@nfdi4plants/arctrl 1.2.0 → 2.0.0-alpha.2

package/ISA/ISA.Json/Material.js

@@ -1,232 +0,0 @@
-import { ErrorReason$1, Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { list as list_2, object, string } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { FSharpResult$2 } from "../../fable_modules/fable-library-js.4.13.0/Result.js";
-import { MaterialType } from "../ISA/JsonTypes/MaterialType.js";
-import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { ofArray, choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
-import { equals } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeContext, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
-import { tryIncludeList, tryInclude } from "./GEncode.js";
-import { list as list_1 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
-import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
-import { context_jsonvalue } from "./context/rocrate/isa_material_attribute_context.js";
-import { object as object_1, uri } from "./Decode.js";
-import { MaterialAttribute } from "../ISA/JsonTypes/MaterialAttribute.js";
-import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
-import { replace, printf, toText } from "../../fable_modules/fable-library-js.4.13.0/String.js";
-import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { Value_decoder, Value_encoder } from "./Factor.js";
-import { context_jsonvalue as context_jsonvalue_1 } from "./context/rocrate/isa_material_attribute_value_context.js";
-import { MaterialAttributeValue } from "../ISA/JsonTypes/MaterialAttributeValue.js";
-import { context_jsonvalue as context_jsonvalue_2 } from "./context/rocrate/isa_material_context.js";
-import { Material } from "../ISA/JsonTypes/Material.js";
-
-export function MaterialType_encoder(options, value) {
-    if (value.tag === 1) {
-        return new Json(0, ["Labeled Extract Name"]);
-    }
-    else {
-        return new Json(0, ["Extract Name"]);
-    }
-}
-
-export function MaterialType_decoder(options) {
-    return {
-        Decode(s, json) {
-            const matchValue = string.Decode(s, json);
-            if (matchValue.tag === 1) {
-                return new FSharpResult$2(1, [matchValue.fields[0]]);
-            }
-            else {
-                switch (matchValue.fields[0]) {
-                    case "Extract Name":
-                        return new FSharpResult$2(0, [new MaterialType(0, [])]);
-                    case "Labeled Extract Name":
-                        return new FSharpResult$2(0, [new MaterialType(1, [])]);
-                    default: {
-                        const s_1 = matchValue.fields[0];
-                        return new FSharpResult$2(1, [[`Could not parse ${s_1}No other value than "Extract Name" or "Labeled Extract Name" allowed for materialtype`, new ErrorReason$1(0, [s_1, json])]]);
-                    }
-                }
-            }
-        },
-    };
-}
-
-export function MaterialAttribute_genID(m) {
-    const matchValue = m.ID;
-    if (matchValue == null) {
-        return "#EmptyMaterialAttribute";
-    }
-    else {
-        return URIModule_toString(matchValue);
-    }
-}
-
-export function MaterialAttribute_encoder(options, oa) {
-    return new Json(5, [choose((tupledArg) => {
-        const v = tupledArg[1];
-        if (equals(v, new Json(3, []))) {
-            return void 0;
-        }
-        else {
-            return [tupledArg[0], v];
-        }
-    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [MaterialAttribute_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_1(ofArray([new Json(0, ["MaterialAttribute"]), new Json(0, ["ArcMaterialAttribute"])]))]) : empty(), delay(() => append(singleton(tryInclude("characteristicType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa.CharacteristicType)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty()))))))))))]);
-}
-
-export function MaterialAttribute_decoder(options) {
-    return object((get$) => {
-        let objectArg, arg_3, objectArg_1;
-        return new MaterialAttribute((objectArg = get$.Optional, objectArg.Field("@id", uri)), (arg_3 = OntologyAnnotation_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("characteristicType", arg_3))));
-    });
-}
-
-export function MaterialAttribute_fromJsonString(s) {
-    const matchValue = fromString(MaterialAttribute_decoder(ConverterOptions_$ctor()), s);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function MaterialAttribute_toJsonString(m) {
-    return toString(2, MaterialAttribute_encoder(ConverterOptions_$ctor(), m));
-}
-
-/**
- * exports in json-ld format
- */
-export function MaterialAttribute_toJsonldString(m) {
-    let returnVal;
-    return toString(2, MaterialAttribute_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), m));
-}
-
-export function MaterialAttribute_toJsonldStringWithContext(a) {
-    let returnVal;
-    return toString(2, MaterialAttribute_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
-}
-
-export function MaterialAttributeValue_genID(m) {
-    const matchValue = m.ID;
-    if (matchValue == null) {
-        return "#EmptyMaterialAttributeValue";
-    }
-    else {
-        return URIModule_toString(matchValue);
-    }
-}
-
-export function MaterialAttributeValue_encoder(options, 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];
-        }
-    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [MaterialAttributeValue_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_1(ofArray([new Json(0, ["MaterialAttributeValue"]), new Json(0, ["ArcMaterialAttributeValue"])]))]) : empty(), delay(() => append(singleton(tryInclude("category", (oa_1) => MaterialAttribute_encoder(options, oa_1), oa.Category)), delay(() => append(singleton(tryInclude("value", (value_5) => Value_encoder(options, value_5), oa.Value)), delay(() => append(singleton(tryInclude("unit", (oa_2) => OntologyAnnotation_encoder(options, oa_2), oa.Unit)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue_1]) : empty()))))))))))))))]);
-}
-
-export function MaterialAttributeValue_decoder(options) {
-    return object((get$) => {
-        let objectArg, arg_3, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3;
-        return new MaterialAttributeValue((objectArg = get$.Optional, objectArg.Field("@id", uri)), (arg_3 = MaterialAttribute_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("category", arg_3))), (arg_5 = Value_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("value", arg_5))), (arg_7 = OntologyAnnotation_decoder(options), (objectArg_3 = get$.Optional, objectArg_3.Field("unit", arg_7))));
-    });
-}
-
-export function MaterialAttributeValue_fromJsonString(s) {
-    const matchValue = fromString(MaterialAttributeValue_decoder(ConverterOptions_$ctor()), s);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function MaterialAttributeValue_toJsonString(m) {
-    return toString(2, MaterialAttributeValue_encoder(ConverterOptions_$ctor(), m));
-}
-
-/**
- * exports in json-ld format
- */
-export function MaterialAttributeValue_toJsonldString(m) {
-    let returnVal;
-    return toString(2, MaterialAttributeValue_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), m));
-}
-
-export function MaterialAttributeValue_toJsonldStringWithContext(a) {
-    let returnVal;
-    return toString(2, MaterialAttributeValue_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
-}
-
-export function Material_genID(m) {
-    const matchValue = m.ID;
-    if (matchValue == null) {
-        const matchValue_1 = m.Name;
-        if (matchValue_1 == null) {
-            return "#EmptyMaterial";
-        }
-        else {
-            return "#Material_" + replace(matchValue_1, " ", "_");
-        }
-    }
-    else {
-        return matchValue;
-    }
-}
-
-export function Material_encoder(options, 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];
-        }
-    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [Material_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_1(ofArray([new Json(0, ["Material"]), new Json(0, ["ArcMaterial"])]))]) : empty(), delay(() => append(singleton(tryInclude("name", (value_5) => (new Json(0, [value_5])), oa.Name)), delay(() => append(singleton(tryInclude("type", (value_7) => MaterialType_encoder(options, value_7), oa.MaterialType)), delay(() => append(singleton(tryIncludeList("characteristics", (oa_1) => MaterialAttributeValue_encoder(options, oa_1), oa.Characteristics)), delay(() => append(singleton(tryIncludeList("derivesFrom", (oa_2) => Material_encoder(options, oa_2), oa.DerivesFrom)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue_2]) : empty()))))))))))))))))]);
-}
-
-export const Material_allowedFields = ofArray(["@id", "@type", "name", "type", "characteristics", "derivesFrom", "@context"]);
-
-export function Material_decoder(options) {
-    return object_1(Material_allowedFields, (get$) => {
-        let objectArg, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, arg_9, objectArg_4;
-        return new Material((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = MaterialType_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("type", arg_5))), (arg_7 = list_2(MaterialAttributeValue_decoder(options)), (objectArg_3 = get$.Optional, objectArg_3.Field("characteristics", arg_7))), (arg_9 = list_2(Material_decoder(options)), (objectArg_4 = get$.Optional, objectArg_4.Field("derivesFrom", arg_9))));
-    });
-}
-
-export function Material_fromJsonString(s) {
-    const matchValue = fromString(Material_decoder(ConverterOptions_$ctor()), s);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function Material_toJsonString(m) {
-    return toString(2, Material_encoder(ConverterOptions_$ctor(), m));
-}
-
-/**
- * exports in json-ld format
- */
-export function Material_toJsonldString(m) {
-    let returnVal;
-    return toString(2, Material_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), m));
-}
-
-export function Material_toJsonldStringWithContext(a) {
-    let returnVal;
-    return toString(2, Material_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
-}
-

package/ISA/ISA.Json/Ontology.js

@@ -1,200 +0,0 @@
-import { array, object, string, float, int } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { FSharpResult$2 } from "../../fable_modules/fable-library-js.4.13.0/Result.js";
-import { equals, int32ToString } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { printf, toText, replace } from "../../fable_modules/fable-library-js.4.13.0/String.js";
-import { choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
-import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeContext, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
-import { tryIncludeArray, tryInclude } from "./GEncode.js";
-import { decoder as decoder_1, encoder } from "./Comment.js";
-import { context_jsonvalue } from "./context/rocrate/isa_ontology_source_reference_context.js";
-import { uri } from "./Decode.js";
-import { OntologySourceReference } from "../ISA/JsonTypes/OntologySourceReference.js";
-import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
-import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { context_jsonvalue as context_jsonvalue_1 } from "./context/rocrate/isa_ontology_annotation_context.js";
-import { OntologyAnnotation } from "../ISA/JsonTypes/OntologyAnnotation.js";
-import { unwrap } from "../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { StringTable_decodeString, StringTable_encodeString } from "./StringTable.js";
-
-/**
- * This decodes from integer, float or string to string only!
- */
-export function AnnotationValue_decoder(options) {
-    return {
-        Decode(s, json) {
-            const matchValue = int.Decode(s, json);
-            if (matchValue.tag === 1) {
-                const matchValue_1 = float.Decode(s, json);
-                if (matchValue_1.tag === 1) {
-                    const matchValue_2 = string.Decode(s, json);
-                    return (matchValue_2.tag === 1) ? (new FSharpResult$2(1, [matchValue_2.fields[0]])) : (new FSharpResult$2(0, [matchValue_2.fields[0]]));
-                }
-                else {
-                    return new FSharpResult$2(0, [matchValue_1.fields[0].toString()]);
-                }
-            }
-            else {
-                return new FSharpResult$2(0, [int32ToString(matchValue.fields[0])]);
-            }
-        },
-    };
-}
-
-export function OntologySourceReference_genID(o) {
-    const matchValue = o.File;
-    if (matchValue == null) {
-        const matchValue_1 = o.Name;
-        if (matchValue_1 == null) {
-            return "#DummyOntologySourceRef";
-        }
-        else {
-            return "#OntologySourceRef_" + replace(matchValue_1, " ", "_");
-        }
-    }
-    else {
-        return matchValue;
-    }
-}
-
-export function OntologySourceReference_encoder(options, osr) {
-    return new Json(5, [choose((tupledArg) => {
-        const v = tupledArg[1];
-        if (equals(v, new Json(3, []))) {
-            return void 0;
-        }
-        else {
-            return [tupledArg[0], v];
-        }
-    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [OntologySourceReference_genID(osr)])]) : empty(), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["OntologySourceReference"])]) : empty(), delay(() => append(singleton(tryInclude("description", (value_2) => (new Json(0, [value_2])), osr.Description)), delay(() => append(singleton(tryInclude("file", (value_4) => (new Json(0, [value_4])), osr.File)), delay(() => append(singleton(tryInclude("name", (value_6) => (new Json(0, [value_6])), osr.Name)), delay(() => append(singleton(tryInclude("version", (value_8) => (new Json(0, [value_8])), osr.Version)), delay(() => append(singleton(tryIncludeArray("comments", (comment) => encoder(options, comment), osr.Comments)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty()))))))))))))))))))]);
-}
-
-export function OntologySourceReference_decoder(options) {
-    return object((get$) => {
-        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4;
-        return new OntologySourceReference((objectArg = get$.Optional, objectArg.Field("description", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("file", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("name", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("version", string)), (arg_9 = array(decoder_1(options)), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", arg_9))));
-    });
-}
-
-export function OntologySourceReference_fromJsonString(s) {
-    const matchValue = fromString(OntologySourceReference_decoder(ConverterOptions_$ctor()), s);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function OntologySourceReference_toJsonString(oa) {
-    return toString(2, OntologySourceReference_encoder(ConverterOptions_$ctor(), oa));
-}
-
-/**
- * exports in json-ld format
- */
-export function OntologySourceReference_toJsonldString(oa) {
-    let returnVal;
-    return toString(2, OntologySourceReference_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), oa));
-}
-
-export function OntologySourceReference_toJsonldStringWithContext(a) {
-    let returnVal;
-    return toString(2, OntologySourceReference_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
-}
-
-export function OntologyAnnotation_genID(o) {
-    const matchValue = o.ID;
-    if (matchValue == null) {
-        const matchValue_1 = o.TermAccessionNumber;
-        if (matchValue_1 == null) {
-            const matchValue_2 = o.TermSourceREF;
-            if (matchValue_2 == null) {
-                const matchValue_3 = o.Name;
-                if (matchValue_3 == null) {
-                    return "#DummyOntologyAnnotation";
-                }
-                else {
-                    return "#UserTerm_" + replace(matchValue_3, " ", "_");
-                }
-            }
-            else {
-                return "#" + replace(matchValue_2, " ", "_");
-            }
-        }
-        else {
-            return URIModule_toString(matchValue_1);
-        }
-    }
-    else {
-        return URIModule_toString(matchValue);
-    }
-}
-
-export function OntologyAnnotation_encoder(options, 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];
-        }
-    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [OntologyAnnotation_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["OntologyAnnotation"])]) : empty(), delay(() => append(singleton(tryInclude("annotationValue", (value_4) => (new Json(0, [value_4])), oa.Name)), delay(() => append(singleton(tryInclude("termSource", (value_6) => (new Json(0, [value_6])), oa.TermSourceREF)), delay(() => append(singleton(tryInclude("termAccession", (value_8) => (new Json(0, [value_8])), oa.TermAccessionNumber)), delay(() => append(singleton(tryIncludeArray("comments", (comment) => encoder(options, comment), oa.Comments)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue_1]) : empty()))))))))))))))))]);
-}
-
-export function OntologyAnnotation_decoder(options) {
-    return object((get$) => {
-        let objectArg, arg_3, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4;
-        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((arg_3 = AnnotationValue_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("annotationValue", arg_3)))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termSource", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("termAccession", string))), unwrap((arg_9 = array(decoder_1(options)), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", arg_9)))));
-    });
-}
-
-export function OntologyAnnotation_compressedEncoder(stringTable, options, oa) {
-    return new Json(5, [choose((tupledArg) => {
-        const v = tupledArg[1];
-        if (equals(v, new Json(3, []))) {
-            return void 0;
-        }
-        else {
-            return [tupledArg[0], v];
-        }
-    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [OntologyAnnotation_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["OntologyAnnotation"])]) : empty(), delay(() => append(singleton(tryInclude("a", (s) => StringTable_encodeString(stringTable, s), oa.Name)), delay(() => append(singleton(tryInclude("ts", (s_1) => StringTable_encodeString(stringTable, s_1), oa.TermSourceREF)), delay(() => append(singleton(tryInclude("ta", (s_2) => StringTable_encodeString(stringTable, s_2), oa.TermAccessionNumber)), delay(() => singleton(tryIncludeArray("comments", (comment) => encoder(options, comment), oa.Comments)))))))))))))))]);
-}
-
-export function OntologyAnnotation_compressedDecoder(stringTable, options) {
-    return object((get$) => {
-        let objectArg, arg_3, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, arg_9, objectArg_4;
-        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((arg_3 = StringTable_decodeString(stringTable), (objectArg_1 = get$.Optional, objectArg_1.Field("a", arg_3)))), unwrap((arg_5 = StringTable_decodeString(stringTable), (objectArg_2 = get$.Optional, objectArg_2.Field("ts", arg_5)))), unwrap((arg_7 = StringTable_decodeString(stringTable), (objectArg_3 = get$.Optional, objectArg_3.Field("ta", arg_7)))), unwrap((arg_9 = array(decoder_1(options)), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", arg_9)))));
-    });
-}
-
-export function OntologyAnnotation_fromJsonString(s) {
-    const matchValue = fromString(OntologyAnnotation_decoder(ConverterOptions_$ctor()), s);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function OntologyAnnotation_toJsonString(oa) {
-    return toString(2, OntologyAnnotation_encoder(ConverterOptions_$ctor(), oa));
-}
-
-/**
- * exports in json-ld format
- */
-export function OntologyAnnotation_toJsonldString(oa) {
-    let returnVal;
-    return toString(2, OntologyAnnotation_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), oa));
-}
-
-export function OntologyAnnotation_toJsonldStringWithContext(a) {
-    let returnVal;
-    return toString(2, OntologyAnnotation_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
-}
-

package/ISA/ISA.Json/Person.js

@@ -1,186 +0,0 @@
-import { tryPick } from "../../fable_modules/fable-library-js.4.13.0/Array.js";
-import { printf, toText, replace } from "../../fable_modules/fable-library-js.4.13.0/String.js";
-import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID, ConverterOptions__get_IncludeContext, ConverterOptions__get_IsRoCrate } from "./ConverterOptions.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { context_jsonvalue } from "./context/rocrate/isa_organization_context.js";
-import { Person } from "../ISA/JsonTypes/Person.js";
-import { ofArray, choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
-import { equals } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { tryIncludeArray, 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 { context_jsonvalue as context_jsonvalue_1 } from "./context/rocrate/isa_person_context.js";
-import { uri, object } from "./Decode.js";
-import { array as array_1, string } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
-import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-
-export function genID(p) {
-    const matchValue = p.ID;
-    if (matchValue == null) {
-        let orcid;
-        const matchValue_1 = p.Comments;
-        orcid = ((matchValue_1 == null) ? void 0 : tryPick((c) => {
-            const matchValue_2 = c.Name;
-            const matchValue_3 = c.Value;
-            let matchResult, n, v;
-            if (matchValue_2 != null) {
-                if (matchValue_3 != null) {
-                    matchResult = 0;
-                    n = matchValue_2;
-                    v = matchValue_3;
-                }
-                else {
-                    matchResult = 1;
-                }
-            }
-            else {
-                matchResult = 1;
-            }
-            switch (matchResult) {
-                case 0:
-                    if (((n === "orcid") ? true : (n === "Orcid")) ? true : (n === "ORCID")) {
-                        return v;
-                    }
-                    else {
-                        return void 0;
-                    }
-                default:
-                    return void 0;
-            }
-        }, matchValue_1));
-        if (orcid == null) {
-            const matchValue_5 = p.EMail;
-            if (matchValue_5 == null) {
-                const matchValue_6 = p.FirstName;
-                const matchValue_7 = p.MidInitials;
-                const matchValue_8 = p.LastName;
-                let matchResult_1, fn, ln, mn, fn_1, ln_1, ln_2, fn_2;
-                if (matchValue_6 == null) {
-                    if (matchValue_7 == null) {
-                        if (matchValue_8 != null) {
-                            matchResult_1 = 2;
-                            ln_2 = matchValue_8;
-                        }
-                        else {
-                            matchResult_1 = 4;
-                        }
-                    }
-                    else {
-                        matchResult_1 = 4;
-                    }
-                }
-                else if (matchValue_7 == null) {
-                    if (matchValue_8 == null) {
-                        matchResult_1 = 3;
-                        fn_2 = matchValue_6;
-                    }
-                    else {
-                        matchResult_1 = 1;
-                        fn_1 = matchValue_6;
-                        ln_1 = matchValue_8;
-                    }
-                }
-                else if (matchValue_8 != null) {
-                    matchResult_1 = 0;
-                    fn = matchValue_6;
-                    ln = matchValue_8;
-                    mn = matchValue_7;
-                }
-                else {
-                    matchResult_1 = 4;
-                }
-                switch (matchResult_1) {
-                    case 0:
-                        return (((("#" + replace(fn, " ", "_")) + "_") + replace(mn, " ", "_")) + "_") + replace(ln, " ", "_");
-                    case 1:
-                        return (("#" + replace(fn_1, " ", "_")) + "_") + replace(ln_1, " ", "_");
-                    case 2:
-                        return "#" + replace(ln_2, " ", "_");
-                    case 3:
-                        return "#" + replace(fn_2, " ", "_");
-                    default:
-                        return "#EmptyPerson";
-                }
-            }
-            else {
-                return matchValue_5;
-            }
-        }
-        else {
-            return orcid;
-        }
-    }
-    else {
-        return URIModule_toString(matchValue);
-    }
-}
-
-export function affiliationEncoder(options, affiliation) {
-    if (ConverterOptions__get_IsRoCrate(options)) {
-        return new Json(5, [toList(delay(() => append(singleton(["@type", new Json(0, ["Organization"])]), delay(() => append(singleton(["@id", new Json(0, [`Organization/${affiliation}`])]), delay(() => append(singleton(["name", new Json(0, [affiliation])]), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty())))))))))]);
-    }
-    else {
-        return new Json(0, [affiliation]);
-    }
-}
-
-export function encoder(options, oa) {
-    const oa_1 = Person.setCommentFromORCID(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];
-        }
-    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [genID(oa_1)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa_1.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["Person"])]) : empty(), delay(() => append(singleton(tryInclude("firstName", (value_4) => (new Json(0, [value_4])), oa_1.FirstName)), delay(() => append(singleton(tryInclude("lastName", (value_6) => (new Json(0, [value_6])), oa_1.LastName)), delay(() => append(singleton(tryInclude("midInitials", (value_8) => (new Json(0, [value_8])), oa_1.MidInitials)), delay(() => append(singleton(tryInclude("email", (value_10) => (new Json(0, [value_10])), oa_1.EMail)), delay(() => append(singleton(tryInclude("phone", (value_12) => (new Json(0, [value_12])), oa_1.Phone)), delay(() => append(singleton(tryInclude("fax", (value_14) => (new Json(0, [value_14])), oa_1.Fax)), delay(() => append(singleton(tryInclude("address", (value_16) => (new Json(0, [value_16])), oa_1.Address)), delay(() => append(singleton(tryInclude("affiliation", (affiliation) => affiliationEncoder(options, affiliation), oa_1.Affiliation)), delay(() => append(singleton(tryIncludeArray("roles", (oa_2) => OntologyAnnotation_encoder(options, oa_2), oa_1.Roles)), delay(() => append(singleton(tryIncludeArray("comments", (comment) => encoder_1(options, comment), oa_1.Comments)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue_1]) : empty()))))))))))))))))))))))))))))]);
-}
-
-export const allowedFields = ofArray(["@id", "firstName", "lastName", "midInitials", "email", "phone", "fax", "address", "affiliation", "roles", "comments", "@type", "@context"]);
-
-export function decoder(options) {
-    return object(allowedFields, (get$) => {
-        let objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
-        let person;
-        let ID;
-        const objectArg = get$.Optional;
-        ID = objectArg.Field("@id", uri);
-        let FirstName;
-        const objectArg_1 = get$.Optional;
-        FirstName = objectArg_1.Field("firstName", string);
-        person = (new Person(ID, void 0, (objectArg_2 = get$.Optional, objectArg_2.Field("lastName", string)), FirstName, (objectArg_3 = get$.Optional, objectArg_3.Field("midInitials", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("email", string)), (objectArg_5 = get$.Optional, objectArg_5.Field("phone", string)), (objectArg_6 = get$.Optional, objectArg_6.Field("fax", string)), (objectArg_7 = get$.Optional, objectArg_7.Field("address", string)), (objectArg_8 = get$.Optional, objectArg_8.Field("affiliation", string)), (arg_19 = array_1(OntologyAnnotation_decoder(options)), (objectArg_9 = get$.Optional, objectArg_9.Field("roles", arg_19))), (arg_21 = array_1(decoder_2(options)), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_21)))));
-        return Person.setOrcidFromComments(person);
-    });
-}
-
-export function fromJsonString(s) {
-    const matchValue = fromString(decoder(ConverterOptions_$ctor()), s);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function toJsonString(p) {
-    return toString(2, encoder(ConverterOptions_$ctor(), p));
-}
-
-/**
- * exports in json-ld format
- */
-export function toJsonldString(p) {
-    let returnVal;
-    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
-}
-
-export function toJsonldStringWithContext(a) {
-    let returnVal;
-    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
-}
-