@nfdi4plants/arctrl 2.0.0-alpha.7 → 2.0.0-alpha.8

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) {

package/Json/Process/ProtocolParameter.js

@@ -1,8 +1,9 @@
-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 { ProtocolParameter } from "../../Core/Process/ProtocolParameter.js";
 import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
@@ -10,8 +11,18 @@ import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/Stri
 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 ProtocolParameter_ISAJson_encoder(value) {
-    return new Json(5, [choose((tupledArg) => {
+export function ProtocolParameter_ISAJson_genID(p) {
+    const matchValue = p.ParameterName;
+    if (matchValue == null) {
+        return "#EmptyProtocolParameter";
+    }
+    else {
+        return `#ProtocolParameter/${OntologyAnnotation_ROCrate_genID(matchValue)}`;
+    }
+}
+
+export function ProtocolParameter_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 ProtocolParameter_ISAJson_encoder(value) {
         else {
             return [tupledArg[0], v];
         }
-    }, singleton(tryInclude("parameterName", OntologyAnnotation_ISAJson_encoder, value.ParameterName)))]);
+    }, ofArray([tryInclude("@id", (value_2) => (new Json(0, [value_2])), ProtocolParameter_ISAJson_genID(value_1)), tryInclude("parameterName", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), value_1.ParameterName)]))]));
+    if (idMap != null) {
+        return encode(ProtocolParameter_ISAJson_genID, f, value, idMap);
+    }
+    else {
+        return f(value);
+    }
 }
 
 export const ProtocolParameter_ISAJson_decoder = object((get$) => {
@@ -39,7 +56,7 @@ export function ARCtrl_Process_ProtocolParameter__ProtocolParameter_fromISAJsonS
 
 export function ARCtrl_Process_ProtocolParameter__ProtocolParameter_toISAJsonString_Static_71136F3F(spaces) {
     return (v) => {
-        const value = ProtocolParameter_ISAJson_encoder(v);
+        const value = ProtocolParameter_ISAJson_encoder(void 0, v);
         return toString(defaultSpaces(spaces), value);
     };
 }

package/Json/Process/Sample.js

@@ -14,6 +14,7 @@ import { Option_fromValueWithDefault } from "../../Core/Helper/Collections.js";
 import { Decode_objectNoAdditionalProperties, Decode_uri } from "../Decode.js";
 import { Source_ISAJson_decoder, Source_ISAJson_encoder, Source_ROCrate_decoder } from "./Source.js";
 import { Sample } from "../../Core/Process/Sample.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";
 
@@ -79,8 +80,8 @@ export const Sample_ROCrate_decoder = object((get$) => {
     return new Sample((objectArg_1 = get$.Optional, objectArg_1.Field("@id", Decode_uri)), (objectArg_2 = get$.Optional, objectArg_2.Field("name", string)), patternInput[0], patternInput[1], (arg_7 = list_6(Source_ROCrate_decoder), (objectArg_3 = get$.Optional, objectArg_3.Field("derivesFrom", arg_7))));
 });
 
-export function Sample_ISAJson_encoder(oa) {
-    return new Json(5, [choose((tupledArg) => {
+export function Sample_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;
@@ -88,7 +89,13 @@ export function Sample_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), tryIncludeListOpt("characteristics", MaterialAttributeValue_ISAJson_encoder, oa.Characteristics), tryIncludeListOpt("factorValues", FactorValue_ISAJson_encoder, oa.FactorValues), tryIncludeListOpt("derivesFrom", Source_ISAJson_encoder, oa.DerivesFrom)]))]);
+    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), Sample_ROCrate_genID(oa_1)), tryInclude("name", (value_2) => (new Json(0, [value_2])), oa_1.Name), tryIncludeListOpt("characteristics", (oa_2) => MaterialAttributeValue_ISAJson_encoder(idMap, oa_2), oa_1.Characteristics), tryIncludeListOpt("factorValues", (fv) => FactorValue_ISAJson_encoder(idMap, fv), oa_1.FactorValues), tryIncludeListOpt("derivesFrom", (oa_3) => Source_ISAJson_encoder(idMap, oa_3), oa_1.DerivesFrom)]))]));
+    if (idMap != null) {
+        return encode(Sample_ROCrate_genID, f, oa, idMap);
+    }
+    else {
+        return f(oa);
+    }
 }
 
 export const Sample_ISAJson_allowedFields = ofArray(["@id", "name", "characteristics", "factorValues", "derivesFrom", "@type", "@context"]);
@@ -108,15 +115,16 @@ export function ARCtrl_Process_Sample__Sample_fromISAJsonString_Static_Z721C83C5
     }
 }
 
-export function ARCtrl_Process_Sample__Sample_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_Sample__Sample_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = Sample_ISAJson_encoder(f);
-        return toString(defaultSpaces(spaces), value);
+        const value_1 = Sample_ISAJson_encoder(idMap, f);
+        return toString(defaultSpaces(spaces), value_1);
     };
 }
 
-export function ARCtrl_Process_Sample__Sample_ToISAJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Process_Sample__Sample_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+export function ARCtrl_Process_Sample__Sample_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Process_Sample__Sample_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 
 export function ARCtrl_Process_Sample__Sample_fromROCrateString_Static_Z721C83C5(s) {

package/Json/Process/Source.js

@@ -10,9 +10,10 @@ import { context_jsonvalue } from "../context/rocrate/isa_source_context.js";
 import { list as list_2, string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { Decode_objectNoAdditionalProperties, Decode_uri } from "../Decode.js";
 import { Source } from "../../Core/Process/Source.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 Source_ROCrate_genID(s) {
     const matchValue = s.ID;
@@ -47,8 +48,8 @@ export const Source_ROCrate_decoder = object((get$) => {
     return new Source((objectArg = get$.Optional, objectArg.Field("@id", Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = list_2(MaterialAttributeValue_ROCrate_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("characteristics", arg_5))));
 });
 
-export function Source_ISAJson_encoder(oa) {
-    return new Json(5, [choose((tupledArg) => {
+export function Source_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;
@@ -56,7 +57,13 @@ export function Source_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), tryIncludeListOpt("characteristics", MaterialAttributeValue_ISAJson_encoder, oa.Characteristics)]))]);
+    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), Source_ROCrate_genID(oa_1)), tryInclude("name", (value_2) => (new Json(0, [value_2])), oa_1.Name), tryIncludeListOpt("characteristics", (oa_2) => MaterialAttributeValue_ISAJson_encoder(idMap, oa_2), oa_1.Characteristics)]))]));
+    if (idMap != null) {
+        return encode(Source_ROCrate_genID, f, oa, idMap);
+    }
+    else {
+        return f(oa);
+    }
 }
 
 export const Source_ISAJson_allowedFields = ofArray(["@id", "name", "characteristics", "@type", "@context"]);
@@ -76,15 +83,16 @@ export function ARCtrl_Process_Source__Source_fromISAJsonString_Static_Z721C83C5
     }
 }
 
-export function ARCtrl_Process_Source__Source_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_Source__Source_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = Source_ISAJson_encoder(f);
-        return toString(defaultSpaces(spaces), value);
+        const value_1 = Source_ISAJson_encoder(idMap, f);
+        return toString(defaultSpaces(spaces), value_1);
     };
 }
 
-export function ARCtrl_Process_Source__Source_ToISAJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Process_Source__Source_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+export function ARCtrl_Process_Source__Source_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Process_Source__Source_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 
 export function ARCtrl_Process_Source__Source_fromROCrateString_Static_Z721C83C5(s) {

package/Json/Process/StudyMaterials.js

@@ -7,7 +7,7 @@ import { Source_ISAJson_encoder } from "./Source.js";
 import { Sample_ISAJson_encoder } from "./Sample.js";
 import { Material_ISAJson_encoder } from "./Material.js";
 
-export function encoder(ps) {
+export function encoder(idMap, ps) {
     const source = getSources(ps);
     const samples = getSamples(ps);
     const materials = getMaterials(ps);
@@ -19,6 +19,6 @@ export function encoder(ps) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([tryIncludeList("sources", Source_ISAJson_encoder, source), tryIncludeList("samples", Sample_ISAJson_encoder, samples), tryIncludeList("otherMaterials", Material_ISAJson_encoder, materials)]))]);
+    }, ofArray([tryIncludeList("sources", (oa) => Source_ISAJson_encoder(idMap, oa), source), tryIncludeList("samples", (oa_1) => Sample_ISAJson_encoder(idMap, oa_1), samples), tryIncludeList("otherMaterials", (c) => Material_ISAJson_encoder(idMap, c), materials)]))]);
 }
 

package/Json/Process/Value.js

@@ -8,14 +8,14 @@ import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/Stri
 import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
 import { defaultSpaces } from "../Encode.js";
 
-export function Value_ISAJson_encoder(value) {
+export function Value_ISAJson_encoder(idMap, value) {
     switch (value.tag) {
         case 1:
             return new Json(7, [value.fields[0] >>> 0]);
         case 3:
             return new Json(0, [value.fields[0]]);
         case 0:
-            return OntologyAnnotation_ISAJson_encoder(value.fields[0]);
+            return OntologyAnnotation_ISAJson_encoder(idMap, value.fields[0]);
         default:
             return new Json(2, [value.fields[0]]);
     }
@@ -35,7 +35,7 @@ export function ARCtrl_Process_Value__Value_fromISAJsonString_Static_Z721C83C5(s
 
 export function ARCtrl_Process_Value__Value_toISAJsonString_Static_71136F3F(spaces) {
     return (v) => {
-        const value = Value_ISAJson_encoder(v);
+        const value = Value_ISAJson_encoder(void 0, v);
         return toString(defaultSpaces(spaces), value);
     };
 }

package/Json/Publication.js

@@ -6,7 +6,7 @@ import { OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCra
 import { Comment_ISAJson_encoder, Comment_ROCrate_decoderDisambiguatingDescription, Comment_ROCrate_encoderDisambiguatingDescription, Comment_decoder, Comment_encoder } from "./Comment.js";
 import { string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { Publication } from "../Core/Publication.js";
-import { unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { defaultArg, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { Decode_noAdditionalProperties, Decode_resizeArray, Decode_uri } from "./Decode.js";
 import { printf, toText, replace } from "../fable_modules/fable-library-js.4.16.0/String.js";
 import { Person_ROCrate_decodeAuthorListString, Person_ROCrate_encodeAuthorListString } from "./Person.js";
@@ -70,7 +70,7 @@ export const Publication_ROCrate_decoder = object((get$) => {
     return new Publication(unwrap((objectArg = get$.Optional, objectArg.Field("pubMedID", Decode_uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("doi", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("authorList", Person_ROCrate_decodeAuthorListString))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("title", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("status", OntologyAnnotation_ROCrate_decoderDefinedTerm))), unwrap((arg_11 = Decode_resizeArray(Comment_ROCrate_decoderDisambiguatingDescription), (objectArg_5 = get$.Optional, objectArg_5.Field("comments", arg_11)))));
 });
 
-export function Publication_ISAJson_encoder(oa) {
+export function Publication_ISAJson_encoder(idMap, oa) {
     return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
         if (equals(v, new Json(3, []))) {
@@ -79,7 +79,7 @@ export function Publication_ISAJson_encoder(oa) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([tryInclude("pubMedID", (value) => (new Json(0, [value])), oa.PubMedID), tryInclude("doi", (value_2) => (new Json(0, [value_2])), oa.DOI), tryInclude("authorList", (value_4) => (new Json(0, [value_4])), oa.Authors), tryInclude("title", (value_6) => (new Json(0, [value_6])), oa.Title), tryInclude("status", OntologyAnnotation_encoder, oa.Status), tryIncludeSeq("comments", Comment_ISAJson_encoder, oa.Comments)]))]);
+    }, ofArray([tryInclude("pubMedID", (value) => (new Json(0, [value])), oa.PubMedID), tryInclude("doi", (value_2) => (new Json(0, [value_2])), oa.DOI), tryInclude("authorList", (value_4) => (new Json(0, [value_4])), oa.Authors), tryInclude("title", (value_6) => (new Json(0, [value_6])), oa.Title), tryInclude("status", OntologyAnnotation_encoder, oa.Status), tryIncludeSeq("comments", (comment) => Comment_ISAJson_encoder(idMap, comment), oa.Comments)]))]);
 }
 
 export const Publication_ISAJson_allowedFields = ofArray(["pubMedID", "doi", "authorList", "title", "status", "comments"]);
@@ -141,14 +141,15 @@ export function ARCtrl_Publication__Publication_fromISAJsonString_Static_Z721C83
     }
 }
 
-export function ARCtrl_Publication__Publication_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Publication__Publication_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (obj) => {
-        const value = Publication_ISAJson_encoder(obj);
+        const value = Publication_ISAJson_encoder(idMap, obj);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
-export function ARCtrl_Publication__Publication_ToISAJsonString_71136F3F(this$, spaces) {
-    return ARCtrl_Publication__Publication_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+export function ARCtrl_Publication__Publication_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Publication__Publication_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 

package/Json/Study.js

@@ -1,5 +1,5 @@
 import { Option_fromValueWithDefault, ResizeArray_map } from "../Core/Helper/Collections.js";
-import { defaultArgWith, map, bind, unwrap, value as value_14, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { defaultArgWith, map, bind, unwrap, value as value_17, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { empty, map as map_1, singleton, ofArray, choose, tryFind } from "../fable_modules/fable-library-js.4.16.0/List.js";
 import { ArcStudy, ArcAssay } from "../Core/ArcTypes.js";
 import { disposeSafe, getEnumerator, equals } from "../fable_modules/fable-library-js.4.16.0/Util.js";
@@ -19,22 +19,23 @@ import { list as list_1 } from "../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs
 import { Process_ISAJson_decoder, Process_ISAJson_encoder, Process_ROCrate_decoder, Process_ROCrate_encoder } from "./Process/Process.js";
 import { Assay_ISAJson_decoder, Assay_ISAJson_encoder, Assay_ROCrate_decoder, Assay_ROCrate_encoder } from "./Assay.js";
 import { context_jsonvalue } from "./context/rocrate/isa_study_context.js";
-import { getUnits, getCharacteristics, getFactors, getProtocols } from "../Core/Process/ProcessSequence.js";
-import { Protocol_ISAJson_encoder } from "./Process/Protocol.js";
-import { encoder } from "./Process/StudyMaterials.js";
+import { getProtocols, getCharacteristics, getFactors, getUnits } from "../Core/Process/ProcessSequence.js";
 import { Factor_ISAJson_encoder } from "./Process/Factor.js";
 import { MaterialAttribute_ISAJson_encoder } from "./Process/MaterialAttribute.js";
+import { encoder as encoder_4 } from "./Process/StudyMaterials.js";
+import { Protocol_ISAJson_encoder } from "./Process/Protocol.js";
+import { encode } from "./IDTable.js";
 import { isEmpty } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { fromString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
 import { toString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { encode, decode } from "./Table/Compression.js";
+import { encode as encode_1, decode } from "./Table/Compression.js";
 
 /**
  * Get registered assays or get assays from `assays` if IsSome
  */
 export function Study_Helper_getAssayInformation(assays, study) {
     if (assays != null) {
-        return ResizeArray_map((assayId) => defaultArg(tryFind((a) => (a.Identifier === assayId), value_14(assays)), ArcAssay.init(assayId)), study.RegisteredAssayIdentifiers);
+        return ResizeArray_map((assayId) => defaultArg(tryFind((a) => (a.Identifier === assayId), value_17(assays)), ArcAssay.init(assayId)), study.RegisteredAssayIdentifiers);
     }
     else {
         return study.GetRegisteredAssaysOrIdentifier();
@@ -121,48 +122,60 @@ export const Study_ROCrate_decoder = object((get$) => {
 /**
  * If assays.IsSome then try to get registered assays from external list, otherwise try to access investigation or create empty defaults.
  */
-export function Study_ISAJson_encoder(assays, s) {
-    const study = s.Copy(true);
-    const fileName = Study_fileNameFromIdentifier(study.Identifier);
-    let assays_1;
-    const n = [];
-    let enumerator = getEnumerator(Study_Helper_getAssayInformation(assays, study));
-    try {
-        while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
-            const a = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-            const assay = a.Copy();
-            let enumerator_1 = getEnumerator(assay.Performers);
-            try {
-                while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
-                    const person_1 = Person_setSourceAssayComment(enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"](), assay.Identifier);
-                    void (study.Contacts.push(person_1));
+export function Study_ISAJson_encoder(idMap, assays, s) {
+    const f = (s_1) => {
+        let studyName, studyName_1, studyName_2;
+        const study = s_1.Copy(true);
+        const fileName = Study_fileNameFromIdentifier(study.Identifier);
+        let assays_1;
+        const n = [];
+        let enumerator = getEnumerator(Study_Helper_getAssayInformation(assays, study));
+        try {
+            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+                const a = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                const assay = a.Copy();
+                let enumerator_1 = getEnumerator(assay.Performers);
+                try {
+                    while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+                        const person_1 = Person_setSourceAssayComment(enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"](), assay.Identifier);
+                        void (study.Contacts.push(person_1));
+                    }
                 }
+                finally {
+                    disposeSafe(enumerator_1);
+                }
+                assay.Performers = [];
+                void (n.push(assay));
             }
-            finally {
-                disposeSafe(enumerator_1);
-            }
-            assay.Performers = [];
-            void (n.push(assay));
         }
+        finally {
+            disposeSafe(enumerator);
+        }
+        assays_1 = n;
+        const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(study);
+        const encodedUnits = tryIncludeList("unitCategories", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), getUnits(processes));
+        const encodedFactors = tryIncludeList("factors", (value_1) => Factor_ISAJson_encoder(idMap, value_1), getFactors(processes));
+        const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_3) => MaterialAttribute_ISAJson_encoder(idMap, value_3), getCharacteristics(processes));
+        const encodedMaterials = tryInclude("materials", (ps) => encoder_4(idMap, ps), Option_fromValueWithDefault(empty(), processes));
+        let encodedProtocols;
+        const value_5 = getProtocols(processes);
+        encodedProtocols = tryIncludeList("protocols", (studyName = s_1.Identifier, (oa_1) => Protocol_ISAJson_encoder(studyName, void 0, void 0, idMap, oa_1)), value_5);
+        return new Json(5, [choose((tupledArg) => {
+            const v = tupledArg[1];
+            if (equals(v, new Json(3, []))) {
+                return void 0;
+            }
+            else {
+                return [tupledArg[0], v];
+            }
+        }, ofArray([["@id", new Json(0, [Study_ROCrate_genID(study)])], ["filename", new Json(0, [fileName])], ["identifier", new Json(0, [study.Identifier])], tryInclude("title", (value_9) => (new Json(0, [value_9])), study.Title), tryInclude("description", (value_11) => (new Json(0, [value_11])), study.Description), tryInclude("submissionDate", (value_13) => (new Json(0, [value_13])), study.SubmissionDate), tryInclude("publicReleaseDate", (value_15) => (new Json(0, [value_15])), study.PublicReleaseDate), tryIncludeSeq("publications", (oa_2) => Publication_ISAJson_encoder(idMap, oa_2), study.Publications), tryIncludeSeq("people", (person_2) => Person_ISAJson_encoder(idMap, person_2), study.Contacts), tryIncludeSeq("studyDesignDescriptors", (oa_3) => OntologyAnnotation_ISAJson_encoder(idMap, oa_3), study.StudyDesignDescriptors), encodedProtocols, encodedMaterials, tryIncludeList("processSequence", (studyName_1 = s_1.Identifier, (oa_4) => Process_ISAJson_encoder(studyName_1, void 0, idMap, oa_4)), processes), tryIncludeSeq("assays", (studyName_2 = s_1.Identifier, (a_2) => Assay_ISAJson_encoder(studyName_2, idMap, a_2)), assays_1), encodedFactors, encodedCharacteristics, encodedUnits, tryIncludeSeq("comments", (comment) => Comment_ISAJson_encoder(idMap, comment), study.Comments)]))]);
+    };
+    if (idMap != null) {
+        return encode(Study_ROCrate_genID, f, s, idMap);
     }
-    finally {
-        disposeSafe(enumerator);
+    else {
+        return f(s);
     }
-    assays_1 = n;
-    const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(study);
-    const protocols = getProtocols(processes);
-    const factors = getFactors(processes);
-    const characteristics = getCharacteristics(processes);
-    const units = getUnits(processes);
-    return new Json(5, [choose((tupledArg) => {
-        const v = tupledArg[1];
-        if (equals(v, new Json(3, []))) {
-            return void 0;
-        }
-        else {
-            return [tupledArg[0], v];
-        }
-    }, ofArray([["filename", new Json(0, [fileName])], ["identifier", new Json(0, [study.Identifier])], tryInclude("title", (value_2) => (new Json(0, [value_2])), study.Title), tryInclude("description", (value_4) => (new Json(0, [value_4])), study.Description), tryInclude("submissionDate", (value_6) => (new Json(0, [value_6])), study.SubmissionDate), tryInclude("publicReleaseDate", (value_8) => (new Json(0, [value_8])), study.PublicReleaseDate), tryIncludeSeq("publications", Publication_ISAJson_encoder, study.Publications), tryIncludeSeq("people", Person_ISAJson_encoder, study.Contacts), tryIncludeSeq("studyDesignDescriptors", OntologyAnnotation_ISAJson_encoder, study.StudyDesignDescriptors), tryIncludeList("protocols", Protocol_ISAJson_encoder, protocols), tryInclude("materials", encoder, Option_fromValueWithDefault(empty(), processes)), tryIncludeList("factors", Factor_ISAJson_encoder, factors), tryIncludeList("characteristicCategories", MaterialAttribute_ISAJson_encoder, characteristics), tryIncludeList("unitCategories", OntologyAnnotation_ISAJson_encoder, units), tryIncludeList("processSequence", Process_ISAJson_encoder, processes), tryIncludeSeq("assays", Assay_ISAJson_encoder, assays_1), tryIncludeSeq("comments", Comment_ISAJson_encoder, study.Comments)]))]);
 }
 
 export const Study_ISAJson_allowedFields = ofArray(["@id", "filename", "identifier", "title", "description", "submissionDate", "publicReleaseDate", "publications", "people", "studyDesignDescriptors", "protocols", "materials", "assays", "factors", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
@@ -187,7 +200,7 @@ export const Study_ISAJson_decoder = Decode_objectNoAdditionalProperties(Study_I
     personsRaw = objectArg_4.Field("people", arg_10);
     const persons = [];
     if (personsRaw != null) {
-        let enumerator = getEnumerator(value_14(personsRaw));
+        let enumerator = getEnumerator(value_17(personsRaw));
         try {
             while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
                 const person = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
@@ -196,7 +209,7 @@ export const Study_ISAJson_decoder = Decode_objectNoAdditionalProperties(Study_I
                 try {
                     while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
                         const assayIdentifier = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                        const enumerator_2 = getEnumerator(value_14(assays));
+                        const enumerator_2 = getEnumerator(value_17(assays));
                         try {
                             while (enumerator_2["System.Collections.IEnumerator.MoveNext"]()) {
                                 const assay = enumerator_2["System.Collections.Generic.IEnumerator`1.get_Current"]();
@@ -268,7 +281,7 @@ export function ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C8
 }
 
 export function ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F(spaces) {
-    return (obj) => toString(defaultArg(spaces, 0), encode(Study_encoderCompressed, obj));
+    return (obj) => toString(defaultArg(spaces, 0), encode_1(Study_encoderCompressed, obj));
 }
 
 export function ARCtrl_ArcStudy__ArcStudy_ToCompressedJsonString_71136F3F(this$, spaces) {
@@ -309,14 +322,15 @@ export function ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5(s)
     }
 }
 
-export function ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_3BA23086(assays, spaces) {
+export function ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1(assays, spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (obj) => {
-        const value = Study_ISAJson_encoder(assays, obj);
+        const value = Study_ISAJson_encoder(idMap, assays, obj);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
-export function ARCtrl_ArcStudy__ArcStudy_ToISAJsonString_3BA23086(this$, assays, spaces) {
-    return ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_3BA23086(unwrap(assays), unwrap(spaces))(this$);
+export function ARCtrl_ArcStudy__ArcStudy_ToISAJsonString_Z3FD920F1(this$, assays, spaces, useIDReferencing) {
+    return ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1(unwrap(assays), unwrap(spaces), unwrap(useIDReferencing))(this$);
 }