@nfdi4plants/arctrl 2.0.1 → 2.1.0-alpha.2

package/FileSystem/FileSystemTree.js

@@ -1,12 +1,12 @@
-import { unwrap, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
-import { append as append_1, choose, equalsWith, tail, head, map, tryFind } from "../fable_modules/fable-library-js.4.16.0/Array.js";
-import { singleton, append, delay, toArray } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
-import { Array_distinct, Array_groupBy } from "../fable_modules/fable-library-js.4.16.0/Seq2.js";
-import { curry2, arrayHash, stringHash } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { unwrap, defaultArg } from "../fable_modules/fable-library-js.4.22.0/Option.js";
+import { append as append_1, choose, equalsWith, tail, head, map, tryFind } from "../fable_modules/fable-library-js.4.22.0/Array.js";
+import { singleton, append, delay, toArray } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
+import { Array_distinct, Array_groupBy } from "../fable_modules/fable-library-js.4.22.0/Seq2.js";
+import { curry2, arrayHash, stringHash } from "../fable_modules/fable-library-js.4.22.0/Util.js";
 import { combineMany, split } from "./Path.js";
-import { empty, reverse, toArray as toArray_1, cons } from "../fable_modules/fable-library-js.4.16.0/List.js";
-import { Union } from "../fable_modules/fable-library-js.4.16.0/Types.js";
-import { union_type, array_type, string_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
+import { empty, reverse, toArray as toArray_1, cons } from "../fable_modules/fable-library-js.4.22.0/List.js";
+import { Union } from "../fable_modules/fable-library-js.4.22.0/Types.js";
+import { union_type, array_type, string_type } from "../fable_modules/fable-library-js.4.22.0/Reflection.js";
 
 export class FileSystemTree extends Union {
     constructor(tag, fields) {
@@ -50,7 +50,7 @@ export class FileSystemTree extends Union {
     }
     TryGetChildByName(name) {
         const this$ = this;
-        return (this$.tag === 0) ? void 0 : tryFind((c) => (c.Name === name), this$.fields[1]);
+        return (this$.tag === 0) ? undefined : tryFind((c) => (c.Name === name), this$.fields[1]);
     }
     static tryGetChildByName(name) {
         return (fst) => fst.TryGetChildByName(name);
@@ -139,7 +139,7 @@ export class FileSystemTree extends Union {
                     return new FileSystemTree(0, [n]);
                 }
                 else {
-                    return void 0;
+                    return undefined;
                 }
             }
         };
@@ -157,7 +157,7 @@ export class FileSystemTree extends Union {
                     return new FileSystemTree(1, [n_1, choose(loop, parent.fields[1])]);
                 }
                 else {
-                    return void 0;
+                    return undefined;
                 }
             }
             else {
@@ -177,14 +177,14 @@ export class FileSystemTree extends Union {
                 if (predicate(n_1)) {
                     const filteredChildren = choose(loop, parent.fields[1]);
                     if (filteredChildren.length === 0) {
-                        return void 0;
+                        return undefined;
                     }
                     else {
                         return new FileSystemTree(1, [n_1, filteredChildren]);
                     }
                 }
                 else {
-                    return void 0;
+                    return undefined;
                 }
             }
             else {
@@ -193,7 +193,7 @@ export class FileSystemTree extends Union {
                     return new FileSystemTree(0, [n]);
                 }
                 else {
-                    return void 0;
+                    return undefined;
                 }
             }
         };

package/FileSystem/Path.js

@@ -1,10 +1,10 @@
-import { trim, join, trimStart, trimEnd, split as split_1 } from "../fable_modules/fable-library-js.4.16.0/String.js";
-import { last, mapIndexed } from "../fable_modules/fable-library-js.4.16.0/Array.js";
+import { trim, join, trimStart, trimEnd, split as split_1 } from "../fable_modules/fable-library-js.4.22.0/String.js";
+import { last, mapIndexed } from "../fable_modules/fable-library-js.4.22.0/Array.js";
 
 export const seperators = ["/", "\\"];
 
 export function split(path) {
-    const array = split_1(path, seperators, void 0, 3);
+    const array = split_1(path, seperators, undefined, 3);
     return array.filter((p) => {
         if (p !== "") {
             return p !== ".";

package/Json/ARC.js

@@ -1,25 +1,31 @@
-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 { ofArray, choose } from "../fable_modules/fable-library-js.4.22.0/List.js";
+import { map } from "../fable_modules/fable-library-js.4.22.0/Option.js";
 import { tryInclude } from "./Encode.js";
-import { Investigation_ROCrate_decoder, Investigation_ROCrate_encoder } from "./Investigation.js";
+import { ROCrate_decoder, ROCrate_encoder } from "./Investigation.js";
 import { context_jsonvalue, conformsTo_jsonvalue } from "./context/rocrate/rocrate_context.js";
-import { object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { map as map_1 } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
+import { object } from "../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
 
 export function encoder(isa) {
-    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, isa), ["conformsTo", conformsTo_jsonvalue], ["@context", context_jsonvalue]]))]);
+    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([tryInclude("@type", (value) => ({
+        Encode(helpers) {
+            return helpers.encodeString(value);
+        },
+    }), "CreativeWork"), tryInclude("@id", (value_2) => ({
+        Encode(helpers_1) {
+            return helpers_1.encodeString(value_2);
+        },
+    }), "ro-crate-metadata.json"), tryInclude("about", ROCrate_encoder, isa), ["conformsTo", conformsTo_jsonvalue], ["@context", context_jsonvalue]]));
+    return {
+        Encode(helpers_2) {
+            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_2)], values);
+            return helpers_2.encodeObject(arg);
+        },
+    };
 }
 
 export const decoder = object((get$) => {
     const objectArg = get$.Optional;
-    return objectArg.Field("about", Investigation_ROCrate_decoder);
+    return objectArg.Field("about", ROCrate_decoder);
 });
 

package/Json/Assay.js

@@ -1,69 +1,71 @@
-import { empty, singleton, 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, tryIncludeList, tryIncludeSeq, tryInclude } from "./Encode.js";
+import { empty, singleton, ofArray, choose } from "../fable_modules/fable-library-js.4.22.0/List.js";
+import { bind, defaultArg, unwrap, map } from "../fable_modules/fable-library-js.4.22.0/Option.js";
+import { tryIncludeList, tryIncludeSeq, tryInclude } from "./Encode.js";
 import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_decoderPropertyValue, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_ROCrate_encoderPropertyValue, OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./OntologyAnnotation.js";
-import { decoderCompressed, encoderCompressed, decoder as decoder_1, encoder as encoder_3 } from "./DataMap/DataMap.js";
-import { ArcTable_decoderCompressed, ArcTable_encoderCompressed, ArcTable_decoder, ArcTable_encoder } from "./Table/ArcTable.js";
-import { Person_ROCrate_decoder, Person_ROCrate_encoder, Person_decoder, Person_encoder } from "./Person.js";
-import { Comment_ISAJson_decoder, Comment_ISAJson_encoder, Comment_ROCrate_decoder, Comment_ROCrate_encoder, Comment_decoder, Comment_encoder } from "./Comment.js";
-import { map as map_1, list as list_2, string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { decoderCompressed as decoderCompressed_2, encoderCompressed as encoderCompressed_2, decoder as decoder_2, encoder as encoder_4 } from "./DataMap/DataMap.js";
+import { decoderCompressed as decoderCompressed_1, encoderCompressed as encoderCompressed_1, decoder as decoder_1, encoder as encoder_5 } from "./Table/ArcTable.js";
+import { ROCrate_decoder as ROCrate_decoder_2, ROCrate_encoder as ROCrate_encoder_1, decoder as decoder_3, encoder as encoder_6 } from "./Person.js";
+import { ISAJson_decoder as ISAJson_decoder_2, ISAJson_encoder as ISAJson_encoder_3, ROCrate_decoder as ROCrate_decoder_3, ROCrate_encoder as ROCrate_encoder_4, decoder as decoder_4, encoder as encoder_7 } from "./Comment.js";
+import { map as map_1 } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
+import { map as map_2, list as list_2, resizeArray, string, object } from "../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
 import { ArcAssay } from "../Core/ArcTypes.js";
-import { bind, map, defaultArg, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.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 { replace } from "../fable_modules/fable-library-js.4.22.0/String.js";
 import { Assay_tryIdentifierFromFileName, createMissingIdentifier, Assay_fileNameFromIdentifier } from "../Core/Helper/Identifier.js";
 import { JsonTypes_decomposeTechnologyPlatform, JsonTypes_composeTechnologyPlatform, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D, ARCtrl_ArcTables__ArcTables_GetProcesses } from "../Core/Conversion.js";
 import { getCharacteristics, getUnits, getData } from "../Core/Process/ProcessSequence.js";
-import { list as list_1 } from "../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
-import { Data_ISAJson_encoder, Data_ROCrate_encoder } from "./Data.js";
-import { Process_ISAJson_decoder, Process_ISAJson_encoder, Process_ROCrate_decoder, Process_ROCrate_encoder } from "./Process/Process.js";
+import { list as list_1 } from "../fable_modules/Thoth.Json.Core.0.4.0/Encode.fs.js";
+import { ISAJson_encoder as ISAJson_encoder_1, ROCrate_encoder as ROCrate_encoder_2 } from "./Data.js";
+import { ISAJson_decoder as ISAJson_decoder_1, ISAJson_encoder as ISAJson_encoder_2, ROCrate_decoder as ROCrate_decoder_1, ROCrate_encoder as ROCrate_encoder_3 } from "./Process/Process.js";
 import { context_jsonvalue } from "./context/rocrate/isa_assay_context.js";
-import { MaterialAttribute_ISAJson_encoder } from "./Process/MaterialAttribute.js";
-import { encoder as encoder_4 } from "./Process/AssayMaterials.js";
+import { encoder as encoder_8 } from "./Process/MaterialAttribute.js";
+import { encoder as encoder_9 } from "./Process/AssayMaterials.js";
 import { Option_fromValueWithDefault } from "../Core/Helper/Collections.js";
 import { encode } from "./IDTable.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";
-
-export function Assay_encoder(assay) {
-    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, [assay.Identifier])], tryInclude("MeasurementType", OntologyAnnotation_encoder, assay.MeasurementType), tryInclude("TechnologyType", OntologyAnnotation_encoder, assay.TechnologyType), tryInclude("TechnologyPlatform", OntologyAnnotation_encoder, assay.TechnologyPlatform), tryInclude("DataMap", encoder_3, assay.DataMap), tryIncludeSeq("Tables", ArcTable_encoder, assay.Tables), tryIncludeSeq("Performers", Person_encoder, assay.Performers), tryIncludeSeq("Comments", Comment_encoder, assay.Comments)]))]);
+import { Decode_objectNoAdditionalProperties } from "./Decode.js";
+
+export function encoder(assay) {
+    let value;
+    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = assay.Identifier, {
+        Encode(helpers) {
+            return helpers.encodeString(value);
+        },
+    })], tryInclude("MeasurementType", OntologyAnnotation_encoder, assay.MeasurementType), tryInclude("TechnologyType", OntologyAnnotation_encoder, assay.TechnologyType), tryInclude("TechnologyPlatform", OntologyAnnotation_encoder, assay.TechnologyPlatform), tryInclude("DataMap", encoder_4, assay.DataMap), tryIncludeSeq("Tables", encoder_5, assay.Tables), tryIncludeSeq("Performers", encoder_6, assay.Performers), tryIncludeSeq("Comments", encoder_7, assay.Comments)]));
+    return {
+        Encode(helpers_1) {
+            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_1)], values);
+            return helpers_1.encodeObject(arg);
+        },
+    };
 }
 
-export const Assay_decoder = object((get$) => {
+export const decoder = object((get$) => {
     let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7;
-    return ArcAssay.create((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("MeasurementType", OntologyAnnotation_decoder))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("TechnologyType", OntologyAnnotation_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("TechnologyPlatform", OntologyAnnotation_decoder))), unwrap((arg_9 = Decode_resizeArray(ArcTable_decoder), (objectArg_4 = get$.Optional, objectArg_4.Field("Tables", arg_9)))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("DataMap", decoder_1))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Performers", arg_13)))), unwrap((arg_15 = Decode_resizeArray(Comment_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("Comments", arg_15)))));
+    return ArcAssay.create((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("MeasurementType", OntologyAnnotation_decoder))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("TechnologyType", OntologyAnnotation_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("TechnologyPlatform", OntologyAnnotation_decoder))), unwrap((arg_9 = resizeArray(decoder_1), (objectArg_4 = get$.Optional, objectArg_4.Field("Tables", arg_9)))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("DataMap", decoder_2))), unwrap((arg_13 = resizeArray(decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("Performers", arg_13)))), unwrap((arg_15 = resizeArray(decoder_4), (objectArg_7 = get$.Optional, objectArg_7.Field("Comments", arg_15)))));
 });
 
-export function Assay_encoderCompressed(stringTable, oaTable, cellTable, assay) {
-    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, [assay.Identifier])], tryInclude("MeasurementType", OntologyAnnotation_encoder, assay.MeasurementType), tryInclude("TechnologyType", OntologyAnnotation_encoder, assay.TechnologyType), tryInclude("TechnologyPlatform", OntologyAnnotation_encoder, assay.TechnologyPlatform), tryIncludeSeq("Tables", (table) => ArcTable_encoderCompressed(stringTable, oaTable, cellTable, table), assay.Tables), tryInclude("DataMap", (dm) => encoderCompressed(stringTable, oaTable, cellTable, dm), assay.DataMap), tryIncludeSeq("Performers", Person_encoder, assay.Performers), tryIncludeSeq("Comments", Comment_encoder, assay.Comments)]))]);
+export function encoderCompressed(stringTable, oaTable, cellTable, assay) {
+    let value;
+    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = assay.Identifier, {
+        Encode(helpers) {
+            return helpers.encodeString(value);
+        },
+    })], tryInclude("MeasurementType", OntologyAnnotation_encoder, assay.MeasurementType), tryInclude("TechnologyType", OntologyAnnotation_encoder, assay.TechnologyType), tryInclude("TechnologyPlatform", OntologyAnnotation_encoder, assay.TechnologyPlatform), tryIncludeSeq("Tables", (table) => encoderCompressed_1(stringTable, oaTable, cellTable, table), assay.Tables), tryInclude("DataMap", (dm) => encoderCompressed_2(stringTable, oaTable, cellTable, dm), assay.DataMap), tryIncludeSeq("Performers", encoder_6, assay.Performers), tryIncludeSeq("Comments", encoder_7, assay.Comments)]));
+    return {
+        Encode(helpers_1) {
+            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_1)], values);
+            return helpers_1.encodeObject(arg);
+        },
+    };
 }
 
-export function Assay_decoderCompressed(stringTable, oaTable, cellTable) {
+export function decoderCompressed(stringTable, oaTable, cellTable) {
     return object((get$) => {
         let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7;
-        return ArcAssay.create((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("MeasurementType", OntologyAnnotation_decoder))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("TechnologyType", OntologyAnnotation_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("TechnologyPlatform", OntologyAnnotation_decoder))), unwrap((arg_9 = Decode_resizeArray(ArcTable_decoderCompressed(stringTable, oaTable, cellTable)), (objectArg_4 = get$.Optional, objectArg_4.Field("Tables", arg_9)))), unwrap((arg_11 = decoderCompressed(stringTable, oaTable, cellTable), (objectArg_5 = get$.Optional, objectArg_5.Field("DataMap", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Performers", arg_13)))), unwrap((arg_15 = Decode_resizeArray(Comment_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("Comments", arg_15)))));
+        return ArcAssay.create((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("MeasurementType", OntologyAnnotation_decoder))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("TechnologyType", OntologyAnnotation_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("TechnologyPlatform", OntologyAnnotation_decoder))), unwrap((arg_9 = resizeArray(decoderCompressed_1(stringTable, oaTable, cellTable)), (objectArg_4 = get$.Optional, objectArg_4.Field("Tables", arg_9)))), unwrap((arg_11 = decoderCompressed_2(stringTable, oaTable, cellTable), (objectArg_5 = get$.Optional, objectArg_5.Field("DataMap", arg_11)))), unwrap((arg_13 = resizeArray(decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("Performers", arg_13)))), unwrap((arg_15 = resizeArray(decoder_4), (objectArg_7 = get$.Optional, objectArg_7.Field("Comments", arg_15)))));
     });
 }
 
-export function Assay_ROCrate_genID(a) {
+export function ROCrate_genID(a) {
     const matchValue = a.Identifier;
     if (matchValue === "") {
         return "#EmptyAssay";
@@ -73,160 +75,97 @@ export function Assay_ROCrate_genID(a) {
     }
 }
 
-export function Assay_ROCrate_encoder(studyName, a) {
-    let assayName;
+export function ROCrate_encoder(studyName, a) {
+    let value, value_3, assayName;
     const fileName = Assay_fileNameFromIdentifier(a.Identifier);
     const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(a);
     const dataFiles = getData(processes);
-    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, [Assay_ROCrate_genID(a)])], ["@type", list_1(singleton(new Json(0, ["Assay"])))], ["additionalType", new Json(0, ["Assay"])], ["identifier", new Json(0, [a.Identifier])], ["filename", new Json(0, [fileName])], tryInclude("measurementType", OntologyAnnotation_ROCrate_encoderPropertyValue, a.MeasurementType), tryInclude("technologyType", OntologyAnnotation_ROCrate_encoderDefinedTerm, a.TechnologyType), tryInclude("technologyPlatform", OntologyAnnotation_ROCrate_encoderDefinedTerm, a.TechnologyPlatform), tryIncludeSeq("performers", Person_ROCrate_encoder, a.Performers), tryIncludeList("dataFiles", Data_ROCrate_encoder, dataFiles), tryIncludeList("processSequence", (assayName = a.Identifier, (oa_5) => Process_ROCrate_encoder(studyName, assayName, oa_5)), processes), tryIncludeSeq("comments", Comment_ROCrate_encoder, a.Comments), ["@context", context_jsonvalue]]))]);
+    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = ROCrate_genID(a), {
+        Encode(helpers) {
+            return helpers.encodeString(value);
+        },
+    })], ["@type", list_1(singleton({
+        Encode(helpers_1) {
+            return helpers_1.encodeString("Assay");
+        },
+    }))], ["additionalType", {
+        Encode(helpers_2) {
+            return helpers_2.encodeString("Assay");
+        },
+    }], ["identifier", (value_3 = a.Identifier, {
+        Encode(helpers_3) {
+            return helpers_3.encodeString(value_3);
+        },
+    })], ["filename", {
+        Encode(helpers_4) {
+            return helpers_4.encodeString(fileName);
+        },
+    }], tryInclude("measurementType", OntologyAnnotation_ROCrate_encoderPropertyValue, a.MeasurementType), tryInclude("technologyType", OntologyAnnotation_ROCrate_encoderDefinedTerm, a.TechnologyType), tryInclude("technologyPlatform", OntologyAnnotation_ROCrate_encoderDefinedTerm, a.TechnologyPlatform), tryIncludeSeq("performers", ROCrate_encoder_1, a.Performers), tryIncludeList("dataFiles", ROCrate_encoder_2, dataFiles), tryIncludeList("processSequence", (assayName = a.Identifier, (oa_5) => ROCrate_encoder_3(studyName, assayName, oa_5)), processes), tryIncludeSeq("comments", ROCrate_encoder_4, a.Comments), ["@context", context_jsonvalue]]));
+    return {
+        Encode(helpers_5) {
+            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_5)], values);
+            return helpers_5.encodeObject(arg);
+        },
+    };
 }
 
-export const Assay_ROCrate_decoder = object((get$) => {
+export const ROCrate_decoder = object((get$) => {
     let objectArg, arg_3, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_12, objectArg_5, arg_14, objectArg_6;
     const identifier = defaultArg((objectArg = get$.Optional, objectArg.Field("identifier", string)), createMissingIdentifier());
     const tables = map((arg_4) => {
         const a = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(arg_4);
         return a.Tables;
-    }, (arg_3 = list_2(Process_ROCrate_decoder), (objectArg_1 = get$.Optional, objectArg_1.Field("processSequence", arg_3))));
-    return new ArcAssay(identifier, unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", OntologyAnnotation_ROCrate_decoderPropertyValue))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", OntologyAnnotation_ROCrate_decoderDefinedTerm))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", OntologyAnnotation_ROCrate_decoderDefinedTerm))), unwrap(tables), void 0, unwrap((arg_12 = Decode_resizeArray(Person_ROCrate_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("performers", arg_12)))), unwrap((arg_14 = Decode_resizeArray(Comment_ROCrate_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("comments", arg_14)))));
+    }, (arg_3 = list_2(ROCrate_decoder_1), (objectArg_1 = get$.Optional, objectArg_1.Field("processSequence", arg_3))));
+    return new ArcAssay(identifier, unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", OntologyAnnotation_ROCrate_decoderPropertyValue))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", OntologyAnnotation_ROCrate_decoderDefinedTerm))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", OntologyAnnotation_ROCrate_decoderDefinedTerm))), unwrap(tables), undefined, unwrap((arg_12 = resizeArray(ROCrate_decoder_2), (objectArg_5 = get$.Optional, objectArg_5.Field("performers", arg_12)))), unwrap((arg_14 = resizeArray(ROCrate_decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("comments", arg_14)))));
 });
 
-export function Assay_ISAJson_encoder(studyName, idMap, a) {
+export function ISAJson_encoder(studyName, idMap, a) {
     const f = (a_1) => {
         let assayName;
         const fileName = Assay_fileNameFromIdentifier(a_1.Identifier);
         const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(a_1);
         const encodedUnits = tryIncludeList("unitCategories", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), getUnits(processes));
-        const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_1) => MaterialAttribute_ISAJson_encoder(idMap, value_1), getCharacteristics(processes));
-        const encodedMaterials = tryInclude("materials", (ps) => encoder_4(idMap, ps), Option_fromValueWithDefault(empty(), processes));
-        const encocedDataFiles = tryIncludeList("dataFiles", (oa_1) => Data_ISAJson_encoder(idMap, oa_1), getData(processes));
+        const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_1) => encoder_8(idMap, value_1), getCharacteristics(processes));
+        const encodedMaterials = tryInclude("materials", (ps) => encoder_9(idMap, ps), Option_fromValueWithDefault(empty(), processes));
+        const encocedDataFiles = tryIncludeList("dataFiles", (oa_1) => ISAJson_encoder_1(idMap, oa_1), getData(processes));
         const units = getUnits(processes);
-        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, [fileName])], tryInclude("@id", (value_5) => (new Json(0, [value_5])), Assay_ROCrate_genID(a_1)), tryInclude("measurementType", (oa_2) => OntologyAnnotation_ISAJson_encoder(idMap, oa_2), a_1.MeasurementType), tryInclude("technologyType", (oa_3) => OntologyAnnotation_ISAJson_encoder(idMap, oa_3), a_1.TechnologyType), tryInclude("technologyPlatform", (value_7) => (new Json(0, [value_7])), map(JsonTypes_composeTechnologyPlatform, a_1.TechnologyPlatform)), encocedDataFiles, encodedMaterials, encodedCharacteristics, encodedUnits, tryIncludeList("processSequence", (assayName = a_1.Identifier, (oa_4) => Process_ISAJson_encoder(studyName, assayName, idMap, oa_4)), processes), tryIncludeSeq("comments", (comment) => Comment_ISAJson_encoder(idMap, comment), a_1.Comments)]))]);
+        const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["filename", {
+            Encode(helpers) {
+                return helpers.encodeString(fileName);
+            },
+        }], tryInclude("@id", (value_5) => ({
+            Encode(helpers_1) {
+                return helpers_1.encodeString(value_5);
+            },
+        }), ROCrate_genID(a_1)), tryInclude("measurementType", (oa_2) => OntologyAnnotation_ISAJson_encoder(idMap, oa_2), a_1.MeasurementType), tryInclude("technologyType", (oa_3) => OntologyAnnotation_ISAJson_encoder(idMap, oa_3), a_1.TechnologyType), tryInclude("technologyPlatform", (value_7) => ({
+            Encode(helpers_2) {
+                return helpers_2.encodeString(value_7);
+            },
+        }), map(JsonTypes_composeTechnologyPlatform, a_1.TechnologyPlatform)), encocedDataFiles, encodedMaterials, encodedCharacteristics, encodedUnits, tryIncludeList("processSequence", (assayName = a_1.Identifier, (oa_4) => ISAJson_encoder_2(studyName, assayName, idMap, oa_4)), processes), tryIncludeSeq("comments", (comment) => ISAJson_encoder_3(idMap, comment), a_1.Comments)]));
+        return {
+            Encode(helpers_3) {
+                const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_3)], values);
+                return helpers_3.encodeObject(arg);
+            },
+        };
     };
     if (idMap != null) {
-        return encode(Assay_ROCrate_genID, f, a, idMap);
+        return encode(ROCrate_genID, f, a, idMap);
     }
     else {
         return f(a);
     }
 }
 
-export const Assay_ISAJson_allowedFields = ofArray(["@id", "filename", "measurementType", "technologyType", "technologyPlatform", "dataFiles", "materials", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
+export const ISAJson_allowedFields = ofArray(["@id", "filename", "measurementType", "technologyType", "technologyPlatform", "dataFiles", "materials", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
 
-export const Assay_ISAJson_decoder = Decode_objectNoAdditionalProperties(Assay_ISAJson_allowedFields, (get$) => {
+export const ISAJson_decoder = Decode_objectNoAdditionalProperties(ISAJson_allowedFields, (get$) => {
     let objectArg, arg_3, objectArg_1, objectArg_2, objectArg_3, arg_10, objectArg_4, arg_12, objectArg_5;
     const identifier = defaultArg(bind(Assay_tryIdentifierFromFileName, (objectArg = get$.Optional, objectArg.Field("filename", string))), createMissingIdentifier());
     const tables = map((arg_4) => {
         const a = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(arg_4);
         return a.Tables;
-    }, (arg_3 = list_2(Process_ISAJson_decoder), (objectArg_1 = get$.Optional, objectArg_1.Field("processSequence", arg_3))));
-    return new ArcAssay(identifier, unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", OntologyAnnotation_ISAJson_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", OntologyAnnotation_ISAJson_decoder))), unwrap((arg_10 = map_1(JsonTypes_decomposeTechnologyPlatform, string), (objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", arg_10)))), unwrap(tables), void 0, void 0, unwrap((arg_12 = Decode_resizeArray(Comment_ISAJson_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("comments", arg_12)))));
+    }, (arg_3 = list_2(ISAJson_decoder_1), (objectArg_1 = get$.Optional, objectArg_1.Field("processSequence", arg_3))));
+    return new ArcAssay(identifier, unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", OntologyAnnotation_ISAJson_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", OntologyAnnotation_ISAJson_decoder))), unwrap((arg_10 = map_2(JsonTypes_decomposeTechnologyPlatform, string), (objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", arg_10)))), unwrap(tables), undefined, undefined, unwrap((arg_12 = resizeArray(ISAJson_decoder_2), (objectArg_5 = get$.Optional, objectArg_5.Field("comments", arg_12)))));
 });
 
-export function ARCtrl_ArcAssay__ArcAssay_fromJsonString_Static_Z721C83C5(s) {
-    const matchValue = fromString(Assay_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_ArcAssay__ArcAssay_toJsonString_Static_71136F3F(spaces) {
-    return (obj) => {
-        const value = Assay_encoder(obj);
-        return toString(defaultSpaces(spaces), value);
-    };
-}
-
-export function ARCtrl_ArcAssay__ArcAssay_ToJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
-}
-
-export function ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C83C5(s) {
-    try {
-        const matchValue = fromString(decode(Assay_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_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F(spaces) {
-    return (obj) => toString(defaultArg(spaces, 0), encode_1(Assay_encoderCompressed, obj));
-}
-
-export function ARCtrl_ArcAssay__ArcAssay_ToCompressedJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(this$);
-}
-
-export function ARCtrl_ArcAssay__ArcAssay_fromROCrateJsonString_Static_Z721C83C5(s) {
-    const matchValue = fromString(Assay_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_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47(studyName, spaces) {
-    return (obj) => {
-        const value = Assay_ROCrate_encoder(studyName, obj);
-        return toString(defaultSpaces(spaces), value);
-    };
-}
-
-export function ARCtrl_ArcAssay__ArcAssay_ToROCrateJsonString_5CABCA47(this$, studyName, spaces) {
-    return ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47(unwrap(studyName), unwrap(spaces))(this$);
-}
-
-export function ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
-    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
-    return (obj) => {
-        const value = Assay_ISAJson_encoder(void 0, idMap, obj);
-        return toString(defaultSpaces(spaces), value);
-    };
-}
-
-export function ARCtrl_ArcAssay__ArcAssay_fromISAJsonString_Static_Z721C83C5(s) {
-    const matchValue = fromString(Assay_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_ArcAssay__ArcAssay_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
-    return ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
-}
-