@nfdi4plants/arctrl 1.0.0-alpha10

package/ISA/ISA.Json/Process.js

@@ -0,0 +1,291 @@
+import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { ProtocolParameter_getNameText_Z3A4310A5 } from "../ISA/JsonTypes/ProtocolParameter.js";
+import { Value_getText_72E9EF0F } from "../ISA/JsonTypes/Value.js";
+import { list as list_2, toString, nil, object as object_22 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { map, choose } from "../../fable_modules/fable-library.4.1.4/List.js";
+import { uncurry2, equals } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.1.4/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 { Protocol_decoder, Protocol_encoder, ProtocolParameter_decoder, ProtocolParameter_encoder } from "./Protocol.js";
+import { Value_decoder, Value_encoder } from "./Factor.js";
+import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
+import { list as list_1, string, object as object_23 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { ProcessParameterValue } from "../ISA/JsonTypes/ProcessParameterValue.js";
+import { uri, fromJsonString } from "./Decode.js";
+import { ProcessInput } from "../ISA/JsonTypes/ProcessInput.js";
+import { Data_decoder, Sample_decoder, Source_decoder, Source_encoder, Data_encoder, Sample_encoder } from "./Data.js";
+import { Material_decoder, Material_encoder } from "./Material.js";
+import { FSharpResult$2 } from "../../fable_modules/fable-library.4.1.4/Choice.js";
+import { ProcessOutput } from "../ISA/JsonTypes/ProcessOutput.js";
+import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
+import { decoder as decoder_4, encoder } from "./Comment.js";
+import { Process } from "../ISA/JsonTypes/Process.js";
+
+export function ProcessParameterValue_genID(p) {
+    const matchValue = p.Value;
+    const matchValue_1 = p.Category;
+    let matchResult, c, v;
+    if (matchValue != null) {
+        if (matchValue_1 != null) {
+            matchResult = 0;
+            c = matchValue_1;
+            v = matchValue;
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0:
+            return (("#Param_" + replace(ProtocolParameter_getNameText_Z3A4310A5(c), " ", "_")) + "_") + replace(Value_getText_72E9EF0F(v), " ", "_");
+        default:
+            return "#EmptyParameterValue";
+    }
+}
+
+export function ProcessParameterValue_encoder(options, oa) {
+    return object_22(choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, nil)) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, toList(delay(() => {
+        let value, s;
+        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = ProcessParameterValue_genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : empty(), delay(() => {
+            let value_2, s_1;
+            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_2 = "ProcessParameterValue", (typeof value_2 === "string") ? ((s_1 = value_2, s_1)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("category", (oa_1) => ProtocolParameter_encoder(options, oa_1), oa["Category"])), delay(() => append(singleton(tryInclude("value", (value_4) => Value_encoder(options, value_4), oa["Value"])), delay(() => singleton(tryInclude("unit", (oa_2) => OntologyAnnotation_encoder(options, oa_2), oa["Unit"]))))))));
+        }));
+    }))));
+}
+
+export function ProcessParameterValue_decoder(options) {
+    return (path) => ((v) => object_23((get$) => {
+        let arg_1, objectArg, objectArg_1, arg_5, objectArg_2;
+        return new ProcessParameterValue((arg_1 = ProtocolParameter_decoder(options), (objectArg = get$.Optional, objectArg.Field("category", uncurry2(arg_1)))), (objectArg_1 = get$.Optional, objectArg_1.Field("value", (s, json) => Value_decoder(options, s, json))), (arg_5 = OntologyAnnotation_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("unit", uncurry2(arg_5)))));
+    }, path, v));
+}
+
+export function ProcessParameterValue_fromJsonString(s) {
+    return fromJsonString(uncurry2(ProcessParameterValue_decoder(ConverterOptions_$ctor())), s);
+}
+
+export function ProcessParameterValue_toJsonString(p) {
+    return toString(2, ProcessParameterValue_encoder(ConverterOptions_$ctor(), p));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function ProcessParameterValue_toStringLD(p) {
+    let returnVal;
+    return toString(2, ProcessParameterValue_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
+}
+
+export function ProcessInput_encoder(options, value) {
+    if (value instanceof ProcessInput) {
+        if (value.tag === 1) {
+            return Sample_encoder(options, value.fields[0]);
+        }
+        else if (value.tag === 2) {
+            return Data_encoder(options, value.fields[0]);
+        }
+        else if (value.tag === 3) {
+            return Material_encoder(options, value.fields[0]);
+        }
+        else {
+            return Source_encoder(options, value.fields[0]);
+        }
+    }
+    else {
+        return nil;
+    }
+}
+
+export function ProcessInput_decoder(options, s, json) {
+    const matchValue = Source_decoder(options, s, json);
+    if (matchValue.tag === 1) {
+        const matchValue_1 = Sample_decoder(options, s, json);
+        if (matchValue_1.tag === 1) {
+            const matchValue_2 = Data_decoder(options, s, json);
+            if (matchValue_2.tag === 1) {
+                const matchValue_3 = Material_decoder(options, s, json);
+                if (matchValue_3.tag === 1) {
+                    return new FSharpResult$2(1, [matchValue_3.fields[0]]);
+                }
+                else {
+                    return new FSharpResult$2(0, [new ProcessInput(3, [matchValue_3.fields[0]])]);
+                }
+            }
+            else {
+                return new FSharpResult$2(0, [new ProcessInput(2, [matchValue_2.fields[0]])]);
+            }
+        }
+        else {
+            return new FSharpResult$2(0, [new ProcessInput(1, [matchValue_1.fields[0]])]);
+        }
+    }
+    else {
+        return new FSharpResult$2(0, [new ProcessInput(0, [matchValue.fields[0]])]);
+    }
+}
+
+export function ProcessInput_fromJsonString(s) {
+    let options;
+    return fromJsonString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => ProcessInput_decoder(options, s_1, json)))), s);
+}
+
+export function ProcessInput_toJsonString(m) {
+    return toString(2, ProcessInput_encoder(ConverterOptions_$ctor(), m));
+}
+
+export function ProcessInput_toStringLD(m) {
+    let returnVal;
+    return toString(2, ProcessInput_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), m));
+}
+
+export function ProcessOutput_encoder(options, value) {
+    if (value instanceof ProcessOutput) {
+        if (value.tag === 1) {
+            return Data_encoder(options, value.fields[0]);
+        }
+        else if (value.tag === 2) {
+            return Material_encoder(options, value.fields[0]);
+        }
+        else {
+            return Sample_encoder(options, value.fields[0]);
+        }
+    }
+    else {
+        return nil;
+    }
+}
+
+export function ProcessOutput_decoder(options, s, json) {
+    const matchValue = Sample_decoder(options, s, json);
+    if (matchValue.tag === 1) {
+        const matchValue_1 = Data_decoder(options, s, json);
+        if (matchValue_1.tag === 1) {
+            const matchValue_2 = Material_decoder(options, s, json);
+            if (matchValue_2.tag === 1) {
+                return new FSharpResult$2(1, [matchValue_2.fields[0]]);
+            }
+            else {
+                return new FSharpResult$2(0, [new ProcessOutput(2, [matchValue_2.fields[0]])]);
+            }
+        }
+        else {
+            return new FSharpResult$2(0, [new ProcessOutput(1, [matchValue_1.fields[0]])]);
+        }
+    }
+    else {
+        return new FSharpResult$2(0, [new ProcessOutput(0, [matchValue.fields[0]])]);
+    }
+}
+
+export function ProcessOutput_fromJsonString(s) {
+    let options;
+    return fromJsonString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => ProcessOutput_decoder(options, s_1, json)))), s);
+}
+
+export function ProcessOutput_toJsonString(m) {
+    return toString(2, ProcessOutput_encoder(ConverterOptions_$ctor(), m));
+}
+
+export function Process_genID(p) {
+    const matchValue = p.ID;
+    if (matchValue == null) {
+        const matchValue_1 = p.Name;
+        if (matchValue_1 == null) {
+            return "#EmptyProcess";
+        }
+        else {
+            return "#Process_" + replace(matchValue_1, " ", "_");
+        }
+    }
+    else {
+        return URIModule_toString(matchValue);
+    }
+}
+
+export function Process_encoder(options, oa) {
+    return object_22(choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, nil)) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, toList(delay(() => {
+        let value, s;
+        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = Process_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 = "Process", (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("executesProtocol", (oa_1) => Protocol_encoder(options, oa_1), oa["ExecutesProtocol"])), delay(() => append(singleton(tryInclude("parameterValues", (oa_2) => ProcessParameterValue_encoder(options, oa_2), oa["ParameterValues"])), delay(() => append(singleton(tryInclude("performer", (value_10) => {
+                let s_4;
+                const value_11 = value_10;
+                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
+            }, oa["Performer"])), delay(() => append(singleton(tryInclude("date", (value_13) => {
+                let s_5;
+                const value_14 = value_13;
+                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
+            }, oa["Date"])), delay(() => append(singleton(tryInclude("previousProcess", (oa_3) => Process_encoder(options, oa_3), oa["PreviousProcess"])), delay(() => append(singleton(tryInclude("nextProcess", (oa_4) => Process_encoder(options, oa_4), oa["NextProcess"])), delay(() => append(singleton(tryInclude("inputs", (value_16) => ProcessInput_encoder(options, value_16), oa["Inputs"])), delay(() => append(singleton(tryInclude("outputs", (value_17) => ProcessOutput_encoder(options, value_17), oa["Outputs"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), oa["Comments"]))))))))))))))))))))));
+        }));
+    }))));
+}
+
+export function Process_decoder(options) {
+    return (path_7) => ((v) => object_23((get$) => {
+        let objectArg, objectArg_1, arg_5, objectArg_2, arg_7, decoder, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, objectArg_8, objectArg_9, arg_21, decoder_3, objectArg_10;
+        return new Process((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = Protocol_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("executesProtocol", uncurry2(arg_5)))), (arg_7 = ((decoder = ProcessParameterValue_decoder(options), (path_1) => ((value_1) => list_1(uncurry2(decoder), path_1, value_1)))), (objectArg_3 = get$.Optional, objectArg_3.Field("parameterValues", uncurry2(arg_7)))), (objectArg_4 = get$.Optional, objectArg_4.Field("performer", string)), (objectArg_5 = get$.Optional, objectArg_5.Field("date", string)), (arg_13 = Process_decoder(options), (objectArg_6 = get$.Optional, objectArg_6.Field("previousProcess", uncurry2(arg_13)))), (arg_15 = Process_decoder(options), (objectArg_7 = get$.Optional, objectArg_7.Field("nextProcess", uncurry2(arg_15)))), (objectArg_8 = get$.Optional, objectArg_8.Field("inputs", (path_4, value_4) => list_1((s_1, json_1) => ProcessInput_decoder(options, s_1, json_1), path_4, value_4))), (objectArg_9 = get$.Optional, objectArg_9.Field("outputs", (path_5, value_5) => list_1((s_2, json_2) => ProcessOutput_decoder(options, s_2, json_2), path_5, value_5))), (arg_21 = ((decoder_3 = decoder_4(options), (path_6) => ((value_6) => list_1(uncurry2(decoder_3), path_6, value_6)))), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", uncurry2(arg_21)))));
+    }, path_7, v));
+}
+
+export function Process_fromJsonString(s) {
+    return fromJsonString(uncurry2(Process_decoder(ConverterOptions_$ctor())), s);
+}
+
+export function Process_toJsonString(p) {
+    return toString(2, Process_encoder(ConverterOptions_$ctor(), p));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function Process_toStringLD(p) {
+    let returnVal;
+    return toString(2, Process_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
+}
+
+export function ProcessSequence_fromJsonString(s) {
+    let decoder;
+    return fromJsonString(uncurry2((decoder = Process_decoder(ConverterOptions_$ctor()), (path) => ((value) => list_1(uncurry2(decoder), path, value)))), s);
+}
+
+export function ProcessSequence_toJsonString(p) {
+    let options;
+    return toString(2, list_2(map((options = ConverterOptions_$ctor(), (oa) => Process_encoder(options, oa)), p)));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function ProcessSequence_toStringLD(p) {
+    let options, returnVal;
+    return toString(2, list_2(map((options = ((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal))), (oa) => Process_encoder(options, oa)), p)));
+}
+

package/ISA/ISA.Json/Protocol.js

@@ -0,0 +1,242 @@
+import { value as value_19 } from "../../fable_modules/fable-library.4.1.4/Option.js";
+import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
+import { toString, nil, object as object_18 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { choose } from "../../fable_modules/fable-library.4.1.4/List.js";
+import { uncurry2, equals } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.1.4/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 { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
+import { list as list_1, string, object as object_19 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { fromJsonString, uri } from "./Decode.js";
+import { ProtocolParameter } from "../ISA/JsonTypes/ProtocolParameter.js";
+import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { Result_Map } from "../../fable_modules/fable-library.4.1.4/Choice.js";
+import { Component, Component_decomposeName_Z721C83C5 } from "../ISA/JsonTypes/Component.js";
+import { decoder as decoder_3, encoder } from "./Comment.js";
+import { Protocol } from "../ISA/JsonTypes/Protocol.js";
+
+export function ProtocolParameter_genID(pp) {
+    const matchValue = pp.ID;
+    if (matchValue == null) {
+        const matchValue_1 = pp.ParameterName;
+        let matchResult, n_1;
+        if (matchValue_1 != null) {
+            if (!(matchValue_1.ID == null)) {
+                matchResult = 0;
+                n_1 = matchValue_1;
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+        switch (matchResult) {
+            case 0:
+                return "#Param_" + value_19(n_1.ID);
+            default:
+                return "#EmptyProtocolParameter";
+        }
+    }
+    else {
+        return URIModule_toString(matchValue);
+    }
+}
+
+export function ProtocolParameter_encoder(options, oa) {
+    return object_18(choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, nil)) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, toList(delay(() => {
+        let value, s;
+        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = ProtocolParameter_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 = "ProtocolParameter", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => singleton(tryInclude("parameterName", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["ParameterName"]))));
+        }));
+    }))));
+}
+
+export function ProtocolParameter_decoder(options) {
+    return (path) => ((v) => object_19((get$) => {
+        let objectArg, arg_3, objectArg_1;
+        return new ProtocolParameter((objectArg = get$.Optional, objectArg.Field("@id", uri)), (arg_3 = OntologyAnnotation_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("parameterName", uncurry2(arg_3)))));
+    }, path, v));
+}
+
+export function ProtocolParameter_fromJsonString(s) {
+    return fromJsonString(uncurry2(ProtocolParameter_decoder(ConverterOptions_$ctor())), s);
+}
+
+export function ProtocolParameter_toString(p) {
+    return toString(2, ProtocolParameter_encoder(ConverterOptions_$ctor(), p));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function ProtocolParameter_toStringLD(p) {
+    let returnVal;
+    return toString(2, ProtocolParameter_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
+}
+
+export function Component_genID(c) {
+    const matchValue = c.ComponentName;
+    if (matchValue == null) {
+        return "#EmptyComponent";
+    }
+    else {
+        return "#Component_" + replace(matchValue, " ", "_");
+    }
+}
+
+export function Component_encoder(options, oa) {
+    return object_18(choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, nil)) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, toList(delay(() => {
+        let value, s;
+        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = Component_genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : empty(), delay(() => {
+            let value_2, s_1;
+            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_2 = "Component", (typeof value_2 === "string") ? ((s_1 = value_2, s_1)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("componentName", (value_4) => {
+                let s_2;
+                const value_5 = value_4;
+                return (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil;
+            }, oa["ComponentName"])), delay(() => singleton(tryInclude("componentType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["ComponentType"]))))));
+        }));
+    }))));
+}
+
+export function Component_decoder(options, s, json) {
+    return Result_Map((c) => {
+        let patternInput;
+        const matchValue = c.ComponentName;
+        if (matchValue == null) {
+            patternInput = [void 0, void 0];
+        }
+        else {
+            const tupledArg = Component_decomposeName_Z721C83C5(matchValue);
+            patternInput = [tupledArg[0], tupledArg[1]];
+        }
+        return new Component(c.ComponentName, patternInput[0], patternInput[1], c.ComponentType);
+    }, object_19((get$) => {
+        let objectArg, arg_3, objectArg_1;
+        return new Component((objectArg = get$.Optional, objectArg.Field("componentName", uri)), void 0, void 0, (arg_3 = OntologyAnnotation_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("componentType", uncurry2(arg_3)))));
+    }, s, json));
+}
+
+export function Component_fromJsonString(s) {
+    let options;
+    return fromJsonString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Component_decoder(options, s_1, json)))), s);
+}
+
+export function Component_toJsonString(p) {
+    return toString(2, Component_encoder(ConverterOptions_$ctor(), p));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function Component_toStringLD(p) {
+    let returnVal;
+    return toString(2, Component_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
+}
+
+export function Protocol_genID(p) {
+    const matchValue = p.ID;
+    if (matchValue == null) {
+        const matchValue_1 = p.Uri;
+        if (matchValue_1 == null) {
+            const matchValue_2 = p.Name;
+            if (matchValue_2 == null) {
+                return "#EmptyProtocol";
+            }
+            else {
+                return "#Protocol_" + replace(matchValue_2, " ", "_");
+            }
+        }
+        else {
+            return matchValue_1;
+        }
+    }
+    else {
+        return URIModule_toString(matchValue);
+    }
+}
+
+export function Protocol_encoder(options, oa) {
+    return object_18(choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, nil)) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, toList(delay(() => {
+        let value, s;
+        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = Protocol_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 = "Protocol", (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("protocolType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["ProtocolType"])), delay(() => append(singleton(tryInclude("description", (value_10) => {
+                let s_4;
+                const value_11 = value_10;
+                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
+            }, oa["Description"])), delay(() => append(singleton(tryInclude("uri", (value_13) => {
+                let s_5;
+                const value_14 = value_13;
+                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
+            }, oa["Uri"])), delay(() => append(singleton(tryInclude("version", (value_16) => {
+                let s_6;
+                const value_17 = value_16;
+                return (typeof value_17 === "string") ? ((s_6 = value_17, s_6)) : nil;
+            }, oa["Version"])), delay(() => append(singleton(tryInclude("parameters", (oa_2) => ProtocolParameter_encoder(options, oa_2), oa["Parameters"])), delay(() => append(singleton(tryInclude("components", (oa_3) => Component_encoder(options, oa_3), oa["Components"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), oa["Comments"]))))))))))))))))));
+        }));
+    }))));
+}
+
+export function Protocol_decoder(options) {
+    return (path_6) => ((v) => object_19((get$) => {
+        let objectArg, objectArg_1, arg_5, objectArg_2, objectArg_3, objectArg_4, objectArg_5, arg_13, decoder, objectArg_6, objectArg_7, arg_17, decoder_2, objectArg_8;
+        return new Protocol((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = OntologyAnnotation_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("protocolType", uncurry2(arg_5)))), (objectArg_3 = get$.Optional, objectArg_3.Field("description", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("uri", uri)), (objectArg_5 = get$.Optional, objectArg_5.Field("version", string)), (arg_13 = ((decoder = ProtocolParameter_decoder(options), (path_3) => ((value_3) => list_1(uncurry2(decoder), path_3, value_3)))), (objectArg_6 = get$.Optional, objectArg_6.Field("parameters", uncurry2(arg_13)))), (objectArg_7 = get$.Optional, objectArg_7.Field("components", (path_4, value_4) => list_1((s_2, json_2) => Component_decoder(options, s_2, json_2), path_4, value_4))), (arg_17 = ((decoder_2 = decoder_3(options), (path_5) => ((value_5) => list_1(uncurry2(decoder_2), path_5, value_5)))), (objectArg_8 = get$.Optional, objectArg_8.Field("comments", uncurry2(arg_17)))));
+    }, path_6, v));
+}
+
+export function Protocol_fromJsonString(s) {
+    return fromJsonString(uncurry2(Protocol_decoder(ConverterOptions_$ctor())), s);
+}
+
+export function Protocol_toJsonString(p) {
+    return toString(2, Protocol_encoder(ConverterOptions_$ctor(), p));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function Protocol_toStringLD(p) {
+    let returnVal;
+    return toString(2, Protocol_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
+}
+

package/ISA/ISA.Json/Publication.js

@@ -0,0 +1,92 @@
+import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { toString, nil, object as object_12 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { choose } from "../../fable_modules/fable-library.4.1.4/List.js";
+import { uncurry2, equals } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.1.4/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 { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
+import { decoder as decoder_2, encoder as encoder_1 } from "./Comment.js";
+import { array, string, object as object_13 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { fromJsonString as fromJsonString_1, uri } from "./Decode.js";
+import { Publication } from "../ISA/JsonTypes/Publication.js";
+
+export function genID(p) {
+    const matchValue = p.DOI;
+    if (matchValue == null) {
+        const matchValue_1 = p.PubMedID;
+        if (matchValue_1 == null) {
+            const matchValue_2 = p.Title;
+            if (matchValue_2 == null) {
+                return "#EmptyPublication";
+            }
+            else {
+                return "#Pub_" + replace(matchValue_2, " ", "_");
+            }
+        }
+        else {
+            return matchValue_1;
+        }
+    }
+    else {
+        return matchValue;
+    }
+}
+
+export function encoder(options, oa) {
+    return object_12(choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, nil)) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, toList(delay(() => {
+        let value, s;
+        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : empty(), delay(() => {
+            let value_2, s_1;
+            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_2 = "Publication", (typeof value_2 === "string") ? ((s_1 = value_2, s_1)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("pubMedID", (value_4) => {
+                let s_2;
+                const value_5 = value_4;
+                return (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil;
+            }, oa["PubMedID"])), delay(() => append(singleton(tryInclude("doi", (value_7) => {
+                let s_3;
+                const value_8 = value_7;
+                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
+            }, oa["DOI"])), delay(() => append(singleton(tryInclude("authorList", (value_10) => {
+                let s_4;
+                const value_11 = value_10;
+                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
+            }, oa["Authors"])), delay(() => append(singleton(tryInclude("title", (value_13) => {
+                let s_5;
+                const value_14 = value_13;
+                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
+            }, oa["Title"])), delay(() => append(singleton(tryInclude("status", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["Status"])), delay(() => singleton(tryInclude("comments", (comment) => encoder_1(options, comment), oa["Comments"]))))))))))))));
+        }));
+    }))));
+}
+
+export function decoder(options) {
+    return (path_4) => ((v) => object_13((get$) => {
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4, arg_11, decoder_1, objectArg_5;
+        return new Publication((objectArg = get$.Optional, objectArg.Field("pubMedID", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("doi", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("authorList", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("title", string)), (arg_9 = OntologyAnnotation_decoder(options), (objectArg_4 = get$.Optional, objectArg_4.Field("status", uncurry2(arg_9)))), (arg_11 = ((decoder_1 = decoder_2(options), (path_3) => ((value_3) => array(uncurry2(decoder_1), path_3, value_3)))), (objectArg_5 = get$.Optional, objectArg_5.Field("comments", uncurry2(arg_11)))));
+    }, path_4, v));
+}
+
+export function fromJsonString(s) {
+    return fromJsonString_1(uncurry2(decoder(ConverterOptions_$ctor())), s);
+}
+
+export function toJsonString(p) {
+    return toString(2, encoder(ConverterOptions_$ctor(), p));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function toStringLD(p) {
+    let returnVal;
+    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
+}
+