@nfdi4plants/arctrl 1.0.0-alpha6

package/ISA/ISA.Spreadsheet/Metadata/Contacts.js

@@ -0,0 +1,104 @@
+import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { OntologyAnnotation_toAggregatedStrings, OntologyAnnotation_fromAggregatedStrings, Option_fromValueWithDefault } from "./Conversions.js";
+import { Person } from "../../ISA/JsonTypes/Person.js";
+import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { unwrap, defaultArg } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+
+export const lastNameLabel = "Last Name";
+
+export const firstNameLabel = "First Name";
+
+export const midInitialsLabel = "Mid Initials";
+
+export const emailLabel = "Email";
+
+export const phoneLabel = "Phone";
+
+export const faxLabel = "Fax";
+
+export const addressLabel = "Address";
+
+export const affiliationLabel = "Affiliation";
+
+export const rolesLabel = "Roles";
+
+export const rolesTermAccessionNumberLabel = "Roles Term Accession Number";
+
+export const rolesTermSourceREFLabel = "Roles Term Source REF";
+
+export const labels = ofArray([lastNameLabel, firstNameLabel, midInitialsLabel, emailLabel, phoneLabel, faxLabel, addressLabel, affiliationLabel, rolesLabel, rolesTermAccessionNumberLabel, rolesTermSourceREFLabel]);
+
+export function fromString(lastName, firstName, midInitials, email, phone, fax, address, affiliation, role, rolesTermAccessionNumber, rolesTermSourceREF, comments) {
+    let arg_12;
+    const arg_10 = Option_fromValueWithDefault([], OntologyAnnotation_fromAggregatedStrings(";", role, rolesTermSourceREF, rolesTermAccessionNumber));
+    const arg_11 = Option_fromValueWithDefault([], comments);
+    arg_12 = Person.make(void 0, void 0, lastName, firstName, midInitials, email, phone, fax, address, affiliation, arg_10, arg_11);
+    return Person.setOrcidFromComments(arg_12);
+}
+
+export function fromSparseTable(matrix) {
+    if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
+        const comments = SparseTable_GetEmptyComments_651559CC(matrix);
+        return singleton(Person.create(void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, comments));
+    }
+    else {
+        return initialize(matrix.ColumnCount, (i) => {
+            const comments_1 = toArray(map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys));
+            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);
+        });
+    }
+}
+
+export 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(";", defaultArg(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);
+        const matchValue = p.Comments;
+        if (matchValue != null) {
+            const array = matchValue;
+            array.forEach((comment) => {
+                const patternInput = Comment_toString(comment);
+                const n = patternInput[0];
+                commentKeys = cons(n, commentKeys);
+                addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+            });
+        }
+    }, map((arg) => Person.setCommentFromORCID(arg), persons));
+    return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    })), matrix.ColumnCount);
+}
+
+export 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])];
+}
+
+export function toRows(prefix, persons) {
+    const m = toSparseTable(persons);
+    if (prefix == null) {
+        return SparseTable_ToRows_6A3D4534(m);
+    }
+    else {
+        return SparseTable_ToRows_6A3D4534(m, prefix);
+    }
+}
+

package/ISA/ISA.Spreadsheet/Metadata/Conversions.js

@@ -0,0 +1,180 @@
+import { equals } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { value, some } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { map, equalsWith, fill, map3, fold } from "../../../fable_modules/fable-library.4.1.4/Array.js";
+import { toText, printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
+import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
+import { map as map_1, fold as fold_1, ofArray, empty } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { Array_map4 } from "../CollectionAux.js";
+import { Component_toString_Z609B8895, Component_fromString_Z61E08C1 } from "../../ISA/JsonTypes/Component.js";
+import { ProtocolParameter_toString_Z3A4310A5, ProtocolParameter_make } from "../../ISA/JsonTypes/ProtocolParameter.js";
+
+/**
+ * If the value matches the default, a None is returned, else a Some is returned
+ */
+export function Option_fromValueWithDefault(d, v) {
+    if (equals(d, v)) {
+        return void 0;
+    }
+    else {
+        return some(v);
+    }
+}
+
+/**
+ * Applies the function f on the value of the option if it exists, else applies it on the default value. If the result value matches the default, a None is returned
+ */
+export function Option_mapDefault(d, f, o) {
+    return Option_fromValueWithDefault(d, (o == null) ? f(d) : f(value(o)));
+}
+
+/**
+ * Returns the length of a subpropertylist from the aggregated strings
+ * 
+ * In ISATab format, some subproperties which are stored as lists in ISAJson are stored as semicolon delimited tables
+ * 
+ * These strings should either contain the same number of semicolon delimited elements or be empty.
+ */
+export 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);
+}
+
+/**
+ * Returns a list of ISAJson OntologyAnnotation objects from ISATab aggregated strings
+ */
+export function OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions) {
+    const l = OntologyAnnotation_getLengthOfAggregatedStrings(separator, [terms, source, accessions]) | 0;
+    if (l === 0) {
+        return [];
+    }
+    else {
+        return map3((a, b, c) => OntologyAnnotation.fromString(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));
+    }
+}
+
+/**
+ * Returns the aggregated ISATab OntologyAnnotation Name, ontology source and Accession number from a list of ISAJson OntologyAnnotation objects
+ */
+export function OntologyAnnotation_toAggregatedStrings(separator, oas) {
+    let first = true;
+    if (equalsWith(equals, oas, [])) {
+        return {
+            TermAccessionNumberAgg: "",
+            TermNameAgg: "",
+            TermSourceREFAgg: "",
+        };
+    }
+    else {
+        const tupledArg_1 = fold((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((arg) => OntologyAnnotation.toString(arg), oas));
+        return {
+            TermAccessionNumberAgg: tupledArg_1[2],
+            TermNameAgg: tupledArg_1[0],
+            TermSourceREFAgg: tupledArg_1[1],
+        };
+    }
+}
+
+/**
+ * Returns a list of ISAJson Component objects from ISATab aggregated strings
+ */
+export 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_fromString_Z61E08C1, (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)));
+    }
+}
+
+/**
+ * Returns the aggregated ISATAb Component Name, Ontology Annotation value, Accession number and ontology source from a list of ISAJson Component objects
+ */
+export 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_1(Component_toString_Z609B8895, cs));
+        return {
+            NameAgg: tupledArg_2[0],
+            TermAccessionNumberAgg: tupledArg_2[3],
+            TermNameAgg: tupledArg_2[1],
+            TermSourceREFAgg: tupledArg_2[2],
+        };
+    }
+}
+
+/**
+ * Returns a list of ISAJson ProtocolParameter objects from ISATab aggregated strings
+ */
+export function ProtocolParameter_fromAggregatedStrings(separator, terms, source, accessions) {
+    return map((arg_3) => ((arg_2) => ProtocolParameter_make(void 0, arg_2))(arg_3), OntologyAnnotation_fromAggregatedStrings(separator, terms, source, accessions));
+}
+
+/**
+ * Returns the aggregated ISATAb Ontology Annotation value, Accession number and ontology source from a list of ISAJson ProtocolParameter objects
+ */
+export 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_1(ProtocolParameter_toString_Z3A4310A5, oas));
+        return {
+            TermAccessionNumberAgg: tupledArg_1[2],
+            TermNameAgg: tupledArg_1[0],
+            TermSourceREFAgg: tupledArg_1[1],
+        };
+    }
+}
+

package/ISA/ISA.Spreadsheet/Metadata/DesignDescriptors.js

@@ -0,0 +1,27 @@
+import { ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { toRows as toRows_1, fromRows as fromRows_1, toSparseTable as toSparseTable_1, fromSparseTable as fromSparseTable_1 } from "./OntologyAnnotation.js";
+
+export const designTypeLabel = "Type";
+
+export const designTypeTermAccessionNumberLabel = "Type Term Accession Number";
+
+export const designTypeTermSourceREFLabel = "Type Term Source REF";
+
+export const labels = ofArray([designTypeLabel, designTypeTermAccessionNumberLabel, designTypeTermSourceREFLabel]);
+
+export function fromSparseTable(matrix) {
+    return fromSparseTable_1(designTypeLabel, designTypeTermSourceREFLabel, designTypeTermAccessionNumberLabel, matrix);
+}
+
+export function toSparseTable(designs) {
+    return toSparseTable_1(designTypeLabel, designTypeTermSourceREFLabel, designTypeTermAccessionNumberLabel, designs);
+}
+
+export function fromRows(prefix, lineNumber, rows) {
+    return fromRows_1(prefix, designTypeLabel, designTypeTermSourceREFLabel, designTypeTermAccessionNumberLabel, lineNumber, rows);
+}
+
+export function toRows(prefix, designs) {
+    return toRows_1(prefix, designTypeLabel, designTypeTermSourceREFLabel, designTypeTermAccessionNumberLabel, designs);
+}
+

package/ISA/ISA.Spreadsheet/Metadata/Factors.js

@@ -0,0 +1,85 @@
+import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
+import { Option_fromValueWithDefault } from "./Conversions.js";
+import { Factor } from "../../ISA/JsonTypes/Factor.js";
+import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+
+export const nameLabel = "Name";
+
+export const factorTypeLabel = "Type";
+
+export const typeTermAccessionNumberLabel = "Type Term Accession Number";
+
+export const typeTermSourceREFLabel = "Type Term Source REF";
+
+export const labels = ofArray([nameLabel, factorTypeLabel, typeTermAccessionNumberLabel, typeTermSourceREFLabel]);
+
+export function fromString(name, designType, typeTermSourceREF, typeTermAccessionNumber, comments) {
+    const factorType = OntologyAnnotation.fromString(designType, typeTermSourceREF, typeTermAccessionNumber);
+    const arg_2 = Option_fromValueWithDefault(OntologyAnnotation.empty, factorType);
+    const arg_3 = Option_fromValueWithDefault([], comments);
+    return Factor.make(void 0, name, arg_2, arg_3);
+}
+
+export function fromSparseTable(matrix) {
+    if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
+        const comments = SparseTable_GetEmptyComments_651559CC(matrix);
+        return singleton(Factor.create(void 0, void 0, void 0, comments));
+    }
+    else {
+        return initialize(matrix.ColumnCount, (i) => {
+            const comments_1 = toArray(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, [factorTypeLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermSourceREFLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermAccessionNumberLabel, i]), comments_1);
+        });
+    }
+}
+
+export 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, OntologyAnnotation.empty);
+        ft = OntologyAnnotation.toString(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) {
+            const array = matchValue;
+            array.forEach((comment) => {
+                const patternInput = Comment_toString(comment);
+                const n = patternInput[0];
+                commentKeys = cons(n, commentKeys);
+                addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+            });
+        }
+    }, factors);
+    return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    })), matrix.ColumnCount);
+}
+
+export function fromRows(prefix, lineNumber, rows) {
+    const tupledArg = (prefix == null) ? SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber) : SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber, prefix);
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+
+export function toRows(prefix, factors) {
+    const m = toSparseTable(factors);
+    if (prefix == null) {
+        return SparseTable_ToRows_6A3D4534(m);
+    }
+    else {
+        return SparseTable_ToRows_6A3D4534(m, prefix);
+    }
+}
+

package/ISA/ISA.Spreadsheet/Metadata/OntologyAnnotation.js

@@ -0,0 +1,65 @@
+import { reverse, cons, iterateIndexed, empty, ofArray, map, toArray, initialize, singleton, length } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
+import { Option_fromValueWithDefault } from "./Conversions.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { unwrap } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+
+export function fromSparseTable(label, labelTSR, labelTAN, matrix) {
+    if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
+        const comments = SparseTable_GetEmptyComments_651559CC(matrix);
+        return singleton(OntologyAnnotation.create(void 0, void 0, void 0, void 0, comments));
+    }
+    else {
+        return initialize(matrix.ColumnCount, (i) => {
+            const comments_1 = Option_fromValueWithDefault([], toArray(map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys)));
+            return OntologyAnnotation.fromString(unwrap(SparseTable__TryGetValue_11FD62A8(matrix, [label, i])), unwrap(SparseTable__TryGetValue_11FD62A8(matrix, [labelTSR, i])), unwrap(SparseTable__TryGetValue_11FD62A8(matrix, [labelTAN, i])), unwrap(comments_1));
+        });
+    }
+}
+
+export 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.toString(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);
+        const matchValue = d.Comments;
+        if (matchValue != null) {
+            const array = matchValue;
+            array.forEach((comment) => {
+                const patternInput = Comment_toString(comment);
+                const n = patternInput[0];
+                commentKeys = cons(n, commentKeys);
+                addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+            });
+        }
+    }, designs);
+    return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    })), matrix.ColumnCount);
+}
+
+export function fromRows(prefix, label, labelTSR, labelTAN, lineNumber, rows) {
+    const labels = ofArray([label, labelTAN, labelTSR]);
+    const tupledArg = (prefix == null) ? SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber) : SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber, prefix);
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(label, labelTSR, labelTAN, tupledArg[3])];
+}
+
+export function toRows(prefix, label, labelTSR, labelTAN, designs) {
+    const m = toSparseTable(label, labelTSR, labelTAN, designs);
+    if (prefix == null) {
+        return SparseTable_ToRows_6A3D4534(m);
+    }
+    else {
+        return SparseTable_ToRows_6A3D4534(m, prefix);
+    }
+}
+

package/ISA/ISA.Spreadsheet/Metadata/OntologySourceReference.js

@@ -0,0 +1,73 @@
+import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { Option_fromValueWithDefault } from "./Conversions.js";
+import { OntologySourceReference } from "../../ISA/JsonTypes/OntologySourceReference.js";
+import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+
+export const nameLabel = "Term Source Name";
+
+export const fileLabel = "Term Source File";
+
+export const versionLabel = "Term Source Version";
+
+export const descriptionLabel = "Term Source Description";
+
+export const labels = ofArray([nameLabel, fileLabel, versionLabel, descriptionLabel]);
+
+export function fromString(description, file, name, version, comments) {
+    const arg_4 = Option_fromValueWithDefault([], comments);
+    return OntologySourceReference.make(description, file, name, version, arg_4);
+}
+
+export function fromSparseTable(matrix) {
+    if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
+        const comments = SparseTable_GetEmptyComments_651559CC(matrix);
+        return singleton(OntologySourceReference.create(void 0, void 0, void 0, void 0, comments));
+    }
+    else {
+        return initialize(matrix.ColumnCount, (i) => {
+            const comments_1 = toArray(map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys));
+            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);
+        });
+    }
+}
+
+export 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, ""));
+        const matchValue = o.Comments;
+        if (matchValue != null) {
+            const array = matchValue;
+            array.forEach((comment) => {
+                const patternInput = Comment_toString(comment);
+                const n = patternInput[0];
+                commentKeys = cons(n, commentKeys);
+                addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+            });
+        }
+    }, ontologySources);
+    return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    })), matrix.ColumnCount);
+}
+
+export function fromRows(lineNumber, rows) {
+    const tupledArg = SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber);
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+
+export function toRows(termSources) {
+    return SparseTable_ToRows_6A3D4534(toSparseTable(termSources));
+}
+

package/ISA/ISA.Spreadsheet/Metadata/Protocols.js

@@ -0,0 +1,116 @@
+import { reverse, cons, iterate, iterateIndexed, map as map_1, initialize, singleton, length, empty, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
+import { Component_toAggregatedStrings, ProtocolParameter_toAggregatedStrings, Option_fromValueWithDefault, Component_fromAggregatedStrings, ProtocolParameter_fromAggregatedStrings } from "./Conversions.js";
+import { Protocol_create_Z7DFD6E67, Protocol_make } from "../../ISA/JsonTypes/Protocol.js";
+import { defaultArg, map } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { URIModule_fromString } from "../../ISA/JsonTypes/URI.js";
+import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+
+export const nameLabel = "Name";
+
+export const protocolTypeLabel = "Type";
+
+export const typeTermAccessionNumberLabel = "Type Term Accession Number";
+
+export const typeTermSourceREFLabel = "Type Term Source REF";
+
+export const descriptionLabel = "Description";
+
+export const uriLabel = "URI";
+
+export const versionLabel = "Version";
+
+export const parametersNameLabel = "Parameters Name";
+
+export const parametersTermAccessionNumberLabel = "Parameters Term Accession Number";
+
+export const parametersTermSourceREFLabel = "Parameters Term Source REF";
+
+export const componentsNameLabel = "Components Name";
+
+export const componentsTypeLabel = "Components Type";
+
+export const componentsTypeTermAccessionNumberLabel = "Components Type Term Accession Number";
+
+export const componentsTypeTermSourceREFLabel = "Components Type Term Source REF";
+
+export const labels = ofArray([nameLabel, protocolTypeLabel, typeTermAccessionNumberLabel, typeTermSourceREFLabel, descriptionLabel, uriLabel, versionLabel, parametersNameLabel, parametersTermAccessionNumberLabel, parametersTermSourceREFLabel, componentsNameLabel, componentsTypeLabel, componentsTypeTermAccessionNumberLabel, componentsTypeTermSourceREFLabel]);
+
+export function fromString(name, protocolType, typeTermAccessionNumber, typeTermSourceREF, description, uri, version, parametersName, parametersTermAccessionNumber, parametersTermSourceREF, componentsName, componentsType, componentsTypeTermAccessionNumber, componentsTypeTermSourceREF, comments) {
+    const protocolType_1 = OntologyAnnotation.fromString(protocolType, typeTermSourceREF, typeTermAccessionNumber);
+    const parameters = ofArray(ProtocolParameter_fromAggregatedStrings(";", parametersName, parametersTermSourceREF, parametersTermAccessionNumber));
+    const components = Component_fromAggregatedStrings(";", componentsName, componentsType, componentsTypeTermSourceREF, componentsTypeTermAccessionNumber);
+    return Protocol_make(void 0, map(URIModule_fromString, name), Option_fromValueWithDefault(OntologyAnnotation.empty, protocolType_1), description, map(URIModule_fromString, uri), version, Option_fromValueWithDefault(empty(), parameters), Option_fromValueWithDefault(empty(), components), Option_fromValueWithDefault(empty(), comments));
+}
+
+export function fromSparseTable(matrix) {
+    if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
+        return singleton(Protocol_create_Z7DFD6E67(void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, ofArray(SparseTable_GetEmptyComments_651559CC(matrix))));
+    }
+    else {
+        return initialize(matrix.ColumnCount, (i) => {
+            const comments_1 = map_1((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);
+        });
+    }
+}
+
+export 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, OntologyAnnotation.empty);
+        pt_1 = OntologyAnnotation.toString(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]);
+            }, matchValue);
+        }
+    }, protocols);
+    return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    })), matrix.ColumnCount);
+}
+
+export function fromRows(prefix, lineNumber, rows) {
+    const tupledArg = (prefix == null) ? SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber) : SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber, prefix);
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(tupledArg[3])];
+}
+
+export function toRows(prefix, protocols) {
+    const m = toSparseTable(protocols);
+    if (prefix == null) {
+        return SparseTable_ToRows_6A3D4534(m);
+    }
+    else {
+        return SparseTable_ToRows_6A3D4534(m, prefix);
+    }
+}
+