@nfdi4plants/arctrl 1.0.7 → 1.2.0

package/ISA/ISA.Json/ArcTypes/CompositeHeader.js

@@ -1,71 +1,43 @@
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "../Ontology.js";
 import { ConverterOptions_$ctor } from "../ConverterOptions.js";
-import { empty, singleton } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { empty, singleton } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
 import { IOType_decoder, IOType_encoder } from "./IOType.js";
-import { toString, list, object } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { fromString, index, string, object as object_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
-import { uncurry2 } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { list } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
+import { index, string, object } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { CompositeHeader } from "../../ISA/ArcTypes/CompositeHeader.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
-import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { fromString } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
+import { toString } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
+import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
 
 export function CompositeHeader_encoder(ch) {
     const oaToJsonString = (oa) => OntologyAnnotation_encoder(ConverterOptions_$ctor(), oa);
     const patternInput = (ch.tag === 3) ? ["Parameter", singleton(oaToJsonString(ch.fields[0]))] : ((ch.tag === 2) ? ["Factor", singleton(oaToJsonString(ch.fields[0]))] : ((ch.tag === 1) ? ["Characteristic", singleton(oaToJsonString(ch.fields[0]))] : ((ch.tag === 0) ? ["Component", singleton(oaToJsonString(ch.fields[0]))] : ((ch.tag === 4) ? ["ProtocolType", empty()] : ((ch.tag === 8) ? ["ProtocolREF", empty()] : ((ch.tag === 5) ? ["ProtocolDescription", empty()] : ((ch.tag === 6) ? ["ProtocolUri", empty()] : ((ch.tag === 7) ? ["ProtocolVersion", empty()] : ((ch.tag === 9) ? ["Performer", empty()] : ((ch.tag === 10) ? ["Date", empty()] : ((ch.tag === 11) ? ["Input", singleton(IOType_encoder(ch.fields[0]))] : ((ch.tag === 12) ? ["Output", singleton(IOType_encoder(ch.fields[0]))] : [ch.fields[0], empty()]))))))))))));
-    return object([["headertype", patternInput[0]], ["values", list(patternInput[1])]]);
+    return new Json(5, [[["headertype", new Json(0, [patternInput[0]])], ["values", list(patternInput[1])]]]);
 }
 
-export const CompositeHeader_decoder = (path_3) => ((v) => object_1((get$) => {
+export const CompositeHeader_decoder = object((get$) => {
     let headerType;
     const objectArg = get$.Required;
     headerType = objectArg.Field("headertype", string);
     const oa = () => {
-        let arg_3;
-        const decoder = OntologyAnnotation_decoder(ConverterOptions_$ctor());
-        arg_3 = ((path_1) => ((value_1) => index(0, uncurry2(decoder), path_1, value_1)));
+        const arg_3 = index(0, OntologyAnnotation_decoder(ConverterOptions_$ctor()));
         const objectArg_1 = get$.Required;
-        return objectArg_1.Field("values", uncurry2(arg_3));
+        return objectArg_1.Field("values", arg_3);
     };
     const io = () => {
+        const arg_5 = index(0, IOType_decoder);
         const objectArg_2 = get$.Required;
-        return objectArg_2.Field("values", (path_2, value_2) => index(0, uncurry2(IOType_decoder), path_2, value_2));
+        return objectArg_2.Field("values", arg_5);
     };
-    switch (headerType) {
-        case "Characteristic":
-            return new CompositeHeader(1, [oa()]);
-        case "Parameter":
-            return new CompositeHeader(3, [oa()]);
-        case "Component":
-            return new CompositeHeader(0, [oa()]);
-        case "Factor":
-            return new CompositeHeader(2, [oa()]);
-        case "Input":
-            return new CompositeHeader(11, [io()]);
-        case "Output":
-            return new CompositeHeader(12, [io()]);
-        case "ProtocolType":
-            return new CompositeHeader(4, []);
-        case "ProtocolREF":
-            return new CompositeHeader(8, []);
-        case "ProtocolDescription":
-            return new CompositeHeader(5, []);
-        case "ProtocolUri":
-            return new CompositeHeader(6, []);
-        case "ProtocolVersion":
-            return new CompositeHeader(7, []);
-        case "Performer":
-            return new CompositeHeader(9, []);
-        case "Date":
-            return new CompositeHeader(10, []);
-        default:
-            return new CompositeHeader(13, [headerType]);
-    }
-}, path_3, v));
+    return (headerType === "Characteristic") ? (new CompositeHeader(1, [oa()])) : ((headerType === "Parameter") ? (new CompositeHeader(3, [oa()])) : ((headerType === "Component") ? (new CompositeHeader(0, [oa()])) : ((headerType === "Factor") ? (new CompositeHeader(2, [oa()])) : ((headerType === "Input") ? (new CompositeHeader(11, [io()])) : ((headerType === "Output") ? (new CompositeHeader(12, [io()])) : ((headerType === "ProtocolType") ? (new CompositeHeader(4, [])) : ((headerType === "ProtocolREF") ? (new CompositeHeader(8, [])) : ((headerType === "ProtocolDescription") ? (new CompositeHeader(5, [])) : ((headerType === "ProtocolUri") ? (new CompositeHeader(6, [])) : ((headerType === "ProtocolVersion") ? (new CompositeHeader(7, [])) : ((headerType === "Performer") ? (new CompositeHeader(9, [])) : ((headerType === "Date") ? (new CompositeHeader(10, [])) : (new CompositeHeader(13, [headerType]))))))))))))));
+});
 
 export function ARCtrl_ISA_CompositeHeader__CompositeHeader_fromJsonString_Static_Z721C83C5(jsonString) {
-    const matchValue = fromString(uncurry2(CompositeHeader_decoder), jsonString);
+    const matchValue = fromString(CompositeHeader_decoder, jsonString);
     if (matchValue.tag === 1) {
-        return toFail(printf("Error. Unable to parse json string to CompositeHeader: %s"))(matchValue.fields[0]);
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
     }
     else {
         return matchValue.fields[0];

package/ISA/ISA.Json/ArcTypes/IOType.js

@@ -1,24 +1,22 @@
-import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
-import { fromString, string, succeed, andThen } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
-import { uncurry2, uncurry3 } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { string, succeed, andThen } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { IOType } from "../../ISA/ArcTypes/CompositeHeader.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
-import { toString as toString_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { fromString } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
+import { toString as toString_1 } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
+import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
 
 export function IOType_encoder(io) {
-    return toString(io);
+    return new Json(0, [toString(io)]);
 }
 
-export const IOType_decoder = (path_1) => ((value_1) => andThen(uncurry3((s) => {
-    const output = IOType.ofString(s);
-    return (arg10$0040) => ((arg20$0040) => succeed(output, arg10$0040, arg20$0040));
-}), string, path_1, value_1));
+export const IOType_decoder = andThen((s) => succeed(IOType.ofString(s)), string);
 
 export function ARCtrl_ISA_IOType__IOType_fromJsonString_Static_Z721C83C5(jsonString) {
-    const matchValue = fromString(uncurry2(IOType_decoder), jsonString);
+    const matchValue = fromString(IOType_decoder, jsonString);
     if (matchValue.tag === 1) {
-        return toFail(printf("Error. Unable to parse json string to IOType: %s"))(matchValue.fields[0]);
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
     }
     else {
         return matchValue.fields[0];

package/ISA/ISA.Json/ArcTypes/OATable.js

@@ -0,0 +1,42 @@
+import { sortBy, map, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { comparePrimitives } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { item, map as map_1 } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
+import { ConverterOptions_$ctor } from "../ConverterOptions.js";
+import { OntologyAnnotation_compressedDecoder, OntologyAnnotation_compressedEncoder } from "../Ontology.js";
+import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { int, object, array as array_1 } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { Dict_tryFind } from "../../ISA/Helper.js";
+import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
+
+export function OATable_arrayFromMap(otm) {
+    return toArray(map((kv_1) => kv_1[0], sortBy((kv) => kv[1], otm, {
+        Compare: comparePrimitives,
+    })));
+}
+
+export function OATable_encoder(stringTable, ot) {
+    let options;
+    return new Json(6, [map_1((options = ConverterOptions_$ctor(), (oa) => OntologyAnnotation_compressedEncoder(stringTable, options, oa)), ot)]);
+}
+
+export function OATable_decoder(stringTable) {
+    return array_1(OntologyAnnotation_compressedDecoder(stringTable, ConverterOptions_$ctor()));
+}
+
+export function OATable_encodeOA(otm, oa) {
+    const matchValue = Dict_tryFind(oa, otm);
+    if (matchValue == null) {
+        const i_1 = otm.size | 0;
+        addToDict(otm, oa, i_1);
+        return new Json(7, [i_1 >>> 0]);
+    }
+    else {
+        const i = matchValue | 0;
+        return new Json(7, [i >>> 0]);
+    }
+}
+
+export function OATable_decodeOA(ot) {
+    return object((get$) => item(get$.Required.Raw(int), ot));
+}
+

package/ISA/ISA.Json/Assay.js

@@ -1,37 +1,47 @@
-import { toString, nil, object as object_22 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { ofArray, choose } from "../../fable_modules/fable-library.4.5.0/List.js";
-import { uncurry2, equals } from "../../fable_modules/fable-library.4.5.0/Util.js";
-import { tryInclude } from "./GEncode.js";
+import { ofArray, choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
+import { equals } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { tryInclude, tryIncludeList } from "./GEncode.js";
 import { Data_decoder, Data_encoder, Sample_decoder, Sample_encoder } from "./Data.js";
 import { MaterialAttribute_decoder, MaterialAttribute_encoder, Material_decoder, Material_encoder } from "./Material.js";
-import { string, list as list_1, object as object_23 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { uri, object } from "./Decode.js";
+import { string, list as list_1 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { AssayMaterials } from "../ISA/JsonTypes/AssayMaterials.js";
+import { printf, toText, replace, remove } from "../../fable_modules/fable-library-js.4.13.0/String.js";
+import { max } from "../../fable_modules/fable-library-js.4.13.0/Double.js";
 import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.5.0/Seq.js";
-import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
+import { Operators_FailurePattern } from "../../fable_modules/fable-library-js.4.13.0/FSharp.Core.js";
+import { Assay_identifierFromFileName } from "../ISA/Identifier.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeContext, ConverterOptions__get_IsRoCrate, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
+import { list as list_2 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
 import { Process_decoder, Process_encoder } from "./Process.js";
-import { decoder as decoder_5, encoder } from "./Comment.js";
-import { fromJsonString, uri } from "./Decode.js";
+import { decoder as decoder_1, encoder } from "./Comment.js";
+import { context_jsonvalue } from "./context/rocrate/isa_assay_context.js";
 import { Assay } from "../ISA/JsonTypes/Assay.js";
+import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
 
 export function AssayMaterials_encoder(options, oa) {
-    return object_22(choose((tupledArg) => {
+    return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
-        if (equals(v, nil)) {
+        if (equals(v, new Json(3, []))) {
             return void 0;
         }
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([tryInclude("samples", (oa_1) => Sample_encoder(options, oa_1), oa["Samples"]), tryInclude("otherMaterials", (oa_2) => Material_encoder(options, oa_2), oa["OtherMaterials"])])));
+    }, ofArray([tryIncludeList("samples", (oa_1) => Sample_encoder(options, oa_1), oa.Samples), tryIncludeList("otherMaterials", (oa_2) => Material_encoder(options, oa_2), oa.OtherMaterials)]))]);
 }
 
+export const AssayMaterials_allowedFields = ofArray(["samples", "otherMaterials"]);
+
 export function AssayMaterials_decoder(options) {
-    return (path_2) => ((v) => object_23((get$) => {
-        let objectArg, objectArg_1;
-        return new AssayMaterials((objectArg = get$.Optional, objectArg.Field("samples", (path, value) => list_1((s, json) => Sample_decoder(options, s, json), path, value))), (objectArg_1 = get$.Optional, objectArg_1.Field("otherMaterials", (path_1, value_1) => list_1((s_1, json_1) => Material_decoder(options, s_1, json_1), path_1, value_1))));
-    }, path_2, v));
+    return object(AssayMaterials_allowedFields, (get$) => {
+        let arg_1, objectArg, arg_3, objectArg_1;
+        return new AssayMaterials((arg_1 = list_1(Sample_decoder(options)), (objectArg = get$.Optional, objectArg.Field("samples", arg_1))), (arg_3 = list_1(Material_decoder(options)), (objectArg_1 = get$.Optional, objectArg_1.Field("otherMaterials", arg_3))));
+    });
 }
 
 export function Assay_genID(a) {
@@ -42,7 +52,8 @@ export function Assay_genID(a) {
             return "#EmptyAssay";
         }
         else {
-            return matchValue_1;
+            const n = matchValue_1;
+            return remove(replace(n, " ", "_"), 0, 1 + max(n.lastIndexOf("/"), n.lastIndexOf("\\")));
         }
     }
     else {
@@ -50,56 +61,69 @@ export function Assay_genID(a) {
     }
 }
 
-export function Assay_encoder(options, oa) {
-    return object_22(choose((tupledArg) => {
+export function Assay_encoder(options, studyName, oa) {
+    let assayName;
+    try {
+        const matchValue = oa.FileName;
+        assayName = ((matchValue == null) ? void 0 : Assay_identifierFromFileName(matchValue));
+    }
+    catch (matchValue_1) {
+        const activePatternResult = Operators_FailurePattern(matchValue_1);
+        if (activePatternResult != null) {
+            const msg = activePatternResult;
+            assayName = void 0;
+        }
+        else {
+            throw matchValue_1;
+        }
+    }
+    return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
-        if (equals(v, nil)) {
+        if (equals(v, new Json(3, []))) {
             return void 0;
         }
         else {
             return [tupledArg[0], v];
         }
-    }, toList(delay(() => {
-        let value, s;
-        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = Assay_genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : singleton(tryInclude("@id", (value_2) => {
-            let s_1;
-            const value_3 = value_2;
-            return (typeof value_3 === "string") ? ((s_1 = value_3, s_1)) : nil;
-        }, oa["ID"])), delay(() => {
-            let value_5, s_2;
-            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "Assay", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("filename", (value_7) => {
-                let s_3;
-                const value_8 = value_7;
-                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
-            }, oa["FileName"])), delay(() => append(singleton(tryInclude("measurementType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["MeasurementType"])), delay(() => append(singleton(tryInclude("technologyType", (oa_2) => OntologyAnnotation_encoder(options, oa_2), oa["TechnologyType"])), delay(() => append(singleton(tryInclude("technologyPlatform", (value_10) => {
-                let s_4;
-                const value_11 = value_10;
-                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
-            }, oa["TechnologyPlatform"])), delay(() => append(singleton(tryInclude("dataFiles", (oa_3) => Data_encoder(options, oa_3), oa["DataFiles"])), delay(() => append(singleton(tryInclude("materials", (oa_4) => AssayMaterials_encoder(options, oa_4), oa["Materials"])), delay(() => append(singleton(tryInclude("characteristicCategories", (oa_5) => MaterialAttribute_encoder(options, oa_5), oa["CharacteristicCategories"])), delay(() => append(singleton(tryInclude("unitCategories", (oa_6) => OntologyAnnotation_encoder(options, oa_6), oa["UnitCategories"])), delay(() => append(singleton(tryInclude("processSequence", (oa_7) => Process_encoder(options, oa_7), oa["ProcessSequence"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), oa["Comments"]))))))))))))))))))))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [Assay_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_2(ofArray([new Json(0, ["Assay"]), new Json(0, ["ArcAssay"])]))]) : empty(), delay(() => append(singleton(tryInclude("filename", (value_5) => (new Json(0, [value_5])), oa.FileName)), delay(() => append(singleton(tryInclude("measurementType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa.MeasurementType)), delay(() => append(singleton(tryInclude("technologyType", (oa_2) => OntologyAnnotation_encoder(options, oa_2), oa.TechnologyType)), delay(() => append(singleton(tryInclude("technologyPlatform", (value_7) => (new Json(0, [value_7])), oa.TechnologyPlatform)), delay(() => append(singleton(tryIncludeList("dataFiles", (oa_3) => Data_encoder(options, oa_3), oa.DataFiles)), delay(() => {
+        let matchValue_2, m;
+        return append(ConverterOptions__get_IsRoCrate(options) ? ((matchValue_2 = oa.Materials, (matchValue_2 == null) ? (empty()) : ((m = matchValue_2, append(singleton(tryIncludeList("samples", (oa_4) => Sample_encoder(options, oa_4), m.Samples)), delay(() => singleton(tryIncludeList("materials", (oa_5) => Material_encoder(options, oa_5), m.OtherMaterials)))))))) : empty(), delay(() => append(!ConverterOptions__get_IsRoCrate(options) ? singleton(tryInclude("materials", (oa_6) => AssayMaterials_encoder(options, oa_6), oa.Materials)) : empty(), delay(() => append(singleton(tryIncludeList("characteristicCategories", (oa_7) => MaterialAttribute_encoder(options, oa_7), oa.CharacteristicCategories)), delay(() => append(singleton(tryIncludeList("unitCategories", (oa_8) => OntologyAnnotation_encoder(options, oa_8), oa.UnitCategories)), delay(() => append(singleton(tryIncludeList("processSequence", (oa_9) => Process_encoder(options, studyName, assayName, oa_9), oa.ProcessSequence)), delay(() => append(singleton(tryIncludeList("comments", (comment) => encoder(options, comment), oa.Comments)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty())))))))))))));
+    })))))))))))))))))]);
 }
 
+export const Assay_allowedFields = ofArray(["@id", "filename", "measurementType", "technologyType", "technologyPlatform", "dataFiles", "materials", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
+
 export function Assay_decoder(options) {
-    return (path_7) => ((v) => object_23((get$) => {
-        let objectArg, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, decoder_1, objectArg_7, arg_17, decoder_2, objectArg_8, arg_19, decoder_3, objectArg_9, arg_21, decoder_4, objectArg_10;
-        return new Assay((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("filename", string)), (arg_5 = OntologyAnnotation_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", uncurry2(arg_5)))), (arg_7 = OntologyAnnotation_decoder(options), (objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", uncurry2(arg_7)))), (objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", string)), (objectArg_5 = get$.Optional, objectArg_5.Field("dataFiles", (path_2, value_2) => list_1((s_1, json_1) => Data_decoder(options, s_1, json_1), path_2, value_2))), (arg_13 = AssayMaterials_decoder(options), (objectArg_6 = get$.Optional, objectArg_6.Field("materials", uncurry2(arg_13)))), (arg_15 = ((decoder_1 = MaterialAttribute_decoder(options), (path_3) => ((value_3) => list_1(uncurry2(decoder_1), path_3, value_3)))), (objectArg_7 = get$.Optional, objectArg_7.Field("characteristicCategories", uncurry2(arg_15)))), (arg_17 = ((decoder_2 = OntologyAnnotation_decoder(options), (path_4) => ((value_4) => list_1(uncurry2(decoder_2), path_4, value_4)))), (objectArg_8 = get$.Optional, objectArg_8.Field("unitCategories", uncurry2(arg_17)))), (arg_19 = ((decoder_3 = Process_decoder(options), (path_5) => ((value_5) => list_1(uncurry2(decoder_3), path_5, value_5)))), (objectArg_9 = get$.Optional, objectArg_9.Field("processSequence", uncurry2(arg_19)))), (arg_21 = ((decoder_4 = decoder_5(options), (path_6) => ((value_6) => list_1(uncurry2(decoder_4), path_6, value_6)))), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", uncurry2(arg_21)))));
-    }, path_7, v));
+    return object(Assay_allowedFields, (get$) => {
+        let objectArg, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
+        return new Assay((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("filename", string)), (arg_5 = OntologyAnnotation_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", arg_5))), (arg_7 = OntologyAnnotation_decoder(options), (objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", arg_7))), (objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", string)), (arg_11 = list_1(Data_decoder(options)), (objectArg_5 = get$.Optional, objectArg_5.Field("dataFiles", arg_11))), (arg_13 = AssayMaterials_decoder(options), (objectArg_6 = get$.Optional, objectArg_6.Field("materials", arg_13))), (arg_15 = list_1(MaterialAttribute_decoder(options)), (objectArg_7 = get$.Optional, objectArg_7.Field("characteristicCategories", arg_15))), (arg_17 = list_1(OntologyAnnotation_decoder(options)), (objectArg_8 = get$.Optional, objectArg_8.Field("unitCategories", arg_17))), (arg_19 = list_1(Process_decoder(options)), (objectArg_9 = get$.Optional, objectArg_9.Field("processSequence", arg_19))), (arg_21 = list_1(decoder_1(options)), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_21))));
+    });
 }
 
 export function Assay_fromJsonString(s) {
-    return fromJsonString(uncurry2(Assay_decoder(ConverterOptions_$ctor())), s);
+    const matchValue = fromString(Assay_decoder(ConverterOptions_$ctor()), s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
 }
 
 export function Assay_toJsonString(p) {
-    return toString(2, Assay_encoder(ConverterOptions_$ctor(), p));
+    return toString(2, Assay_encoder(ConverterOptions_$ctor(), void 0, p));
 }
 
 /**
  * exports in json-ld format
  */
-export function Assay_toStringLD(a) {
+export function Assay_toJsonldString(a) {
+    let returnVal;
+    return toString(2, Assay_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), void 0, a));
+}
+
+export function Assay_toJsonldStringWithContext(a) {
     let returnVal;
-    return toString(2, Assay_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), a));
+    return toString(2, Assay_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), void 0, a));
 }
 

package/ISA/ISA.Json/Comment.js

@@ -1,15 +1,18 @@
-import { replace } from "../../fable_modules/fable-library.4.5.0/String.js";
-import { value as value_13 } from "../../fable_modules/fable-library.4.5.0/Option.js";
+import { printf, toText, replace } from "../../fable_modules/fable-library-js.4.13.0/String.js";
+import { value as value_8 } from "../../fable_modules/fable-library-js.4.13.0/Option.js";
 import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { toString, nil, object as object_6 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { choose } from "../../fable_modules/fable-library.4.5.0/List.js";
-import { uncurry2, equals } from "../../fable_modules/fable-library.4.5.0/Util.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.5.0/Seq.js";
-import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
+import { choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
+import { equals } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeContext, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
 import { tryInclude } from "./GEncode.js";
-import { string, object as object_7 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
-import { fromJsonString as fromJsonString_1, uri } from "./Decode.js";
+import { context_jsonvalue } from "./context/rocrate/isa_comment_context.js";
+import { string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { uri } from "./Decode.js";
 import { Comment$ } from "../ISA/JsonTypes/Comment.js";
+import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
 
 export function genID(c) {
     const matchValue = c.ID;
@@ -20,7 +23,7 @@ export function genID(c) {
         }
         else {
             const n = matchValue_1;
-            const v = (c.Value != null) ? ("_" + replace(value_13(c.Value), " ", "_")) : "";
+            const v = (c.Value != null) ? ("_" + replace(value_8(c.Value), " ", "_")) : "";
             return ("#Comment_" + replace(n, " ", "_")) + v;
         }
     }
@@ -30,44 +33,32 @@ export function genID(c) {
 }
 
 export function encoder(options, comment) {
-    return object_6(choose((tupledArg) => {
+    return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
-        if (equals(v, nil)) {
+        if (equals(v, new Json(3, []))) {
             return void 0;
         }
         else {
             return [tupledArg[0], v];
         }
-    }, toList(delay(() => {
-        let value, s;
-        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = genID(comment), (typeof value === "string") ? ((s = value, s)) : nil)]) : singleton(tryInclude("@id", (value_2) => {
-            let s_1;
-            const value_3 = value_2;
-            return (typeof value_3 === "string") ? ((s_1 = value_3, s_1)) : nil;
-        }, comment["ID"])), delay(() => {
-            let value_5, s_2;
-            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "Comment", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("name", (value_7) => {
-                let s_3;
-                const value_8 = value_7;
-                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
-            }, comment["Name"])), delay(() => singleton(tryInclude("value", (value_10) => {
-                let s_4;
-                const value_11 = value_10;
-                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
-            }, comment["Value"]))))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [genID(comment)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), comment.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["Comment"])]) : empty(), delay(() => append(singleton(tryInclude("name", (value_4) => (new Json(0, [value_4])), comment.Name)), delay(() => append(singleton(tryInclude("value", (value_6) => (new Json(0, [value_6])), comment.Value)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty()))))))))))))]);
 }
 
 export function decoder(options) {
-    return (path_2) => ((v) => object_7((get$) => {
+    return object((get$) => {
         let objectArg, objectArg_1, objectArg_2;
         return new Comment$((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("value", string)));
-    }, path_2, v));
+    });
 }
 
 export function fromJsonString(s) {
-    return fromJsonString_1(uncurry2(decoder(ConverterOptions_$ctor())), s);
+    const matchValue = fromString(decoder(ConverterOptions_$ctor()), s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
 }
 
 export function toJsonString(c) {
@@ -77,8 +68,13 @@ export function toJsonString(c) {
 /**
  * exports in json-ld format
  */
-export function toStringLD(c) {
+export function toJsonldString(c) {
     let returnVal;
     return toString(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), c));
 }
 
+export function toJsonldStringWithContext(a) {
+    let returnVal;
+    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
+}
+

package/ISA/ISA.Json/ConverterOptions.js

@@ -1,9 +1,11 @@
-import { class_type } from "../../fable_modules/fable-library.4.5.0/Reflection.js";
+import { class_type } from "../../fable_modules/fable-library-js.4.13.0/Reflection.js";
 
 export class ConverterOptions {
     constructor() {
         this.setID = false;
         this.includeType = false;
+        this.includeContext = false;
+        this.isRoCrate = false;
     }
 }
 
@@ -31,3 +33,19 @@ export function ConverterOptions__set_IncludeType_Z1FBCCD16(this$, iT) {
     this$.includeType = iT;
 }
 
+export function ConverterOptions__get_IncludeContext(this$) {
+    return this$.includeContext;
+}
+
+export function ConverterOptions__set_IncludeContext_Z1FBCCD16(this$, iC) {
+    this$.includeContext = iC;
+}
+
+export function ConverterOptions__get_IsRoCrate(this$) {
+    return this$.isRoCrate;
+}
+
+export function ConverterOptions__set_IsRoCrate_Z1FBCCD16(this$, iR) {
+    this$.isRoCrate = iR;
+}
+