@nfdi4plants/arctrl 2.0.0-beta.8 → 2.0.1

package/Core/Table/ArcTable.js

@@ -1,19 +1,19 @@
-import { boxHashValues, Unchecked_alignByHeaders, Unchecked_extendToRowCount, Unchecked_removeRowCells_withIndexChange, Unchecked_addRows, Unchecked_addRow, Unchecked_getEmptyCellForHeader, Unchecked_moveColumnTo, 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, SanityChecks_validate } from "./ArcTableAux.js";
+import { boxHashValues, Unchecked_alignByHeaders, Unchecked_extendToRowCount, Unchecked_removeRowCells_withIndexChange, Unchecked_addRows, Unchecked_addRow, Unchecked_getEmptyCellForHeader, Unchecked_moveColumnTo, Unchecked_removeColumnCells_withIndexChange, tryFindDuplicateUniqueInArray, Unchecked_removeColumnCells, Unchecked_removeHeader, Unchecked_fillMissingCells, Unchecked_addColumn, SanityChecks_validateColumn, tryFindDuplicateUnique, Unchecked_setCellAt, SanityChecks_validateRowIndex, SanityChecks_validateColumnIndex, Unchecked_tryGetCellAt, getRowCount, getColumnCount, SanityChecks_validate } from "./ArcTableAux.js";
 import { Dictionary } from "../../fable_modules/fable-library-js.4.16.0/MutableMap.js";
-import { compareArrays, safeHash, comparePrimitives, equals, arrayHash, equalArrays } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+import { compareArrays, safeHash, comparePrimitives, equals, disposeSafe, getEnumerator, arrayHash, equalArrays } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 import { value as value_3, map as map_2, unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { item as item_1, fold, append as append_1, toList, indexed as indexed_1, choose, filter, length, tryFindIndex, empty, singleton, collect, removeAt, map, delay, toArray } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { rangeDouble } from "../../fable_modules/fable-library-js.4.16.0/Range.js";
+import { join, printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { getItemFromDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
 import { CompositeColumn } from "./CompositeColumn.js";
-import { sortBy, indexed, mapIndexed, initialize, item, sortDescending, iterateIndexed, map as map_1 } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+import { sortBy, indexed, mapIndexed, item, sortDescending, iterateIndexed, initialize, map as map_1 } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
 import { append, iterate, isEmpty } from "../../fable_modules/fable-library-js.4.16.0/List.js";
 import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../fable_modules/fable-library-js.4.16.0/System.Text.js";
 import { toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
-import { join, printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
 import { CompositeCell } from "./CompositeCell.js";
 import { CompositeHeader } from "./CompositeHeader.js";
 import { Array_groupBy } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
-import { getItemFromDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
 import { boxHashSeq, boxHashArray } from "../Helper/HashCodes.js";
 import { class_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
@@ -104,6 +104,19 @@ export class ArcTable {
     static tryGetCellAt(column, row) {
         return (table) => table.TryGetCellAt(column, row);
     }
+    GetCellAt(column, row) {
+        const this$ = this;
+        try {
+            return getItemFromDict(this$.Values, [column, row]);
+        }
+        catch (matchValue) {
+            const arg_2 = this$.Name;
+            return toFail(printf("Unable to find cell for index: (%i, %i) in table %s"))(column)(row)(arg_2);
+        }
+    }
+    static getCellAt(column, row) {
+        return (table) => table.GetCellAt(column, row);
+    }
     IterColumns(action) {
         const this$ = this;
         for (let columnIndex = 0; columnIndex <= (this$.ColumnCount - 1); columnIndex++) {
@@ -130,20 +143,83 @@ export class ArcTable {
             return copy;
         };
     }
-    UpdateCellAt(columnIndex, rowIndex, c) {
+    UpdateCellAt(columnIndex, rowIndex, c, skipValidation) {
         const this$ = this;
-        SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);
-        SanityChecks_validateRowIndex(rowIndex, this$.RowCount, false);
-        SanityChecks_validateColumn(CompositeColumn.create(this$.Headers[columnIndex], [c]));
+        if (!defaultArg(skipValidation, false)) {
+            SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);
+            SanityChecks_validateRowIndex(rowIndex, this$.RowCount, false);
+            c.ValidateAgainstHeader(this$.Headers[columnIndex], true);
+        }
+        Unchecked_setCellAt(columnIndex, rowIndex, c, this$.Values);
+    }
+    static updateCellAt(columnIndex, rowIndex, cell, skipValidation) {
+        return (table) => {
+            const newTable = table.Copy();
+            newTable.UpdateCellAt(columnIndex, rowIndex, cell, unwrap(skipValidation));
+            return newTable;
+        };
+    }
+    SetCellAt(columnIndex, rowIndex, c, skipValidation) {
+        const this$ = this;
+        if (!defaultArg(skipValidation, false)) {
+            SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);
+            c.ValidateAgainstHeader(this$.Headers[columnIndex], true);
+        }
         Unchecked_setCellAt(columnIndex, rowIndex, c, this$.Values);
     }
-    static updateCellAt(columnIndex, rowIndex, cell) {
+    static setCellAt(columnIndex, rowIndex, cell, skipValidation) {
         return (table) => {
             const newTable = table.Copy();
-            newTable.UpdateCellAt(columnIndex, rowIndex, cell);
+            newTable.SetCellAt(columnIndex, rowIndex, cell, unwrap(skipValidation));
             return newTable;
         };
     }
+    UpdateCellsBy(f, skipValidation) {
+        const this$ = this;
+        const skipValidation_1 = defaultArg(skipValidation, false);
+        let enumerator = getEnumerator(this$.Values);
+        try {
+            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+                const kv = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                const patternInput = kv[0];
+                const ri = patternInput[1] | 0;
+                const ci = patternInput[0] | 0;
+                const newCell = f(ci, ri, kv[1]);
+                if (!skipValidation_1) {
+                    newCell.ValidateAgainstHeader(this$.Headers[ci], true);
+                }
+                Unchecked_setCellAt(ci, ri, newCell, this$.Values);
+            }
+        }
+        finally {
+            disposeSafe(enumerator);
+        }
+    }
+    static updateCellsBy(f, skipValidation) {
+        return (table) => {
+            const newTable = table.Copy();
+            newTable.UpdateCellsBy(f, unwrap(skipValidation));
+        };
+    }
+    UpdateCellBy(columnIndex, rowIndex, f, skipValidation) {
+        const this$ = this;
+        const skipValidation_1 = defaultArg(skipValidation, false);
+        if (!skipValidation_1) {
+            SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);
+            SanityChecks_validateRowIndex(rowIndex, this$.RowCount, false);
+        }
+        const newCell = f(this$.GetCellAt(columnIndex, rowIndex));
+        if (!skipValidation_1) {
+            newCell.ValidateAgainstHeader(this$.Headers[columnIndex], true);
+        }
+        Unchecked_setCellAt(columnIndex, rowIndex, newCell, this$.Values);
+    }
+    static updateCellBy(columnIndex, rowIndex, f, skipValidation) {
+        return (table) => {
+            const newTable = table.Copy();
+            newTable.UpdateCellBy(columnIndex, rowIndex, f, unwrap(skipValidation));
+        };
+    }
     UpdateHeader(index, newHeader, forceConvertCells) {
         const this$ = this;
         const forceConvertCells_1 = defaultArg(forceConvertCells, false);
@@ -199,6 +275,18 @@ export class ArcTable {
             return newTable;
         };
     }
+    AddColumnFill(header, cell, index, forceReplace) {
+        const this$ = this;
+        const cells = initialize(this$.RowCount, (_arg) => cell.Copy());
+        this$.AddColumn(header, cells, index, forceReplace);
+    }
+    static addColumnFill(header, cell, index, forceReplace) {
+        return (table) => {
+            const newTable = table.Copy();
+            newTable.AddColumnFill(header, cell, unwrap(index), unwrap(forceReplace));
+            return newTable;
+        };
+    }
     UpdateColumn(columnIndex, header, cells, skipFillMissing) {
         const this$ = this;
         SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);

package/Core/Table/CompositeCell.js

@@ -165,6 +165,32 @@ export class CompositeCell extends Union {
         const this$ = this;
         return (this$.tag === 1) ? (new CompositeCell(1, [this$.fields[0]])) : ((this$.tag === 2) ? (new CompositeCell(2, [this$.fields[0], this$.fields[1].Copy()])) : ((this$.tag === 3) ? (new CompositeCell(3, [this$.fields[0].Copy()])) : (new CompositeCell(0, [this$.fields[0].Copy()]))));
     }
+    ValidateAgainstHeader(header, raiseException) {
+        const this$ = this;
+        const raiseExeption = defaultArg(raiseException, false);
+        const cell = this$;
+        if (header.IsDataColumn && (cell.isData ? true : cell.isFreeText)) {
+            return true;
+        }
+        else if (header.IsDataColumn) {
+            if (raiseExeption) {
+                throw new Error(`Invalid combination of header \`${header}\` and cell \`${cell}\`, Data header should have either Data or Freetext cells`);
+            }
+            return false;
+        }
+        else if (header.IsTermColumn && (cell.isTerm ? true : cell.isUnitized)) {
+            return true;
+        }
+        else if (!header.IsTermColumn && cell.isFreeText) {
+            return true;
+        }
+        else {
+            if (raiseExeption) {
+                throw new Error(`Invalid combination of header \`${header}\` and cell \`${cell}\``);
+            }
+            return false;
+        }
+    }
     static term(oa) {
         return new CompositeCell(0, [oa]);
     }

package/Core/Table/CompositeColumn.js

@@ -1,6 +1,5 @@
-import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
-import { item } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
-import { fold, empty, singleton, collect, delay, toArray } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { fold, empty, singleton, collect, delay, toArray, exists } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { CompositeCell_$reflection, CompositeCell } from "./CompositeCell.js";
 import { Record } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
 import { CompositeHeader_$reflection } from "./CompositeHeader.js";
@@ -17,33 +16,7 @@ export class CompositeColumn extends Record {
     }
     Validate(raiseException) {
         const this$ = this;
-        const raiseExeption = defaultArg(raiseException, false);
-        const header = this$.Header;
-        const cells = this$.Cells;
-        if (cells.length === 0) {
-            return true;
-        }
-        else if (header.IsDataColumn && (item(0, cells).isData ? true : item(0, cells).isFreeText)) {
-            return true;
-        }
-        else if (header.IsDataColumn) {
-            if (raiseExeption) {
-                throw new Error(`Invalid combination of header \`${header}\` and cells \`${item(0, cells)}\`, Data header should have either Data or Freetext cells`);
-            }
-            return false;
-        }
-        else if (header.IsTermColumn && (item(0, cells).isTerm ? true : item(0, cells).isUnitized)) {
-            return true;
-        }
-        else if (!header.IsTermColumn && item(0, cells).isFreeText) {
-            return true;
-        }
-        else {
-            if (raiseExeption) {
-                throw new Error(`Invalid combination of header \`${header}\` and cells \`${item(0, cells)}\``);
-            }
-            return false;
-        }
+        return !exists((c) => !c.ValidateAgainstHeader(this$.Header, unwrap(raiseException)), this$.Cells);
     }
     TryGetColumnUnits() {
         const this$ = this;
@@ -71,6 +44,10 @@ export class CompositeColumn extends Record {
             return (patternInput[1] >= patternInput[0]) ? CompositeCell.emptyTerm : CompositeCell.emptyUnitized;
         }
     }
+    get IsUnique() {
+        const this$ = this;
+        return this$.Header.IsUnique;
+    }
 }
 
 export function CompositeColumn_$reflection() {

package/Core/Table/CompositeHeader.js

@@ -2,7 +2,6 @@ import { map } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
 import { union_type, string_type, getUnionCases, name } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 import { Union, toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
 import { ActivePatterns_$007CTermColumn$007C_$007C, Pattern_CommentPattern, Pattern_OutputPattern, Pattern_InputPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseIOTypeHeader } from "../Helper/Regex.js";
-import { equals } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
 import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../OntologyAnnotation.js";
 
@@ -98,79 +97,6 @@ export class IOType extends Union {
             return IOType.ofString(s);
         }
     }
-    GetUITooltip() {
-        const this$ = this;
-        return IOType.getUITooltip(this$);
-    }
-    static getUITooltip(iotype) {
-        let matchResult;
-        if (typeof iotype === "string") {
-            if (equals(iotype, "Source")) {
-                matchResult = 0;
-            }
-            else if (equals(iotype, "Sample")) {
-                matchResult = 1;
-            }
-            else if (equals(iotype, "RawDataFile")) {
-                matchResult = 2;
-            }
-            else if (equals(iotype, "DerivedDataFile")) {
-                matchResult = 3;
-            }
-            else if (equals(iotype, "ImageFile")) {
-                matchResult = 4;
-            }
-            else if (equals(iotype, "Material")) {
-                matchResult = 5;
-            }
-            else if (equals(iotype, "FreeText")) {
-                matchResult = 6;
-            }
-            else {
-                matchResult = 7;
-            }
-        }
-        else {
-            switch (iotype.tag) {
-                case 1: {
-                    matchResult = 1;
-                    break;
-                }
-                case 2: {
-                    matchResult = 2;
-                    break;
-                }
-                case 3: {
-                    matchResult = 5;
-                    break;
-                }
-                case 4: {
-                    matchResult = 6;
-                    break;
-                }
-                default:
-                    matchResult = 0;
-            }
-        }
-        switch (matchResult) {
-            case 0:
-                return "The source value must be a unique identifier for an organism or a sample.";
-            case 1:
-                return "The Sample Name column describes specifc laboratory samples with a unique identifier.";
-            case 2:
-                return "The Raw Data File column defines untransformed and unprocessed data files.";
-            case 3:
-                return "The Derived Data File column defines transformed and/or processed data files.";
-            case 4:
-                return "Placeholder";
-            case 5:
-                return "Placeholder";
-            case 6:
-                return "Placeholder";
-            default:
-                throw new Error(`Unable to parse combination to existing IOType: \`${iotype}\``);
-        }
-    }
     static source() {
         return new IOType(0, []);
     }
@@ -543,157 +469,21 @@ export class CompositeHeader extends Union {
                 return void 0;
         }
     }
-    GetUITooltip() {
+    get IsUnique() {
         const this$ = this;
-        return CompositeHeader.getUITooltip(this$);
-    }
-    static getUITooltip(header) {
-        let matchResult;
-        if (typeof header === "string") {
-            if (equals(header, "Component")) {
-                matchResult = 0;
-            }
-            else if (equals(header, "Characteristic")) {
-                matchResult = 1;
-            }
-            else if (equals(header, "Factor")) {
-                matchResult = 2;
-            }
-            else if (equals(header, "Parameter")) {
-                matchResult = 3;
-            }
-            else if (equals(header, "ProtocolType")) {
-                matchResult = 4;
-            }
-            else if (equals(header, "ProtocolDescription")) {
-                matchResult = 5;
-            }
-            else if (equals(header, "ProtocolUri")) {
-                matchResult = 6;
-            }
-            else if (equals(header, "ProtocolVersion")) {
-                matchResult = 7;
-            }
-            else if (equals(header, "ProtocolREF")) {
-                matchResult = 8;
-            }
-            else if (equals(header, "Performer")) {
-                matchResult = 9;
-            }
-            else if (equals(header, "Date")) {
-                matchResult = 10;
-            }
-            else if (equals(header, "Input")) {
-                matchResult = 11;
-            }
-            else if (equals(header, "Output")) {
-                matchResult = 12;
-            }
-            else if (equals(header, "FreeText")) {
-                matchResult = 13;
-            }
-            else if (equals(header, "Comment")) {
-                matchResult = 14;
-            }
-            else {
-                matchResult = 15;
-            }
-        }
-        else {
-            switch (header.tag) {
-                case 1: {
-                    matchResult = 1;
-                    break;
-                }
-                case 2: {
-                    matchResult = 2;
-                    break;
-                }
-                case 3: {
-                    matchResult = 3;
-                    break;
-                }
-                case 4: {
-                    matchResult = 4;
-                    break;
-                }
-                case 5: {
-                    matchResult = 5;
-                    break;
-                }
-                case 6: {
-                    matchResult = 6;
-                    break;
-                }
-                case 7: {
-                    matchResult = 7;
-                    break;
-                }
-                case 8: {
-                    matchResult = 8;
-                    break;
-                }
-                case 9: {
-                    matchResult = 9;
-                    break;
-                }
-                case 10: {
-                    matchResult = 10;
-                    break;
-                }
-                case 11: {
-                    matchResult = 11;
-                    break;
-                }
-                case 12: {
-                    matchResult = 12;
-                    break;
-                }
-                case 13: {
-                    matchResult = 13;
-                    break;
-                }
-                case 14: {
-                    matchResult = 14;
-                    break;
-                }
-                default:
-                    matchResult = 0;
-            }
-        }
-        switch (matchResult) {
-            case 0:
-                return "Component columns are used to describe physical components of a experiment, e.g. instrument names, software names, and reagents names.";
-            case 1:
-                return "Characteristic columns are used for study descriptions and describe inherent properties of the source material, e.g. a certain strain or organism part.";
-            case 2:
-                return "Use Factor columns to describe independent variables that result in a specific output of your experiment, e.g. the light intensity under which an organism was grown.";
-            case 3:
-                return "Parameter columns describe steps in your experimental workflow, e.g. the centrifugation time or the temperature used for your assay.";
+        switch (this$.tag) {
             case 4:
-                return "Defines the protocol type according to your preferred endpoint repository.";
+            case 8:
             case 5:
-                return "Describe the protocol in free text.";
             case 6:
-                return "Web or local address where the in-depth protocol is stored.";
             case 7:
-                return "Defines the protocol version.";
-            case 8:
-                return "Defines the protocol name.";
             case 9:
-                return "Defines the protocol performer.";
             case 10:
-                return "Defines the date the protocol was performed.";
             case 11:
-                return "Only one input column per table. E.g. experimental samples or files.";
             case 12:
-                return "Only one output column per table. E.g. experimental samples or files.";
-            case 13:
-                return "Placeholder";
-            case 14:
-                return "Comment";
+                return true;
             default:
-                throw new Error(`Unable to parse combination to existing CompositeHeader: \`${header}\``);
+                return false;
         }
     }
     static component(oa) {

package/FileSystem/Path.js

@@ -4,7 +4,15 @@ import { last, mapIndexed } from "../fable_modules/fable-library-js.4.16.0/Array
 export const seperators = ["/", "\\"];
 
 export function split(path) {
-    return split_1(path, seperators, void 0, 3);
+    const array = split_1(path, seperators, void 0, 3);
+    return array.filter((p) => {
+        if (p !== "") {
+            return p !== ".";
+        }
+        else {
+            return false;
+        }
+    });
 }
 
 export function combine(path1, path2) {

package/Json/context/rocrate/isa_data_context.js

@@ -21,5 +21,5 @@ export function IContext_$reflection() {
 
 export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["Data", new Json(0, ["sdo:MediaObject"])], ["type", new Json(0, ["sdo:disambiguatingDescription"])], ["encodingFormat", new Json(0, ["sdo:encodingFormat"])], ["usageInfo", new Json(0, ["sdo:usageInfo"])], ["name", new Json(0, ["sdo:name"])], ["comments", new Json(0, ["sdo:comment"])]]]);
 
-export const context_str = "\n{\n  \"@context\": {\n    \"sdo\": \"http://schema.org/\",\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\n\n    \"Data\": \"sdo:MediaObject\",\n    \"ArcData\": \"arc:ARC#ARC_00000076\",\n\n    \"type\": \"arc:ARC#ARC_00000107\",\n\n    \"name\": \"sdo:name\",\n    \"comments\": \"sdo:disambiguatingDescription\"\n  }\n}\n    ";
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Data\": \"sdo:MediaObject\",\r\n    \"ArcData\": \"arc:ARC#ARC_00000076\",\r\n\r\n    \"type\": \"arc:ARC#ARC_00000107\",\r\n\r\n    \"name\": \"sdo:name\",\r\n    \"comments\": \"sdo:disambiguatingDescription\"\r\n  }\r\n}\r\n    ";
 

package/Json/context/rocrate/isa_investigation_context.js

@@ -29,5 +29,5 @@ export function IContext_$reflection() {
 
 export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["Investigation", new Json(0, ["sdo:Dataset"])], ["identifier", new Json(0, ["sdo:identifier"])], ["title", new Json(0, ["sdo:headline"])], ["additionalType", new Json(0, ["sdo:additionalType"])], ["description", new Json(0, ["sdo:description"])], ["submissionDate", new Json(0, ["sdo:dateCreated"])], ["publicReleaseDate", new Json(0, ["sdo:datePublished"])], ["publications", new Json(0, ["sdo:citation"])], ["people", new Json(0, ["sdo:creator"])], ["studies", new Json(0, ["sdo:hasPart"])], ["ontologySourceReferences", new Json(0, ["sdo:mentions"])], ["comments", new Json(0, ["sdo:comment"])], ["filename", new Json(0, ["sdo:alternateName"])]]]);
 
-export const context_str = "\n{\n  \"@context\": {\n    \"sdo\": \"http://schema.org/\",\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\n\n    \"Investigation\": \"sdo:Dataset\",\n\n    \"identifier\" : \"sdo:identifier\",\n    \"title\": \"sdo:headline\",\n    \"description\": \"sdo:description\",\n    \"submissionDate\": \"sdo:dateCreated\",\n    \"publicReleaseDate\": \"sdo:datePublished\",\n    \"publications\": \"sdo:citation\",\n    \"people\": \"sdo:creator\",\n    \"studies\": \"sdo:hasPart\",\n    \"ontologySourceReferences\": \"sdo:mentions\",\n    \"comments\": \"sdo:disambiguatingDescription\",\n\n    \"publications?\": \"sdo:SubjectOf?\",\n    \"filename\": \"sdo:alternateName\"\n  }\n}\n    ";
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Investigation\": \"sdo:Dataset\",\r\n\r\n    \"identifier\" : \"sdo:identifier\",\r\n    \"title\": \"sdo:headline\",\r\n    \"description\": \"sdo:description\",\r\n    \"submissionDate\": \"sdo:dateCreated\",\r\n    \"publicReleaseDate\": \"sdo:datePublished\",\r\n    \"publications\": \"sdo:citation\",\r\n    \"people\": \"sdo:creator\",\r\n    \"studies\": \"sdo:hasPart\",\r\n    \"ontologySourceReferences\": \"sdo:mentions\",\r\n    \"comments\": \"sdo:disambiguatingDescription\",\r\n\r\n    \"publications?\": \"sdo:SubjectOf?\",\r\n    \"filename\": \"sdo:alternateName\"\r\n  }\r\n}\r\n    ";
 

package/Spreadsheet/AnnotationTable/ArcTable.js

@@ -118,7 +118,7 @@ export function tryFromFsWorksheet(sheet) {
     }
 }
 
-export function toFsWorksheet(table) {
+export function toFsWorksheet(index, table) {
     const stringCount = new Map([]);
     const ws = new FsWorksheet(table.Name);
     if (table.Columns.length === 0) {
@@ -130,7 +130,8 @@ export function toFsWorksheet(table) {
         }));
         const maxRow = length(head(columns)) | 0;
         const maxCol = length(columns) | 0;
-        const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
+        const name = (index == null) ? "annotationTable" : (`${"annotationTable"}${index}`);
+        const fsTable = ws.Table(name, FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
         iterateIndexed((colI, col) => {
             iterateIndexed((rowI, stringCell) => {
                 let value;

package/Spreadsheet/ArcAssay.js

@@ -1,5 +1,5 @@
 import { FsWorksheet } from "../fable_modules/FsSpreadsheet.6.2.0/FsWorksheet.fs.js";
-import { iterate, isEmpty as isEmpty_1, tryPick, choose, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { iterate, isEmpty as isEmpty_1, tryPick, choose, tryFind, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { SparseRowModule_tryGetValueAt, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_writeToSheet } from "./Metadata/SparseTable.js";
 import { fromRows as fromRows_1, toRows as toRows_1 } from "./Metadata/Assays.js";
 import { empty, isEmpty, ofSeq, singleton as singleton_1 } from "../fable_modules/fable-library-js.4.16.0/List.js";
@@ -8,7 +8,7 @@ import { toConsole, printf, toFail } from "../fable_modules/fable-library-js.4.1
 import { getEnumerator } from "../fable_modules/fable-library-js.4.16.0/Util.js";
 import { ArcAssay } from "../Core/ArcTypes.js";
 import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
-import { toArray, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { unwrap, toArray, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { toFsWorksheet as toFsWorksheet_1, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
 import { toFsWorksheet, tryFromFsWorksheet as tryFromFsWorksheet_1 } from "./DataMapTable/DataMapTable.js";
 import { FsWorkbook } from "../fable_modules/FsSpreadsheet.6.2.0/FsWorkbook.fs.js";
@@ -115,34 +115,45 @@ export function ArcAssay_fromMetadataSheet(sheet) {
     }
 }
 
+export function ArcAssay_isMetadataSheetName(name) {
+    if (name === "isa_assay") {
+        return true;
+    }
+    else {
+        return name === "Assay";
+    }
+}
+
+export function ArcAssay_isMetadataSheet(sheet) {
+    return ArcAssay_isMetadataSheetName(sheet.Name);
+}
+
+export function ArcAssay_tryGetMetadataSheet(doc) {
+    return tryFind(ArcAssay_isMetadataSheet, doc.GetWorksheets());
+}
+
 /**
  * Reads an assay from a spreadsheet
  */
 export function ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D(doc) {
     try {
-        let assayMetaData;
-        const matchValue = doc.TryGetWorksheetByName("isa_assay");
+        let assayMetadata;
+        const matchValue = ArcAssay_tryGetMetadataSheet(doc);
         if (matchValue == null) {
-            const matchValue_1 = doc.TryGetWorksheetByName("Assay");
-            if (matchValue_1 == null) {
-                toConsole(printf("Cannot retrieve metadata: Assay file does not contain \"%s\" or \"%s\" sheet."))("isa_assay")("Assay");
-                assayMetaData = ArcAssay.create(createMissingIdentifier());
-            }
-            else {
-                assayMetaData = ArcAssay_fromMetadataSheet(matchValue_1);
-            }
+            toConsole(printf("Cannot retrieve metadata: Assay file does not contain \"%s\" or \"%s\" sheet."))("isa_assay")("Assay");
+            assayMetadata = ArcAssay.create(createMissingIdentifier());
         }
         else {
-            assayMetaData = ArcAssay_fromMetadataSheet(matchValue);
+            assayMetadata = ArcAssay_fromMetadataSheet(matchValue);
         }
         const sheets = doc.GetWorksheets();
         const annotationTables = choose(tryFromFsWorksheet, sheets);
         const datamapSheet = tryPick(tryFromFsWorksheet_1, sheets);
         if (!isEmpty_1(annotationTables)) {
-            assayMetaData.Tables = Array.from(annotationTables);
+            assayMetadata.Tables = Array.from(annotationTables);
         }
-        assayMetaData.DataMap = datamapSheet;
-        return assayMetaData;
+        assayMetadata.DataMap = datamapSheet;
+        return assayMetadata;
     }
     catch (err) {
         const arg_2 = err.message;
@@ -158,18 +169,27 @@ export function ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D(doc) {
 export function ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(assay, datamapSheet) {
     const datamapSheet_1 = defaultArg(datamapSheet, true);
     const doc = new FsWorkbook();
-    const metaDataSheet = ArcAssay_toMetadataSheet(assay);
-    doc.AddWorksheet(metaDataSheet);
+    const metadataSheet = ArcAssay_toMetadataSheet(assay);
+    doc.AddWorksheet(metadataSheet);
     if (datamapSheet_1) {
         iterate((arg) => {
             const sheet = toFsWorksheet(arg);
             doc.AddWorksheet(sheet);
         }, toArray(assay.DataMap));
     }
-    iterate((arg_1) => {
-        const sheet_1 = toFsWorksheet_1(arg_1);
+    iterateIndexed((i, arg_1) => {
+        const sheet_1 = toFsWorksheet_1(i, arg_1);
         doc.AddWorksheet(sheet_1);
     }, assay.Tables);
     return doc;
 }
 
+/**
+ * Write an assay to a spreadsheet
+ * 
+ * If datamapSheet is true, the datamap will be written to a worksheet inside assay workbook.
+ */
+export function ARCtrl_ArcAssay__ArcAssay_ToFsWorkbook_6FCE9E49(this$, datamapSheet) {
+    return ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(this$, unwrap(datamapSheet));
+}
+