@nfdi4plants/arctrl 2.5.1 → 3.0.0-alpha.2

package/dist/ts/esm/ts/Spreadsheet/Metadata/Comment.js

@@ -0,0 +1,59 @@
+import { ActivePatterns_$007CRegex$007C_$007C } from "../../Core/Helper/Regex.js";
+import { bind, defaultArg, value as value_1 } from "@fable-org/fable-library-js/Option.js";
+import { printf, toText } from "@fable-org/fable-library-js/String.js";
+import { Option_fromValueWithDefault } from "./Conversions.js";
+import { Comment$ } from "../../Core/Comment.js";
+export const Comment_commentValueKey = "commentValue";
+export const Comment_commentPattern = `Comment\\s*\\[<(?<${Comment_commentValueKey}>.+)>\\]`;
+export const Comment_commentPatternNoAngleBrackets = `Comment\\s*\\[(?<${Comment_commentValueKey}>.+)\\]`;
+export function Comment_$007CComment$007C_$007C(key) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Comment_commentPattern, key);
+    if (activePatternResult != null) {
+        const r = value_1(activePatternResult);
+        return (r.groups && r.groups[Comment_commentValueKey]) || "";
+    }
+    else {
+        const activePatternResult_1 = ActivePatterns_$007CRegex$007C_$007C(Comment_commentPatternNoAngleBrackets, key);
+        if (activePatternResult_1 != null) {
+            const r_1 = value_1(activePatternResult_1);
+            const v = (r_1.groups && r_1.groups[Comment_commentValueKey]) || "";
+            if (v === "<>") {
+                return undefined;
+            }
+            else {
+                return v;
+            }
+        }
+        else {
+            return undefined;
+        }
+    }
+}
+export function Comment_wrapCommentKey(k) {
+    return toText(printf("Comment[%s]"))(k);
+}
+export function Comment_fromString(k, v) {
+    const name = Option_fromValueWithDefault("", k);
+    const value = Option_fromValueWithDefault("", v);
+    return Comment$.make(name, value);
+}
+export function Comment_toString(c) {
+    return [defaultArg(c.Name, ""), defaultArg(c.Value, "")];
+}
+export const Remark_remarkValueKey = "remarkValue";
+export const Remark_remarkPattern = `#(?<${Remark_remarkValueKey}>.+)`;
+export function Remark_$007CRemark$007C_$007C(key) {
+    return bind((k) => {
+        const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Remark_remarkPattern, k);
+        if (activePatternResult != null) {
+            const r = value_1(activePatternResult);
+            return (r.groups && r.groups[Remark_remarkValueKey]) || "";
+        }
+        else {
+            return undefined;
+        }
+    }, key);
+}
+export function Remark_wrapRemark(r) {
+    return toText(printf("#%s"))(r);
+}

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

@@ -0,0 +1,84 @@
+import { reverse, cons, iterateIndexed, empty, map, initialize, singleton, length, ofArray } from "@fable-org/fable-library-js/List.js";
+import { Person_setCommentFromORCID, Person_setOrcidFromComments } from "../../Core/Conversion.js";
+import { OntologyAnnotation_toAggregatedStrings, OntologyAnnotation_fromAggregatedStrings } from "./Conversions.js";
+import { Person } from "../../Core/Person.js";
+import { value as value_1, unwrap, defaultArg } from "@fable-org/fable-library-js/Option.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable_Create_Z2192E64B, SparseTable, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { addToDict } from "@fable-org/fable-library-js/MapUtil.js";
+import { ResizeArray_iter } from "../../Core/Helper/Collections.js";
+import { List_distinct } from "@fable-org/fable-library-js/Seq2.js";
+import { stringHash } from "@fable-org/fable-library-js/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 roles_1;
+    return Person_setOrcidFromComments((roles_1 = OntologyAnnotation_fromAggregatedStrings(";", role, rolesTermSourceREF, rolesTermAccessionNumber), Person.make(undefined, lastName, firstName, midInitials, email, phone, fax, address, affiliation, roles_1, comments)));
+}
+export 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);
+        });
+    }
+}
+export function toSparseTable(persons) {
+    const matrix = SparseTable_Create_Z2192E64B(undefined, labels, undefined, 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);
+}
+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_759CAFC1(m);
+    }
+    else {
+        return SparseTable_ToRows_759CAFC1(m, value_1(prefix));
+    }
+}

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

@@ -0,0 +1,176 @@
+import { equals } from "@fable-org/fable-library-js/Util.js";
+import { defaultArg, value, some } from "@fable-org/fable-library-js/Option.js";
+import { equalsWith, fill, map3, fold } from "@fable-org/fable-library-js/Array.js";
+import { toText, printf, toFail } from "@fable-org/fable-library-js/String.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { Component_toStringObject_Z685B8F25, Component_fromISAString_7C9A7CF8 } from "../../Core/Process/Component.js";
+import { map, fold as fold_1, ofArray, empty } from "@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";
+/**
+ * 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 undefined;
+    }
+    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 {
+        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);
+    }
+}
+/**
+ * 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) => {
+            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],
+        };
+    }
+}
+/**
+ * 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_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)));
+    }
+}
+/**
+ * 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(Component_toStringObject_Z685B8F25, 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 ResizeArray_map((arg) => ((parameterName) => ProtocolParameter.make(undefined, parameterName))(arg), 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((pp) => ProtocolParameter.toStringObject(pp), oas));
+        return {
+            TermAccessionNumberAgg: tupledArg_1[2],
+            TermNameAgg: tupledArg_1[0],
+            TermSourceREFAgg: tupledArg_1[1],
+        };
+    }
+}

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

@@ -0,0 +1,18 @@
+import { ofArray } from "@fable-org/fable-library-js/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/dist/ts/esm/ts/Spreadsheet/Metadata/Factors.js

@@ -0,0 +1,75 @@
+import { reverse, cons, iterateIndexed, empty, map, initialize, singleton, length, ofArray } from "@fable-org/fable-library-js/List.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { value as value_1, defaultArg, unwrap } from "@fable-org/fable-library-js/Option.js";
+import { ResizeArray_iter, Option_fromValueWithDefault } from "../../Core/Helper/Collections.js";
+import { Factor } from "../../Core/Process/Factor.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable_Create_Z2192E64B, SparseTable, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { addToDict } from "@fable-org/fable-library-js/MapUtil.js";
+import { List_distinct } from "@fable-org/fable-library-js/Seq2.js";
+import { stringHash } from "@fable-org/fable-library-js/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.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);
+}
+export function fromSparseTable(matrix) {
+    if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
+        const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+        return singleton(Factor.create(undefined, undefined, 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);
+        });
+    }
+}
+export function toSparseTable(factors) {
+    const matrix = SparseTable_Create_Z2192E64B(undefined, labels, undefined, 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_1(matchValue));
+        }
+    }, 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, value_1(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_759CAFC1(m);
+    }
+    else {
+        return SparseTable_ToRows_759CAFC1(m, value_1(prefix));
+    }
+}

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

@@ -0,0 +1,59 @@
+import { reverse, cons, iterateIndexed, empty, ofArray, map, initialize, singleton, length } from "@fable-org/fable-library-js/List.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable_Create_Z2192E64B, SparseTable, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { value as value_1, unwrap } from "@fable-org/fable-library-js/Option.js";
+import { addToDict } from "@fable-org/fable-library-js/MapUtil.js";
+import { ResizeArray_iter } from "../../Core/Helper/Collections.js";
+import { List_distinct } from "@fable-org/fable-library-js/Seq2.js";
+import { stringHash } from "@fable-org/fable-library-js/Util.js";
+export 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);
+        });
+    }
+}
+export function toSparseTable(label, labelTSR, labelTAN, designs) {
+    const matrix = SparseTable_Create_Z2192E64B(undefined, ofArray([label, labelTAN, labelTSR]), undefined, 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);
+}
+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, value_1(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_759CAFC1(m);
+    }
+    else {
+        return SparseTable_ToRows_759CAFC1(m, value_1(prefix));
+    }
+}

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

@@ -0,0 +1,60 @@
+import { reverse, cons, iterateIndexed, empty, map, initialize, singleton, length, ofArray } from "@fable-org/fable-library-js/List.js";
+import { OntologySourceReference } from "../../Core/OntologySourceReference.js";
+import { defaultArg } from "@fable-org/fable-library-js/Option.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable_Create_Z2192E64B, SparseTable, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { addToDict } from "@fable-org/fable-library-js/MapUtil.js";
+import { ResizeArray_iter } from "../../Core/Helper/Collections.js";
+import { List_distinct } from "@fable-org/fable-library-js/Seq2.js";
+import { stringHash } from "@fable-org/fable-library-js/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) {
+    return OntologySourceReference.make(description, file, name, version, comments);
+}
+export 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);
+        });
+    }
+}
+export function toSparseTable(ontologySources) {
+    const matrix = SparseTable_Create_Z2192E64B(undefined, labels, undefined, 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);
+}
+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_759CAFC1(toSparseTable(termSources));
+}

package/dist/ts/esm/ts/Spreadsheet/Metadata/Protocols.js

@@ -0,0 +1,95 @@
+import { reverse, cons, iterate, iterateIndexed, map as map_1, initialize, singleton, length, empty, ofSeq, ofArray } from "@fable-org/fable-library-js/List.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { value as value_3, defaultArg, map, unwrap } from "@fable-org/fable-library-js/Option.js";
+import { Component_toAggregatedStrings, ProtocolParameter_toAggregatedStrings, Option_fromValueWithDefault, Component_fromAggregatedStrings, ProtocolParameter_fromAggregatedStrings } from "./Conversions.js";
+import { Protocol_create_Z414665E7, Protocol_make } from "../../Core/Process/Protocol.js";
+import { URIModule_fromString } from "../../Core/URI.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable_Create_Z2192E64B, SparseTable, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { addToDict } from "@fable-org/fable-library-js/MapUtil.js";
+import { List_distinct } from "@fable-org/fable-library-js/Seq2.js";
+import { stringHash } from "@fable-org/fable-library-js/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.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(undefined, map(URIModule_fromString, name), Option_fromValueWithDefault(new OntologyAnnotation(), 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_Z414665E7(undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, ofSeq(SparseTable_GetEmptyComments_3ECCA699(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(undefined, labels, undefined, 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_3(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, value_3(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_759CAFC1(m);
+    }
+    else {
+        return SparseTable_ToRows_759CAFC1(m, value_3(prefix));
+    }
+}