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

package/dist/ts/ts/ROCrateIO.d.ts

@@ -0,0 +1,16 @@
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { LDNode } from './ROCrate/LDObject.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { ArcInvestigation } from './Core/ArcTypes.js';
+import { FileSystem } from './FileSystem/FileSystem.js';
+import { Decoder$1, IEncodable } from './fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
+export declare class ROCrate {
+    constructor();
+}
+export declare function ROCrate_$reflection(): TypeInfo;
+export declare function ROCrate_getDefaultLicense(): string;
+export declare function ROCrate_get_metadataFileDescriptor(): LDNode;
+export declare function ROCrate_encoder_B568605(isa: ArcInvestigation, license?: Option<any>, fs?: FileSystem): IEncodable;
+export declare function ROCrate_get_decoder(): Decoder$1<[ArcInvestigation, string[]]>;
+export declare function ROCrate_get_decoderDeprecated(): Decoder$1<ArcInvestigation>;
+//# sourceMappingURL=ROCrateIO.d.ts.map

package/dist/ts/ts/ROCrateIO.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ROCrateIO.d.ts","sourceRoot":"","sources":["../../../src/ARCtrl/ts/ROCrateIO.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAkB,MAAM,EAAE,MAAM,uBAAuB,CAAC;AAC/D,OAAO,EAAE,MAAM,EAA4B,MAAM,uCAAuC,CAAC;AAOzF,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,UAAU,EAAE,MAAM,4BAA4B,CAAC;AACxD,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,mDAAmD,CAAC;AAO1F,qBAAa,OAAO;;CAGnB;AAED,wBAAgB,mBAAmB,IAAI,QAAQ,CAE9C;AAED,wBAAgB,yBAAyB,IAAI,MAAM,CAElD;AAED,wBAAgB,kCAAkC,IAAI,MAAM,CAK3D;AAED,wBAAgB,uBAAuB,CAAC,GAAG,EAAE,gBAAgB,EAAE,OAAO,CAAC,EAAE,MAAM,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,UAAU,CAWjH;AAED,wBAAgB,mBAAmB,IAAI,SAAS,CAAC,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC,CAAC,CAmB7E;AAED,wBAAgB,6BAA6B,IAAI,SAAS,CAAC,gBAAgB,CAAC,CAE3E"}

package/dist/ts/ts/ROCrateIO.js

@@ -0,0 +1,58 @@
+import { LDNode, LDRef } from './ROCrate/LDObject.js';
+import { value, unwrap } from '../node_modules/@fable-org/fable-library-js/Option.js';
+import { ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8, ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_1695DD5C } from './Conversion.js';
+import { LDDataset } from './ROCrate/Generic/Dataset.js';
+import { now } from '../node_modules/@fable-org/fable-library-js/Date.js';
+import { LDContext } from './ROCrate/LDContext.js';
+import { initV1_1, initBioschemasContext } from './ROCrate/ROCrateContext.js';
+import { decoder as decoder$1, encoder } from './Json/ROCrate/LDGraph.js';
+import { map } from './fable_modules/Thoth.Json.Core.0.7.0/Decode.fs.js';
+import { ResizeArray_choose } from './Core/Helper/Collections.js';
+import { LDFile } from './ROCrate/Generic/File.js';
+import { exactlyOne } from '../node_modules/@fable-org/fable-library-js/Seq.js';
+import { decoder } from './Json/ROCrate/LDNode.js';
+
+function ROCrate_getDefaultLicense() {
+  return "ALL RIGHTS RESERVED BY THE AUTHORS";
+}
+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;
+}
+function ROCrate_encoder_B568605(isa, license, fs) {
+  const license_2 = ROCrate_getDefaultLicense() ;
+  const isa_1 = ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_1695DD5C(isa, unwrap(fs));
+  LDDataset.setSDDatePublishedAsDateTime(isa_1, now());
+  LDDataset.setLicenseAsCreativeWork(isa_1, license_2);
+  const graph = isa_1.Flatten();
+  const context = new LDContext(void 0, [initV1_1(), initBioschemasContext()]);
+  graph.SetContext(context);
+  graph.AddNode(ROCrate_get_metadataFileDescriptor());
+  graph.Compact_InPlace();
+  return encoder(graph);
+}
+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(matchValue);
+      const files = ResizeArray_choose((n) => {
+        if (LDFile.validate(n, unwrap(graph.TryGetContext())) && !(n.Id.indexOf("#") >= 0) && !n.HasType(LDDataset.schemaType, unwrap(graph.TryGetContext()))) {
+          return n.Id;
+        } else {
+          return void 0;
+        }
+      }, graph.Nodes);
+      return [ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(node, graph, unwrap(graph.TryGetContext())), files];
+    }
+  }, decoder$1);
+}
+function ROCrate_get_decoderDeprecated() {
+  return map((ldnode) => ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(exactlyOne(LDDataset.getAbouts(ldnode)), void 0, initV1_1()), decoder);
+}
+
+export { ROCrate_encoder_B568605, ROCrate_getDefaultLicense, ROCrate_get_decoder, ROCrate_get_decoderDeprecated, ROCrate_get_metadataFileDescriptor };

package/dist/ts/ts/Spreadsheet/AnnotationTable/ArcTable.d.ts

@@ -0,0 +1,40 @@
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { CompositeHeader_$union } from '../../Core/Table/CompositeHeader.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { CompositeColumn } from '../../Core/Table/CompositeColumn.js';
+import { FsTable } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/Tables/FsTable.fs.js';
+import { FsWorksheet } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorksheet.fs.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { ArcTableValues } from '../../Core/Table/ArcTableAux.js';
+import { ArcTable } from '../../Core/Table/ArcTable.js';
+/**
+ * Iterates over elements of the input list and groups adjacent elements.
+ * A new group is started when the specified predicate holds about the element
+ * of the list (and at the beginning of the iteration).
+ *
+ * For example:
+ * List.groupWhen isOdd [3;3;2;4;1;2] = [[3]; [3; 2; 4]; [1; 2]]
+ */
+export declare function Aux_List_groupWhen<$a>(f: ((arg0: $a) => boolean), list: FSharpList<$a>): FSharpList<FSharpList<$a>>;
+export declare function classifyHeaderOrder(header: CompositeHeader_$union): int32;
+export declare function classifyColumnOrder(column: CompositeColumn): int32;
+export declare const helperColumnStrings: FSharpList<string>;
+export declare function groupColumnsByHeader(stringCellColumns: string[][]): string[][][];
+/**
+ * Returns the annotation table of the worksheet if it exists, else returns None
+ */
+export declare function tryAnnotationTable(sheet: FsWorksheet): Option<FsTable>;
+/**
+ * Groups and parses a collection of single columns into the according ISA composite columns
+ */
+export declare function composeColumns(stringCellColumns: string[][]): CompositeColumn[];
+/**
+ * Groups and parses a collection of single columns into the according ISA composite columns
+ */
+export declare function composeArcTableValues(stringCellColumns: string[][]): [CompositeHeader_$union[], ArcTableValues];
+/**
+ * Returns the protocol described by the headers and a function for parsing the values of the matrix to the processes of this protocol
+ */
+export declare function tryFromFsWorksheet(sheet: FsWorksheet): Option<ArcTable>;
+export declare function toFsWorksheet(index: Option<int32>, table: ArcTable): FsWorksheet;
+//# sourceMappingURL=ArcTable.d.ts.map

package/dist/ts/ts/Spreadsheet/AnnotationTable/ArcTable.d.ts.map

@@ -0,0 +1 @@
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package/dist/ts/ts/Spreadsheet/AnnotationTable/ArcTable.js

@@ -0,0 +1,149 @@
+import { ofArray, collect, sortBy, ofSeq, length, iterateIndexed, toArray as toArray$1, exists, reverse, map as map$2, fold as fold$1, empty, cons, singleton as singleton$1, isEmpty, tail, head } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { map, item, unzip } from '../../../node_modules/@fable-org/fable-library-js/Array.js';
+import { fold, toArray, delay, map as map$1, collect as collect$1, singleton, tryFind } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { FsWorksheet } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorksheet.fs.js';
+import { value } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { toStringCellColumns, fixDeprecatedIOHeader, ColumnValueRefs_fromStringCellColumns } from './CompositeColumn.js';
+import { comparePrimitives } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+import { ArcTableValues } from '../../Core/Table/ArcTableAux.js';
+import { toFail, printf } from '../../../node_modules/@fable-org/fable-library-js/String.js';
+import { rangeDouble } from '../../../node_modules/@fable-org/fable-library-js/Range.js';
+import { ArcTable } from '../../Core/Table/ArcTable.js';
+import { max } from '../../../node_modules/@fable-org/fable-library-js/Double.js';
+import { FsRangeAddress } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/Ranges/FsRangeAddress.fs.js';
+import { FsAddress } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsAddress.fs.js';
+import { Dictionary_tryGet } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/Cells/FsCellsCollection.fs.js';
+import { addToDict } from '../../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+
+function Aux_List_groupWhen(f, list) {
+  return reverse(map$2(reverse, fold$1((acc, e) => {
+    const matchValue = f(e);
+    if (matchValue) {
+      return cons(singleton$1(e), acc);
+    } else if (!isEmpty(acc)) {
+      return cons(cons(e, head(acc)), tail(acc));
+    } else {
+      return singleton$1(singleton$1(e));
+    }
+  }, empty(), list)));
+}
+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;
+  }
+}
+function classifyColumnOrder(column) {
+  return classifyHeaderOrder(column.Header);
+}
+const helperColumnStrings = ofArray(["Term Source REF", "Term Accession Number", "Unit", "Data Format", "Data Selector Format"]);
+function groupColumnsByHeader(stringCellColumns) {
+  return map(toArray$1, toArray$1(Aux_List_groupWhen((c) => {
+    const v = item(0, c);
+    return !exists((s) => v.startsWith(s), helperColumnStrings);
+  }, ofArray(stringCellColumns))));
+}
+function tryAnnotationTable(sheet) {
+  return tryFind((t) => t.Name.startsWith("annotationTable"), sheet.Tables);
+}
+function composeArcTableValues(stringCellColumns) {
+  const valueMap = /* @__PURE__ */ new Map([]);
+  const rowCount = item(0, stringCellColumns).length - 1 | 0;
+  const patternInput = unzip(map((columns) => ColumnValueRefs_fromStringCellColumns(valueMap, columns), groupColumnsByHeader(stringCellColumns)));
+  return [patternInput[0], ArcTableValues.fromRefColumns(patternInput[1], valueMap, rowCount)];
+}
+function tryFromFsWorksheet(sheet) {
+  try {
+    const matchValue = tryAnnotationTable(sheet);
+    if (matchValue == null) {
+      return void 0;
+    } else {
+      const t = value(matchValue);
+      const patternInput = composeArcTableValues(map(fixDeprecatedIOHeader, toArray(delay(() => map$1((c) => toArray(delay(() => collect$1((r) => {
+        const matchValue_1 = sheet.CellCollection.TryGetCell(r, c);
+        if (matchValue_1 == null) {
+          return singleton("");
+        } else {
+          const cell = value(matchValue_1);
+          return singleton(cell.ValueAsString());
+        }
+      }, rangeDouble(1, 1, t.RangeAddress.LastAddress.RowNumber)))), rangeDouble(1, 1, t.RangeAddress.LastAddress.ColumnNumber))))));
+      return ArcTable.fromArcTableValues(sheet.Name, Array.from(patternInput[0]), patternInput[1]);
+    }
+  } catch (err) {
+    const arg = sheet.Name;
+    const arg_1 = err.message;
+    return toFail(printf('Could not parse table with name "%s":\n%s'))(arg)(arg_1);
+  }
+}
+function toFsWorksheet(index, table) {
+  const stringCount = /* @__PURE__ */ new Map([]);
+  const ws = new FsWorksheet(table.Name);
+  if (table.ColumnCount === 0) {
+    return ws;
+  } else {
+    const columns = collect(toStringCellColumns, sortBy(classifyColumnOrder, ofSeq(table.Columns), {
+      Compare: comparePrimitives
+    }));
+    let tableRowCount;
+    const maxRow = fold((acc, c) => max(acc, length(c)), 0, columns) | 0;
+    tableRowCount = maxRow === 1 ? 2 : maxRow;
+    const tableColumnCount = length(columns) | 0;
+    const name = index == null ? "annotationTable" : `${"annotationTable"}${value(index)}`;
+    const fsTable = ws.Table(name, new FsRangeAddress(new FsAddress(1, 1), new FsAddress(tableRowCount, tableColumnCount)));
+    iterateIndexed((colI, col) => {
+      iterateIndexed((rowI, stringCell) => {
+        let value$1;
+        if (rowI === 0) {
+          const matchValue = Dictionary_tryGet(stringCell, stringCount);
+          if (matchValue == null) {
+            addToDict(stringCount, stringCell, "");
+            value$1 = stringCell;
+          } else {
+            const spaces = value(matchValue);
+            stringCount.set(stringCell, spaces + " ");
+            value$1 = stringCell + " " + spaces;
+          }
+        } else {
+          value$1 = stringCell;
+        }
+        const address = new FsAddress(rowI + 1, colI + 1);
+        fsTable.Cell(address, ws.CellCollection).SetValueAs(value$1);
+      }, col);
+    }, columns);
+    return ws;
+  }
+}
+
+export { Aux_List_groupWhen, classifyColumnOrder, classifyHeaderOrder, composeArcTableValues, groupColumnsByHeader, helperColumnStrings, toFsWorksheet, tryAnnotationTable, tryFromFsWorksheet };

package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeCell.d.ts

@@ -0,0 +1,9 @@
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { CompositeCell_$union } from '../../Core/Table/CompositeCell.js';
+export declare function termFromStringCells(tsrCol: Option<int32>, tanCol: Option<int32>, cellValues: string[]): CompositeCell_$union;
+export declare function unitizedFromStringCells(unitCol: int32, tsrCol: Option<int32>, tanCol: Option<int32>, cellValues: string[]): CompositeCell_$union;
+export declare function freeTextFromStringCells(cellValues: string[]): CompositeCell_$union;
+export declare function dataFromStringCells(format: Option<int32>, selectorFormat: Option<int32>, cellValues: string[]): CompositeCell_$union;
+export declare function toStringCells(isTerm: boolean, hasUnit: boolean, cell: CompositeCell_$union): string[];
+//# sourceMappingURL=CompositeCell.d.ts.map

package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeCell.d.ts.map

@@ -0,0 +1 @@
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package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeCell.js

@@ -0,0 +1,63 @@
+import { defaultArg, bind, unwrap, map } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { item } from '../../../node_modules/@fable-org/fable-library-js/Array.js';
+import { CompositeCell } from '../../Core/Table/CompositeCell.js';
+import { Option_fromValueWithDefault } from '../../Core/Helper/Collections.js';
+
+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));
+}
+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));
+}
+function freeTextFromStringCells(cellValues) {
+  return CompositeCell.createFreeText(item(0, cellValues));
+}
+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));
+}
+function toStringCells(isTerm, hasUnit, cell) {
+  switch (cell.tag) {
+    case /* Term */
+    0:
+      if (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 (cell.fields[0], hasUnit) {
+        const v_3 = cell.fields[0];
+        return [v_3, "", "", ""];
+      } else if (cell.fields[0], isTerm) {
+        const v_4 = cell.fields[0];
+        return [v_4, "", ""];
+      } else {
+        const v_5 = cell.fields[0];
+        return [v_5];
+      }
+  }
+}
+
+export { dataFromStringCells, freeTextFromStringCells, termFromStringCells, toStringCells, unitizedFromStringCells };

package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeColumn.d.ts

@@ -0,0 +1,24 @@
+import { CompositeHeader_$union } from '../../Core/Table/CompositeHeader.js';
+import { CompositeCell_$union } from '../../Core/Table/CompositeCell.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { CompositeColumn } from '../../Core/Table/CompositeColumn.js';
+import { FsCell } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/Cells/FsCell.fs.js';
+import { FsColumn } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsColumn.fs.js';
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { IMap } from '@fable-org/fable-library-js/Util.js';
+import { ColumnValueRefs_$union } from '../../Core/Table/ArcTableAux.js';
+/**
+ * Checks if the column header is a deprecated IO Header. If so, fixes it.
+ *
+ * The old format of IO Headers was only the type of IO so, e.g. "Source Name" or "Raw Data File".
+ *
+ * A "Source Name" column will now be mapped to the propper "Input [Source Name]", and all other IO types will be mapped to "Output [<IO Type>]".
+ */
+export declare function fixDeprecatedIOHeader(stringCellCol: string[]): string[];
+export declare function fromStringCellColumns(columns: string[][]): CompositeColumn;
+export declare function stringCellColumnsOfFsColumns(columns: FsColumn[]): string[][];
+export declare function fromFsColumns(columns: FsColumn[]): CompositeColumn;
+export declare function toStringCellColumns(column: CompositeColumn): FSharpList<FSharpList<string>>;
+export declare function toFsColumns(column: CompositeColumn): FSharpList<FSharpList<FsCell>>;
+export declare function ColumnValueRefs_fromStringCellColumns(valueMap: IMap<int32, CompositeCell_$union>, columns: string[][]): [CompositeHeader_$union, ColumnValueRefs_$union];
+//# sourceMappingURL=CompositeColumn.d.ts.map

package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeColumn.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"CompositeColumn.d.ts","sourceRoot":"","sources":["../../../../../src/ARCtrl/ts/Spreadsheet/AnnotationTable/CompositeColumn.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,sBAAsB,EAAuF,MAAM,qCAAqC,CAAC;AAGlK,OAAO,EAAE,oBAAoB,EAAE,MAAM,mCAAmC,CAAC;AACzE,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAG7D,OAAO,EAAE,eAAe,EAAE,MAAM,qCAAqC,CAAC;AACtE,OAAO,EAAE,MAAM,EAAE,MAAM,oEAAoE,CAAC;AAC5F,OAAO,EAAE,QAAQ,EAAE,MAAM,gEAAgE,CAAC;AAG1F,OAAO,EAAgB,UAAU,EAAqC,MAAM,qCAAqC,CAAC;AAClH,OAAO,EAAyB,IAAI,EAAE,MAAM,qCAAqC,CAAC;AAClF,OAAO,EAAsD,sBAAsB,EAA0B,MAAM,iCAAiC,CAAC;AAIrJ;;;;;;GAMG;AACH,wBAAgB,qBAAqB,CAAC,aAAa,EAAE,MAAM,EAAE,GAAG,MAAM,EAAE,CAkBvE;AAED,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE,GAAG,eAAe,CAK1E;AAED,wBAAgB,4BAA4B,CAAC,OAAO,EAAE,QAAQ,EAAE,GAAG,MAAM,EAAE,EAAE,CAK5E;AAED,wBAAgB,aAAa,CAAC,OAAO,EAAE,QAAQ,EAAE,GAAG,eAAe,CAKlE;AAED,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,eAAe,GAAG,UAAU,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAoB3F;AAED,wBAAgB,WAAW,CAAC,MAAM,EAAE,eAAe,GAAG,UAAU,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAEnF;AAED,wBAAgB,qCAAqC,CAAC,QAAQ,EAAE,IAAI,CAAC,KAAK,EAAE,oBAAoB,CAAC,EAAE,OAAO,EAAE,MAAM,EAAE,EAAE,GAAG,CAAC,sBAAsB,EAAE,sBAAsB,CAAC,CAyDxK"}

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

@@ -0,0 +1,108 @@
+import { map, skip, item, setItem, tryItem } from '../../../node_modules/@fable-org/fable-library-js/Array.js';
+import { IOType, CompositeHeader_Output, CompositeHeader_Input, IOType_Source } from '../../Core/Table/CompositeHeader.js';
+import { toString, FSharpRef } from '../../../node_modules/@fable-org/fable-library-js/Types.js';
+import { toStringCells, fromStringCells } from './CompositeHeader.js';
+import { exists, toArray, toList, delay, reduce, map as map$1, append, singleton as singleton$1 } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { rangeDouble } from '../../../node_modules/@fable-org/fable-library-js/Range.js';
+import { value, defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import '../../Core/Helper/Url.js';
+import { defaultOf, stringHash } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+import { ofArray, singleton } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { tryGetValue, getItemFromDict } from '../../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+import { mergeHashes } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/HashCodes.fs.js';
+import { toStringCells as toStringCells$1 } from './CompositeCell.js';
+import { ColumnValueRefs_Sparse, ensureCellHashInValueMap, ColumnValueRefs_Constant } from '../../Core/Table/ArcTableAux.js';
+
+function fixDeprecatedIOHeader(stringCellCol) {
+  if (stringCellCol.length === 0) {
+    throw new Error("Can't fix IOHeader Invalid column, neither header nor values given");
+  }
+  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;
+    }
+  }
+}
+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$1(item(0, header)), delay(() => map$1((i) => getCellOrDefault(i, 0, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton$1(item(1, header)), delay(() => map$1((i_1) => getCellOrDefault(i_1, 1, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton$1(item(2, header)), delay(() => map$1((i_2) => getCellOrDefault(i_2, 2, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton$1(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$1(item(0, header)), delay(() => map$1((i_4) => getCellOrDefault(i_4, 0, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton$1(item(1, header)), delay(() => map$1((i_5) => getCellOrDefault(i_5, 1, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton$1(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$1(item(0, header)), delay(() => map$1((i_7) => getCellOrDefault(i_7, 0, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton$1(item(1, header)), delay(() => map$1((i_8) => getCellOrDefault(i_8, 1, cells), rangeDouble(0, 1, compositeCells.length - 1)))))), toList(delay(() => append(singleton$1(item(2, header)), delay(() => map$1((i_9) => getCellOrDefault(i_9, 2, cells), rangeDouble(0, 1, compositeCells.length - 1))))))]);
+  } else {
+    return singleton(toList(delay(() => append(singleton$1(item(0, header)), delay(() => map$1((i_10) => item(0, item(i_10, cells)), rangeDouble(0, 1, compositeCells.length - 1)))))));
+  }
+}
+function ColumnValueRefs_fromStringCellColumns(valueMap, columns) {
+  const hashMap = /* @__PURE__ */ new Map([]);
+  const cells = /* @__PURE__ */ 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] : void 0;
+      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 (value(matchValue) | 0, constant) {
+        value(matchValue) | 0;
+      } else {
+        const cellHash_2 = value(matchValue) | 0;
+        cells.set(i - 1, cellHash_2);
+      }
+    }
+    if (constant) {
+      return [header, ColumnValueRefs_Constant(getItemFromDict(cells, 0))];
+    } else {
+      return [header, ColumnValueRefs_Sparse(cells)];
+    }
+  }
+}
+
+export { ColumnValueRefs_fromStringCellColumns, fixDeprecatedIOHeader, toStringCellColumns };

package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeHeader.d.ts

@@ -0,0 +1,22 @@
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
+import { CompositeCell_$union } from '../../Core/Table/CompositeCell.js';
+import { CompositeHeader_$union } from '../../Core/Table/CompositeHeader.js';
+export declare function ActivePattern_mergeIDInfo(idSpace1: string, localID1: string, idSpace2: string, localID2: string): {
+    TermAccessionNumber: string;
+    TermSourceRef: string;
+};
+export declare function ActivePattern_$007CTerm$007C_$007C(categoryParser: ((arg0: string) => Option<string>), f: ((arg0: OntologyAnnotation) => CompositeHeader_$union), cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007CParameter$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007CFactor$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007CCharacteristic$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007CComponent$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007CInput$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007COutput$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007CComment$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007CProtocolType$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007CProtocolHeader$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function ActivePattern_$007CFreeText$007C_$007C(cellValues: string[]): Option<[CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)]>;
+export declare function fromStringCells(cellValues: string[]): [CompositeHeader_$union, ((arg0: string[]) => CompositeCell_$union)];
+export declare function toStringCells(hasUnit: boolean, header: CompositeHeader_$union): string[];
+//# sourceMappingURL=CompositeHeader.d.ts.map

package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeHeader.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"CompositeHeader.d.ts","sourceRoot":"","sources":["../../../../../src/ARCtrl/ts/Spreadsheet/AnnotationTable/CompositeHeader.ts"],"names":[],"mappings":"AACA,OAAO,EAAc,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAC3E,OAAO,EAAE,kBAAkB,EAAE,MAAM,kCAAkC,CAAC;AAEtE,OAAO,EAAE,oBAAoB,EAAE,MAAM,mCAAmC,CAAC;AACzE,OAAO,EAAqc,sBAAsB,EAAE,MAAM,qCAAqC,CAAC;AAQhhB,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG;IAAE,mBAAmB,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,CAAA;CAAE,CAWxK;AAED,wBAAgB,kCAAkC,CAAC,cAAc,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,KAAK,MAAM,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,kBAAkB,KAAK,sBAAsB,CAAC,EAAE,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAwKpQ;AAED,wBAAgB,uCAAuC,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAS1J;AAED,wBAAgB,oCAAoC,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CASvJ;AAED,wBAAgB,4CAA4C,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAS/J;AAED,wBAAgB,uCAAuC,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAS1J;AAED,wBAAgB,mCAAmC,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAwBtJ;AAED,wBAAgB,oCAAoC,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAwBvJ;AAED,wBAAgB,qCAAqC,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAqBxJ;AAED,wBAAgB,0CAA0C,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAgB7J;AAED,wBAAgB,4CAA4C,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CA4C/J;AAED,wBAAgB,sCAAsC,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAOzJ;AAED,wBAAgB,eAAe,CAAC,UAAU,EAAE,MAAM,EAAE,GAAG,CAAC,sBAAsB,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,oBAAoB,CAAC,CAAC,CAwE1H;AAED,wBAAgB,aAAa,CAAC,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,sBAAsB,GAAG,MAAM,EAAE,CAaxF"}