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

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

@@ -0,0 +1,62 @@
+import { ofArray, length, singleton, initialize, map, empty, iterateIndexed, cons, reverse } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { OntologySourceReference } from '../../Core/OntologySourceReference.js';
+import { defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { SparseTable_FromRows_Z5579EC29, SparseTable_GetEmptyComments_3ECCA699, SparseTable__TryGetValueDefault_5BAE6133, SparseTable__TryGetValue_11FD62A8, SparseTable_ToRows_759CAFC1, SparseTable_Create_Z2192E64B, SparseTable } from './SparseTable.js';
+import { Comment_fromString, Comment_toString } from './Comment.js';
+import { addToDict } from '../../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+import { ResizeArray_iter } from '../../Core/Helper/Collections.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 nameLabel = "Term Source Name";
+const fileLabel = "Term Source File";
+const versionLabel = "Term Source Version";
+const descriptionLabel = "Term Source Description";
+const labels = ofArray([nameLabel, fileLabel, versionLabel, descriptionLabel]);
+function fromString(description, file, name, version, comments) {
+  return OntologySourceReference.make(description, file, name, version, comments);
+}
+function fromSparseTable(matrix) {
+  let returnVal;
+  if (matrix.ColumnCount === 0 && length(matrix.CommentKeys) !== 0) {
+    const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+    return singleton((returnVal = OntologySourceReference.create(), returnVal.Comments = comments, returnVal));
+  } else {
+    return initialize(matrix.ColumnCount, (i) => {
+      let comments_1;
+      const collection = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys);
+      comments_1 = Array.from(collection);
+      return fromString(SparseTable__TryGetValue_11FD62A8(matrix, [descriptionLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [fileLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [nameLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [versionLabel, i]), comments_1);
+    });
+  }
+}
+function toSparseTable(ontologySources) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, labels, void 0, length(ontologySources) + 1);
+  let commentKeys = empty();
+  iterateIndexed((i, o) => {
+    const i_1 = i + 1 | 0;
+    addToDict(matrix.Matrix, [nameLabel, i_1], defaultArg(o.Name, ""));
+    addToDict(matrix.Matrix, [fileLabel, i_1], defaultArg(o.File, ""));
+    addToDict(matrix.Matrix, [versionLabel, i_1], defaultArg(o.Version, ""));
+    addToDict(matrix.Matrix, [descriptionLabel, i_1], defaultArg(o.Description, ""));
+    ResizeArray_iter((comment) => {
+      const patternInput = Comment_toString(comment);
+      const n = patternInput[0];
+      commentKeys = cons(n, commentKeys);
+      addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+    }, o.Comments);
+  }, ontologySources);
+  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);
+  return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(termSources) {
+  return SparseTable_ToRows_759CAFC1(toSparseTable(termSources));
+}
+
+export { descriptionLabel, fileLabel, fromRows, fromSparseTable, fromString, labels, nameLabel, toRows, toSparseTable, versionLabel };

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

@@ -0,0 +1,28 @@
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { Protocol } from '../../Core/Process/Protocol.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 nameLabel = "Name";
+export declare const protocolTypeLabel = "Type";
+export declare const typeTermAccessionNumberLabel = "Type Term Accession Number";
+export declare const typeTermSourceREFLabel = "Type Term Source REF";
+export declare const descriptionLabel = "Description";
+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 labels: FSharpList<string>;
+export declare function fromString(name: Option<string>, protocolType: Option<string>, typeTermAccessionNumber: Option<string>, typeTermSourceREF: Option<string>, description: Option<string>, uri: Option<string>, version: Option<string>, parametersName: string, parametersTermAccessionNumber: string, parametersTermSourceREF: string, componentsName: string, componentsType: string, componentsTypeTermAccessionNumber: string, componentsTypeTermSourceREF: string, comments: FSharpList<Comment$>): Protocol;
+export declare function fromSparseTable(matrix: SparseTable): FSharpList<Protocol>;
+export declare function toSparseTable(protocols: FSharpList<Protocol>): SparseTable;
+export declare function fromRows(prefix: Option<string>, lineNumber: int32, rows: IEnumerator<Iterable<[int32, string]>>): [Option<string>, int32, FSharpList<Remark>, FSharpList<Protocol>];
+export declare function toRows(prefix: Option<string>, protocols: FSharpList<Protocol>): Iterable<Iterable<[int32, string]>>;
+//# sourceMappingURL=Protocols.d.ts.map

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

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

@@ -0,0 +1,94 @@
+import { ofArray, length, singleton, ofSeq, initialize, map, empty, iterateIndexed, iterate, cons, reverse } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
+import { value, unwrap, map as map$1, defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { ProtocolParameter_fromAggregatedStrings, Component_fromAggregatedStrings, Option_fromValueWithDefault, ProtocolParameter_toAggregatedStrings, Component_toAggregatedStrings } from './Conversions.js';
+import { Protocol_create_Z414665E7, Protocol_make } from '../../Core/Process/Protocol.js';
+import { URIModule_fromString } from '../../Core/URI.js';
+import { SparseTable_FromRows_Z5579EC29, SparseTable_GetEmptyComments_3ECCA699, SparseTable__TryGetValueDefault_5BAE6133, SparseTable__TryGetValue_11FD62A8, SparseTable_ToRows_759CAFC1, SparseTable_Create_Z2192E64B, SparseTable } from './SparseTable.js';
+import { Comment_fromString, Comment_toString } from './Comment.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 nameLabel = "Name";
+const protocolTypeLabel = "Type";
+const typeTermAccessionNumberLabel = "Type Term Accession Number";
+const typeTermSourceREFLabel = "Type Term Source REF";
+const descriptionLabel = "Description";
+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 labels = ofArray([nameLabel, protocolTypeLabel, typeTermAccessionNumberLabel, typeTermSourceREFLabel, descriptionLabel, uriLabel, versionLabel, parametersNameLabel, parametersTermAccessionNumberLabel, parametersTermSourceREFLabel, componentsNameLabel, componentsTypeLabel, componentsTypeTermAccessionNumberLabel, componentsTypeTermSourceREFLabel]);
+function fromString(name, protocolType, typeTermAccessionNumber, typeTermSourceREF, description, uri, version, parametersName, parametersTermAccessionNumber, parametersTermSourceREF, componentsName, componentsType, componentsTypeTermAccessionNumber, componentsTypeTermSourceREF, comments) {
+  const protocolType_1 = OntologyAnnotation.create(unwrap(protocolType), unwrap(typeTermSourceREF), unwrap(typeTermAccessionNumber));
+  const parameters = ofSeq(ProtocolParameter_fromAggregatedStrings(";", parametersName, parametersTermSourceREF, parametersTermAccessionNumber));
+  const components = Component_fromAggregatedStrings(";", componentsName, componentsType, componentsTypeTermSourceREF, componentsTypeTermAccessionNumber);
+  return Protocol_make(void 0, map$1(URIModule_fromString, name), Option_fromValueWithDefault(new OntologyAnnotation(), protocolType_1), description, map$1(URIModule_fromString, uri), version, Option_fromValueWithDefault(empty(), parameters), Option_fromValueWithDefault(empty(), components), Option_fromValueWithDefault(empty(), comments));
+}
+function fromSparseTable(matrix) {
+  if (matrix.ColumnCount === 0 && length(matrix.CommentKeys) !== 0) {
+    return singleton(Protocol_create_Z414665E7(void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, ofSeq(SparseTable_GetEmptyComments_3ECCA699(matrix))));
+  } else {
+    return initialize(matrix.ColumnCount, (i) => {
+      const comments_1 = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys);
+      return fromString(SparseTable__TryGetValue_11FD62A8(matrix, [nameLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [protocolTypeLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermAccessionNumberLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermSourceREFLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [descriptionLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [uriLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [versionLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [parametersNameLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [parametersTermAccessionNumberLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [parametersTermSourceREFLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [componentsNameLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [componentsTypeLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [componentsTypeTermAccessionNumberLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [componentsTypeTermSourceREFLabel, i]), comments_1);
+    });
+  }
+}
+function toSparseTable(protocols) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, labels, void 0, length(protocols) + 1);
+  let commentKeys = empty();
+  iterateIndexed((i, p) => {
+    const i_1 = i + 1 | 0;
+    let pt_1;
+    const pt = defaultArg(p.ProtocolType, new OntologyAnnotation());
+    pt_1 = OntologyAnnotation.toStringObject(pt, true);
+    const pAgg = ProtocolParameter_toAggregatedStrings(";", defaultArg(p.Parameters, empty()));
+    const cAgg = Component_toAggregatedStrings(";", defaultArg(p.Components, empty()));
+    addToDict(matrix.Matrix, [nameLabel, i_1], defaultArg(p.Name, ""));
+    addToDict(matrix.Matrix, [protocolTypeLabel, i_1], pt_1.TermName);
+    addToDict(matrix.Matrix, [typeTermAccessionNumberLabel, i_1], pt_1.TermAccessionNumber);
+    addToDict(matrix.Matrix, [typeTermSourceREFLabel, i_1], pt_1.TermSourceREF);
+    addToDict(matrix.Matrix, [descriptionLabel, i_1], defaultArg(p.Description, ""));
+    addToDict(matrix.Matrix, [uriLabel, i_1], defaultArg(p.Uri, ""));
+    addToDict(matrix.Matrix, [versionLabel, i_1], defaultArg(p.Version, ""));
+    addToDict(matrix.Matrix, [parametersNameLabel, i_1], pAgg.TermNameAgg);
+    addToDict(matrix.Matrix, [parametersTermAccessionNumberLabel, i_1], pAgg.TermAccessionNumberAgg);
+    addToDict(matrix.Matrix, [parametersTermSourceREFLabel, i_1], pAgg.TermSourceREFAgg);
+    addToDict(matrix.Matrix, [componentsNameLabel, i_1], cAgg.NameAgg);
+    addToDict(matrix.Matrix, [componentsTypeLabel, i_1], cAgg.TermNameAgg);
+    addToDict(matrix.Matrix, [componentsTypeTermAccessionNumberLabel, i_1], cAgg.TermAccessionNumberAgg);
+    addToDict(matrix.Matrix, [componentsTypeTermSourceREFLabel, i_1], cAgg.TermSourceREFAgg);
+    const matchValue = p.Comments;
+    if (matchValue != null) {
+      iterate((comment) => {
+        const patternInput = Comment_toString(comment);
+        const n = patternInput[0];
+        commentKeys = cons(n, commentKeys);
+        addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+      }, value(matchValue));
+    }
+  }, protocols);
+  return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+    Equals: (x, y) => x === y,
+    GetHashCode: stringHash
+  })), matrix.ColumnCount);
+}
+function fromRows(prefix, lineNumber, rows) {
+  const tupledArg = SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber, value(prefix));
+  return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(prefix, protocols) {
+  const m = toSparseTable(protocols);
+  {
+    return SparseTable_ToRows_759CAFC1(m, value(prefix));
+  }
+}
+
+export { componentsNameLabel, componentsTypeLabel, componentsTypeTermAccessionNumberLabel, componentsTypeTermSourceREFLabel, descriptionLabel, fromRows, fromSparseTable, fromString, labels, nameLabel, parametersNameLabel, parametersTermAccessionNumberLabel, parametersTermSourceREFLabel, protocolTypeLabel, toRows, toSparseTable, typeTermAccessionNumberLabel, typeTermSourceREFLabel, uriLabel, versionLabel };

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

@@ -0,0 +1,21 @@
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { Publication } from '../../Core/Publication.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 pubMedIDLabel = "PubMed ID";
+export declare const doiLabel = "DOI";
+export declare const authorListLabel = "Author List";
+export declare const titleLabel = "Title";
+export declare const statusLabel = "Status";
+export declare const statusTermAccessionNumberLabel = "Status Term Accession Number";
+export declare const statusTermSourceREFLabel = "Status Term Source REF";
+export declare const labels: FSharpList<string>;
+export declare function fromString(pubMedID: Option<string>, doi: Option<string>, author: Option<string>, title: Option<string>, status: Option<string>, statusTermSourceREF: Option<string>, statusTermAccessionNumber: Option<string>, comments: Comment$[]): Publication;
+export declare function fromSparseTable(matrix: SparseTable): FSharpList<Publication>;
+export declare function toSparseTable(publications: FSharpList<Publication>): SparseTable;
+export declare function fromRows(prefix: Option<string>, lineNumber: int32, rows: IEnumerator<Iterable<[int32, string]>>): [Option<string>, int32, FSharpList<Remark>, FSharpList<Publication>];
+export declare function toRows(prefix: Option<string>, publications: FSharpList<Publication>): Iterable<Iterable<[int32, string]>>;
+//# sourceMappingURL=Publication.d.ts.map

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

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

@@ -0,0 +1,81 @@
+import { ofArray, length, singleton, initialize, map, empty, iterateIndexed, cons, reverse } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
+import { value, unwrap, map as map$1, defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { URIModule_fromString } from '../../Core/URI.js';
+import { Option_fromValueWithDefault, ResizeArray_iter } from '../../Core/Helper/Collections.js';
+import { Publication } from '../../Core/Publication.js';
+import { SparseTable_FromRows_Z5579EC29, SparseTable_GetEmptyComments_3ECCA699, SparseTable__TryGetValueDefault_5BAE6133, SparseTable__TryGetValue_11FD62A8, SparseTable_ToRows_759CAFC1, SparseTable_Create_Z2192E64B, SparseTable } from './SparseTable.js';
+import { Comment_fromString, Comment_toString } from './Comment.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 pubMedIDLabel = "PubMed ID";
+const doiLabel = "DOI";
+const authorListLabel = "Author List";
+const titleLabel = "Title";
+const statusLabel = "Status";
+const statusTermAccessionNumberLabel = "Status Term Accession Number";
+const statusTermSourceREFLabel = "Status Term Source REF";
+const labels = ofArray([pubMedIDLabel, doiLabel, authorListLabel, titleLabel, statusLabel, statusTermAccessionNumberLabel, statusTermSourceREFLabel]);
+function fromString(pubMedID, doi, author, title, status, statusTermSourceREF, statusTermAccessionNumber, comments) {
+  const status_1 = new OntologyAnnotation(unwrap(status), unwrap(statusTermSourceREF), unwrap(statusTermAccessionNumber));
+  const pubMedID_1 = map$1(URIModule_fromString, pubMedID);
+  const status_2 = Option_fromValueWithDefault(new OntologyAnnotation(), status_1);
+  return Publication.make(pubMedID_1, doi, author, title, status_2, comments);
+}
+function fromSparseTable(matrix) {
+  let returnVal;
+  if (matrix.ColumnCount === 0 && length(matrix.CommentKeys) !== 0) {
+    const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+    return singleton((returnVal = Publication.create(), returnVal.Comments = comments, returnVal));
+  } else {
+    return initialize(matrix.ColumnCount, (i) => {
+      let comments_1;
+      const collection = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys);
+      comments_1 = Array.from(collection);
+      return fromString(SparseTable__TryGetValue_11FD62A8(matrix, [pubMedIDLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [doiLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [authorListLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [titleLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [statusLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [statusTermSourceREFLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [statusTermAccessionNumberLabel, i]), comments_1);
+    });
+  }
+}
+function toSparseTable(publications) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, labels, void 0, length(publications) + 1);
+  let commentKeys = empty();
+  iterateIndexed((i, p) => {
+    const i_1 = i + 1 | 0;
+    let s_1;
+    const s = defaultArg(p.Status, new OntologyAnnotation());
+    s_1 = OntologyAnnotation.toStringObject(s, true);
+    addToDict(matrix.Matrix, [pubMedIDLabel, i_1], defaultArg(p.PubMedID, ""));
+    addToDict(matrix.Matrix, [doiLabel, i_1], defaultArg(p.DOI, ""));
+    addToDict(matrix.Matrix, [authorListLabel, i_1], defaultArg(p.Authors, ""));
+    addToDict(matrix.Matrix, [titleLabel, i_1], defaultArg(p.Title, ""));
+    addToDict(matrix.Matrix, [statusLabel, i_1], s_1.TermName);
+    addToDict(matrix.Matrix, [statusTermAccessionNumberLabel, i_1], s_1.TermAccessionNumber);
+    addToDict(matrix.Matrix, [statusTermSourceREFLabel, i_1], s_1.TermSourceREF);
+    ResizeArray_iter((comment) => {
+      const patternInput = Comment_toString(comment);
+      const n = patternInput[0];
+      commentKeys = cons(n, commentKeys);
+      addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+    }, p.Comments);
+  }, publications);
+  return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+    Equals: (x, y) => x === y,
+    GetHashCode: stringHash
+  })), matrix.ColumnCount);
+}
+function fromRows(prefix, lineNumber, rows) {
+  const tupledArg = prefix == null ? SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber) : SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber, value(prefix));
+  return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(prefix, publications) {
+  const m = toSparseTable(publications);
+  if (prefix == null) {
+    return SparseTable_ToRows_759CAFC1(m);
+  } else {
+    return SparseTable_ToRows_759CAFC1(m, value(prefix));
+  }
+}
+
+export { authorListLabel, doiLabel, fromRows, fromSparseTable, fromString, labels, pubMedIDLabel, statusLabel, statusTermAccessionNumberLabel, statusTermSourceREFLabel, titleLabel, toRows, toSparseTable };

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

@@ -0,0 +1,14 @@
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { ArcRun } 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 labels: FSharpList<string>;
+export declare function fromString(identifier: Option<string>, title: Option<string>, description: Option<string>, workflowIdentifiers: Option<string>, measurementType: Option<string>, measurementTypeTermSourceREF: Option<string>, measurementTypeTermAccessionNumber: Option<string>, technologyType: Option<string>, technologyTypeTermSourceREF: Option<string>, technologyTypeTermAccessionNumber: Option<string>, technologyPlatform: Option<string>, fileName: Option<string>, comments: Comment$[]): ArcRun;
+export declare function fromSparseTable(matrix: SparseTable): ArcRun;
+export declare function toSparseTable(run: ArcRun): SparseTable;
+export declare function fromRows(lineNumber: int32, rows: IEnumerator<Iterable<[int32, string]>>): [Option<string>, int32, FSharpList<Remark>, ArcRun];
+export declare function toRows(run: ArcRun): Iterable<Iterable<[int32, string]>>;
+//# sourceMappingURL=Run.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"Run.d.ts","sourceRoot":"","sources":["../../../../../src/ARCtrl/ts/Spreadsheet/Metadata/Run.ts"],"names":[],"mappings":"AAAA,OAAO,EAAsC,UAAU,EAAW,MAAM,qCAAqC,CAAC;AAC9G,OAAO,EAAmB,MAAM,EAAiB,MAAM,uCAAuC,CAAC;AAK/F,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAChD,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,uBAAuB,CAAC;AAEzD,OAAO,EAA6F,WAAW,EAA+E,MAAM,kBAAkB,CAAC;AACvN,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAI7D,OAAO,EAAE,WAAW,EAAc,MAAM,qCAAqC,CAAC;AAE9E,eAAO,MAAM,MAAM,EAAE,UAAU,CAAC,MAAM,CAAgT,CAAC;AAEvV,wBAAgB,UAAU,CAAC,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,WAAW,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,mBAAmB,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,eAAe,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,4BAA4B,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,kCAAkC,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,cAAc,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,2BAA2B,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,iCAAiC,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,kBAAkB,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,MAAM,CA6B7e;AAED,wBAAgB,eAAe,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,CAK3D;AAED,wBAAgB,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAiCtD;AAED,wBAAgB,QAAQ,CAAC,UAAU,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,UAAU,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC,CAG7I;AAED,wBAAgB,MAAM,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,CAEvE"}

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

@@ -0,0 +1,91 @@
+import { ofArray, map, empty, cons, reverse } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { value, unwrap, map as map$1, defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
+import { createMissingIdentifier, Assay_tryIdentifierFromFileName, Run_fileNameFromIdentifier } from '../../Core/Helper/Identifier.js';
+import { Option_fromValueWithDefault, ResizeArray_iter } from '../../Core/Helper/Collections.js';
+import { JsonTypes_decomposeTechnologyPlatform, JsonTypes_composeTechnologyPlatform } from '../../Core/Conversion.js';
+import { ArcRun } from '../../Core/ArcTypes.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 labels = ofArray(["Identifier", "Title", "Description", "Workflow Identifiers", "Measurement Type", "Measurement Type Term Accession Number", "Measurement Type Term Source REF", "Technology Type", "Technology Type Term Accession Number", "Technology Type Term Source REF", "Technology Platform", "File Name"]);
+function fromString(identifier, title, description, workflowIdentifiers, measurementType, measurementTypeTermSourceREF, measurementTypeTermAccessionNumber, technologyType, technologyTypeTermSourceREF, technologyTypeTermAccessionNumber, technologyPlatform, fileName, comments) {
+  let workflowIdentifiers_1;
+  if (workflowIdentifiers == null) {
+    workflowIdentifiers_1 = [];
+  } else {
+    const wi = value(workflowIdentifiers);
+    const collection = wi.split(";");
+    workflowIdentifiers_1 = Array.from(collection);
+  }
+  const measurementType_1 = OntologyAnnotation.create(unwrap(measurementType), unwrap(measurementTypeTermSourceREF), unwrap(measurementTypeTermAccessionNumber));
+  const technologyType_1 = OntologyAnnotation.create(unwrap(technologyType), unwrap(technologyTypeTermSourceREF), unwrap(technologyTypeTermAccessionNumber));
+  let identifier_4;
+  if (identifier == null) {
+    if (fileName == null) {
+      identifier_4 = createMissingIdentifier();
+    } else {
+      const matchValue = Assay_tryIdentifierFromFileName(value(fileName));
+      identifier_4 = matchValue != null ? value(matchValue) : createMissingIdentifier();
+    }
+  } else {
+    identifier_4 = value(identifier);
+  }
+  const measurementType_2 = Option_fromValueWithDefault(new OntologyAnnotation(), measurementType_1);
+  const technologyType_2 = Option_fromValueWithDefault(new OntologyAnnotation(), technologyType_1);
+  const technologyPlatform_1 = map$1(JsonTypes_decomposeTechnologyPlatform, technologyPlatform);
+  return ArcRun.make(identifier_4, title, description, measurementType_2, technologyType_2, technologyPlatform_1, workflowIdentifiers_1, [], void 0, [], comments);
+}
+function fromSparseTable(matrix) {
+  let comments;
+  const collection = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, 0])), matrix.CommentKeys);
+  comments = Array.from(collection);
+  return fromString(SparseTable__TryGetValue_11FD62A8(matrix, ["Identifier", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Title", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Description", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Workflow Identifiers", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Measurement Type", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Measurement Type Term Source REF", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Measurement Type Term Accession Number", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Technology Type", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Technology Type Term Source REF", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Technology Type Term Accession Number", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["Technology Platform", 0]), SparseTable__TryGetValue_11FD62A8(matrix, ["File Name", 0]), comments);
+}
+function toSparseTable(run) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, labels, void 0, 2);
+  let commentKeys = empty();
+  const patternInput = run.Identifier.startsWith("MISSING_IDENTIFIER_") ? ["", ""] : [run.Identifier, Run_fileNameFromIdentifier(run.Identifier)];
+  const workflowIdentifiers = join(";", run.WorkflowIdentifiers);
+  let mt_1;
+  const mt = defaultArg(run.MeasurementType, new OntologyAnnotation());
+  mt_1 = OntologyAnnotation.toStringObject(mt, true);
+  let tt_1;
+  const tt = defaultArg(run.TechnologyType, new OntologyAnnotation());
+  tt_1 = OntologyAnnotation.toStringObject(tt, true);
+  addToDict(matrix.Matrix, ["Identifier", 1], patternInput[0]);
+  addToDict(matrix.Matrix, ["Title", 1], defaultArg(run.Title, ""));
+  addToDict(matrix.Matrix, ["Description", 1], defaultArg(run.Description, ""));
+  addToDict(matrix.Matrix, ["Workflow Identifiers", 1], workflowIdentifiers);
+  addToDict(matrix.Matrix, ["Measurement Type", 1], mt_1.TermName);
+  addToDict(matrix.Matrix, ["Measurement Type Term Accession Number", 1], mt_1.TermAccessionNumber);
+  addToDict(matrix.Matrix, ["Measurement Type Term Source REF", 1], mt_1.TermSourceREF);
+  addToDict(matrix.Matrix, ["Technology Type", 1], tt_1.TermName);
+  addToDict(matrix.Matrix, ["Technology Type Term Accession Number", 1], tt_1.TermAccessionNumber);
+  addToDict(matrix.Matrix, ["Technology Type Term Source REF", 1], tt_1.TermSourceREF);
+  addToDict(matrix.Matrix, ["Technology Platform", 1], defaultArg(map$1(JsonTypes_composeTechnologyPlatform, run.TechnologyPlatform), ""));
+  addToDict(matrix.Matrix, ["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]);
+  }, run.Comments);
+  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, "Run");
+  return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(run) {
+  return SparseTable_ToRows_759CAFC1(toSparseTable(run), "Run");
+}
+
+export { fromRows, fromSparseTable, fromString, labels, toRows, toSparseTable };

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

@@ -0,0 +1,37 @@
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { IEnumerator, IEquatable, IMap } from '@fable-org/fable-library-js/Util.js';
+import { FsRow } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsRow.fs.js';
+import { RowElement_$union } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/DSL/Types.fs.js';
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { FsWorksheet } from '../../fable_modules/FsSpreadsheet.7.0.0-alpha.1/FsWorksheet.fs.js';
+import { Record } from '@fable-org/fable-library-js/Types.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { Comment$, Remark } from '../../Core/Comment.js';
+export declare function SparseRowModule_fromValues(v: Iterable<string>): Iterable<[int32, string]>;
+export declare function SparseRowModule_getValues(i: Iterable<[int32, string]>): Iterable<string>;
+export declare function SparseRowModule_fromAllValues(v: Iterable<Option<string>>): Iterable<[int32, string]>;
+export declare function SparseRowModule_getAllValues(i: Iterable<[int32, string]>): Iterable<Option<string>>;
+export declare function SparseRowModule_fromFsRow(r: FsRow): Iterable<[int32, string]>;
+export declare function SparseRowModule_tryGetValueAt(i: int32, vs: Iterable<[int32, string]>): Option<string>;
+export declare function SparseRowModule_toDSLRow(vs: Iterable<[int32, string]>): FSharpList<RowElement_$union>;
+export declare function SparseRowModule_readFromSheet(sheet: FsWorksheet): Iterable<Iterable<[int32, string]>>;
+export declare function SparseRowModule_writeToSheet(rowI: int32, row: Iterable<[int32, string]>, sheet: FsWorksheet): void;
+export declare class SparseTable extends Record implements IEquatable<SparseTable> {
+    readonly Matrix: IMap<[string, int32], string>;
+    readonly Keys: FSharpList<string>;
+    readonly CommentKeys: FSharpList<string>;
+    readonly ColumnCount: int32;
+    constructor(Matrix: IMap<[string, int32], string>, Keys: FSharpList<string>, CommentKeys: FSharpList<string>, ColumnCount: int32);
+}
+export declare function SparseTable_$reflection(): TypeInfo;
+export declare function SparseTable__TryGetValue_11FD62A8(this$: SparseTable, key: [string, int32]): Option<string>;
+export declare function SparseTable__TryGetValueDefault_5BAE6133(this$: SparseTable, defaultValue: string, key: [string, int32]): string;
+export declare function SparseTable_Create_Z2192E64B(matrix?: IMap<[string, int32], string>, keys?: FSharpList<string>, commentKeys?: FSharpList<string>, length?: int32): SparseTable;
+export declare function SparseTable_AddRow(key: string, values: Iterable<[int32, string]>, matrix: SparseTable): SparseTable;
+export declare function SparseTable_AddEmptyComment(key: string, matrix: SparseTable): SparseTable;
+export declare function SparseTable_AddComment(key: string, values: Iterable<[int32, string]>, matrix: SparseTable): SparseTable;
+export declare function SparseTable_FromRows_Z5579EC29(en: IEnumerator<Iterable<[int32, string]>>, labels: FSharpList<string>, lineNumber: int32, prefix?: string): [Option<string>, int32, FSharpList<Remark>, SparseTable];
+export declare function SparseTable_ToRows_759CAFC1(matrix: SparseTable, prefix?: string): Iterable<Iterable<[int32, string]>>;
+export declare function SparseTable_GetEmptyComments_3ECCA699(matrix: SparseTable): Comment$[];
+//# sourceMappingURL=SparseTable.d.ts.map

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

@@ -0,0 +1 @@
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