@nfdi4plants/arctrl 1.1.0 → 1.2.0

package/ISA/ISA.Json/Material.js

@@ -1,53 +1,57 @@
+import { ErrorReason$1, Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { list as list_2, object, string } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { FSharpResult$2 } from "../../fable_modules/fable-library-js.4.13.0/Result.js";
 import { MaterialType } from "../ISA/JsonTypes/MaterialType.js";
-import { toString, object as object_10, nil } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { list as list_1, object as object_11, string } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
-import { FSharpResult$2 } from "../../fable_modules/fable-library.4.5.0/Choice.js";
-import { ErrorReason } from "../../fable_modules/Thoth.Json.10.1.0/Types.fs.js";
 import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { ofArray, choose } from "../../fable_modules/fable-library.4.5.0/List.js";
-import { uncurry2, equals } from "../../fable_modules/fable-library.4.5.0/Util.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.5.0/Seq.js";
-import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
-import { 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 { 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 { tryIncludeList, tryInclude } from "./GEncode.js";
+import { list as list_1 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
-import { hasUnknownFields, fromJsonString, uri } from "./Decode.js";
+import { context_jsonvalue } from "./context/rocrate/isa_material_attribute_context.js";
+import { object as object_1, uri } from "./Decode.js";
 import { MaterialAttribute } from "../ISA/JsonTypes/MaterialAttribute.js";
+import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { replace, 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 { Value_decoder, Value_encoder } from "./Factor.js";
+import { context_jsonvalue as context_jsonvalue_1 } from "./context/rocrate/isa_material_attribute_value_context.js";
 import { MaterialAttributeValue } from "../ISA/JsonTypes/MaterialAttributeValue.js";
-import { replace } from "../../fable_modules/fable-library.4.5.0/String.js";
+import { context_jsonvalue as context_jsonvalue_2 } from "./context/rocrate/isa_material_context.js";
 import { Material } from "../ISA/JsonTypes/Material.js";
 
 export function MaterialType_encoder(options, value) {
-    if (value instanceof MaterialType) {
-        if (value.tag === 1) {
-            return "Labeled Extract Name";
-        }
-        else {
-            return "Extract Name";
-        }
+    if (value.tag === 1) {
+        return new Json(0, ["Labeled Extract Name"]);
     }
     else {
-        return nil;
+        return new Json(0, ["Extract Name"]);
     }
 }
 
-export function MaterialType_decoder(options, s, json) {
-    const matchValue = string(s, json);
-    if (matchValue.tag === 1) {
-        return new FSharpResult$2(1, [matchValue.fields[0]]);
-    }
-    else {
-        switch (matchValue.fields[0]) {
-            case "Extract Name":
-                return new FSharpResult$2(0, [new MaterialType(0, [])]);
-            case "Labeled Extract Name":
-                return new FSharpResult$2(0, [new MaterialType(1, [])]);
-            default: {
-                const s_1 = matchValue.fields[0];
-                return new FSharpResult$2(1, [[`Could not parse ${s_1}No other value than "Extract Name" or "Labeled Extract Name" allowed for materialtype`, new ErrorReason(0, [s_1, nil])]]);
+export function MaterialType_decoder(options) {
+    return {
+        Decode(s, json) {
+            const matchValue = string.Decode(s, json);
+            if (matchValue.tag === 1) {
+                return new FSharpResult$2(1, [matchValue.fields[0]]);
             }
-        }
-    }
+            else {
+                switch (matchValue.fields[0]) {
+                    case "Extract Name":
+                        return new FSharpResult$2(0, [new MaterialType(0, [])]);
+                    case "Labeled Extract Name":
+                        return new FSharpResult$2(0, [new MaterialType(1, [])]);
+                    default: {
+                        const s_1 = matchValue.fields[0];
+                        return new FSharpResult$2(1, [[`Could not parse ${s_1}No other value than "Extract Name" or "Labeled Extract Name" allowed for materialtype`, new ErrorReason$1(0, [s_1, json])]]);
+                    }
+                }
+            }
+        },
+    };
 }
 
 export function MaterialAttribute_genID(m) {
@@ -61,36 +65,32 @@ export function MaterialAttribute_genID(m) {
 }
 
 export function MaterialAttribute_encoder(options, oa) {
-    return object_10(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 = MaterialAttribute_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 = "MaterialAttribute", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => singleton(tryInclude("characteristicType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["CharacteristicType"]))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [MaterialAttribute_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_1(ofArray([new Json(0, ["MaterialAttribute"]), new Json(0, ["ArcMaterialAttribute"])]))]) : empty(), delay(() => append(singleton(tryInclude("characteristicType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa.CharacteristicType)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty()))))))))))]);
 }
 
 export function MaterialAttribute_decoder(options) {
-    return (path) => ((v) => object_11((get$) => {
+    return object((get$) => {
         let objectArg, arg_3, objectArg_1;
-        return new MaterialAttribute((objectArg = get$.Optional, objectArg.Field("@id", uri)), (arg_3 = OntologyAnnotation_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("characteristicType", uncurry2(arg_3)))));
-    }, path, v));
+        return new MaterialAttribute((objectArg = get$.Optional, objectArg.Field("@id", uri)), (arg_3 = OntologyAnnotation_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("characteristicType", arg_3))));
+    });
 }
 
 export function MaterialAttribute_fromJsonString(s) {
-    return fromJsonString(uncurry2(MaterialAttribute_decoder(ConverterOptions_$ctor())), s);
+    const matchValue = fromString(MaterialAttribute_decoder(ConverterOptions_$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 MaterialAttribute_toJsonString(m) {
@@ -100,11 +100,16 @@ export function MaterialAttribute_toJsonString(m) {
 /**
  * exports in json-ld format
  */
-export function MaterialAttribute_toStringLD(m) {
+export function MaterialAttribute_toJsonldString(m) {
     let returnVal;
     return toString(2, MaterialAttribute_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), m));
 }
 
+export function MaterialAttribute_toJsonldStringWithContext(a) {
+    let returnVal;
+    return toString(2, MaterialAttribute_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
+}
+
 export function MaterialAttributeValue_genID(m) {
     const matchValue = m.ID;
     if (matchValue == null) {
@@ -116,36 +121,32 @@ export function MaterialAttributeValue_genID(m) {
 }
 
 export function MaterialAttributeValue_encoder(options, oa) {
-    return object_10(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 = MaterialAttributeValue_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 = "MaterialAttributeValue", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("category", (oa_1) => MaterialAttribute_encoder(options, oa_1), oa["Category"])), delay(() => append(singleton(tryInclude("value", (value_7) => Value_encoder(options, value_7), oa["Value"])), delay(() => singleton(tryInclude("unit", (oa_2) => OntologyAnnotation_encoder(options, oa_2), oa["Unit"]))))))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [MaterialAttributeValue_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_1(ofArray([new Json(0, ["MaterialAttributeValue"]), new Json(0, ["ArcMaterialAttributeValue"])]))]) : empty(), delay(() => append(singleton(tryInclude("category", (oa_1) => MaterialAttribute_encoder(options, oa_1), oa.Category)), delay(() => append(singleton(tryInclude("value", (value_5) => Value_encoder(options, value_5), oa.Value)), delay(() => append(singleton(tryInclude("unit", (oa_2) => OntologyAnnotation_encoder(options, oa_2), oa.Unit)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue_1]) : empty()))))))))))))))]);
 }
 
 export function MaterialAttributeValue_decoder(options) {
-    return (path) => ((v) => object_11((get$) => {
-        let objectArg, arg_3, objectArg_1, objectArg_2, arg_7, objectArg_3;
-        return new MaterialAttributeValue((objectArg = get$.Optional, objectArg.Field("@id", uri)), (arg_3 = MaterialAttribute_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("category", uncurry2(arg_3)))), (objectArg_2 = get$.Optional, objectArg_2.Field("value", (s_1, json_1) => Value_decoder(options, s_1, json_1))), (arg_7 = OntologyAnnotation_decoder(options), (objectArg_3 = get$.Optional, objectArg_3.Field("unit", uncurry2(arg_7)))));
-    }, path, v));
+    return object((get$) => {
+        let objectArg, arg_3, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3;
+        return new MaterialAttributeValue((objectArg = get$.Optional, objectArg.Field("@id", uri)), (arg_3 = MaterialAttribute_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("category", arg_3))), (arg_5 = Value_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("value", arg_5))), (arg_7 = OntologyAnnotation_decoder(options), (objectArg_3 = get$.Optional, objectArg_3.Field("unit", arg_7))));
+    });
 }
 
 export function MaterialAttributeValue_fromJsonString(s) {
-    return fromJsonString(uncurry2(MaterialAttributeValue_decoder(ConverterOptions_$ctor())), s);
+    const matchValue = fromString(MaterialAttributeValue_decoder(ConverterOptions_$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 MaterialAttributeValue_toJsonString(m) {
@@ -155,11 +156,16 @@ export function MaterialAttributeValue_toJsonString(m) {
 /**
  * exports in json-ld format
  */
-export function MaterialAttributeValue_toStringLD(m) {
+export function MaterialAttributeValue_toJsonldString(m) {
     let returnVal;
     return toString(2, MaterialAttributeValue_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), m));
 }
 
+export function MaterialAttributeValue_toJsonldStringWithContext(a) {
+    let returnVal;
+    return toString(2, MaterialAttributeValue_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
+}
+
 export function Material_genID(m) {
     const matchValue = m.ID;
     if (matchValue == null) {
@@ -177,46 +183,34 @@ export function Material_genID(m) {
 }
 
 export function Material_encoder(options, oa) {
-    return object_10(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 = Material_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 = "Material", (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;
-            }, oa["Name"])), delay(() => append(singleton(tryInclude("type", (value_10) => MaterialType_encoder(options, value_10), oa["MaterialType"])), delay(() => append(singleton(tryInclude("characteristics", (oa_1) => MaterialAttributeValue_encoder(options, oa_1), oa["Characteristics"])), delay(() => singleton(tryInclude("derivesFrom", (oa_2) => Material_encoder(options, oa_2), oa["DerivesFrom"]))))))))));
-        }));
-    }))));
-}
-
-export function Material_decoder(options, s, json) {
-    if (hasUnknownFields(ofArray(["@id", "@type", "name", "type", "characteristics", "derivesFrom"]), json)) {
-        return new FSharpResult$2(1, [["Unknown fields in material", new ErrorReason(0, [s, nil])]]);
-    }
-    else {
-        return object_11((get$) => {
-            let objectArg, objectArg_1, objectArg_2, arg_7, decoder, objectArg_3, objectArg_4;
-            return new Material((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("type", (s_2, json_2) => MaterialType_decoder(options, s_2, json_2))), (arg_7 = ((decoder = MaterialAttributeValue_decoder(options), (path_1) => ((value_1) => list_1(uncurry2(decoder), path_1, value_1)))), (objectArg_3 = get$.Optional, objectArg_3.Field("characteristics", uncurry2(arg_7)))), (objectArg_4 = get$.Optional, objectArg_4.Field("derivesFrom", (path_2, value_2) => list_1((s_3, json_3) => Material_decoder(options, s_3, json_3), path_2, value_2))));
-        }, s, json);
-    }
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [Material_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_1(ofArray([new Json(0, ["Material"]), new Json(0, ["ArcMaterial"])]))]) : empty(), delay(() => append(singleton(tryInclude("name", (value_5) => (new Json(0, [value_5])), oa.Name)), delay(() => append(singleton(tryInclude("type", (value_7) => MaterialType_encoder(options, value_7), oa.MaterialType)), delay(() => append(singleton(tryIncludeList("characteristics", (oa_1) => MaterialAttributeValue_encoder(options, oa_1), oa.Characteristics)), delay(() => append(singleton(tryIncludeList("derivesFrom", (oa_2) => Material_encoder(options, oa_2), oa.DerivesFrom)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue_2]) : empty()))))))))))))))))]);
+}
+
+export const Material_allowedFields = ofArray(["@id", "@type", "name", "type", "characteristics", "derivesFrom", "@context"]);
+
+export function Material_decoder(options) {
+    return object_1(Material_allowedFields, (get$) => {
+        let objectArg, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, arg_9, objectArg_4;
+        return new Material((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = MaterialType_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("type", arg_5))), (arg_7 = list_2(MaterialAttributeValue_decoder(options)), (objectArg_3 = get$.Optional, objectArg_3.Field("characteristics", arg_7))), (arg_9 = list_2(Material_decoder(options)), (objectArg_4 = get$.Optional, objectArg_4.Field("derivesFrom", arg_9))));
+    });
 }
 
 export function Material_fromJsonString(s) {
-    let options;
-    return fromJsonString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Material_decoder(options, s_1, json)))), s);
+    const matchValue = fromString(Material_decoder(ConverterOptions_$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 Material_toJsonString(m) {
@@ -226,8 +220,13 @@ export function Material_toJsonString(m) {
 /**
  * exports in json-ld format
  */
-export function Material_toStringLD(m) {
+export function Material_toJsonldString(m) {
     let returnVal;
     return toString(2, Material_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), m));
 }
 
+export function Material_toJsonldStringWithContext(a) {
+    let returnVal;
+    return toString(2, Material_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/Ontology.js

@@ -1,43 +1,46 @@
-import { array, object as object_11, string, float, int } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
-import { FSharpResult$2 } from "../../fable_modules/fable-library.4.5.0/Choice.js";
-import { uncurry2, equals, int32ToString } from "../../fable_modules/fable-library.4.5.0/Util.js";
-import { replace } from "../../fable_modules/fable-library.4.5.0/String.js";
-import { toString, nil, object as object_10 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { choose } from "../../fable_modules/fable-library.4.5.0/List.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.5.0/Seq.js";
-import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
-import { tryInclude } from "./GEncode.js";
+import { array, object, string, float, int } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { FSharpResult$2 } from "../../fable_modules/fable-library-js.4.13.0/Result.js";
+import { equals, int32ToString } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { printf, toText, replace } from "../../fable_modules/fable-library-js.4.13.0/String.js";
+import { choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
+import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeContext, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
+import { tryIncludeArray, tryInclude } from "./GEncode.js";
 import { decoder as decoder_1, encoder } from "./Comment.js";
-import { fromJsonString, uri } from "./Decode.js";
+import { context_jsonvalue } from "./context/rocrate/isa_ontology_source_reference_context.js";
+import { uri } from "./Decode.js";
 import { OntologySourceReference } from "../ISA/JsonTypes/OntologySourceReference.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";
 import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
+import { context_jsonvalue as context_jsonvalue_1 } from "./context/rocrate/isa_ontology_annotation_context.js";
 import { OntologyAnnotation } from "../ISA/JsonTypes/OntologyAnnotation.js";
-import { unwrap } from "../../fable_modules/fable-library.4.5.0/Option.js";
+import { unwrap } from "../../fable_modules/fable-library-js.4.13.0/Option.js";
 import { StringTable_decodeString, StringTable_encodeString } from "./StringTable.js";
 
 /**
  * This decodes from integer, float or string to string only!
  */
-export function AnnotationValue_decoder(options, s, json) {
-    const matchValue = int(s)(json);
-    if (matchValue.tag === 1) {
-        const matchValue_1 = float(s, json);
-        if (matchValue_1.tag === 1) {
-            const matchValue_2 = string(s, json);
-            if (matchValue_2.tag === 1) {
-                return new FSharpResult$2(1, [matchValue_2.fields[0]]);
+export function AnnotationValue_decoder(options) {
+    return {
+        Decode(s, json) {
+            const matchValue = int.Decode(s, json);
+            if (matchValue.tag === 1) {
+                const matchValue_1 = float.Decode(s, json);
+                if (matchValue_1.tag === 1) {
+                    const matchValue_2 = string.Decode(s, json);
+                    return (matchValue_2.tag === 1) ? (new FSharpResult$2(1, [matchValue_2.fields[0]])) : (new FSharpResult$2(0, [matchValue_2.fields[0]]));
+                }
+                else {
+                    return new FSharpResult$2(0, [matchValue_1.fields[0].toString()]);
+                }
             }
             else {
-                return new FSharpResult$2(0, [matchValue_2.fields[0]]);
+                return new FSharpResult$2(0, [int32ToString(matchValue.fields[0])]);
             }
-        }
-        else {
-            return new FSharpResult$2(0, [matchValue_1.fields[0].toString()]);
-        }
-    }
-    else {
-        return new FSharpResult$2(0, [int32ToString(matchValue.fields[0])]);
-    }
+        },
+    };
 }
 
 export function OntologySourceReference_genID(o) {
@@ -57,48 +60,32 @@ export function OntologySourceReference_genID(o) {
 }
 
 export function OntologySourceReference_encoder(options, osr) {
-    return object_10(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 = OntologySourceReference_genID(osr), (typeof value === "string") ? ((s = value, s)) : nil)]) : empty(), delay(() => {
-            let value_2, s_1;
-            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_2 = "OntologySourceReference", (typeof value_2 === "string") ? ((s_1 = value_2, s_1)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("description", (value_4) => {
-                let s_2;
-                const value_5 = value_4;
-                return (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil;
-            }, osr["Description"])), delay(() => append(singleton(tryInclude("file", (value_7) => {
-                let s_3;
-                const value_8 = value_7;
-                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
-            }, osr["File"])), delay(() => append(singleton(tryInclude("name", (value_10) => {
-                let s_4;
-                const value_11 = value_10;
-                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
-            }, osr["Name"])), delay(() => append(singleton(tryInclude("version", (value_13) => {
-                let s_5;
-                const value_14 = value_13;
-                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
-            }, osr["Version"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), osr["Comments"]))))))))))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [OntologySourceReference_genID(osr)])]) : empty(), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["OntologySourceReference"])]) : empty(), delay(() => append(singleton(tryInclude("description", (value_2) => (new Json(0, [value_2])), osr.Description)), delay(() => append(singleton(tryInclude("file", (value_4) => (new Json(0, [value_4])), osr.File)), delay(() => append(singleton(tryInclude("name", (value_6) => (new Json(0, [value_6])), osr.Name)), delay(() => append(singleton(tryInclude("version", (value_8) => (new Json(0, [value_8])), osr.Version)), delay(() => append(singleton(tryIncludeArray("comments", (comment) => encoder(options, comment), osr.Comments)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty()))))))))))))))))))]);
 }
 
 export function OntologySourceReference_decoder(options) {
-    return (path_4) => ((v) => object_11((get$) => {
-        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, decoder, objectArg_4;
-        return new OntologySourceReference((objectArg = get$.Optional, objectArg.Field("description", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("file", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("name", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("version", string)), (arg_9 = ((decoder = decoder_1(options), (path_3) => ((value_3) => array(uncurry2(decoder), path_3, value_3)))), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", uncurry2(arg_9)))));
-    }, path_4, v));
+    return object((get$) => {
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4;
+        return new OntologySourceReference((objectArg = get$.Optional, objectArg.Field("description", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("file", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("name", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("version", string)), (arg_9 = array(decoder_1(options)), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", arg_9))));
+    });
 }
 
 export function OntologySourceReference_fromJsonString(s) {
-    return fromJsonString(uncurry2(OntologySourceReference_decoder(ConverterOptions_$ctor())), s);
+    const matchValue = fromString(OntologySourceReference_decoder(ConverterOptions_$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 OntologySourceReference_toJsonString(oa) {
@@ -108,11 +95,16 @@ export function OntologySourceReference_toJsonString(oa) {
 /**
  * exports in json-ld format
  */
-export function OntologySourceReference_toStringLD(oa) {
+export function OntologySourceReference_toJsonldString(oa) {
     let returnVal;
     return toString(2, OntologySourceReference_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), oa));
 }
 
+export function OntologySourceReference_toJsonldStringWithContext(a) {
+    let returnVal;
+    return toString(2, OntologySourceReference_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
+}
+
 export function OntologyAnnotation_genID(o) {
     const matchValue = o.ID;
     if (matchValue == null) {
@@ -120,14 +112,20 @@ export function OntologyAnnotation_genID(o) {
         if (matchValue_1 == null) {
             const matchValue_2 = o.TermSourceREF;
             if (matchValue_2 == null) {
-                return "#DummyOntologyAnnotation";
+                const matchValue_3 = o.Name;
+                if (matchValue_3 == null) {
+                    return "#DummyOntologyAnnotation";
+                }
+                else {
+                    return "#UserTerm_" + replace(matchValue_3, " ", "_");
+                }
             }
             else {
                 return "#" + replace(matchValue_2, " ", "_");
             }
         }
         else {
-            return matchValue_1;
+            return URIModule_toString(matchValue_1);
         }
     }
     else {
@@ -136,77 +134,51 @@ export function OntologyAnnotation_genID(o) {
 }
 
 export function OntologyAnnotation_encoder(options, oa) {
-    return object_10(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 = OntologyAnnotation_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 = "OntologyAnnotation", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("annotationValue", (value_7) => {
-                let s_3;
-                const value_8 = value_7;
-                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
-            }, oa["Name"])), delay(() => append(singleton(tryInclude("termSource", (value_10) => {
-                let s_4;
-                const value_11 = value_10;
-                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
-            }, oa["TermSourceREF"])), delay(() => append(singleton(tryInclude("termAccession", (value_13) => {
-                let s_5;
-                const value_14 = value_13;
-                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
-            }, oa["TermAccessionNumber"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), oa["Comments"]))))))))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [OntologyAnnotation_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["OntologyAnnotation"])]) : empty(), delay(() => append(singleton(tryInclude("annotationValue", (value_4) => (new Json(0, [value_4])), oa.Name)), delay(() => append(singleton(tryInclude("termSource", (value_6) => (new Json(0, [value_6])), oa.TermSourceREF)), delay(() => append(singleton(tryInclude("termAccession", (value_8) => (new Json(0, [value_8])), oa.TermAccessionNumber)), delay(() => append(singleton(tryIncludeArray("comments", (comment) => encoder(options, comment), oa.Comments)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue_1]) : empty()))))))))))))))))]);
 }
 
 export function OntologyAnnotation_decoder(options) {
-    return (path_3) => ((v) => object_11((get$) => {
-        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, decoder, objectArg_4;
-        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("annotationValue", (s_1, json_1) => AnnotationValue_decoder(options, s_1, json_1)))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termSource", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("termAccession", string))), unwrap((arg_9 = ((decoder = decoder_1(options), (path_2) => ((value_2) => array(uncurry2(decoder), path_2, value_2)))), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", uncurry2(arg_9))))));
-    }, path_3, v));
+    return object((get$) => {
+        let objectArg, arg_3, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4;
+        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((arg_3 = AnnotationValue_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("annotationValue", arg_3)))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termSource", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("termAccession", string))), unwrap((arg_9 = array(decoder_1(options)), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", arg_9)))));
+    });
 }
 
 export function OntologyAnnotation_compressedEncoder(stringTable, options, oa) {
-    return object_10(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 = OntologyAnnotation_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 = "OntologyAnnotation", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("a", (s_3) => StringTable_encodeString(stringTable, s_3), oa["Name"])), delay(() => append(singleton(tryInclude("ts", (s_4) => StringTable_encodeString(stringTable, s_4), oa["TermSourceREF"])), delay(() => append(singleton(tryInclude("ta", (s_5) => StringTable_encodeString(stringTable, s_5), oa["TermAccessionNumber"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), oa["Comments"]))))))))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [OntologyAnnotation_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["OntologyAnnotation"])]) : empty(), delay(() => append(singleton(tryInclude("a", (s) => StringTable_encodeString(stringTable, s), oa.Name)), delay(() => append(singleton(tryInclude("ts", (s_1) => StringTable_encodeString(stringTable, s_1), oa.TermSourceREF)), delay(() => append(singleton(tryInclude("ta", (s_2) => StringTable_encodeString(stringTable, s_2), oa.TermAccessionNumber)), delay(() => singleton(tryIncludeArray("comments", (comment) => encoder(options, comment), oa.Comments)))))))))))))))]);
 }
 
 export function OntologyAnnotation_compressedDecoder(stringTable, options) {
-    return (path_1) => ((v) => object_11((get$) => {
-        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, decoder, objectArg_4;
-        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("a", (s_1, o) => StringTable_decodeString(stringTable, s_1, o)))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("ts", (s_2, o_1) => StringTable_decodeString(stringTable, s_2, o_1)))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("ta", (s_3, o_2) => StringTable_decodeString(stringTable, s_3, o_2)))), unwrap((arg_9 = ((decoder = decoder_1(options), (path) => ((value) => array(uncurry2(decoder), path, value)))), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", uncurry2(arg_9))))));
-    }, path_1, v));
+    return object((get$) => {
+        let objectArg, arg_3, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, arg_9, objectArg_4;
+        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((arg_3 = StringTable_decodeString(stringTable), (objectArg_1 = get$.Optional, objectArg_1.Field("a", arg_3)))), unwrap((arg_5 = StringTable_decodeString(stringTable), (objectArg_2 = get$.Optional, objectArg_2.Field("ts", arg_5)))), unwrap((arg_7 = StringTable_decodeString(stringTable), (objectArg_3 = get$.Optional, objectArg_3.Field("ta", arg_7)))), unwrap((arg_9 = array(decoder_1(options)), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", arg_9)))));
+    });
 }
 
 export function OntologyAnnotation_fromJsonString(s) {
-    return fromJsonString(uncurry2(OntologyAnnotation_decoder(ConverterOptions_$ctor())), s);
+    const matchValue = fromString(OntologyAnnotation_decoder(ConverterOptions_$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 OntologyAnnotation_toJsonString(oa) {
@@ -216,8 +188,13 @@ export function OntologyAnnotation_toJsonString(oa) {
 /**
  * exports in json-ld format
  */
-export function OntologyAnnotation_toStringLD(oa) {
+export function OntologyAnnotation_toJsonldString(oa) {
     let returnVal;
     return toString(2, OntologyAnnotation_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), oa));
 }
 
+export function OntologyAnnotation_toJsonldStringWithContext(a) {
+    let returnVal;
+    return toString(2, OntologyAnnotation_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
+}
+