@nfdi4plants/arctrl 2.0.0-alpha.7 → 2.0.0-beta.1

package/Json/Process/MaterialAttribute.js

@@ -1,17 +1,28 @@
-import { singleton, choose } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_genID } from "../OntologyAnnotation.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 { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
 import { defaultSpaces, tryInclude } from "../Encode.js";
-import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder } from "../OntologyAnnotation.js";
+import { encode } from "../IDTable.js";
 import { object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { MaterialAttribute } from "../../Core/Process/MaterialAttribute.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 { unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { unwrap } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 
-export function MaterialAttribute_ISAJson_encoder(value) {
-    return new Json(5, [choose((tupledArg) => {
+export function MaterialAttribute_ISAJson_genID(m) {
+    const matchValue = m.CharacteristicType;
+    if (matchValue == null) {
+        return "#EmptyFactor";
+    }
+    else {
+        return `#MaterialAttribute/${OntologyAnnotation_ROCrate_genID(matchValue)}`;
+    }
+}
+
+export function MaterialAttribute_ISAJson_encoder(idMap, value) {
+    const f = (value_1) => (new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
         if (equals(v, new Json(3, []))) {
             return void 0;
@@ -19,7 +30,13 @@ export function MaterialAttribute_ISAJson_encoder(value) {
         else {
             return [tupledArg[0], v];
         }
-    }, singleton(tryInclude("characteristicType", OntologyAnnotation_ISAJson_encoder, value.CharacteristicType)))]);
+    }, ofArray([tryInclude("@id", (value_2) => (new Json(0, [value_2])), MaterialAttribute_ISAJson_genID(value_1)), tryInclude("characteristicType", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), value_1.CharacteristicType)]))]));
+    if (idMap != null) {
+        return encode(MaterialAttribute_ISAJson_genID, f, value, idMap);
+    }
+    else {
+        return f(value);
+    }
 }
 
 export const MaterialAttribute_ISAJson_decoder = object((get$) => {
@@ -37,14 +54,15 @@ export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_fromISAJsonS
     }
 }
 
-export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (v) => {
-        const value = MaterialAttribute_ISAJson_encoder(v);
+        const value = MaterialAttribute_ISAJson_encoder(idMap, v);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
-export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_ToJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Process_MaterialAttribute__MaterialAttribute_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_ToJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Process_MaterialAttribute__MaterialAttribute_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 

package/Json/Process/MaterialAttributeValue.js

@@ -1,4 +1,4 @@
-import { 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";
@@ -7,19 +7,24 @@ import { defaultSpaces, tryInclude } from "../Encode.js";
 import { MaterialAttribute_ISAJson_decoder, MaterialAttribute_ISAJson_encoder } from "./MaterialAttribute.js";
 import { Value_ISAJson_decoder, Value_ISAJson_encoder } from "./Value.js";
 import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder } from "../OntologyAnnotation.js";
+import { encode } from "../IDTable.js";
 import { object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { Decode_uri } from "../Decode.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 { unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { unwrap } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 
 export const MaterialAttributeValue_ROCrate_encoder = encoder;
 
 export const MaterialAttributeValue_ROCrate_decoder = decoder_1(MaterialAttributeValue_createAsPV);
 
-export function MaterialAttributeValue_ISAJson_encoder(oa) {
-    return new Json(5, [choose((tupledArg) => {
+export function MaterialAttributeValue_ISAJson_genID(oa) {
+    return genID(oa);
+}
+
+export function MaterialAttributeValue_ISAJson_encoder(idMap, oa) {
+    const f = (oa_1) => (new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
         if (equals(v, new Json(3, []))) {
             return void 0;
@@ -27,7 +32,13 @@ export function MaterialAttributeValue_ISAJson_encoder(oa) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), oa.ID), tryInclude("category", MaterialAttribute_ISAJson_encoder, oa.Category), tryInclude("value", Value_ISAJson_encoder, oa.Value), tryInclude("unit", OntologyAnnotation_ISAJson_encoder, oa.Unit)]))]);
+    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), MaterialAttributeValue_ISAJson_genID(oa_1)), tryInclude("category", (value_2) => MaterialAttribute_ISAJson_encoder(idMap, value_2), oa_1.Category), tryInclude("value", (value_3) => Value_ISAJson_encoder(idMap, value_3), oa_1.Value), tryInclude("unit", (oa_3) => OntologyAnnotation_ISAJson_encoder(idMap, oa_3), oa_1.Unit)]))]));
+    if (idMap != null) {
+        return encode(MaterialAttributeValue_ISAJson_genID, f, oa, idMap);
+    }
+    else {
+        return f(oa);
+    }
 }
 
 export const MaterialAttributeValue_ISAJson_decoder = object((get$) => {
@@ -45,15 +56,16 @@ export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_fr
     }
 }
 
-export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = MaterialAttributeValue_ISAJson_encoder(f);
+        const value = MaterialAttributeValue_ISAJson_encoder(idMap, f);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
-export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_ToISAJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 
 export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_fromROCrateJsonString_Static_Z721C83C5(s) {

package/Json/Process/Process.js

@@ -15,9 +15,10 @@ import { context_jsonvalue } from "../context/rocrate/isa_process_context.js";
 import { list as list_2, string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { Decode_uri } from "../Decode.js";
 import { Process } from "../../Core/Process/Process.js";
+import { encode } from "../IDTable.js";
 import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { unwrap } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 
 export function Process_ROCrate_genID(p) {
     const matchValue = p.ID;
@@ -52,8 +53,8 @@ export const Process_ROCrate_decoder = object((get$) => {
     return new Process((objectArg = get$.Optional, objectArg.Field("@id", Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("executesProtocol", Protocol_ROCrate_decoder)), (arg_7 = list_2(ProcessParameterValue_ROCrate_decoder), (objectArg_3 = get$.Optional, objectArg_3.Field("parameterValues", arg_7))), (objectArg_4 = get$.Optional, objectArg_4.Field("performer", Person_ROCrate_decodeAuthorListString)), (objectArg_5 = get$.Optional, objectArg_5.Field("date", string)), void 0, void 0, (arg_13 = list_2(ProcessInput_ROCrate_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("inputs", arg_13))), (arg_15 = list_2(ProcessOutput_ROCrate_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("outputs", arg_15))), (arg_17 = list_2(Comment_ROCrate_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("comments", arg_17))));
 });
 
-export function Process_ISAJson_encoder(oa) {
-    return new Json(5, [choose((tupledArg) => {
+export function Process_ISAJson_encoder(studyName, assayName, idMap, oa) {
+    const f = (oa_1) => (new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
         if (equals(v, new Json(3, []))) {
             return void 0;
@@ -61,7 +62,13 @@ export function Process_ISAJson_encoder(oa) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), oa.ID), tryInclude("name", (value_2) => (new Json(0, [value_2])), oa.Name), tryInclude("executesProtocol", Protocol_ISAJson_encoder, oa.ExecutesProtocol), tryIncludeListOpt("parameterValues", ProcessParameterValue_ISAJson_encoder, oa.ParameterValues), tryInclude("performer", (value_4) => (new Json(0, [value_4])), oa.Performer), tryInclude("date", (value_6) => (new Json(0, [value_6])), oa.Date), tryInclude("previousProcess", Process_ISAJson_encoder, oa.PreviousProcess), tryInclude("nextProcess", Process_ISAJson_encoder, oa.NextProcess), tryIncludeListOpt("inputs", ProcessInput_ISAJson_encoder, oa.Inputs), tryIncludeListOpt("outputs", ProcessOutput_ISAJson_encoder, oa.Outputs), tryIncludeListOpt("comments", Comment_ISAJson_encoder, oa.Comments)]))]);
+    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), Process_ROCrate_genID(oa_1)), tryInclude("name", (value_2) => (new Json(0, [value_2])), oa_1.Name), tryInclude("executesProtocol", (oa_2) => Protocol_ISAJson_encoder(studyName, assayName, oa_1.Name, idMap, oa_2), oa_1.ExecutesProtocol), tryIncludeListOpt("parameterValues", (oa_3) => ProcessParameterValue_ISAJson_encoder(idMap, oa_3), oa_1.ParameterValues), tryInclude("performer", (value_4) => (new Json(0, [value_4])), oa_1.Performer), tryInclude("date", (value_6) => (new Json(0, [value_6])), oa_1.Date), tryInclude("previousProcess", (oa_4) => Process_ISAJson_encoder(studyName, assayName, idMap, oa_4), oa_1.PreviousProcess), tryInclude("nextProcess", (oa_5) => Process_ISAJson_encoder(studyName, assayName, idMap, oa_5), oa_1.NextProcess), tryIncludeListOpt("inputs", (value_8) => ProcessInput_ISAJson_encoder(idMap, value_8), oa_1.Inputs), tryIncludeListOpt("outputs", (value_9) => ProcessOutput_ISAJson_encoder(idMap, value_9), oa_1.Outputs), tryIncludeListOpt("comments", (comment) => Comment_ISAJson_encoder(idMap, comment), oa_1.Comments)]))]));
+    if (idMap != null) {
+        return encode(Process_ROCrate_genID, f, oa, idMap);
+    }
+    else {
+        return f(oa);
+    }
 }
 
 export const Process_ISAJson_decoder = (() => {
@@ -82,15 +89,16 @@ export function ARCtrl_Process_Process__Process_fromISAJsonString_Static_Z721C83
     }
 }
 
-export function ARCtrl_Process_Process__Process_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_Process__Process_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = Process_ISAJson_encoder(f);
+        const value = Process_ISAJson_encoder(void 0, void 0, idMap, f);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
-export function ARCtrl_Process_Process__Process_ToISAJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Process_Process__Process_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+export function ARCtrl_Process_Process__Process_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Process_Process__Process_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 
 export function ARCtrl_Process_Process__Process_fromROCrateString_Static_Z721C83C5(s) {

package/Json/Process/ProcessInput.js

@@ -7,9 +7,9 @@ import { ProcessInput } from "../../Core/Process/ProcessInput.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";
+import { unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.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 ProcessInput_ROCrate_encoder(value) {
     switch (value.tag) {
@@ -26,16 +26,16 @@ export function ProcessInput_ROCrate_encoder(value) {
 
 export const ProcessInput_ROCrate_decoder = oneOf(ofArray([map((Item) => (new ProcessInput(0, [Item])), Source_ROCrate_decoder), map((Item_1) => (new ProcessInput(1, [Item_1])), Sample_ROCrate_decoder), map((Item_2) => (new ProcessInput(2, [Item_2])), Data_ROCrate_decoder), map((Item_3) => (new ProcessInput(3, [Item_3])), Material_ROCrate_decoder)]));
 
-export function ProcessInput_ISAJson_encoder(value) {
+export function ProcessInput_ISAJson_encoder(idMap, value) {
     switch (value.tag) {
         case 1:
-            return Sample_ISAJson_encoder(value.fields[0]);
+            return Sample_ISAJson_encoder(idMap, value.fields[0]);
         case 2:
-            return Data_ISAJson_encoder(value.fields[0]);
+            return Data_ISAJson_encoder(idMap, value.fields[0]);
         case 3:
-            return Material_ISAJson_encoder(value.fields[0]);
+            return Material_ISAJson_encoder(idMap, value.fields[0]);
         default:
-            return Source_ISAJson_encoder(value.fields[0]);
+            return Source_ISAJson_encoder(idMap, value.fields[0]);
     }
 }
 
@@ -51,14 +51,15 @@ export function ARCtrl_Process_ProcessInput__ProcessInput_fromISAJsonString_Stat
     }
 }
 
-export function ARCtrl_Process_ProcessInput__ProcessInput_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_ProcessInput__ProcessInput_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = ProcessInput_ISAJson_encoder(f);
+        const value = ProcessInput_ISAJson_encoder(idMap, f);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
-export function ARCtrl_Process_ProcessInput__ProcessInput_ToISAJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Process_ProcessInput__ProcessInput_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+export function ARCtrl_Process_ProcessInput__ProcessInput_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Process_ProcessInput__ProcessInput_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 

package/Json/Process/ProcessOutput.js

@@ -6,9 +6,9 @@ import { ProcessOutput } from "../../Core/Process/ProcessOutput.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";
+import { unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.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 ProcessOutput_ROCrate_encoder(value) {
     switch (value.tag) {
@@ -23,14 +23,14 @@ export function ProcessOutput_ROCrate_encoder(value) {
 
 export const ProcessOutput_ROCrate_decoder = oneOf(ofArray([map((Item) => (new ProcessOutput(0, [Item])), Sample_ROCrate_decoder), map((Item_1) => (new ProcessOutput(1, [Item_1])), Data_ROCrate_decoder), map((Item_2) => (new ProcessOutput(2, [Item_2])), Material_ROCrate_decoder)]));
 
-export function ProcessOutput_ISAJson_encoder(value) {
+export function ProcessOutput_ISAJson_encoder(idMap, value) {
     switch (value.tag) {
         case 1:
-            return Data_ISAJson_encoder(value.fields[0]);
+            return Data_ISAJson_encoder(idMap, value.fields[0]);
         case 2:
-            return Material_ISAJson_encoder(value.fields[0]);
+            return Material_ISAJson_encoder(idMap, value.fields[0]);
         default:
-            return Sample_ISAJson_encoder(value.fields[0]);
+            return Sample_ISAJson_encoder(idMap, value.fields[0]);
     }
 }
 
@@ -46,15 +46,16 @@ export function ARCtrl_Process_ProcessOutput__ProcessOutput_fromISAJsonString_St
     }
 }
 
-export function ARCtrl_Process_ProcessOutput__ProcessOutput_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_ProcessOutput__ProcessOutput_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = ProcessOutput_ISAJson_encoder(f);
+        const value = ProcessOutput_ISAJson_encoder(idMap, f);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
-export function ARCtrl_Process_ProcessOutput__ProcessOutput_toISAJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Process_ProcessOutput__ProcessOutput_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+export function ARCtrl_Process_ProcessOutput__ProcessOutput_toISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Process_ProcessOutput__ProcessOutput_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 
 export function ARCtrl_Process_ProcessOutput__ProcessOutput_fromROCrateJsonString_Static_Z721C83C5(s) {

package/Json/Process/ProcessParameterValue.js

@@ -10,14 +10,18 @@ import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder
 import { object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.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 { unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { unwrap } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 
 export const ProcessParameterValue_ROCrate_encoder = encoder;
 
 export const ProcessParameterValue_ROCrate_decoder = decoder_1((category, value, unit) => ProcessParameterValue.createAsPV(category, value, unit));
 
-export function ProcessParameterValue_ISAJson_encoder(oa) {
+export function ProcessParameterValue_ISAJson_genID(oa) {
+    throw new Error("Not implemented");
+}
+
+export function ProcessParameterValue_ISAJson_encoder(idMap, oa) {
     return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
         if (equals(v, new Json(3, []))) {
@@ -26,7 +30,7 @@ export function ProcessParameterValue_ISAJson_encoder(oa) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([tryInclude("category", ProtocolParameter_ISAJson_encoder, oa.Category), tryInclude("value", Value_ISAJson_encoder, oa.Value), tryInclude("unit", OntologyAnnotation_ISAJson_encoder, oa.Unit)]))]);
+    }, ofArray([tryInclude("category", (value) => ProtocolParameter_ISAJson_encoder(idMap, value), oa.Category), tryInclude("value", (value_1) => Value_ISAJson_encoder(idMap, value_1), oa.Value), tryInclude("unit", (oa_1) => OntologyAnnotation_ISAJson_encoder(idMap, oa_1), oa.Unit)]))]);
 }
 
 export const ProcessParameterValue_ISAJson_decoder = object((get$) => {
@@ -44,15 +48,16 @@ export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_from
     }
 }
 
-export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = ProcessParameterValue_ISAJson_encoder(f);
+        const value = ProcessParameterValue_ISAJson_encoder(idMap, f);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
-export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_ToISAJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 
 export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_fromROCrateJsonString_Static_Z721C83C5(s) {

package/Json/Process/ProcessSequence.js

@@ -3,6 +3,7 @@ import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Deco
 import { list as list_1 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { Process_ROCrate_encoder, Process_ROCrate_decoder, Process_ISAJson_encoder, Process_ISAJson_decoder } from "./Process.js";
 import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { list as list_2 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
 import { map } from "../../fable_modules/fable-library-js.4.16.0/List.js";
 import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
@@ -27,9 +28,10 @@ export function ProcessSequence_fromISAJsonString_Z721C83C5(s) {
     }
 }
 
-export function ProcessSequence_toISAJsonString_71136F3F(spaces) {
+export function ProcessSequence_toISAJsonString_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = list_2(map(Process_ISAJson_encoder, f));
+        const value = list_2(map((oa) => Process_ISAJson_encoder(void 0, void 0, idMap, oa), f));
         return toString(defaultSpaces(spaces), value);
     };
 }

package/Json/Process/PropertyValue.js

@@ -11,12 +11,37 @@ import { Value } from "../../Core/Process/Value.js";
 
 export function genID(p) {
     const matchValue = p.GetCategory();
-    if (matchValue == null) {
-        return `#Empty${p.GetAdditionalType()}`;
+    const matchValue_1 = p.GetValue();
+    const matchValue_2 = p.GetUnit();
+    let matchResult, t, u, v, t_1, v_1;
+    if (matchValue != null) {
+        if (matchValue_1 != null) {
+            if (matchValue_2 == null) {
+                matchResult = 1;
+                t_1 = matchValue;
+                v_1 = matchValue_1;
+            }
+            else {
+                matchResult = 0;
+                t = matchValue;
+                u = matchValue_2;
+                v = matchValue_1;
+            }
+        }
+        else {
+            matchResult = 2;
+        }
     }
     else {
-        const t = matchValue;
-        return `${p.GetAdditionalType()}/${t}${p.GetValue()}${p.GetUnit()}`;
+        matchResult = 2;
+    }
+    switch (matchResult) {
+        case 0:
+            return `#${p.GetAdditionalType()}/${t.NameText}=${v.Text}${u.NameText}`;
+        case 1:
+            return `#${p.GetAdditionalType()}/${t_1.NameText}=${v_1.Text}`;
+        default:
+            return `#Empty${p.GetAdditionalType()}`;
     }
 }
 

package/Json/Process/Protocol.js

@@ -14,65 +14,86 @@ import { unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/
 import { Decode_uri } from "../Decode.js";
 import { Protocol } from "../../Core/Process/Protocol.js";
 import { ProtocolParameter_ISAJson_decoder, ProtocolParameter_ISAJson_encoder } from "./ProtocolParameter.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 Protocol_ROCrate_genID(studyName, assayName, processName, p) {
-    const matchValue = p.Uri;
-    if (matchValue == null) {
-        const matchValue_1 = p.Name;
-        if (matchValue_1 == null) {
-            let matchResult, an, pn, sn, pn_1, sn_1, pn_2;
-            if (studyName == null) {
-                if (assayName == null) {
-                    if (processName != null) {
-                        matchResult = 2;
-                        pn_2 = processName;
+    const matchValue = p.ID;
+    let matchResult, id_1;
+    if (matchValue != null) {
+        if (matchValue !== "") {
+            matchResult = 0;
+            id_1 = matchValue;
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0:
+            return id_1;
+        default: {
+            const matchValue_1 = p.Uri;
+            if (matchValue_1 == null) {
+                const matchValue_2 = p.Name;
+                if (matchValue_2 == null) {
+                    let matchResult_1, an, pn, sn, pn_1, sn_1, pn_2;
+                    if (studyName == null) {
+                        if (assayName == null) {
+                            if (processName != null) {
+                                matchResult_1 = 2;
+                                pn_2 = processName;
+                            }
+                            else {
+                                matchResult_1 = 3;
+                            }
+                        }
+                        else {
+                            matchResult_1 = 3;
+                        }
+                    }
+                    else if (assayName == null) {
+                        if (processName != null) {
+                            matchResult_1 = 1;
+                            pn_1 = processName;
+                            sn_1 = studyName;
+                        }
+                        else {
+                            matchResult_1 = 3;
+                        }
+                    }
+                    else if (processName != null) {
+                        matchResult_1 = 0;
+                        an = assayName;
+                        pn = processName;
+                        sn = studyName;
                     }
                     else {
-                        matchResult = 3;
+                        matchResult_1 = 3;
+                    }
+                    switch (matchResult_1) {
+                        case 0:
+                            return (((("#Protocol_" + replace(sn, " ", "_")) + "_") + replace(an, " ", "_")) + "_") + replace(pn, " ", "_");
+                        case 1:
+                            return (("#Protocol_" + replace(sn_1, " ", "_")) + "_") + replace(pn_1, " ", "_");
+                        case 2:
+                            return "#Protocol_" + replace(pn_2, " ", "_");
+                        default:
+                            return "#EmptyProtocol";
                     }
                 }
                 else {
-                    matchResult = 3;
-                }
-            }
-            else if (assayName == null) {
-                if (processName != null) {
-                    matchResult = 1;
-                    pn_1 = processName;
-                    sn_1 = studyName;
-                }
-                else {
-                    matchResult = 3;
+                    return "#Protocol_" + replace(matchValue_2, " ", "_");
                 }
             }
-            else if (processName != null) {
-                matchResult = 0;
-                an = assayName;
-                pn = processName;
-                sn = studyName;
-            }
             else {
-                matchResult = 3;
-            }
-            switch (matchResult) {
-                case 0:
-                    return (((("#Protocol_" + replace(sn, " ", "_")) + "_") + replace(an, " ", "_")) + "_") + replace(pn, " ", "_");
-                case 1:
-                    return (("#Protocol_" + replace(sn_1, " ", "_")) + "_") + replace(pn_1, " ", "_");
-                case 2:
-                    return "#Protocol_" + replace(pn_2, " ", "_");
-                default:
-                    return "#EmptyProtocol";
+                return matchValue_1;
             }
         }
-        else {
-            return "#Protocol_" + replace(matchValue_1, " ", "_");
-        }
-    }
-    else {
-        return matchValue;
     }
 }
 
@@ -94,8 +115,8 @@ export const Protocol_ROCrate_decoder = object((get$) => {
     return new Protocol((objectArg_3 = get$.Optional, objectArg_3.Field("@id", Decode_uri)), (objectArg_4 = get$.Optional, objectArg_4.Field("name", string)), (objectArg_5 = get$.Optional, objectArg_5.Field("protocolType", OntologyAnnotation_ROCrate_decoderDefinedTerm)), (objectArg_6 = get$.Optional, objectArg_6.Field("description", string)), (objectArg_7 = get$.Optional, objectArg_7.Field("uri", Decode_uri)), (objectArg_8 = get$.Optional, objectArg_8.Field("version", string)), void 0, components, (arg_19 = list_5(Comment_ROCrate_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("comments", arg_19))));
 });
 
-export function Protocol_ISAJson_encoder(oa) {
-    return new Json(5, [choose((tupledArg) => {
+export function Protocol_ISAJson_encoder(studyName, assayName, processName, idMap, oa) {
+    const f = (oa_1) => (new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
         if (equals(v, new Json(3, []))) {
             return void 0;
@@ -103,7 +124,13 @@ export function Protocol_ISAJson_encoder(oa) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), oa.ID), tryInclude("name", (value_2) => (new Json(0, [value_2])), oa.Name), tryInclude("protocolType", OntologyAnnotation_ISAJson_encoder, oa.ProtocolType), tryInclude("description", (value_4) => (new Json(0, [value_4])), oa.Description), tryInclude("uri", (value_6) => (new Json(0, [value_6])), oa.Uri), tryInclude("version", (value_8) => (new Json(0, [value_8])), oa.Version), tryIncludeListOpt("parameters", ProtocolParameter_ISAJson_encoder, oa.Parameters), tryIncludeListOpt("components", Component_ISAJson_encoder, oa.Components), tryIncludeListOpt("comments", Comment_ISAJson_encoder, oa.Comments)]))]);
+    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), Protocol_ROCrate_genID(studyName, assayName, processName, oa_1)), tryInclude("name", (value_2) => (new Json(0, [value_2])), oa_1.Name), tryInclude("protocolType", (oa_2) => OntologyAnnotation_ISAJson_encoder(idMap, oa_2), oa_1.ProtocolType), tryInclude("description", (value_4) => (new Json(0, [value_4])), oa_1.Description), tryInclude("uri", (value_6) => (new Json(0, [value_6])), oa_1.Uri), tryInclude("version", (value_8) => (new Json(0, [value_8])), oa_1.Version), tryIncludeListOpt("parameters", (value_10) => ProtocolParameter_ISAJson_encoder(idMap, value_10), oa_1.Parameters), tryIncludeListOpt("components", (c) => Component_ISAJson_encoder(idMap, c), oa_1.Components), tryIncludeListOpt("comments", (comment) => Comment_ISAJson_encoder(idMap, comment), oa_1.Comments)]))]));
+    if (idMap != null) {
+        return encode((p_1) => Protocol_ROCrate_genID(studyName, assayName, processName, p_1), f, oa, idMap);
+    }
+    else {
+        return f(oa);
+    }
 }
 
 export const Protocol_ISAJson_decoder = object((get$) => {
@@ -121,15 +148,16 @@ export function ARCtrl_Process_Protocol__Protocol_fromISAJsonString_Static_Z721C
     }
 }
 
-export function ARCtrl_Process_Protocol__Protocol_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_Protocol__Protocol_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = Protocol_ISAJson_encoder(f);
+        const value = Protocol_ISAJson_encoder(void 0, void 0, void 0, idMap, f);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
 export function ARCtrl_Process_Protocol__Protocol_ToISAJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Process_Protocol__Protocol_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+    return ARCtrl_Process_Protocol__Protocol_toISAJsonString_Static_Z3B036AA(spaces)(this$);
 }
 
 export function ARCtrl_Process_Protocol__Protocol_fromROCrateString_Static_Z721C83C5(s) {