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

package/dist/ts/ts/Spreadsheet/ArcWorkflow.js

@@ -0,0 +1,125 @@
+import { getEnumerator } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { fromRows as fromRows$1, toRows } from './Metadata/Workflow.js';
+import { value } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { empty, ofSeq } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { ArcWorkflow_create_Z3BB02240, ArcWorkflow__set_DataMap_51F1E59E, ArcWorkflow__set_Contacts_Z7E0D1CA3, ArcWorkflow__get_Contacts } from '../Core/ArcTypes.js';
+import { fromRows, toRows as toRows$1 } from './Metadata/Contacts.js';
+import { createMissingIdentifier } from '../Core/Helper/Identifier.js';
+import { SparseRowModule_fromFsRow, SparseRowModule_tryGetValueAt, SparseRowModule_writeToSheet, SparseRowModule_fromValues } from './Metadata/SparseTable.js';
+import { iterateIndexed, tryPick, tryFind, map, delay, append, singleton } 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 { toConsole, printf, toFail } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { FsWorkbook } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorkbook.fs.js';
+import { tryFromFsWorksheet } from './DataMapTable/DataMapTable.js';
+
+function ArcWorkflow_fromRows(rows) {
+  const en = getEnumerator(rows);
+  const loop = (lastRow_mut, workflow_mut, contacts_mut, rowNumber_mut) => {
+    loop:
+      while (true) {
+        const lastRow = lastRow_mut, workflow = workflow_mut, contacts = contacts_mut, rowNumber = rowNumber_mut;
+        let matchResult;
+        if (lastRow != null) {
+          switch (value(lastRow)) {
+            case "WORKFLOW": {
+              matchResult = 0;
+              value(lastRow);
+              break;
+            }
+            case "WORKFLOW CONTACTS": {
+              matchResult = 1;
+              value(lastRow);
+              break;
+            }
+            default:
+              matchResult = 2;
+          }
+        } else {
+          matchResult = 2;
+        }
+        switch (matchResult) {
+          case 0: {
+            const patternInput = fromRows$1(rowNumber + 1, en);
+            lastRow_mut = patternInput[0];
+            workflow_mut = patternInput[3];
+            contacts_mut = contacts;
+            rowNumber_mut = patternInput[1];
+            continue loop;
+          }
+          case 1: {
+            const patternInput_1 = fromRows("Workflow Person", rowNumber + 1, en);
+            lastRow_mut = patternInput_1[0];
+            workflow_mut = workflow;
+            contacts_mut = patternInput_1[3];
+            rowNumber_mut = patternInput_1[1];
+            continue loop;
+          }
+          default:
+            if (workflow != null) {
+              const workflow_2 = value(workflow);
+              ArcWorkflow__set_Contacts_Z7E0D1CA3(workflow_2, Array.from(contacts));
+              return workflow_2;
+            } else {
+              return ArcWorkflow_create_Z3BB02240(createMissingIdentifier(), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, Array.from(contacts));
+            }
+        }
+      }
+  };
+  if (en["System.Collections.IEnumerator.MoveNext"]()) {
+    return loop(SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), void 0, empty(), 1);
+  } else {
+    throw new Error("empty workflow metadata sheet");
+  }
+}
+function ArcWorkflow_toRows(workflow) {
+  return delay(() => append(singleton(SparseRowModule_fromValues(["WORKFLOW"])), delay(() => append(toRows(workflow), delay(() => append(singleton(SparseRowModule_fromValues(["WORKFLOW CONTACTS"])), delay(() => toRows$1("Workflow Person", ofSeq(ArcWorkflow__get_Contacts(workflow))))))))));
+}
+function ArcWorkflow_toMetadataSheet(workflow) {
+  const sheet = new FsWorksheet("isa_workflow");
+  iterateIndexed((rowI, r) => {
+    SparseRowModule_writeToSheet(rowI + 1, r, sheet);
+  }, ArcWorkflow_toRows(workflow));
+  return sheet;
+}
+function ArcWorkflow_fromMetadataSheet(sheet) {
+  try {
+    return ArcWorkflow_fromRows(map(SparseRowModule_fromFsRow, sheet.Rows));
+  } catch (err) {
+    const arg = err.message;
+    return toFail(printf("Failed while parsing metadatasheet: %s"))(arg);
+  }
+}
+function ArcWorkflow_isMetadataSheetName(name) {
+  return name === "isa_workflow";
+}
+function ArcWorkflow_isMetadataSheet(sheet) {
+  return ArcWorkflow_isMetadataSheetName(sheet.Name);
+}
+function ArcWorkflow_tryGetMetadataSheet(doc) {
+  return tryFind(ArcWorkflow_isMetadataSheet, doc.GetWorksheets());
+}
+function ARCtrl_ArcWorkflow__ArcWorkflow_fromFsWorkbook_Static_32154C9D(doc) {
+  try {
+    let workflowMetadata;
+    const matchValue = ArcWorkflow_tryGetMetadataSheet(doc);
+    if (matchValue == null) {
+      toConsole(printf('Cannot retrieve metadata: Workflow file does not contain "%s" sheet.'))("isa_workflow");
+      workflowMetadata = ArcWorkflow_create_Z3BB02240(createMissingIdentifier());
+    } else {
+      workflowMetadata = ArcWorkflow_fromMetadataSheet(value(matchValue));
+    }
+    ArcWorkflow__set_DataMap_51F1E59E(workflowMetadata, tryPick(tryFromFsWorksheet, doc.GetWorksheets()));
+    return workflowMetadata;
+  } catch (err) {
+    const arg_1 = err.message;
+    return toFail(printf("Could not parse assay: \n%s"))(arg_1);
+  }
+}
+function ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E(workflow) {
+  const doc = new FsWorkbook();
+  const metadataSheet = ArcWorkflow_toMetadataSheet(workflow);
+  doc.AddWorksheet(metadataSheet);
+  return doc;
+}
+
+export { ARCtrl_ArcWorkflow__ArcWorkflow_fromFsWorkbook_Static_32154C9D, ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E, ArcWorkflow_fromMetadataSheet, ArcWorkflow_fromRows, ArcWorkflow_isMetadataSheet, ArcWorkflow_isMetadataSheetName, ArcWorkflow_toMetadataSheet, ArcWorkflow_toRows, ArcWorkflow_tryGetMetadataSheet };

package/dist/ts/ts/Spreadsheet/CollectionAux.d.ts

@@ -0,0 +1,23 @@
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { IMap } from '@fable-org/fable-library-js/Util.js';
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+/**
+ * If at least i values exist in seq a, builds a new array that contains the elements of the given seq, exluding the first i elements
+ */
+export declare function Seq_trySkip<$a>(i: int32, s: Iterable<$a>): Option<Iterable<$a>>;
+export declare function Array_ofIndexedSeq(s: Iterable<[int32, string]>): string[];
+/**
+ * If at least i values exist in array a, builds a new array that contains the elements of the given array, exluding the first i elements
+ */
+export declare function Array_trySkip<$a>(i: int32, a: $a[]): Option<$a[]>;
+/**
+ * Returns Item of array at index i if existing, else returns default value
+ */
+export declare function Array_tryItemDefault<$a>(i: int32, d: $a, a: $a[]): $a;
+export declare function Array_map4<A, B, C, D, T>(f: ((arg0: A, arg1: B, arg2: C, arg3: D) => T), aa: A[], ba: B[], ca: C[], da: D[]): T[];
+export declare function List_tryPickDefault<T, U>(chooser: ((arg0: T) => Option<U>), d: U, list: FSharpList<T>): U;
+export declare function List_unzip4<A, B, C, D>(l: FSharpList<[A, B, C, D]>): [FSharpList<A>, FSharpList<B>, FSharpList<C>, FSharpList<D>];
+export declare function Dictionary_tryGetValue<K, V>(k: K, dict: IMap<K, V>): Option<V>;
+export declare function Dictionary_tryGetString<K>(k: K, dict: IMap<K, string>): Option<string>;
+//# sourceMappingURL=CollectionAux.d.ts.map

package/dist/ts/ts/Spreadsheet/CollectionAux.d.ts.map

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

@@ -0,0 +1,34 @@
+import { skip } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { some } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { initialize, item } from '../../node_modules/@fable-org/fable-library-js/Array.js';
+import { defaultOf } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { tryGetValue } from '../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+import { FSharpRef } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+
+function Seq_trySkip(i, s) {
+  try {
+    return skip(i, s);
+  } catch (matchValue) {
+    return void 0;
+  }
+}
+function Array_map4(f, aa, ba, ca, da) {
+  if (!(aa.length === ba.length && ba.length === ca.length && ca.length === da.length)) {
+    throw new Error("");
+  }
+  return initialize(aa.length, (i) => f(item(i, aa), item(i, ba), item(i, ca), item(i, da)));
+}
+function Dictionary_tryGetValue(k, dict) {
+  let patternInput;
+  let outArg = defaultOf();
+  patternInput = [tryGetValue(dict, k, new FSharpRef(() => outArg, (v) => {
+    outArg = v;
+  })), outArg];
+  if (patternInput[0]) {
+    return some(patternInput[1]);
+  } else {
+    return void 0;
+  }
+}
+
+export { Array_map4, Dictionary_tryGetValue, Seq_trySkip };

package/dist/ts/ts/Spreadsheet/DataMap.d.ts

@@ -0,0 +1,8 @@
+import { DataMap } from '../Core/DataMap.js';
+import { FsWorkbook } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorkbook.fs.js';
+/**
+ * Reads an datamap from a spreadsheet
+ */
+export declare function fromFsWorkbook(doc: FsWorkbook): DataMap;
+export declare function toFsWorkbook(dataMap: DataMap): FsWorkbook;
+//# sourceMappingURL=DataMap.d.ts.map

package/dist/ts/ts/Spreadsheet/DataMap.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DataMap.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Spreadsheet/DataMap.ts"],"names":[],"mappings":"AAKA,OAAO,EAAgB,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,EAAE,UAAU,EAAE,MAAM,+DAA+D,CAAC;AAE3F;;GAEG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,UAAU,GAAG,OAAO,CAoBvD;AAED,wBAAgB,YAAY,CAAC,OAAO,EAAE,OAAO,GAAG,UAAU,CAKzD"}

package/dist/ts/ts/Spreadsheet/DataMap.js

@@ -0,0 +1,33 @@
+import { toFail, printf } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { tryPick, forAll } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { toFsWorksheet, tryFromFsWorksheet } from './DataMapTable/DataMapTable.js';
+import { value } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { DataMap_init } from '../Core/DataMap.js';
+import { FsWorkbook } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorkbook.fs.js';
+
+function fromFsWorkbook(doc) {
+  try {
+    const worksheets = doc.GetWorksheets();
+    const dataMapTable = tryPick(tryFromFsWorksheet, worksheets);
+    if (dataMapTable == null) {
+      if (forAll((sheet) => sheet.CellCollection.Count === 0, worksheets)) {
+        return DataMap_init();
+      } else {
+        throw new Error("No DataMapTable was found in any of the sheets of the workbook");
+      }
+    } else {
+      return value(dataMapTable);
+    }
+  } catch (err) {
+    const arg = err.message;
+    return toFail(printf("Could not parse datamap: \n%s"))(arg);
+  }
+}
+function toFsWorkbook(dataMap) {
+  const doc = new FsWorkbook();
+  const sheet = toFsWorksheet(dataMap);
+  doc.AddWorksheet(sheet);
+  return doc;
+}
+
+export { fromFsWorkbook, toFsWorkbook };

package/dist/ts/ts/Spreadsheet/DataMapTable/DataMapColumn.d.ts

@@ -0,0 +1,7 @@
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { FsColumn } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsColumn.fs.js';
+import { FsCell } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/Cells/FsCell.fs.js';
+import { DataContext } from '../../Core/DataContext.js';
+export declare function setFromFsColumns(dc: DataContext[], columns: FSharpList<FsColumn>): DataContext[];
+export declare function toFsColumns(dc: DataContext[]): FSharpList<FSharpList<FsCell>>;
+//# sourceMappingURL=DataMapColumn.d.ts.map

package/dist/ts/ts/Spreadsheet/DataMapTable/DataMapColumn.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DataMapColumn.d.ts","sourceRoot":"","sources":["../../../../../src/ARCtrl/ts/Spreadsheet/DataMapTable/DataMapColumn.ts"],"names":[],"mappings":"AACA,OAAO,EAAiC,UAAU,EAAO,MAAM,qCAAqC,CAAC;AACrG,OAAO,EAAE,QAAQ,EAAE,MAAM,gEAAgE,CAAC;AAC1F,OAAO,EAAE,MAAM,EAAE,MAAM,oEAAoE,CAAC;AAC5F,OAAO,EAAwK,WAAW,EAAE,MAAM,2BAA2B,CAAC;AAS9N,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,WAAW,EAAE,EAAE,OAAO,EAAE,UAAU,CAAC,QAAQ,CAAC,GAAG,WAAW,EAAE,CAMhG;AAED,wBAAgB,WAAW,CAAC,EAAE,EAAE,WAAW,EAAE,GAAG,UAAU,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAuB7E"}

package/dist/ts/ts/Spreadsheet/DataMapTable/DataMapColumn.js

@@ -0,0 +1,41 @@
+import { toFsCells, fromFsCells } from './DataMapHeader.js';
+import { transpose, map, ofArray, singleton } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { FsCell } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/Cells/FsCell.fs.js';
+import { DataContext__get_Explication, DataContext__get_Unit, DataContext__get_ObjectType, DataContext__get_Description, DataContext__get_GeneratedBy, DataContext__get_Label } from '../../Core/DataContext.js';
+import { toList, delay, collect, append, map as map$1, tryFind, singleton as singleton$1 } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { distinct } from '../../../node_modules/@fable-org/fable-library-js/Seq2.js';
+import { defaultArg, bind, value } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { stringHash } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+
+function setFromFsColumns(dc, columns) {
+  const cellParser = fromFsCells(map((c) => c.Item(1), columns));
+  for (let i = 0; i <= dc.length - 1; i++) {
+    cellParser(dc[i])(map((c_1) => c_1.Item(i + 2), columns));
+  }
+  return dc;
+}
+function toFsColumns(dc) {
+  const commentKeys = toList(distinct(collect((dc_1) => map$1((c) => defaultArg(c.Name, ""), dc_1.Comments), dc), {
+    Equals: (x, y) => x === y,
+    GetHashCode: stringHash
+  }));
+  const headers = toFsCells(commentKeys);
+  const createTerm = (oa) => {
+    if (oa == null) {
+      return ofArray([new FsCell(""), new FsCell(""), new FsCell("")]);
+    } else {
+      const oa_1 = value(oa);
+      return ofArray([new FsCell(defaultArg(oa_1.Name, "")), new FsCell(defaultArg(oa_1.TermSourceREF, "")), new FsCell(defaultArg(oa_1.TermAccessionNumber, ""))]);
+    }
+  };
+  const createText = (s) => singleton(new FsCell(defaultArg(s, "")));
+  return transpose(toList(delay(() => append(singleton$1(headers), delay(() => map$1((dc_4) => {
+    const dc_3 = dc_4;
+    return toList(delay(() => {
+      let dc_2;
+      return append((dc_2 = dc_3, ofArray([new FsCell(defaultArg(dc_2.Name, "")), new FsCell(defaultArg(dc_2.Format, "")), new FsCell(defaultArg(dc_2.SelectorFormat, ""))])), delay(() => append(createTerm(DataContext__get_Explication(dc_3)), delay(() => append(createTerm(DataContext__get_Unit(dc_3)), delay(() => append(createTerm(DataContext__get_ObjectType(dc_3)), delay(() => append(createText(DataContext__get_Description(dc_3)), delay(() => append(createText(DataContext__get_GeneratedBy(dc_3)), delay(() => append(createText(DataContext__get_Label(dc_3)), delay(() => map((key) => new FsCell(defaultArg(bind((c_2) => c_2.Value, tryFind((c_1) => defaultArg(c_1.Name, "") === key, dc_3.Comments)), "")), commentKeys)))))))))))))));
+    }));
+  }, dc))))));
+}
+
+export { setFromFsColumns, toFsColumns };

package/dist/ts/ts/Spreadsheet/DataMapTable/DataMapHeader.d.ts

@@ -0,0 +1,23 @@
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { FsCell } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/Cells/FsCell.fs.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
+import { Data } from '../../Core/Data.js';
+import { DataContext } from '../../Core/DataContext.js';
+export declare function ActivePattern_ontologyAnnotationFromFsCells(tsrCol: Option<int32>, tanCol: Option<int32>, cells: FSharpList<FsCell>): OntologyAnnotation;
+export declare function ActivePattern_freeTextFromFsCells(cells: FSharpList<FsCell>): string;
+export declare function ActivePattern_dataFromFsCells(format: Option<int32>, selectorFormat: Option<int32>, cells: FSharpList<FsCell>): Data;
+export declare function ActivePattern_$007CTerm$007C_$007C(categoryString: string, cells: FSharpList<FsCell>): Option<((arg0: FSharpList<FsCell>) => OntologyAnnotation)>;
+export declare function ActivePattern_$007CExplication$007C_$007C(cells: FSharpList<FsCell>): Option<((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext))>;
+export declare function ActivePattern_$007CUnit$007C_$007C(cells: FSharpList<FsCell>): Option<((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext))>;
+export declare function ActivePattern_$007CObjectType$007C_$007C(cells: FSharpList<FsCell>): Option<((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext))>;
+export declare function ActivePattern_$007CDescription$007C_$007C(cells: FSharpList<FsCell>): Option<((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext))>;
+export declare function ActivePattern_$007CGeneratedBy$007C_$007C(cells: FSharpList<FsCell>): Option<((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext))>;
+export declare function ActivePattern_$007CLabel$007C_$007C(cells: FSharpList<FsCell>): Option<((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext))>;
+export declare function ActivePattern_$007CData$007C_$007C(cells: FSharpList<FsCell>): Option<((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext))>;
+export declare function ActivePattern_$007CComment$007C_$007C(cells: FSharpList<FsCell>): Option<((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext))>;
+export declare function ActivePattern_$007CFreetext$007C_$007C(cells: FSharpList<FsCell>): Option<((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext))>;
+export declare function fromFsCells(cells: FSharpList<FsCell>): ((arg0: DataContext) => ((arg0: FSharpList<FsCell>) => DataContext));
+export declare function toFsCells(commentKeys: FSharpList<string>): FSharpList<FsCell>;
+//# sourceMappingURL=DataMapHeader.d.ts.map

package/dist/ts/ts/Spreadsheet/DataMapTable/DataMapHeader.d.ts.map

@@ -0,0 +1 @@
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