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

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

@@ -1,65 +0,0 @@
-import { class_type } from "@fable-org/fable-library-js/Reflection.js";
-import { LDRef, LDNode } from "./ROCrate/LDObject.js";
-import { unwrap, value as value_1 } from "@fable-org/fable-library-js/Option.js";
-import { ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8, ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation } from "./Conversion.js";
-import { LDDataset } from "./ROCrate/Generic/Dataset.js";
-import { now } from "@fable-org/fable-library-js/Date.js";
-import { LDContext } from "./ROCrate/LDContext.js";
-import { initBioschemasContext, initV1_1 } from "./ROCrate/ROCrateContext.js";
-import { decoder, encoder } from "./Json/ROCrate/LDGraph.js";
-import { map } from "./fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
-import { ResizeArray_choose } from "./Core/Helper/Collections.js";
-import { LDFile } from "./ROCrate/Generic/File.js";
-import { exactlyOne } from "@fable-org/fable-library-js/Seq.js";
-import { decoder as decoder_1 } from "./Json/ROCrate/LDNode.js";
-export class ROCrate {
-    constructor() {
-    }
-}
-export function ROCrate_$reflection() {
-    return class_type("ARCtrl.Json.ARC.ROCrate", undefined, ROCrate);
-}
-export function ROCrate_getDefaultLicense() {
-    return "ALL RIGHTS RESERVED BY THE AUTHORS";
-}
-export function ROCrate_get_metadataFileDescriptor() {
-    const node = new LDNode("ro-crate-metadata.json", ["http://schema.org/CreativeWork"]);
-    node.SetProperty("http://purl.org/dc/terms/conformsTo", new LDRef("https://w3id.org/ro/crate/1.1"));
-    node.SetProperty("http://schema.org/about", new LDRef("./"));
-    return node;
-}
-export function ROCrate_encoder_8A8D439(isa, license) {
-    const license_2 = (license == null) ? ROCrate_getDefaultLicense() : value_1(license);
-    const isa_1 = ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation(isa);
-    LDDataset.setSDDatePublishedAsDateTime(isa_1, now());
-    LDDataset.setLicenseAsCreativeWork(isa_1, license_2);
-    const graph = isa_1.Flatten();
-    const context = new LDContext(undefined, [initV1_1(), initBioschemasContext()]);
-    graph.SetContext(context);
-    graph.AddNode(ROCrate_get_metadataFileDescriptor());
-    graph.Compact_InPlace();
-    return encoder(graph);
-}
-export function ROCrate_get_decoder() {
-    return map((graph) => {
-        const matchValue = graph.TryGetNode("./");
-        if (matchValue == null) {
-            throw new Error("RO-Crate graph did not contain root data Entity");
-        }
-        else {
-            const node = value_1(matchValue);
-            const files = ResizeArray_choose((n) => {
-                if (LDFile.validate(n, unwrap(graph.TryGetContext())) && !(n.Id.indexOf("#") >= 0)) {
-                    return n.Id;
-                }
-                else {
-                    return undefined;
-                }
-            }, graph.Nodes);
-            return [ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(node, graph, unwrap(graph.TryGetContext())), files];
-        }
-    }, decoder);
-}
-export function ROCrate_get_decoderDeprecated() {
-    return map((ldnode) => ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(exactlyOne(LDDataset.getAbouts(ldnode)), undefined, initV1_1()), decoder_1);
-}

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

@@ -1,164 +0,0 @@
-import { iterateIndexed, length, ofSeq, sortBy, collect as collect_1, exists, toArray, ofArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "@fable-org/fable-library-js/List.js";
-import { unzip, item, map as map_1 } from "@fable-org/fable-library-js/Array.js";
-import { fold as fold_1, singleton as singleton_1, collect, map as map_2, delay, toArray as toArray_1, tryFind } from "@fable-org/fable-library-js/Seq.js";
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.6.3.1/FsWorksheet.fs.js";
-import { value as value_1 } from "@fable-org/fable-library-js/Option.js";
-import { toStringCellColumns, fixDeprecatedIOHeader, ColumnValueRefs_fromStringCellColumns, fromStringCellColumns } from "./CompositeColumn.js";
-import { comparePrimitives } from "@fable-org/fable-library-js/Util.js";
-import { ArcTableValues } from "../../Core/Table/ArcTableAux.js";
-import { printf, toFail } from "@fable-org/fable-library-js/String.js";
-import { Dictionary_tryGet, FsCellsCollection__TryGetCell_Z37302880 } from "../../fable_modules/FsSpreadsheet.6.3.1/Cells/FsCellsCollection.fs.js";
-import { rangeDouble } from "@fable-org/fable-library-js/Range.js";
-import { FsAddress_$ctor_Z37302880, FsAddress__get_ColumnNumber, FsAddress__get_RowNumber } from "../../fable_modules/FsSpreadsheet.6.3.1/FsAddress.fs.js";
-import { FsRangeAddress_$ctor_7E77A4A0, FsRangeAddress__get_LastAddress } from "../../fable_modules/FsSpreadsheet.6.3.1/Ranges/FsRangeAddress.fs.js";
-import { FsRangeBase__Cell_Z3407A44B, FsRangeBase__get_RangeAddress } from "../../fable_modules/FsSpreadsheet.6.3.1/Ranges/FsRangeBase.fs.js";
-import { ArcTable } from "../../Core/Table/ArcTable.js";
-import { max } from "@fable-org/fable-library-js/Double.js";
-import { addToDict } from "@fable-org/fable-library-js/MapUtil.js";
-/**
- * Iterates over elements of the input list and groups adjacent elements.
- * A new group is started when the specified predicate holds about the element
- * of the list (and at the beginning of the iteration).
- *
- * For example:
- * List.groupWhen isOdd [3;3;2;4;1;2] = [[3]; [3; 2; 4]; [1; 2]]
- */
-export function Aux_List_groupWhen(f, list) {
-    return reverse(map(reverse, fold((acc, e) => {
-        const matchValue = f(e);
-        if (matchValue) {
-            return cons(singleton(e), acc);
-        }
-        else if (!isEmpty(acc)) {
-            return cons(cons(e, head(acc)), tail(acc));
-        }
-        else {
-            return singleton(singleton(e));
-        }
-    }, empty(), list)));
-}
-export function classifyHeaderOrder(header) {
-    switch (header.tag) {
-        case /* ProtocolType */ 4:
-        case /* ProtocolDescription */ 5:
-        case /* ProtocolUri */ 6:
-        case /* ProtocolVersion */ 7:
-        case /* ProtocolREF */ 8:
-        case /* Performer */ 9:
-        case /* Date */ 10:
-            return 2;
-        case /* Component */ 0:
-        case /* Characteristic */ 1:
-        case /* Factor */ 2:
-        case /* Parameter */ 3:
-        case /* Comment */ 14:
-        case /* FreeText */ 13:
-            return 3;
-        case /* Output */ 12:
-            return 4;
-        default:
-            return 1;
-    }
-}
-export function classifyColumnOrder(column) {
-    return classifyHeaderOrder(column.Header);
-}
-export const helperColumnStrings = ofArray(["Term Source REF", "Term Accession Number", "Unit", "Data Format", "Data Selector Format"]);
-export function groupColumnsByHeader(stringCellColumns) {
-    return map_1(toArray, toArray(Aux_List_groupWhen((c) => {
-        const v = item(0, c);
-        return !exists((s) => v.startsWith(s), helperColumnStrings);
-    }, ofArray(stringCellColumns))));
-}
-/**
- * Returns the annotation table of the worksheet if it exists, else returns None
- */
-export function tryAnnotationTable(sheet) {
-    return tryFind((t) => t.Name.startsWith("annotationTable"), sheet.Tables);
-}
-/**
- * Groups and parses a collection of single columns into the according ISA composite columns
- */
-export function composeColumns(stringCellColumns) {
-    return map_1(fromStringCellColumns, groupColumnsByHeader(stringCellColumns));
-}
-/**
- * Groups and parses a collection of single columns into the according ISA composite columns
- */
-export function composeArcTableValues(stringCellColumns) {
-    const valueMap = new Map([]);
-    const rowCount = (item(0, stringCellColumns).length - 1) | 0;
-    const patternInput = unzip(map_1((columns) => ColumnValueRefs_fromStringCellColumns(valueMap, columns), groupColumnsByHeader(stringCellColumns)));
-    return [patternInput[0], ArcTableValues.fromRefColumns(patternInput[1], valueMap, rowCount)];
-}
-/**
- * Returns the protocol described by the headers and a function for parsing the values of the matrix to the processes of this protocol
- */
-export function tryFromFsWorksheet(sheet) {
-    try {
-        const matchValue = tryAnnotationTable(sheet);
-        if (matchValue == null) {
-            return undefined;
-        }
-        else {
-            const t = value_1(matchValue);
-            const patternInput = composeArcTableValues(map_1(fixDeprecatedIOHeader, toArray_1(delay(() => map_2((c) => toArray_1(delay(() => collect((r) => {
-                const matchValue_1 = FsCellsCollection__TryGetCell_Z37302880(sheet.CellCollection, r, c);
-                if (matchValue_1 == null) {
-                    return singleton_1("");
-                }
-                else {
-                    const cell = value_1(matchValue_1);
-                    return singleton_1(cell.ValueAsString());
-                }
-            }, rangeDouble(1, 1, FsAddress__get_RowNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(t))))))), rangeDouble(1, 1, FsAddress__get_ColumnNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(t)))))))));
-            return ArcTable.fromArcTableValues(sheet.Name, Array.from(patternInput[0]), patternInput[1]);
-        }
-    }
-    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(index, table) {
-    const stringCount = new Map([]);
-    const ws = new FsWorksheet(table.Name);
-    if (table.ColumnCount === 0) {
-        return ws;
-    }
-    else {
-        const columns = collect_1(toStringCellColumns, sortBy(classifyColumnOrder, ofSeq(table.Columns), {
-            Compare: comparePrimitives,
-        }));
-        let tableRowCount;
-        const maxRow = fold_1((acc, c) => max(acc, length(c)), 0, columns) | 0;
-        tableRowCount = ((maxRow === 1) ? 2 : maxRow);
-        const tableColumnCount = length(columns) | 0;
-        const name = (index == null) ? "annotationTable" : (`${"annotationTable"}${value_1(index)}`);
-        const fsTable = ws.Table(name, FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(tableRowCount, tableColumnCount)));
-        iterateIndexed((colI, col) => {
-            iterateIndexed((rowI, stringCell) => {
-                let value;
-                if (rowI === 0) {
-                    const matchValue = Dictionary_tryGet(stringCell, stringCount);
-                    if (matchValue == null) {
-                        addToDict(stringCount, stringCell, "");
-                        value = stringCell;
-                    }
-                    else {
-                        const spaces = value_1(matchValue);
-                        stringCount.set(stringCell, spaces + " ");
-                        value = ((stringCell + " ") + spaces);
-                    }
-                }
-                else {
-                    value = stringCell;
-                }
-                const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
-                FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);
-            }, col);
-        }, columns);
-        return ws;
-    }
-}

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

@@ -1,61 +0,0 @@
-import { defaultArg, bind, unwrap, map } from "@fable-org/fable-library-js/Option.js";
-import { item } from "@fable-org/fable-library-js/Array.js";
-import { CompositeCell } from "../../Core/Table/CompositeCell.js";
-import { Option_fromValueWithDefault } from "../../Core/Helper/Collections.js";
-export function termFromStringCells(tsrCol, tanCol, cellValues) {
-    const tan = map((i) => item(i, cellValues), tanCol);
-    const tsr = map((i_1) => item(i_1, cellValues), tsrCol);
-    return CompositeCell.createTermFromString(item(0, cellValues), unwrap(tsr), unwrap(tan));
-}
-export function unitizedFromStringCells(unitCol, tsrCol, tanCol, cellValues) {
-    const unit = item(unitCol, cellValues);
-    const tan = map((i) => item(i, cellValues), tanCol);
-    const tsr = map((i_1) => item(i_1, cellValues), tsrCol);
-    return CompositeCell.createUnitizedFromString(item(0, cellValues), unit, unwrap(tsr), unwrap(tan));
-}
-export function freeTextFromStringCells(cellValues) {
-    return CompositeCell.createFreeText(item(0, cellValues));
-}
-export function dataFromStringCells(format, selectorFormat, cellValues) {
-    const format_1 = bind((i) => Option_fromValueWithDefault("", item(i, cellValues)), format);
-    const selectorFormat_1 = bind((i_1) => Option_fromValueWithDefault("", item(i_1, cellValues)), selectorFormat);
-    return CompositeCell.createDataFromString(item(0, cellValues), unwrap(format_1), unwrap(selectorFormat_1));
-}
-export function toStringCells(isTerm, hasUnit, cell) {
-    let v, v_1, v_2;
-    switch (cell.tag) {
-        case /* Term */ 0:
-            if ((v = cell.fields[0], hasUnit)) {
-                const v_6 = cell.fields[0];
-                return [v_6.NameText, "", defaultArg(v_6.TermSourceREF, ""), v_6.TermAccessionOntobeeUrl];
-            }
-            else {
-                const v_7 = cell.fields[0];
-                return [v_7.NameText, defaultArg(v_7.TermSourceREF, ""), v_7.TermAccessionOntobeeUrl];
-            }
-        case /* Unitized */ 2: {
-            const unit = cell.fields[1];
-            const v_8 = cell.fields[0];
-            return [v_8, unit.NameText, defaultArg(unit.TermSourceREF, ""), unit.TermAccessionOntobeeUrl];
-        }
-        case /* Data */ 3: {
-            const d = cell.fields[0];
-            const format = defaultArg(d.Format, "");
-            const selectorFormat = defaultArg(d.SelectorFormat, "");
-            return [defaultArg(d.Name, ""), format, selectorFormat];
-        }
-        default:
-            if ((v_1 = cell.fields[0], hasUnit)) {
-                const v_3 = cell.fields[0];
-                return [v_3, "", "", ""];
-            }
-            else if ((v_2 = cell.fields[0], isTerm)) {
-                const v_4 = cell.fields[0];
-                return [v_4, "", ""];
-            }
-            else {
-                const v_5 = cell.fields[0];
-                return [v_5];
-            }
-    }
-}

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

@@ -1,141 +0,0 @@
-import { tryItem, map, setItem, item, skip } from "@fable-org/fable-library-js/Array.js";
-import { CompositeHeader_Output, CompositeHeader_Input, IOType_Source, IOType } from "../../Core/Table/CompositeHeader.js";
-import { FSharpRef, toString } from "@fable-org/fable-library-js/Types.js";
-import { toStringCells, fromStringCells } from "./CompositeHeader.js";
-import { reduce, singleton, append, toList, exists, map as map_1, delay, toArray } from "@fable-org/fable-library-js/Seq.js";
-import { rangeDouble } from "@fable-org/fable-library-js/Range.js";
-import { CompositeColumn } from "../../Core/Table/CompositeColumn.js";
-import { FsCell } from "../../fable_modules/FsSpreadsheet.6.3.1/Cells/FsCell.fs.js";
-import { toStringCells as toStringCells_1 } from "./CompositeCell.js";
-import { value as value_1, defaultArg } from "@fable-org/fable-library-js/Option.js";
-import { map as map_2, singleton as singleton_1, ofArray } from "@fable-org/fable-library-js/List.js";
-import { defaultOf, stringHash } from "@fable-org/fable-library-js/Util.js";
-import { ColumnValueRefs_Constant, ensureCellHashInValueMap, ColumnValueRefs_Sparse } from "../../Core/Table/ArcTableAux.js";
-import { mergeHashes } from "../../Core/Helper/HashCodes.js";
-import { getItemFromDict, tryGetValue } from "@fable-org/fable-library-js/MapUtil.js";
-/**
- * Checks if the column header is a deprecated IO Header. If so, fixes it.
- *
- * The old format of IO Headers was only the type of IO so, e.g. "Source Name" or "Raw Data File".
- *
- * A "Source Name" column will now be mapped to the propper "Input [Source Name]", and all other IO types will be mapped to "Output [<IO Type>]".
- */
-export function fixDeprecatedIOHeader(stringCellCol) {
-    if (stringCellCol.length === 0) {
-        throw new Error("Can\'t fix IOHeader Invalid column, neither header nor values given");
-    }
-    const values = skip(1, stringCellCol);
-    const matchValue = IOType.ofString(item(0, stringCellCol));
-    switch (matchValue.tag) {
-        case /* FreeText */ 4:
-            return stringCellCol;
-        case /* Source */ 0: {
-            setItem(stringCellCol, 0, toString(CompositeHeader_Input(IOType_Source())));
-            return stringCellCol;
-        }
-        default: {
-            setItem(stringCellCol, 0, toString(CompositeHeader_Output(matchValue)));
-            return stringCellCol;
-        }
-    }
-}
-export function fromStringCellColumns(columns) {
-    const patternInput = fromStringCells(map((c) => item(0, c), columns));
-    const l = item(0, columns).length | 0;
-    const cells = Array.from(toArray(delay(() => map_1((i) => patternInput[1](map((c_1) => item(i, c_1), columns)), rangeDouble(1, 1, l - 1)))));
-    return CompositeColumn.create(patternInput[0], cells);
-}
-export function stringCellColumnsOfFsColumns(columns) {
-    return map((c) => {
-        c.ToDenseColumn();
-        return map((cell) => cell.ValueAsString(), toArray(c.Cells));
-    }, columns);
-}
-export function fromFsColumns(columns) {
-    return fromStringCellColumns(map((c) => {
-        c.ToDenseColumn();
-        return map((c_1) => c_1.ValueAsString(), toArray(c.Cells));
-    }, columns));
-}
-export function toStringCellColumns(column) {
-    const hasUnit = exists((c) => c.isUnitized, column.Cells);
-    const isTerm = column.Header.IsTermColumn;
-    const isData = column.Header.IsDataColumn && exists((c_1) => c_1.isData, column.Cells);
-    const header = toStringCells(hasUnit, column.Header);
-    const compositeCells = toArray(column.Cells);
-    const cells = map((cell) => toStringCells_1(isTerm, hasUnit, cell), toArray(column.Cells));
-    const getCellOrDefault = (ri, ci, cells_1) => defaultArg(tryItem(ci, item(ri, cells_1)), "");
-    if (hasUnit) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i) => getCellOrDefault(i, 0, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_1) => getCellOrDefault(i_1, 1, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_2) => getCellOrDefault(i_2, 2, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(3, header)), delay(() => map_1((i_3) => getCellOrDefault(i_3, 3, cells), rangeDouble(0, 1, compositeCells.length - 1))))))]);
-    }
-    else if (isTerm) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_4) => getCellOrDefault(i_4, 0, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_5) => getCellOrDefault(i_5, 1, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_6) => getCellOrDefault(i_6, 2, cells), rangeDouble(0, 1, compositeCells.length - 1))))))]);
-    }
-    else if (isData) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_7) => getCellOrDefault(i_7, 0, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_8) => getCellOrDefault(i_8, 1, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_9) => getCellOrDefault(i_9, 2, cells), rangeDouble(0, 1, compositeCells.length - 1))))))]);
-    }
-    else {
-        return singleton_1(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_10) => item(0, item(i_10, cells)), rangeDouble(0, 1, compositeCells.length - 1)))))));
-    }
-}
-export function toFsColumns(column) {
-    return map_2((c) => map_2((s) => (new FsCell(s)), c), toStringCellColumns(column));
-}
-export function ColumnValueRefs_fromStringCellColumns(valueMap, columns) {
-    let cellHash;
-    const hashMap = new Map([]);
-    const cells = new Map([]);
-    let constant = true;
-    const patternInput = fromStringCells(map((c) => item(0, c), columns));
-    const header = patternInput[0];
-    const cellParser = patternInput[1];
-    const l = item(0, columns).length | 0;
-    if (l === 1) {
-        return [header, ColumnValueRefs_Sparse(cells)];
-    }
-    else {
-        for (let i = 1; i <= (l - 1); i++) {
-            const strings = map((c_1) => item(i, c_1), columns);
-            const hash_2 = reduce(mergeHashes, map_1(stringHash, strings)) | 0;
-            let matchValue;
-            let patternInput_1;
-            let outArg = defaultOf();
-            patternInput_1 = [tryGetValue(hashMap, hash_2, new FSharpRef(() => outArg, (v) => {
-                    outArg = (v | 0);
-                })), outArg];
-            matchValue = (patternInput_1[0] ? patternInput_1[1] : undefined);
-            if (matchValue == null) {
-                if (i === 1) {
-                    const cellHash_3 = ensureCellHashInValueMap(cellParser(strings), valueMap) | 0;
-                    hashMap.set(hash_2, cellHash_3);
-                    cells.set(i - 1, cellHash_3);
-                }
-                else {
-                    if (constant) {
-                        constant = false;
-                        for (let j = 0; j <= (i - 1); j++) {
-                            const cellHash_4 = getItemFromDict(cells, 0) | 0;
-                            cells.set(j, cellHash_4);
-                        }
-                    }
-                    const cellHash_5 = ensureCellHashInValueMap(cellParser(strings), valueMap) | 0;
-                    hashMap.set(hash_2, cellHash_5);
-                    cells.set(i - 1, cellHash_5);
-                }
-            }
-            else if ((cellHash = (value_1(matchValue) | 0), constant)) {
-                const cellHash_1 = value_1(matchValue) | 0;
-            }
-            else {
-                const cellHash_2 = value_1(matchValue) | 0;
-                cells.set(i - 1, cellHash_2);
-            }
-        }
-        if (constant) {
-            return [header, ColumnValueRefs_Constant(getItemFromDict(cells, 0))];
-        }
-        else {
-            return [header, ColumnValueRefs_Sparse(cells)];
-        }
-    }
-}