@nfdi4plants/arctrl 1.1.0 → 2.0.0-alpha.1

package/Json/Investigation.js

@@ -0,0 +1,220 @@
+import { empty, unzip, ofArray, choose } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { stringHash, equals } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { defaultSpaces, tryIncludeSeq, tryInclude } from "./Encode.js";
+import { OntologySourceReference_ISAJson_decoder, OntologySourceReference_ISAJson_encoder, OntologySourceReference_ROCrate_decoder, OntologySourceReference_ROCrate_encoder, OntologySourceReference_decoder, OntologySourceReference_encoder } from "./OntologySourceReference.js";
+import { Publication_ISAJson_decoder, Publication_ISAJson_encoder, Publication_ROCrate_decoder, Publication_ROCrate_encoder, Publication_decoder, Publication_encoder } from "./Publication.js";
+import { Person_ISAJson_decoder, Person_ISAJson_encoder, Person_ROCrate_decoder, Person_ROCrate_encoder, Person_decoder, Person_encoder } from "./Person.js";
+import { Assay_decoderCompressed, Assay_encoderCompressed, Assay_decoder, Assay_encoder } from "./Assay.js";
+import { Study_ISAJson_decoder, Study_ISAJson_encoder, Study_ROCrate_decoder, Study_ROCrate_encoder, Study_decoderCompressed, Study_encoderCompressed, Study_decoder, Study_encoder } from "./Study.js";
+import { Comment_ISAJson_decoder, Comment_ISAJson_encoder, Comment_ROCrate_decoder, Comment_ROCrate_encoder, Comment_decoder, Comment_encoder } from "./Comment.js";
+import { list as list_1, string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { ArcInvestigation } from "../Core/ArcTypes.js";
+import { Decode_objectNoAdditionalProperties, Decode_resizeArray } from "./Decode.js";
+import { context_jsonvalue } from "./context/rocrate/isa_investigation_context.js";
+import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
+import { defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { distinctBy } from "../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { map, concat } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { context_jsonvalue as context_jsonvalue_1, conformsTo_jsonvalue } from "./context/rocrate/rocrate_context.js";
+import { fromString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { toFail, printf, toText } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { toString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
+import { encode, decode } from "./Table/Compression.js";
+
+export function Investigation_encoder(inv) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([["Identifier", new Json(0, [inv.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), inv.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), inv.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), inv.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), inv.PublicReleaseDate), tryIncludeSeq("OntologySourceReferences", OntologySourceReference_encoder, inv.OntologySourceReferences), tryIncludeSeq("Publications", Publication_encoder, inv.Publications), tryIncludeSeq("Contacts", Person_encoder, inv.Contacts), tryIncludeSeq("Assays", Assay_encoder, inv.Assays), tryIncludeSeq("Studies", Study_encoder, inv.Studies), tryIncludeSeq("RegisteredStudyIdentifiers", (value_9) => (new Json(0, [value_9])), inv.RegisteredStudyIdentifiers), tryIncludeSeq("Comments", Comment_encoder, inv.Comments)]))]);
+}
+
+export const Investigation_decoder = object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
+    return new ArcInvestigation((objectArg = get$.Required, objectArg.Field("Identifier", string)), (objectArg_1 = get$.Optional, objectArg_1.Field("Title", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("Description", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string)), (arg_11 = Decode_resizeArray(OntologySourceReference_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("OntologySourceReferences", arg_11))), (arg_13 = Decode_resizeArray(Publication_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Publications", arg_13))), (arg_15 = Decode_resizeArray(Person_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("Contacts", arg_15))), (arg_17 = Decode_resizeArray(Assay_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("Assays", arg_17))), (arg_19 = Decode_resizeArray(Study_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("Studies", arg_19))), (arg_21 = Decode_resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredStudyIdentifiers", arg_21))), (arg_23 = Decode_resizeArray(Comment_decoder), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23))));
+});
+
+export function Investigation_encoderCompressed(stringTable, oaTable, cellTable, inv) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([["Identifier", new Json(0, [inv.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), inv.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), inv.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), inv.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), inv.PublicReleaseDate), tryIncludeSeq("OntologySourceReferences", OntologySourceReference_encoder, inv.OntologySourceReferences), tryIncludeSeq("Publications", Publication_encoder, inv.Publications), tryIncludeSeq("Contacts", Person_encoder, inv.Contacts), tryIncludeSeq("Assays", (assay) => Assay_encoderCompressed(stringTable, oaTable, cellTable, assay), inv.Assays), tryIncludeSeq("Studies", (study) => Study_encoderCompressed(stringTable, oaTable, cellTable, study), inv.Studies), tryIncludeSeq("RegisteredStudyIdentifiers", (value_9) => (new Json(0, [value_9])), inv.RegisteredStudyIdentifiers), tryIncludeSeq("Comments", Comment_encoder, inv.Comments)]))]);
+}
+
+export function Investigation_decoderCompressed(stringTable, oaTable, cellTable) {
+    return object((get$) => {
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
+        return new ArcInvestigation((objectArg = get$.Required, objectArg.Field("Identifier", string)), (objectArg_1 = get$.Optional, objectArg_1.Field("Title", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("Description", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string)), (arg_11 = Decode_resizeArray(OntologySourceReference_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("OntologySourceReferences", arg_11))), (arg_13 = Decode_resizeArray(Publication_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Publications", arg_13))), (arg_15 = Decode_resizeArray(Person_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("Contacts", arg_15))), (arg_17 = Decode_resizeArray(Assay_decoderCompressed(stringTable, oaTable, cellTable)), (objectArg_8 = get$.Optional, objectArg_8.Field("Assays", arg_17))), (arg_19 = Decode_resizeArray(Study_decoderCompressed(stringTable, oaTable, cellTable)), (objectArg_9 = get$.Optional, objectArg_9.Field("Studies", arg_19))), (arg_21 = Decode_resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredStudyIdentifiers", arg_21))), (arg_23 = Decode_resizeArray(Comment_decoder), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23))));
+    });
+}
+
+export function Investigation_ROCrate_genID(i) {
+    return "./";
+}
+
+export function Investigation_ROCrate_encoder(oa) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([["@id", new Json(0, [Investigation_ROCrate_genID(oa)])], ["@type", new Json(0, ["Investigation"])], ["additionalType", new Json(0, ["Investigation"])], ["identifier", new Json(0, [oa.Identifier])], ["filename", new Json(0, [ArcInvestigation.FileName])], tryInclude("title", (value_5) => (new Json(0, [value_5])), oa.Title), tryInclude("description", (value_7) => (new Json(0, [value_7])), oa.Description), tryInclude("submissionDate", (value_9) => (new Json(0, [value_9])), oa.SubmissionDate), tryInclude("publicReleaseDate", (value_11) => (new Json(0, [value_11])), oa.PublicReleaseDate), tryIncludeSeq("ontologySourceReferences", OntologySourceReference_ROCrate_encoder, oa.OntologySourceReferences), tryIncludeSeq("publications", Publication_ROCrate_encoder, oa.Publications), tryIncludeSeq("people", Person_ROCrate_encoder, oa.Contacts), tryIncludeSeq("studies", (s) => Study_ROCrate_encoder(void 0, s), oa.Studies), tryIncludeSeq("comments", Comment_ROCrate_encoder, oa.Comments), ["@context", context_jsonvalue]]))]);
+}
+
+export const Investigation_ROCrate_decoder = object((get$) => {
+    let arg_3, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9;
+    let identifier;
+    let matchValue;
+    const objectArg = get$.Optional;
+    matchValue = objectArg.Field("identifier", string);
+    identifier = ((matchValue == null) ? createMissingIdentifier() : matchValue);
+    const patternInput = unzip(defaultArg((arg_3 = list_1(Study_ROCrate_decoder), (objectArg_1 = get$.Optional, objectArg_1.Field("studies", arg_3))), empty()));
+    const studiesRaw = patternInput[0];
+    let assays;
+    const collection = distinctBy((a) => a.Identifier, concat(patternInput[1]), {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    });
+    assays = Array.from(collection);
+    const studies = Array.from(studiesRaw);
+    let studyIdentifiers;
+    const collection_1 = map((a_1) => a_1.Identifier, studiesRaw);
+    studyIdentifiers = Array.from(collection_1);
+    return new ArcInvestigation(identifier, (objectArg_2 = get$.Optional, objectArg_2.Field("title", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("description", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("submissionDate", string)), (objectArg_5 = get$.Optional, objectArg_5.Field("publicReleaseDate", string)), (arg_13 = Decode_resizeArray(OntologySourceReference_ROCrate_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("ontologySourceReferences", arg_13))), (arg_15 = Decode_resizeArray(Publication_ROCrate_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("publications", arg_15))), (arg_17 = Decode_resizeArray(Person_ROCrate_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("people", arg_17))), assays, studies, studyIdentifiers, (arg_19 = Decode_resizeArray(Comment_ROCrate_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("comments", arg_19))));
+});
+
+export function Investigation_ROCrate_encodeRoCrate(oa) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([tryInclude("@type", (value) => (new Json(0, [value])), "CreativeWork"), tryInclude("@id", (value_2) => (new Json(0, [value_2])), "ro-crate-metadata.json"), tryInclude("about", Investigation_ROCrate_encoder, oa), ["conformsTo", conformsTo_jsonvalue], ["@context", context_jsonvalue_1]]))]);
+}
+
+export const Investigation_ISAJson_allowedFields = ofArray(["@id", "filename", "identifier", "title", "description", "submissionDate", "publicReleaseDate", "ontologySourceReferences", "publications", "people", "studies", "comments", "@type", "@context"]);
+
+export function Investigation_ISAJson_encoder(inv) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([["filename", new Json(0, [ArcInvestigation.FileName])], ["identifier", new Json(0, [inv.Identifier])], tryInclude("title", (value_2) => (new Json(0, [value_2])), inv.Title), tryInclude("description", (value_4) => (new Json(0, [value_4])), inv.Description), tryInclude("submissionDate", (value_6) => (new Json(0, [value_6])), inv.SubmissionDate), tryInclude("publicReleaseDate", (value_8) => (new Json(0, [value_8])), inv.PublicReleaseDate), tryIncludeSeq("ontologySourceReferences", OntologySourceReference_ISAJson_encoder, inv.OntologySourceReferences), tryIncludeSeq("publications", Publication_ISAJson_encoder, inv.Publications), tryIncludeSeq("people", Person_ISAJson_encoder, inv.Contacts), tryIncludeSeq("studies", (s) => Study_ISAJson_encoder(void 0, s), inv.Studies), tryIncludeSeq("comments", Comment_ISAJson_encoder, inv.Comments)]))]);
+}
+
+export const Investigation_ISAJson_decoder = Decode_objectNoAdditionalProperties(Investigation_ISAJson_allowedFields, (get$) => {
+    let arg_3, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9;
+    let identifer;
+    let matchValue;
+    const objectArg = get$.Optional;
+    matchValue = objectArg.Field("identifier", string);
+    identifer = ((matchValue == null) ? createMissingIdentifier() : matchValue);
+    const patternInput = unzip(defaultArg((arg_3 = list_1(Study_ISAJson_decoder), (objectArg_1 = get$.Optional, objectArg_1.Field("studies", arg_3))), empty()));
+    const studiesRaw = patternInput[0];
+    let assays;
+    const collection = distinctBy((a) => a.Identifier, concat(patternInput[1]), {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    });
+    assays = Array.from(collection);
+    const studies = Array.from(studiesRaw);
+    let studyIdentifiers;
+    const collection_1 = map((a_1) => a_1.Identifier, studiesRaw);
+    studyIdentifiers = Array.from(collection_1);
+    return new ArcInvestigation(identifer, (objectArg_2 = get$.Optional, objectArg_2.Field("title", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("description", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("submissionDate", string)), (objectArg_5 = get$.Optional, objectArg_5.Field("publicReleaseDate", string)), (arg_13 = Decode_resizeArray(OntologySourceReference_ISAJson_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("ontologySourceReferences", arg_13))), (arg_15 = Decode_resizeArray(Publication_ISAJson_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("publications", arg_15))), (arg_17 = Decode_resizeArray(Person_ISAJson_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("people", arg_17))), assays, studies, studyIdentifiers, (arg_19 = Decode_resizeArray(Comment_ISAJson_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("comments", arg_19))));
+});
+
+export function ARCtrl_ArcInvestigation__ArcInvestigation_fromJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Investigation_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = Investigation_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_ArcInvestigation__ArcInvestigation_fromCompressedJsonString_Static_Z721C83C5(s) {
+    try {
+        const matchValue = fromString(decode(Investigation_decoderCompressed), s);
+        if (matchValue.tag === 1) {
+            throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+        }
+        else {
+            return matchValue.fields[0];
+        }
+    }
+    catch (e_1) {
+        const arg_1 = e_1.message;
+        return toFail(printf("Error. Unable to parse json string to ArcStudy: %s"))(arg_1);
+    }
+}
+
+export function ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F(spaces) {
+    return (obj) => toString(defaultArg(spaces, 0), encode(Investigation_encoderCompressed, obj));
+}
+
+export function ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Investigation_ROCrate_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+/**
+ * exports in json-ld format
+ */
+export function ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = Investigation_ROCrate_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = Investigation_ISAJson_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_ArcInvestigation__ArcInvestigation_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Investigation_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+

package/Json/OntologyAnnotation.js

@@ -0,0 +1,169 @@
+import { object, string, float, int, map, oneOf } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { equals, int32ToString } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { choose, ofArray } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { defaultSpaces, tryIncludeSeq, tryInclude } from "./Encode.js";
+import { Comment_ROCrate_decoderDisambiguatingDescription, Comment_ROCrate_encoderDisambiguatingDescription, Comment_decoder, Comment_encoder } from "./Comment.js";
+import { OntologyAnnotation } from "../Core/OntologyAnnotation.js";
+import { unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { Decode_resizeArray } from "./Decode.js";
+import { decodeString, encodeString } from "./StringTable.js";
+import { printf, toText, replace } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { URIModule_toString } from "../Core/URI.js";
+import { context_jsonvalue } from "./context/rocrate/isa_ontology_annotation_context.js";
+import { context_jsonvalue as context_jsonvalue_1 } from "./context/rocrate/property_value_context.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 const AnnotationValue_decoder = oneOf(ofArray([map(int32ToString, int), map((value_1) => value_1.toString(), float), string]));
+
+export function OntologyAnnotation_encoder(oa) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([tryInclude("annotationValue", (value) => (new Json(0, [value])), oa.Name), tryInclude("termSource", (value_2) => (new Json(0, [value_2])), oa.TermSourceREF), tryInclude("termAccession", (value_4) => (new Json(0, [value_4])), oa.TermAccessionNumber), tryIncludeSeq("comments", Comment_encoder, oa.Comments)]))]);
+}
+
+export const OntologyAnnotation_decoder = object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, arg_7, objectArg_3;
+    return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("annotationValue", AnnotationValue_decoder))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("termSource", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termAccession", string))), unwrap((arg_7 = Decode_resizeArray(Comment_decoder), (objectArg_3 = get$.Optional, objectArg_3.Field("comments", arg_7)))));
+});
+
+export function OntologyAnnotation_compressedEncoder(stringTable, oa) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([tryInclude("a", (s) => encodeString(stringTable, s), oa.Name), tryInclude("ts", (s_1) => encodeString(stringTable, s_1), oa.TermSourceREF), tryInclude("ta", (s_2) => encodeString(stringTable, s_2), oa.TermAccessionNumber), tryIncludeSeq("comments", Comment_encoder, oa.Comments)]))]);
+}
+
+export function OntologyAnnotation_compressedDecoder(stringTable) {
+    return object((get$) => {
+        let arg_1, objectArg, arg_3, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3;
+        return new OntologyAnnotation(unwrap((arg_1 = decodeString(stringTable), (objectArg = get$.Optional, objectArg.Field("a", arg_1)))), unwrap((arg_3 = decodeString(stringTable), (objectArg_1 = get$.Optional, objectArg_1.Field("ts", arg_3)))), unwrap((arg_5 = decodeString(stringTable), (objectArg_2 = get$.Optional, objectArg_2.Field("ta", arg_5)))), unwrap((arg_7 = Decode_resizeArray(Comment_decoder), (objectArg_3 = get$.Optional, objectArg_3.Field("comments", arg_7)))));
+    });
+}
+
+export function OntologyAnnotation_ROCrate_genID(o) {
+    const matchValue = o.TermAccessionNumber;
+    if (matchValue == null) {
+        const matchValue_1 = o.TermSourceREF;
+        if (matchValue_1 == null) {
+            const matchValue_2 = o.Name;
+            if (matchValue_2 == null) {
+                return "#DummyOntologyAnnotation";
+            }
+            else {
+                return "#UserTerm_" + replace(matchValue_2, " ", "_");
+            }
+        }
+        else {
+            return "#" + replace(matchValue_1, " ", "_");
+        }
+    }
+    else {
+        return URIModule_toString(matchValue);
+    }
+}
+
+export function OntologyAnnotation_ROCrate_encoderDefinedTerm(oa) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([["@id", new Json(0, [OntologyAnnotation_ROCrate_genID(oa)])], ["@type", new Json(0, ["OntologyAnnotation"])], tryInclude("annotationValue", (value_2) => (new Json(0, [value_2])), oa.Name), tryInclude("termSource", (value_4) => (new Json(0, [value_4])), oa.TermSourceREF), tryInclude("termAccession", (value_6) => (new Json(0, [value_6])), oa.TermAccessionNumber), tryIncludeSeq("comments", Comment_ROCrate_encoderDisambiguatingDescription, oa.Comments), ["@context", context_jsonvalue]]))]);
+}
+
+export const OntologyAnnotation_ROCrate_decoderDefinedTerm = object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, arg_7, objectArg_3;
+    return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("annotationValue", AnnotationValue_decoder))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("termSource", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termAccession", string))), unwrap((arg_7 = Decode_resizeArray(Comment_ROCrate_decoderDisambiguatingDescription), (objectArg_3 = get$.Optional, objectArg_3.Field("comments", arg_7)))));
+});
+
+export function OntologyAnnotation_ROCrate_encoderPropertyValue(oa) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([["@id", new Json(0, [OntologyAnnotation_ROCrate_genID(oa)])], ["@type", new Json(0, ["PropertyValue"])], tryInclude("category", (value_2) => (new Json(0, [value_2])), oa.Name), tryInclude("categoryCode", (value_4) => (new Json(0, [value_4])), oa.TermAccessionNumber), tryIncludeSeq("comments", Comment_ROCrate_encoderDisambiguatingDescription, oa.Comments), ["@context", context_jsonvalue_1]]))]);
+}
+
+export const OntologyAnnotation_ROCrate_decoderPropertyValue = object((get$) => {
+    let objectArg, objectArg_1, arg_5, objectArg_2;
+    return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("category", string))), void 0, unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("categoryCode", string))), unwrap((arg_5 = Decode_resizeArray(Comment_ROCrate_decoderDisambiguatingDescription), (objectArg_2 = get$.Optional, objectArg_2.Field("comments", arg_5)))));
+});
+
+export const OntologyAnnotation_ISAJson_encoder = OntologyAnnotation_encoder;
+
+export const OntologyAnnotation_ISAJson_decoder = OntologyAnnotation_decoder;
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_fromJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(OntologyAnnotation_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_toJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = OntologyAnnotation_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_fromROCrateJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(OntologyAnnotation_ROCrate_decoderDefinedTerm, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+/**
+ * exports in json-ld format
+ */
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_toROCrateJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = OntologyAnnotation_ROCrate_encoderDefinedTerm(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_toISAJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = OntologyAnnotation_ISAJson_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(OntologyAnnotation_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+

package/Json/OntologySourceReference.js

@@ -0,0 +1,122 @@
+import { ofArray, choose } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { equals } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { defaultSpaces, tryIncludeSeq, tryInclude } from "./Encode.js";
+import { Comment_decoder, Comment_encoder } from "./Comment.js";
+import { string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { OntologySourceReference } from "../Core/OntologySourceReference.js";
+import { unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { Decode_resizeArray, Decode_uri } from "./Decode.js";
+import { printf, toText, replace } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { context_jsonvalue } from "./context/rocrate/isa_ontology_source_reference_context.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 OntologySourceReference_encoder(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];
+        }
+    }, ofArray([tryInclude("description", (value) => (new Json(0, [value])), osr.Description), tryInclude("file", (value_2) => (new Json(0, [value_2])), osr.File), tryInclude("name", (value_4) => (new Json(0, [value_4])), osr.Name), tryInclude("version", (value_6) => (new Json(0, [value_6])), osr.Version), tryIncludeSeq("comments", Comment_encoder, osr.Comments)]))]);
+}
+
+export const OntologySourceReference_decoder = object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4;
+    return new OntologySourceReference(unwrap((objectArg = get$.Optional, objectArg.Field("description", Decode_uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("file", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("name", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("version", string))), unwrap((arg_9 = Decode_resizeArray(Comment_decoder), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", arg_9)))));
+});
+
+export function OntologySourceReference_ROCrate_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_ROCrate_encoder(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];
+        }
+    }, ofArray([["@id", new Json(0, [OntologySourceReference_ROCrate_genID(osr)])], ["@type", new Json(0, ["OntologySourceReference"])], tryInclude("description", (value_2) => (new Json(0, [value_2])), osr.Description), tryInclude("file", (value_4) => (new Json(0, [value_4])), osr.File), tryInclude("name", (value_6) => (new Json(0, [value_6])), osr.Name), tryInclude("version", (value_8) => (new Json(0, [value_8])), osr.Version), tryIncludeSeq("comments", Comment_encoder, osr.Comments), ["@context", context_jsonvalue]]))]);
+}
+
+export const OntologySourceReference_ROCrate_decoder = object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4;
+    return new OntologySourceReference(unwrap((objectArg = get$.Optional, objectArg.Field("description", Decode_uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("file", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("name", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("version", string))), unwrap((arg_9 = Decode_resizeArray(Comment_decoder), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", arg_9)))));
+});
+
+export const OntologySourceReference_ISAJson_encoder = OntologySourceReference_encoder;
+
+export const OntologySourceReference_ISAJson_decoder = OntologySourceReference_decoder;
+
+export function ARCtrl_OntologySourceReference__OntologySourceReference_fromJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(OntologySourceReference_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_OntologySourceReference__OntologySourceReference_toJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = OntologySourceReference_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_OntologySourceReference__OntologySourceReference_fromROCrateJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(OntologySourceReference_ROCrate_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+/**
+ * exports in json-ld format
+ */
+export function ARCtrl_OntologySourceReference__OntologySourceReference_toROCrateJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = OntologySourceReference_ROCrate_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_OntologySourceReference__OntologySourceReference_toISAJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = OntologySourceReference_ISAJson_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_OntologySourceReference__OntologySourceReference_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(OntologySourceReference_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+