@nfdi4plants/arctrl 1.0.6 → 1.1.0

package/ISA/ISA.Json/ArcTypes/ArcTable.js

@@ -1,15 +1,21 @@
 import { toString, tuple2, map as map_1, list, object } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { collect, empty, map, singleton, append, delay, toList } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { iterate, toArray, collect, empty, map, singleton, append, delay, toList } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
 import { CompositeHeader_decoder, CompositeHeader_encoder } from "./CompositeHeader.js";
 import { CompositeCell_decoder, CompositeCell_encoder } from "./CompositeCell.js";
 import { empty as empty_2, ofSeq } from "../../../fable_modules/fable-library.4.5.0/Map.js";
-import { arrayHash, equalArrays, uncurry2, compareArrays } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { fromString, string, int, tuple2 as tuple2_1, map$0027, list as list_1, object as object_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
-import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { safeHash, equals, arrayHash, equalArrays, uncurry2, compareArrays } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { fromString, value as value_5, array as array_1, string, int, tuple2 as tuple2_1, map$0027, list as list_1, object as object_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { toArray as toArray_1, defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
 import { empty as empty_1 } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { Dictionary } from "../../../fable_modules/fable-library.4.5.0/MutableMap.js";
 import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
+import { CellTable_arrayFromMap, CellTable_encoder, CellTable_decoder, CellTable_decodeCell, CellTable_encodeCell } from "./CellTable.js";
+import { addToDict, getItemFromDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
+import { rangeDouble } from "../../../fable_modules/fable-library.4.5.0/Range.js";
+import { iterateIndexed } from "../../../fable_modules/fable-library.4.5.0/Array.js";
+import { StringTable_arrayFromMap, StringTable_encoder, StringTable_decoder, StringTable_decodeString, StringTable_encodeString } from "../StringTable.js";
 import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { OATable_arrayFromMap, OATable_encoder, OATable_decoder } from "./OATable.js";
 
 export function ArcTable_encoder(table) {
     return object(toList(delay(() => append(singleton(["name", table.Name]), delay(() => append((table.Headers.length !== 0) ? singleton(["header", list(toList(delay(() => map(CompositeHeader_encoder, table.Headers))))]) : empty(), delay(() => ((table.Values.size !== 0) ? singleton(["values", map_1((tupledArg) => tuple2((value) => value, (value_2) => value_2, tupledArg[0], tupledArg[1]), CompositeCell_encoder, ofSeq(toList(delay(() => collect((matchValue) => {
@@ -37,6 +43,80 @@ export const ArcTable_decoder = (path_2) => ((v) => object_1((get$) => {
     return ArcTable.create((objectArg_2 = get$.Required, objectArg_2.Field("name", string)), decodedHeader, decodedValues);
 }, path_2, v));
 
+export function ArcTable_compressedColumnEncoder(columnIndex, rowCount, cellTable, table) {
+    if (table.Headers[columnIndex].IsIOType ? true : (rowCount < 100)) {
+        return toArray(delay(() => map((r) => CellTable_encodeCell(cellTable, getItemFromDict(table.Values, [columnIndex, r])), rangeDouble(0, 1, rowCount - 1))));
+    }
+    else {
+        let current = getItemFromDict(table.Values, [columnIndex, 0]);
+        let from = 0;
+        return toArray(delay(() => append(collect((i) => {
+            const next = getItemFromDict(table.Values, [columnIndex, i]);
+            return !equals(next, current) ? append(singleton(object([["f", from], ["t", i - 1], ["v", CellTable_encodeCell(cellTable, current)]])), delay(() => {
+                current = next;
+                from = (i | 0);
+                return empty();
+            })) : empty();
+        }, rangeDouble(1, 1, rowCount - 1)), delay(() => singleton(object([["f", from], ["t", rowCount - 1], ["v", CellTable_encodeCell(cellTable, current)]]))))));
+    }
+}
+
+export function ArcTable_compressedColumnDecoder(columnIndex, cellTable, table, column) {
+    const matchValue = array_1((s, o) => CellTable_decodeCell(cellTable, s, o), "", column);
+    if (matchValue.tag === 1) {
+        array_1((s_1, jv) => object_1((get$) => {
+            let from;
+            const objectArg = get$.Required;
+            from = objectArg.Field("f", uncurry2(int));
+            let to_;
+            const objectArg_1 = get$.Required;
+            to_ = objectArg_1.Field("t", uncurry2(int));
+            let value;
+            const objectArg_2 = get$.Required;
+            value = objectArg_2.Field("v", (s_2, o_1) => CellTable_decodeCell(cellTable, s_2, o_1));
+            for (let i = from; i <= to_; i++) {
+                addToDict(table.Values, [columnIndex, i], value);
+            }
+        }, s_1, jv), "", column);
+    }
+    else {
+        iterateIndexed((r, cell) => {
+            addToDict(table.Values, [columnIndex, r], cell);
+        }, matchValue.fields[0]);
+    }
+}
+
+export function ArcTable_compressedEncoder(stringTable, oaTable, cellTable, table) {
+    return object(toList(delay(() => append(singleton(["n", StringTable_encodeString(stringTable, table.Name)]), delay(() => append((table.Headers.length !== 0) ? singleton(["h", list(toList(delay(() => map(CompositeHeader_encoder, table.Headers))))]) : empty(), delay(() => {
+        if (table.Values.size !== 0) {
+            const rowCount = table.RowCount | 0;
+            return singleton(["c", toArray(delay(() => map((c) => ArcTable_compressedColumnEncoder(c, rowCount, cellTable, table), rangeDouble(0, 1, table.ColumnCount - 1))))]);
+        }
+        else {
+            return empty();
+        }
+    })))))));
+}
+
+export function ArcTable_compressedDecoder(stringTable, oaTable, cellTable) {
+    return (path_2) => ((v_1) => object_1((get$) => {
+        let objectArg, objectArg_1, objectArg_2;
+        let decodedHeader;
+        const collection = defaultArg((objectArg = get$.Optional, objectArg.Field("h", (path, value) => list_1(uncurry2(CompositeHeader_decoder), path, value))), empty_1());
+        decodedHeader = Array.from(collection);
+        const table = ArcTable.create((objectArg_1 = get$.Required, objectArg_1.Field("n", (s, o) => StringTable_decodeString(stringTable, s, o))), decodedHeader, new Dictionary([], {
+            Equals: equalArrays,
+            GetHashCode: arrayHash,
+        }));
+        iterate((array) => {
+            iterateIndexed((c, col) => {
+                ArcTable_compressedColumnDecoder(c, cellTable, table, col);
+            }, array);
+        }, toArray_1((objectArg_2 = get$.Optional, objectArg_2.Field("c", (path_1, value_2) => array_1(value_5, path_1, value_2)))));
+        return table;
+    }, path_2, v_1));
+}
+
 export function ARCtrl_ISA_ArcTable__ArcTable_fromJsonString_Static_Z721C83C5(jsonString) {
     const matchValue = fromString(uncurry2(ArcTable_decoder), jsonString);
     if (matchValue.tag === 1) {
@@ -55,3 +135,44 @@ export function ARCtrl_ISA_ArcTable__ArcTable_toJsonString_Static_1B2566EA(a) {
     return ARCtrl_ISA_ArcTable__ArcTable_ToJsonString_71136F3F(a);
 }
 
+export function ARCtrl_ISA_ArcTable__ArcTable_fromCompressedJsonString_Static_Z721C83C5(jsonString) {
+    const matchValue = fromString((path, v) => object_1((get$) => {
+        let arg_5, objectArg_2;
+        let stringTable;
+        const objectArg = get$.Required;
+        stringTable = objectArg.Field("stringTable", uncurry2(StringTable_decoder));
+        let oaTable;
+        const arg_3 = OATable_decoder(stringTable);
+        const objectArg_1 = get$.Required;
+        oaTable = objectArg_1.Field("oaTable", uncurry2(arg_3));
+        const arg_7 = ArcTable_compressedDecoder(stringTable, oaTable, (arg_5 = CellTable_decoder(stringTable, oaTable), (objectArg_2 = get$.Required, objectArg_2.Field("cellTable", uncurry2(arg_5)))));
+        const objectArg_3 = get$.Required;
+        return objectArg_3.Field("table", uncurry2(arg_7));
+    }, path, v), jsonString);
+    if (matchValue.tag === 1) {
+        return toFail(printf("Error. Unable to parse json string to ArcTable: %s"))(matchValue.fields[0]);
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ISA_ArcTable__ArcTable_ToCompressedJsonString_71136F3F(this$, spaces) {
+    const spaces_1 = defaultArg(spaces, 0) | 0;
+    const stringTable = new Map([]);
+    const oaTable = new Dictionary([], {
+        Equals: equals,
+        GetHashCode: safeHash,
+    });
+    const cellTable = new Dictionary([], {
+        Equals: equals,
+        GetHashCode: safeHash,
+    });
+    const arcTable = ArcTable_compressedEncoder(stringTable, oaTable, cellTable, this$);
+    return toString(spaces_1, object([["cellTable", CellTable_encoder(stringTable, oaTable, CellTable_arrayFromMap(cellTable))], ["oaTable", OATable_encoder(stringTable, OATable_arrayFromMap(oaTable))], ["stringTable", StringTable_encoder(StringTable_arrayFromMap(stringTable))], ["table", arcTable]]));
+}
+
+export function ARCtrl_ISA_ArcTable__ArcTable_toCompressedJsonString_Static_1B2566EA(a) {
+    return ARCtrl_ISA_ArcTable__ArcTable_ToCompressedJsonString_71136F3F(a);
+}
+

package/ISA/ISA.Json/ArcTypes/CellTable.js

@@ -0,0 +1,46 @@
+import { sortBy, map, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { uncurry2, comparePrimitives } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { map as map_1 } from "../../../fable_modules/fable-library.4.5.0/Array.js";
+import { CompositeCell_compressedDecoder, CompositeCell_compressedEncoder } from "./CompositeCell.js";
+import { int, array as array_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { Dict_tryFind } from "../../ISA/Helper.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
+import { FSharpResult$2 } from "../../../fable_modules/fable-library.4.5.0/Choice.js";
+
+export function CellTable_arrayFromMap(otm) {
+    return toArray(map((kv_1) => kv_1[0], sortBy((kv) => kv[1], otm, {
+        Compare: comparePrimitives,
+    })));
+}
+
+export function CellTable_encoder(stringTable, oaTable, ot) {
+    return map_1((cc) => CompositeCell_compressedEncoder(stringTable, oaTable, cc), ot);
+}
+
+export function CellTable_decoder(stringTable, oaTable) {
+    const decoder = CompositeCell_compressedDecoder(stringTable, oaTable);
+    return (path) => ((value) => array_1(uncurry2(decoder), path, value));
+}
+
+export function CellTable_encodeCell(otm, cc) {
+    const matchValue = Dict_tryFind(cc, otm);
+    if (matchValue == null) {
+        const i_1 = otm.size | 0;
+        addToDict(otm, cc, i_1);
+        return i_1;
+    }
+    else {
+        return matchValue;
+    }
+}
+
+export function CellTable_decodeCell(ot, s, o) {
+    const matchValue = int(s)(o);
+    if (matchValue.tag === 1) {
+        return new FSharpResult$2(1, [matchValue.fields[0]]);
+    }
+    else {
+        return new FSharpResult$2(0, [ot[matchValue.fields[0]]]);
+    }
+}
+

package/ISA/ISA.Json/ArcTypes/CompositeCell.js

@@ -6,6 +6,8 @@ import { fromString, index, string, object as object_1 } from "../../../fable_mo
 import { CompositeCell } from "../../ISA/ArcTypes/CompositeCell.js";
 import { uncurry2 } from "../../../fable_modules/fable-library.4.5.0/Util.js";
 import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { OATable_decodeOA, OATable_encodeOA } from "./OATable.js";
+import { StringTable_decodeString, StringTable_encodeString } from "../StringTable.js";
 import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
 
 export function CompositeCell_encoder(cc) {
@@ -31,6 +33,30 @@ export const CompositeCell_decoder = (path_7) => ((v_1) => object_1((get$) => {
     }
 }, path_7, v_1));
 
+export function CompositeCell_compressedEncoder(stringTable, oaTable, cc) {
+    const patternInput = (cc.tag === 0) ? ["Term", singleton(OATable_encodeOA(oaTable, cc.fields[0]))] : ((cc.tag === 2) ? ["Unitized", ofArray([StringTable_encodeString(stringTable, cc.fields[0]), OATable_encodeOA(oaTable, cc.fields[1])])] : ["FreeText", singleton(StringTable_encodeString(stringTable, cc.fields[0]))]);
+    return object([["t", StringTable_encodeString(stringTable, patternInput[0])], ["v", list(patternInput[1])]]);
+}
+
+export function CompositeCell_compressedDecoder(stringTable, oaTable) {
+    return (path_4) => ((v_1) => object_1((get$) => {
+        let objectArg_1, objectArg_2, objectArg_3, objectArg_4;
+        let matchValue;
+        const objectArg = get$.Required;
+        matchValue = objectArg.Field("t", (s, o) => StringTable_decodeString(stringTable, s, o));
+        switch (matchValue) {
+            case "FreeText":
+                return new CompositeCell(1, [(objectArg_1 = get$.Required, objectArg_1.Field("v", (path, value) => index(0, (s_1, o_1) => StringTable_decodeString(stringTable, s_1, o_1), path, value)))]);
+            case "Term":
+                return new CompositeCell(0, [(objectArg_2 = get$.Required, objectArg_2.Field("v", (path_1, value_1) => index(0, (s_3, o_2) => OATable_decodeOA(oaTable, s_3, o_2), path_1, value_1)))]);
+            case "Unitized":
+                return new CompositeCell(2, [(objectArg_3 = get$.Required, objectArg_3.Field("v", (path_2, value_2) => index(0, (s_4, o_3) => StringTable_decodeString(stringTable, s_4, o_3), path_2, value_2))), (objectArg_4 = get$.Required, objectArg_4.Field("v", (path_3, value_3) => index(1, (s_5, o_4) => OATable_decodeOA(oaTable, s_5, o_4), path_3, value_3)))]);
+            default:
+                return toFail(printf("Error reading CompositeCell from json string: %A"))(matchValue);
+        }
+    }, path_4, v_1));
+}
+
 export function ARCtrl_ISA_CompositeCell__CompositeCell_fromJsonString_Static_Z721C83C5(jsonString) {
     const matchValue = fromString(uncurry2(CompositeCell_decoder), jsonString);
     if (matchValue.tag === 1) {

package/ISA/ISA.Json/ArcTypes/OATable.js

@@ -0,0 +1,48 @@
+import { sortBy, map, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { uncurry2, comparePrimitives } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { map as map_1 } from "../../../fable_modules/fable-library.4.5.0/Array.js";
+import { ConverterOptions_$ctor } from "../ConverterOptions.js";
+import { OntologyAnnotation_compressedDecoder, OntologyAnnotation_compressedEncoder } from "../Ontology.js";
+import { int, array as array_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { Dict_tryFind } from "../../ISA/Helper.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
+import { FSharpResult$2 } from "../../../fable_modules/fable-library.4.5.0/Choice.js";
+
+export function OATable_arrayFromMap(otm) {
+    return toArray(map((kv_1) => kv_1[0], sortBy((kv) => kv[1], otm, {
+        Compare: comparePrimitives,
+    })));
+}
+
+export function OATable_encoder(stringTable, ot) {
+    let options;
+    return map_1((options = ConverterOptions_$ctor(), (oa) => OntologyAnnotation_compressedEncoder(stringTable, options, oa)), ot);
+}
+
+export function OATable_decoder(stringTable) {
+    const decoder = OntologyAnnotation_compressedDecoder(stringTable, ConverterOptions_$ctor());
+    return (path) => ((value) => array_1(uncurry2(decoder), path, value));
+}
+
+export function OATable_encodeOA(otm, oa) {
+    const matchValue = Dict_tryFind(oa, otm);
+    if (matchValue == null) {
+        const i_1 = otm.size | 0;
+        addToDict(otm, oa, i_1);
+        return i_1;
+    }
+    else {
+        return matchValue;
+    }
+}
+
+export function OATable_decodeOA(ot, s, o) {
+    const matchValue = int(s)(o);
+    if (matchValue.tag === 1) {
+        return new FSharpResult$2(1, [matchValue.fields[0]]);
+    }
+    else {
+        return new FSharpResult$2(0, [ot[matchValue.fields[0]]]);
+    }
+}
+

package/ISA/ISA.Json/Ontology.js

@@ -13,6 +13,7 @@ import { OntologySourceReference } from "../ISA/JsonTypes/OntologySourceReferenc
 import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
 import { OntologyAnnotation } from "../ISA/JsonTypes/OntologyAnnotation.js";
 import { unwrap } from "../../fable_modules/fable-library.4.5.0/Option.js";
+import { StringTable_decodeString, StringTable_encodeString } from "./StringTable.js";
 
 /**
  * This decodes from integer, float or string to string only!
@@ -175,6 +176,35 @@ export function OntologyAnnotation_decoder(options) {
     }, path_3, v));
 }
 
+export function OntologyAnnotation_compressedEncoder(stringTable, options, oa) {
+    return object_10(choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, nil)) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, toList(delay(() => {
+        let value, s;
+        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = OntologyAnnotation_genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : singleton(tryInclude("@id", (value_2) => {
+            let s_1;
+            const value_3 = value_2;
+            return (typeof value_3 === "string") ? ((s_1 = value_3, s_1)) : nil;
+        }, oa["ID"])), delay(() => {
+            let value_5, s_2;
+            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "OntologyAnnotation", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("a", (s_3) => StringTable_encodeString(stringTable, s_3), oa["Name"])), delay(() => append(singleton(tryInclude("ts", (s_4) => StringTable_encodeString(stringTable, s_4), oa["TermSourceREF"])), delay(() => append(singleton(tryInclude("ta", (s_5) => StringTable_encodeString(stringTable, s_5), oa["TermAccessionNumber"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), oa["Comments"]))))))))));
+        }));
+    }))));
+}
+
+export function OntologyAnnotation_compressedDecoder(stringTable, options) {
+    return (path_1) => ((v) => object_11((get$) => {
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, decoder, objectArg_4;
+        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("a", (s_1, o) => StringTable_decodeString(stringTable, s_1, o)))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("ts", (s_2, o_1) => StringTable_decodeString(stringTable, s_2, o_1)))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("ta", (s_3, o_2) => StringTable_decodeString(stringTable, s_3, o_2)))), unwrap((arg_9 = ((decoder = decoder_1(options), (path) => ((value) => array(uncurry2(decoder), path, value)))), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", uncurry2(arg_9))))));
+    }, path_1, v));
+}
+
 export function OntologyAnnotation_fromJsonString(s) {
     return fromJsonString(uncurry2(OntologyAnnotation_decoder(ConverterOptions_$ctor())), s);
 }

package/ISA/ISA.Json/StringTable.js

@@ -0,0 +1,43 @@
+import { sortBy, map, toArray } from "../../fable_modules/fable-library.4.5.0/Seq.js";
+import { comparePrimitives } from "../../fable_modules/fable-library.4.5.0/Util.js";
+import { map as map_1 } from "../../fable_modules/fable-library.4.5.0/Array.js";
+import { int, string, array as array_1 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { Dict_tryFind } from "../ISA/Helper.js";
+import { addToDict } from "../../fable_modules/fable-library.4.5.0/MapUtil.js";
+import { FSharpResult$2 } from "../../fable_modules/fable-library.4.5.0/Choice.js";
+
+export function StringTable_arrayFromMap(otm) {
+    return toArray(map((kv_1) => kv_1[0], sortBy((kv) => kv[1], otm, {
+        Compare: comparePrimitives,
+    })));
+}
+
+export function StringTable_encoder(ot) {
+    return map_1((value) => value, ot);
+}
+
+export const StringTable_decoder = (path_1) => ((value_1) => array_1(string, path_1, value_1));
+
+export function StringTable_encodeString(otm, s) {
+    const s_1 = s;
+    const matchValue = Dict_tryFind(s_1, otm);
+    if (matchValue == null) {
+        const i_1 = otm.size | 0;
+        addToDict(otm, s_1, i_1);
+        return i_1;
+    }
+    else {
+        return matchValue;
+    }
+}
+
+export function StringTable_decodeString(ot, s, o) {
+    const matchValue = int(s)(o);
+    if (matchValue.tag === 1) {
+        return new FSharpResult$2(1, [matchValue.fields[0]]);
+    }
+    else {
+        return new FSharpResult$2(0, [ot[matchValue.fields[0]]]);
+    }
+}
+

package/ISA/ISA.Spreadsheet/AnnotationTable/ArcTable.js

@@ -2,14 +2,15 @@ import { iterateIndexed, length, ofArray, sortBy, collect, toArray, empty, tail,
 import { tryParseReferenceColumnHeader } from "../../ISA/Regex.js";
 import { map as map_1, toList, tryFind } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
 import { toFsColumns, fixDeprecatedIOHeader, fromFsColumns } from "./CompositeColumn.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
 import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
-import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.5.1.1/FsWorksheet.fs.js";
+import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
 import { comparePrimitives } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.1/Ranges/FsRangeAddress.fs.js";
-import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.1/FsAddress.fs.js";
-import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.5.1.1/Cells/FsCellsCollection.fs.js";
+import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
+import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCellsCollection.fs.js";
 import { addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
-import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.5.1.1/Ranges/FsRangeBase.fs.js";
+import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeBase.fs.js";
 
 /**
  * Iterates over elements of the input list and groups adjacent elements.
@@ -91,49 +92,61 @@ export function composeColumns(columns) {
  * Returns the protocol described by the headers and a function for parsing the values of the matrix to the processes of this protocol
  */
 export function tryFromFsWorksheet(sheet) {
-    const matchValue = tryAnnotationTable(sheet);
-    if (matchValue == null) {
-        return void 0;
+    try {
+        const matchValue = tryAnnotationTable(sheet);
+        if (matchValue == null) {
+            return void 0;
+        }
+        else {
+            const t = matchValue;
+            const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
+            return ArcTable.addColumns(compositeColumns, void 0, true)(ArcTable.init(sheet.Name));
+        }
     }
-    else {
-        const t = matchValue;
-        const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
-        return ArcTable.addColumns(compositeColumns, void 0, true)(ArcTable.init(sheet.Name));
+    catch (err) {
+        const arg = sheet.Name;
+        const arg_1 = err.message;
+        return toFail(printf("Could not parse table with name \"%s\":\n%s"))(arg)(arg_1);
     }
 }
 
 export function toFsWorksheet(table) {
     const stringCount = new Map([]);
     const ws = new FsWorksheet(table.Name);
-    const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
-        Compare: comparePrimitives,
-    }));
-    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_$ctor_Z37302880(maxRow, maxCol)));
-    iterateIndexed((colI, col) => {
-        iterateIndexed((rowI, cell) => {
-            let value;
-            const v = cell.ValueAsString();
-            if (rowI === 0) {
-                const matchValue = Dictionary_tryGet(v, stringCount);
-                if (matchValue == null) {
-                    addToDict(stringCount, cell.ValueAsString(), "");
-                    value = v;
+    if (table.Columns.length === 0) {
+        return ws;
+    }
+    else {
+        const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
+            Compare: comparePrimitives,
+        }));
+        const maxRow = length(head(columns)) | 0;
+        const maxCol = length(columns) | 0;
+        const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
+        iterateIndexed((colI, col) => {
+            iterateIndexed((rowI, cell) => {
+                let value;
+                const v = cell.ValueAsString();
+                if (rowI === 0) {
+                    const matchValue = Dictionary_tryGet(v, stringCount);
+                    if (matchValue == null) {
+                        addToDict(stringCount, cell.ValueAsString(), "");
+                        value = v;
+                    }
+                    else {
+                        const spaces = matchValue;
+                        stringCount.set(v, spaces + " ");
+                        value = ((v + " ") + spaces);
+                    }
                 }
                 else {
-                    const spaces = matchValue;
-                    stringCount.set(v, spaces + " ");
-                    value = ((v + " ") + spaces);
+                    value = v;
                 }
-            }
-            else {
-                value = v;
-            }
-            const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
-            FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);
-        }, col);
-    }, columns);
-    return ws;
+                const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
+                FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);
+            }, col);
+        }, columns);
+        return ws;
+    }
 }
 

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeCell.js

@@ -1,7 +1,7 @@
 import { singleton, ofArray, head, tail, isEmpty, map } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { CompositeCell } from "../../ISA/ArcTypes/CompositeCell.js";
 import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
-import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.1/Cells/FsCell.fs.js";
+import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
 
 export function fromFsCells(cells) {
     const cellValues = map((c) => c.ValueAsString(), cells);

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeColumn.js

@@ -2,9 +2,9 @@ import { CompositeHeader, IOType } from "../../ISA/ArcTypes/CompositeHeader.js";
 import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { toFsCells, fromFsCells } from "./CompositeHeader.js";
 import { singleton as singleton_1, ofArray, item, map } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { FsAddress__get_RowNumber } from "../../../fable_modules/FsSpreadsheet.5.1.1/FsAddress.fs.js";
-import { FsRangeAddress__get_LastAddress } from "../../../fable_modules/FsSpreadsheet.5.1.1/Ranges/FsRangeAddress.fs.js";
-import { FsRangeBase__get_RangeAddress } from "../../../fable_modules/FsSpreadsheet.5.1.1/Ranges/FsRangeBase.fs.js";
+import { FsAddress__get_RowNumber } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
+import { FsRangeAddress__get_LastAddress } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsRangeBase__get_RangeAddress } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeBase.fs.js";
 import { singleton, append, toList, exists, map as map_1, delay, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
 import { toFsCells as toFsCells_1, fromFsCells as fromFsCells_1 } from "./CompositeCell.js";
 import { rangeDouble } from "../../../fable_modules/fable-library.4.5.0/Range.js";

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeHeader.js

@@ -3,7 +3,7 @@ import { singleton, tail, head, isEmpty, map } from "../../../fable_modules/fabl
 import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
 import { ActivePatterns_$007COutputColumnHeader$007C_$007C, ActivePatterns_$007CInputColumnHeader$007C_$007C, tryParseComponentColumnHeader, tryParseCharacteristicColumnHeader, tryParseFactorColumnHeader, tryParseParameterColumnHeader, ActivePatterns_$007CUnitColumnHeader$007C_$007C, ActivePatterns_$007CTANColumnHeader$007C_$007C, ActivePatterns_$007CTSRColumnHeader$007C_$007C } from "../../ISA/Regex.js";
 import { IOType, CompositeHeader } from "../../ISA/ArcTypes/CompositeHeader.js";
-import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.1/Cells/FsCell.fs.js";
+import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
 import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { empty, singleton as singleton_1, append, delay, toList } from "../../../fable_modules/fable-library.4.5.0/Seq.js";