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

package/dist/ts/ts/Spreadsheet/Metadata/SparseTable.js

@@ -0,0 +1,193 @@
+import { iterate, indexed, choose, tryPick, map, tryItem, isEmpty, maxBy, length, delay, append as append$1 } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { value, map as map$1, defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { equals, comparePrimitives } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+import { Record } from '../../../node_modules/@fable-org/fable-library-js/Types.js';
+import { FsAddress } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsAddress.fs.js';
+import { exists, find, cons, empty, append, singleton, map as map$2, initialize } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { toFail, printf } from '../../../node_modules/@fable-org/fable-library-js/String.js';
+import { FsRangeAddress } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/Ranges/FsRangeAddress.fs.js';
+import { Seq_trySkip, Dictionary_tryGetValue } from '../CollectionAux.js';
+import { getItemFromDict, addToDict } from '../../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+import { Dictionary_init } from '../../Core/Helper/Collections.js';
+import { Remark, Comment$ } from '../../Core/Comment.js';
+import { Comment_$007CComment$007C_$007C, Remark_$007CRemark$007C_$007C, Comment_wrapCommentKey } from './Comment.js';
+
+function SparseRowModule_fromValues(v) {
+  return indexed(v);
+}
+function SparseRowModule_fromFsRow(r) {
+  return choose((c) => {
+    if (equals(c.Value, "")) {
+      return void 0;
+    } else {
+      return [c.ColumnNumber - 1, c.ValueAsString()];
+    }
+  }, r.Cells);
+}
+function SparseRowModule_tryGetValueAt(i, vs) {
+  return tryPick((tupledArg) => {
+    if (tupledArg[0] === i) {
+      return tupledArg[1];
+    } else {
+      return void 0;
+    }
+  }, vs);
+}
+function SparseRowModule_writeToSheet(rowI, row, sheet) {
+  const fsRow = sheet.RowWithRange(new FsRangeAddress(new FsAddress(rowI, 1), new FsAddress(rowI, 1)), true);
+  iterate((tupledArg) => {
+    const v = tupledArg[1];
+    if (v.trim() !== "") {
+      fsRow.Item(tupledArg[0] + 1).SetValueAs(v);
+    }
+  }, row);
+}
+class SparseTable extends Record {
+  constructor(Matrix, Keys, CommentKeys, ColumnCount) {
+    super();
+    this.Matrix = Matrix;
+    this.Keys = Keys;
+    this.CommentKeys = CommentKeys;
+    this.ColumnCount = ColumnCount | 0;
+  }
+}
+function SparseTable__TryGetValue_11FD62A8(this$, key) {
+  return Dictionary_tryGetValue(key, this$.Matrix);
+}
+function SparseTable__TryGetValueDefault_5BAE6133(this$, defaultValue, key) {
+  if (this$.Matrix.has(key)) {
+    return getItemFromDict(this$.Matrix, key);
+  } else {
+    return defaultValue;
+  }
+}
+function SparseTable_Create_Z2192E64B(matrix, keys, commentKeys, length) {
+  return new SparseTable(defaultArg(matrix, Dictionary_init()), defaultArg(keys, empty()), defaultArg(commentKeys, empty()), defaultArg(length, 0));
+}
+function SparseTable_AddRow(key, values, matrix) {
+  iterate((tupledArg) => {
+    addToDict(matrix.Matrix, [key, tupledArg[0]], tupledArg[1]);
+  }, values);
+  const length = (isEmpty(values) ? 0 : 1 + maxBy((tuple) => tuple[0], values, {
+    Compare: comparePrimitives
+  })[0]) | 0;
+  return new SparseTable(matrix.Matrix, append(matrix.Keys, singleton(key)), matrix.CommentKeys, length > matrix.ColumnCount ? length : matrix.ColumnCount);
+}
+function SparseTable_AddEmptyComment(key, matrix) {
+  return new SparseTable(matrix.Matrix, matrix.Keys, append(matrix.CommentKeys, singleton(key)), matrix.ColumnCount);
+}
+function SparseTable_AddComment(key, values, matrix) {
+  if (length(values) === 0) {
+    return SparseTable_AddEmptyComment(key, matrix);
+  } else {
+    iterate((tupledArg) => {
+      addToDict(matrix.Matrix, [key, tupledArg[0]], tupledArg[1]);
+    }, values);
+    const length = (isEmpty(values) ? 0 : 1 + maxBy((tuple) => tuple[0], values, {
+      Compare: comparePrimitives
+    })[0]) | 0;
+    return new SparseTable(matrix.Matrix, matrix.Keys, append(matrix.CommentKeys, singleton(key)), length > matrix.ColumnCount ? length : matrix.ColumnCount);
+  }
+}
+function SparseTable_FromRows_Z5579EC29(en, labels, lineNumber, prefix) {
+  try {
+    const prefix_1 = prefix == null ? "" : value(prefix) + " ";
+    const loop = (matrix_mut, remarks_mut, lineNumber_1_mut) => {
+      let v_2, k_1;
+      loop:
+        while (true) {
+          const matrix = matrix_mut, remarks = remarks_mut, lineNumber_1 = lineNumber_1_mut;
+          if (en["System.Collections.IEnumerator.MoveNext"]()) {
+            const row = map((tupledArg) => [tupledArg[0] - 1, tupledArg[1]], en["System.Collections.Generic.IEnumerator`1.get_Current"]());
+            const matchValue = map$1((tuple) => tuple[1], tryItem(0, row));
+            const vals = Seq_trySkip(1, row);
+            const key = matchValue;
+            let matchResult, k, v_1;
+            if (key != null) {
+              const activePatternResult = Comment_$007CComment$007C_$007C(value(key));
+              if (activePatternResult != null) {
+                if (vals != null) {
+                  matchResult = 0;
+                  k = value(activePatternResult);
+                  v_1 = value(vals);
+                } else {
+                  matchResult = 1;
+                }
+              } else {
+                matchResult = 1;
+              }
+            } else {
+              matchResult = 1;
+            }
+            switch (matchResult) {
+              case 0: {
+                matrix_mut = SparseTable_AddComment(k, v_1, matrix);
+                remarks_mut = remarks;
+                lineNumber_1_mut = lineNumber_1 + 1;
+                continue loop;
+              }
+              default: {
+                let matchResult_1, k_2, k_3, v_3, k_4;
+                const activePatternResult_1 = Remark_$007CRemark$007C_$007C(key);
+                if (activePatternResult_1 != null) {
+                  matchResult_1 = 0;
+                  k_2 = value(activePatternResult_1);
+                } else if (key != null) {
+                  if (vals != null) {
+                    if (v_2 = value(vals), k_1 = value(key), exists((label) => k_1 === prefix_1 + label, labels)) {
+                      matchResult_1 = 1;
+                      k_3 = value(key);
+                      v_3 = value(vals);
+                    } else {
+                      matchResult_1 = 2;
+                      k_4 = value(key);
+                    }
+                  } else {
+                    matchResult_1 = 2;
+                    k_4 = value(key);
+                  }
+                } else {
+                  matchResult_1 = 3;
+                }
+                switch (matchResult_1) {
+                  case 0: {
+                    matrix_mut = matrix;
+                    remarks_mut = cons(Remark.make(lineNumber_1, k_2), remarks);
+                    lineNumber_1_mut = lineNumber_1 + 1;
+                    continue loop;
+                  }
+                  case 1: {
+                    matrix_mut = SparseTable_AddRow(find((label_1) => k_3 === prefix_1 + label_1, labels), v_3, matrix);
+                    remarks_mut = remarks;
+                    lineNumber_1_mut = lineNumber_1 + 1;
+                    continue loop;
+                  }
+                  case 2:
+                    return [k_4, lineNumber_1, remarks, matrix];
+                  default:
+                    return [void 0, lineNumber_1, remarks, matrix];
+                }
+              }
+            }
+          } else {
+            return [void 0, lineNumber_1, remarks, matrix];
+          }
+          break;
+        }
+    };
+    return loop(SparseTable_Create_Z2192E64B(), empty(), lineNumber);
+  } catch (err) {
+    const arg_1 = err.message;
+    return toFail(printf("Error parsing block in investigation file starting from line number %i: %s"))(lineNumber)(arg_1);
+  }
+}
+function SparseTable_ToRows_759CAFC1(matrix, prefix) {
+  const prefix_1 = prefix == null ? "" : value(prefix) + " ";
+  return delay(() => append$1(map((key) => SparseRowModule_fromValues(cons(prefix_1 + key, initialize(matrix.ColumnCount - 1, (i) => SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [key, i + 1])))), matrix.Keys), delay(() => map((key_1) => SparseRowModule_fromValues(cons(Comment_wrapCommentKey(key_1), initialize(matrix.ColumnCount - 1, (i_1) => SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [key_1, i_1 + 1])))), matrix.CommentKeys))));
+}
+function SparseTable_GetEmptyComments_3ECCA699(matrix) {
+  const collection = map$2((key) => Comment$.create(key), matrix.CommentKeys);
+  return Array.from(collection);
+}
+
+export { SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt, SparseRowModule_writeToSheet, SparseTable, SparseTable_AddComment, SparseTable_AddEmptyComment, SparseTable_AddRow, SparseTable_Create_Z2192E64B, SparseTable_FromRows_Z5579EC29, SparseTable_GetEmptyComments_3ECCA699, SparseTable_ToRows_759CAFC1, SparseTable__TryGetValueDefault_5BAE6133, SparseTable__TryGetValue_11FD62A8 };

package/dist/ts/ts/Spreadsheet/Metadata/Study.d.ts

@@ -0,0 +1,38 @@
+import { Record } from '@fable-org/fable-library-js/Types.js';
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { Remark, Comment$ } from '../../Core/Comment.js';
+import { IEnumerator, IEquatable } from '@fable-org/fable-library-js/Util.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { SparseTable } from './SparseTable.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { ArcAssay, ArcStudy } from '../../Core/ArcTypes.js';
+import { Publication } from '../../Core/Publication.js';
+import { Person } from '../../Core/Person.js';
+import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
+import { Factor } from '../../Core/Process/Factor.js';
+import { Protocol } from '../../Core/Process/Protocol.js';
+export declare class StudyInfo extends Record implements IEquatable<StudyInfo> {
+    readonly Identifier: string;
+    readonly Title: string;
+    readonly Description: string;
+    readonly SubmissionDate: string;
+    readonly PublicReleaseDate: string;
+    readonly FileName: string;
+    readonly Comments: FSharpList<Comment$>;
+    constructor(Identifier: string, Title: string, Description: string, SubmissionDate: string, PublicReleaseDate: string, FileName: string, Comments: FSharpList<Comment$>);
+}
+export declare function StudyInfo_$reflection(): TypeInfo;
+export declare function StudyInfo_create(identifier: string, title: string, description: string, submissionDate: string, publicReleaseDate: string, fileName: string, comments: FSharpList<Comment$>): StudyInfo;
+export declare function StudyInfo_get_Labels(): FSharpList<string>;
+export declare function StudyInfo_FromSparseTable_3ECCA699(matrix: SparseTable): StudyInfo;
+export declare function StudyInfo_ToSparseTable_1680536E(study: ArcStudy): SparseTable;
+export declare function StudyInfo_fromRows(lineNumber: int32, rows: IEnumerator<Iterable<[int32, string]>>): [Option<string>, int32, FSharpList<Remark>, StudyInfo];
+export declare function StudyInfo_toRows_1680536E(study: ArcStudy): Iterable<Iterable<[int32, string]>>;
+/**
+ * FACTORS AND PROTOCOLS ARE NOT USED ANYMORE, Lukas, 21.03.24
+ */
+export declare function fromParts(studyInfo: StudyInfo, designDescriptors: FSharpList<OntologyAnnotation>, publications: FSharpList<Publication>, factors: FSharpList<Factor>, assays: FSharpList<ArcAssay>, protocols: FSharpList<Protocol>, contacts: FSharpList<Person>): Option<[ArcStudy, FSharpList<ArcAssay>]>;
+export declare function fromRows(lineNumber: int32, en: IEnumerator<Iterable<[int32, string]>>): [Option<string>, int32, FSharpList<Remark>, Option<[ArcStudy, FSharpList<ArcAssay>]>];
+export declare function toRows(study: ArcStudy, assays: Option<FSharpList<ArcAssay>>): Iterable<Iterable<[int32, string]>>;
+//# sourceMappingURL=Study.d.ts.map

package/dist/ts/ts/Spreadsheet/Metadata/Study.d.ts.map

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

@@ -0,0 +1,238 @@
+import { Record } from '../../../node_modules/@fable-org/fable-library-js/Types.js';
+import { ofSeq, empty, append, ofArray, map, cons, reverse } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { defaultArg, value } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { stringHash } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+import { collect, delay, append as append$1, singleton } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { Comment_fromString, Comment_toString } from './Comment.js';
+import { SparseTable_FromRows_Z5579EC29, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_ToRows_759CAFC1, SparseTable_Create_Z2192E64B, SparseTable, SparseRowModule_fromValues } from './SparseTable.js';
+import { createMissingIdentifier, Study_fileNameFromIdentifier } from '../../Core/Helper/Identifier.js';
+import { addToDict } from '../../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+import { Option_fromValueWithDefault, ResizeArray_iter } from '../../Core/Helper/Collections.js';
+import { List_distinct } from '../../../node_modules/@fable-org/fable-library-js/Seq2.js';
+import { ArcStudy } from '../../Core/ArcTypes.js';
+import { fromRows as fromRows$6, toRows as toRows$1 } from './DesignDescriptors.js';
+import { fromRows as fromRows$5, toRows as toRows$2 } from './Publication.js';
+import { fromRows as fromRows$4, toRows as toRows$3 } from './Factors.js';
+import { fromRows as fromRows$3, toRows as toRows$4 } from './Assays.js';
+import { fromRows as fromRows$2, toRows as toRows$5 } from './Protocols.js';
+import { fromRows as fromRows$1, toRows as toRows$6 } from './Contacts.js';
+import { ARCtrl_ArcTable__ArcTable_GetProtocols, ARCtrl_ArcTable__ArcTable_GetProcesses } from '../../Core/Conversion.js';
+import { getFactors } from '../../Core/Process/ProcessSequence.js';
+
+class StudyInfo extends Record {
+  constructor(Identifier, Title, Description, SubmissionDate, PublicReleaseDate, FileName, Comments) {
+    super();
+    this.Identifier = Identifier;
+    this.Title = Title;
+    this.Description = Description;
+    this.SubmissionDate = SubmissionDate;
+    this.PublicReleaseDate = PublicReleaseDate;
+    this.FileName = FileName;
+    this.Comments = Comments;
+  }
+}
+function StudyInfo_create(identifier, title, description, submissionDate, publicReleaseDate, fileName, comments) {
+  return new StudyInfo(identifier, title, description, submissionDate, publicReleaseDate, fileName, comments);
+}
+function StudyInfo_get_Labels() {
+  return ofArray(["Study Identifier", "Study Title", "Study Description", "Study Submission Date", "Study Public Release Date", "Study File Name"]);
+}
+function StudyInfo_FromSparseTable_3ECCA699(matrix) {
+  const comments = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, 0])), matrix.CommentKeys);
+  return StudyInfo_create(SparseTable__TryGetValueDefault_5BAE6133(matrix, createMissingIdentifier(), ["Study Identifier", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study Title", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study Description", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study Submission Date", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study Public Release Date", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study File Name", 0]), comments);
+}
+function StudyInfo_ToSparseTable_1680536E(study) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, StudyInfo_get_Labels(), void 0, 2);
+  let commentKeys = empty();
+  const patternInput = study.Identifier.startsWith("MISSING_IDENTIFIER_") ? ["", ""] : [study.Identifier, Study_fileNameFromIdentifier(study.Identifier)];
+  addToDict(matrix.Matrix, ["Study Identifier", 1], patternInput[0]);
+  addToDict(matrix.Matrix, ["Study Title", 1], defaultArg(study.Title, ""));
+  addToDict(matrix.Matrix, ["Study Description", 1], defaultArg(study.Description, ""));
+  addToDict(matrix.Matrix, ["Study Submission Date", 1], defaultArg(study.SubmissionDate, ""));
+  addToDict(matrix.Matrix, ["Study Public Release Date", 1], defaultArg(study.PublicReleaseDate, ""));
+  addToDict(matrix.Matrix, ["Study File Name", 1], patternInput[1]);
+  ResizeArray_iter((comment) => {
+    const patternInput_1 = Comment_toString(comment);
+    const n = patternInput_1[0];
+    commentKeys = cons(n, commentKeys);
+    addToDict(matrix.Matrix, [n, 1], patternInput_1[1]);
+  }, study.Comments);
+  return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+    Equals: (x, y) => x === y,
+    GetHashCode: stringHash
+  })), matrix.ColumnCount);
+}
+function StudyInfo_fromRows(lineNumber, rows) {
+  const tupledArg = SparseTable_FromRows_Z5579EC29(rows, StudyInfo_get_Labels(), lineNumber);
+  return [tupledArg[0], tupledArg[1], tupledArg[2], StudyInfo_FromSparseTable_3ECCA699(tupledArg[3])];
+}
+function StudyInfo_toRows_1680536E(study) {
+  return SparseTable_ToRows_759CAFC1(StudyInfo_ToSparseTable_1680536E(study));
+}
+function fromParts(studyInfo, designDescriptors, publications, factors, assays, protocols, contacts) {
+  const assayIdentifiers = map((assay) => assay.Identifier, assays);
+  let arcstudy;
+  const title = Option_fromValueWithDefault("", studyInfo.Title);
+  const description = Option_fromValueWithDefault("", studyInfo.Description);
+  const submissionDate = Option_fromValueWithDefault("", studyInfo.SubmissionDate);
+  const publicReleaseDate = Option_fromValueWithDefault("", studyInfo.PublicReleaseDate);
+  const publications_1 = Array.from(publications);
+  const contacts_1 = Array.from(contacts);
+  const studyDesignDescriptors = Array.from(designDescriptors);
+  const registeredAssayIdentifiers = Array.from(assayIdentifiers);
+  const comments = Array.from(studyInfo.Comments);
+  arcstudy = ArcStudy.make(studyInfo.Identifier, title, description, submissionDate, publicReleaseDate, publications_1, contacts_1, studyDesignDescriptors, [], void 0, registeredAssayIdentifiers, comments);
+  if (arcstudy.isEmpty && arcstudy.Identifier === "") {
+    return void 0;
+  } else {
+    return [arcstudy, assays];
+  }
+}
+function fromRows(lineNumber, en) {
+  const loop = (lastLine_mut, studyInfo_mut, designDescriptors_mut, publications_mut, factors_mut, assays_mut, protocols_mut, contacts_mut, remarks_mut, lineNumber_1_mut) => {
+    loop:
+      while (true) {
+        const lastLine = lastLine_mut, studyInfo = studyInfo_mut, designDescriptors = designDescriptors_mut, publications = publications_mut, factors = factors_mut, assays = assays_mut, protocols = protocols_mut, contacts = contacts_mut, remarks = remarks_mut, lineNumber_1 = lineNumber_1_mut;
+        let matchResult, k_12;
+        if (lastLine != null) {
+          switch (value(lastLine)) {
+            case "STUDY DESIGN DESCRIPTORS": {
+              matchResult = 0;
+              value(lastLine);
+              break;
+            }
+            case "STUDY PUBLICATIONS": {
+              matchResult = 1;
+              value(lastLine);
+              break;
+            }
+            case "STUDY FACTORS": {
+              matchResult = 2;
+              value(lastLine);
+              break;
+            }
+            case "STUDY ASSAYS": {
+              matchResult = 3;
+              value(lastLine);
+              break;
+            }
+            case "STUDY PROTOCOLS": {
+              matchResult = 4;
+              value(lastLine);
+              break;
+            }
+            case "STUDY CONTACTS": {
+              matchResult = 5;
+              value(lastLine);
+              break;
+            }
+            default: {
+              matchResult = 6;
+              k_12 = lastLine;
+            }
+          }
+        } else {
+          matchResult = 6;
+          k_12 = lastLine;
+        }
+        switch (matchResult) {
+          case 0: {
+            const patternInput = fromRows$6("Study Design", lineNumber_1 + 1, en);
+            lastLine_mut = patternInput[0];
+            studyInfo_mut = studyInfo;
+            designDescriptors_mut = patternInput[3];
+            publications_mut = publications;
+            factors_mut = factors;
+            assays_mut = assays;
+            protocols_mut = protocols;
+            contacts_mut = contacts;
+            remarks_mut = append(remarks, patternInput[2]);
+            lineNumber_1_mut = patternInput[1];
+            continue loop;
+          }
+          case 1: {
+            const patternInput_1 = fromRows$5("Study Publication", lineNumber_1 + 1, en);
+            lastLine_mut = patternInput_1[0];
+            studyInfo_mut = studyInfo;
+            designDescriptors_mut = designDescriptors;
+            publications_mut = patternInput_1[3];
+            factors_mut = factors;
+            assays_mut = assays;
+            protocols_mut = protocols;
+            contacts_mut = contacts;
+            remarks_mut = append(remarks, patternInput_1[2]);
+            lineNumber_1_mut = patternInput_1[1];
+            continue loop;
+          }
+          case 2: {
+            const patternInput_2 = fromRows$4("Study Factor", lineNumber_1 + 1, en);
+            lastLine_mut = patternInput_2[0];
+            studyInfo_mut = studyInfo;
+            designDescriptors_mut = designDescriptors;
+            publications_mut = publications;
+            factors_mut = patternInput_2[3];
+            assays_mut = assays;
+            protocols_mut = protocols;
+            contacts_mut = contacts;
+            remarks_mut = append(remarks, patternInput_2[2]);
+            lineNumber_1_mut = patternInput_2[1];
+            continue loop;
+          }
+          case 3: {
+            const patternInput_3 = fromRows$3("Study Assay", lineNumber_1 + 1, en);
+            lastLine_mut = patternInput_3[0];
+            studyInfo_mut = studyInfo;
+            designDescriptors_mut = designDescriptors;
+            publications_mut = publications;
+            factors_mut = factors;
+            assays_mut = patternInput_3[3];
+            protocols_mut = protocols;
+            contacts_mut = contacts;
+            remarks_mut = append(remarks, patternInput_3[2]);
+            lineNumber_1_mut = patternInput_3[1];
+            continue loop;
+          }
+          case 4: {
+            const patternInput_4 = fromRows$2("Study Protocol", lineNumber_1 + 1, en);
+            lastLine_mut = patternInput_4[0];
+            studyInfo_mut = studyInfo;
+            designDescriptors_mut = designDescriptors;
+            publications_mut = publications;
+            factors_mut = factors;
+            assays_mut = assays;
+            protocols_mut = patternInput_4[3];
+            contacts_mut = contacts;
+            remarks_mut = append(remarks, patternInput_4[2]);
+            lineNumber_1_mut = patternInput_4[1];
+            continue loop;
+          }
+          case 5: {
+            const patternInput_5 = fromRows$1("Study Person", lineNumber_1 + 1, en);
+            lastLine_mut = patternInput_5[0];
+            studyInfo_mut = studyInfo;
+            designDescriptors_mut = designDescriptors;
+            publications_mut = publications;
+            factors_mut = factors;
+            assays_mut = assays;
+            protocols_mut = protocols;
+            contacts_mut = patternInput_5[3];
+            remarks_mut = append(remarks, patternInput_5[2]);
+            lineNumber_1_mut = patternInput_5[1];
+            continue loop;
+          }
+          default:
+            return [k_12, lineNumber_1, remarks, fromParts(studyInfo, designDescriptors, publications, factors, assays, protocols, contacts)];
+        }
+      }
+  };
+  const patternInput_6 = StudyInfo_fromRows(lineNumber, en);
+  return loop(patternInput_6[0], patternInput_6[3], empty(), empty(), empty(), empty(), empty(), empty(), patternInput_6[2], patternInput_6[1]);
+}
+function toRows(study, assays) {
+  const protocols = ofSeq(collect(ARCtrl_ArcTable__ArcTable_GetProtocols, study.Tables));
+  const factors = ofSeq(collect((f) => getFactors(ARCtrl_ArcTable__ArcTable_GetProcesses(f)), study.Tables));
+  const assays_1 = defaultArg(assays, ofSeq(study.GetRegisteredAssaysOrIdentifier()));
+  return delay(() => append$1(StudyInfo_toRows_1680536E(study), delay(() => append$1(singleton(SparseRowModule_fromValues(["STUDY DESIGN DESCRIPTORS"])), delay(() => append$1(toRows$1("Study Design", ofSeq(study.StudyDesignDescriptors)), delay(() => append$1(singleton(SparseRowModule_fromValues(["STUDY PUBLICATIONS"])), delay(() => append$1(toRows$2("Study Publication", ofSeq(study.Publications)), delay(() => append$1(singleton(SparseRowModule_fromValues(["STUDY FACTORS"])), delay(() => append$1(toRows$3("Study Factor", factors), delay(() => append$1(singleton(SparseRowModule_fromValues(["STUDY ASSAYS"])), delay(() => append$1(toRows$4("Study Assay", assays_1), delay(() => append$1(singleton(SparseRowModule_fromValues(["STUDY PROTOCOLS"])), delay(() => append$1(toRows$5("Study Protocol", protocols), delay(() => append$1(singleton(SparseRowModule_fromValues(["STUDY CONTACTS"])), delay(() => toRows$6("Study Person", ofSeq(study.Contacts)))))))))))))))))))))))))));
+}
+
+export { StudyInfo, StudyInfo_FromSparseTable_3ECCA699, StudyInfo_ToSparseTable_1680536E, StudyInfo_create, StudyInfo_fromRows, StudyInfo_get_Labels, StudyInfo_toRows_1680536E, fromParts, fromRows, toRows };

package/dist/ts/ts/Spreadsheet/Metadata/Workflow.d.ts

@@ -0,0 +1,31 @@
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { ArcWorkflow } from '../../Core/ArcTypes.js';
+import { Remark, Comment$ } from '../../Core/Comment.js';
+import { SparseTable } from './SparseTable.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { IEnumerator } from '@fable-org/fable-library-js/Util.js';
+export declare const identifierLabel = "Identifier";
+export declare const titleLabel = "Title";
+export declare const descriptionLabel = "Description";
+export declare const workflowTypeLabel = "Type";
+export declare const typeTermAccessionNumberLabel = "Type Term Accession Number";
+export declare const typeTermSourceREFLabel = "Type Term Source REF";
+export declare const subWorkflowIdentifiersLabel = "Sub Workflow Identifiers";
+export declare const uriLabel = "URI";
+export declare const versionLabel = "Version";
+export declare const parametersNameLabel = "Parameters Name";
+export declare const parametersTermAccessionNumberLabel = "Parameters Term Accession Number";
+export declare const parametersTermSourceREFLabel = "Parameters Term Source REF";
+export declare const componentsNameLabel = "Components Name";
+export declare const componentsTypeLabel = "Components Type";
+export declare const componentsTypeTermAccessionNumberLabel = "Components Type Term Accession Number";
+export declare const componentsTypeTermSourceREFLabel = "Components Type Term Source REF";
+export declare const fileNameLabel = "File Name";
+export declare const labels: FSharpList<string>;
+export declare function fromString(identifier: Option<string>, title: Option<string>, description: Option<string>, workflowType: Option<string>, workflowTypeTermAccessionNumber: Option<string>, workflowTypeTermSourceREF: Option<string>, subworkflowIdentifiers: Option<string>, uri: Option<string>, version: Option<string>, parametersName: string, parametersTermAccessionNumber: string, parametersTermSourceREF: string, componentsName: string, componentsType: string, componentsTypeTermAccessionNumber: string, componentsTypeTermSourceREF: string, fileName: Option<string>, comments: Comment$[]): ArcWorkflow;
+export declare function fromSparseTable(matrix: SparseTable): ArcWorkflow;
+export declare function toSparseTable(workflow: ArcWorkflow): SparseTable;
+export declare function fromRows(lineNumber: int32, rows: IEnumerator<Iterable<[int32, string]>>): [Option<string>, int32, FSharpList<Remark>, ArcWorkflow];
+export declare function toRows(workflow: ArcWorkflow): Iterable<Iterable<[int32, string]>>;
+//# sourceMappingURL=Workflow.d.ts.map

package/dist/ts/ts/Spreadsheet/Metadata/Workflow.d.ts.map

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

@@ -0,0 +1,105 @@
+import { ofArray, map, empty, ofSeq, cons, reverse } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { value, unwrap, defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { map as map$1 } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
+import { Option_fromValueWithDefault, ResizeArray_iter } from '../../Core/Helper/Collections.js';
+import { ProtocolParameter_fromAggregatedStrings, Component_fromAggregatedStrings, ProtocolParameter_toAggregatedStrings, Component_toAggregatedStrings } from './Conversions.js';
+import { ArcWorkflow_make, ArcWorkflow__get_Identifier, ArcWorkflow__get_WorkflowType, ArcWorkflow__get_Parameters, ArcWorkflow__get_Components, ArcWorkflow__get_SubWorkflowIdentifiers, ArcWorkflow__get_Title, ArcWorkflow__get_Description, ArcWorkflow__get_URI, ArcWorkflow__get_Version, ArcWorkflow__get_Comments } from '../../Core/ArcTypes.js';
+import { createMissingIdentifier, Workflow_tryIdentifierFromFileName, Workflow_fileNameFromIdentifier } from '../../Core/Helper/Identifier.js';
+import { Comment_fromString, Comment_toString } from './Comment.js';
+import { SparseTable_FromRows_Z5579EC29, SparseTable__TryGetValueDefault_5BAE6133, SparseTable__TryGetValue_11FD62A8, SparseTable_ToRows_759CAFC1, SparseTable_Create_Z2192E64B, SparseTable } from './SparseTable.js';
+import { join } from '../../../node_modules/@fable-org/fable-library-js/String.js';
+import { addToDict } from '../../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+import { List_distinct } from '../../../node_modules/@fable-org/fable-library-js/Seq2.js';
+import { stringHash } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+
+const identifierLabel = "Identifier";
+const titleLabel = "Title";
+const descriptionLabel = "Description";
+const workflowTypeLabel = "Type";
+const typeTermAccessionNumberLabel = "Type Term Accession Number";
+const typeTermSourceREFLabel = "Type Term Source REF";
+const subWorkflowIdentifiersLabel = "Sub Workflow Identifiers";
+const uriLabel = "URI";
+const versionLabel = "Version";
+const parametersNameLabel = "Parameters Name";
+const parametersTermAccessionNumberLabel = "Parameters Term Accession Number";
+const parametersTermSourceREFLabel = "Parameters Term Source REF";
+const componentsNameLabel = "Components Name";
+const componentsTypeLabel = "Components Type";
+const componentsTypeTermAccessionNumberLabel = "Components Type Term Accession Number";
+const componentsTypeTermSourceREFLabel = "Components Type Term Source REF";
+const fileNameLabel = "File Name";
+const labels = ofArray([identifierLabel, titleLabel, descriptionLabel, workflowTypeLabel, typeTermAccessionNumberLabel, typeTermSourceREFLabel, subWorkflowIdentifiersLabel, uriLabel, versionLabel, parametersNameLabel, parametersTermAccessionNumberLabel, parametersTermSourceREFLabel, componentsNameLabel, componentsTypeLabel, componentsTypeTermAccessionNumberLabel, componentsTypeTermSourceREFLabel, fileNameLabel]);
+function fromString(identifier, title, description, workflowType, workflowTypeTermAccessionNumber, workflowTypeTermSourceREF, subworkflowIdentifiers, uri, version, parametersName, parametersTermAccessionNumber, parametersTermSourceREF, componentsName, componentsType, componentsTypeTermAccessionNumber, componentsTypeTermSourceREF, fileName, comments) {
+  let matchValue;
+  let subworkflowIdentifiers_2;
+  if (subworkflowIdentifiers == null) {
+    subworkflowIdentifiers_2 = [];
+  } else {
+    const subworkflowIdentifiers_1 = value(subworkflowIdentifiers);
+    const collection = map$1((s) => s.trim(), subworkflowIdentifiers_1.split(";"));
+    subworkflowIdentifiers_2 = Array.from(collection);
+  }
+  let workflowType_1;
+  const v = OntologyAnnotation.create(unwrap(workflowType), unwrap(workflowTypeTermSourceREF), unwrap(workflowTypeTermAccessionNumber));
+  workflowType_1 = Option_fromValueWithDefault(new OntologyAnnotation(), v);
+  let parameters;
+  const collection_1 = ProtocolParameter_fromAggregatedStrings(";", parametersName, parametersTermSourceREF, parametersTermAccessionNumber);
+  parameters = Array.from(collection_1);
+  let components;
+  const collection_2 = Component_fromAggregatedStrings(";", componentsName, componentsType, componentsTypeTermSourceREF, componentsTypeTermAccessionNumber);
+  components = Array.from(collection_2);
+  return ArcWorkflow_make(identifier == null ? fileName == null ? createMissingIdentifier() : (matchValue = Workflow_tryIdentifierFromFileName(value(fileName)), matchValue != null ? value(matchValue) : createMissingIdentifier()) : value(identifier), title, description, workflowType_1, uri, version, subworkflowIdentifiers_2, parameters, components, void 0, [], comments);
+}
+function fromSparseTable(matrix) {
+  const comments = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, 0])), matrix.CommentKeys);
+  return fromString(SparseTable__TryGetValue_11FD62A8(matrix, [identifierLabel, 0]), SparseTable__TryGetValue_11FD62A8(matrix, [titleLabel, 0]), SparseTable__TryGetValue_11FD62A8(matrix, [descriptionLabel, 0]), SparseTable__TryGetValue_11FD62A8(matrix, [workflowTypeLabel, 0]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermAccessionNumberLabel, 0]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermSourceREFLabel, 0]), SparseTable__TryGetValue_11FD62A8(matrix, [subWorkflowIdentifiersLabel, 0]), SparseTable__TryGetValue_11FD62A8(matrix, [uriLabel, 0]), SparseTable__TryGetValue_11FD62A8(matrix, [versionLabel, 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [parametersNameLabel, 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [parametersTermAccessionNumberLabel, 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [parametersTermSourceREFLabel, 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [componentsNameLabel, 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [componentsTypeLabel, 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [componentsTypeTermAccessionNumberLabel, 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [componentsTypeTermSourceREFLabel, 0]), SparseTable__TryGetValue_11FD62A8(matrix, [fileNameLabel, 0]), Array.from(comments));
+}
+function toSparseTable(workflow) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, labels, void 0, 2);
+  let commentKeys = empty();
+  const patternInput = ArcWorkflow__get_Identifier(workflow).startsWith("MISSING_IDENTIFIER_") ? ["", ""] : [ArcWorkflow__get_Identifier(workflow), Workflow_fileNameFromIdentifier(ArcWorkflow__get_Identifier(workflow))];
+  let wt;
+  const tt = defaultArg(ArcWorkflow__get_WorkflowType(workflow), new OntologyAnnotation());
+  wt = OntologyAnnotation.toStringObject(tt, true);
+  const pAgg = ProtocolParameter_toAggregatedStrings(";", ofSeq(ArcWorkflow__get_Parameters(workflow)));
+  const cAgg = Component_toAggregatedStrings(";", ofSeq(ArcWorkflow__get_Components(workflow)));
+  const subWorkflowsAgg = join(";", ArcWorkflow__get_SubWorkflowIdentifiers(workflow));
+  addToDict(matrix.Matrix, [identifierLabel, 1], patternInput[0]);
+  addToDict(matrix.Matrix, [titleLabel, 1], defaultArg(ArcWorkflow__get_Title(workflow), ""));
+  addToDict(matrix.Matrix, [descriptionLabel, 1], defaultArg(ArcWorkflow__get_Description(workflow), ""));
+  addToDict(matrix.Matrix, [workflowTypeLabel, 1], wt.TermName);
+  addToDict(matrix.Matrix, [typeTermAccessionNumberLabel, 1], wt.TermAccessionNumber);
+  addToDict(matrix.Matrix, [typeTermSourceREFLabel, 1], wt.TermSourceREF);
+  addToDict(matrix.Matrix, [subWorkflowIdentifiersLabel, 1], subWorkflowsAgg);
+  addToDict(matrix.Matrix, [uriLabel, 1], defaultArg(ArcWorkflow__get_URI(workflow), ""));
+  addToDict(matrix.Matrix, [versionLabel, 1], defaultArg(ArcWorkflow__get_Version(workflow), ""));
+  addToDict(matrix.Matrix, [parametersNameLabel, 1], pAgg.TermNameAgg);
+  addToDict(matrix.Matrix, [parametersTermAccessionNumberLabel, 1], pAgg.TermAccessionNumberAgg);
+  addToDict(matrix.Matrix, [parametersTermSourceREFLabel, 1], pAgg.TermSourceREFAgg);
+  addToDict(matrix.Matrix, [componentsNameLabel, 1], cAgg.NameAgg);
+  addToDict(matrix.Matrix, [componentsTypeLabel, 1], cAgg.TermNameAgg);
+  addToDict(matrix.Matrix, [componentsTypeTermAccessionNumberLabel, 1], cAgg.TermAccessionNumberAgg);
+  addToDict(matrix.Matrix, [componentsTypeTermSourceREFLabel, 1], cAgg.TermSourceREFAgg);
+  addToDict(matrix.Matrix, [fileNameLabel, 1], patternInput[1]);
+  ResizeArray_iter((comment) => {
+    const patternInput_1 = Comment_toString(comment);
+    const n = patternInput_1[0];
+    commentKeys = cons(n, commentKeys);
+    addToDict(matrix.Matrix, [n, 1], patternInput_1[1]);
+  }, ArcWorkflow__get_Comments(workflow));
+  return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+    Equals: (x, y) => x === y,
+    GetHashCode: stringHash
+  })), matrix.ColumnCount);
+}
+function fromRows(lineNumber, rows) {
+  const tupledArg = SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber, "Workflow");
+  return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(workflow) {
+  return SparseTable_ToRows_759CAFC1(toSparseTable(workflow), "Workflow");
+}
+
+export { componentsNameLabel, componentsTypeLabel, componentsTypeTermAccessionNumberLabel, componentsTypeTermSourceREFLabel, descriptionLabel, fileNameLabel, fromRows, fromSparseTable, fromString, identifierLabel, labels, parametersNameLabel, parametersTermAccessionNumberLabel, parametersTermSourceREFLabel, subWorkflowIdentifiersLabel, titleLabel, toRows, toSparseTable, typeTermAccessionNumberLabel, typeTermSourceREFLabel, uriLabel, versionLabel, workflowTypeLabel };

package/dist/ts/ts/Template.Web.d.ts

@@ -0,0 +1,11 @@
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { Async } from '@fable-org/fable-library-js/AsyncBuilder.js';
+import { Template } from './Core/Template.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+export declare function getTemplates(url: Option<string>): Async<Template[]>;
+export declare class WebController {
+    constructor();
+    static getTemplates(url: Option<string>): Promise<Template[]>;
+}
+export declare function WebController_$reflection(): TypeInfo;
+//# sourceMappingURL=Template.Web.d.ts.map

package/dist/ts/ts/Template.Web.d.ts.map

@@ -0,0 +1 @@
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