.JsonHelper_OntologyAnnotationJson_$ctor = JsonHelper_OntologyAnnotationJson_$ctor;
 exports.JsonHelper_AssayJson_$reflection = JsonHelper_AssayJson_$reflection;
@@ -11,6 +11,10 @@ exports.JsonHelper_InvestigationJson_$reflection = JsonHelper_InvestigationJson_
 exports.JsonHelper_InvestigationJson_$ctor = JsonHelper_InvestigationJson_$ctor;
 exports.JsonHelper_ARCJson_$reflection = JsonHelper_ARCJson_$reflection;
 exports.JsonHelper_ARCJson_$ctor = JsonHelper_ARCJson_$ctor;
+exports.JsonHelper_LDGraphJson_$reflection = JsonHelper_LDGraphJson_$reflection;
+exports.JsonHelper_LDGraphJson_$ctor = JsonHelper_LDGraphJson_$ctor;
+exports.JsonHelper_LDNodeJson_$reflection = JsonHelper_LDNodeJson_$reflection;
+exports.JsonHelper_LDNodeJson_$ctor = JsonHelper_LDNodeJson_$ctor;
 exports.JsonController_$reflection = JsonController_$reflection;
 const OntologyAnnotation_js_1 = require("./JsonIO/OntologyAnnotation.js");
 const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
@@ -19,6 +23,7 @@ const Assay_js_1 = require("./JsonIO/Assay.js");
 const Study_js_1 = require("./JsonIO/Study.js");
 const Investigation_js_1 = require("./JsonIO/Investigation.js");
 const ARC_js_1 = require("./ARC.js");
+const LDObject_js_1 = require("./JsonIO/LDObject.js");
 class JsonHelper_OntologyAnnotationJson {
     constructor() {
     }
@@ -170,6 +175,40 @@ function JsonHelper_ARCJson_$reflection() {
 function JsonHelper_ARCJson_$ctor() {
     return new JsonHelper_ARCJson();
 }
+class JsonHelper_LDGraphJson {
+    constructor() {
+    }
+    fromROCrateJsonString(s) {
+        return (0, LDObject_js_1.ARCtrl_ROCrate_LDGraph__LDGraph_fromROCrateJsonString_Static_Z721C83C5)(s);
+    }
+    toROCrateJsonString(spaces) {
+        return (0, LDObject_js_1.ARCtrl_ROCrate_LDGraph__LDGraph_toROCrateJsonString_Static_71136F3F)((0, Option_js_1.unwrap)(spaces));
+    }
+}
+exports.JsonHelper_LDGraphJson = JsonHelper_LDGraphJson;
+function JsonHelper_LDGraphJson_$reflection() {
+    return (0, Reflection_js_1.class_type)("ARCtrl.JsonHelper.LDGraphJson", undefined, JsonHelper_LDGraphJson);
+}
+function JsonHelper_LDGraphJson_$ctor() {
+    return new JsonHelper_LDGraphJson();
+}
+class JsonHelper_LDNodeJson {
+    constructor() {
+    }
+    fromROCrateJsonString(s) {
+        return (0, LDObject_js_1.ARCtrl_ROCrate_LDNode__LDNode_fromROCrateJsonString_Static_Z721C83C5)(s);
+    }
+    toROCrateJsonString(spaces) {
+        return (0, LDObject_js_1.ARCtrl_ROCrate_LDNode__LDNode_toROCrateJsonString_Static_71136F3F)((0, Option_js_1.unwrap)(spaces));
+    }
+}
+exports.JsonHelper_LDNodeJson = JsonHelper_LDNodeJson;
+function JsonHelper_LDNodeJson_$reflection() {
+    return (0, Reflection_js_1.class_type)("ARCtrl.JsonHelper.LDNodeJson", undefined, JsonHelper_LDNodeJson);
+}
+function JsonHelper_LDNodeJson_$ctor() {
+    return new JsonHelper_LDNodeJson();
+}
 class JsonController {
     constructor() {
     }
@@ -188,6 +227,12 @@ class JsonController {
     static get ARC() {
         return new JsonHelper_ARCJson();
     }
+    static get LDGraph() {
+        return new JsonHelper_LDGraphJson();
+    }
+    static get LDNode() {
+        return new JsonHelper_LDNodeJson();
+    }
 }
 exports.JsonController = JsonController;
 function JsonController_$reflection() {

package/dist/ts/cjs/ts/ROCrateIO.js

@@ -17,6 +17,8 @@ const LDContext_js_1 = require("./ROCrate/LDContext.js");
 const ROCrateContext_js_1 = require("./ROCrate/ROCrateContext.js");
 const LDGraph_js_1 = require("./Json/ROCrate/LDGraph.js");
 const Decode_fs_js_1 = require("./fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const Collections_js_1 = require("./Core/Helper/Collections.js");
+const File_js_1 = require("./ROCrate/Generic/File.js");
 const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
 const LDNode_js_1 = require("./Json/ROCrate/LDNode.js");
 class ROCrate {
@@ -55,7 +57,16 @@ function ROCrate_get_decoder() {
             throw new Error("RO-Crate graph did not contain root data Entity");
         }
         else {
-            return (0, Conversion_js_1.ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8)((0, Option_js_1.value)(matchValue), graph, (0, Option_js_1.unwrap)(graph.TryGetContext()));
+            const node = (0, Option_js_1.value)(matchValue);
+            const files = (0, Collections_js_1.ResizeArray_choose)((n) => {
+                if (File_js_1.LDFile.validate(n, (0, Option_js_1.unwrap)(graph.TryGetContext())) && !(n.Id.indexOf("#") >= 0)) {
+                    return n.Id;
+                }
+                else {
+                    return undefined;
+                }
+            }, graph.Nodes);
+            return [(0, Conversion_js_1.ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8)(node, graph, (0, Option_js_1.unwrap)(graph.TryGetContext())), files];
         }
     }, LDGraph_js_1.decoder);
 }

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

@@ -7,6 +7,7 @@ exports.classifyColumnOrder = classifyColumnOrder;
 exports.groupColumnsByHeader = groupColumnsByHeader;
 exports.tryAnnotationTable = tryAnnotationTable;
 exports.composeColumns = composeColumns;
+exports.composeArcTableValues = composeArcTableValues;
 exports.tryFromFsWorksheet = tryFromFsWorksheet;
 exports.toFsWorksheet = toFsWorksheet;
 const List_js_1 = require("@fable-org/fable-library-js/List.js");
@@ -15,6 +16,8 @@ const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
 const FsWorksheet_fs_js_1 = require("../../fable_modules/FsSpreadsheet.6.3.1/FsWorksheet.fs.js");
 const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
 const CompositeColumn_js_1 = require("./CompositeColumn.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+const ArcTableAux_js_1 = require("../../Core/Table/ArcTableAux.js");
 const String_js_1 = require("@fable-org/fable-library-js/String.js");
 const FsCellsCollection_fs_js_1 = require("../../fable_modules/FsSpreadsheet.6.3.1/Cells/FsCellsCollection.fs.js");
 const Range_js_1 = require("@fable-org/fable-library-js/Range.js");
@@ -22,7 +25,6 @@ const FsAddress_fs_js_1 = require("../../fable_modules/FsSpreadsheet.6.3.1/FsAdd
 const FsRangeAddress_fs_js_1 = require("../../fable_modules/FsSpreadsheet.6.3.1/Ranges/FsRangeAddress.fs.js");
 const FsRangeBase_fs_js_1 = require("../../fable_modules/FsSpreadsheet.6.3.1/Ranges/FsRangeBase.fs.js");
 const ArcTable_js_1 = require("../../Core/Table/ArcTable.js");
-const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
 const Double_js_1 = require("@fable-org/fable-library-js/Double.js");
 const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
 /**
@@ -92,6 +94,15 @@ function tryAnnotationTable(sheet) {
 function composeColumns(stringCellColumns) {
     return (0, Array_js_1.map)(CompositeColumn_js_1.fromStringCellColumns, groupColumnsByHeader(stringCellColumns));
 }
+/**
+ * Groups and parses a collection of single columns into the according ISA composite columns
+ */
+function composeArcTableValues(stringCellColumns) {
+    const valueMap = new Map([]);
+    const rowCount = ((0, Array_js_1.item)(0, stringCellColumns).length - 1) | 0;
+    const patternInput = (0, Array_js_1.unzip)((0, Array_js_1.map)((columns) => (0, CompositeColumn_js_1.ColumnValueRefs_fromStringCellColumns)(valueMap, columns), groupColumnsByHeader(stringCellColumns)));
+    return [patternInput[0], ArcTableAux_js_1.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
  */
@@ -103,7 +114,7 @@ function tryFromFsWorksheet(sheet) {
         }
         else {
             const t = (0, Option_js_1.value)(matchValue);
-            const compositeColumns = composeColumns((0, Array_js_1.map)(CompositeColumn_js_1.fixDeprecatedIOHeader, (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((c) => (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.collect)((r) => {
+            const patternInput = composeArcTableValues((0, Array_js_1.map)(CompositeColumn_js_1.fixDeprecatedIOHeader, (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((c) => (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.collect)((r) => {
                 const matchValue_1 = (0, FsCellsCollection_fs_js_1.FsCellsCollection__TryGetCell_Z37302880)(sheet.CellCollection, r, c);
                 if (matchValue_1 == null) {
                     return (0, Seq_js_1.singleton)("");
@@ -113,7 +124,7 @@ function tryFromFsWorksheet(sheet) {
                     return (0, Seq_js_1.singleton)(cell.ValueAsString());
                 }
             }, (0, Range_js_1.rangeDouble)(1, 1, (0, FsAddress_fs_js_1.FsAddress__get_RowNumber)((0, FsRangeAddress_fs_js_1.FsRangeAddress__get_LastAddress)((0, FsRangeBase_fs_js_1.FsRangeBase__get_RangeAddress)(t))))))), (0, Range_js_1.rangeDouble)(1, 1, (0, FsAddress_fs_js_1.FsAddress__get_ColumnNumber)((0, FsRangeAddress_fs_js_1.FsRangeAddress__get_LastAddress)((0, FsRangeBase_fs_js_1.FsRangeBase__get_RangeAddress)(t)))))))));
-            return ArcTable_js_1.ArcTable.addColumns(compositeColumns, undefined, true)(ArcTable_js_1.ArcTable.init(sheet.Name));
+            return ArcTable_js_1.ArcTable.fromArcTableValues(sheet.Name, Array.from(patternInput[0]), patternInput[1]);
         }
     }
     catch (err) {
@@ -129,7 +140,7 @@ function toFsWorksheet(index, table) {
         return ws;
     }
     else {
-        const columns = (0, List_js_1.collect)(CompositeColumn_js_1.toStringCellColumns, (0, List_js_1.sortBy)(classifyColumnOrder, (0, List_js_1.ofArray)(table.Columns), {
+        const columns = (0, List_js_1.collect)(CompositeColumn_js_1.toStringCellColumns, (0, List_js_1.sortBy)(classifyColumnOrder, (0, List_js_1.ofSeq)(table.Columns), {
             Compare: Util_js_1.comparePrimitives,
         }));
         let tableRowCount;

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

@@ -2,9 +2,11 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fixDeprecatedIOHeader = fixDeprecatedIOHeader;
 exports.fromStringCellColumns = fromStringCellColumns;
+exports.stringCellColumnsOfFsColumns = stringCellColumnsOfFsColumns;
 exports.fromFsColumns = fromFsColumns;
 exports.toStringCellColumns = toStringCellColumns;
 exports.toFsColumns = toFsColumns;
+exports.ColumnValueRefs_fromStringCellColumns = ColumnValueRefs_fromStringCellColumns;
 const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
 const CompositeHeader_js_1 = require("../../Core/Table/CompositeHeader.js");
 const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
@@ -16,6 +18,10 @@ const FsCell_fs_js_1 = require("../../fable_modules/FsSpreadsheet.6.3.1/Cells/Fs
 const CompositeCell_js_1 = require("./CompositeCell.js");
 const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
 const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+const ArcTableAux_js_1 = require("../../Core/Table/ArcTableAux.js");
+const HashCodes_js_1 = require("../../Core/Helper/HashCodes.js");
+const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
 /**
  * Checks if the column header is a deprecated IO Header. If so, fixes it.
  *
@@ -45,9 +51,15 @@ function fixDeprecatedIOHeader(stringCellCol) {
 function fromStringCellColumns(columns) {
     const patternInput = (0, CompositeHeader_js_2.fromStringCells)((0, Array_js_1.map)((c) => (0, Array_js_1.item)(0, c), columns));
     const l = (0, Array_js_1.item)(0, columns).length | 0;
-    const cells = (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i) => patternInput[1]((0, Array_js_1.map)((c_1) => (0, Array_js_1.item)(i, c_1), columns)), (0, Range_js_1.rangeDouble)(1, 1, l - 1))));
+    const cells = Array.from((0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i) => patternInput[1]((0, Array_js_1.map)((c_1) => (0, Array_js_1.item)(i, c_1), columns)), (0, Range_js_1.rangeDouble)(1, 1, l - 1)))));
     return CompositeColumn_js_1.CompositeColumn.create(patternInput[0], cells);
 }
+function stringCellColumnsOfFsColumns(columns) {
+    return (0, Array_js_1.map)((c) => {
+        c.ToDenseColumn();
+        return (0, Array_js_1.map)((cell) => cell.ValueAsString(), (0, Seq_js_1.toArray)(c.Cells));
+    }, columns);
+}
 function fromFsColumns(columns) {
     return fromStringCellColumns((0, Array_js_1.map)((c) => {
         c.ToDenseColumn();
@@ -59,21 +71,80 @@ function toStringCellColumns(column) {
     const isTerm = column.Header.IsTermColumn;
     const isData = column.Header.IsDataColumn && (0, Seq_js_1.exists)((c_1) => c_1.isData, column.Cells);
     const header = (0, CompositeHeader_js_2.toStringCells)(hasUnit, column.Header);
-    const cells = (0, Array_js_1.map)((cell) => (0, CompositeCell_js_1.toStringCells)(isTerm, hasUnit, cell), column.Cells);
+    const compositeCells = (0, Seq_js_1.toArray)(column.Cells);
+    const cells = (0, Array_js_1.map)((cell) => (0, CompositeCell_js_1.toStringCells)(isTerm, hasUnit, cell), (0, Seq_js_1.toArray)(column.Cells));
     const getCellOrDefault = (ri, ci, cells_1) => (0, Option_js_1.defaultArg)((0, Array_js_1.tryItem)(ci, (0, Array_js_1.item)(ri, cells_1)), "");
     if (hasUnit) {
-        return (0, List_js_1.ofArray)([(0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(0, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i) => getCellOrDefault(i, 0, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(1, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_1) => getCellOrDefault(i_1, 1, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(2, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_2) => getCellOrDefault(i_2, 2, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(3, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_3) => getCellOrDefault(i_3, 3, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1))))))]);
+        return (0, List_js_1.ofArray)([(0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(0, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i) => getCellOrDefault(i, 0, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(1, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_1) => getCellOrDefault(i_1, 1, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(2, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_2) => getCellOrDefault(i_2, 2, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(3, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_3) => getCellOrDefault(i_3, 3, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1))))))]);
     }
     else if (isTerm) {
-        return (0, List_js_1.ofArray)([(0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(0, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_4) => getCellOrDefault(i_4, 0, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(1, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_5) => getCellOrDefault(i_5, 1, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(2, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_6) => getCellOrDefault(i_6, 2, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1))))))]);
+        return (0, List_js_1.ofArray)([(0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(0, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_4) => getCellOrDefault(i_4, 0, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(1, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_5) => getCellOrDefault(i_5, 1, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(2, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_6) => getCellOrDefault(i_6, 2, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1))))))]);
     }
     else if (isData) {
-        return (0, List_js_1.ofArray)([(0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(0, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_7) => getCellOrDefault(i_7, 0, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(1, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_8) => getCellOrDefault(i_8, 1, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(2, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_9) => getCellOrDefault(i_9, 2, cells), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1))))))]);
+        return (0, List_js_1.ofArray)([(0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(0, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_7) => getCellOrDefault(i_7, 0, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(1, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_8) => getCellOrDefault(i_8, 1, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1)))))), (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(2, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_9) => getCellOrDefault(i_9, 2, cells), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1))))))]);
     }
     else {
-        return (0, List_js_1.singleton)((0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(0, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_10) => (0, Array_js_1.item)(0, (0, Array_js_1.item)(i_10, cells)), (0, Range_js_1.rangeDouble)(0, 1, column.Cells.length - 1)))))));
+        return (0, List_js_1.singleton)((0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Array_js_1.item)(0, header)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i_10) => (0, Array_js_1.item)(0, (0, Array_js_1.item)(i_10, cells)), (0, Range_js_1.rangeDouble)(0, 1, compositeCells.length - 1)))))));
     }
 }
 function toFsColumns(column) {
     return (0, List_js_1.map)((c) => (0, List_js_1.map)((s) => (new FsCell_fs_js_1.FsCell(s)), c), toStringCellColumns(column));
 }
+function ColumnValueRefs_fromStringCellColumns(valueMap, columns) {
+    let cellHash;
+    const hashMap = new Map([]);
+    const cells = new Map([]);
+    let constant = true;
+    const patternInput = (0, CompositeHeader_js_2.fromStringCells)((0, Array_js_1.map)((c) => (0, Array_js_1.item)(0, c), columns));
+    const header = patternInput[0];
+    const cellParser = patternInput[1];
+    const l = (0, Array_js_1.item)(0, columns).length | 0;
+    if (l === 1) {
+        return [header, (0, ArcTableAux_js_1.ColumnValueRefs_Sparse)(cells)];
+    }
+    else {
+        for (let i = 1; i <= (l - 1); i++) {
+            const strings = (0, Array_js_1.map)((c_1) => (0, Array_js_1.item)(i, c_1), columns);
+            const hash_2 = (0, Seq_js_1.reduce)(HashCodes_js_1.mergeHashes, (0, Seq_js_1.map)(Util_js_1.stringHash, strings)) | 0;
+            let matchValue;
+            let patternInput_1;
+            let outArg = (0, Util_js_1.defaultOf)();
+            patternInput_1 = [(0, MapUtil_js_1.tryGetValue)(hashMap, hash_2, new Types_js_1.FSharpRef(() => outArg, (v) => {
+                    outArg = (v | 0);
+                })), outArg];
+            matchValue = (patternInput_1[0] ? patternInput_1[1] : undefined);
+            if (matchValue == null) {
+                if (i === 1) {
+                    const cellHash_3 = (0, ArcTableAux_js_1.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 = (0, MapUtil_js_1.getItemFromDict)(cells, 0) | 0;
+                            cells.set(j, cellHash_4);
+                        }
+                    }
+                    const cellHash_5 = (0, ArcTableAux_js_1.ensureCellHashInValueMap)(cellParser(strings), valueMap) | 0;
+                    hashMap.set(hash_2, cellHash_5);
+                    cells.set(i - 1, cellHash_5);
+                }
+            }
+            else if ((cellHash = ((0, Option_js_1.value)(matchValue) | 0), constant)) {
+                const cellHash_1 = (0, Option_js_1.value)(matchValue) | 0;
+            }
+            else {
+                const cellHash_2 = (0, Option_js_1.value)(matchValue) | 0;
+                cells.set(i - 1, cellHash_2);
+            }
+        }
+        if (constant) {
+            return [header, (0, ArcTableAux_js_1.ColumnValueRefs_Constant)((0, MapUtil_js_1.getItemFromDict)(cells, 0))];
+        }
+        else {
+            return [header, (0, ArcTableAux_js_1.ColumnValueRefs_Sparse)(cells)];
+        }
+    }
+}

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

@@ -31,11 +31,11 @@ const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
 const Collections_js_1 = require("../Core/Helper/Collections.js");
 const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
 const ArcTypes_js_1 = require("../Core/ArcTypes.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
 const OntologySourceReference_js_1 = require("./Metadata/OntologySourceReference.js");
 const Publication_js_1 = require("./Metadata/Publication.js");
 const Contacts_js_1 = require("./Metadata/Contacts.js");
 const Study_js_1 = require("./Metadata/Study.js");
-const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
 const Map_js_1 = require("@fable-org/fable-library-js/Map.js");
 const FsWorksheet_fs_js_1 = require("../fable_modules/FsSpreadsheet.6.3.1/FsWorksheet.fs.js");
 const FsWorkbook_fs_js_1 = require("../fable_modules/FsSpreadsheet.6.3.1/FsWorkbook.fs.js");
@@ -108,6 +108,9 @@ function ArcInvestigation_fromParts(investigationInfo, ontologySourceReference,
     return ArcTypes_js_1.ArcInvestigation.make(investigationInfo.Identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications_1, contacts_1, assays_1, studies_1, [], [], registeredStudyIdentifiers, comments, remarks_1);
 }
 function ArcInvestigation_fromRows(rows) {
+    if ((0, Seq_js_1.isEmpty)(rows)) {
+        throw new Error("isa_investigation sheet in Investigation file is empty");
+    }
     const en = (0, Util_js_1.getEnumerator)(rows);
     const emptyInvestigationInfo = ArcInvestigation_InvestigationInfo_create("", "", "", "", "", (0, List_js_1.empty)());
     const loop = (lastLine_mut, ontologySourceReferences_mut, investigationInfo_mut, publications_mut, contacts_mut, studies_mut, remarks_mut, lineNumber_mut) => {
@@ -226,25 +229,38 @@ function ArcInvestigation_fromRows(rows) {
                         continue loop;
                     }
                 }
-                default: {
-                    let patternInput_5;
-                    const tupledArg = (0, List_js_1.unzip)(studies);
-                    patternInput_5 = [(0, List_js_1.reverse)(tupledArg[0]), (0, Seq2_js_1.List_distinctBy)((a_1) => a_1.Identifier, (0, List_js_1.concat)(tupledArg[1]), {
-                            Equals: (x, y) => (x === y),
-                            GetHashCode: Util_js_1.stringHash,
-                        })];
-                    return ArcInvestigation_fromParts(investigationInfo, ontologySourceReferences, publications, contacts, patternInput_5[0], patternInput_5[1], remarks);
-                }
+                default:
+                    if (en["System.Collections.IEnumerator.MoveNext"]()) {
+                        lastLine_mut = (0, SparseTable_js_1.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 = (0, List_js_1.unzip)(studies);
+                        patternInput_5 = [(0, List_js_1.reverse)(tupledArg[0]), (0, Seq2_js_1.List_distinctBy)((a_1) => a_1.Identifier, (0, List_js_1.concat)(tupledArg[1]), {
+                                Equals: (x, y) => (x === y),
+                                GetHashCode: Util_js_1.stringHash,
+                            })];
+                        return ArcInvestigation_fromParts(investigationInfo, ontologySourceReferences, publications, contacts, patternInput_5[0], patternInput_5[1], remarks);
+                    }
             }
             break;
         }
     };
-    if (en["System.Collections.IEnumerator.MoveNext"]()) {
-        return loop((0, SparseTable_js_1.SparseRowModule_tryGetValueAt)(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), (0, List_js_1.empty)(), emptyInvestigationInfo, (0, List_js_1.empty)(), (0, List_js_1.empty)(), (0, List_js_1.empty)(), (0, List_js_1.empty)(), 1);
-    }
-    else {
-        throw new Error("emptyInvestigationFile");
+    let arcInvestigation;
+    en["System.Collections.IEnumerator.MoveNext"]();
+    arcInvestigation = loop((0, SparseTable_js_1.SparseRowModule_tryGetValueAt)(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), (0, List_js_1.empty)(), emptyInvestigationInfo, (0, List_js_1.empty)(), (0, List_js_1.empty)(), (0, List_js_1.empty)(), (0, List_js_1.empty)(), 1);
+    if (arcInvestigation.Identifier === "") {
+        throw new Error("Mandatory Investigation identifier is not present");
     }
+    return arcInvestigation;
 }
 function ArcInvestigation_toRows(investigation) {
     let remarks, rows;

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

@@ -476,5 +476,5 @@ function fromFsCells(cells) {
     }
 }
 function toFsCells(commentKeys) {
-    return (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Data"), new FsCell_fs_js_1.FsCell("Data Format"), new FsCell_fs_js_1.FsCell("Data Selector Format")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Explication"), new FsCell_fs_js_1.FsCell("Term Source REF"), new FsCell_fs_js_1.FsCell("Term Accession Number")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Unit"), new FsCell_fs_js_1.FsCell("Term Source REF"), new FsCell_fs_js_1.FsCell("Term Accession Number")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Object Type"), new FsCell_fs_js_1.FsCell("Term Source REF"), new FsCell_fs_js_1.FsCell("Term Accession Number")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Description")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Generated By")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Label")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((ck) => (new FsCell_fs_js_1.FsCell(ck)), commentKeys)))))))))))))))));
+    return (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Data"), new FsCell_fs_js_1.FsCell("Data Format"), new FsCell_fs_js_1.FsCell("Data Selector Format")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Explication"), new FsCell_fs_js_1.FsCell("Term Source REF"), new FsCell_fs_js_1.FsCell("Term Accession Number")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Unit"), new FsCell_fs_js_1.FsCell("Term Source REF"), new FsCell_fs_js_1.FsCell("Term Accession Number")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Object Type"), new FsCell_fs_js_1.FsCell("Term Source REF"), new FsCell_fs_js_1.FsCell("Term Accession Number")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Description")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Generated By")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)([new FsCell_fs_js_1.FsCell("Label")], (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((ck) => (new FsCell_fs_js_1.FsCell(`Comment [${ck}]`)), commentKeys)))))))))))))))));
 }

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

@@ -36,7 +36,7 @@ const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
 const Reflection_js_1 = require("@fable-org/fable-library-js/Reflection.js");
 const CollectionAux_js_1 = require("../CollectionAux.js");
 const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
-const MutableMap_js_1 = require("@fable-org/fable-library-js/MutableMap.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
 const String_js_1 = require("@fable-org/fable-library-js/String.js");
 const Comment_js_1 = require("../../Core/Comment.js");
 const Comment_js_2 = require("./Comment.js");
@@ -319,10 +319,7 @@ function SparseTable__TryGetValueDefault_5BAE6133(this$, defaultValue, key) {
     }
 }
 function SparseTable_Create_Z2192E64B(matrix, keys, commentKeys, length) {
-    return new SparseTable((0, Option_js_1.defaultArg)(matrix, new MutableMap_js_1.Dictionary([], {
-        Equals: Util_js_1.equalArrays,
-        GetHashCode: Util_js_1.arrayHash,
-    })), (0, Option_js_1.defaultArg)(keys, (0, List_js_1.empty)()), (0, Option_js_1.defaultArg)(commentKeys, (0, List_js_1.empty)()), (0, Option_js_1.defaultArg)(length, 0));
+    return new SparseTable((0, Option_js_1.defaultArg)(matrix, (0, Collections_js_1.Dictionary_init)()), (0, Option_js_1.defaultArg)(keys, (0, List_js_1.empty)()), (0, Option_js_1.defaultArg)(commentKeys, (0, List_js_1.empty)()), (0, Option_js_1.defaultArg)(length, 0));
 }
 function SparseTable_AddRow(key, values, matrix) {
     (0, Seq_js_1.iterate)((tupledArg) => {

package/dist/ts/esm/ts/ARC.js

@@ -8,15 +8,16 @@ import { PromiseBuilder__Delay_62FBFDE1, PromiseBuilder__Run_212F1D4B } from "./
 import { promise } from "./fable_modules/Fable.Promise.3.2.0/PromiseImpl.fs.js";
 import { getAllFilePathsAsync } from "./ContractIO/FileSystemHelper.js";
 import { toList, collect, empty, find, tryFind, iterate, map, singleton, append, delay, contains, toArray } from "@fable-org/fable-library-js/Seq.js";
-import { defaultOf, disposeSafe, getEnumerator, safeHash, curry2, comparePrimitives, stringHash } from "@fable-org/fable-library-js/Util.js";
+import { equals, defaultOf, disposeSafe, getEnumerator, safeHash, curry2, comparePrimitives, stringHash } from "@fable-org/fable-library-js/Util.js";
 import { getStudyFolderPath, getAssayFolderPath } from "./FileSystem/Path.js";
 import { ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToDeleteContract } from "./Contract/ArcAssay.js";
 import { ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract } from "./Contract/ArcInvestigation.js";
 import { ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract } from "./Contract/ArcStudy.js";
-import { exactlyOne, tryPick, append as append_1, contains as contains_2, concat, fold, choose, map as map_1 } from "@fable-org/fable-library-js/Array.js";
+import { item, equalsWith, tryPick, append as append_1, contains as contains_2, concat, fold, choose, map as map_1 } from "@fable-org/fable-library-js/Array.js";
 import { toText, printf, toFail, join, replace } from "@fable-org/fable-library-js/String.js";
 import { Run_datamapFileNameFromIdentifier, Run_fileNameFromIdentifier, Workflow_datamapFileNameFromIdentifier, Workflow_fileNameFromIdentifier, Assay_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Study_fileNameFromIdentifier, createMissingIdentifier } from "./Core/Helper/Identifier.js";
 import { FSharpSet__Contains, unionMany, contains as contains_1, ofSeq } from "@fable-org/fable-library-js/Set.js";
+import { ResizeArray_map, ResizeArray_iter } from "./Core/Helper/Collections.js";
 import { DataMap__get_StaticHash, DataMap__set_StaticHash_Z524259A4, DataMap__get_DataContexts } from "./Core/DataMap.js";
 import { FileSystemTree_Folder, FileSystemTree } from "./FileSystem/FileSystemTree.js";
 import { tryISAReadContractFromPath } from "./Contract/ARC.js";
@@ -33,8 +34,7 @@ import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.6.3.1/Cells/FsC
 import { ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static, ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5 } from "./Contract/Datamap.js";
 import { ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49 } from "./Contract/ArcWorkflow.js";
 import { ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49 } from "./Contract/ArcRun.js";
-import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, gitattributesContract, Init_createInitContract_6DFDD678 } from "./Contract/Git.js";
-import { ResizeArray_map } from "./Core/Helper/Collections.js";
+import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitattributesContract, gitignoreContract, Init_createInitContract_6DFDD678 } from "./Contract/Git.js";
 import { ofSeq as ofSeq_1 } from "@fable-org/fable-library-js/Map.js";
 import { fromString } from "./fable_modules/Thoth.Json.JavaScript.0.3.0/Decode.fs.js";
 import { ROCrate_encoder_8A8D439, ROCrate_get_decoder, ROCrate_get_decoderDeprecated } from "./ROCrateIO.js";
@@ -53,7 +53,7 @@ export class ARC extends ArcInvestigation {
         this._fs = ((fs_1 = defaultArg(fs, FileSystem.create({
             tree: FileSystemTree_Folder("", []),
         })), ARCAux_updateFSByISA(this$.contents, fs_1)));
-        this["init@89"] = 1;
+        this["init@90"] = 1;
     }
     get FileSystem() {
         const this$ = this;
@@ -287,12 +287,12 @@ export class ARC extends ArcInvestigation {
             }
             switch (matchResult) {
                 case 0: {
-                    col_2.Cells.forEach((c) => {
+                    ResizeArray_iter((c) => {
                         if (c.AsData.FilePath != null) {
                             const newFilePath = dataNameFunction(c.AsData);
                             c.AsData.FilePath = newFilePath;
                         }
-                    });
+                    }, col_2.Cells);
                     break;
                 }
                 case 1: {
@@ -313,19 +313,19 @@ export class ARC extends ArcInvestigation {
             }, DataMap__get_DataContexts(dm));
         };
         iterate((s) => {
-            const f = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
+            const f_1 = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
             const source_1 = s.Tables;
-            iterate(curry2(updateTable)(f), source_1);
+            iterate(curry2(updateTable)(f_1), source_1);
             if (s.DataMap != null) {
-                updateDataMap(f, value_3(s.DataMap));
+                updateDataMap(f_1, value_3(s.DataMap));
             }
         }, this$.Studies);
-        iterate((a) => {
-            const f_1 = (d_1) => d_1.GetAbsolutePathForAssay(a.Identifier, checkExistenceFromRoot);
-            const source_3 = a.Tables;
-            iterate(curry2(updateTable)(f_1), source_3);
-            if (a.DataMap != null) {
-                updateDataMap(f_1, value_3(a.DataMap));
+        iterate((a_1) => {
+            const f_2 = (d_1) => d_1.GetAbsolutePathForAssay(a_1.Identifier, checkExistenceFromRoot);
+            const source_3 = a_1.Tables;
+            iterate(curry2(updateTable)(f_2), source_3);
+            if (a_1.DataMap != null) {
+                updateDataMap(f_2, value_3(a_1.DataMap));
             }
         }, this$.Assays);
     }
@@ -381,7 +381,7 @@ export class ARC extends ArcInvestigation {
                 const registeredStudy = value_3(registeredStudyOpt);
                 registeredStudy.UpdateReferenceByStudyFile(study, true);
             }
-            const datamap = ARCAux_getAssayDataMapFromContracts(study.Identifier, contracts);
+            const datamap = ARCAux_getStudyDataMapFromContracts(study.Identifier, contracts);
             if (study.DataMap == null) {
                 study.DataMap = datamap;
             }
@@ -663,9 +663,10 @@ export class ARC extends ArcInvestigation {
             }));
         }
     }
-    GetGitInitContracts(branch, repositoryAddress, defaultGitignore) {
+    GetGitInitContracts(branch, repositoryAddress, defaultGitignore, defaultGitattributes) {
         const defaultGitignore_1 = defaultArg(defaultGitignore, false);
-        return toArray(delay(() => append(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append(singleton(gitattributesContract), delay(() => append(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => ((repositoryAddress != null) ? singleton(Init_createAddRemoteContract_Z721C83C5(value_3(repositoryAddress))) : empty())))))))));
+        const defaultGitattributes_1 = defaultArg(defaultGitattributes, false);
+        return toArray(delay(() => append(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => append(defaultGitattributes_1 ? singleton(gitattributesContract) : empty(), delay(() => ((repositoryAddress != null) ? singleton(Init_createAddRemoteContract_Z721C83C5(value_3(repositoryAddress))) : empty())))))))));
     }
     static getCloneContract(remoteUrl, merge, branch, token, nolfs) {
         return Clone_createCloneContract_5000466F(remoteUrl, unwrap(merge), unwrap(branch), unwrap(token), unwrap(nolfs));
@@ -820,15 +821,18 @@ export class ARC extends ArcInvestigation {
     static fromROCrateJsonString(s) {
         let arg;
         try {
-            let isa;
+            let patternInput;
             const matchValue = fromString(ROCrate_get_decoder(), s);
             if (matchValue.tag === /* Error */ 1) {
                 throw new Error((arg = matchValue.fields[0], toText(printf("Error decoding string: %O"))(arg)));
             }
             else {
-                isa = matchValue.fields[0];
+                patternInput = matchValue.fields[0];
             }
-            return ARC.fromArcInvestigation(isa);
+            let fileSystem;
+            const paths = Array.from(patternInput[1]);
+            fileSystem = FileSystem.fromFilePaths(paths);
+            return ARC.fromArcInvestigation(patternInput[0], undefined, fileSystem);
         }
         catch (ex) {
             const arg_1 = ex.message;
@@ -913,7 +917,14 @@ export function ARCAux_getRunDataMapFromContracts(runIdentifier, contracts) {
     return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static(runIdentifier, c), contracts);
 }
 export function ARCAux_getArcInvestigationFromContracts(contracts) {
-    return exactlyOne(choose(ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts));
+    const matchValue = choose(ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts);
+    if (!equalsWith(equals, matchValue, defaultOf()) && (matchValue.length === 1)) {
+        return item(0, matchValue);
+    }
+    else {
+        const arg = matchValue.length | 0;
+        return toFail(printf("Could not find investigation in contracts. Expected exactly one investigation, but found %d."))(arg);
+    }
 }
 export function ARCAux_updateFSByISA(isa, fs) {
     let assaysFolder;