@nfdi4plants/arctrl 2.0.0-beta.1 → 2.0.0-beta.8

package/Core/Process/FactorValue.js

@@ -2,7 +2,7 @@ import { Record, toString } from "../../fable_modules/fable-library-js.4.16.0/Ty
 import { unwrap, defaultArg, bind, map } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { record_type, option_type, string_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 import { Factor, Factor_$reflection } from "./Factor.js";
-import { Value_$reflection } from "./Value.js";
+import { Value_$reflection } from "../Value.js";
 import { OntologyAnnotation_$reflection } from "../OntologyAnnotation.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";
@@ -35,6 +35,15 @@ export class FactorValue extends Record {
         }, this$.Value);
         return (category == null) ? ((value == null) ? "" : ((value_2 = value, value_2))) : ((value == null) ? ((category_2 = category, (category_2 + ":") + "No Value")) : ((category_1 = category, (value_1 = value, (category_1 + ":") + value_1))));
     }
+    AlternateName() {
+        return void 0;
+    }
+    MeasurementMethod() {
+        return void 0;
+    }
+    Description() {
+        return void 0;
+    }
     GetCategory() {
         const this$ = this;
         return bind((f) => f.FactorType, this$.Category);
@@ -60,12 +69,12 @@ export function FactorValue_make(id, category, value, unit) {
     return new FactorValue(id, category, value, unit);
 }
 
-export function FactorValue_create_29259B2C(Id, Category, Value, Unit) {
+export function FactorValue_create_30BDC49(Id, Category, Value, Unit) {
     return FactorValue_make(Id, Category, Value, Unit);
 }
 
 export function FactorValue_get_empty() {
-    return FactorValue_create_29259B2C();
+    return FactorValue_create_30BDC49();
 }
 
 export function FactorValue__get_ValueText(this$) {
@@ -122,7 +131,7 @@ export function FactorValue_nameEqualsString(name, fv) {
     return FactorValue__get_NameText(fv) === name;
 }
 
-export function FactorValue_createAsPV(category, value, unit) {
-    return FactorValue_create_29259B2C(void 0, unwrap(map((c) => Factor.create(void 0, c), category)), unwrap(value), unwrap(unit));
+export function FactorValue_createAsPV(alternateName, measurementMethod, description, category, value, unit) {
+    return FactorValue_create_30BDC49(void 0, unwrap(map((c) => Factor.create(void 0, c), category)), unwrap(value), unwrap(unit));
 }
 

package/Core/Process/MaterialAttributeValue.js

@@ -2,7 +2,7 @@ import { Record, toString } from "../../fable_modules/fable-library-js.4.16.0/Ty
 import { unwrap, defaultArg, bind, map } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { MaterialAttribute__SetCategory_ZDED3A0F, MaterialAttribute_create_A220A8A, MaterialAttribute__MapCategory_658CFBF6, MaterialAttribute__get_TryNameText, MaterialAttribute_$reflection, MaterialAttribute__get_NameText } from "./MaterialAttribute.js";
 import { record_type, option_type, string_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
-import { Value_$reflection } from "./Value.js";
+import { Value_$reflection } from "../Value.js";
 import { OntologyAnnotation_$reflection } from "../OntologyAnnotation.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";
@@ -35,6 +35,15 @@ export class MaterialAttributeValue extends Record {
         }, this$.Value);
         return (category == null) ? ((value == null) ? "" : ((value_2 = value, value_2))) : ((value == null) ? ((category_2 = category, (category_2 + ":") + "No Value")) : ((category_1 = category, (value_1 = value, (category_1 + ":") + value_1))));
     }
+    AlternateName() {
+        return void 0;
+    }
+    MeasurementMethod() {
+        return void 0;
+    }
+    Description() {
+        return void 0;
+    }
     GetCategory() {
         const this$ = this;
         return bind((x) => x.CharacteristicType, this$.Category);
@@ -60,12 +69,12 @@ export function MaterialAttributeValue_make(id, category, value, unit) {
     return new MaterialAttributeValue(id, category, value, unit);
 }
 
-export function MaterialAttributeValue_create_BE8DE56(Id, Category, Value, Unit) {
+export function MaterialAttributeValue_create_ZE1D108D(Id, Category, Value, Unit) {
     return MaterialAttributeValue_make(Id, Category, Value, Unit);
 }
 
 export function MaterialAttributeValue_get_empty() {
-    return MaterialAttributeValue_create_BE8DE56();
+    return MaterialAttributeValue_create_ZE1D108D();
 }
 
 /**
@@ -139,7 +148,7 @@ export function MaterialAttributeValue_nameEqualsString(name, mv) {
     return MaterialAttributeValue__get_NameText(mv) === name;
 }
 
-export function MaterialAttributeValue_createAsPV(category, value, unit) {
-    return MaterialAttributeValue_create_BE8DE56(void 0, unwrap(map((c) => MaterialAttribute_create_A220A8A(void 0, c), category)), unwrap(value), unwrap(unit));
+export function MaterialAttributeValue_createAsPV(alternateName, measurementMethod, description, category, value, unit) {
+    return MaterialAttributeValue_create_ZE1D108D(void 0, unwrap(map((c) => MaterialAttribute_create_A220A8A(void 0, c), category)), unwrap(value), unwrap(unit));
 }
 

package/Core/Process/ProcessParameterValue.js

@@ -4,7 +4,7 @@ import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/Stri
 import { ProtocolParameter_$reflection, ProtocolParameter } from "./ProtocolParameter.js";
 import { Record, toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
 import { record_type, option_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
-import { Value_$reflection } from "./Value.js";
+import { Value_$reflection } from "../Value.js";
 import { OntologyAnnotation_$reflection } from "../OntologyAnnotation.js";
 
 export class ProcessParameterValue extends Record {
@@ -79,7 +79,7 @@ export class ProcessParameterValue extends Record {
     static getCategory(pv) {
         return pv.Category;
     }
-    static createAsPV(category, value, unit) {
+    static createAsPV(alternateName, measurementMethod, description, category, value, unit) {
         const category_1 = map((c) => ProtocolParameter.create(void 0, c), category);
         return ProcessParameterValue.create(unwrap(category_1), unwrap(value), unwrap(unit));
     }
@@ -103,6 +103,15 @@ export class ProcessParameterValue extends Record {
         }, this$.Value);
         return (category == null) ? ((value == null) ? "" : ((value_2 = value, value_2))) : ((value == null) ? ((category_2 = category, (category_2 + ":") + "No Value")) : ((category_1 = category, (value_1 = value, (category_1 + ":") + value_1))));
     }
+    AlternateName() {
+        return void 0;
+    }
+    MeasurementMethod() {
+        return void 0;
+    }
+    Description() {
+        return void 0;
+    }
     GetCategory() {
         const this$ = this;
         return bind((p) => p.ParameterName, this$.Category);

package/Core/Table/CompositeCell.js

@@ -54,33 +54,19 @@ export class CompositeCell extends Union {
     }
     ToUnitizedCell() {
         const this$ = this;
-        switch (this$.tag) {
-            case 1:
-                return new CompositeCell(2, ["", OntologyAnnotation.create(this$.fields[0])]);
-            case 0:
-                return new CompositeCell(2, ["", this$.fields[0]]);
-            case 3:
-                throw new Error("Data cell cannot be converted to Unitized cell.");
-            default:
-                return this$;
-        }
+        return (this$.tag === 1) ? (new CompositeCell(2, ["", OntologyAnnotation.create(this$.fields[0])])) : ((this$.tag === 0) ? (new CompositeCell(2, ["", this$.fields[0]])) : ((this$.tag === 3) ? (new CompositeCell(2, ["", OntologyAnnotation.create(this$.fields[0].NameText)])) : this$));
     }
     ToTermCell() {
         const this$ = this;
-        switch (this$.tag) {
-            case 2:
-                return new CompositeCell(0, [this$.fields[1]]);
-            case 1:
-                return new CompositeCell(0, [OntologyAnnotation.create(this$.fields[0])]);
-            case 3:
-                throw new Error("Data cell cannot be converted to Term cell.");
-            default:
-                return this$;
-        }
+        return (this$.tag === 2) ? (new CompositeCell(0, [this$.fields[1]])) : ((this$.tag === 1) ? (new CompositeCell(0, [OntologyAnnotation.create(this$.fields[0])])) : ((this$.tag === 3) ? (new CompositeCell(0, [new OntologyAnnotation(this$.fields[0].NameText)])) : this$));
     }
     ToFreeTextCell() {
         const this$ = this;
-        return (this$.tag === 0) ? (new CompositeCell(1, [this$.fields[0].NameText])) : ((this$.tag === 2) ? (new CompositeCell(1, [this$.fields[1].NameText])) : ((this$.tag === 3) ? (new CompositeCell(1, [defaultArg(this$.fields[0].Name, "")])) : this$));
+        return (this$.tag === 0) ? (new CompositeCell(1, [this$.fields[0].NameText])) : ((this$.tag === 2) ? (new CompositeCell(1, [this$.fields[1].NameText])) : ((this$.tag === 3) ? (new CompositeCell(1, [this$.fields[0].NameText])) : this$));
+    }
+    ToDataCell() {
+        const this$ = this;
+        return (this$.tag === 1) ? CompositeCell.createDataFromString(this$.fields[0]) : ((this$.tag === 0) ? CompositeCell.createDataFromString(this$.fields[0].NameText) : ((this$.tag === 3) ? this$ : CompositeCell.createDataFromString(this$.fields[1].NameText)));
     }
     get AsUnitized() {
         const this$ = this;
@@ -159,8 +145,11 @@ export class CompositeCell extends Union {
                 return CompositeCell.createUnitized(this$.fields[0], oa);
             case 1:
                 return CompositeCell.createFreeText(oa.NameText);
-            case 3:
-                throw new Error("Data cell cannot be updated with OntologyAnnotation.");
+            case 3: {
+                const d = this$.fields[0];
+                d.Name = oa.NameText;
+                return new CompositeCell(3, [d]);
+            }
             default:
                 return CompositeCell.createTerm(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);

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

@@ -1,13 +1,13 @@
-import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { unwrap, map } from "../../fable_modules/fable-library-js.4.16.0/Option.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";
-import { tryInclude } from "../Encode.js";
-import { context_jsonvalue } from "../context/rocrate/property_value_context.js";
-import { string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
-import { AnnotationValue_decoder } from "../OntologyAnnotation.js";
-import { Value } from "../../Core/Process/Value.js";
+import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { unwrap, map } from "../fable_modules/fable-library-js.4.16.0/Option.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";
+import { tryInclude } from "./Encode.js";
+import { context_jsonvalue } from "./context/rocrate/property_value_context.js";
+import { string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { OntologyAnnotation } from "../Core/OntologyAnnotation.js";
+import { AnnotationValue_decoder } from "./OntologyAnnotation.js";
+import { Value } from "../Core/Value.js";
 
 export function genID(p) {
     const matchValue = p.GetCategory();
@@ -97,19 +97,28 @@ export function encoder(pv) {
         else {
             return [tupledArg[0], v_1];
         }
-    }, ofArray([["@id", new Json(0, [genID(pv)])], ["@type", new Json(0, ["PropertyValue"])], ["additionalType", new Json(0, [pv.GetAdditionalType()])], tryInclude("category", (value_11) => (new Json(0, [value_11])), patternInput[0]), tryInclude("categoryCode", (value_13) => (new Json(0, [value_13])), patternInput[1]), tryInclude("value", (x) => x, patternInput_1[0]), tryInclude("valueCode", (x_1) => x_1, patternInput_1[1]), tryInclude("unit", (value_15) => (new Json(0, [value_15])), patternInput_2[0]), tryInclude("unitCode", (value_17) => (new Json(0, [value_17])), patternInput_2[1]), ["@context", context_jsonvalue]]))]);
+    }, ofArray([["@id", new Json(0, [genID(pv)])], ["@type", new Json(0, ["PropertyValue"])], ["additionalType", new Json(0, [pv.GetAdditionalType()])], tryInclude("alternateName", (value_11) => (new Json(0, [value_11])), pv.AlternateName()), tryInclude("measurementMethod", (value_13) => (new Json(0, [value_13])), pv.MeasurementMethod()), tryInclude("description", (value_15) => (new Json(0, [value_15])), pv.Description()), tryInclude("category", (value_17) => (new Json(0, [value_17])), patternInput[0]), tryInclude("categoryCode", (value_19) => (new Json(0, [value_19])), patternInput[1]), tryInclude("value", (x) => x, patternInput_1[0]), tryInclude("valueCode", (x_1) => x_1, patternInput_1[1]), tryInclude("unit", (value_21) => (new Json(0, [value_21])), patternInput_2[0]), tryInclude("unitCode", (value_23) => (new Json(0, [value_23])), patternInput_2[1]), ["@context", context_jsonvalue]]))]);
 }
 
 export function decoder(create) {
     return object((get$) => {
-        let value, objectArg_4, code_4, objectArg_5;
+        let value, objectArg_7, code_4, objectArg_8;
+        let alternateName;
+        const objectArg = get$.Optional;
+        alternateName = objectArg.Field("alternateName", string);
+        let measurementMethod;
+        const objectArg_1 = get$.Optional;
+        measurementMethod = objectArg_1.Field("measurementMethod", string);
+        let description;
+        const objectArg_2 = get$.Optional;
+        description = objectArg_2.Field("description", string);
         let category;
         let name;
-        const objectArg = get$.Optional;
-        name = objectArg.Field("category", string);
+        const objectArg_3 = get$.Optional;
+        name = objectArg_3.Field("category", string);
         let code;
-        const objectArg_1 = get$.Optional;
-        code = objectArg_1.Field("categoryCode", string);
+        const objectArg_4 = get$.Optional;
+        code = objectArg_4.Field("categoryCode", string);
         let matchResult, code_1;
         if (name == null) {
             if (code != null) {
@@ -161,11 +170,11 @@ export function decoder(create) {
         }
         let unit;
         let name_1;
-        const objectArg_2 = get$.Optional;
-        name_1 = objectArg_2.Field("unit", string);
+        const objectArg_5 = get$.Optional;
+        name_1 = objectArg_5.Field("unit", string);
         let code_2;
-        const objectArg_3 = get$.Optional;
-        code_2 = objectArg_3.Field("unitCode", string);
+        const objectArg_6 = get$.Optional;
+        code_2 = objectArg_6.Field("unitCode", string);
         let matchResult_1, code_3;
         if (name_1 == null) {
             if (code_2 != null) {
@@ -215,7 +224,7 @@ export function decoder(create) {
                     throw new Error(`Error while decoding unit (name:${name_1}, code:${code_3}): ${err_3}`);
                 }
         }
-        return create(category, (value = ((objectArg_4 = get$.Optional, objectArg_4.Field("value", AnnotationValue_decoder))), (code_4 = ((objectArg_5 = get$.Optional, objectArg_5.Field("valueCode", string))), ((value == null) && (code_4 == null)) ? void 0 : (() => {
+        return create(alternateName, measurementMethod, description, category, (value = ((objectArg_7 = get$.Optional, objectArg_7.Field("value", AnnotationValue_decoder))), (code_4 = ((objectArg_8 = get$.Optional, objectArg_8.Field("valueCode", string))), ((value == null) && (code_4 == null)) ? void 0 : (() => {
             try {
                 return Value.fromOptions(value, void 0, code_4);
             }