@nfdi4plants/arctrl 1.0.0-alpha6

package/ISA/ISA.Json/Ontology.js

@@ -0,0 +1,204 @@
+import { AnnotationValue } from "../ISA/JsonTypes/AnnotationValue.js";
+import { toString, object as object_10, nil } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { array, object as object_11, string, float, int } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { FSharpResult$2 } from "../../fable_modules/fable-library.4.1.4/Choice.js";
+import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { choose } from "../../fable_modules/fable-library.4.1.4/List.js";
+import { uncurry2, equals } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.1.4/Seq.js";
+import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
+import { tryInclude } from "./GEncode.js";
+import { decoder as decoder_1, encoder } from "./Comment.js";
+import { fromString, uri } from "./Decode.js";
+import { OntologySourceReference } from "../ISA/JsonTypes/OntologySourceReference.js";
+import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
+import { OntologyAnnotation } from "../ISA/JsonTypes/OntologyAnnotation.js";
+import { unwrap } from "../../fable_modules/fable-library.4.1.4/Option.js";
+
+export function AnnotationValue_encoder(options, value) {
+    if (value instanceof AnnotationValue) {
+        if (value.tag === 2) {
+            return value.fields[0];
+        }
+        else if (value.tag === 0) {
+            return value.fields[0];
+        }
+        else {
+            return value.fields[0];
+        }
+    }
+    else {
+        return nil;
+    }
+}
+
+export function AnnotationValue_decoder(options, s, json) {
+    const matchValue = int(s)(json);
+    if (matchValue.tag === 1) {
+        const matchValue_1 = float(s, json);
+        if (matchValue_1.tag === 1) {
+            const matchValue_2 = string(s, json);
+            if (matchValue_2.tag === 1) {
+                return new FSharpResult$2(1, [matchValue_2.fields[0]]);
+            }
+            else {
+                return new FSharpResult$2(0, [new AnnotationValue(0, [matchValue_2.fields[0]])]);
+            }
+        }
+        else {
+            return new FSharpResult$2(0, [new AnnotationValue(1, [matchValue_1.fields[0]])]);
+        }
+    }
+    else {
+        return new FSharpResult$2(0, [new AnnotationValue(2, [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 object_10(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 = OntologySourceReference_genID(osr), (typeof value === "string") ? ((s = value, s)) : nil)]) : empty(), delay(() => {
+            let value_2, s_1;
+            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_2 = "OntologySourceReference", (typeof value_2 === "string") ? ((s_1 = value_2, s_1)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("description", (value_4) => {
+                let s_2;
+                const value_5 = value_4;
+                return (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil;
+            }, osr["Description"])), delay(() => append(singleton(tryInclude("file", (value_7) => {
+                let s_3;
+                const value_8 = value_7;
+                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
+            }, osr["File"])), delay(() => append(singleton(tryInclude("name", (value_10) => {
+                let s_4;
+                const value_11 = value_10;
+                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
+            }, osr["Name"])), delay(() => append(singleton(tryInclude("version", (value_13) => {
+                let s_5;
+                const value_14 = value_13;
+                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
+            }, osr["Version"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), osr["Comments"]))))))))))));
+        }));
+    }))));
+}
+
+export function OntologySourceReference_decoder(options) {
+    return (path_4) => ((v) => object_11((get$) => {
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, decoder, objectArg_4;
+        return new OntologySourceReference((objectArg = get$.Optional, objectArg.Field("description", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("file", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("name", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("version", string)), (arg_9 = ((decoder = decoder_1(options), (path_3) => ((value_3) => array(uncurry2(decoder), path_3, value_3)))), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", uncurry2(arg_9)))));
+    }, path_4, v));
+}
+
+export function OntologySourceReference_fromString(s) {
+    return fromString(uncurry2(OntologySourceReference_decoder(ConverterOptions_$ctor())), s);
+}
+
+export function OntologySourceReference_toString(oa) {
+    return toString(2, OntologySourceReference_encoder(ConverterOptions_$ctor(), oa));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function OntologySourceReference_toStringLD(oa) {
+    let returnVal;
+    return toString(2, OntologySourceReference_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), oa));
+}
+
+export function 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) {
+                return "#DummyOntologyAnnotation";
+            }
+            else {
+                return "#" + replace(matchValue_2, " ", "_");
+            }
+        }
+        else {
+            return matchValue_1;
+        }
+    }
+    else {
+        return URIModule_toString(matchValue);
+    }
+}
+
+export function OntologyAnnotation_encoder(options, oa) {
+    return object_10(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 = OntologyAnnotation_genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : singleton(tryInclude("@id", (value_2) => {
+            let s_1;
+            const value_3 = value_2;
+            return (typeof value_3 === "string") ? ((s_1 = value_3, s_1)) : nil;
+        }, oa["ID"])), delay(() => {
+            let value_5, s_2;
+            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "OntologyAnnotation", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("annotationValue", (value_7) => AnnotationValue_encoder(options, value_7), oa["Name"])), delay(() => append(singleton(tryInclude("termSource", (value_8) => {
+                let s_3;
+                const value_9 = value_8;
+                return (typeof value_9 === "string") ? ((s_3 = value_9, s_3)) : nil;
+            }, oa["TermSourceREF"])), delay(() => append(singleton(tryInclude("termAccession", (value_11) => {
+                let s_4;
+                const value_12 = value_11;
+                return (typeof value_12 === "string") ? ((s_4 = value_12, s_4)) : nil;
+            }, oa["TermAccessionNumber"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), oa["Comments"]))))))))));
+        }));
+    }))));
+}
+
+export function OntologyAnnotation_decoder(options) {
+    return (path_3) => ((v) => object_11((get$) => {
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, decoder, objectArg_4;
+        return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("@id", uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("annotationValue", (s_1, json_1) => AnnotationValue_decoder(options, s_1, json_1)))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termSource", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("termAccession", string))), unwrap((arg_9 = ((decoder = decoder_1(options), (path_2) => ((value_2) => array(uncurry2(decoder), path_2, value_2)))), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", uncurry2(arg_9))))));
+    }, path_3, v));
+}
+
+export function OntologyAnnotation_fromString(s) {
+    return fromString(uncurry2(OntologyAnnotation_decoder(ConverterOptions_$ctor())), s);
+}
+
+export function OntologyAnnotation_toString(oa) {
+    return toString(2, OntologyAnnotation_encoder(ConverterOptions_$ctor(), oa));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function OntologyAnnotation_toStringLD(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));
+}
+

package/ISA/ISA.Json/Person.js

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+import { tryPick } from "../../fable_modules/fable-library.4.1.4/Array.js";
+import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
+import { Person } from "../ISA/JsonTypes/Person.js";
+import { toString as toString_1, nil, object as object_22 } 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_3, encoder as encoder_1 } from "./Comment.js";
+import { array as array_1, string, object as object_23 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { fromString as fromString_1, uri } from "./Decode.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 encoder(options, oa) {
+    let oa_1;
+    const arg = oa;
+    oa_1 = Person.setCommentFromORCID(arg);
+    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 = genID(oa_1), (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_1["ID"])), delay(() => {
+            let value_5, s_2;
+            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "Person", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("firstName", (value_7) => {
+                let s_3;
+                const value_8 = value_7;
+                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
+            }, oa_1["FirstName"])), delay(() => append(singleton(tryInclude("lastName", (value_10) => {
+                let s_4;
+                const value_11 = value_10;
+                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
+            }, oa_1["LastName"])), delay(() => append(singleton(tryInclude("midInitials", (value_13) => {
+                let s_5;
+                const value_14 = value_13;
+                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
+            }, oa_1["MidInitials"])), delay(() => append(singleton(tryInclude("email", (value_16) => {
+                let s_6;
+                const value_17 = value_16;
+                return (typeof value_17 === "string") ? ((s_6 = value_17, s_6)) : nil;
+            }, oa_1["EMail"])), delay(() => append(singleton(tryInclude("phone", (value_19) => {
+                let s_7;
+                const value_20 = value_19;
+                return (typeof value_20 === "string") ? ((s_7 = value_20, s_7)) : nil;
+            }, oa_1["Phone"])), delay(() => append(singleton(tryInclude("fax", (value_22) => {
+                let s_8;
+                const value_23 = value_22;
+                return (typeof value_23 === "string") ? ((s_8 = value_23, s_8)) : nil;
+            }, oa_1["Fax"])), delay(() => append(singleton(tryInclude("address", (value_25) => {
+                let s_9;
+                const value_26 = value_25;
+                return (typeof value_26 === "string") ? ((s_9 = value_26, s_9)) : nil;
+            }, oa_1["Address"])), delay(() => append(singleton(tryInclude("affiliation", (value_28) => {
+                let s_10;
+                const value_29 = value_28;
+                return (typeof value_29 === "string") ? ((s_10 = value_29, s_10)) : nil;
+            }, oa_1["Affiliation"])), delay(() => append(singleton(tryInclude("roles", (oa_2) => OntologyAnnotation_encoder(options, oa_2), oa_1["Roles"])), delay(() => singleton(tryInclude("comments", (comment) => encoder_1(options, comment), oa_1["Comments"]))))))))))))))))))))));
+        }));
+    }))));
+}
+
+export function decoder(options) {
+    return (path_10) => ((v) => object_23((get$) => {
+        let objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, objectArg_8, arg_19, decoder_1, objectArg_9, arg_21, decoder_2, objectArg_10;
+        let arg_22;
+        let ID;
+        const objectArg = get$.Optional;
+        ID = objectArg.Field("@id", uri);
+        let FirstName;
+        const objectArg_1 = get$.Optional;
+        FirstName = objectArg_1.Field("firstName", string);
+        arg_22 = (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$.Optional, objectArg_8.Field("affiliation", string)), (arg_19 = ((decoder_1 = OntologyAnnotation_decoder(options), (path_8) => ((value_8) => array_1(uncurry2(decoder_1), path_8, value_8)))), (objectArg_9 = get$.Optional, objectArg_9.Field("roles", uncurry2(arg_19)))), (arg_21 = ((decoder_2 = decoder_3(options), (path_9) => ((value_9) => array_1(uncurry2(decoder_2), path_9, value_9)))), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", uncurry2(arg_21))))));
+        return Person.setOrcidFromComments(arg_22);
+    }, path_10, v));
+}
+
+export function fromString(s) {
+    return fromString_1(uncurry2(decoder(ConverterOptions_$ctor())), s);
+}
+
+export function toString(p) {
+    return toString_1(2, encoder(ConverterOptions_$ctor(), p));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function toStringLD(p) {
+    let returnVal;
+    return toString_1(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
+}
+