@nfdi4plants/arctrl 1.2.0 → 2.0.0-alpha.2

package/Json/Process/PropertyValue.js

@@ -0,0 +1,82 @@
+import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { map } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+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 { tryInclude } from "../Encode.js";
+import { context_jsonvalue } from "../context/rocrate/property_value_context.js";
+import { string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { Value } from "../../Core/Process/Value.js";
+
+export function genID(p) {
+    const matchValue = p.GetCategory();
+    if (matchValue == null) {
+        return `#Empty${() => p.GetAdditionalType()}`;
+    }
+    else {
+        return `${() => p.GetAdditionalType()}/${matchValue}${p.GetValue()}${p.GetUnit()}`;
+    }
+}
+
+export function encoder(pv) {
+    let patternInput;
+    const matchValue = pv.GetCategory();
+    if (matchValue == null) {
+        patternInput = [void 0, void 0];
+    }
+    else {
+        const oa = matchValue;
+        patternInput = [oa.Name, oa.TermAccessionNumber];
+    }
+    let patternInput_1;
+    const matchValue_1 = pv.GetValue();
+    if (matchValue_1 == null) {
+        patternInput_1 = [void 0, void 0];
+    }
+    else {
+        const v = matchValue_1;
+        switch (v.tag) {
+            case 1: {
+                patternInput_1 = [new Json(7, [v.fields[0] >>> 0]), void 0];
+                break;
+            }
+            case 2: {
+                patternInput_1 = [new Json(2, [v.fields[0]]), void 0];
+                break;
+            }
+            case 0: {
+                const oa_1 = v.fields[0];
+                patternInput_1 = [map((value_3) => (new Json(0, [value_3])), oa_1.Name), map((value_5) => (new Json(0, [value_5])), oa_1.TermAccessionNumber)];
+                break;
+            }
+            default:
+                patternInput_1 = [new Json(0, [v.fields[0]]), void 0];
+        }
+    }
+    let patternInput_2;
+    const matchValue_2 = pv.GetUnit();
+    if (matchValue_2 == null) {
+        patternInput_2 = [void 0, void 0];
+    }
+    else {
+        const oa_2 = matchValue_2;
+        patternInput_2 = [oa_2.Name, oa_2.TermAccessionNumber];
+    }
+    return new Json(5, [choose((tupledArg) => {
+        const v_1 = tupledArg[1];
+        if (equals(v_1, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v_1];
+        }
+    }, ofArray([["@id", new Json(0, [genID(pv)])], ["@type", new Json(0, ["PropertyValue"])], ["additionalType", new Json(0, [pv.GetAdditionalType()])], tryInclude("category", (value_11) => (new Json(0, [value_11])), patternInput[0]), tryInclude("categoryCode", (value_13) => (new Json(0, [value_13])), patternInput[1]), tryInclude("value", (x) => x, patternInput_1[0]), tryInclude("valueCode", (x_1) => x_1, patternInput_1[1]), tryInclude("unit", (value_15) => (new Json(0, [value_15])), patternInput_2[0]), tryInclude("unitCode", (value_17) => (new Json(0, [value_17])), patternInput_2[1]), ["@context", context_jsonvalue]]))]);
+}
+
+export function decoder(create) {
+    return object((get$) => {
+        let name, objectArg, code, objectArg_1, value, objectArg_2, code_1, objectArg_3, name_1, objectArg_4, code_2, objectArg_5;
+        return create((name = ((objectArg = get$.Optional, objectArg.Field("category", string))), (code = ((objectArg_1 = get$.Optional, objectArg_1.Field("categoryCode", string))), ((name == null) && (code == null)) ? void 0 : OntologyAnnotation.create(name, void 0, code))), (value = ((objectArg_2 = get$.Optional, objectArg_2.Field("value", string))), (code_1 = ((objectArg_3 = get$.Optional, objectArg_3.Field("valueCode", string))), ((value == null) && (code_1 == null)) ? void 0 : Value.fromOptions(value, void 0, code_1))), (name_1 = ((objectArg_4 = get$.Optional, objectArg_4.Field("unit", string))), (code_2 = ((objectArg_5 = get$.Optional, objectArg_5.Field("unitCode", string))), ((name_1 == null) && (code_2 == null)) ? void 0 : OntologyAnnotation.create(name_1, void 0, code_2))));
+    });
+}
+

package/Json/Process/Protocol.js

@@ -0,0 +1,147 @@
+import { printf, toText, replace } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { append, empty, ofArray, singleton, 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 { list as list_4 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
+import { defaultSpaces, tryIncludeListOpt, tryInclude } from "../Encode.js";
+import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_encoderDefinedTerm } from "../OntologyAnnotation.js";
+import { Component_ISAJson_decoder, Component_ISAJson_encoder, Component_ROCrate_decoder, Component_ROCrate_encoder } from "./Component.js";
+import { Comment_ISAJson_decoder, Comment_ISAJson_encoder, Comment_ROCrate_decoder, Comment_ROCrate_encoder } from "../Comment.js";
+import { context_jsonvalue } from "../context/rocrate/isa_protocol_context.js";
+import { string, list as list_5, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { Option_fromValueWithDefault } from "../../Core/Helper/Collections.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { Decode_uri } from "../Decode.js";
+import { Protocol } from "../../Core/Process/Protocol.js";
+import { ProtocolParameter_ISAJson_decoder, ProtocolParameter_ISAJson_encoder } from "./ProtocolParameter.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 Protocol_ROCrate_genID(studyName, assayName, processName, p) {
+    const matchValue = p.Uri;
+    if (matchValue == null) {
+        const matchValue_1 = p.Name;
+        if (matchValue_1 == null) {
+            let matchResult, an, pn, sn, pn_1, sn_1, pn_2;
+            if (studyName == null) {
+                if (assayName == null) {
+                    if (processName != null) {
+                        matchResult = 2;
+                        pn_2 = processName;
+                    }
+                    else {
+                        matchResult = 3;
+                    }
+                }
+                else {
+                    matchResult = 3;
+                }
+            }
+            else if (assayName == null) {
+                if (processName != null) {
+                    matchResult = 1;
+                    pn_1 = processName;
+                    sn_1 = studyName;
+                }
+                else {
+                    matchResult = 3;
+                }
+            }
+            else if (processName != null) {
+                matchResult = 0;
+                an = assayName;
+                pn = processName;
+                sn = studyName;
+            }
+            else {
+                matchResult = 3;
+            }
+            switch (matchResult) {
+                case 0:
+                    return (((("#Protocol_" + replace(sn, " ", "_")) + "_") + replace(an, " ", "_")) + "_") + replace(pn, " ", "_");
+                case 1:
+                    return (("#Protocol_" + replace(sn_1, " ", "_")) + "_") + replace(pn_1, " ", "_");
+                case 2:
+                    return "#Protocol_" + replace(pn_2, " ", "_");
+                default:
+                    return "#EmptyProtocol";
+            }
+        }
+        else {
+            return "#Protocol_" + replace(matchValue_1, " ", "_");
+        }
+    }
+    else {
+        return matchValue;
+    }
+}
+
+export function Protocol_ROCrate_encoder(studyName, assayName, processName, oa) {
+    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([["@id", new Json(0, [Protocol_ROCrate_genID(studyName, assayName, processName, oa)])], ["@type", list_4(singleton(new Json(0, ["Protocol"])))], tryInclude("name", (value_2) => (new Json(0, [value_2])), oa.Name), tryInclude("protocolType", OntologyAnnotation_ROCrate_encoderDefinedTerm, oa.ProtocolType), tryInclude("description", (value_4) => (new Json(0, [value_4])), oa.Description), tryInclude("uri", (value_6) => (new Json(0, [value_6])), oa.Uri), tryInclude("version", (value_8) => (new Json(0, [value_8])), oa.Version), tryIncludeListOpt("components", Component_ROCrate_encoder, oa.Components), tryIncludeListOpt("comments", Comment_ROCrate_encoder, oa.Comments), ["@context", context_jsonvalue]]))]);
+}
+
+export const Protocol_ROCrate_decoder = object((get$) => {
+    let list_3, list_1, arg_1, objectArg, arg_3, objectArg_1, arg_5, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, objectArg_8, arg_19, objectArg_9;
+    const components = Option_fromValueWithDefault(empty(), (list_3 = ((list_1 = defaultArg((arg_1 = list_5(Component_ROCrate_decoder), (objectArg = get$.Optional, objectArg.Field("components", arg_1))), empty()), append(defaultArg((arg_3 = list_5(Component_ROCrate_decoder), (objectArg_1 = get$.Optional, objectArg_1.Field("reagents", arg_3))), empty()), list_1))), append(defaultArg((arg_5 = list_5(Component_ROCrate_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("computationalTools", arg_5))), empty()), list_3)));
+    return new Protocol((objectArg_3 = get$.Optional, objectArg_3.Field("@id", Decode_uri)), (objectArg_4 = get$.Optional, objectArg_4.Field("name", string)), (objectArg_5 = get$.Optional, objectArg_5.Field("protocolType", OntologyAnnotation_ROCrate_decoderDefinedTerm)), (objectArg_6 = get$.Optional, objectArg_6.Field("description", string)), (objectArg_7 = get$.Optional, objectArg_7.Field("uri", Decode_uri)), (objectArg_8 = get$.Optional, objectArg_8.Field("version", string)), void 0, components, (arg_19 = list_5(Comment_ROCrate_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("comments", arg_19))));
+});
+
+export function Protocol_ISAJson_encoder(oa) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), oa.ID), tryInclude("name", (value_2) => (new Json(0, [value_2])), oa.Name), tryInclude("protocolType", OntologyAnnotation_ISAJson_encoder, oa.ProtocolType), tryInclude("description", (value_4) => (new Json(0, [value_4])), oa.Description), tryInclude("uri", (value_6) => (new Json(0, [value_6])), oa.Uri), tryInclude("version", (value_8) => (new Json(0, [value_8])), oa.Version), tryIncludeListOpt("parameters", ProtocolParameter_ISAJson_encoder, oa.Parameters), tryIncludeListOpt("components", Component_ISAJson_encoder, oa.Components), tryIncludeListOpt("comments", Comment_ISAJson_encoder, oa.Comments)]))]);
+}
+
+export const Protocol_ISAJson_decoder = object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8;
+    return new Protocol((objectArg = get$.Optional, objectArg.Field("@id", Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("protocolType", OntologyAnnotation_ISAJson_decoder)), (objectArg_3 = get$.Optional, objectArg_3.Field("description", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("uri", Decode_uri)), (objectArg_5 = get$.Optional, objectArg_5.Field("version", string)), (arg_13 = list_5(ProtocolParameter_ISAJson_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("parameters", arg_13))), (arg_15 = list_5(Component_ISAJson_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("components", arg_15))), (arg_17 = list_5(Comment_ISAJson_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("comments", arg_17))));
+});
+
+export function ARCtrl_Process_Protocol__Protocol_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Protocol_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_Process_Protocol__Protocol_toISAJsonString_Static_71136F3F(spaces) {
+    return (f) => {
+        const value = Protocol_ISAJson_encoder(f);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_Process_Protocol__Protocol_fromROCrateString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Protocol_ROCrate_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_Process_Protocol__Protocol_toROCrateString_Static(studyName, assayName, processName, spaces) {
+    return (f) => {
+        const value = Protocol_ROCrate_encoder(studyName, assayName, processName, f);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+

package/Json/Process/ProtocolParameter.js

@@ -0,0 +1,45 @@
+import { singleton, 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 { defaultSpaces, tryInclude } from "../Encode.js";
+import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder } from "../OntologyAnnotation.js";
+import { object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { ProtocolParameter } from "../../Core/Process/ProtocolParameter.js";
+import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
+
+export function ProtocolParameter_ISAJson_encoder(value) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, singleton(tryInclude("parameterName", OntologyAnnotation_ISAJson_encoder, value.ParameterName)))]);
+}
+
+export const ProtocolParameter_ISAJson_decoder = object((get$) => {
+    let objectArg;
+    return new ProtocolParameter(void 0, (objectArg = get$.Optional, objectArg.Field("parameterName", OntologyAnnotation_ISAJson_decoder)));
+});
+
+export function ARCtrl_Process_ProtocolParameter__ProtocolParameter_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(ProtocolParameter_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_Process_ProtocolParameter__ProtocolParameter_toISAJsonString_Static_71136F3F(spaces) {
+    return (v) => {
+        const value = ProtocolParameter_ISAJson_encoder(v);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+

package/Json/Process/Sample.js

@@ -0,0 +1,134 @@
+import { printf, toText, replace } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { ofArray, singleton, choose, append, empty, map } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { MaterialAttributeValue_ISAJson_decoder, MaterialAttributeValue_ISAJson_encoder, MaterialAttributeValue_ROCrate_decoder, MaterialAttributeValue_ROCrate_encoder } from "./MaterialAttributeValue.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { FactorValue_ISAJson_decoder, FactorValue_ISAJson_encoder, FactorValue_ROCrate_decoder, FactorValue_ROCrate_encoder } from "./FactorValue.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 { list as list_5 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
+import { defaultSpaces, tryIncludeListOpt, tryIncludeList, tryInclude } from "../Encode.js";
+import { context_jsonvalue } from "../context/rocrate/isa_sample_context.js";
+import { list as list_6, object, string } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { FSharpResult$2 } from "../../fable_modules/fable-library-js.4.16.0/Result.js";
+import { Option_fromValueWithDefault } from "../../Core/Helper/Collections.js";
+import { Decode_objectNoAdditionalProperties, Decode_uri } from "../Decode.js";
+import { Source_ISAJson_decoder, Source_ISAJson_encoder, Source_ROCrate_decoder } from "./Source.js";
+import { Sample } from "../../Core/Process/Sample.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 Sample_ROCrate_genID(s) {
+    const matchValue = s.ID;
+    if (matchValue == null) {
+        const matchValue_1 = s.Name;
+        if (matchValue_1 == null) {
+            return "#EmptySample";
+        }
+        else {
+            return "#Sample_" + replace(matchValue_1, " ", "_");
+        }
+    }
+    else {
+        return matchValue;
+    }
+}
+
+export function Sample_ROCrate_encoder(oa) {
+    let additionalProperties;
+    const list_3 = map(MaterialAttributeValue_ROCrate_encoder, defaultArg(oa.Characteristics, empty()));
+    additionalProperties = append(map(FactorValue_ROCrate_encoder, defaultArg(oa.FactorValues, empty())), list_3);
+    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([["@id", new Json(0, [Sample_ROCrate_genID(oa)])], ["@type", list_5(singleton(new Json(0, ["Sample"])))], tryInclude("name", (value_4) => (new Json(0, [value_4])), oa.Name), tryIncludeList("additionalProperties", (x) => x, additionalProperties), ["@context", context_jsonvalue]]))]);
+}
+
+export const Sample_ROCrate_additionalPropertyDecoder = {
+    Decode(s, json) {
+        let matchValue;
+        if ((s.hasProperty("additionalType", json) ? ((matchValue = string.Decode(s, s.getProperty("additionalType", json)), (matchValue.tag === 0) ? matchValue.fields[0] : "")) : "") === "FactorValue") {
+            const matchValue_1 = FactorValue_ROCrate_decoder.Decode(s, json);
+            return (matchValue_1.tag === 1) ? (new FSharpResult$2(1, [matchValue_1.fields[0]])) : (new FSharpResult$2(0, [[void 0, matchValue_1.fields[0]]]));
+        }
+        else {
+            const matchValue_2 = MaterialAttributeValue_ROCrate_decoder.Decode(s, json);
+            return (matchValue_2.tag === 1) ? (new FSharpResult$2(1, [matchValue_2.fields[0]])) : (new FSharpResult$2(0, [[matchValue_2.fields[0], void 0]]));
+        }
+    },
+};
+
+export const Sample_ROCrate_decoder = object((get$) => {
+    let objectArg_1, objectArg_2, arg_7, objectArg_3;
+    let additionalProperties;
+    const arg_1 = list_6(Sample_ROCrate_additionalPropertyDecoder);
+    const objectArg = get$.Optional;
+    additionalProperties = objectArg.Field("additionalProperties", arg_1);
+    let patternInput;
+    if (additionalProperties != null) {
+        const additionalProperties_1 = additionalProperties;
+        patternInput = [Option_fromValueWithDefault(empty(), choose((tuple) => tuple[0], additionalProperties_1)), Option_fromValueWithDefault(empty(), choose((tuple_1) => tuple_1[1], additionalProperties_1))];
+    }
+    else {
+        patternInput = [void 0, void 0];
+    }
+    return new Sample((objectArg_1 = get$.Optional, objectArg_1.Field("@id", Decode_uri)), (objectArg_2 = get$.Optional, objectArg_2.Field("name", string)), patternInput[0], patternInput[1], (arg_7 = list_6(Source_ROCrate_decoder), (objectArg_3 = get$.Optional, objectArg_3.Field("derivesFrom", arg_7))));
+});
+
+export function Sample_ISAJson_encoder(oa) {
+    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("@id", (value) => (new Json(0, [value])), oa.ID), tryInclude("name", (value_2) => (new Json(0, [value_2])), oa.Name), tryIncludeListOpt("characteristics", MaterialAttributeValue_ISAJson_encoder, oa.Characteristics), tryIncludeListOpt("factorValues", FactorValue_ISAJson_encoder, oa.FactorValues), tryIncludeListOpt("derivesFrom", Source_ISAJson_encoder, oa.DerivesFrom)]))]);
+}
+
+export const Sample_ISAJson_allowedFields = ofArray(["@id", "name", "characteristics", "factorValues", "derivesFrom", "@type", "@context"]);
+
+export const Sample_ISAJson_decoder = Decode_objectNoAdditionalProperties(Sample_ISAJson_allowedFields, (get$) => {
+    let objectArg, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, arg_9, objectArg_4;
+    return new Sample((objectArg = get$.Optional, objectArg.Field("@id", Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = list_6(MaterialAttributeValue_ISAJson_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("characteristics", arg_5))), (arg_7 = list_6(FactorValue_ISAJson_decoder), (objectArg_3 = get$.Optional, objectArg_3.Field("factorValues", arg_7))), (arg_9 = list_6(Source_ISAJson_decoder), (objectArg_4 = get$.Optional, objectArg_4.Field("derivesFrom", arg_9))));
+});
+
+export function ARCtrl_Process_Sample__Sample_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Sample_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_Process_Sample__Sample_toISAJsonString_Static_71136F3F(spaces) {
+    return (f) => {
+        const value = Sample_ISAJson_encoder(f);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_Process_Sample__Sample_fromROCrateString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Sample_ROCrate_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_Process_Sample__Sample_toROCrateString_Static_71136F3F(spaces) {
+    return (f) => {
+        const value = Sample_ROCrate_encoder(f);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+

package/Json/Process/Source.js

@@ -0,0 +1,101 @@
+import { printf, toText, replace } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { URIModule_toString } from "../../Core/URI.js";
+import { ofArray, singleton, 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 { list as list_1 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
+import { defaultSpaces, tryIncludeListOpt, tryInclude } from "../Encode.js";
+import { MaterialAttributeValue_ISAJson_decoder, MaterialAttributeValue_ISAJson_encoder, MaterialAttributeValue_ROCrate_decoder, MaterialAttributeValue_ROCrate_encoder } from "./MaterialAttributeValue.js";
+import { context_jsonvalue } from "../context/rocrate/isa_source_context.js";
+import { list as list_2, string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { Decode_objectNoAdditionalProperties, Decode_uri } from "../Decode.js";
+import { Source } from "../../Core/Process/Source.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 Source_ROCrate_genID(s) {
+    const matchValue = s.ID;
+    if (matchValue == null) {
+        const matchValue_1 = s.Name;
+        if (matchValue_1 == null) {
+            return "#EmptySource";
+        }
+        else {
+            return "#Source_" + replace(matchValue_1, " ", "_");
+        }
+    }
+    else {
+        return URIModule_toString(matchValue);
+    }
+}
+
+export function Source_ROCrate_encoder(oa) {
+    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([["@id", new Json(0, [Source_ROCrate_genID(oa)])], ["@type", list_1(singleton(new Json(0, ["Source"])))], tryInclude("name", (value_2) => (new Json(0, [value_2])), oa.Name), tryIncludeListOpt("characteristics", MaterialAttributeValue_ROCrate_encoder, oa.Characteristics), ["@context", context_jsonvalue]]))]);
+}
+
+export const Source_ROCrate_decoder = object((get$) => {
+    let objectArg, objectArg_1, arg_5, objectArg_2;
+    return new Source((objectArg = get$.Optional, objectArg.Field("@id", Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = list_2(MaterialAttributeValue_ROCrate_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("characteristics", arg_5))));
+});
+
+export function Source_ISAJson_encoder(oa) {
+    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("@id", (value) => (new Json(0, [value])), oa.ID), tryInclude("name", (value_2) => (new Json(0, [value_2])), oa.Name), tryIncludeListOpt("characteristics", MaterialAttributeValue_ISAJson_encoder, oa.Characteristics)]))]);
+}
+
+export const Source_ISAJson_allowedFields = ofArray(["@id", "name", "characteristics", "@type", "@context"]);
+
+export const Source_ISAJson_decoder = Decode_objectNoAdditionalProperties(Source_ISAJson_allowedFields, (get$) => {
+    let objectArg, objectArg_1, arg_5, objectArg_2;
+    return new Source((objectArg = get$.Optional, objectArg.Field("@id", Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = list_2(MaterialAttributeValue_ISAJson_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("characteristics", arg_5))));
+});
+
+export function ARCtrl_Process_Source__Source_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Source_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_Process_Source__Source_toISAJsonString_Static_71136F3F(spaces) {
+    return (f) => {
+        const value = Source_ISAJson_encoder(f);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_Process_Source__Source_fromROCrateString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Source_ROCrate_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_Process_Source__Source_toROCrateString_Static_71136F3F(spaces) {
+    return (f) => {
+        const value = Source_ROCrate_encoder(f);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+

package/Json/Process/StudyMaterials.js

@@ -0,0 +1,24 @@
+import { getMaterials, getSamples, getSources } from "../../Core/Process/ProcessSequence.js";
+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 { tryIncludeList } from "../Encode.js";
+import { Source_ISAJson_encoder } from "./Source.js";
+import { Sample_ISAJson_encoder } from "./Sample.js";
+import { Material_ISAJson_encoder } from "./Material.js";
+
+export function encoder(ps) {
+    const source = getSources(ps);
+    const samples = getSamples(ps);
+    const materials = getMaterials(ps);
+    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([tryIncludeList("sources", Source_ISAJson_encoder, source), tryIncludeList("samples", Sample_ISAJson_encoder, samples), tryIncludeList("otherMaterials", Material_ISAJson_encoder, materials)]))]);
+}
+

package/Json/Process/Value.js

@@ -0,0 +1,42 @@
+import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder } from "../OntologyAnnotation.js";
+import { string, float, int, map, oneOf } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { Value } from "../../Core/Process/Value.js";
+import { ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
+import { defaultSpaces } from "../Encode.js";
+
+export function Value_ISAJson_encoder(value) {
+    switch (value.tag) {
+        case 1:
+            return new Json(7, [value.fields[0] >>> 0]);
+        case 3:
+            return new Json(0, [value.fields[0]]);
+        case 0:
+            return OntologyAnnotation_ISAJson_encoder(value.fields[0]);
+        default:
+            return new Json(2, [value.fields[0]]);
+    }
+}
+
+export const Value_ISAJson_decoder = oneOf(ofArray([map((Item) => (new Value(1, [Item])), int), map((Item_1) => (new Value(2, [Item_1])), float), map((Item_2) => (new Value(0, [Item_2])), OntologyAnnotation_ISAJson_decoder), map((Item_3) => (new Value(3, [Item_3])), string)]));
+
+export function ARCtrl_Process_Value__Value_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Value_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_Process_Value__Value_toISAJsonString_Static_71136F3F(spaces) {
+    return (v) => {
+        const value = Value_ISAJson_encoder(v);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+