@nfdi4plants/arctrl 2.0.1 → 2.1.0-alpha.2

package/Json/Study.js

@@ -1,40 +1,36 @@
 import { Option_fromValueWithDefault, ResizeArray_map } from "../Core/Helper/Collections.js";
-import { defaultArgWith, map, bind, unwrap, value as value_17, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
-import { empty, map as map_1, singleton, ofArray, choose, tryFind } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { defaultArgWith, bind, unwrap, map, value as value_17, defaultArg } from "../fable_modules/fable-library-js.4.22.0/Option.js";
+import { empty, map as map_2, singleton, ofArray, choose, tryFind } from "../fable_modules/fable-library-js.4.22.0/List.js";
 import { ArcStudy, ArcAssay } from "../Core/ArcTypes.js";
-import { disposeSafe, getEnumerator, 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, tryIncludeList, tryIncludeSeq, tryInclude } from "./Encode.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 { tryIncludeList, tryIncludeSeq, tryInclude } from "./Encode.js";
+import { ISAJson_decoder as ISAJson_decoder_4, ISAJson_encoder as ISAJson_encoder_2, ROCrate_decoder as ROCrate_decoder_3, ROCrate_encoder as ROCrate_encoder_1, decoder as decoder_2, encoder as encoder_5 } from "./Publication.js";
+import { ISAJson_decoder as ISAJson_decoder_3, ISAJson_encoder as ISAJson_encoder_3, ROCrate_decoder as ROCrate_decoder_4, ROCrate_encoder as ROCrate_encoder_2, decoder as decoder_3, encoder as encoder_6 } from "./Person.js";
 import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./OntologyAnnotation.js";
-import { ArcTable_decoderCompressed, ArcTable_encoderCompressed, ArcTable_decoder, ArcTable_encoder } from "./Table/ArcTable.js";
-import { decoderCompressed, encoderCompressed, decoder as decoder_1, encoder as encoder_4 } from "./DataMap/DataMap.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_2, string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { Decode_objectNoAdditionalProperties, Decode_resizeArray } from "./Decode.js";
-import { toFail, printf, toText, replace } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { decoderCompressed as decoderCompressed_1, encoderCompressed as encoderCompressed_1, decoder as decoder_4, encoder as encoder_7 } from "./Table/ArcTable.js";
+import { decoderCompressed as decoderCompressed_2, encoderCompressed as encoderCompressed_2, decoder as decoder_5, encoder as encoder_8 } from "./DataMap/DataMap.js";
+import { ISAJson_decoder as ISAJson_decoder_5, ISAJson_encoder as ISAJson_encoder_6, ROCrate_decoder as ROCrate_decoder_5, ROCrate_encoder as ROCrate_encoder_5, decoder as decoder_6, encoder as encoder_9 } from "./Comment.js";
+import { isEmpty, map as map_1 } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
+import { list as list_2, resizeArray, string, object } from "../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
+import { replace } from "../fable_modules/fable-library-js.4.22.0/String.js";
 import { Study_fileNameFromIdentifier, createMissingIdentifier, Study_tryIdentifierFromFileName, Study_tryFileNameFromIdentifier } from "../Core/Helper/Identifier.js";
 import { Person_removeSourceAssayComments, Person_getSourceAssayIdentifiersFromComments, Person_setSourceAssayComment, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D, ARCtrl_ArcTables__ArcTables_GetProcesses } from "../Core/Conversion.js";
-import { list as list_1 } from "../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
-import { Process_ISAJson_decoder, Process_ISAJson_encoder, Process_ROCrate_decoder, Process_ROCrate_encoder } from "./Process/Process.js";
-import { Assay_ISAJson_decoder, Assay_ISAJson_encoder, Assay_ROCrate_decoder, Assay_ROCrate_encoder } from "./Assay.js";
+import { list as list_1 } from "../fable_modules/Thoth.Json.Core.0.4.0/Encode.fs.js";
+import { ISAJson_decoder as ISAJson_decoder_1, ISAJson_encoder as ISAJson_encoder_4, ROCrate_decoder as ROCrate_decoder_2, ROCrate_encoder as ROCrate_encoder_3 } from "./Process/Process.js";
+import { ISAJson_decoder as ISAJson_decoder_2, ISAJson_encoder as ISAJson_encoder_5, ROCrate_decoder as ROCrate_decoder_1, ROCrate_encoder as ROCrate_encoder_4 } from "./Assay.js";
 import { context_jsonvalue } from "./context/rocrate/isa_study_context.js";
+import { disposeSafe, getEnumerator } from "../fable_modules/fable-library-js.4.22.0/Util.js";
 import { getProtocols, getCharacteristics, getFactors, getUnits } from "../Core/Process/ProcessSequence.js";
-import { Factor_ISAJson_encoder } from "./Process/Factor.js";
-import { MaterialAttribute_ISAJson_encoder } from "./Process/MaterialAttribute.js";
-import { encoder as encoder_5 } from "./Process/StudyMaterials.js";
-import { Protocol_ISAJson_encoder } from "./Process/Protocol.js";
+import { encoder as encoder_10 } from "./Process/Factor.js";
+import { encoder as encoder_11 } from "./Process/MaterialAttribute.js";
+import { encoder as encoder_12 } from "./Process/StudyMaterials.js";
+import { ISAJson_encoder as ISAJson_encoder_1 } from "./Process/Protocol.js";
 import { encode } from "./IDTable.js";
-import { isEmpty } from "../fable_modules/fable-library-js.4.16.0/Seq.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 { encode as encode_1, decode } from "./Table/Compression.js";
+import { Decode_objectNoAdditionalProperties } from "./Decode.js";
 
 /**
  * Get registered assays or get assays from `assays` if IsSome
  */
-export function Study_Helper_getAssayInformation(assays, study) {
+export function Helper_getAssayInformation(assays, study) {
     if (assays != null) {
         return ResizeArray_map((assayId) => defaultArg(tryFind((a) => (a.Identifier === assayId), value_17(assays)), ArcAssay.init(assayId)), study.RegisteredAssayIdentifiers);
     }
@@ -43,43 +39,89 @@ export function Study_Helper_getAssayInformation(assays, study) {
     }
 }
 
-export function Study_encoder(study) {
-    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, [study.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), study.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), study.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), study.PublicReleaseDate), tryIncludeSeq("Publications", Publication_encoder, study.Publications), tryIncludeSeq("Contacts", Person_encoder, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", ArcTable_encoder, study.Tables), tryInclude("DataMap", encoder_4, study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => (new Json(0, [value_9])), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", Comment_encoder, study.Comments)]))]);
+export function encoder(study) {
+    let value;
+    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = study.Identifier, {
+        Encode(helpers) {
+            return helpers.encodeString(value);
+        },
+    })], tryInclude("Title", (value_1) => ({
+        Encode(helpers_1) {
+            return helpers_1.encodeString(value_1);
+        },
+    }), study.Title), tryInclude("Description", (value_3) => ({
+        Encode(helpers_2) {
+            return helpers_2.encodeString(value_3);
+        },
+    }), study.Description), tryInclude("SubmissionDate", (value_5) => ({
+        Encode(helpers_3) {
+            return helpers_3.encodeString(value_5);
+        },
+    }), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => ({
+        Encode(helpers_4) {
+            return helpers_4.encodeString(value_7);
+        },
+    }), study.PublicReleaseDate), tryIncludeSeq("Publications", encoder_5, study.Publications), tryIncludeSeq("Contacts", encoder_6, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", encoder_7, study.Tables), tryInclude("DataMap", encoder_8, study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => ({
+        Encode(helpers_5) {
+            return helpers_5.encodeString(value_9);
+        },
+    }), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", encoder_9, study.Comments)]));
+    return {
+        Encode(helpers_6) {
+            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values);
+            return helpers_6.encodeObject(arg);
+        },
+    };
 }
 
-export const Study_decoder = object((get$) => {
+export const decoder = object((get$) => {
     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, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
-    return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = Decode_resizeArray(Publication_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = Decode_resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = Decode_resizeArray(ArcTable_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", decoder_1))), unwrap((arg_21 = Decode_resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21)))), unwrap((arg_23 = Decode_resizeArray(Comment_decoder), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23)))));
+    return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = resizeArray(decoder_2), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = resizeArray(decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = resizeArray(decoder_4), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", decoder_5))), unwrap((arg_21 = resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21)))), unwrap((arg_23 = resizeArray(decoder_6), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23)))));
 });
 
-export function Study_encoderCompressed(stringTable, oaTable, cellTable, study) {
-    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, [study.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), study.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), study.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), study.PublicReleaseDate), tryIncludeSeq("Publications", Publication_encoder, study.Publications), tryIncludeSeq("Contacts", Person_encoder, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", (table) => ArcTable_encoderCompressed(stringTable, oaTable, cellTable, table), study.Tables), tryInclude("DataMap", (dm) => encoderCompressed(stringTable, oaTable, cellTable, dm), study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => (new Json(0, [value_9])), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", Comment_encoder, study.Comments)]))]);
+export function encoderCompressed(stringTable, oaTable, cellTable, study) {
+    let value;
+    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = study.Identifier, {
+        Encode(helpers) {
+            return helpers.encodeString(value);
+        },
+    })], tryInclude("Title", (value_1) => ({
+        Encode(helpers_1) {
+            return helpers_1.encodeString(value_1);
+        },
+    }), study.Title), tryInclude("Description", (value_3) => ({
+        Encode(helpers_2) {
+            return helpers_2.encodeString(value_3);
+        },
+    }), study.Description), tryInclude("SubmissionDate", (value_5) => ({
+        Encode(helpers_3) {
+            return helpers_3.encodeString(value_5);
+        },
+    }), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => ({
+        Encode(helpers_4) {
+            return helpers_4.encodeString(value_7);
+        },
+    }), study.PublicReleaseDate), tryIncludeSeq("Publications", encoder_5, study.Publications), tryIncludeSeq("Contacts", encoder_6, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", (table) => encoderCompressed_1(stringTable, oaTable, cellTable, table), study.Tables), tryInclude("DataMap", (dm) => encoderCompressed_2(stringTable, oaTable, cellTable, dm), study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => ({
+        Encode(helpers_5) {
+            return helpers_5.encodeString(value_9);
+        },
+    }), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", encoder_9, study.Comments)]));
+    return {
+        Encode(helpers_6) {
+            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values);
+            return helpers_6.encodeObject(arg);
+        },
+    };
 }
 
-export function Study_decoderCompressed(stringTable, oaTable, cellTable) {
+export function decoderCompressed(stringTable, oaTable, cellTable) {
     return object((get$) => {
         let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
-        return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = Decode_resizeArray(Publication_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = Decode_resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = Decode_resizeArray(ArcTable_decoderCompressed(stringTable, oaTable, cellTable)), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((arg_19 = decoderCompressed(stringTable, oaTable, cellTable), (objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", arg_19)))), unwrap((arg_21 = Decode_resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21)))), unwrap((arg_23 = Decode_resizeArray(Comment_decoder), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23)))));
+        return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = resizeArray(decoder_2), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = resizeArray(decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = resizeArray(decoderCompressed_1(stringTable, oaTable, cellTable)), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((arg_19 = decoderCompressed_2(stringTable, oaTable, cellTable), (objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", arg_19)))), unwrap((arg_21 = resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21)))), unwrap((arg_23 = resizeArray(decoder_6), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23)))));
     });
 }
 
-export function Study_ROCrate_genID(a) {
+export function ROCrate_genID(a) {
     const matchValue = a.Identifier;
     if (matchValue === "") {
         return "#EmptyStudy";
@@ -89,48 +131,82 @@ export function Study_ROCrate_genID(a) {
     }
 }
 
-export function Study_ROCrate_encoder(assays, s) {
-    let studyName, studyName_1;
+export function ROCrate_encoder(assays, s) {
+    let value, value_3, studyName, studyName_1;
     const fileName = Study_tryFileNameFromIdentifier(s.Identifier);
     const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(s);
-    const assays_1 = Study_Helper_getAssayInformation(assays, s);
-    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, [Study_ROCrate_genID(s)])], ["@type", list_1(singleton(new Json(0, ["Study"])))], ["additionalType", new Json(0, ["Study"])], ["identifier", new Json(0, [s.Identifier])], tryInclude("filename", (value_4) => (new Json(0, [value_4])), fileName), tryInclude("title", (value_6) => (new Json(0, [value_6])), s.Title), tryInclude("description", (value_8) => (new Json(0, [value_8])), s.Description), tryIncludeSeq("studyDesignDescriptors", OntologyAnnotation_ROCrate_encoderDefinedTerm, s.StudyDesignDescriptors), tryInclude("submissionDate", (value_10) => (new Json(0, [value_10])), s.SubmissionDate), tryInclude("publicReleaseDate", (value_12) => (new Json(0, [value_12])), s.PublicReleaseDate), tryIncludeSeq("publications", Publication_ROCrate_encoder, s.Publications), tryIncludeSeq("people", Person_ROCrate_encoder, s.Contacts), tryIncludeList("processSequence", (studyName = s.Identifier, (oa_3) => Process_ROCrate_encoder(studyName, void 0, oa_3)), processes), tryIncludeSeq("assays", (studyName_1 = s.Identifier, (a_1) => Assay_ROCrate_encoder(studyName_1, a_1)), assays_1), tryIncludeSeq("comments", Comment_ROCrate_encoder, s.Comments), ["@context", context_jsonvalue]]))]);
+    const assays_1 = Helper_getAssayInformation(assays, s);
+    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = ROCrate_genID(s), {
+        Encode(helpers) {
+            return helpers.encodeString(value);
+        },
+    })], ["@type", list_1(singleton({
+        Encode(helpers_1) {
+            return helpers_1.encodeString("Study");
+        },
+    }))], ["additionalType", {
+        Encode(helpers_2) {
+            return helpers_2.encodeString("Study");
+        },
+    }], ["identifier", (value_3 = s.Identifier, {
+        Encode(helpers_3) {
+            return helpers_3.encodeString(value_3);
+        },
+    })], tryInclude("filename", (value_4) => ({
+        Encode(helpers_4) {
+            return helpers_4.encodeString(value_4);
+        },
+    }), fileName), tryInclude("title", (value_6) => ({
+        Encode(helpers_5) {
+            return helpers_5.encodeString(value_6);
+        },
+    }), s.Title), tryInclude("description", (value_8) => ({
+        Encode(helpers_6) {
+            return helpers_6.encodeString(value_8);
+        },
+    }), s.Description), tryIncludeSeq("studyDesignDescriptors", OntologyAnnotation_ROCrate_encoderDefinedTerm, s.StudyDesignDescriptors), tryInclude("submissionDate", (value_10) => ({
+        Encode(helpers_7) {
+            return helpers_7.encodeString(value_10);
+        },
+    }), s.SubmissionDate), tryInclude("publicReleaseDate", (value_12) => ({
+        Encode(helpers_8) {
+            return helpers_8.encodeString(value_12);
+        },
+    }), s.PublicReleaseDate), tryIncludeSeq("publications", ROCrate_encoder_1, s.Publications), tryIncludeSeq("people", ROCrate_encoder_2, s.Contacts), tryIncludeList("processSequence", (studyName = s.Identifier, (oa_3) => ROCrate_encoder_3(studyName, undefined, oa_3)), processes), tryIncludeSeq("assays", (studyName_1 = s.Identifier, (a_1) => ROCrate_encoder_4(studyName_1, a_1)), assays_1), tryIncludeSeq("comments", ROCrate_encoder_5, s.Comments), ["@context", context_jsonvalue]]));
+    return {
+        Encode(helpers_9) {
+            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_9)], values);
+            return helpers_9.encodeObject(arg);
+        },
+    };
 }
 
-export const Study_ROCrate_decoder = object((get$) => {
+export const ROCrate_decoder = object((get$) => {
     let objectArg, arg_6, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, arg_16, objectArg_7, arg_18, objectArg_8, arg_20, objectArg_9, arg_22, objectArg_10;
     const identifier = defaultArg(bind(Study_tryIdentifierFromFileName, (objectArg = get$.Optional, objectArg.Field("filename", string))), createMissingIdentifier());
     let assays;
-    const arg_3 = list_2(Assay_ROCrate_decoder);
+    const arg_3 = list_2(ROCrate_decoder_1);
     const objectArg_1 = get$.Optional;
     assays = objectArg_1.Field("assays", arg_3);
     const assayIdentifiers = map((arg_4) => {
-        const collection = map_1((a) => a.Identifier, arg_4);
+        const collection = map_2((a) => a.Identifier, arg_4);
         return Array.from(collection);
     }, assays);
-    const tables = map((ps) => ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(ps).Tables, (arg_6 = list_2(Process_ROCrate_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("processSequence", arg_6))));
-    return [new ArcStudy(identifier, unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("title", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("description", string))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("submissionDate", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("publicReleaseDate", string))), unwrap((arg_16 = Decode_resizeArray(Publication_ROCrate_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("publications", arg_16)))), unwrap((arg_18 = Decode_resizeArray(Person_ROCrate_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("people", arg_18)))), unwrap((arg_20 = Decode_resizeArray(OntologyAnnotation_ROCrate_decoderDefinedTerm), (objectArg_9 = get$.Optional, objectArg_9.Field("studyDesignDescriptors", arg_20)))), unwrap(tables), void 0, unwrap(assayIdentifiers), unwrap((arg_22 = Decode_resizeArray(Comment_ROCrate_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_22))))), defaultArg(assays, empty())];
+    const tables = map((ps) => ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(ps).Tables, (arg_6 = list_2(ROCrate_decoder_2), (objectArg_2 = get$.Optional, objectArg_2.Field("processSequence", arg_6))));
+    return [new ArcStudy(identifier, unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("title", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("description", string))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("submissionDate", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("publicReleaseDate", string))), unwrap((arg_16 = resizeArray(ROCrate_decoder_3), (objectArg_7 = get$.Optional, objectArg_7.Field("publications", arg_16)))), unwrap((arg_18 = resizeArray(ROCrate_decoder_4), (objectArg_8 = get$.Optional, objectArg_8.Field("people", arg_18)))), unwrap((arg_20 = resizeArray(OntologyAnnotation_ROCrate_decoderDefinedTerm), (objectArg_9 = get$.Optional, objectArg_9.Field("studyDesignDescriptors", arg_20)))), unwrap(tables), undefined, unwrap(assayIdentifiers), unwrap((arg_22 = resizeArray(ROCrate_decoder_5), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_22))))), defaultArg(assays, empty())];
 });
 
 /**
  * If assays.IsSome then try to get registered assays from external list, otherwise try to access investigation or create empty defaults.
  */
-export function Study_ISAJson_encoder(idMap, assays, s) {
+export function ISAJson_encoder(idMap, assays, s) {
     const f = (s_1) => {
-        let studyName, studyName_1, studyName_2;
+        let studyName, value_6, value_8, studyName_1, studyName_2;
         const study = s_1.Copy(true);
         const fileName = Study_fileNameFromIdentifier(study.Identifier);
         let assays_1;
         const n = [];
-        let enumerator = getEnumerator(Study_Helper_getAssayInformation(assays, study));
+        let enumerator = getEnumerator(Helper_getAssayInformation(assays, study));
         try {
             while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
                 const a = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
@@ -155,33 +231,59 @@ export function Study_ISAJson_encoder(idMap, assays, s) {
         assays_1 = n;
         const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(study);
         const encodedUnits = tryIncludeList("unitCategories", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), getUnits(processes));
-        const encodedFactors = tryIncludeList("factors", (value_1) => Factor_ISAJson_encoder(idMap, value_1), getFactors(processes));
-        const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_3) => MaterialAttribute_ISAJson_encoder(idMap, value_3), getCharacteristics(processes));
-        const encodedMaterials = tryInclude("materials", (ps) => encoder_5(idMap, ps), Option_fromValueWithDefault(empty(), processes));
+        const encodedFactors = tryIncludeList("factors", (value_1) => encoder_10(idMap, value_1), getFactors(processes));
+        const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_3) => encoder_11(idMap, value_3), getCharacteristics(processes));
+        const encodedMaterials = tryInclude("materials", (ps) => encoder_12(idMap, ps), Option_fromValueWithDefault(empty(), processes));
         let encodedProtocols;
         const value_5 = getProtocols(processes);
-        encodedProtocols = tryIncludeList("protocols", (studyName = s_1.Identifier, (oa_1) => Protocol_ISAJson_encoder(studyName, void 0, void 0, idMap, oa_1)), value_5);
-        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, [Study_ROCrate_genID(study)])], ["filename", new Json(0, [fileName])], ["identifier", new Json(0, [study.Identifier])], tryInclude("title", (value_9) => (new Json(0, [value_9])), study.Title), tryInclude("description", (value_11) => (new Json(0, [value_11])), study.Description), tryInclude("submissionDate", (value_13) => (new Json(0, [value_13])), study.SubmissionDate), tryInclude("publicReleaseDate", (value_15) => (new Json(0, [value_15])), study.PublicReleaseDate), tryIncludeSeq("publications", (oa_2) => Publication_ISAJson_encoder(idMap, oa_2), study.Publications), tryIncludeSeq("people", (person_2) => Person_ISAJson_encoder(idMap, person_2), study.Contacts), tryIncludeSeq("studyDesignDescriptors", (oa_3) => OntologyAnnotation_ISAJson_encoder(idMap, oa_3), study.StudyDesignDescriptors), encodedProtocols, encodedMaterials, tryIncludeList("processSequence", (studyName_1 = s_1.Identifier, (oa_4) => Process_ISAJson_encoder(studyName_1, void 0, idMap, oa_4)), processes), tryIncludeSeq("assays", (studyName_2 = s_1.Identifier, (a_2) => Assay_ISAJson_encoder(studyName_2, idMap, a_2)), assays_1), encodedFactors, encodedCharacteristics, encodedUnits, tryIncludeSeq("comments", (comment) => Comment_ISAJson_encoder(idMap, comment), study.Comments)]))]);
+        encodedProtocols = tryIncludeList("protocols", (studyName = s_1.Identifier, (oa_1) => ISAJson_encoder_1(studyName, undefined, undefined, idMap, oa_1)), value_5);
+        const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value_6 = ROCrate_genID(study), {
+            Encode(helpers) {
+                return helpers.encodeString(value_6);
+            },
+        })], ["filename", {
+            Encode(helpers_1) {
+                return helpers_1.encodeString(fileName);
+            },
+        }], ["identifier", (value_8 = study.Identifier, {
+            Encode(helpers_2) {
+                return helpers_2.encodeString(value_8);
+            },
+        })], tryInclude("title", (value_9) => ({
+            Encode(helpers_3) {
+                return helpers_3.encodeString(value_9);
+            },
+        }), study.Title), tryInclude("description", (value_11) => ({
+            Encode(helpers_4) {
+                return helpers_4.encodeString(value_11);
+            },
+        }), study.Description), tryInclude("submissionDate", (value_13) => ({
+            Encode(helpers_5) {
+                return helpers_5.encodeString(value_13);
+            },
+        }), study.SubmissionDate), tryInclude("publicReleaseDate", (value_15) => ({
+            Encode(helpers_6) {
+                return helpers_6.encodeString(value_15);
+            },
+        }), study.PublicReleaseDate), tryIncludeSeq("publications", (oa_2) => ISAJson_encoder_2(idMap, oa_2), study.Publications), tryIncludeSeq("people", (person_2) => ISAJson_encoder_3(idMap, person_2), study.Contacts), tryIncludeSeq("studyDesignDescriptors", (oa_3) => OntologyAnnotation_ISAJson_encoder(idMap, oa_3), study.StudyDesignDescriptors), encodedProtocols, encodedMaterials, tryIncludeList("processSequence", (studyName_1 = s_1.Identifier, (oa_4) => ISAJson_encoder_4(studyName_1, undefined, idMap, oa_4)), processes), tryIncludeSeq("assays", (studyName_2 = s_1.Identifier, (a_2) => ISAJson_encoder_5(studyName_2, idMap, a_2)), assays_1), encodedFactors, encodedCharacteristics, encodedUnits, tryIncludeSeq("comments", (comment) => ISAJson_encoder_6(idMap, comment), study.Comments)]));
+        return {
+            Encode(helpers_7) {
+                const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_7)], values);
+                return helpers_7.encodeObject(arg);
+            },
+        };
     };
     if (idMap != null) {
-        return encode(Study_ROCrate_genID, f, s, idMap);
+        return encode(ROCrate_genID, f, s, idMap);
     }
     else {
         return f(s);
     }
 }
 
-export const Study_ISAJson_allowedFields = ofArray(["@id", "filename", "identifier", "title", "description", "submissionDate", "publicReleaseDate", "publications", "people", "studyDesignDescriptors", "protocols", "materials", "assays", "factors", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
+export const ISAJson_allowedFields = ofArray(["@id", "filename", "identifier", "title", "description", "submissionDate", "publicReleaseDate", "publications", "people", "studyDesignDescriptors", "protocols", "materials", "assays", "factors", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
 
-export const Study_ISAJson_decoder = Decode_objectNoAdditionalProperties(Study_ISAJson_allowedFields, (get$) => {
+export const ISAJson_decoder = Decode_objectNoAdditionalProperties(ISAJson_allowedFields, (get$) => {
     let objectArg, arg_5, objectArg_2, objectArg_5, objectArg_6, objectArg_7, objectArg_8, arg_21, objectArg_9, arg_23, objectArg_10, arg_25, objectArg_11;
     const identifier = defaultArgWith((objectArg = get$.Optional, objectArg.Field("identifier", string)), () => {
         let objectArg_1;
@@ -190,13 +292,13 @@ export const Study_ISAJson_decoder = Decode_objectNoAdditionalProperties(Study_I
     const tables = map((arg_6) => {
         const a = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(arg_6);
         return a.Tables;
-    }, (arg_5 = list_2(Process_ISAJson_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("processSequence", arg_5))));
+    }, (arg_5 = list_2(ISAJson_decoder_1), (objectArg_2 = get$.Optional, objectArg_2.Field("processSequence", arg_5))));
     let assays;
-    const arg_8 = list_2(Assay_ISAJson_decoder);
+    const arg_8 = list_2(ISAJson_decoder_2);
     const objectArg_3 = get$.Optional;
     assays = objectArg_3.Field("assays", arg_8);
     let personsRaw;
-    const arg_10 = Decode_resizeArray(Person_ISAJson_decoder);
+    const arg_10 = resizeArray(ISAJson_decoder_3);
     const objectArg_4 = get$.Optional;
     personsRaw = objectArg_4.Field("people", arg_10);
     const persons = [];
@@ -238,100 +340,9 @@ export const Study_ISAJson_decoder = Decode_objectNoAdditionalProperties(Study_I
         }
     }
     const assayIdentifiers = map((arg_11) => {
-        const collection = map_1((a_1) => a_1.Identifier, arg_11);
+        const collection = map_2((a_1) => a_1.Identifier, arg_11);
         return Array.from(collection);
     }, assays);
-    return [new ArcStudy(identifier, unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("title", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("description", string))), unwrap((objectArg_7 = get$.Optional, objectArg_7.Field("submissionDate", string))), unwrap((objectArg_8 = get$.Optional, objectArg_8.Field("publicReleaseDate", string))), unwrap((arg_21 = Decode_resizeArray(Publication_ISAJson_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("publications", arg_21)))), unwrap((persons.length === 0) ? void 0 : persons), unwrap((arg_23 = Decode_resizeArray(OntologyAnnotation_ISAJson_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("studyDesignDescriptors", arg_23)))), unwrap(tables), void 0, unwrap(assayIdentifiers), unwrap((arg_25 = Decode_resizeArray(Comment_ISAJson_decoder), (objectArg_11 = get$.Optional, objectArg_11.Field("comments", arg_25))))), defaultArg(assays, empty())];
+    return [new ArcStudy(identifier, unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("title", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("description", string))), unwrap((objectArg_7 = get$.Optional, objectArg_7.Field("submissionDate", string))), unwrap((objectArg_8 = get$.Optional, objectArg_8.Field("publicReleaseDate", string))), unwrap((arg_21 = resizeArray(ISAJson_decoder_4), (objectArg_9 = get$.Optional, objectArg_9.Field("publications", arg_21)))), unwrap((persons.length === 0) ? undefined : persons), unwrap((arg_23 = resizeArray(OntologyAnnotation_ISAJson_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("studyDesignDescriptors", arg_23)))), unwrap(tables), undefined, unwrap(assayIdentifiers), unwrap((arg_25 = resizeArray(ISAJson_decoder_5), (objectArg_11 = get$.Optional, objectArg_11.Field("comments", arg_25))))), defaultArg(assays, empty())];
 });
 
-export function ARCtrl_ArcStudy__ArcStudy_fromJsonString_Static_Z721C83C5(s) {
-    const matchValue = fromString(Study_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_ArcStudy__ArcStudy_toJsonString_Static_71136F3F(spaces) {
-    return (obj) => {
-        const value = Study_encoder(obj);
-        return toString(defaultSpaces(spaces), value);
-    };
-}
-
-export function ARCtrl_ArcStudy__ArcStudy_ToJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
-}
-
-export function ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5(s) {
-    try {
-        const matchValue = fromString(decode(Study_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_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F(spaces) {
-    return (obj) => toString(defaultArg(spaces, 0), encode_1(Study_encoderCompressed, obj));
-}
-
-export function ARCtrl_ArcStudy__ArcStudy_ToCompressedJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(this$);
-}
-
-export function ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5(s) {
-    const matchValue = fromString(Study_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_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086(assays, spaces) {
-    return (obj) => {
-        const value = Study_ROCrate_encoder(assays, obj);
-        return toString(defaultSpaces(spaces), value);
-    };
-}
-
-export function ARCtrl_ArcStudy__ArcStudy_ToROCrateJsonString_3BA23086(this$, assays, spaces) {
-    return ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086(unwrap(assays), unwrap(spaces))(this$);
-}
-
-export function ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5(s) {
-    const matchValue = fromString(Study_ISAJson_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_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1(assays, spaces, useIDReferencing) {
-    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
-    return (obj) => {
-        const value = Study_ISAJson_encoder(idMap, assays, obj);
-        return toString(defaultSpaces(spaces), value);
-    };
-}
-
-export function ARCtrl_ArcStudy__ArcStudy_ToISAJsonString_Z3FD920F1(this$, assays, spaces, useIDReferencing) {
-    return ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1(unwrap(assays), unwrap(spaces), unwrap(useIDReferencing))(this$);
-}
-