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

package/dist/ts/ts/Spreadsheet/ArcInvestigation.js

@@ -0,0 +1,316 @@
+import { Record } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+import { ofSeq, map, isEmpty, tail, cons, head, reverse, empty, unzip, concat, append, ofArray } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { Remark } from '../Core/Comment.js';
+import { comparePrimitives, getEnumerator, stringHash } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { Remark_wrapRemark, Comment_fromString, Comment_toString } from './Metadata/Comment.js';
+import { SparseRowModule_writeToSheet, SparseRowModule_fromValues, SparseRowModule_fromFsRow, SparseRowModule_tryGetValueAt, SparseTable_FromRows_Z5579EC29, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_ToRows_759CAFC1, SparseTable_Create_Z2192E64B, SparseTable } from './Metadata/SparseTable.js';
+import { addToDict } from '../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+import { value, defaultArg } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { Option_fromValueWithDefault, ResizeArray_iter } from '../Core/Helper/Collections.js';
+import { List_distinctBy, List_distinct } from '../../node_modules/@fable-org/fable-library-js/Seq2.js';
+import { ArcInvestigation, ArcStudy } from '../Core/ArcTypes.js';
+import { iterateIndexed, toList, map as map$1, isEmpty as isEmpty$1, tryFind as tryFind$1, delay, append as append$1, singleton, collect } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { fromRows as fromRows$3, toRows } from './Metadata/OntologySourceReference.js';
+import { fromRows as fromRows$2, toRows as toRows$1 } from './Metadata/Publication.js';
+import { fromRows as fromRows$1, toRows as toRows$2 } from './Metadata/Contacts.js';
+import { fromRows, toRows as toRows$3 } from './Metadata/Study.js';
+import { ofList, tryFind } from '../../node_modules/@fable-org/fable-library-js/Map.js';
+import { FsWorksheet } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorksheet.fs.js';
+import { FsWorkbook } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorkbook.fs.js';
+import { toFail, printf } from '../../node_modules/@fable-org/fable-library-js/String.js';
+
+class ArcInvestigation_InvestigationInfo extends Record {
+  constructor(Identifier, Title, Description, SubmissionDate, PublicReleaseDate, Comments) {
+    super();
+    this.Identifier = Identifier;
+    this.Title = Title;
+    this.Description = Description;
+    this.SubmissionDate = SubmissionDate;
+    this.PublicReleaseDate = PublicReleaseDate;
+    this.Comments = Comments;
+  }
+}
+function ArcInvestigation_InvestigationInfo_create(identifier, title, description, submissionDate, publicReleaseDate, comments) {
+  return new ArcInvestigation_InvestigationInfo(identifier, title, description, submissionDate, publicReleaseDate, comments);
+}
+function ArcInvestigation_InvestigationInfo_get_Labels() {
+  return ofArray(["Investigation Identifier", "Investigation Title", "Investigation Description", "Investigation Submission Date", "Investigation Public Release Date"]);
+}
+function ArcInvestigation_InvestigationInfo_FromSparseTable_3ECCA699(matrix) {
+  const comments = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, 0])), matrix.CommentKeys);
+  return ArcInvestigation_InvestigationInfo_create(SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Identifier", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Title", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Description", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Submission Date", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Investigation Public Release Date", 0]), comments);
+}
+function ArcInvestigation_InvestigationInfo_ToSparseTable_Z720BD3FF(investigation) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, ArcInvestigation_InvestigationInfo_get_Labels(), void 0, 2);
+  let commentKeys = empty();
+  addToDict(matrix.Matrix, ["Investigation Identifier", 1], investigation.Identifier);
+  addToDict(matrix.Matrix, ["Investigation Title", 1], defaultArg(investigation.Title, ""));
+  addToDict(matrix.Matrix, ["Investigation Description", 1], defaultArg(investigation.Description, ""));
+  addToDict(matrix.Matrix, ["Investigation Submission Date", 1], defaultArg(investigation.SubmissionDate, ""));
+  addToDict(matrix.Matrix, ["Investigation Public Release Date", 1], defaultArg(investigation.PublicReleaseDate, ""));
+  ResizeArray_iter((comment) => {
+    const patternInput = Comment_toString(comment);
+    const n = patternInput[0];
+    commentKeys = cons(n, commentKeys);
+    addToDict(matrix.Matrix, [n, 1], patternInput[1]);
+  }, investigation.Comments);
+  return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+    Equals: (x, y) => x === y,
+    GetHashCode: stringHash
+  })), matrix.ColumnCount);
+}
+function ArcInvestigation_InvestigationInfo_fromRows(lineNumber, rows) {
+  const tupledArg = SparseTable_FromRows_Z5579EC29(rows, ArcInvestigation_InvestigationInfo_get_Labels(), lineNumber);
+  return [tupledArg[0], tupledArg[1], tupledArg[2], ArcInvestigation_InvestigationInfo_FromSparseTable_3ECCA699(tupledArg[3])];
+}
+function ArcInvestigation_InvestigationInfo_toRows_Z720BD3FF(investigation) {
+  return SparseTable_ToRows_759CAFC1(ArcInvestigation_InvestigationInfo_ToSparseTable_Z720BD3FF(investigation));
+}
+function ArcInvestigation_fromParts(investigationInfo, ontologySourceReference, publications, contacts, studies, assays, remarks) {
+  const studyIdentifiers = map((s) => s.Identifier, studies);
+  const title = Option_fromValueWithDefault("", investigationInfo.Title);
+  const description = Option_fromValueWithDefault("", investigationInfo.Description);
+  const submissionDate = Option_fromValueWithDefault("", investigationInfo.SubmissionDate);
+  const publicReleaseDate = Option_fromValueWithDefault("", investigationInfo.PublicReleaseDate);
+  const ontologySourceReferences = Array.from(ontologySourceReference);
+  const publications_1 = Array.from(publications);
+  const contacts_1 = Array.from(contacts);
+  const assays_1 = Array.from(assays);
+  const studies_1 = Array.from(studies);
+  const registeredStudyIdentifiers = Array.from(studyIdentifiers);
+  const comments = Array.from(investigationInfo.Comments);
+  const remarks_1 = Array.from(remarks);
+  return ArcInvestigation.make(investigationInfo.Identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications_1, contacts_1, assays_1, studies_1, [], [], registeredStudyIdentifiers, comments, remarks_1);
+}
+function ArcInvestigation_fromRows(rows) {
+  if (isEmpty$1(rows)) {
+    throw new Error("isa_investigation sheet in Investigation file is empty");
+  }
+  const en = getEnumerator(rows);
+  const emptyInvestigationInfo = ArcInvestigation_InvestigationInfo_create("", "", "", "", "", empty());
+  const loop = (lastLine_mut, ontologySourceReferences_mut, investigationInfo_mut, publications_mut, contacts_mut, studies_mut, remarks_mut, lineNumber_mut) => {
+    loop:
+      while (true) {
+        const lastLine = lastLine_mut, ontologySourceReferences = ontologySourceReferences_mut, investigationInfo = investigationInfo_mut, publications = publications_mut, contacts = contacts_mut, studies = studies_mut, remarks = remarks_mut, lineNumber = lineNumber_mut;
+        let matchResult;
+        if (lastLine != null) {
+          switch (value(lastLine)) {
+            case "ONTOLOGY SOURCE REFERENCE": {
+              matchResult = 0;
+              value(lastLine);
+              break;
+            }
+            case "INVESTIGATION": {
+              matchResult = 1;
+              value(lastLine);
+              break;
+            }
+            case "INVESTIGATION PUBLICATIONS": {
+              matchResult = 2;
+              value(lastLine);
+              break;
+            }
+            case "INVESTIGATION CONTACTS": {
+              matchResult = 3;
+              value(lastLine);
+              break;
+            }
+            case "STUDY": {
+              matchResult = 4;
+              value(lastLine);
+              break;
+            }
+            default:
+              matchResult = 5;
+          }
+        } else {
+          matchResult = 5;
+        }
+        switch (matchResult) {
+          case 0: {
+            const patternInput = fromRows$3(lineNumber + 1, en);
+            lastLine_mut = patternInput[0];
+            ontologySourceReferences_mut = patternInput[3];
+            investigationInfo_mut = investigationInfo;
+            publications_mut = publications;
+            contacts_mut = contacts;
+            studies_mut = studies;
+            remarks_mut = append(remarks, patternInput[2]);
+            lineNumber_mut = patternInput[1];
+            continue loop;
+          }
+          case 1: {
+            const patternInput_1 = ArcInvestigation_InvestigationInfo_fromRows(lineNumber + 1, en);
+            lastLine_mut = patternInput_1[0];
+            ontologySourceReferences_mut = ontologySourceReferences;
+            investigationInfo_mut = patternInput_1[3];
+            publications_mut = publications;
+            contacts_mut = contacts;
+            studies_mut = studies;
+            remarks_mut = append(remarks, patternInput_1[2]);
+            lineNumber_mut = patternInput_1[1];
+            continue loop;
+          }
+          case 2: {
+            const patternInput_2 = fromRows$2("Investigation Publication", lineNumber + 1, en);
+            lastLine_mut = patternInput_2[0];
+            ontologySourceReferences_mut = ontologySourceReferences;
+            investigationInfo_mut = investigationInfo;
+            publications_mut = patternInput_2[3];
+            contacts_mut = contacts;
+            studies_mut = studies;
+            remarks_mut = append(remarks, patternInput_2[2]);
+            lineNumber_mut = patternInput_2[1];
+            continue loop;
+          }
+          case 3: {
+            const patternInput_3 = fromRows$1("Investigation Person", lineNumber + 1, en);
+            lastLine_mut = patternInput_3[0];
+            ontologySourceReferences_mut = ontologySourceReferences;
+            investigationInfo_mut = investigationInfo;
+            publications_mut = publications;
+            contacts_mut = patternInput_3[3];
+            studies_mut = studies;
+            remarks_mut = append(remarks, patternInput_3[2]);
+            lineNumber_mut = patternInput_3[1];
+            continue loop;
+          }
+          case 4: {
+            const patternInput_4 = fromRows(lineNumber + 1, en);
+            const study = patternInput_4[3];
+            const newRemarks_4 = patternInput_4[2];
+            const lineNumber_6 = patternInput_4[1] | 0;
+            const currentLine_4 = patternInput_4[0];
+            if (study != null) {
+              lastLine_mut = currentLine_4;
+              ontologySourceReferences_mut = ontologySourceReferences;
+              investigationInfo_mut = investigationInfo;
+              publications_mut = publications;
+              contacts_mut = contacts;
+              studies_mut = cons(value(study), studies);
+              remarks_mut = append(remarks, newRemarks_4);
+              lineNumber_mut = lineNumber_6;
+              continue loop;
+            } else {
+              lastLine_mut = currentLine_4;
+              ontologySourceReferences_mut = ontologySourceReferences;
+              investigationInfo_mut = investigationInfo;
+              publications_mut = publications;
+              contacts_mut = contacts;
+              studies_mut = studies;
+              remarks_mut = append(remarks, newRemarks_4);
+              lineNumber_mut = lineNumber_6;
+              continue loop;
+            }
+          }
+          default:
+            if (en["System.Collections.IEnumerator.MoveNext"]()) {
+              lastLine_mut = SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]());
+              ontologySourceReferences_mut = ontologySourceReferences;
+              investigationInfo_mut = investigationInfo;
+              publications_mut = publications;
+              contacts_mut = contacts;
+              studies_mut = studies;
+              remarks_mut = remarks;
+              lineNumber_mut = lineNumber;
+              continue loop;
+            } else {
+              let patternInput_5;
+              const tupledArg = unzip(studies);
+              patternInput_5 = [reverse(tupledArg[0]), List_distinctBy((a_1) => a_1.Identifier, concat(tupledArg[1]), {
+                Equals: (x, y) => x === y,
+                GetHashCode: stringHash
+              })];
+              return ArcInvestigation_fromParts(investigationInfo, ontologySourceReferences, publications, contacts, patternInput_5[0], patternInput_5[1], remarks);
+            }
+        }
+      }
+  };
+  let arcInvestigation;
+  en["System.Collections.IEnumerator.MoveNext"]();
+  arcInvestigation = loop(SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), empty(), emptyInvestigationInfo, empty(), empty(), empty(), empty(), 1);
+  if (arcInvestigation.Identifier === "") {
+    throw new Error("Mandatory Investigation identifier is not present");
+  }
+  return arcInvestigation;
+}
+function ArcInvestigation_toRows(investigation) {
+  let remarks, rows;
+  return remarks = ofSeq(investigation.Remarks), rows = delay(() => append$1(singleton(SparseRowModule_fromValues(["ONTOLOGY SOURCE REFERENCE"])), delay(() => append$1(toRows(ofSeq(investigation.OntologySourceReferences)), delay(() => append$1(singleton(SparseRowModule_fromValues(["INVESTIGATION"])), delay(() => append$1(ArcInvestigation_InvestigationInfo_toRows_Z720BD3FF(investigation), delay(() => append$1(singleton(SparseRowModule_fromValues(["INVESTIGATION PUBLICATIONS"])), delay(() => append$1(toRows$1("Investigation Publication", ofSeq(investigation.Publications)), delay(() => append$1(singleton(SparseRowModule_fromValues(["INVESTIGATION CONTACTS"])), delay(() => append$1(toRows$2("Investigation Person", ofSeq(investigation.Contacts)), delay(() => collect((studyIdentifier) => {
+    const study = defaultArg(investigation.TryGetStudy(studyIdentifier), new ArcStudy(studyIdentifier));
+    return append$1(singleton(SparseRowModule_fromValues(["STUDY"])), delay(() => toRows$3(study, void 0)));
+  }, investigation.RegisteredStudyIdentifiers)))))))))))))))))), (() => {
+    try {
+      const rm = ofList(map((remark) => Remark.toTuple(remark), remarks), {
+        Compare: comparePrimitives
+      });
+      const loop = (i_mut, l_mut, nl_mut) => {
+        loop:
+          while (true) {
+            const i = i_mut, l = l_mut, nl = nl_mut;
+            const matchValue = tryFind(i, rm);
+            if (matchValue == null) {
+              if (!isEmpty(l)) {
+                i_mut = i + 1;
+                l_mut = tail(l);
+                nl_mut = cons(head(l), nl);
+                continue loop;
+              } else {
+                return nl;
+              }
+            } else {
+              const remark_1 = value(matchValue);
+              i_mut = i + 1;
+              l_mut = l;
+              nl_mut = cons(SparseRowModule_fromValues([Remark_wrapRemark(remark_1)]), nl);
+              continue loop;
+            }
+            break;
+          }
+      };
+      return reverse(loop(1, ofSeq(rows), empty()));
+    } catch (matchValue_1) {
+      return toList(rows);
+    }
+  })();
+}
+function ArcInvestigation_isMetadataSheetName(name) {
+  if (name === "isa_investigation") {
+    return true;
+  } else {
+    return name === "Investigation";
+  }
+}
+function ArcInvestigation_isMetadataSheet(sheet) {
+  return ArcInvestigation_isMetadataSheetName(sheet.Name);
+}
+function ArcInvestigation_tryGetMetadataSheet(doc) {
+  return tryFind$1(ArcInvestigation_isMetadataSheet, doc.GetWorksheets());
+}
+function ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D(doc) {
+  let sheet_1, matchValue;
+  try {
+    return ArcInvestigation_fromRows(map$1(SparseRowModule_fromFsRow, (sheet_1 = (matchValue = ArcInvestigation_tryGetMetadataSheet(doc), matchValue == null ? (() => {
+      throw new Error('Could not find metadata sheet with sheetname "isa_investigation" or deprecated sheetname "Investigation"');
+    })() : value(matchValue)), FsWorksheet.getRows(sheet_1))));
+  } catch (err) {
+    const arg = err.message;
+    return toFail(printf("Could not read investigation from spreadsheet: %s"))(arg);
+  }
+}
+function ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(investigation) {
+  try {
+    const wb = new FsWorkbook();
+    const sheet = new FsWorksheet("isa_investigation");
+    iterateIndexed((rowI, r) => {
+      SparseRowModule_writeToSheet(rowI + 1, r, sheet);
+    }, ArcInvestigation_toRows(investigation));
+    wb.AddWorksheet(sheet);
+    return wb;
+  } catch (err) {
+    const arg = err.message;
+    return toFail(printf("Could not write investigation to spreadsheet: %s"))(arg);
+  }
+}
+
+export { ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D, ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF, ArcInvestigation_InvestigationInfo, ArcInvestigation_InvestigationInfo_FromSparseTable_3ECCA699, ArcInvestigation_InvestigationInfo_ToSparseTable_Z720BD3FF, ArcInvestigation_InvestigationInfo_create, ArcInvestigation_InvestigationInfo_fromRows, ArcInvestigation_InvestigationInfo_get_Labels, ArcInvestigation_InvestigationInfo_toRows_Z720BD3FF, ArcInvestigation_fromParts, ArcInvestigation_fromRows, ArcInvestigation_isMetadataSheet, ArcInvestigation_isMetadataSheetName, ArcInvestigation_toRows, ArcInvestigation_tryGetMetadataSheet };

package/dist/ts/ts/Spreadsheet/ArcRun.d.ts

@@ -0,0 +1,27 @@
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { ArcRun } from '../Core/ArcTypes.js';
+import { FsWorksheet } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorksheet.fs.js';
+import { FsWorkbook } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorkbook.fs.js';
+export declare function ArcRun_fromRows(rows: Iterable<Iterable<[int32, string]>>): ArcRun;
+export declare function ArcRun_toRows(run: ArcRun): Iterable<Iterable<[int32, string]>>;
+export declare function ArcRun_toMetadataSheet(run: ArcRun): FsWorksheet;
+export declare function ArcRun_fromMetadataSheet(sheet: FsWorksheet): ArcRun;
+export declare function ArcRun_toMetadataCollection(run: ArcRun): Iterable<Iterable<Option<string>>>;
+export declare function ArcRun_fromMetadataCollection(collection: Iterable<Iterable<Option<string>>>): ArcRun;
+export declare function ArcRun_isMetadataSheetName(name: string): boolean;
+export declare function ArcRun_isMetadataSheet(sheet: FsWorksheet): boolean;
+export declare function ArcRun_tryGetMetadataSheet(doc: FsWorkbook): Option<FsWorksheet>;
+/**
+ * Reads an run from a spreadsheet
+ */
+export declare function ARCtrl_ArcRun__ArcRun_fromFsWorkbook_Static_32154C9D(doc: FsWorkbook): ArcRun;
+/**
+ * Write a run to a spreadsheet
+ */
+export declare function ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8(run: ArcRun): FsWorkbook;
+/**
+ * Write a run to a spreadsheet
+ */
+export declare function ARCtrl_ArcRun__ArcRun_ToFsWorkbook(this$: ArcRun): FsWorkbook;
+//# sourceMappingURL=ArcRun.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ArcRun.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Spreadsheet/ArcRun.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAE7D,OAAO,EAAoB,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAGjF,OAAO,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAM7C,OAAO,EAAE,WAAW,EAAE,MAAM,gEAAgE,CAAC;AAG7F,OAAO,EAAE,UAAU,EAAE,MAAM,+DAA+D,CAAC;AAM3F,wBAAgB,eAAe,CAAC,IAAI,EAAE,QAAQ,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,CA8DjF;AAED,wBAAgB,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,CAE9E;AAED,wBAAgB,sBAAsB,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAM/D;AAED,wBAAgB,wBAAwB,CAAC,KAAK,EAAE,WAAW,GAAG,MAAM,CAQnE;AAED,wBAAgB,2BAA2B,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAE3F;AAED,wBAAgB,6BAA6B,CAAC,UAAU,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,CAQpG;AAED,wBAAgB,0BAA0B,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAEhE;AAED,wBAAgB,sBAAsB,CAAC,KAAK,EAAE,WAAW,GAAG,OAAO,CAElE;AAED,wBAAgB,0BAA0B,CAAC,GAAG,EAAE,UAAU,GAAG,MAAM,CAAC,WAAW,CAAC,CAE/E;AAED;;GAEG;AACH,wBAAgB,oDAAoD,CAAC,GAAG,EAAE,UAAU,GAAG,MAAM,CAwB5F;AAED;;GAEG;AACH,wBAAgB,mDAAmD,CAAC,GAAG,EAAE,MAAM,GAAG,UAAU,CAS3F;AAED;;GAEG;AACH,wBAAgB,kCAAkC,CAAC,KAAK,EAAE,MAAM,GAAG,UAAU,CAE5E"}

package/dist/ts/ts/Spreadsheet/ArcRun.js

@@ -0,0 +1,136 @@
+import { getEnumerator } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { fromRows as fromRows$1, toRows } from './Metadata/Run.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 { ArcRun } 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, choose, tryPick, isEmpty, 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 { toFsWorksheet, tryFromFsWorksheet } from './AnnotationTable/ArcTable.js';
+import { tryFromFsWorksheet as tryFromFsWorksheet$1 } from './DataMapTable/DataMapTable.js';
+
+function ArcRun_fromRows(rows) {
+  const en = getEnumerator(rows);
+  const loop = (lastRow_mut, run_mut, performers_mut, rowNumber_mut) => {
+    loop:
+      while (true) {
+        const lastRow = lastRow_mut, run = run_mut, performers = performers_mut, rowNumber = rowNumber_mut;
+        let matchResult;
+        if (lastRow != null) {
+          switch (value(lastRow)) {
+            case "RUN": {
+              matchResult = 0;
+              value(lastRow);
+              break;
+            }
+            case "RUN PERFORMERS": {
+              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];
+            run_mut = patternInput[3];
+            performers_mut = performers;
+            rowNumber_mut = patternInput[1];
+            continue loop;
+          }
+          case 1: {
+            const patternInput_1 = fromRows("Run Person", rowNumber + 1, en);
+            lastRow_mut = patternInput_1[0];
+            run_mut = run;
+            performers_mut = patternInput_1[3];
+            rowNumber_mut = patternInput_1[1];
+            continue loop;
+          }
+          default:
+            if (run != null) {
+              const run_2 = value(run);
+              run_2.Performers = Array.from(performers);
+              return run_2;
+            } else {
+              return ArcRun.create(createMissingIdentifier(), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, Array.from(performers));
+            }
+        }
+      }
+  };
+  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 run metadata sheet");
+  }
+}
+function ArcRun_toRows(run) {
+  return delay(() => append(singleton(SparseRowModule_fromValues(["RUN"])), delay(() => append(toRows(run), delay(() => append(singleton(SparseRowModule_fromValues(["RUN PERFORMERS"])), delay(() => toRows$1("Run Person", ofSeq(run.Performers)))))))));
+}
+function ArcRun_toMetadataSheet(run) {
+  const sheet = new FsWorksheet("isa_run");
+  iterateIndexed((rowI, r) => {
+    SparseRowModule_writeToSheet(rowI + 1, r, sheet);
+  }, ArcRun_toRows(run));
+  return sheet;
+}
+function ArcRun_fromMetadataSheet(sheet) {
+  try {
+    return ArcRun_fromRows(map(SparseRowModule_fromFsRow, sheet.Rows));
+  } catch (err) {
+    const arg = err.message;
+    return toFail(printf("Failed while parsing metadatasheet: %s"))(arg);
+  }
+}
+function ArcRun_isMetadataSheetName(name) {
+  return name === "isa_run";
+}
+function ArcRun_isMetadataSheet(sheet) {
+  return ArcRun_isMetadataSheetName(sheet.Name);
+}
+function ArcRun_tryGetMetadataSheet(doc) {
+  return tryFind(ArcRun_isMetadataSheet, doc.GetWorksheets());
+}
+function ARCtrl_ArcRun__ArcRun_fromFsWorkbook_Static_32154C9D(doc) {
+  try {
+    let runMetadata;
+    const matchValue = ArcRun_tryGetMetadataSheet(doc);
+    if (matchValue == null) {
+      toConsole(printf('Cannot retrieve metadata: Run file does not contain "%s" sheet.'))("isa_run");
+      runMetadata = ArcRun.create(createMissingIdentifier());
+    } else {
+      runMetadata = ArcRun_fromMetadataSheet(value(matchValue));
+    }
+    const sheets = doc.GetWorksheets();
+    const annotationTables = choose(tryFromFsWorksheet, sheets);
+    const datamapSheet = tryPick(tryFromFsWorksheet$1, sheets);
+    runMetadata.DataMap = datamapSheet;
+    if (!isEmpty(annotationTables)) {
+      runMetadata.Tables = Array.from(annotationTables);
+    }
+    return runMetadata;
+  } catch (err) {
+    const arg_1 = err.message;
+    return toFail(printf("Could not parse assay: \n%s"))(arg_1);
+  }
+}
+function ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8(run) {
+  const doc = new FsWorkbook();
+  const metadataSheet = ArcRun_toMetadataSheet(run);
+  doc.AddWorksheet(metadataSheet);
+  iterateIndexed((i, arg) => {
+    const sheet = toFsWorksheet(i, arg);
+    doc.AddWorksheet(sheet);
+  }, run.Tables);
+  return doc;
+}
+
+export { ARCtrl_ArcRun__ArcRun_fromFsWorkbook_Static_32154C9D, ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8, ArcRun_fromMetadataSheet, ArcRun_fromRows, ArcRun_isMetadataSheet, ArcRun_isMetadataSheetName, ArcRun_toMetadataSheet, ArcRun_toRows, ArcRun_tryGetMetadataSheet };

package/dist/ts/ts/Spreadsheet/ArcStudy.d.ts

@@ -0,0 +1,26 @@
+import { FsWorksheet } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorksheet.fs.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { ArcAssay, ArcStudy } from '../Core/ArcTypes.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { FsWorkbook } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorkbook.fs.js';
+export declare function ArcStudy_toMetadataSheet(study: ArcStudy, assays: Option<FSharpList<ArcAssay>>): FsWorksheet;
+export declare function ArcStudy_fromRows(rows: Iterable<Iterable<[int32, string]>>): Option<[ArcStudy, FSharpList<ArcAssay>]>;
+export declare function ArcStudy_fromMetadataSheet(sheet: FsWorksheet): [ArcStudy, FSharpList<ArcAssay>];
+export declare function ArcStudy_toMetadataCollection(study: ArcStudy, assays: Option<FSharpList<ArcAssay>>): Iterable<Iterable<Option<string>>>;
+export declare function ArcStudy_fromMetadataCollection(collection: Iterable<Iterable<Option<string>>>): [ArcStudy, FSharpList<ArcAssay>];
+export declare function ArcStudy_isMetadataSheetName(name: string): boolean;
+export declare function ArcStudy_isMetadataSheet(sheet: FsWorksheet): boolean;
+export declare function ArcStudy_tryGetMetadataSheet(doc: FsWorkbook): Option<FsWorksheet>;
+/**
+ * Reads an assay from a spreadsheet
+ */
+export declare function ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(doc: FsWorkbook): [ArcStudy, FSharpList<ArcAssay>];
+/**
+ * Write a study to a spreadsheet
+ *
+ * If datamapSheet is true, the datamap will be written to a worksheet inside study workbook. Default: true
+ */
+export declare function ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(study: ArcStudy, assays?: FSharpList<ArcAssay>, datamapSheet?: boolean): FsWorkbook;
+export declare function ARCtrl_ArcStudy__ArcStudy_ToFsWorkbook_257FC1F0(this$: ArcStudy, assays: Option<FSharpList<ArcAssay>>, datamapSheet: Option<boolean>): FsWorkbook;
+//# sourceMappingURL=ArcStudy.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ArcStudy.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Spreadsheet/ArcStudy.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,gEAAgE,CAAC;AAG7F,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAE7D,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AACzD,OAAO,EAAiD,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAC9G,OAAO,EAAS,UAAU,EAAE,MAAM,qCAAqC,CAAC;AAKxE,OAAO,EAAE,UAAU,EAAE,MAAM,+DAA+D,CAAC;AAO3F,wBAAgB,wBAAwB,CAAC,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC,GAAG,WAAW,CAO3G;AAED,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,QAAQ,EAAE,UAAU,CAAC,QAAQ,CAAC,CAAC,CAAC,CAIrH;AAED,wBAAgB,0BAA0B,CAAC,KAAK,EAAE,WAAW,GAAG,CAAC,QAAQ,EAAE,UAAU,CAAC,QAAQ,CAAC,CAAC,CAQ/F;AAED,wBAAgB,6BAA6B,CAAC,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAGvI;AAED,wBAAgB,+BAA+B,CAAC,UAAU,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,EAAE,UAAU,CAAC,QAAQ,CAAC,CAAC,CAQhI;AAED,wBAAgB,4BAA4B,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAOlE;AAED,wBAAgB,wBAAwB,CAAC,KAAK,EAAE,WAAW,GAAG,OAAO,CAEpE;AAED,wBAAgB,4BAA4B,CAAC,GAAG,EAAE,UAAU,GAAG,MAAM,CAAC,WAAW,CAAC,CAEjF;AAED;;GAEG;AACH,wBAAgB,wDAAwD,CAAC,GAAG,EAAE,UAAU,GAAG,CAAC,QAAQ,EAAE,UAAU,CAAC,QAAQ,CAAC,CAAC,CAyB1H;AAED;;;;GAIG;AACH,wBAAgB,uDAAuD,CAAC,KAAK,EAAE,QAAQ,EAAE,MAAM,CAAC,EAAE,UAAU,CAAC,QAAQ,CAAC,EAAE,YAAY,CAAC,EAAE,OAAO,GAAG,UAAU,CAgB1J;AAED,wBAAgB,+CAA+C,CAAC,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC,EAAE,YAAY,EAAE,MAAM,CAAC,OAAO,CAAC,GAAG,UAAU,CAEhK"}

package/dist/ts/ts/Spreadsheet/ArcStudy.js

@@ -0,0 +1,92 @@
+import { FsWorksheet } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorksheet.fs.js';
+import { iterate, iterateIndexed, append, tryPick, tryFind, map } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { SparseRowModule_writeToSheet, SparseRowModule_fromFsRow, SparseRowModule_fromValues } from './Metadata/SparseTable.js';
+import { toRows, fromRows } from './Metadata/Study.js';
+import { ArcStudy } from '../Core/ArcTypes.js';
+import { defaultArg, toArray, value } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { empty } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { getEnumerator } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { toConsole, printf, toFail } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { createMissingIdentifier } from '../Core/Helper/Identifier.js';
+import { FsWorkbook } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorkbook.fs.js';
+import { ResizeArray_choose, ResizeArray_isEmpty } from '../Core/Helper/Collections.js';
+import { toFsWorksheet as toFsWorksheet$1, tryFromFsWorksheet } from './AnnotationTable/ArcTable.js';
+import { toFsWorksheet, tryFromFsWorksheet as tryFromFsWorksheet$1 } from './DataMapTable/DataMapTable.js';
+
+function ArcStudy_toMetadataSheet(study, assays) {
+  let source_1;
+  const sheet = new FsWorksheet("isa_study");
+  iterateIndexed((rowI, r) => {
+    SparseRowModule_writeToSheet(rowI + 1, r, sheet);
+  }, (source_1 = toRows(study, assays), append([SparseRowModule_fromValues(["STUDY"])], source_1)));
+  return sheet;
+}
+function ArcStudy_fromRows(rows) {
+  const en = getEnumerator(rows);
+  en["System.Collections.IEnumerator.MoveNext"]();
+  return fromRows(2, en)[3];
+}
+function ArcStudy_fromMetadataSheet(sheet) {
+  try {
+    return defaultArg(ArcStudy_fromRows(map(SparseRowModule_fromFsRow, sheet.Rows)), [ArcStudy.create(createMissingIdentifier()), empty()]);
+  } catch (err) {
+    const arg = err.message;
+    return toFail(printf("Failed while parsing metadatasheet: %s"))(arg);
+  }
+}
+function ArcStudy_isMetadataSheetName(name) {
+  if (name === "isa_study") {
+    return true;
+  } else {
+    return name === "Study";
+  }
+}
+function ArcStudy_isMetadataSheet(sheet) {
+  return ArcStudy_isMetadataSheetName(sheet.Name);
+}
+function ArcStudy_tryGetMetadataSheet(doc) {
+  return tryFind(ArcStudy_isMetadataSheet, doc.GetWorksheets());
+}
+function ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(doc) {
+  try {
+    let patternInput;
+    const matchValue = ArcStudy_tryGetMetadataSheet(doc);
+    if (matchValue == null) {
+      toConsole(printf('Cannot retrieve metadata: Study file does not contain "%s" or "%s" sheet.'))("isa_study")("Study");
+      patternInput = [ArcStudy.create(createMissingIdentifier()), empty()];
+    } else {
+      patternInput = ArcStudy_fromMetadataSheet(value(matchValue));
+    }
+    const studyMetadata = patternInput[0];
+    const sheets = doc.GetWorksheets();
+    const annotationTables = ResizeArray_choose(tryFromFsWorksheet, sheets);
+    const datamapSheet = tryPick(tryFromFsWorksheet$1, sheets);
+    if (!ResizeArray_isEmpty(annotationTables)) {
+      studyMetadata.Tables = annotationTables;
+    }
+    studyMetadata.DataMap = datamapSheet;
+    return [studyMetadata, patternInput[1]];
+  } catch (err) {
+    const arg_2 = err.message;
+    return toFail(printf("Could not parse study: \n%s"))(arg_2);
+  }
+}
+function ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(study, assays, datamapSheet) {
+  const datamapSheet_1 = defaultArg(datamapSheet, true);
+  const doc = new FsWorkbook();
+  const metadataSheet = ArcStudy_toMetadataSheet(study, assays);
+  doc.AddWorksheet(metadataSheet);
+  if (datamapSheet_1) {
+    iterate((arg) => {
+      const sheet = toFsWorksheet(arg);
+      doc.AddWorksheet(sheet);
+    }, toArray(study.DataMap));
+  }
+  iterateIndexed((i, arg_1) => {
+    const sheet_1 = toFsWorksheet$1(i, arg_1);
+    doc.AddWorksheet(sheet_1);
+  }, study.Tables);
+  return doc;
+}
+
+export { ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D, ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522, ArcStudy_fromMetadataSheet, ArcStudy_fromRows, ArcStudy_isMetadataSheet, ArcStudy_isMetadataSheetName, ArcStudy_toMetadataSheet, ArcStudy_tryGetMetadataSheet };

package/dist/ts/ts/Spreadsheet/ArcWorkflow.d.ts

@@ -0,0 +1,27 @@
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { ArcWorkflow } from '../Core/ArcTypes.js';
+import { FsWorksheet } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorksheet.fs.js';
+import { FsWorkbook } from '../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorkbook.fs.js';
+export declare function ArcWorkflow_fromRows(rows: Iterable<Iterable<[int32, string]>>): ArcWorkflow;
+export declare function ArcWorkflow_toRows(workflow: ArcWorkflow): Iterable<Iterable<[int32, string]>>;
+export declare function ArcWorkflow_toMetadataSheet(workflow: ArcWorkflow): FsWorksheet;
+export declare function ArcWorkflow_fromMetadataSheet(sheet: FsWorksheet): ArcWorkflow;
+export declare function ArcWorkflow_toMetadataCollection(workflow: ArcWorkflow): Iterable<Iterable<Option<string>>>;
+export declare function ArcWorkflow_fromMetadataCollection(collection: Iterable<Iterable<Option<string>>>): ArcWorkflow;
+export declare function ArcWorkflow_isMetadataSheetName(name: string): boolean;
+export declare function ArcWorkflow_isMetadataSheet(sheet: FsWorksheet): boolean;
+export declare function ArcWorkflow_tryGetMetadataSheet(doc: FsWorkbook): Option<FsWorksheet>;
+/**
+ * Reads an workflow from a spreadsheet
+ */
+export declare function ARCtrl_ArcWorkflow__ArcWorkflow_fromFsWorkbook_Static_32154C9D(doc: FsWorkbook): ArcWorkflow;
+/**
+ * Write a workflow to a spreadsheet
+ */
+export declare function ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E(workflow: ArcWorkflow): FsWorkbook;
+/**
+ * Write a workflow to a spreadsheet
+ */
+export declare function ARCtrl_ArcWorkflow__ArcWorkflow_ToFsWorkbook(this$: ArcWorkflow): FsWorkbook;
+//# sourceMappingURL=ArcWorkflow.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ArcWorkflow.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Spreadsheet/ArcWorkflow.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAE7D,OAAO,EAAS,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAGtE,OAAO,EAAmI,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAMnL,OAAO,EAAE,WAAW,EAAE,MAAM,gEAAgE,CAAC;AAG7F,OAAO,EAAE,UAAU,EAAE,MAAM,+DAA+D,CAAC;AAI3F,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,QAAQ,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,WAAW,CA8D3F;AAED,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,CAE7F;AAED,wBAAgB,2BAA2B,CAAC,QAAQ,EAAE,WAAW,GAAG,WAAW,CAM9E;AAED,wBAAgB,6BAA6B,CAAC,KAAK,EAAE,WAAW,GAAG,WAAW,CAQ7E;AAED,wBAAgB,gCAAgC,CAAC,QAAQ,EAAE,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAE1G;AAED,wBAAgB,kCAAkC,CAAC,UAAU,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,WAAW,CAQ9G;AAED,wBAAgB,+BAA+B,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAErE;AAED,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,WAAW,GAAG,OAAO,CAEvE;AAED,wBAAgB,+BAA+B,CAAC,GAAG,EAAE,UAAU,GAAG,MAAM,CAAC,WAAW,CAAC,CAEpF;AAED;;GAEG;AACH,wBAAgB,8DAA8D,CAAC,GAAG,EAAE,UAAU,GAAG,WAAW,CAkB3G;AAED;;GAEG;AACH,wBAAgB,6DAA6D,CAAC,QAAQ,EAAE,WAAW,GAAG,UAAU,CAK/G;AAED;;GAEG;AACH,wBAAgB,4CAA4C,CAAC,KAAK,EAAE,WAAW,GAAG,UAAU,CAE3F"}