@nfdi4plants/arctrl 1.2.0 → 2.0.0-alpha.2

package/{ISA/ISA/ArcTypes → Core/Table}/CompositeCell.js

@@ -1,8 +1,7 @@
-import { int32ToString } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
-import { Union } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
-import { union_type, string_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../OntologyAnnotation.js";
+import { Union } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { union_type, string_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class CompositeCell extends Union {
     constructor(tag, fields) {
@@ -13,69 +12,6 @@ export class CompositeCell extends Union {
     cases() {
         return ["Term", "FreeText", "Unitized"];
     }
-    static fromValue(value, unit) {
-        let matchResult, t, i, i_1, u, f, f_1, u_1, s;
-        switch (value.tag) {
-            case 1: {
-                if (unit != null) {
-                    matchResult = 2;
-                    i_1 = value.fields[0];
-                    u = unit;
-                }
-                else {
-                    matchResult = 1;
-                    i = value.fields[0];
-                }
-                break;
-            }
-            case 2: {
-                if (unit != null) {
-                    matchResult = 4;
-                    f_1 = value.fields[0];
-                    u_1 = unit;
-                }
-                else {
-                    matchResult = 3;
-                    f = value.fields[0];
-                }
-                break;
-            }
-            case 3: {
-                if (unit == null) {
-                    matchResult = 5;
-                    s = value.fields[0];
-                }
-                else {
-                    matchResult = 6;
-                }
-                break;
-            }
-            default:
-                if (unit == null) {
-                    matchResult = 0;
-                    t = value.fields[0];
-                }
-                else {
-                    matchResult = 6;
-                }
-        }
-        switch (matchResult) {
-            case 0:
-                return new CompositeCell(0, [t]);
-            case 1:
-                return new CompositeCell(1, [int32ToString(i)]);
-            case 2:
-                return new CompositeCell(2, [int32ToString(i_1), u]);
-            case 3:
-                return new CompositeCell(1, [f.toString()]);
-            case 4:
-                return new CompositeCell(2, [f_1.toString(), u_1]);
-            case 5:
-                return new CompositeCell(1, [s]);
-            default:
-                throw new Error("could not convert value to cell, invalid combination of value and unit");
-        }
-    }
     get isUnitized() {
         const this$ = this;
         return this$.tag === 2;
@@ -109,11 +45,11 @@ export class CompositeCell extends Union {
     }
     ToUnitizedCell() {
         const this$ = this;
-        return (this$.tag === 1) ? (new CompositeCell(2, ["", OntologyAnnotation.create(void 0, this$.fields[0])])) : ((this$.tag === 0) ? (new CompositeCell(2, ["", this$.fields[0]])) : this$);
+        return (this$.tag === 1) ? (new CompositeCell(2, ["", OntologyAnnotation.create(this$.fields[0])])) : ((this$.tag === 0) ? (new CompositeCell(2, ["", this$.fields[0]])) : this$);
     }
     ToTermCell() {
         const this$ = this;
-        return (this$.tag === 2) ? (new CompositeCell(0, [this$.fields[1]])) : ((this$.tag === 1) ? (new CompositeCell(0, [OntologyAnnotation.create(void 0, this$.fields[0])])) : this$);
+        return (this$.tag === 2) ? (new CompositeCell(0, [this$.fields[1]])) : ((this$.tag === 1) ? (new CompositeCell(0, [OntologyAnnotation.create(this$.fields[0])])) : this$);
     }
     ToFreeTextCell() {
         const this$ = this;
@@ -150,26 +86,33 @@ export class CompositeCell extends Union {
         return new CompositeCell(0, [oa]);
     }
     static createTermFromString(name, tsr, tan) {
-        return new CompositeCell(0, [OntologyAnnotation.fromString(name, tsr, tan)]);
+        return new CompositeCell(0, [OntologyAnnotation.create(name, tsr, tan)]);
     }
     static createUnitized(value, oa) {
-        return new CompositeCell(2, [value, defaultArg(oa, OntologyAnnotation.empty)]);
+        return new CompositeCell(2, [value, defaultArg(oa, new OntologyAnnotation())]);
     }
     static createUnitizedFromString(value, name, tsr, tan) {
-        const tupledArg = [value, OntologyAnnotation.fromString(name, tsr, tan)];
+        const tupledArg = [value, OntologyAnnotation.create(name, tsr, tan)];
         return new CompositeCell(2, [tupledArg[0], tupledArg[1]]);
     }
     static createFreeText(value) {
         return new CompositeCell(1, [value]);
     }
     static get emptyTerm() {
-        return new CompositeCell(0, [OntologyAnnotation.empty]);
+        return new CompositeCell(0, [new OntologyAnnotation()]);
     }
     static get emptyFreeText() {
         return new CompositeCell(1, [""]);
     }
     static get emptyUnitized() {
-        return new CompositeCell(2, ["", OntologyAnnotation.empty]);
+        return new CompositeCell(2, ["", new OntologyAnnotation()]);
+    }
+    UpdateWithOA(oa) {
+        const this$ = this;
+        return (this$.tag === 2) ? CompositeCell.createUnitized(this$.fields[0], oa) : ((this$.tag === 1) ? CompositeCell.createFreeText(oa.NameText) : CompositeCell.createTerm(oa));
+    }
+    static updateWithOA(oa, cell) {
+        return cell.UpdateWithOA(oa);
     }
     toString() {
         const this$ = this;
@@ -187,6 +130,6 @@ export class CompositeCell extends Union {
 }
 
 export function CompositeCell_$reflection() {
-    return union_type("ARCtrl.ISA.CompositeCell", [], CompositeCell, () => [[["Item", OntologyAnnotation_$reflection()]], [["Item", string_type]], [["Item1", string_type], ["Item2", OntologyAnnotation_$reflection()]]]);
+    return union_type("ARCtrl.CompositeCell", [], CompositeCell, () => [[["Item", OntologyAnnotation_$reflection()]], [["Item", string_type]], [["Item1", string_type], ["Item2", OntologyAnnotation_$reflection()]]]);
 }
 

package/{ISA/ISA/ArcTypes → Core/Table}/CompositeColumn.js

@@ -1,10 +1,10 @@
-import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { item } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
-import { fold, empty, singleton, collect, delay, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { item } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+import { fold, empty, singleton, collect, delay, toArray } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { CompositeCell_$reflection, CompositeCell } from "./CompositeCell.js";
-import { Record } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { Record } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
 import { CompositeHeader_$reflection } from "./CompositeHeader.js";
-import { record_type, array_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { record_type, array_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class CompositeColumn extends Record {
     constructor(Header, Cells) {
@@ -65,6 +65,6 @@ export class CompositeColumn extends Record {
 }
 
 export function CompositeColumn_$reflection() {
-    return record_type("ARCtrl.ISA.CompositeColumn", [], CompositeColumn, () => [["Header", CompositeHeader_$reflection()], ["Cells", array_type(CompositeCell_$reflection())]]);
+    return record_type("ARCtrl.CompositeColumn", [], CompositeColumn, () => [["Header", CompositeHeader_$reflection()], ["Cells", array_type(CompositeCell_$reflection())]]);
 }
 

package/{ISA/ISA/ArcTypes → Core/Table}/CompositeHeader.js

@@ -1,14 +1,10 @@
-import { map } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
-import { union_type, string_type, getUnionCases, name } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
-import { Union, toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
-import { ActivePatterns_$007CTermColumn$007C_$007C, Pattern_OutputPattern, Pattern_InputPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseIOTypeHeader } from "../Regex.js";
-import { equals } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
-import { ProtocolParameter } from "../JsonTypes/ProtocolParameter.js";
-import { Factor } from "../JsonTypes/Factor.js";
-import { MaterialAttribute_create_Z6C54B221 } from "../JsonTypes/MaterialAttribute.js";
-import { Component_create_61502994 } from "../JsonTypes/Component.js";
+import { map } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+import { union_type, string_type, getUnionCases, name } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
+import { Union, toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { ActivePatterns_$007CTermColumn$007C_$007C, Pattern_OutputPattern, Pattern_InputPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseIOTypeHeader } from "../Helper/Regex.js";
+import { equals } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../OntologyAnnotation.js";
 
 export class IOType extends Union {
     constructor(tag, fields) {
@@ -239,7 +235,7 @@ export class IOType extends Union {
 }
 
 export function IOType_$reflection() {
-    return union_type("ARCtrl.ISA.IOType", [], IOType, () => [[], [], [], [], [], [], [["Item", string_type]]]);
+    return union_type("ARCtrl.IOType", [], IOType, () => [[], [], [], [], [], [], [["Item", string_type]]]);
 }
 
 export class CompositeHeader extends Union {
@@ -263,7 +259,7 @@ export class CompositeHeader extends Union {
     }
     ToTerm() {
         const this$ = this;
-        return (this$.tag === 2) ? this$.fields[0] : ((this$.tag === 1) ? this$.fields[0] : ((this$.tag === 0) ? this$.fields[0] : ((this$.tag === 4) ? OntologyAnnotation.fromString(toString(this$), void 0, this$.GetFeaturedColumnAccession) : ((this$.tag === 8) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 5) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 6) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 7) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 9) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 10) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 11) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 12) ? OntologyAnnotation.fromString(toString(this$)) : ((this$.tag === 13) ? OntologyAnnotation.fromString(toString(this$)) : this$.fields[0]))))))))))));
+        return (this$.tag === 2) ? this$.fields[0] : ((this$.tag === 1) ? this$.fields[0] : ((this$.tag === 0) ? this$.fields[0] : ((this$.tag === 4) ? OntologyAnnotation.create(toString(this$), void 0, this$.GetFeaturedColumnAccession) : ((this$.tag === 8) ? OntologyAnnotation.create(toString(this$)) : ((this$.tag === 5) ? OntologyAnnotation.create(toString(this$)) : ((this$.tag === 6) ? OntologyAnnotation.create(toString(this$)) : ((this$.tag === 7) ? OntologyAnnotation.create(toString(this$)) : ((this$.tag === 9) ? OntologyAnnotation.create(toString(this$)) : ((this$.tag === 10) ? OntologyAnnotation.create(toString(this$)) : ((this$.tag === 11) ? OntologyAnnotation.create(toString(this$)) : ((this$.tag === 12) ? OntologyAnnotation.create(toString(this$)) : ((this$.tag === 13) ? OntologyAnnotation.create(toString(this$)) : this$.fields[0]))))))))))));
     }
     static OfHeaderString(str) {
         const matchValue = str.trim();
@@ -288,16 +284,16 @@ export class CompositeHeader extends Union {
                     switch (matchValue_1) {
                         case "Parameter":
                         case "Parameter Value":
-                            return new CompositeHeader(3, [OntologyAnnotation.fromString(r_2.TermName)]);
+                            return new CompositeHeader(3, [OntologyAnnotation.create(r_2.TermName)]);
                         case "Factor":
                         case "Factor Value":
-                            return new CompositeHeader(2, [OntologyAnnotation.fromString(r_2.TermName)]);
+                            return new CompositeHeader(2, [OntologyAnnotation.create(r_2.TermName)]);
                         case "Characteristic":
                         case "Characteristics":
                         case "Characteristics Value":
-                            return new CompositeHeader(1, [OntologyAnnotation.fromString(r_2.TermName)]);
+                            return new CompositeHeader(1, [OntologyAnnotation.create(r_2.TermName)]);
                         case "Component":
-                            return new CompositeHeader(0, [OntologyAnnotation.fromString(r_2.TermName)]);
+                            return new CompositeHeader(0, [OntologyAnnotation.create(r_2.TermName)]);
                         default:
                             return new CompositeHeader(13, [str]);
                     }
@@ -545,22 +541,6 @@ export class CompositeHeader extends Union {
                 return void 0;
         }
     }
-    TryParameter() {
-        const this$ = this;
-        return (this$.tag === 3) ? ProtocolParameter.create(void 0, this$.fields[0]) : void 0;
-    }
-    TryFactor() {
-        const this$ = this;
-        return (this$.tag === 2) ? Factor.create(void 0, void 0, this$.fields[0]) : void 0;
-    }
-    TryCharacteristic() {
-        const this$ = this;
-        return (this$.tag === 1) ? MaterialAttribute_create_Z6C54B221(void 0, this$.fields[0]) : void 0;
-    }
-    TryComponent() {
-        const this$ = this;
-        return (this$.tag === 0) ? Component_create_61502994(void 0, void 0, void 0, this$.fields[0]) : void 0;
-    }
     GetUITooltip() {
         const this$ = this;
         return CompositeHeader.getUITooltip(this$);
@@ -750,6 +730,6 @@ export class CompositeHeader extends Union {
 }
 
 export function CompositeHeader_$reflection() {
-    return union_type("ARCtrl.ISA.CompositeHeader", [], CompositeHeader, () => [[["Item", OntologyAnnotation_$reflection()]], [["Item", OntologyAnnotation_$reflection()]], [["Item", OntologyAnnotation_$reflection()]], [["Item", OntologyAnnotation_$reflection()]], [], [], [], [], [], [], [], [["Item", IOType_$reflection()]], [["Item", IOType_$reflection()]], [["Item", string_type]]]);
+    return union_type("ARCtrl.CompositeHeader", [], CompositeHeader, () => [[["Item", OntologyAnnotation_$reflection()]], [["Item", OntologyAnnotation_$reflection()]], [["Item", OntologyAnnotation_$reflection()]], [["Item", OntologyAnnotation_$reflection()]], [], [], [], [], [], [], [], [["Item", IOType_$reflection()]], [["Item", IOType_$reflection()]], [["Item", string_type]]]);
 }
 

package/{Templates → Core}/Template.js

@@ -1,12 +1,12 @@
-import { identityHash, safeHash, stringHash, equals } from "../fable_modules/fable-library-js.4.13.0/Util.js";
-import { Union } from "../fable_modules/fable-library-js.4.13.0/Types.js";
-import { class_type, union_type, string_type } from "../fable_modules/fable-library-js.4.13.0/Reflection.js";
-import { defaultArg, unwrap } from "../fable_modules/fable-library-js.4.13.0/Option.js";
-import { newGuid } from "../fable_modules/fable-library-js.4.13.0/Guid.js";
-import { ArcTable } from "../ISA/ISA/ArcTypes/ArcTable.js";
-import { SemVer_tryOfString_Z721C83C5 } from "../SemVer.js";
-import { equalsWith } from "../fable_modules/fable-library-js.4.13.0/Array.js";
-import { toUniversalTime, now, equals as equals_1 } from "../fable_modules/fable-library-js.4.13.0/Date.js";
+import { safeHash, equals } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { Union } from "../fable_modules/fable-library-js.4.16.0/Types.js";
+import { class_type, union_type, string_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
+import { defaultArg, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { newGuid } from "../fable_modules/fable-library-js.4.16.0/Guid.js";
+import { ArcTable } from "./Table/ArcTable.js";
+import { SemVer_tryOfString_Z721C83C5 } from "./Helper/SemVer.js";
+import { hashDateTime, boxHashSeq, boxHashArray } from "./Helper/HashCodes.js";
+import { now } from "../fable_modules/fable-library-js.4.16.0/Date.js";
 
 export class Organisation extends Union {
     constructor(tag, fields) {
@@ -31,12 +31,11 @@ export class Organisation extends Union {
 }
 
 export function Organisation_$reflection() {
-    return union_type("ARCtrl.Template.Organisation", [], Organisation, () => [[], [["Item", string_type]]]);
+    return union_type("ARCtrl.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"]));
@@ -44,7 +43,7 @@ export class Template {
         const authors_1 = defaultArg(authors, []);
         const repos_1 = defaultArg(repos, []);
         const tags_1 = defaultArg(tags, []);
-        const lastUpdated_1 = defaultArg(lastUpdated, (copyOfStruct = now(), toUniversalTime(copyOfStruct)));
+        const lastUpdated_1 = defaultArg(lastUpdated, now());
         this["Id@"] = id;
         this["Table@"] = table;
         this["Name@"] = name_1;
@@ -155,7 +154,7 @@ export class Template {
     }
     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$.LastUpdated, other.LastUpdated);
+        return safeHash(this$) === safeHash(other);
     }
     Equals(other) {
         let template;
@@ -163,17 +162,17 @@ export class Template {
         return (other instanceof Template) && ((template = other, this$.StructurallyEquals(template)));
     }
     GetHashCode() {
-        let copyOfStruct, copyOfStruct_1;
+        let copyOfStruct;
         const this$ = 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$.LastUpdated, safeHash(copyOfStruct_1)))) | 0;
+        return boxHashArray([(copyOfStruct = this$.Id, copyOfStruct), safeHash(this$.Table), this$.Name, safeHash(this$.Organisation), this$.Version, boxHashSeq(this$.Authors), boxHashSeq(this$.EndpointRepositories), boxHashSeq(this$.Tags), hashDateTime(this$.LastUpdated)]) | 0;
     }
 }
 
 export function Template_$reflection() {
-    return class_type("ARCtrl.Template.Template", void 0, Template);
+    return class_type("ARCtrl.Template", void 0, Template);
 }
 
-export function Template_$ctor_4AC720A8(id, table, name, description, organisation, version, authors, repos, tags, lastUpdated) {
+export function Template_$ctor_Z17EA765C(id, table, name, description, organisation, version, authors, repos, tags, lastUpdated) {
     return new Template(id, table, name, description, organisation, version, authors, repos, tags, lastUpdated);
 }
 

package/Core/Templates.js

@@ -0,0 +1,84 @@
+import { defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { ResizeArray_append, ResizeArray_collect, ResizeArray_distinct, ResizeArray_filter } from "./Helper/Collections.js";
+import { uncurry2, safeHash, equals, disposeSafe, getEnumerator } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { contains as contains_1 } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { addRangeInPlace, item } from "../fable_modules/fable-library-js.4.16.0/Array.js";
+import { Array_distinct } from "../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { class_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
+
+export function TemplatesAux_getComparer(matchAll) {
+    if (defaultArg(matchAll, false)) {
+        return (e) => ((e_1) => (e && e_1));
+    }
+    else {
+        return (e_2) => ((e_3) => (e_2 || e_3));
+    }
+}
+
+export function TemplatesAux_filterOnTags(tagGetter, queryTags, comparer, templates) {
+    return ResizeArray_filter((t) => {
+        const templateTags = tagGetter(t);
+        let isValid = void 0;
+        let enumerator = getEnumerator(queryTags);
+        try {
+            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+                const contains = contains_1(enumerator["System.Collections.Generic.IEnumerator`1.get_Current"](), templateTags, {
+                    Equals: equals,
+                    GetHashCode: safeHash,
+                });
+                const isValid_1 = isValid;
+                if (isValid_1 != null) {
+                    const maybe = isValid_1;
+                    isValid = comparer(maybe, contains);
+                }
+                else {
+                    isValid = contains;
+                }
+            }
+        }
+        finally {
+            disposeSafe(enumerator);
+        }
+        return defaultArg(isValid, false);
+    }, templates);
+}
+
+export class Templates {
+    constructor() {
+    }
+    static getDistinctTags(templates) {
+        return ResizeArray_distinct(ResizeArray_collect((t) => t.Tags, templates));
+    }
+    static getDistinctEndpointRepositories(templates) {
+        return ResizeArray_distinct(ResizeArray_collect((t) => t.EndpointRepositories, templates));
+    }
+    static getDistinctOntologyAnnotations(templates) {
+        const oas = [];
+        for (let idx = 0; idx <= (templates.length - 1); idx++) {
+            const t = item(idx, templates);
+            addRangeInPlace(t.Tags, oas);
+            addRangeInPlace(t.EndpointRepositories, oas);
+        }
+        return Array_distinct(Array.from(oas), {
+            Equals: equals,
+            GetHashCode: safeHash,
+        });
+    }
+    static filterByTags(queryTags, matchAll) {
+        return (templates) => TemplatesAux_filterOnTags((t) => t.Tags, queryTags, uncurry2(TemplatesAux_getComparer(matchAll)), templates);
+    }
+    static filterByEndpointRepositories(queryTags, matchAll) {
+        return (templates) => TemplatesAux_filterOnTags((t) => t.EndpointRepositories, queryTags, uncurry2(TemplatesAux_getComparer(matchAll)), templates);
+    }
+    static filterByOntologyAnnotation(queryTags, matchAll) {
+        return (templates) => TemplatesAux_filterOnTags((t) => ResizeArray_append(t.Tags, t.EndpointRepositories), queryTags, uncurry2(TemplatesAux_getComparer(matchAll)), templates);
+    }
+    static filterByDataPLANT(templates) {
+        return ResizeArray_filter((t) => t.Organisation.IsOfficial(), templates);
+    }
+}
+
+export function Templates_$reflection() {
+    return class_type("ARCtrl.Templates", void 0, Templates);
+}
+

package/FileSystem/Commit.js

@@ -1,5 +1,5 @@
-import { Record } from "../fable_modules/fable-library-js.4.13.0/Types.js";
-import { record_type, class_type, string_type } from "../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Record } from "../fable_modules/fable-library-js.4.16.0/Types.js";
+import { record_type, class_type, string_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class Commit extends Record {
     constructor(Hash, UserName, UserEmail, Date$, Message) {

package/FileSystem/FileSystem.js

@@ -1,9 +1,9 @@
-import { defaultArg } from "../fable_modules/fable-library-js.4.13.0/Option.js";
+import { defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { FileSystemTree_$reflection, FileSystemTree } from "./FileSystemTree.js";
-import { map, append } from "../fable_modules/fable-library-js.4.13.0/Array.js";
-import { Record } from "../fable_modules/fable-library-js.4.13.0/Types.js";
+import { map, append } from "../fable_modules/fable-library-js.4.16.0/Array.js";
+import { Record } from "../fable_modules/fable-library-js.4.16.0/Types.js";
 import { Commit_$reflection } from "./Commit.js";
-import { record_type, array_type } from "../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { record_type, array_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class FileSystem extends Record {
     constructor(Tree, History) {

package/FileSystem/FileSystemTree.js

@@ -1,12 +1,12 @@
-import { unwrap, defaultArg } from "../fable_modules/fable-library-js.4.13.0/Option.js";
-import { append as append_1, choose, equalsWith, tail, head, map, tryFind } from "../fable_modules/fable-library-js.4.13.0/Array.js";
-import { singleton, append, delay, toArray } from "../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { Array_distinct, Array_groupBy } from "../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { curry2, arrayHash, stringHash } from "../fable_modules/fable-library-js.4.13.0/Util.js";
+import { unwrap, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { append as append_1, choose, equalsWith, tail, head, map, tryFind } from "../fable_modules/fable-library-js.4.16.0/Array.js";
+import { singleton, append, delay, toArray } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { Array_distinct, Array_groupBy } from "../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { curry2, arrayHash, stringHash } from "../fable_modules/fable-library-js.4.16.0/Util.js";
 import { combineMany, split } from "./Path.js";
-import { empty, reverse, toArray as toArray_1, cons } from "../fable_modules/fable-library-js.4.13.0/List.js";
-import { Union } from "../fable_modules/fable-library-js.4.13.0/Types.js";
-import { union_type, array_type, string_type } from "../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { empty, reverse, toArray as toArray_1, cons } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { Union } from "../fable_modules/fable-library-js.4.16.0/Types.js";
+import { union_type, array_type, string_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class FileSystemTree extends Union {
     constructor(tag, fields) {
@@ -215,6 +215,44 @@ export class FileSystemTree extends Union {
         const this$ = this;
         return (this$.tag === 0) ? (new FileSystemTree(0, [this$.fields[0]])) : (new FileSystemTree(1, [this$.fields[0], map((c) => c.Copy(), this$.fields[1])]));
     }
+    static createGitKeepFile() {
+        return FileSystemTree.createFile(".gitkeep");
+    }
+    static createReadmeFile() {
+        return FileSystemTree.createFile("README.md");
+    }
+    static createEmptyFolder(name) {
+        return FileSystemTree.createFolder(name, [FileSystemTree.createGitKeepFile()]);
+    }
+    static createAssayFolder(assayName) {
+        const dataset = FileSystemTree.createEmptyFolder("dataset");
+        const protocols = FileSystemTree.createEmptyFolder("protocols");
+        const readme = FileSystemTree.createReadmeFile();
+        const assayFile = FileSystemTree.createFile("isa.assay.xlsx");
+        return FileSystemTree.createFolder(assayName, [dataset, protocols, assayFile, readme]);
+    }
+    static createStudyFolder(studyName) {
+        const resources = FileSystemTree.createEmptyFolder("resources");
+        const protocols = FileSystemTree.createEmptyFolder("protocols");
+        const readme = FileSystemTree.createReadmeFile();
+        const studyFile = FileSystemTree.createFile("isa.study.xlsx");
+        return FileSystemTree.createFolder(studyName, [resources, protocols, studyFile, readme]);
+    }
+    static createInvestigationFile() {
+        return FileSystemTree.createFile("isa.investigation.xlsx");
+    }
+    static createAssaysFolder(assays) {
+        return FileSystemTree.createFolder("assays", append_1([FileSystemTree.createGitKeepFile()], assays));
+    }
+    static createStudiesFolder(studies) {
+        return FileSystemTree.createFolder("studies", append_1([FileSystemTree.createGitKeepFile()], studies));
+    }
+    static createWorkflowsFolder(workflows) {
+        return FileSystemTree.createFolder("workflows", append_1([FileSystemTree.createGitKeepFile()], workflows));
+    }
+    static createRunsFolder(runs) {
+        return FileSystemTree.createFolder("runs", append_1([FileSystemTree.createGitKeepFile()], runs));
+    }
 }
 
 export function FileSystemTree_$reflection() {

package/FileSystem/Path.js

@@ -1,5 +1,5 @@
-import { trim, join, trimStart, trimEnd, split as split_1 } from "../fable_modules/fable-library-js.4.13.0/String.js";
-import { last, mapIndexed } from "../fable_modules/fable-library-js.4.13.0/Array.js";
+import { trim, join, trimStart, trimEnd, split as split_1 } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { last, mapIndexed } from "../fable_modules/fable-library-js.4.16.0/Array.js";
 
 export const seperators = ["/", "\\"];
 
@@ -36,3 +36,11 @@ export function isFile(fileName, path) {
     return getFileName(path) === fileName;
 }
 
+export function getAssayFolderPath(assayIdentifier) {
+    return combine("assays", assayIdentifier);
+}
+
+export function getStudyFolderPath(studyIdentifier) {
+    return combine("studies", studyIdentifier);
+}
+

package/Json/ARC.js

@@ -0,0 +1,25 @@
+import { ofArray, choose } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { equals } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { tryInclude } from "./Encode.js";
+import { Investigation_ROCrate_decoder, Investigation_ROCrate_encoder } from "./Investigation.js";
+import { context_jsonvalue, conformsTo_jsonvalue } from "./context/rocrate/rocrate_context.js";
+import { object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+
+export function encoder(isa) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([tryInclude("@type", (value) => (new Json(0, [value])), "CreativeWork"), tryInclude("@id", (value_2) => (new Json(0, [value_2])), "ro-crate-metadata.json"), tryInclude("about", Investigation_ROCrate_encoder, isa), ["conformsTo", conformsTo_jsonvalue], ["@context", context_jsonvalue]]))]);
+}
+
+export const decoder = object((get$) => {
+    const objectArg = get$.Optional;
+    return objectArg.Field("about", Investigation_ROCrate_decoder);
+});
+