@nfdi4plants/arctrl 2.5.1 → 3.0.0-alpha.2

package/dist/ts/cjs/ts/Json/Process/MaterialAttribute.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.decoder = void 0;
+exports.genID = genID;
+exports.encoder = encoder;
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const OntologyAnnotation_js_1 = require("../OntologyAnnotation.js");
+const MaterialAttribute_js_1 = require("../../Core/Process/MaterialAttribute.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_js_1 = require("../Encode.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const IDTable_js_1 = require("../IDTable.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+function genID(m) {
+    const matchValue = m.CharacteristicType;
+    if (matchValue == null) {
+        return "#EmptyFactor";
+    }
+    else {
+        return `#MaterialAttribute/${(0, OntologyAnnotation_js_1.OntologyAnnotation_ROCrate_genID)((0, Option_js_1.value)(matchValue))}`;
+    }
+}
+function encoder(idMap, value) {
+    const f = (value_1) => {
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("@id", (value_2) => ({
+                Encode(helpers) {
+                    return helpers.encodeString(value_2);
+                },
+            }), genID(value_1)), (0, Encode_js_1.tryInclude)("characteristicType", (oa) => (0, OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_encoder)(idMap, oa), value_1.CharacteristicType)]));
+        return {
+            Encode(helpers_1) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_1)], values_1);
+                return helpers_1.encodeObject(arg);
+            },
+        };
+    };
+    if (idMap != null) {
+        return (0, IDTable_js_1.encode)(genID, f, value, (0, Option_js_1.value)(idMap));
+    }
+    else {
+        return f(value);
+    }
+}
+exports.decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg;
+    return new MaterialAttribute_js_1.MaterialAttribute(undefined, (objectArg = get$.Optional, objectArg.Field("characteristicType", OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_decoder)));
+});

package/dist/ts/cjs/ts/Json/Process/MaterialAttributeValue.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ROCrate_decoder = exports.ROCrate_encoder = void 0;
+exports.ISAJson_genID = ISAJson_genID;
+exports.ISAJson_encoder = ISAJson_encoder;
+const PropertyValue_js_1 = require("../PropertyValue.js");
+const MaterialAttributeValue_js_1 = require("../../Core/Process/MaterialAttributeValue.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_js_1 = require("../Encode.js");
+const MaterialAttribute_js_1 = require("./MaterialAttribute.js");
+const Value_js_1 = require("./Value.js");
+const OntologyAnnotation_js_1 = require("../OntologyAnnotation.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const IDTable_js_1 = require("../IDTable.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const Decode_js_1 = require("../Decode.js");
+exports.ROCrate_encoder = PropertyValue_js_1.encoder;
+exports.ROCrate_decoder = (0, PropertyValue_js_1.decoder)(MaterialAttributeValue_js_1.MaterialAttributeValue_createAsPV);
+function ISAJson_genID(oa) {
+    return (0, PropertyValue_js_1.genID)(oa);
+}
+function ISAJson_encoder(idMap, oa) {
+    const f = (oa_1) => {
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("@id", (value) => ({
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            }), ISAJson_genID(oa_1)), (0, Encode_js_1.tryInclude)("category", (value_2) => (0, MaterialAttribute_js_1.encoder)(idMap, value_2), oa_1.Category), (0, Encode_js_1.tryInclude)("value", (value_3) => (0, Value_js_1.encoder)(idMap, value_3), oa_1.Value), (0, Encode_js_1.tryInclude)("unit", (oa_3) => (0, OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_encoder)(idMap, oa_3), oa_1.Unit)]));
+        return {
+            Encode(helpers_1) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_1)], values_1);
+                return helpers_1.encodeObject(arg);
+            },
+        };
+    };
+    if (idMap != null) {
+        return (0, IDTable_js_1.encode)(ISAJson_genID, f, oa, (0, Option_js_1.value)(idMap));
+    }
+    else {
+        return f(oa);
+    }
+}
+exports.ISAJson_decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3;
+    return new MaterialAttributeValue_js_1.MaterialAttributeValue((objectArg = get$.Optional, objectArg.Field("@id", Decode_js_1.Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("category", MaterialAttribute_js_1.decoder)), (objectArg_2 = get$.Optional, objectArg_2.Field("value", Value_js_1.decoder)), (objectArg_3 = get$.Optional, objectArg_3.Field("unit", OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_decoder)));
+});

package/dist/ts/cjs/ts/Json/Process/MaterialType.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ISAJson_encoder = exports.ROCrate_decoder = void 0;
+exports.ROCrate_encoder = ROCrate_encoder;
+const Types_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Types.fs.js");
+const MaterialType_js_1 = require("../../Core/Process/MaterialType.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const Result_js_1 = require("@fable-org/fable-library-js/Result.js");
+function ROCrate_encoder(value) {
+    if (value.tag === /* LabeledExtractName */ 1) {
+        return {
+            Encode(helpers_1) {
+                return helpers_1.encodeString("Labeled Extract Name");
+            },
+        };
+    }
+    else {
+        return {
+            Encode(helpers) {
+                return helpers.encodeString("Extract Name");
+            },
+        };
+    }
+}
+exports.ROCrate_decoder = {
+    Decode(s, json) {
+        const matchValue = Decode_fs_js_1.string.Decode(s, json);
+        if (matchValue.tag === /* Error */ 1) {
+            return (0, Result_js_1.FSharpResult$2_Error)(matchValue.fields[0]);
+        }
+        else {
+            switch (matchValue.fields[0]) {
+                case "Extract Name":
+                    return (0, Result_js_1.FSharpResult$2_Ok)((0, MaterialType_js_1.MaterialType_ExtractName)());
+                case "Labeled Extract Name":
+                    return (0, Result_js_1.FSharpResult$2_Ok)((0, MaterialType_js_1.MaterialType_LabeledExtractName)());
+                default: {
+                    const s_1 = matchValue.fields[0];
+                    return (0, Result_js_1.FSharpResult$2_Error)([`Could not parse ${s_1}No other value than "Extract Name" or "Labeled Extract Name" allowed for materialtype`, (0, Types_fs_js_1.ErrorReason$1_BadPrimitive)(s_1, json)]);
+                }
+            }
+        }
+    },
+};
+exports.ISAJson_encoder = ROCrate_encoder;
+exports.ISAJson_decoder = exports.ROCrate_decoder;

package/dist/ts/cjs/ts/Json/Process/Process.js

@@ -0,0 +1,109 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ROCrate_decoder = void 0;
+exports.ROCrate_genID = ROCrate_genID;
+exports.ROCrate_encoder = ROCrate_encoder;
+exports.ISAJson_encoder = ISAJson_encoder;
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const URI_js_1 = require("../../Core/URI.js");
+const Process_js_1 = require("../../Core/Process/Process.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Encode.fs.js");
+const Encode_js_1 = require("../Encode.js");
+const Protocol_js_1 = require("./Protocol.js");
+const ProcessParameterValue_js_1 = require("./ProcessParameterValue.js");
+const Person_js_1 = require("../Person.js");
+const ProcessInput_js_1 = require("./ProcessInput.js");
+const ProcessOutput_js_1 = require("./ProcessOutput.js");
+const Comment_js_1 = require("../Comment.js");
+const isa_process_context_js_1 = require("../context/rocrate/isa_process_context.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const Decode_js_1 = require("../Decode.js");
+const IDTable_js_1 = require("../IDTable.js");
+function ROCrate_genID(p) {
+    const matchValue = p.ID;
+    if (matchValue == null) {
+        const matchValue_1 = p.Name;
+        if (matchValue_1 == null) {
+            return "#EmptyProcess";
+        }
+        else {
+            return "#Process_" + (0, String_js_1.replace)((0, Option_js_1.value)(matchValue_1), " ", "_");
+        }
+    }
+    else {
+        return (0, URI_js_1.URIModule_toString)((0, Option_js_1.value)(matchValue));
+    }
+}
+function ROCrate_encoder(studyName, assayName, oa) {
+    let value;
+    const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([["@id", (value = ROCrate_genID(oa), {
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            })], ["@type", (0, Encode_fs_js_1.list)((0, List_js_1.singleton)({
+                Encode(helpers_1) {
+                    return helpers_1.encodeString("Process");
+                },
+            }))], (0, Encode_js_1.tryInclude)("name", (value_2) => ({
+            Encode(helpers_2) {
+                return helpers_2.encodeString(value_2);
+            },
+        }), oa.Name), (0, Encode_js_1.tryInclude)("executesProtocol", (oa_1) => (0, Protocol_js_1.ROCrate_encoder)(studyName, assayName, oa.Name, oa_1), oa.ExecutesProtocol), (0, Encode_js_1.tryIncludeListOpt)("parameterValues", ProcessParameterValue_js_1.ROCrate_encoder, oa.ParameterValues), (0, Encode_js_1.tryInclude)("performer", Person_js_1.ROCrate_encodeAuthorListString, oa.Performer), (0, Encode_js_1.tryInclude)("date", (value_4) => ({
+            Encode(helpers_3) {
+                return helpers_3.encodeString(value_4);
+            },
+        }), oa.Date), (0, Encode_js_1.tryIncludeListOpt)("inputs", ProcessInput_js_1.ROCrate_encoder, oa.Inputs), (0, Encode_js_1.tryIncludeListOpt)("outputs", ProcessOutput_js_1.ROCrate_encoder, oa.Outputs), (0, Encode_js_1.tryIncludeListOpt)("comments", Comment_js_1.ROCrate_encoder, oa.Comments), ["@context", isa_process_context_js_1.context_jsonvalue]]));
+    return {
+        Encode(helpers_4) {
+            const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_4)], values_1);
+            return helpers_4.encodeObject(arg);
+        },
+    };
+}
+exports.ROCrate_decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg, objectArg_1, objectArg_2, arg_7, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8;
+    return new Process_js_1.Process((objectArg = get$.Optional, objectArg.Field("@id", Decode_js_1.Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", Decode_fs_js_1.string)), (objectArg_2 = get$.Optional, objectArg_2.Field("executesProtocol", Protocol_js_1.ROCrate_decoder)), (arg_7 = (0, Decode_fs_js_1.list)(ProcessParameterValue_js_1.ROCrate_decoder), (objectArg_3 = get$.Optional, objectArg_3.Field("parameterValues", arg_7))), (objectArg_4 = get$.Optional, objectArg_4.Field("performer", Person_js_1.ROCrate_decodeAuthorListString)), (objectArg_5 = get$.Optional, objectArg_5.Field("date", Decode_fs_js_1.string)), undefined, undefined, (arg_13 = (0, Decode_fs_js_1.list)(ProcessInput_js_1.ROCrate_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("inputs", arg_13))), (arg_15 = (0, Decode_fs_js_1.list)(ProcessOutput_js_1.ROCrate_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("outputs", arg_15))), (arg_17 = (0, Decode_fs_js_1.list)(Comment_js_1.ROCrate_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("comments", arg_17))));
+});
+function ISAJson_encoder(studyName, assayName, idMap, oa) {
+    const f = (oa_1) => {
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("@id", (value) => ({
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            }), ROCrate_genID(oa_1)), (0, Encode_js_1.tryInclude)("name", (value_2) => ({
+                Encode(helpers_1) {
+                    return helpers_1.encodeString(value_2);
+                },
+            }), oa_1.Name), (0, Encode_js_1.tryInclude)("executesProtocol", (oa_2) => (0, Protocol_js_1.ISAJson_encoder)(studyName, assayName, oa_1.Name, idMap, oa_2), oa_1.ExecutesProtocol), (0, Encode_js_1.tryIncludeListOpt)("parameterValues", (oa_3) => (0, ProcessParameterValue_js_1.ISAJson_encoder)(idMap, oa_3), oa_1.ParameterValues), (0, Encode_js_1.tryInclude)("performer", (value_4) => ({
+                Encode(helpers_2) {
+                    return helpers_2.encodeString(value_4);
+                },
+            }), oa_1.Performer), (0, Encode_js_1.tryInclude)("date", (value_6) => ({
+                Encode(helpers_3) {
+                    return helpers_3.encodeString(value_6);
+                },
+            }), oa_1.Date), (0, Encode_js_1.tryInclude)("previousProcess", (oa_4) => ISAJson_encoder(studyName, assayName, idMap, oa_4), oa_1.PreviousProcess), (0, Encode_js_1.tryInclude)("nextProcess", (oa_5) => ISAJson_encoder(studyName, assayName, idMap, oa_5), oa_1.NextProcess), (0, Encode_js_1.tryIncludeListOpt)("inputs", (value_8) => (0, ProcessInput_js_1.ISAJson_encoder)(idMap, value_8), oa_1.Inputs), (0, Encode_js_1.tryIncludeListOpt)("outputs", (value_9) => (0, ProcessOutput_js_1.ISAJson_encoder)(idMap, value_9), oa_1.Outputs), (0, Encode_js_1.tryIncludeListOpt)("comments", (comment) => (0, Comment_js_1.ISAJson_encoder)(idMap, comment), oa_1.Comments)]));
+        return {
+            Encode(helpers_4) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_4)], values_1);
+                return helpers_4.encodeObject(arg);
+            },
+        };
+    };
+    if (idMap != null) {
+        return (0, IDTable_js_1.encode)(ROCrate_genID, f, oa, (0, Option_js_1.value)(idMap));
+    }
+    else {
+        return f(oa);
+    }
+}
+exports.ISAJson_decoder = (() => {
+    const decode = () => (0, Decode_fs_js_1.object)((get$) => {
+        let objectArg, objectArg_1, objectArg_2, arg_7, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
+        return new Process_js_1.Process((objectArg = get$.Optional, objectArg.Field("@id", Decode_js_1.Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", Decode_fs_js_1.string)), (objectArg_2 = get$.Optional, objectArg_2.Field("executesProtocol", Protocol_js_1.ISAJson_decoder)), (arg_7 = (0, Decode_fs_js_1.list)(ProcessParameterValue_js_1.ISAJson_decoder), (objectArg_3 = get$.Optional, objectArg_3.Field("parameterValues", arg_7))), (objectArg_4 = get$.Optional, objectArg_4.Field("performer", Decode_fs_js_1.string)), (objectArg_5 = get$.Optional, objectArg_5.Field("date", Decode_fs_js_1.string)), (arg_13 = decode(), (objectArg_6 = get$.Optional, objectArg_6.Field("previousProcess", arg_13))), (arg_15 = decode(), (objectArg_7 = get$.Optional, objectArg_7.Field("nextProcess", arg_15))), (arg_17 = (0, Decode_fs_js_1.list)(ProcessInput_js_1.ISAJson_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("inputs", arg_17))), (arg_19 = (0, Decode_fs_js_1.list)(ProcessOutput_js_1.ISAJson_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("outputs", arg_19))), (arg_21 = (0, Decode_fs_js_1.list)(Comment_js_1.ISAJson_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_21))));
+    });
+    return decode();
+})();

package/dist/ts/cjs/ts/Json/Process/ProcessInput.js

@@ -0,0 +1,38 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ROCrate_decoder = void 0;
+exports.ROCrate_encoder = ROCrate_encoder;
+exports.ISAJson_encoder = ISAJson_encoder;
+const Sample_js_1 = require("./Sample.js");
+const Data_js_1 = require("../Data.js");
+const Material_js_1 = require("./Material.js");
+const Source_js_1 = require("./Source.js");
+const ProcessInput_js_1 = require("../../Core/Process/ProcessInput.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+function ROCrate_encoder(value) {
+    switch (value.tag) {
+        case /* Sample */ 1:
+            return (0, Sample_js_1.ROCrate_encoder)(value.fields[0]);
+        case /* Data */ 2:
+            return (0, Data_js_1.ROCrate_encoder)(value.fields[0]);
+        case /* Material */ 3:
+            return (0, Material_js_1.ROCrate_encoder)(value.fields[0]);
+        default:
+            return (0, Source_js_1.ROCrate_encoder)(value.fields[0]);
+    }
+}
+exports.ROCrate_decoder = (0, Decode_fs_js_1.oneOf)((0, List_js_1.ofArray)([(0, Decode_fs_js_1.map)(ProcessInput_js_1.ProcessInput_Sample, Sample_js_1.ROCrate_decoder), (0, Decode_fs_js_1.map)(ProcessInput_js_1.ProcessInput_Source, Source_js_1.ROCrate_decoder), (0, Decode_fs_js_1.map)(ProcessInput_js_1.ProcessInput_Data, Data_js_1.ROCrate_decoder), (0, Decode_fs_js_1.map)(ProcessInput_js_1.ProcessInput_Material, Material_js_1.ROCrate_decoder)]));
+function ISAJson_encoder(idMap, value) {
+    switch (value.tag) {
+        case /* Sample */ 1:
+            return (0, Sample_js_1.ISAJson_encoder)(idMap, value.fields[0]);
+        case /* Data */ 2:
+            return (0, Data_js_1.ISAJson_encoder)(idMap, value.fields[0]);
+        case /* Material */ 3:
+            return (0, Material_js_1.ISAJson_encoder)(idMap, value.fields[0]);
+        default:
+            return (0, Source_js_1.ISAJson_encoder)(idMap, value.fields[0]);
+    }
+}
+exports.ISAJson_decoder = (0, Decode_fs_js_1.oneOf)((0, List_js_1.ofArray)([(0, Decode_fs_js_1.map)(ProcessInput_js_1.ProcessInput_Source, Source_js_1.ISAJson_decoder), (0, Decode_fs_js_1.map)(ProcessInput_js_1.ProcessInput_Sample, Sample_js_1.ISAJson_decoder), (0, Decode_fs_js_1.map)(ProcessInput_js_1.ProcessInput_Data, Data_js_1.ISAJson_decoder), (0, Decode_fs_js_1.map)(ProcessInput_js_1.ProcessInput_Material, Material_js_1.ISAJson_decoder)]));

package/dist/ts/cjs/ts/Json/Process/ProcessOutput.js

@@ -0,0 +1,33 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ROCrate_decoder = void 0;
+exports.ROCrate_encoder = ROCrate_encoder;
+exports.ISAJson_encoder = ISAJson_encoder;
+const Data_js_1 = require("../Data.js");
+const Material_js_1 = require("./Material.js");
+const Sample_js_1 = require("./Sample.js");
+const ProcessOutput_js_1 = require("../../Core/Process/ProcessOutput.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+function ROCrate_encoder(value) {
+    switch (value.tag) {
+        case /* Data */ 1:
+            return (0, Data_js_1.ROCrate_encoder)(value.fields[0]);
+        case /* Material */ 2:
+            return (0, Material_js_1.ROCrate_encoder)(value.fields[0]);
+        default:
+            return (0, Sample_js_1.ROCrate_encoder)(value.fields[0]);
+    }
+}
+exports.ROCrate_decoder = (0, Decode_fs_js_1.oneOf)((0, List_js_1.ofArray)([(0, Decode_fs_js_1.map)(ProcessOutput_js_1.ProcessOutput_Sample, Sample_js_1.ROCrate_decoder), (0, Decode_fs_js_1.map)(ProcessOutput_js_1.ProcessOutput_Data, Data_js_1.ROCrate_decoder), (0, Decode_fs_js_1.map)(ProcessOutput_js_1.ProcessOutput_Material, Material_js_1.ROCrate_decoder)]));
+function ISAJson_encoder(idMap, value) {
+    switch (value.tag) {
+        case /* Data */ 1:
+            return (0, Data_js_1.ISAJson_encoder)(idMap, value.fields[0]);
+        case /* Material */ 2:
+            return (0, Material_js_1.ISAJson_encoder)(idMap, value.fields[0]);
+        default:
+            return (0, Sample_js_1.ISAJson_encoder)(idMap, value.fields[0]);
+    }
+}
+exports.ISAJson_decoder = (0, Decode_fs_js_1.oneOf)((0, List_js_1.ofArray)([(0, Decode_fs_js_1.map)(ProcessOutput_js_1.ProcessOutput_Sample, Sample_js_1.ISAJson_decoder), (0, Decode_fs_js_1.map)(ProcessOutput_js_1.ProcessOutput_Data, Data_js_1.ISAJson_decoder), (0, Decode_fs_js_1.map)(ProcessOutput_js_1.ProcessOutput_Material, Material_js_1.ISAJson_decoder)]));

package/dist/ts/cjs/ts/Json/Process/ProcessParameterValue.js

@@ -0,0 +1,33 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ROCrate_decoder = exports.ROCrate_encoder = void 0;
+exports.ISAJson_genID = ISAJson_genID;
+exports.ISAJson_encoder = ISAJson_encoder;
+const PropertyValue_js_1 = require("../PropertyValue.js");
+const ProcessParameterValue_js_1 = require("../../Core/Process/ProcessParameterValue.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_js_1 = require("../Encode.js");
+const ProtocolParameter_js_1 = require("./ProtocolParameter.js");
+const Value_js_1 = require("./Value.js");
+const OntologyAnnotation_js_1 = require("../OntologyAnnotation.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+exports.ROCrate_encoder = PropertyValue_js_1.encoder;
+exports.ROCrate_decoder = (0, PropertyValue_js_1.decoder)((alternateName, measurementMethod, description, category, value, unit) => ProcessParameterValue_js_1.ProcessParameterValue.createAsPV(alternateName, measurementMethod, description, category, value, unit));
+function ISAJson_genID(oa) {
+    throw new Error("Not implemented");
+}
+function ISAJson_encoder(idMap, oa) {
+    const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("category", (value) => (0, ProtocolParameter_js_1.encoder)(idMap, value), oa.Category), (0, Encode_js_1.tryInclude)("value", (value_1) => (0, Value_js_1.encoder)(idMap, value_1), oa.Value), (0, Encode_js_1.tryInclude)("unit", (oa_1) => (0, OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_encoder)(idMap, oa_1), oa.Unit)]));
+    return {
+        Encode(helpers) {
+            const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers)], values_1);
+            return helpers.encodeObject(arg);
+        },
+    };
+}
+exports.ISAJson_decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg, objectArg_1, objectArg_2;
+    return new ProcessParameterValue_js_1.ProcessParameterValue((objectArg = get$.Optional, objectArg.Field("category", ProtocolParameter_js_1.decoder)), (objectArg_1 = get$.Optional, objectArg_1.Field("value", Value_js_1.decoder)), (objectArg_2 = get$.Optional, objectArg_2.Field("unit", OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_decoder)));
+});

package/dist/ts/cjs/ts/Json/Process/Protocol.js

@@ -0,0 +1,180 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ROCrate_decoder = void 0;
+exports.ROCrate_genID = ROCrate_genID;
+exports.ROCrate_encoder = ROCrate_encoder;
+exports.ISAJson_encoder = ISAJson_encoder;
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const Protocol_js_1 = require("../../Core/Process/Protocol.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Encode.fs.js");
+const Encode_js_1 = require("../Encode.js");
+const OntologyAnnotation_js_1 = require("../OntologyAnnotation.js");
+const Component_js_1 = require("./Component.js");
+const Comment_js_1 = require("../Comment.js");
+const isa_protocol_context_js_1 = require("../context/rocrate/isa_protocol_context.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
+const Decode_js_1 = require("../Decode.js");
+const ProtocolParameter_js_1 = require("./ProtocolParameter.js");
+const IDTable_js_1 = require("../IDTable.js");
+function ROCrate_genID(studyName, assayName, processName, p) {
+    const matchValue = p.ID;
+    let matchResult, id_1;
+    if (matchValue != null) {
+        if ((0, Option_js_1.value)(matchValue) !== "") {
+            matchResult = 0;
+            id_1 = (0, Option_js_1.value)(matchValue);
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0:
+            return id_1;
+        default: {
+            const matchValue_1 = p.Uri;
+            if (matchValue_1 == null) {
+                const matchValue_2 = p.Name;
+                if (matchValue_2 == null) {
+                    let matchResult_1, an, pn, sn, pn_1, sn_1, pn_2;
+                    if (studyName == null) {
+                        if (assayName == null) {
+                            if (processName != null) {
+                                matchResult_1 = 2;
+                                pn_2 = (0, Option_js_1.value)(processName);
+                            }
+                            else {
+                                matchResult_1 = 3;
+                            }
+                        }
+                        else {
+                            matchResult_1 = 3;
+                        }
+                    }
+                    else if (assayName == null) {
+                        if (processName != null) {
+                            matchResult_1 = 1;
+                            pn_1 = (0, Option_js_1.value)(processName);
+                            sn_1 = (0, Option_js_1.value)(studyName);
+                        }
+                        else {
+                            matchResult_1 = 3;
+                        }
+                    }
+                    else if (processName != null) {
+                        matchResult_1 = 0;
+                        an = (0, Option_js_1.value)(assayName);
+                        pn = (0, Option_js_1.value)(processName);
+                        sn = (0, Option_js_1.value)(studyName);
+                    }
+                    else {
+                        matchResult_1 = 3;
+                    }
+                    switch (matchResult_1) {
+                        case 0:
+                            return (((("#Protocol_" + (0, String_js_1.replace)(sn, " ", "_")) + "_") + (0, String_js_1.replace)(an, " ", "_")) + "_") + (0, String_js_1.replace)(pn, " ", "_");
+                        case 1:
+                            return (("#Protocol_" + (0, String_js_1.replace)(sn_1, " ", "_")) + "_") + (0, String_js_1.replace)(pn_1, " ", "_");
+                        case 2:
+                            return "#Protocol_" + (0, String_js_1.replace)(pn_2, " ", "_");
+                        default:
+                            return "#EmptyProtocol";
+                    }
+                }
+                else {
+                    return "#Protocol_" + (0, String_js_1.replace)((0, Option_js_1.value)(matchValue_2), " ", "_");
+                }
+            }
+            else {
+                return (0, Option_js_1.value)(matchValue_1);
+            }
+        }
+    }
+}
+function ROCrate_encoder(studyName, assayName, processName, oa) {
+    let value;
+    const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([["@id", (value = ROCrate_genID(studyName, assayName, processName, oa), {
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            })], ["@type", (0, Encode_fs_js_1.list)((0, List_js_1.singleton)({
+                Encode(helpers_1) {
+                    return helpers_1.encodeString("Protocol");
+                },
+            }))], (0, Encode_js_1.tryInclude)("name", (value_2) => ({
+            Encode(helpers_2) {
+                return helpers_2.encodeString(value_2);
+            },
+        }), oa.Name), (0, Encode_js_1.tryInclude)("protocolType", OntologyAnnotation_js_1.OntologyAnnotation_ROCrate_encoderDefinedTerm, oa.ProtocolType), (0, Encode_js_1.tryInclude)("description", (value_4) => ({
+            Encode(helpers_3) {
+                return helpers_3.encodeString(value_4);
+            },
+        }), oa.Description), (0, Encode_js_1.tryInclude)("uri", (value_6) => ({
+            Encode(helpers_4) {
+                return helpers_4.encodeString(value_6);
+            },
+        }), oa.Uri), (0, Encode_js_1.tryInclude)("version", (value_8) => ({
+            Encode(helpers_5) {
+                return helpers_5.encodeString(value_8);
+            },
+        }), oa.Version), (0, Encode_js_1.tryIncludeListOpt)("components", Component_js_1.ROCrate_encoder, oa.Components), (0, Encode_js_1.tryIncludeListOpt)("comments", Comment_js_1.ROCrate_encoder, oa.Comments), ["@context", isa_protocol_context_js_1.context_jsonvalue]]));
+    return {
+        Encode(helpers_6) {
+            const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values_1);
+            return helpers_6.encodeObject(arg);
+        },
+    };
+}
+exports.ROCrate_decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let list_3, list_1, arg_1, objectArg, arg_3, objectArg_1, arg_5, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, objectArg_8, arg_19, objectArg_9;
+    const components = (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (list_3 = ((list_1 = (0, Option_js_1.defaultArg)((arg_1 = (0, Decode_fs_js_1.list)(Component_js_1.ROCrate_decoder), (objectArg = get$.Optional, objectArg.Field("components", arg_1))), (0, List_js_1.empty)()), (0, List_js_1.append)((0, Option_js_1.defaultArg)((arg_3 = (0, Decode_fs_js_1.list)(Component_js_1.ROCrate_decoder), (objectArg_1 = get$.Optional, objectArg_1.Field("reagents", arg_3))), (0, List_js_1.empty)()), list_1))), (0, List_js_1.append)((0, Option_js_1.defaultArg)((arg_5 = (0, Decode_fs_js_1.list)(Component_js_1.ROCrate_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("computationalTools", arg_5))), (0, List_js_1.empty)()), list_3)));
+    return new Protocol_js_1.Protocol((objectArg_3 = get$.Optional, objectArg_3.Field("@id", Decode_js_1.Decode_uri)), (objectArg_4 = get$.Optional, objectArg_4.Field("name", Decode_fs_js_1.string)), (objectArg_5 = get$.Optional, objectArg_5.Field("protocolType", OntologyAnnotation_js_1.OntologyAnnotation_ROCrate_decoderDefinedTerm)), (objectArg_6 = get$.Optional, objectArg_6.Field("description", Decode_fs_js_1.string)), (objectArg_7 = get$.Optional, objectArg_7.Field("uri", Decode_js_1.Decode_uri)), (objectArg_8 = get$.Optional, objectArg_8.Field("version", Decode_fs_js_1.string)), undefined, components, (arg_19 = (0, Decode_fs_js_1.list)(Comment_js_1.ROCrate_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("comments", arg_19))));
+});
+function ISAJson_encoder(studyName, assayName, processName, idMap, oa) {
+    const f = (oa_1) => {
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("@id", (value) => ({
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            }), ROCrate_genID(studyName, assayName, processName, oa_1)), (0, Encode_js_1.tryInclude)("name", (value_2) => ({
+                Encode(helpers_1) {
+                    return helpers_1.encodeString(value_2);
+                },
+            }), oa_1.Name), (0, Encode_js_1.tryInclude)("protocolType", (oa_2) => (0, OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_encoder)(idMap, oa_2), oa_1.ProtocolType), (0, Encode_js_1.tryInclude)("description", (value_4) => ({
+                Encode(helpers_2) {
+                    return helpers_2.encodeString(value_4);
+                },
+            }), oa_1.Description), (0, Encode_js_1.tryInclude)("uri", (value_6) => ({
+                Encode(helpers_3) {
+                    return helpers_3.encodeString(value_6);
+                },
+            }), oa_1.Uri), (0, Encode_js_1.tryInclude)("version", (value_8) => ({
+                Encode(helpers_4) {
+                    return helpers_4.encodeString(value_8);
+                },
+            }), oa_1.Version), (0, Encode_js_1.tryIncludeListOpt)("parameters", (value_10) => (0, ProtocolParameter_js_1.encoder)(idMap, value_10), oa_1.Parameters), (0, Encode_js_1.tryIncludeListOpt)("components", (c) => (0, Component_js_1.ISAJson_encoder)(idMap, c), oa_1.Components), (0, Encode_js_1.tryIncludeListOpt)("comments", (comment) => (0, Comment_js_1.ISAJson_encoder)(idMap, comment), oa_1.Comments)]));
+        return {
+            Encode(helpers_5) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_5)], values_1);
+                return helpers_5.encodeObject(arg);
+            },
+        };
+    };
+    if (idMap != null) {
+        return (0, IDTable_js_1.encode)((p_1) => ROCrate_genID(studyName, assayName, processName, p_1), f, oa, (0, Option_js_1.value)(idMap));
+    }
+    else {
+        return f(oa);
+    }
+}
+exports.ISAJson_decoder = (0, Decode_fs_js_1.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_js_1.Protocol((objectArg = get$.Optional, objectArg.Field("@id", Decode_js_1.Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", Decode_fs_js_1.string)), (objectArg_2 = get$.Optional, objectArg_2.Field("protocolType", OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_decoder)), (objectArg_3 = get$.Optional, objectArg_3.Field("description", Decode_fs_js_1.string)), (objectArg_4 = get$.Optional, objectArg_4.Field("uri", Decode_js_1.Decode_uri)), (objectArg_5 = get$.Optional, objectArg_5.Field("version", Decode_fs_js_1.string)), (arg_13 = (0, Decode_fs_js_1.list)(ProtocolParameter_js_1.decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("parameters", arg_13))), (arg_15 = (0, Decode_fs_js_1.list)(Component_js_1.ISAJson_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("components", arg_15))), (arg_17 = (0, Decode_fs_js_1.list)(Comment_js_1.ISAJson_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("comments", arg_17))));
+});

package/dist/ts/cjs/ts/Json/Process/ProtocolParameter.js

@@ -0,0 +1,47 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.decoder = void 0;
+exports.genID = genID;
+exports.encoder = encoder;
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const OntologyAnnotation_js_1 = require("../OntologyAnnotation.js");
+const ProtocolParameter_js_1 = require("../../Core/Process/ProtocolParameter.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_js_1 = require("../Encode.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const IDTable_js_1 = require("../IDTable.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+function genID(p) {
+    const matchValue = p.ParameterName;
+    if (matchValue == null) {
+        return "#EmptyProtocolParameter";
+    }
+    else {
+        return `#ProtocolParameter/${(0, OntologyAnnotation_js_1.OntologyAnnotation_ROCrate_genID)((0, Option_js_1.value)(matchValue))}`;
+    }
+}
+function encoder(idMap, value) {
+    const f = (value_1) => {
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("@id", (value_2) => ({
+                Encode(helpers) {
+                    return helpers.encodeString(value_2);
+                },
+            }), genID(value_1)), (0, Encode_js_1.tryInclude)("parameterName", (oa) => (0, OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_encoder)(idMap, oa), value_1.ParameterName)]));
+        return {
+            Encode(helpers_1) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_1)], values_1);
+                return helpers_1.encodeObject(arg);
+            },
+        };
+    };
+    if (idMap != null) {
+        return (0, IDTable_js_1.encode)(genID, f, value, (0, Option_js_1.value)(idMap));
+    }
+    else {
+        return f(value);
+    }
+}
+exports.decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg;
+    return new ProtocolParameter_js_1.ProtocolParameter(undefined, (objectArg = get$.Optional, objectArg.Field("parameterName", OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_decoder)));
+});