@nfdi4plants/arctrl 2.0.0-alpha.6 → 2.0.0-alpha.8

package/Json/Assay.js

@@ -13,17 +13,18 @@ import { Decode_objectNoAdditionalProperties, Decode_resizeArray } from "./Decod
 import { toFail, printf, toText, replace } from "../fable_modules/fable-library-js.4.16.0/String.js";
 import { Assay_tryIdentifierFromFileName, createMissingIdentifier, Assay_fileNameFromIdentifier } from "../Core/Helper/Identifier.js";
 import { JsonTypes_decomposeTechnologyPlatform, JsonTypes_composeTechnologyPlatform, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D, ARCtrl_ArcTables__ArcTables_GetProcesses } from "../Core/Conversion.js";
-import { getUnits, getCharacteristics, getData } from "../Core/Process/ProcessSequence.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 { 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 { encoder } from "./Process/AssayMaterials.js";
-import { Option_fromValueWithDefault } from "../Core/Helper/Collections.js";
 import { MaterialAttribute_ISAJson_encoder } from "./Process/MaterialAttribute.js";
+import { encoder as encoder_3 } from "./Process/AssayMaterials.js";
+import { Option_fromValueWithDefault } from "../Core/Helper/Collections.js";
+import { encode } from "./IDTable.js";
 import { fromString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
 import { toString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { encode, decode } from "./Table/Compression.js";
+import { encode as encode_1, decode } from "./Table/Compression.js";
 
 export function Assay_encoder(assay) {
     return new Json(5, [choose((tupledArg) => {
@@ -97,21 +98,32 @@ export const Assay_ROCrate_decoder = object((get$) => {
     return new ArcAssay(identifier, unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", OntologyAnnotation_ROCrate_decoderPropertyValue))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", OntologyAnnotation_ROCrate_decoderDefinedTerm))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", OntologyAnnotation_ROCrate_decoderDefinedTerm))), unwrap(tables), void 0, unwrap((arg_12 = Decode_resizeArray(Person_ROCrate_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("performers", arg_12)))), unwrap((arg_14 = Decode_resizeArray(Comment_ROCrate_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("comments", arg_14)))));
 });
 
-export function Assay_ISAJson_encoder(a) {
-    const fileName = Assay_fileNameFromIdentifier(a.Identifier);
-    const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(a);
-    const dataFiles = getData(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])], tryInclude("measurementType", OntologyAnnotation_ISAJson_encoder, a.MeasurementType), tryInclude("technologyType", OntologyAnnotation_ISAJson_encoder, a.TechnologyType), tryInclude("technologyPlatform", (value_1) => (new Json(0, [value_1])), map(JsonTypes_composeTechnologyPlatform, a.TechnologyPlatform)), tryIncludeList("dataFiles", Data_ISAJson_encoder, dataFiles), tryInclude("materials", encoder, Option_fromValueWithDefault(empty(), processes)), tryIncludeList("characteristicCategories", MaterialAttribute_ISAJson_encoder, characteristics), tryIncludeList("unitCategories", OntologyAnnotation_ISAJson_encoder, units), tryIncludeList("processSequence", Process_ISAJson_encoder, processes), tryIncludeSeq("comments", Comment_ISAJson_encoder, a.Comments)]))]);
+export function Assay_ISAJson_encoder(studyName, idMap, a) {
+    const f = (a_1) => {
+        let assayName;
+        const fileName = Assay_fileNameFromIdentifier(a_1.Identifier);
+        const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(a_1);
+        const encodedUnits = tryIncludeList("unitCategories", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), getUnits(processes));
+        const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_1) => MaterialAttribute_ISAJson_encoder(idMap, value_1), getCharacteristics(processes));
+        const encodedMaterials = tryInclude("materials", (ps) => encoder_3(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) => {
+            const v = tupledArg[1];
+            if (equals(v, new Json(3, []))) {
+                return void 0;
+            }
+            else {
+                return [tupledArg[0], v];
+            }
+        }, ofArray([["filename", new Json(0, [fileName])], tryInclude("@id", (value_5) => (new Json(0, [value_5])), Assay_ROCrate_genID(a_1)), tryInclude("measurementType", (oa_2) => OntologyAnnotation_ISAJson_encoder(idMap, oa_2), a_1.MeasurementType), tryInclude("technologyType", (oa_3) => OntologyAnnotation_ISAJson_encoder(idMap, oa_3), a_1.TechnologyType), tryInclude("technologyPlatform", (value_7) => (new Json(0, [value_7])), map(JsonTypes_composeTechnologyPlatform, a_1.TechnologyPlatform)), encocedDataFiles, encodedMaterials, encodedCharacteristics, encodedUnits, tryIncludeList("processSequence", (assayName = a_1.Identifier, (oa_4) => Process_ISAJson_encoder(studyName, assayName, idMap, oa_4)), processes), tryIncludeSeq("comments", (comment) => Comment_ISAJson_encoder(idMap, comment), a_1.Comments)]))]);
+    };
+    if (idMap != null) {
+        return encode(Assay_ROCrate_genID, f, a, idMap);
+    }
+    else {
+        return f(a);
+    }
 }
 
 export const Assay_ISAJson_allowedFields = ofArray(["@id", "filename", "measurementType", "technologyType", "technologyPlatform", "dataFiles", "materials", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
@@ -143,6 +155,10 @@ export function ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F(spaces) {
     };
 }
 
+export function ARCtrl_ArcAssay__ArcAssay_ToJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C83C5(s) {
     try {
         const matchValue = fromString(decode(Assay_decoderCompressed), s);
@@ -160,7 +176,11 @@ export function ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C8
 }
 
 export function ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F(spaces) {
-    return (obj) => toString(defaultArg(spaces, 0), encode(Assay_encoderCompressed, obj));
+    return (obj) => toString(defaultArg(spaces, 0), encode_1(Assay_encoderCompressed, obj));
+}
+
+export function ARCtrl_ArcAssay__ArcAssay_ToCompressedJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(this$);
 }
 
 export function ARCtrl_ArcAssay__ArcAssay_fromROCrateJsonString_Static_Z721C83C5(s) {
@@ -183,9 +203,14 @@ export function ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47(st
     };
 }
 
-export function ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_ArcAssay__ArcAssay_ToROCrateJsonString_5CABCA47(this$, studyName, spaces) {
+    return ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47(unwrap(studyName), unwrap(spaces))(this$);
+}
+
+export function ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (obj) => {
-        const value = Assay_ISAJson_encoder(obj);
+        const value = Assay_ISAJson_encoder(void 0, idMap, obj);
         return toString(defaultSpaces(spaces), value);
     };
 }
@@ -200,3 +225,7 @@ export function ARCtrl_ArcAssay__ArcAssay_fromISAJsonString_Static_Z721C83C5(s)
     }
 }
 
+export function ARCtrl_ArcAssay__ArcAssay_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
+}
+

package/Json/Comment.js

@@ -9,6 +9,7 @@ import { printf, toText, replace } from "../fable_modules/fable-library-js.4.16.
 import { context_jsonvalue } from "./context/rocrate/isa_comment_context.js";
 import { toString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
 import { fromString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { encode } from "./IDTable.js";
 
 export function Comment_encoder(comment) {
     return new Json(5, [choose((tupledArg) => {
@@ -70,7 +71,23 @@ export const Comment_ROCrate_decoderDisambiguatingDescription = map((s) => {
     }
 }, string);
 
-export const Comment_ISAJson_encoder = Comment_encoder;
+export function Comment_ISAJson_encoder(idMap, comment) {
+    const f = (comment_1) => (new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), Comment_ROCrate_genID(comment_1)), tryInclude("name", (value_2) => (new Json(0, [value_2])), comment_1.Name), tryInclude("value", (value_4) => (new Json(0, [value_4])), comment_1.Value)]))]));
+    if (idMap == null) {
+        return f(comment);
+    }
+    else {
+        return encode(Comment_ROCrate_genID, f, comment, idMap);
+    }
+}
 
 export const Comment_ISAJson_decoder = Comment_decoder;
 
@@ -91,6 +108,10 @@ export function ARCtrl_Comment__Comment_toJsonString_Static_71136F3F(spaces) {
     };
 }
 
+export function ARCtrl_Comment__Comment_toJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_Comment__Comment_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_Comment__Comment_fromROCrateJsonString_Static_Z721C83C5(s) {
     const matchValue = fromString(Comment_ROCrate_decoder, s);
     if (matchValue.tag === 1) {
@@ -111,11 +132,8 @@ export function ARCtrl_Comment__Comment_toROCrateJsonString_Static_71136F3F(spac
     };
 }
 
-export function ARCtrl_Comment__Comment_toISAJsonString_Static_71136F3F(spaces) {
-    return (c) => {
-        const value = Comment_ISAJson_encoder(c);
-        return toString(defaultSpaces(spaces), value);
-    };
+export function ARCtrl_Comment__Comment_toROCrateJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_Comment__Comment_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(this$);
 }
 
 export function ARCtrl_Comment__Comment_fromISAJsonString_Static_Z721C83C5(s) {
@@ -128,3 +146,14 @@ export function ARCtrl_Comment__Comment_fromISAJsonString_Static_Z721C83C5(s) {
     }
 }
 
+export function ARCtrl_Comment__Comment_toISAJsonString_Static_71136F3F(spaces) {
+    return (c) => {
+        const value = Comment_ISAJson_encoder(void 0, c);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_Comment__Comment_toISAJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_Comment__Comment_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+

package/Json/IDTable.js

@@ -0,0 +1,19 @@
+import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { addToDict } from "../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+
+export function encodeID(id) {
+    return new Json(5, [[["@id", new Json(0, [id])]]]);
+}
+
+export function encode(genID, encoder, value, table) {
+    const id = genID(value);
+    if (table.has(id)) {
+        return encodeID(id);
+    }
+    else {
+        const v = encoder(value);
+        addToDict(table, genID(value), v);
+        return v;
+    }
+}
+

package/Json/Investigation.js

@@ -13,7 +13,7 @@ import { ArcInvestigation } from "../Core/ArcTypes.js";
 import { Decode_objectNoAdditionalProperties, Decode_resizeArray } from "./Decode.js";
 import { context_jsonvalue } from "./context/rocrate/isa_investigation_context.js";
 import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
-import { defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { unwrap, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { distinctBy } from "../fable_modules/fable-library-js.4.16.0/Seq2.js";
 import { map, concat } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { context_jsonvalue as context_jsonvalue_1, conformsTo_jsonvalue } from "./context/rocrate/rocrate_context.js";
@@ -110,7 +110,7 @@ export function Investigation_ROCrate_encodeRoCrate(oa) {
 
 export const Investigation_ISAJson_allowedFields = ofArray(["@id", "filename", "identifier", "title", "description", "submissionDate", "publicReleaseDate", "ontologySourceReferences", "publications", "people", "studies", "comments", "@type", "@context"]);
 
-export function Investigation_ISAJson_encoder(inv) {
+export function Investigation_ISAJson_encoder(idMap, inv) {
     return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
         if (equals(v, new Json(3, []))) {
@@ -119,7 +119,7 @@ export function Investigation_ISAJson_encoder(inv) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([["filename", new Json(0, [ArcInvestigation.FileName])], ["identifier", new Json(0, [inv.Identifier])], tryInclude("title", (value_2) => (new Json(0, [value_2])), inv.Title), tryInclude("description", (value_4) => (new Json(0, [value_4])), inv.Description), tryInclude("submissionDate", (value_6) => (new Json(0, [value_6])), inv.SubmissionDate), tryInclude("publicReleaseDate", (value_8) => (new Json(0, [value_8])), inv.PublicReleaseDate), tryIncludeSeq("ontologySourceReferences", OntologySourceReference_ISAJson_encoder, inv.OntologySourceReferences), tryIncludeSeq("publications", Publication_ISAJson_encoder, inv.Publications), tryIncludeSeq("people", Person_ISAJson_encoder, inv.Contacts), tryIncludeSeq("studies", (s) => Study_ISAJson_encoder(void 0, s), inv.Studies), tryIncludeSeq("comments", Comment_ISAJson_encoder, inv.Comments)]))]);
+    }, ofArray([["@id", new Json(0, [Investigation_ROCrate_genID(inv)])], ["filename", new Json(0, [ArcInvestigation.FileName])], ["identifier", new Json(0, [inv.Identifier])], tryInclude("title", (value_3) => (new Json(0, [value_3])), inv.Title), tryInclude("description", (value_5) => (new Json(0, [value_5])), inv.Description), tryInclude("submissionDate", (value_7) => (new Json(0, [value_7])), inv.SubmissionDate), tryInclude("publicReleaseDate", (value_9) => (new Json(0, [value_9])), inv.PublicReleaseDate), tryIncludeSeq("ontologySourceReferences", (osr) => OntologySourceReference_ISAJson_encoder(idMap, osr), inv.OntologySourceReferences), tryIncludeSeq("publications", (oa) => Publication_ISAJson_encoder(idMap, oa), inv.Publications), tryIncludeSeq("people", (person) => Person_ISAJson_encoder(idMap, person), inv.Contacts), tryIncludeSeq("studies", (s) => Study_ISAJson_encoder(idMap, void 0, s), inv.Studies), tryIncludeSeq("comments", (comment) => Comment_ISAJson_encoder(idMap, comment), inv.Comments)]))]);
 }
 
 export const Investigation_ISAJson_decoder = Decode_objectNoAdditionalProperties(Investigation_ISAJson_allowedFields, (get$) => {
@@ -161,6 +161,10 @@ export function ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71
     };
 }
 
+export function ARCtrl_ArcInvestigation__ArcInvestigation_ToJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_ArcInvestigation__ArcInvestigation_fromCompressedJsonString_Static_Z721C83C5(s) {
     try {
         const matchValue = fromString(decode(Investigation_decoderCompressed), s);
@@ -181,6 +185,10 @@ export function ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString
     return (obj) => toString(defaultArg(spaces, 0), encode(Investigation_encoderCompressed, obj));
 }
 
+export function ARCtrl_ArcInvestigation__ArcInvestigation_ToCompressedJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateJsonString_Static_Z721C83C5(s) {
     const matchValue = fromString(Investigation_ROCrate_decoder, s);
     if (matchValue.tag === 1) {
@@ -201,9 +209,14 @@ export function ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_St
     };
 }
 
-export function ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
+export function ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (obj) => {
-        const value = Investigation_ISAJson_encoder(obj);
+        const value = Investigation_ISAJson_encoder(idMap, obj);
         return toString(defaultSpaces(spaces), value);
     };
 }
@@ -218,3 +231,7 @@ export function ARCtrl_ArcInvestigation__ArcInvestigation_fromISAJsonString_Stat
     }
 }
 
+export function ARCtrl_ArcInvestigation__ArcInvestigation_ToISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
+}
+

package/Json/OntologyAnnotation.js

@@ -12,6 +12,9 @@ import { printf, toText, replace } from "../fable_modules/fable-library-js.4.16.
 import { URIModule_toString } from "../Core/URI.js";
 import { context_jsonvalue } from "./context/rocrate/isa_ontology_annotation_context.js";
 import { context_jsonvalue as context_jsonvalue_1 } from "./context/rocrate/property_value_context.js";
+import { filter } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { orderName } from "../Core/Process/ColumnIndex.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";
 
@@ -109,7 +112,47 @@ export const OntologyAnnotation_ROCrate_decoderPropertyValue = object((get$) =>
     return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("category", string))), void 0, unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("categoryCode", string))), unwrap((arg_5 = Decode_resizeArray(Comment_ROCrate_decoderDisambiguatingDescription), (objectArg_2 = get$.Optional, objectArg_2.Field("comments", arg_5)))));
 });
 
-export const OntologyAnnotation_ISAJson_encoder = OntologyAnnotation_encoder;
+export function OntologyAnnotation_ISAJson_encoder(idMap, oa) {
+    const f = (oa_1) => {
+        const comments = filter((c) => {
+            const matchValue = c.Name;
+            let matchResult, n_1;
+            if (matchValue != null) {
+                if (matchValue === orderName) {
+                    matchResult = 0;
+                    n_1 = matchValue;
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else {
+                matchResult = 1;
+            }
+            switch (matchResult) {
+                case 0:
+                    return false;
+                default:
+                    return true;
+            }
+        }, oa_1.Comments);
+        return new Json(5, [choose((tupledArg) => {
+            const v = tupledArg[1];
+            if (equals(v, new Json(3, []))) {
+                return void 0;
+            }
+            else {
+                return [tupledArg[0], v];
+            }
+        }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), OntologyAnnotation_ROCrate_genID(oa_1)), tryInclude("annotationValue", (value_2) => (new Json(0, [value_2])), oa_1.Name), tryInclude("termSource", (value_4) => (new Json(0, [value_4])), oa_1.TermSourceREF), tryInclude("termAccession", (value_6) => (new Json(0, [value_6])), oa_1.TermAccessionNumber), tryIncludeSeq("comments", Comment_encoder, comments)]))]);
+    };
+    if (idMap != null) {
+        return encode(OntologyAnnotation_ROCrate_genID, f, oa, idMap);
+    }
+    else {
+        return f(oa);
+    }
+}
 
 export const OntologyAnnotation_ISAJson_decoder = OntologyAnnotation_decoder;
 
@@ -130,6 +173,10 @@ export function ARCtrl_OntologyAnnotation__OntologyAnnotation_toJsonString_Stati
     };
 }
 
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_ToJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_OntologyAnnotation__OntologyAnnotation_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_OntologyAnnotation__OntologyAnnotation_fromROCrateJsonString_Static_Z721C83C5(s) {
     const matchValue = fromString(OntologyAnnotation_ROCrate_decoderDefinedTerm, s);
     if (matchValue.tag === 1) {
@@ -150,11 +197,8 @@ export function ARCtrl_OntologyAnnotation__OntologyAnnotation_toROCrateJsonStrin
     };
 }
 
-export function ARCtrl_OntologyAnnotation__OntologyAnnotation_toISAJsonString_Static_71136F3F(spaces) {
-    return (obj) => {
-        const value = OntologyAnnotation_ISAJson_encoder(obj);
-        return toString(defaultSpaces(spaces), value);
-    };
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_ToROCrateJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_OntologyAnnotation__OntologyAnnotation_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(this$);
 }
 
 export function ARCtrl_OntologyAnnotation__OntologyAnnotation_fromISAJsonString_Static_Z721C83C5(s) {
@@ -167,3 +211,14 @@ export function ARCtrl_OntologyAnnotation__OntologyAnnotation_fromISAJsonString_
     }
 }
 
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_toISAJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = OntologyAnnotation_ISAJson_encoder(void 0, obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_ToISAJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_OntologyAnnotation__OntologyAnnotation_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+

package/Json/OntologySourceReference.js

@@ -2,7 +2,7 @@ import { ofArray, choose } from "../fable_modules/fable-library-js.4.16.0/List.j
 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 { Comment_decoder, Comment_encoder } from "./Comment.js";
+import { Comment_ISAJson_encoder, Comment_decoder, Comment_encoder } from "./Comment.js";
 import { string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { OntologySourceReference } from "../Core/OntologySourceReference.js";
 import { unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
@@ -62,7 +62,17 @@ export const OntologySourceReference_ROCrate_decoder = object((get$) => {
     return new OntologySourceReference(unwrap((objectArg = get$.Optional, objectArg.Field("description", Decode_uri))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("file", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("name", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("version", string))), unwrap((arg_9 = Decode_resizeArray(Comment_decoder), (objectArg_4 = get$.Optional, objectArg_4.Field("comments", arg_9)))));
 });
 
-export const OntologySourceReference_ISAJson_encoder = OntologySourceReference_encoder;
+export function OntologySourceReference_ISAJson_encoder(idMap, osr) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([tryInclude("description", (value) => (new Json(0, [value])), osr.Description), tryInclude("file", (value_2) => (new Json(0, [value_2])), osr.File), tryInclude("name", (value_4) => (new Json(0, [value_4])), osr.Name), tryInclude("version", (value_6) => (new Json(0, [value_6])), osr.Version), tryIncludeSeq("comments", (comment) => Comment_ISAJson_encoder(idMap, comment), osr.Comments)]))]);
+}
 
 export const OntologySourceReference_ISAJson_decoder = OntologySourceReference_decoder;
 
@@ -83,6 +93,10 @@ export function ARCtrl_OntologySourceReference__OntologySourceReference_toJsonSt
     };
 }
 
+export function ARCtrl_OntologySourceReference__OntologySourceReference_ToJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_OntologySourceReference__OntologySourceReference_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_OntologySourceReference__OntologySourceReference_fromROCrateJsonString_Static_Z721C83C5(s) {
     const matchValue = fromString(OntologySourceReference_ROCrate_decoder, s);
     if (matchValue.tag === 1) {
@@ -103,11 +117,8 @@ export function ARCtrl_OntologySourceReference__OntologySourceReference_toROCrat
     };
 }
 
-export function ARCtrl_OntologySourceReference__OntologySourceReference_toISAJsonString_Static_71136F3F(spaces) {
-    return (obj) => {
-        const value = OntologySourceReference_ISAJson_encoder(obj);
-        return toString(defaultSpaces(spaces), value);
-    };
+export function ARCtrl_OntologySourceReference__OntologySourceReference_ToROCrateJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_OntologySourceReference__OntologySourceReference_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(this$);
 }
 
 export function ARCtrl_OntologySourceReference__OntologySourceReference_fromISAJsonString_Static_Z721C83C5(s) {
@@ -120,3 +131,14 @@ export function ARCtrl_OntologySourceReference__OntologySourceReference_fromISAJ
     }
 }
 
+export function ARCtrl_OntologySourceReference__OntologySourceReference_toISAJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = OntologySourceReference_ISAJson_encoder(void 0, obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_OntologySourceReference__OntologySourceReference_ToISAJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_OntologySourceReference__OntologySourceReference_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+

package/Json/Person.js

@@ -14,6 +14,7 @@ import { context_jsonvalue } from "./context/rocrate/isa_organization_context.js
 import { contextMinimal_jsonValue, context_jsonvalue as context_jsonvalue_1 } from "./context/rocrate/isa_person_context.js";
 import { map } from "../fable_modules/fable-library-js.4.16.0/Array.js";
 import { Person_setOrcidFromComments, Person_setCommentFromORCID } from "../Core/Conversion.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";
 
@@ -176,17 +177,25 @@ export const Person_ROCrate_decodeAuthorListString = map_1((v) => join(", ", v),
 
 export const Person_ISAJson_allowedFields = ofArray(["@id", "firstName", "lastName", "midInitials", "email", "phone", "fax", "address", "affiliation", "roles", "comments", "@type", "@context"]);
 
-export function Person_ISAJson_encoder(person) {
-    const person_1 = Person_setCommentFromORCID(person);
-    return new Json(5, [choose((tupledArg) => {
-        const v = tupledArg[1];
-        if (equals(v, new Json(3, []))) {
-            return void 0;
-        }
-        else {
-            return [tupledArg[0], v];
-        }
-    }, ofArray([tryInclude("firstName", (value) => (new Json(0, [value])), person_1.FirstName), tryInclude("lastName", (value_2) => (new Json(0, [value_2])), person_1.LastName), tryInclude("midInitials", (value_4) => (new Json(0, [value_4])), person_1.MidInitials), tryInclude("email", (value_6) => (new Json(0, [value_6])), person_1.EMail), tryInclude("phone", (value_8) => (new Json(0, [value_8])), person_1.Phone), tryInclude("fax", (value_10) => (new Json(0, [value_10])), person_1.Fax), tryInclude("address", (value_12) => (new Json(0, [value_12])), person_1.Address), tryInclude("affiliation", (value_14) => (new Json(0, [value_14])), person_1.Affiliation), tryIncludeSeq("roles", OntologyAnnotation_encoder, person_1.Roles), tryIncludeSeq("comments", Comment_encoder, person_1.Comments)]))]);
+export function Person_ISAJson_encoder(idMap, person) {
+    const f = (person_1) => {
+        const person_2 = Person_setCommentFromORCID(person_1);
+        return new Json(5, [choose((tupledArg) => {
+            const v = tupledArg[1];
+            if (equals(v, new Json(3, []))) {
+                return void 0;
+            }
+            else {
+                return [tupledArg[0], v];
+            }
+        }, ofArray([tryInclude("@id", (value) => (new Json(0, [value])), Person_ROCrate_genID(person_2)), tryInclude("firstName", (value_2) => (new Json(0, [value_2])), person_2.FirstName), tryInclude("lastName", (value_4) => (new Json(0, [value_4])), person_2.LastName), tryInclude("midInitials", (value_6) => (new Json(0, [value_6])), person_2.MidInitials), tryInclude("email", (value_8) => (new Json(0, [value_8])), person_2.EMail), tryInclude("phone", (value_10) => (new Json(0, [value_10])), person_2.Phone), tryInclude("fax", (value_12) => (new Json(0, [value_12])), person_2.Fax), tryInclude("address", (value_14) => (new Json(0, [value_14])), person_2.Address), tryInclude("affiliation", (value_16) => (new Json(0, [value_16])), person_2.Affiliation), tryIncludeSeq("roles", OntologyAnnotation_encoder, person_2.Roles), tryIncludeSeq("comments", Comment_encoder, person_2.Comments)]))]);
+    };
+    if (idMap != null) {
+        return encode(Person_ROCrate_genID, f, person, idMap);
+    }
+    else {
+        return f(person);
+    }
 }
 
 export const Person_ISAJson_decoder = Decode_objectNoAdditionalProperties(Person_ISAJson_allowedFields, (get$) => {
@@ -211,6 +220,10 @@ export function ARCtrl_Person__Person_toJsonString_Static_71136F3F(spaces) {
     };
 }
 
+export function ARCtrl_Person__Person_toJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_Person__Person_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_Person__Person_fromROCrateJsonString_Static_Z721C83C5(s) {
     const matchValue = fromString(Person_ROCrate_decoder, s);
     if (matchValue.tag === 1) {
@@ -231,11 +244,8 @@ export function ARCtrl_Person__Person_toROCrateJsonString_Static_71136F3F(spaces
     };
 }
 
-export function ARCtrl_Person__Person_toISAJsonString_Static_71136F3F(spaces) {
-    return (obj) => {
-        const value = Person_ISAJson_encoder(obj);
-        return toString(defaultSpaces(spaces), value);
-    };
+export function ARCtrl_Person__Person_toROCrateJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_Person__Person_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(this$);
 }
 
 export function ARCtrl_Person__Person_fromISAJsonString_Static_Z721C83C5(s) {
@@ -248,3 +258,15 @@ export function ARCtrl_Person__Person_fromISAJsonString_Static_Z721C83C5(s) {
     }
 }
 
+export function ARCtrl_Person__Person_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
+    return (obj) => {
+        const value = Person_ISAJson_encoder(idMap, obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_Person__Person_toISAJsonString_Z3B036AA(this$, spaces, useIDReferencing) {
+    return ARCtrl_Person__Person_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(this$);
+}
+

package/Json/Process/AssayMaterials.js

@@ -6,7 +6,7 @@ import { tryIncludeList } from "../Encode.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 samples = getSamples(ps);
     const materials = getMaterials(ps);
     return new Json(5, [choose((tupledArg) => {
@@ -17,6 +17,6 @@ export function encoder(ps) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([tryIncludeList("samples", Sample_ISAJson_encoder, samples), tryIncludeList("otherMaterials", Material_ISAJson_encoder, materials)]))]);
+    }, ofArray([tryIncludeList("samples", (oa) => Sample_ISAJson_encoder(idMap, oa), samples), tryIncludeList("otherMaterials", (c) => Material_ISAJson_encoder(idMap, c), materials)]))]);
 }
 

package/Json/Process/Component.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 { 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";
@@ -9,13 +9,18 @@ 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";
 
 export const Component_ROCrate_encoder = encoder;
 
 export const Component_ROCrate_decoder = decoder_1(Component_createAsPV);
 
-export function Component_ISAJson_encoder(c) {
+export function Component_ISAJson_genID(c) {
+    return genID(c);
+}
+
+export function Component_ISAJson_encoder(idMap, c) {
     return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
         if (equals(v, new Json(3, []))) {
@@ -24,7 +29,7 @@ export function Component_ISAJson_encoder(c) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([tryInclude("componentName", (value) => (new Json(0, [value])), Component__get_ComponentName(c)), tryInclude("componentType", OntologyAnnotation_ISAJson_encoder, c.ComponentType)]))]);
+    }, ofArray([tryInclude("componentName", (value) => (new Json(0, [value])), Component__get_ComponentName(c)), tryInclude("componentType", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), c.ComponentType)]))]);
 }
 
 export const Component_ISAJson_decoder = object((get$) => {
@@ -53,13 +58,18 @@ export function ARCtrl_Process_Component__Component_fromISAJsonString_Static_Z72
     }
 }
 
-export function ARCtrl_Process_Component__Component_toISAJsonString_Static_71136F3F(spaces) {
+export function ARCtrl_Process_Component__Component_toISAJsonString_Static_Z3B036AA(spaces, useIDReferencing) {
+    const idMap = defaultArg(useIDReferencing, false) ? (new Map([])) : void 0;
     return (f) => {
-        const value = Component_ISAJson_encoder(f);
+        const value = Component_ISAJson_encoder(idMap, f);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
+export function ARCtrl_Process_Component__Component_toISAJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_Process_Component__Component_toISAJsonString_Static_Z3B036AA(spaces)(this$);
+}
+
 export function ARCtrl_Process_Component__Component_fromROCrateJsonString_Static_Z721C83C5(s) {
     const matchValue = fromString(Component_ROCrate_decoder, s);
     if (matchValue.tag === 1) {
@@ -77,3 +87,7 @@ export function ARCtrl_Process_Component__Component_toROCrateJsonString_Static_7
     };
 }
 
+export function ARCtrl_Process_Component__Component_toROCrateJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_Process_Component__Component_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+