@nfdi4plants/arctrl 1.0.0-alpha6

package/Templates/Templates.Spreadsheet.js

@@ -0,0 +1,315 @@
+import { toArray as toArray_1, append as append_1, reverse, map, empty, ofArray } from "../fable_modules/fable-library.4.1.4/List.js";
+import { toRows, fromRows, toSparseTable, fromSparseTable } from "../ISA/ISA.Spreadsheet/Metadata/OntologyAnnotation.js";
+import { toString, Record } from "../fable_modules/fable-library.4.1.4/Types.js";
+import { record_type, list_type, string_type } from "../fable_modules/fable-library.4.1.4/Reflection.js";
+import { Comment$_$reflection } from "../ISA/ISA/JsonTypes/Comment.js";
+import { Comment_fromString } from "../ISA/ISA.Spreadsheet/Metadata/Comment.js";
+import { SparseRowModule_fromFsRow, SparseRowModule_writeToSheet, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt, SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "../ISA/ISA.Spreadsheet/Metadata/SparseTable.js";
+import { createMissingIdentifier } from "../ISA/ISA/Identifier.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 { getEnumerator, stringHash } from "../fable_modules/fable-library.4.1.4/Util.js";
+import { tryPick, iterateIndexed, delay, singleton, append, head, exists, map as map_1 } from "../fable_modules/fable-library.4.1.4/Seq.js";
+import { Person } from "../ISA/ISA/JsonTypes/Person.js";
+import { toArray } from "../fable_modules/fable-library.4.1.4/Option.js";
+import { toRows as toRows_1, fromRows as fromRows_1 } from "../ISA/ISA.Spreadsheet/Metadata/Contacts.js";
+import { parse } from "../fable_modules/fable-library.4.1.4/Guid.js";
+import { Template, Organisation } from "./Templates.js";
+import { FsWorksheet } from "../fable_modules/FsSpreadsheet.4.1.0/FsWorksheet.fs.js";
+import { printf, toFail } from "../fable_modules/fable-library.4.1.4/String.js";
+import { toFsWorksheet, tryFromFsWorksheet } from "../ISA/ISA.Spreadsheet/AnnotationTable/ArcTable.js";
+import { now } from "../fable_modules/fable-library.4.1.4/Date.js";
+import { FsWorkbook } from "../fable_modules/FsSpreadsheet.4.1.0/FsWorkbook.fs.js";
+
+export const Metadata_ER_labels = ofArray(["ER", "ER Term Accession Number", "ER Term Source REF"]);
+
+export function Metadata_ER_fromSparseTable(matrix) {
+    return fromSparseTable("ER", "ER Term Source REF", "ER Term Accession Number", matrix);
+}
+
+export function Metadata_ER_toSparseTable(designs) {
+    return toSparseTable("ER", "ER Term Source REF", "ER Term Accession Number", designs);
+}
+
+export function Metadata_ER_fromRows(prefix, rows) {
+    const patternInput = fromRows(prefix, "ER", "ER Term Source REF", "ER Term Accession Number", 0, rows);
+    return [patternInput[0], patternInput[3]];
+}
+
+export function Metadata_ER_toRows(prefix, designs) {
+    return toRows(prefix, "ER", "ER Term Source REF", "ER Term Accession Number", designs);
+}
+
+export const Metadata_Tags_labels = ofArray(["Tags", "Tags Term Accession Number", "Tags Term Source REF"]);
+
+export function Metadata_Tags_fromSparseTable(matrix) {
+    return fromSparseTable("Tags", "Tags Term Source REF", "Tags Term Accession Number", matrix);
+}
+
+export function Metadata_Tags_toSparseTable(designs) {
+    return toSparseTable("Tags", "Tags Term Source REF", "Tags Term Accession Number", designs);
+}
+
+export function Metadata_Tags_fromRows(prefix, rows) {
+    const patternInput = fromRows(prefix, "Tags", "Tags Term Source REF", "Tags Term Accession Number", 0, rows);
+    return [patternInput[0], patternInput[3]];
+}
+
+export function Metadata_Tags_toRows(prefix, designs) {
+    return toRows(prefix, "Tags", "Tags Term Source REF", "Tags Term Accession Number", designs);
+}
+
+export class Metadata_Template_TemplateInfo extends Record {
+    constructor(Id, Name, Version, Description, Organisation, Table, Comments) {
+        super();
+        this.Id = Id;
+        this.Name = Name;
+        this.Version = Version;
+        this.Description = Description;
+        this.Organisation = Organisation;
+        this.Table = Table;
+        this.Comments = Comments;
+    }
+}
+
+export function Metadata_Template_TemplateInfo_$reflection() {
+    return record_type("ARCtrl.Templates.Spreadsheet.Metadata.Template.TemplateInfo", [], Metadata_Template_TemplateInfo, () => [["Id", string_type], ["Name", string_type], ["Version", string_type], ["Description", string_type], ["Organisation", string_type], ["Table", string_type], ["Comments", list_type(Comment$_$reflection())]]);
+}
+
+export function Metadata_Template_TemplateInfo_create(id, name, version, description, organisation, table, comments) {
+    return new Metadata_Template_TemplateInfo(id, name, version, description, organisation, table, comments);
+}
+
+export function Metadata_Template_TemplateInfo_get_empty() {
+    return Metadata_Template_TemplateInfo_create("", "", "", "", "", "", empty());
+}
+
+export function Metadata_Template_TemplateInfo_get_Labels() {
+    return ofArray(["Id", "Name", "Version", "Description", "Organisation", "Table"]);
+}
+
+export function Metadata_Template_TemplateInfo_FromSparseTable_651559CC(matrix) {
+    const comments = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, 0])), matrix.CommentKeys);
+    return Metadata_Template_TemplateInfo_create(SparseTable__TryGetValueDefault_5BAE6133(matrix, createMissingIdentifier(), ["Id", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Name", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Version", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Description", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Organisation", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Table", 0]), comments);
+}
+
+export function Metadata_Template_TemplateInfo_ToSparseTable_Z71FCD534(template) {
+    let copyOfStruct, copyOfStruct_1;
+    const matrix = SparseTable_Create_Z2192E64B(void 0, Metadata_Template_TemplateInfo_get_Labels(), void 0, 2);
+    let commentKeys = empty();
+    addToDict(matrix.Matrix, ["Id", 1], (((copyOfStruct = template.Id, copyOfStruct)).indexOf("MISSING_IDENTIFIER_") === 0) ? "" : ((copyOfStruct_1 = template.Id, copyOfStruct_1)));
+    addToDict(matrix.Matrix, ["Name", 1], template.Name);
+    addToDict(matrix.Matrix, ["Version", 1], template.Version);
+    addToDict(matrix.Matrix, ["Description", 1], template.Description);
+    addToDict(matrix.Matrix, ["Organisation", 1], toString(template.Organisation));
+    addToDict(matrix.Matrix, ["Table", 1], template.Table.Name);
+    return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    })), matrix.ColumnCount);
+}
+
+export function Metadata_Template_TemplateInfo_fromRows_9F97F2A(rows) {
+    const tupledArg = SparseTable_FromRows_Z5579EC29(rows, Metadata_Template_TemplateInfo_get_Labels(), 0);
+    return [tupledArg[0], Metadata_Template_TemplateInfo_FromSparseTable_651559CC(tupledArg[3])];
+}
+
+export function Metadata_Template_TemplateInfo_toRows_Z71FCD534(template) {
+    return SparseTable_ToRows_6A3D4534(Metadata_Template_TemplateInfo_ToSparseTable_Z71FCD534(template));
+}
+
+export function Metadata_Template_mapDeprecatedKeys(rows) {
+    const s = map_1((r) => map_1((tupledArg) => {
+        const k = tupledArg[0] | 0;
+        const v = tupledArg[1];
+        if (k === 0) {
+            switch (v) {
+                case "#AUTHORS list":
+                    return [k, "AUTHORS"];
+                case "#ER list":
+                    return [k, "ERS"];
+                case "#TAGS list":
+                    return [k, "TAGS"];
+                case "Authors ORCID":
+                    return [k, `Comment[${Person.orcidKey}]`];
+                case "Authors Last Name":
+                    return [k, "Author Last Name"];
+                case "Authors First Name":
+                    return [k, "Author First Name"];
+                case "Authors Mid Initials":
+                    return [k, "Author Mid Initials"];
+                case "Authors Email":
+                    return [k, "Author Email"];
+                case "Authors Phone":
+                    return [k, "Author Phone"];
+                case "Authors Fax":
+                    return [k, "Author Fax"];
+                case "Authors Address":
+                    return [k, "Author Address"];
+                case "Authors Affiliation":
+                    return [k, "Author Affiliation"];
+                case "Authors Role":
+                    return [k, "Author Roles"];
+                case "Authors Role Term Accession Number":
+                    return [k, "Author Roles Term Accession Number"];
+                case "Authors Role Term Source REF":
+                    return [k, "Author Roles Term Source REF"];
+                default:
+                    return [k, v];
+            }
+        }
+        else {
+            return [k, v];
+        }
+    }, r), rows);
+    if (exists((v_32) => (v_32 === "TEMPLATE"), toArray(SparseRowModule_tryGetValueAt(0, head(s))))) {
+        return s;
+    }
+    else {
+        return append(singleton(SparseRowModule_fromValues(["TEMPLATE"])), s);
+    }
+}
+
+export function Metadata_Template_fromRows(rows) {
+    const loop = (en_mut, lastLine_mut, templateInfo_mut, ers_mut, tags_mut, authors_mut) => {
+        loop:
+        while (true) {
+            const en = en_mut, lastLine = lastLine_mut, templateInfo = templateInfo_mut, ers = ers_mut, tags = tags_mut, authors = authors_mut;
+            let matchResult, k_3, k_4, k_5, k_6;
+            if (lastLine != null) {
+                switch (lastLine) {
+                    case "ERS": {
+                        matchResult = 0;
+                        k_3 = lastLine;
+                        break;
+                    }
+                    case "TAGS": {
+                        matchResult = 1;
+                        k_4 = lastLine;
+                        break;
+                    }
+                    case "AUTHORS": {
+                        matchResult = 2;
+                        k_5 = lastLine;
+                        break;
+                    }
+                    default: {
+                        matchResult = 3;
+                        k_6 = lastLine;
+                    }
+                }
+            }
+            else {
+                matchResult = 3;
+                k_6 = lastLine;
+            }
+            switch (matchResult) {
+                case 0: {
+                    const patternInput = Metadata_ER_fromRows(void 0, en);
+                    en_mut = en;
+                    lastLine_mut = patternInput[0];
+                    templateInfo_mut = templateInfo;
+                    ers_mut = append_1(ers, patternInput[1]);
+                    tags_mut = tags;
+                    authors_mut = authors;
+                    continue loop;
+                }
+                case 1: {
+                    const patternInput_1 = Metadata_Tags_fromRows(void 0, en);
+                    en_mut = en;
+                    lastLine_mut = patternInput_1[0];
+                    templateInfo_mut = templateInfo;
+                    ers_mut = ers;
+                    tags_mut = append_1(tags, patternInput_1[1]);
+                    authors_mut = authors;
+                    continue loop;
+                }
+                case 2: {
+                    const patternInput_2 = fromRows_1("Author", 0, en);
+                    en_mut = en;
+                    lastLine_mut = patternInput_2[0];
+                    templateInfo_mut = templateInfo;
+                    ers_mut = ers;
+                    tags_mut = tags;
+                    authors_mut = append_1(authors, patternInput_2[3]);
+                    continue loop;
+                }
+                default:
+                    return [templateInfo, ers, tags, authors];
+            }
+            break;
+        }
+    };
+    const en_1 = getEnumerator(Metadata_Template_mapDeprecatedKeys(rows));
+    en_1["System.Collections.IEnumerator.MoveNext"]();
+    const patternInput_3 = Metadata_Template_TemplateInfo_fromRows_9F97F2A(en_1);
+    return loop(en_1, patternInput_3[0], patternInput_3[1], empty(), empty(), empty());
+}
+
+export function Metadata_Template_toRows(template) {
+    return delay(() => append(singleton(SparseRowModule_fromValues(["TEMPLATE"])), delay(() => append(Metadata_Template_TemplateInfo_toRows_Z71FCD534(template), delay(() => append(singleton(SparseRowModule_fromValues(["ERS"])), delay(() => append(Metadata_ER_toRows(void 0, ofArray(template.EndpointRepositories)), delay(() => append(singleton(SparseRowModule_fromValues(["TAGS"])), delay(() => append(Metadata_Tags_toRows(void 0, ofArray(template.Tags)), delay(() => append(singleton(SparseRowModule_fromValues(["AUTHORS"])), delay(() => toRows_1("Author", ofArray(template.Authors)))))))))))))))));
+}
+
+export function Template_fromParts(templateInfo, ers, tags, authors, table, lastUpdated) {
+    const arg = parse(templateInfo.Id);
+    const arg_4 = Organisation.ofString(templateInfo.Organisation);
+    const arg_6 = toArray_1(authors);
+    const arg_7 = toArray_1(ers);
+    const arg_8 = toArray_1(tags);
+    return Template.make(arg, table, templateInfo.Name, templateInfo.Description, arg_4, templateInfo.Version, arg_6, arg_7, arg_8, lastUpdated);
+}
+
+export function Template_toMetadataSheet(template) {
+    const sheet = new FsWorksheet("isa_template");
+    iterateIndexed((rowI, r) => {
+        SparseRowModule_writeToSheet(rowI + 1, r, sheet);
+    }, Metadata_Template_toRows(template));
+    return sheet;
+}
+
+export function Template_fromMetadataSheet(sheet) {
+    return Metadata_Template_fromRows(map_1(SparseRowModule_fromFsRow, sheet.Rows));
+}
+
+/**
+ * Reads an assay from a spreadsheet
+ */
+export function Template_fromFsWorkbook(doc) {
+    let matchValue_2, matchValue_4, ws_3, matchValue_5, arg_1, ws_2, matchValue_3, arg;
+    let patternInput;
+    const matchValue = doc.TryGetWorksheetByName("isa_template");
+    if (matchValue == null) {
+        const matchValue_1 = doc.TryGetWorksheetByName("SwateTemplateMetadata");
+        patternInput = ((matchValue_1 == null) ? [Metadata_Template_TemplateInfo_get_empty(), empty(), empty(), empty()] : Template_fromMetadataSheet(matchValue_1));
+    }
+    else {
+        patternInput = Template_fromMetadataSheet(matchValue);
+    }
+    const templateInfo = patternInput[0];
+    const sheets = doc.GetWorksheets();
+    return Template_fromParts(templateInfo, patternInput[1], patternInput[2], patternInput[3], (matchValue_2 = tryPick((ws) => {
+        if (exists((t) => (t.Name === templateInfo.Table), ws.Tables)) {
+            return ws;
+        }
+        else {
+            return void 0;
+        }
+    }, sheets), (matchValue_2 == null) ? ((matchValue_4 = tryPick((ws_1) => {
+        if (ws_1.Name === templateInfo.Table) {
+            return ws_1;
+        }
+        else {
+            return void 0;
+        }
+    }, sheets), (matchValue_4 == null) ? toFail(printf("No worksheet with name %s found"))(templateInfo.Table) : ((ws_3 = matchValue_4, (matchValue_5 = tryFromFsWorksheet(ws_3), (matchValue_5 == null) ? ((arg_1 = ws_3.Name, toFail(printf("Ws with name %s could not be converted to a table"))(arg_1))) : matchValue_5))))) : ((ws_2 = matchValue_2, (matchValue_3 = tryFromFsWorksheet(ws_2), (matchValue_3 == null) ? ((arg = ws_2.Name, toFail(printf("Ws with name %s could not be converted to a table"))(arg))) : matchValue_3)))), now());
+}
+
+export function Template_toFsWorkbook(template) {
+    const doc = new FsWorkbook();
+    const metaDataSheet = Template_toMetadataSheet(template);
+    doc.AddWorksheet(metaDataSheet);
+    const arg = toFsWorksheet(template.Table);
+    doc.AddWorksheet(arg);
+    return doc;
+}
+

package/Templates/Templates.js

@@ -0,0 +1,179 @@
+import { identityHash, safeHash, stringHash, equals } from "../fable_modules/fable-library.4.1.4/Util.js";
+import { Union } from "../fable_modules/fable-library.4.1.4/Types.js";
+import { class_type, union_type, string_type } from "../fable_modules/fable-library.4.1.4/Reflection.js";
+import { defaultArg, unwrap } from "../fable_modules/fable-library.4.1.4/Option.js";
+import { newGuid } from "../fable_modules/fable-library.4.1.4/Guid.js";
+import { ArcTable } from "../ISA/ISA/ArcTypes/ArcTable.js";
+import { SemVer_tryOfString_Z721C83C5 } from "../SemVer.js";
+import { equalsWith } from "../fable_modules/fable-library.4.1.4/Array.js";
+import { toUniversalTime, now, equals as equals_1 } from "../fable_modules/fable-library.4.1.4/Date.js";
+
+export class Organisation extends Union {
+    constructor(tag, fields) {
+        super();
+        this.tag = tag;
+        this.fields = fields;
+    }
+    cases() {
+        return ["DataPLANT", "Other"];
+    }
+    static ofString(str) {
+        return (str.toLocaleLowerCase() === "dataplant") ? (new Organisation(0, [])) : (new Organisation(1, [str]));
+    }
+    toString() {
+        const this$ = this;
+        return (this$.tag === 1) ? this$.fields[0] : "DataPLANT";
+    }
+    IsOfficial() {
+        const this$ = this;
+        return equals(this$, new Organisation(0, []));
+    }
+}
+
+export function Organisation_$reflection() {
+    return union_type("ARCtrl.Templates.Organisation", [], Organisation, () => [[], [["Item", string_type]]]);
+}
+
+export class Template {
+    constructor(id, table, name, description, organisation, version, authors, repos, tags, lastUpdated) {
+        let copyOfStruct;
+        const name_1 = defaultArg(name, "");
+        const description_1 = defaultArg(description, "");
+        const organisation_1 = defaultArg(organisation, new Organisation(1, ["Custom Organisation"]));
+        const version_1 = defaultArg(version, "0.0.0");
+        const authors_1 = defaultArg(authors, []);
+        const repos_1 = defaultArg(repos, []);
+        const tags_1 = defaultArg(tags, []);
+        const lastUpdated_1 = defaultArg(lastUpdated, (copyOfStruct = now(), toUniversalTime(copyOfStruct)));
+        this["Id@"] = id;
+        this["Table@"] = table;
+        this["Name@"] = name_1;
+        this["Description@"] = description_1;
+        this["Organisation@"] = organisation_1;
+        this["Version@"] = version_1;
+        this["Authors@"] = authors_1;
+        this["EndpointRepositories@"] = repos_1;
+        this["Tags@"] = tags_1;
+        this["LastUpdated@"] = lastUpdated_1;
+    }
+    get Id() {
+        const __ = this;
+        return __["Id@"];
+    }
+    set Id(v) {
+        const __ = this;
+        __["Id@"] = v;
+    }
+    get Table() {
+        const __ = this;
+        return __["Table@"];
+    }
+    set Table(v) {
+        const __ = this;
+        __["Table@"] = v;
+    }
+    get Name() {
+        const __ = this;
+        return __["Name@"];
+    }
+    set Name(v) {
+        const __ = this;
+        __["Name@"] = v;
+    }
+    get Description() {
+        const __ = this;
+        return __["Description@"];
+    }
+    set Description(v) {
+        const __ = this;
+        __["Description@"] = v;
+    }
+    get Organisation() {
+        const __ = this;
+        return __["Organisation@"];
+    }
+    set Organisation(v) {
+        const __ = this;
+        __["Organisation@"] = v;
+    }
+    get Version() {
+        const __ = this;
+        return __["Version@"];
+    }
+    set Version(v) {
+        const __ = this;
+        __["Version@"] = v;
+    }
+    get Authors() {
+        const __ = this;
+        return __["Authors@"];
+    }
+    set Authors(v) {
+        const __ = this;
+        __["Authors@"] = v;
+    }
+    get EndpointRepositories() {
+        const __ = this;
+        return __["EndpointRepositories@"];
+    }
+    set EndpointRepositories(v) {
+        const __ = this;
+        __["EndpointRepositories@"] = v;
+    }
+    get Tags() {
+        const __ = this;
+        return __["Tags@"];
+    }
+    set Tags(v) {
+        const __ = this;
+        __["Tags@"] = v;
+    }
+    get LastUpdated() {
+        const __ = this;
+        return __["LastUpdated@"];
+    }
+    set LastUpdated(v) {
+        const __ = this;
+        __["LastUpdated@"] = v;
+    }
+    static make(id, table, name, description, organisation, version, authors, repos, tags, lastUpdated) {
+        return new Template(id, table, name, description, organisation, version, authors, repos, tags, lastUpdated);
+    }
+    static create(id, table, name, description, organisation, version, authors, repos, tags, lastUpdated) {
+        return new Template(id, table, unwrap(name), unwrap(description), unwrap(organisation), unwrap(version), unwrap(authors), unwrap(repos), unwrap(tags), unwrap(lastUpdated));
+    }
+    static init(templateName) {
+        return new Template(newGuid(), ArcTable.init(templateName), templateName);
+    }
+    get SemVer() {
+        const this$ = this;
+        return unwrap(SemVer_tryOfString_Z721C83C5(this$.Version));
+    }
+    ReferenceEquals(other) {
+        const this$ = this;
+        return this$ === other;
+    }
+    StructurallyEquals(other) {
+        const this$ = this;
+        return ((((((((this$.Id === other.Id) && equals(this$.Table, other.Table)) && (this$.Name === other.Name)) && equals(this$.Organisation, other.Organisation)) && (this$.Version === other.Version)) && equalsWith(equals, this$.Authors, other.Authors)) && equalsWith(equals, this$.EndpointRepositories, other.EndpointRepositories)) && equalsWith(equals, this$.Tags, other.Tags)) && equals_1(this$.LastUpdated, other.LastUpdated);
+    }
+    Equals(other) {
+        let template;
+        const this$ = this;
+        return (other instanceof Template) && ((template = other, this$.StructurallyEquals(template)));
+    }
+    GetHashCode() {
+        let copyOfStruct, copyOfStruct_1;
+        const this$ = this;
+        return ((((((((((copyOfStruct = this$.Id, stringHash(copyOfStruct))) + safeHash(this$.Table)) + stringHash(this$.Name)) + safeHash(this$.Organisation)) + stringHash(this$.Version)) + identityHash(this$.Authors)) + identityHash(this$.EndpointRepositories)) + identityHash(this$.Tags)) + ((copyOfStruct_1 = this$.LastUpdated, safeHash(copyOfStruct_1)))) | 0;
+    }
+}
+
+export function Template_$reflection() {
+    return class_type("ARCtrl.Templates.Template", void 0, Template);
+}
+
+export function Template_$ctor_67157A5B(id, table, name, description, organisation, version, authors, repos, tags, lastUpdated) {
+    return new Template(id, table, name, description, organisation, version, authors, repos, tags, lastUpdated);
+}
+