@nfdi4plants/arctrl 2.0.0-beta.2 → 2.0.0

package/Core/Table/CompositeHeader.js

@@ -2,7 +2,6 @@ import { map } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
 import { union_type, string_type, getUnionCases, name } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 import { Union, toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
 import { ActivePatterns_$007CTermColumn$007C_$007C, Pattern_CommentPattern, Pattern_OutputPattern, Pattern_InputPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseIOTypeHeader } from "../Helper/Regex.js";
-import { equals } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
 import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../OntologyAnnotation.js";
 
@@ -98,79 +97,6 @@ export class IOType extends Union {
             return IOType.ofString(s);
         }
     }
-    GetUITooltip() {
-        const this$ = this;
-        return IOType.getUITooltip(this$);
-    }
-    static getUITooltip(iotype) {
-        let matchResult;
-        if (typeof iotype === "string") {
-            if (equals(iotype, "Source")) {
-                matchResult = 0;
-            }
-            else if (equals(iotype, "Sample")) {
-                matchResult = 1;
-            }
-            else if (equals(iotype, "RawDataFile")) {
-                matchResult = 2;
-            }
-            else if (equals(iotype, "DerivedDataFile")) {
-                matchResult = 3;
-            }
-            else if (equals(iotype, "ImageFile")) {
-                matchResult = 4;
-            }
-            else if (equals(iotype, "Material")) {
-                matchResult = 5;
-            }
-            else if (equals(iotype, "FreeText")) {
-                matchResult = 6;
-            }
-            else {
-                matchResult = 7;
-            }
-        }
-        else {
-            switch (iotype.tag) {
-                case 1: {
-                    matchResult = 1;
-                    break;
-                }
-                case 2: {
-                    matchResult = 2;
-                    break;
-                }
-                case 3: {
-                    matchResult = 5;
-                    break;
-                }
-                case 4: {
-                    matchResult = 6;
-                    break;
-                }
-                default:
-                    matchResult = 0;
-            }
-        }
-        switch (matchResult) {
-            case 0:
-                return "The source value must be a unique identifier for an organism or a sample.";
-            case 1:
-                return "The Sample Name column describes specifc laboratory samples with a unique identifier.";
-            case 2:
-                return "The Raw Data File column defines untransformed and unprocessed data files.";
-            case 3:
-                return "The Derived Data File column defines transformed and/or processed data files.";
-            case 4:
-                return "Placeholder";
-            case 5:
-                return "Placeholder";
-            case 6:
-                return "Placeholder";
-            default:
-                throw new Error(`Unable to parse combination to existing IOType: \`${iotype}\``);
-        }
-    }
     static source() {
         return new IOType(0, []);
     }
@@ -543,157 +469,21 @@ export class CompositeHeader extends Union {
                 return void 0;
         }
     }
-    GetUITooltip() {
+    get IsUnique() {
         const this$ = this;
-        return CompositeHeader.getUITooltip(this$);
-    }
-    static getUITooltip(header) {
-        let matchResult;
-        if (typeof header === "string") {
-            if (equals(header, "Component")) {
-                matchResult = 0;
-            }
-            else if (equals(header, "Characteristic")) {
-                matchResult = 1;
-            }
-            else if (equals(header, "Factor")) {
-                matchResult = 2;
-            }
-            else if (equals(header, "Parameter")) {
-                matchResult = 3;
-            }
-            else if (equals(header, "ProtocolType")) {
-                matchResult = 4;
-            }
-            else if (equals(header, "ProtocolDescription")) {
-                matchResult = 5;
-            }
-            else if (equals(header, "ProtocolUri")) {
-                matchResult = 6;
-            }
-            else if (equals(header, "ProtocolVersion")) {
-                matchResult = 7;
-            }
-            else if (equals(header, "ProtocolREF")) {
-                matchResult = 8;
-            }
-            else if (equals(header, "Performer")) {
-                matchResult = 9;
-            }
-            else if (equals(header, "Date")) {
-                matchResult = 10;
-            }
-            else if (equals(header, "Input")) {
-                matchResult = 11;
-            }
-            else if (equals(header, "Output")) {
-                matchResult = 12;
-            }
-            else if (equals(header, "FreeText")) {
-                matchResult = 13;
-            }
-            else if (equals(header, "Comment")) {
-                matchResult = 14;
-            }
-            else {
-                matchResult = 15;
-            }
-        }
-        else {
-            switch (header.tag) {
-                case 1: {
-                    matchResult = 1;
-                    break;
-                }
-                case 2: {
-                    matchResult = 2;
-                    break;
-                }
-                case 3: {
-                    matchResult = 3;
-                    break;
-                }
-                case 4: {
-                    matchResult = 4;
-                    break;
-                }
-                case 5: {
-                    matchResult = 5;
-                    break;
-                }
-                case 6: {
-                    matchResult = 6;
-                    break;
-                }
-                case 7: {
-                    matchResult = 7;
-                    break;
-                }
-                case 8: {
-                    matchResult = 8;
-                    break;
-                }
-                case 9: {
-                    matchResult = 9;
-                    break;
-                }
-                case 10: {
-                    matchResult = 10;
-                    break;
-                }
-                case 11: {
-                    matchResult = 11;
-                    break;
-                }
-                case 12: {
-                    matchResult = 12;
-                    break;
-                }
-                case 13: {
-                    matchResult = 13;
-                    break;
-                }
-                case 14: {
-                    matchResult = 14;
-                    break;
-                }
-                default:
-                    matchResult = 0;
-            }
-        }
-        switch (matchResult) {
-            case 0:
-                return "Component columns are used to describe physical components of a experiment, e.g. instrument names, software names, and reagents names.";
-            case 1:
-                return "Characteristic columns are used for study descriptions and describe inherent properties of the source material, e.g. a certain strain or organism part.";
-            case 2:
-                return "Use Factor columns to describe independent variables that result in a specific output of your experiment, e.g. the light intensity under which an organism was grown.";
-            case 3:
-                return "Parameter columns describe steps in your experimental workflow, e.g. the centrifugation time or the temperature used for your assay.";
+        switch (this$.tag) {
             case 4:
-                return "Defines the protocol type according to your preferred endpoint repository.";
+            case 8:
             case 5:
-                return "Describe the protocol in free text.";
             case 6:
-                return "Web or local address where the in-depth protocol is stored.";
             case 7:
-                return "Defines the protocol version.";
-            case 8:
-                return "Defines the protocol name.";
             case 9:
-                return "Defines the protocol performer.";
             case 10:
-                return "Defines the date the protocol was performed.";
             case 11:
-                return "Only one input column per table. E.g. experimental samples or files.";
             case 12:
-                return "Only one output column per table. E.g. experimental samples or files.";
-            case 13:
-                return "Placeholder";
-            case 14:
-                return "Comment";
+                return true;
             default:
-                throw new Error(`Unable to parse combination to existing CompositeHeader: \`${header}\``);
+                return false;
         }
     }
     static component(oa) {

package/Core/{Process/Value.js → Value.js}

@@ -1,11 +1,11 @@
-import { tryParse } from "../../fable_modules/fable-library-js.4.16.0/Int32.js";
-import { Union, toString, FSharpRef } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
-import { tryParse as tryParse_1 } from "../../fable_modules/fable-library-js.4.16.0/Double.js";
-import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../OntologyAnnotation.js";
-import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
-import { int32ToString } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
-import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
-import { union_type, string_type, float64_type, int32_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
+import { tryParse } from "../fable_modules/fable-library-js.4.16.0/Int32.js";
+import { Union, toString, FSharpRef } from "../fable_modules/fable-library-js.4.16.0/Types.js";
+import { tryParse as tryParse_1 } from "../fable_modules/fable-library-js.4.16.0/Double.js";
+import { OntologyAnnotation_$reflection, OntologyAnnotation } from "./OntologyAnnotation.js";
+import { defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { int32ToString } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { printf, toText } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { union_type, string_type, float64_type, int32_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class Value extends Union {
     constructor(tag, fields) {
@@ -132,6 +132,6 @@ export class Value extends Union {
 }
 
 export function Value_$reflection() {
-    return union_type("ARCtrl.Process.Value", [], Value, () => [[["Item", OntologyAnnotation_$reflection()]], [["Item", int32_type]], [["Item", float64_type]], [["Item", string_type]]]);
+    return union_type("ARCtrl.Value", [], Value, () => [[["Item", OntologyAnnotation_$reflection()]], [["Item", int32_type]], [["Item", float64_type]], [["Item", string_type]]]);
 }
 

package/Json/Assay.js

@@ -3,6 +3,7 @@ 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 { 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";
@@ -15,11 +16,11 @@ import { Assay_tryIdentifierFromFileName, createMissingIdentifier, Assay_fileNam
 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 "./Process/Data.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 { context_jsonvalue } from "./context/rocrate/isa_assay_context.js";
 import { MaterialAttribute_ISAJson_encoder } from "./Process/MaterialAttribute.js";
-import { encoder as encoder_3 } from "./Process/AssayMaterials.js";
+import { encoder as encoder_4 } 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";
@@ -35,12 +36,12 @@ export function Assay_encoder(assay) {
         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", ArcTable_encoder, assay.Tables), tryIncludeSeq("Performers", Person_encoder, assay.Performers), tryIncludeSeq("Comments", Comment_encoder, assay.Comments)]))]);
+    }, 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)]))]);
 }
 
 export const Assay_decoder = object((get$) => {
-    let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6;
-    return ArcAssay.create((objectArg = get$.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)))), void 0, unwrap((arg_11 = Decode_resizeArray(Person_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Performers", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Comment_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Comments", arg_13)))));
+    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)))));
 });
 
 export function Assay_encoderCompressed(stringTable, oaTable, cellTable, assay) {
@@ -52,13 +53,13 @@ export function Assay_encoderCompressed(stringTable, oaTable, cellTable, assay)
         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), tryIncludeSeq("Performers", Person_encoder, assay.Performers), tryIncludeSeq("Comments", Comment_encoder, assay.Comments)]))]);
+    }, 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 Assay_decoderCompressed(stringTable, oaTable, cellTable) {
     return object((get$) => {
-        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6;
-        return ArcAssay.create((objectArg = get$.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)))), void 0, unwrap((arg_11 = Decode_resizeArray(Person_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Performers", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Comment_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Comments", arg_13)))));
+        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)))));
     });
 }
 
@@ -105,7 +106,7 @@ export function Assay_ISAJson_encoder(studyName, idMap, a) {
         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_3(idMap, ps), Option_fromValueWithDefault(empty(), 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 units = getUnits(processes);
         return new Json(5, [choose((tupledArg) => {

package/Json/{Process/Data.js → Data.js}

@@ -1,21 +1,21 @@
-import { 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, tryIncludeSeq, tryInclude } from "../Encode.js";
+import { 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, tryIncludeSeq, tryInclude } from "./Encode.js";
 import { DataFile_ROCrate_decoder, DataFile_ROCrate_encoder, DataFile_ISAJson_decoder, DataFile_ISAJson_encoder } from "./DataFile.js";
-import { Comment_ISAJson_decoder, Comment_ISAJson_encoder, Comment_ROCrate_decoder, Comment_ROCrate_encoder, Comment_decoder, Comment_encoder } from "../Comment.js";
-import { string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { Data } from "../../Core/Data.js";
-import { defaultArg, unwrap } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
-import { Decode_objectNoAdditionalProperties, Decode_resizeArray, Decode_uri } 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 { list as list_1 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
-import { context_jsonvalue } from "../context/rocrate/isa_data_context.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 { Comment_ISAJson_decoder, Comment_ISAJson_encoder, Comment_ROCrate_decoder, Comment_ROCrate_encoder, Comment_decoder, Comment_encoder } from "./Comment.js";
+import { string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { Data } from "../Core/Data.js";
+import { defaultArg, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { Decode_objectNoAdditionalProperties, Decode_resizeArray, Decode_uri } 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 { list as list_1 } from "../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
+import { context_jsonvalue } from "./context/rocrate/isa_data_context.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";
 
 export function Data_encoder(d) {
     return new Json(5, [choose((tupledArg) => {

package/Json/{Process/DataFile.js → DataFile.js}

@@ -1,12 +1,12 @@
-import { ErrorReason$1, Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { string } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { FSharpResult$2 } from "../../fable_modules/fable-library-js.4.16.0/Result.js";
-import { DataFile } from "../../Core/DataFile.js";
-import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
-import { 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 { defaultSpaces } from "../Encode.js";
-import { unwrap } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { ErrorReason$1, Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { string } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { FSharpResult$2 } from "../fable_modules/fable-library-js.4.16.0/Result.js";
+import { DataFile } from "../Core/DataFile.js";
+import { fromString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { 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 { defaultSpaces } from "./Encode.js";
+import { unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 
 export function DataFile_ROCrate_encoder(value) {
     switch (value.tag) {

package/Json/DataMap/DataContext.js

@@ -0,0 +1,30 @@
+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 { Data_decoder, Data_encoder } from "../Data.js";
+import { tryInclude } from "../Encode.js";
+import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "../OntologyAnnotation.js";
+import { DataContext_$ctor_Z780A8A2A, DataContext__get_Label, DataContext__get_GeneratedBy, DataContext__get_Description, DataContext__get_ObjectType, DataContext__get_Unit, DataContext__get_Explication } from "../../Core/DataContext.js";
+import { string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { unwrap } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+
+export function encoder(dc) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([["data", Data_encoder(dc)], tryInclude("explication", OntologyAnnotation_encoder, DataContext__get_Explication(dc)), tryInclude("unit", OntologyAnnotation_encoder, DataContext__get_Unit(dc)), tryInclude("objectType", OntologyAnnotation_encoder, DataContext__get_ObjectType(dc)), tryInclude("description", (value) => (new Json(0, [value])), DataContext__get_Description(dc)), tryInclude("generatedBy", (value_2) => (new Json(0, [value_2])), DataContext__get_GeneratedBy(dc)), tryInclude("label", (value_4) => (new Json(0, [value_4])), DataContext__get_Label(dc))]))]);
+}
+
+export const decoder = object((get$) => {
+    let objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6;
+    let data;
+    const objectArg = get$.Required;
+    data = objectArg.Field("data", Data_decoder);
+    return DataContext_$ctor_Z780A8A2A(unwrap(data.ID), unwrap(data.Name), unwrap(data.DataType), unwrap(data.Format), unwrap(data.SelectorFormat), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("explication", OntologyAnnotation_decoder))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("unit", OntologyAnnotation_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("objectType", OntologyAnnotation_decoder))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("label", string))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("description", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("generatedBy", string))), data.Comments);
+});
+

package/Json/DataMap/DataMap.js

@@ -0,0 +1,25 @@
+import { seq } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
+import { map } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { decoder as decoder_1, encoder as encoder_1 } from "./DataContext.js";
+import { DataMap_$ctor_4E3220A7, DataMap__get_DataContexts } from "../../Core/DataMap.js";
+import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { Decode_resizeArray } from "../Decode.js";
+
+export function encoder(dm) {
+    return new Json(5, [[["dataContexts", seq(map(encoder_1, DataMap__get_DataContexts(dm)))]]]);
+}
+
+export const decoder = object((get$) => {
+    let arg_1, objectArg;
+    return DataMap_$ctor_4E3220A7((arg_1 = Decode_resizeArray(decoder_1), (objectArg = get$.Required, objectArg.Field("dataContexts", arg_1))));
+});
+
+export function encoderCompressed(stringTable, oaTable, cellTable, dm) {
+    return encoder(dm);
+}
+
+export function decoderCompressed(stringTable, oaTable, cellTable) {
+    return decoder;
+}
+

package/Json/Encode.js

@@ -1,6 +1,6 @@
 import { defaultArg, value as value_2 } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { map, isEmpty } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { append, map, isEmpty } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { list as list_1, seq } from "../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
 import { item, map as map_1 } from "../fable_modules/fable-library-js.4.16.0/Array.js";
 import { map as map_2, isEmpty as isEmpty_1 } from "../fable_modules/fable-library-js.4.16.0/List.js";
@@ -43,3 +43,12 @@ export function dateTime(d) {
     return new Json(0, [item(0, toString(d, "O", {}).split("+"))]);
 }
 
+export function addPropertyToObject(name, value, obj) {
+    if (obj.tag === 5) {
+        return new Json(5, [append(obj.fields[0], [[name, value]])]);
+    }
+    else {
+        throw new Error("Expected object");
+    }
+}
+

package/Json/Process/Component.js

@@ -1,4 +1,4 @@
-import { genID, decoder as decoder_1, encoder } from "./PropertyValue.js";
+import { genID, decoder as decoder_1, encoder } from "../PropertyValue.js";
 import { Component, Component_decomposeName_Z721C83C5, Component__get_ComponentName, Component_createAsPV } from "../../Core/Process/Component.js";
 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";

package/Json/Process/FactorValue.js

@@ -1,4 +1,4 @@
-import { genID, decoder as decoder_1, encoder } from "./PropertyValue.js";
+import { genID, decoder as decoder_1, encoder } from "../PropertyValue.js";
 import { FactorValue, FactorValue_createAsPV } from "../../Core/Process/FactorValue.js";
 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";

package/Json/Process/MaterialAttributeValue.js

@@ -1,4 +1,4 @@
-import { genID, decoder as decoder_1, encoder } from "./PropertyValue.js";
+import { genID, decoder as decoder_1, encoder } from "../PropertyValue.js";
 import { MaterialAttributeValue, MaterialAttributeValue_createAsPV } from "../../Core/Process/MaterialAttributeValue.js";
 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";

package/Json/Process/ProcessInput.js

@@ -1,5 +1,5 @@
 import { Sample_ISAJson_decoder, Sample_ISAJson_encoder, Sample_ROCrate_decoder, Sample_ROCrate_encoder } from "./Sample.js";
-import { Data_ISAJson_decoder, Data_ISAJson_encoder, Data_ROCrate_decoder, Data_ROCrate_encoder } from "./Data.js";
+import { Data_ISAJson_decoder, Data_ISAJson_encoder, Data_ROCrate_decoder, Data_ROCrate_encoder } from "../Data.js";
 import { Material_ISAJson_decoder, Material_ISAJson_encoder, Material_ROCrate_decoder, Material_ROCrate_encoder } from "./Material.js";
 import { Source_ISAJson_decoder, Source_ISAJson_encoder, Source_ROCrate_decoder, Source_ROCrate_encoder } from "./Source.js";
 import { map, oneOf } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";

package/Json/Process/ProcessOutput.js

@@ -1,4 +1,4 @@
-import { Data_ISAJson_decoder, Data_ISAJson_encoder, Data_ROCrate_decoder, Data_ROCrate_encoder } from "./Data.js";
+import { Data_ISAJson_decoder, Data_ISAJson_encoder, Data_ROCrate_decoder, Data_ROCrate_encoder } from "../Data.js";
 import { Material_ISAJson_decoder, Material_ISAJson_encoder, Material_ROCrate_decoder, Material_ROCrate_encoder } from "./Material.js";
 import { Sample_ISAJson_decoder, Sample_ISAJson_encoder, Sample_ROCrate_decoder, Sample_ROCrate_encoder } from "./Sample.js";
 import { map, oneOf } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";

package/Json/Process/ProcessParameterValue.js

@@ -1,4 +1,4 @@
-import { decoder as decoder_1, encoder } from "./PropertyValue.js";
+import { decoder as decoder_1, encoder } from "../PropertyValue.js";
 import { ProcessParameterValue } from "../../Core/Process/ProcessParameterValue.js";
 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";
@@ -15,7 +15,7 @@ import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode
 
 export const ProcessParameterValue_ROCrate_encoder = encoder;
 
-export const ProcessParameterValue_ROCrate_decoder = decoder_1((category, value, unit) => ProcessParameterValue.createAsPV(category, value, unit));
+export const ProcessParameterValue_ROCrate_decoder = decoder_1((alternateName, measurementMethod, description, category, value, unit) => ProcessParameterValue.createAsPV(alternateName, measurementMethod, description, category, value, unit));
 
 export function ProcessParameterValue_ISAJson_genID(oa) {
     throw new Error("Not implemented");

package/Json/Process/Value.js

@@ -1,7 +1,7 @@
 import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
 import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder } from "../OntologyAnnotation.js";
 import { string, float, int, map, oneOf } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { Value } from "../../Core/Process/Value.js";
+import { Value } from "../../Core/Value.js";
 import { ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
 import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
 import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
@@ -23,7 +23,7 @@ export function Value_ISAJson_encoder(idMap, value) {
 
 export const Value_ISAJson_decoder = oneOf(ofArray([map((Item) => (new Value(1, [Item])), int), map((Item_1) => (new Value(2, [Item_1])), float), map((Item_2) => (new Value(0, [Item_2])), OntologyAnnotation_ISAJson_decoder), map((Item_3) => (new Value(3, [Item_3])), string)]));
 
-export function ARCtrl_Process_Value__Value_fromISAJsonString_Static_Z721C83C5(s) {
+export function ARCtrl_Value__Value_fromISAJsonString_Static_Z721C83C5(s) {
     const matchValue = fromString(Value_ISAJson_decoder, s);
     if (matchValue.tag === 1) {
         throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
@@ -33,7 +33,7 @@ export function ARCtrl_Process_Value__Value_fromISAJsonString_Static_Z721C83C5(s
     }
 }
 
-export function ARCtrl_Process_Value__Value_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Value__Value_toISAJsonString_Static_71136F3F(spaces) {
     return (v) => {
         const value = Value_ISAJson_encoder(void 0, v);
         return toString(defaultSpaces(spaces), value);