@nfdi4plants/arctrl 3.0.0-beta.3 → 3.0.0-beta.4

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

@@ -0,0 +1,85 @@
+import { ofArray, length, singleton, initialize, map, empty, iterateIndexed, cons, reverse } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { Person_setOrcidFromComments, Person_setCommentFromORCID } from '../../Core/Conversion.js';
+import { OntologyAnnotation_fromAggregatedStrings, OntologyAnnotation_toAggregatedStrings } from './Conversions.js';
+import { Person } from '../../Core/Person.js';
+import { unwrap, value, 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 lastNameLabel = "Last Name";
+const firstNameLabel = "First Name";
+const midInitialsLabel = "Mid Initials";
+const emailLabel = "Email";
+const phoneLabel = "Phone";
+const faxLabel = "Fax";
+const addressLabel = "Address";
+const affiliationLabel = "Affiliation";
+const rolesLabel = "Roles";
+const rolesTermAccessionNumberLabel = "Roles Term Accession Number";
+const rolesTermSourceREFLabel = "Roles Term Source REF";
+const labels = ofArray([lastNameLabel, firstNameLabel, midInitialsLabel, emailLabel, phoneLabel, faxLabel, addressLabel, affiliationLabel, rolesLabel, rolesTermAccessionNumberLabel, rolesTermSourceREFLabel]);
+function fromString(lastName, firstName, midInitials, email, phone, fax, address, affiliation, role, rolesTermAccessionNumber, rolesTermSourceREF, comments) {
+  let roles_1;
+  return Person_setOrcidFromComments((roles_1 = OntologyAnnotation_fromAggregatedStrings(";", role, rolesTermSourceREF, rolesTermAccessionNumber), Person.make(void 0, lastName, firstName, midInitials, email, phone, fax, address, affiliation, roles_1, comments)));
+}
+function fromSparseTable(matrix) {
+  let returnVal;
+  if (matrix.ColumnCount === 0 && length(matrix.CommentKeys) !== 0) {
+    const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+    return singleton((returnVal = Person.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, [lastNameLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [firstNameLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [midInitialsLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [emailLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [phoneLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [faxLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [addressLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [affiliationLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [rolesLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [rolesTermAccessionNumberLabel, i]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [rolesTermSourceREFLabel, i]), comments_1);
+    });
+  }
+}
+function toSparseTable(persons) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, labels, void 0, length(persons) + 1);
+  let commentKeys = empty();
+  iterateIndexed((i, p) => {
+    const i_1 = i + 1 | 0;
+    const rAgg = OntologyAnnotation_toAggregatedStrings(";", Array.from(p.Roles));
+    addToDict(matrix.Matrix, [lastNameLabel, i_1], defaultArg(p.LastName, ""));
+    addToDict(matrix.Matrix, [firstNameLabel, i_1], defaultArg(p.FirstName, ""));
+    addToDict(matrix.Matrix, [midInitialsLabel, i_1], defaultArg(p.MidInitials, ""));
+    addToDict(matrix.Matrix, [emailLabel, i_1], defaultArg(p.EMail, ""));
+    addToDict(matrix.Matrix, [phoneLabel, i_1], defaultArg(p.Phone, ""));
+    addToDict(matrix.Matrix, [faxLabel, i_1], defaultArg(p.Fax, ""));
+    addToDict(matrix.Matrix, [addressLabel, i_1], defaultArg(p.Address, ""));
+    addToDict(matrix.Matrix, [affiliationLabel, i_1], defaultArg(p.Affiliation, ""));
+    addToDict(matrix.Matrix, [rolesLabel, i_1], rAgg.TermNameAgg);
+    addToDict(matrix.Matrix, [rolesTermAccessionNumberLabel, i_1], rAgg.TermAccessionNumberAgg);
+    addToDict(matrix.Matrix, [rolesTermSourceREFLabel, i_1], rAgg.TermSourceREFAgg);
+    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);
+  }, map(Person_setCommentFromORCID, persons));
+  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, unwrap(prefix));
+  return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+function toRows(prefix, persons) {
+  const m = toSparseTable(persons);
+  if (prefix == null) {
+    return SparseTable_ToRows_759CAFC1(m);
+  } else {
+    return SparseTable_ToRows_759CAFC1(m, value(prefix));
+  }
+}
+
+export { addressLabel, affiliationLabel, emailLabel, faxLabel, firstNameLabel, fromRows, fromSparseTable, fromString, labels, lastNameLabel, midInitialsLabel, phoneLabel, rolesLabel, rolesTermAccessionNumberLabel, rolesTermSourceREFLabel, toRows, toSparseTable };

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

@@ -0,0 +1,133 @@
+import { equals } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+import { some, defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { map3, fill, fold, equalsWith } from '../../../node_modules/@fable-org/fable-library-js/Array.js';
+import { toFail, printf, toText } from '../../../node_modules/@fable-org/fable-library-js/String.js';
+import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
+import { Component_fromISAString_7C9A7CF8, Component_toStringObject_Z685B8F25 } from '../../Core/Process/Component.js';
+import { empty, ofArray, fold as fold$1, map } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { Array_map4 } from '../CollectionAux.js';
+import { ResizeArray_map } from '../../Core/Helper/Collections.js';
+import { ProtocolParameter } from '../../Core/Process/ProtocolParameter.js';
+
+function Option_fromValueWithDefault(d, v) {
+  if (equals(d, v)) {
+    return void 0;
+  } else {
+    return some(v);
+  }
+}
+function OntologyAnnotation_getLengthOfAggregatedStrings(separator, strings) {
+  return fold((l, s) => {
+    if (s === "") {
+      return l | 0;
+    } else if (l === 0) {
+      return s.split(separator).length | 0;
+    } else if (l === s.split(separator).length) {
+      return l | 0;
+    } else {
+      return toFail(printf("The length of the aggregated string %s does not match the length of the others"))(s) | 0;
+    }
+  }, 0, strings);
+}
+function OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions) {
+  const l = OntologyAnnotation_getLengthOfAggregatedStrings(separator, [terms, source, accessions]) | 0;
+  if (l === 0) {
+    return [];
+  } else {
+    const collection = map3((a, b, c) => OntologyAnnotation.create(a, b, c), terms === "" ? fill(new Array(l), 0, l, "") : terms.split(separator), source === "" ? fill(new Array(l), 0, l, "") : source.split(separator), accessions === "" ? fill(new Array(l), 0, l, "") : accessions.split(separator));
+    return Array.from(collection);
+  }
+}
+function OntologyAnnotation_toAggregatedStrings(separator, oas) {
+  let first = true;
+  if (equalsWith(equals, oas, [])) {
+    return {
+      TermAccessionNumberAgg: "",
+      TermNameAgg: "",
+      TermSourceREFAgg: ""
+    };
+  } else {
+    const tupledArg_1 = fold((tupledArg, term) => {
+      const matchValue = defaultArg(term.Name, "");
+      const tsr = defaultArg(term.TermSourceREF, "");
+      const tan = defaultArg(term.TermAccessionNumber, "");
+      const name = matchValue;
+      if (first) {
+        first = false;
+        return [name, tsr, tan];
+      } else {
+        return [toText(printf("%s%c%s"))(tupledArg[0])(separator)(name), toText(printf("%s%c%s"))(tupledArg[1])(separator)(tsr), toText(printf("%s%c%s"))(tupledArg[2])(separator)(tan)];
+      }
+    }, ["", "", ""], oas);
+    return {
+      TermAccessionNumberAgg: tupledArg_1[2],
+      TermNameAgg: tupledArg_1[0],
+      TermSourceREFAgg: tupledArg_1[1]
+    };
+  }
+}
+function Component_fromAggregatedStrings(separator, names, terms, source, accessions) {
+  const l = OntologyAnnotation_getLengthOfAggregatedStrings(separator, [names, terms, source, accessions]) | 0;
+  if (l === 0) {
+    return empty();
+  } else {
+    return ofArray(Array_map4(Component_fromISAString_7C9A7CF8, names === "" ? fill(new Array(l), 0, l, "") : names.split(separator), terms === "" ? fill(new Array(l), 0, l, "") : terms.split(separator), source === "" ? fill(new Array(l), 0, l, "") : source.split(separator), accessions === "" ? fill(new Array(l), 0, l, "") : accessions.split(separator)));
+  }
+}
+function Component_toAggregatedStrings(separator, cs) {
+  let first = true;
+  if (equals(cs, empty())) {
+    return {
+      NameAgg: "",
+      TermAccessionNumberAgg: "",
+      TermNameAgg: "",
+      TermSourceREFAgg: ""
+    };
+  } else {
+    const tupledArg_2 = fold$1((tupledArg, tupledArg_1) => {
+      const name = tupledArg_1[0];
+      const term = tupledArg_1[1];
+      if (first) {
+        first = false;
+        return [name, term.TermName, term.TermSourceREF, term.TermAccessionNumber];
+      } else {
+        return [toText(printf("%s%c%s"))(tupledArg[0])(separator)(name), toText(printf("%s%c%s"))(tupledArg[1])(separator)(term.TermName), toText(printf("%s%c%s"))(tupledArg[2])(separator)(term.TermSourceREF), toText(printf("%s%c%s"))(tupledArg[3])(separator)(term.TermAccessionNumber)];
+      }
+    }, ["", "", "", ""], map(Component_toStringObject_Z685B8F25, cs));
+    return {
+      NameAgg: tupledArg_2[0],
+      TermAccessionNumberAgg: tupledArg_2[3],
+      TermNameAgg: tupledArg_2[1],
+      TermSourceREFAgg: tupledArg_2[2]
+    };
+  }
+}
+function ProtocolParameter_fromAggregatedStrings(separator, terms, source, accessions) {
+  return ResizeArray_map((arg) => ((parameterName) => ProtocolParameter.make(void 0, parameterName))(arg), OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions));
+}
+function ProtocolParameter_toAggregatedStrings(separator, oas) {
+  let first = true;
+  if (equals(oas, empty())) {
+    return {
+      TermAccessionNumberAgg: "",
+      TermNameAgg: "",
+      TermSourceREFAgg: ""
+    };
+  } else {
+    const tupledArg_1 = fold$1((tupledArg, term) => {
+      if (first) {
+        first = false;
+        return [term.TermName, term.TermSourceREF, term.TermAccessionNumber];
+      } else {
+        return [toText(printf("%s%c%s"))(tupledArg[0])(separator)(term.TermName), toText(printf("%s%c%s"))(tupledArg[1])(separator)(term.TermSourceREF), toText(printf("%s%c%s"))(tupledArg[2])(separator)(term.TermAccessionNumber)];
+      }
+    }, ["", "", ""], map((pp) => ProtocolParameter.toStringObject(pp), oas));
+    return {
+      TermAccessionNumberAgg: tupledArg_1[2],
+      TermNameAgg: tupledArg_1[0],
+      TermSourceREFAgg: tupledArg_1[1]
+    };
+  }
+}
+
+export { Component_fromAggregatedStrings, Component_toAggregatedStrings, OntologyAnnotation_fromAggregatedStrings, OntologyAnnotation_getLengthOfAggregatedStrings, OntologyAnnotation_toAggregatedStrings, Option_fromValueWithDefault, ProtocolParameter_fromAggregatedStrings, ProtocolParameter_toAggregatedStrings };

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

@@ -0,0 +1,15 @@
+import { ofArray } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { fromRows as fromRows$1, toRows as toRows$1 } from './OntologyAnnotation.js';
+
+const designTypeLabel = "Type";
+const designTypeTermAccessionNumberLabel = "Type Term Accession Number";
+const designTypeTermSourceREFLabel = "Type Term Source REF";
+ofArray([designTypeLabel, designTypeTermAccessionNumberLabel, designTypeTermSourceREFLabel]);
+function fromRows(prefix, lineNumber, rows) {
+  return fromRows$1(prefix, designTypeLabel, designTypeTermSourceREFLabel, designTypeTermAccessionNumberLabel, lineNumber, rows);
+}
+function toRows(prefix, designs) {
+  return toRows$1(prefix, designTypeLabel, designTypeTermSourceREFLabel, designTypeTermAccessionNumberLabel, designs);
+}
+
+export { designTypeLabel, designTypeTermAccessionNumberLabel, designTypeTermSourceREFLabel, fromRows, toRows };

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

@@ -0,0 +1,74 @@
+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, defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { Option_fromValueWithDefault, ResizeArray_iter } from '../../Core/Helper/Collections.js';
+import { Factor } from '../../Core/Process/Factor.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 factorTypeLabel = "Type";
+const typeTermAccessionNumberLabel = "Type Term Accession Number";
+const typeTermSourceREFLabel = "Type Term Source REF";
+const labels = ofArray([nameLabel, factorTypeLabel, typeTermAccessionNumberLabel, typeTermSourceREFLabel]);
+function fromString(name, designType, typeTermSourceREF, typeTermAccessionNumber, comments) {
+  const factorType = OntologyAnnotation.create(unwrap(designType), unwrap(typeTermSourceREF), unwrap(typeTermAccessionNumber));
+  const factorType_1 = Option_fromValueWithDefault(new OntologyAnnotation(), factorType);
+  const comments_1 = Option_fromValueWithDefault([], comments);
+  return Factor.make(name, factorType_1, comments_1);
+}
+function fromSparseTable(matrix) {
+  if (matrix.ColumnCount === 0 && length(matrix.CommentKeys) !== 0) {
+    const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+    return singleton(Factor.create(void 0, void 0, comments));
+  } 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, [nameLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [factorTypeLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermSourceREFLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermAccessionNumberLabel, i]), comments_1);
+    });
+  }
+}
+function toSparseTable(factors) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, labels, void 0, length(factors) + 1);
+  let commentKeys = empty();
+  iterateIndexed((i, f) => {
+    const i_1 = i + 1 | 0;
+    let ft;
+    const f_1 = defaultArg(f.FactorType, new OntologyAnnotation());
+    ft = OntologyAnnotation.toStringObject(f_1, true);
+    addToDict(matrix.Matrix, [nameLabel, i_1], defaultArg(f.Name, ""));
+    addToDict(matrix.Matrix, [factorTypeLabel, i_1], ft.TermName);
+    addToDict(matrix.Matrix, [typeTermAccessionNumberLabel, i_1], ft.TermAccessionNumber);
+    addToDict(matrix.Matrix, [typeTermSourceREFLabel, i_1], ft.TermSourceREF);
+    const matchValue = f.Comments;
+    if (matchValue != null) {
+      ResizeArray_iter((comment) => {
+        const patternInput = Comment_toString(comment);
+        const n = patternInput[0];
+        commentKeys = cons(n, commentKeys);
+        addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+      }, value(matchValue));
+    }
+  }, factors);
+  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, factors) {
+  const m = toSparseTable(factors);
+  {
+    return SparseTable_ToRows_759CAFC1(m, value(prefix));
+  }
+}
+
+export { factorTypeLabel, fromRows, fromSparseTable, fromString, labels, nameLabel, toRows, toSparseTable, typeTermAccessionNumberLabel, typeTermSourceREFLabel };

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

@@ -0,0 +1,58 @@
+import { ofArray, length, singleton, initialize, map, empty, iterateIndexed, cons, reverse } from '../../../node_modules/@fable-org/fable-library-js/List.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 { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
+import { Comment_fromString, Comment_toString } from './Comment.js';
+import { value, unwrap } from '../../../node_modules/@fable-org/fable-library-js/Option.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';
+
+function fromSparseTable(label, labelTSR, labelTAN, matrix) {
+  let returnVal;
+  if (matrix.ColumnCount === 0 && length(matrix.CommentKeys) !== 0) {
+    const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+    return singleton((returnVal = OntologyAnnotation.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 new OntologyAnnotation(unwrap(SparseTable__TryGetValue_11FD62A8(matrix, [label, i])), unwrap(SparseTable__TryGetValue_11FD62A8(matrix, [labelTSR, i])), unwrap(SparseTable__TryGetValue_11FD62A8(matrix, [labelTAN, i])), comments_1);
+    });
+  }
+}
+function toSparseTable(label, labelTSR, labelTAN, designs) {
+  const matrix = SparseTable_Create_Z2192E64B(void 0, ofArray([label, labelTAN, labelTSR]), void 0, length(designs) + 1);
+  let commentKeys = empty();
+  iterateIndexed((i, d) => {
+    const i_1 = i + 1 | 0;
+    const oa = OntologyAnnotation.toStringObject(d, true);
+    addToDict(matrix.Matrix, [label, i_1], oa.TermName);
+    addToDict(matrix.Matrix, [labelTAN, i_1], oa.TermAccessionNumber);
+    addToDict(matrix.Matrix, [labelTSR, i_1], oa.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]);
+    }, d.Comments);
+  }, designs);
+  return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+    Equals: (x, y) => x === y,
+    GetHashCode: stringHash
+  })), matrix.ColumnCount);
+}
+function fromRows(prefix, label, labelTSR, labelTAN, lineNumber, rows) {
+  const labels = ofArray([label, labelTAN, labelTSR]);
+  const tupledArg = SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber, value(prefix));
+  return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(label, labelTSR, labelTAN, tupledArg[3])];
+}
+function toRows(prefix, label, labelTSR, labelTAN, designs) {
+  const m = toSparseTable(label, labelTSR, labelTAN, designs);
+  {
+    return SparseTable_ToRows_759CAFC1(m, value(prefix));
+  }
+}
+
+export { fromRows, fromSparseTable, toRows, toSparseTable };

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.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.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 };