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

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$, assays, spaces, useIDReferencing) {
+    return ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1(unwrap(assays), unwrap(spaces), unwrap(useIDReferencing))(this$);
 }
 

package/Json.js

@@ -1,9 +1,9 @@
 import { ARCtrl_OntologyAnnotation__OntologyAnnotation_toROCrateJsonString_Static_71136F3F, ARCtrl_OntologyAnnotation__OntologyAnnotation_toISAJsonString_Static_71136F3F, ARCtrl_OntologyAnnotation__OntologyAnnotation_toJsonString_Static_71136F3F, ARCtrl_OntologyAnnotation__OntologyAnnotation_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_OntologyAnnotation__OntologyAnnotation_fromISAJsonString_Static_Z721C83C5, ARCtrl_OntologyAnnotation__OntologyAnnotation_fromJsonString_Static_Z721C83C5 } from "./Json/OntologyAnnotation.js";
 import { unwrap } from "./fable_modules/fable-library-js.4.16.0/Option.js";
 import { class_type } from "./fable_modules/fable-library-js.4.16.0/Reflection.js";
-import { ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47, ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromJsonString_Static_Z721C83C5 } from "./Json/Assay.js";
-import { ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086, ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_3BA23086, ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromJsonString_Static_Z721C83C5 } from "./Json/Study.js";
-import { ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromJsonString_Static_Z721C83C5 } from "./Json/Investigation.js";
+import { ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47, ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_Z3B036AA, ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromJsonString_Static_Z721C83C5 } from "./Json/Assay.js";
+import { ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086, ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1, ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromJsonString_Static_Z721C83C5 } from "./Json/Study.js";
+import { ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_Z3B036AA, ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromJsonString_Static_Z721C83C5 } from "./Json/Investigation.js";
 import { ARC } from "./ARC.js";
 
 export class JsonHelper_OntologyAnnotationJson {
@@ -58,8 +58,8 @@ export class JsonHelper_AssayJson {
     toCompressedJsonString(assay, spaces) {
         return ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(assay);
     }
-    toISAJsonString(assay, spaces) {
-        return ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_71136F3F(unwrap(spaces))(assay);
+    toISAJsonString(assay, spaces, useIDReferencing) {
+        return ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(assay);
     }
     toROCrateJsonString(assay, studyName, spaces) {
         return ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47(studyName, unwrap(spaces))(assay);
@@ -95,8 +95,8 @@ export class JsonHelper_StudyJson {
     toCompressedJsonString(study, spaces) {
         return ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(study);
     }
-    toISAJsonString(study, assays, spaces) {
-        return ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_3BA23086(unwrap(assays), unwrap(spaces))(study);
+    toISAJsonString(study, assays, spaces, useIDReferencing) {
+        return ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1(unwrap(assays), unwrap(spaces), unwrap(useIDReferencing))(study);
     }
     toROCrateJsonString(study, assays, spaces) {
         return ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086(unwrap(assays), unwrap(spaces))(study);
@@ -132,8 +132,8 @@ export class JsonHelper_InvestigationJson {
     toCompressedJsonString(investigation, spaces) {
         return ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(investigation);
     }
-    toISAJsonString(investigation, spaces) {
-        return ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_71136F3F(unwrap(spaces))(investigation);
+    toISAJsonString(investigation, spaces, useIDReferencing) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_Z3B036AA(unwrap(spaces), unwrap(useIDReferencing))(investigation);
     }
     toROCrateJsonString(investigation, spaces) {
         return ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(investigation);

package/Spreadsheet/AnnotationTable/ArcTable.js

@@ -1,15 +1,17 @@
-import { iterateIndexed, length, sortBy, collect, toArray, exists, ofArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../fable_modules/fable-library-js.4.16.0/List.js";
-import { map as map_1, toList, tryFind } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
-import { toFsColumns, fixDeprecatedIOHeader, fromFsColumns } from "./CompositeColumn.js";
+import { iterateIndexed, length, sortBy, collect as collect_1, exists, toArray, ofArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { item, map as map_1 } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+import { singleton as singleton_1, collect, map as map_2, delay, toArray as toArray_1, tryFind } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { toStringCellColumns, fixDeprecatedIOHeader, fromStringCellColumns } from "./CompositeColumn.js";
 import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { Dictionary_tryGet, FsCellsCollection__TryGetCell_Z37302880 } from "../../fable_modules/FsSpreadsheet.6.1.2/Cells/FsCellsCollection.fs.js";
+import { rangeDouble } from "../../fable_modules/fable-library-js.4.16.0/Range.js";
+import { FsAddress_$ctor_Z37302880, FsAddress__get_ColumnNumber, FsAddress__get_RowNumber } from "../../fable_modules/FsSpreadsheet.6.1.2/FsAddress.fs.js";
+import { FsRangeAddress_$ctor_7E77A4A0, FsRangeAddress__get_LastAddress } from "../../fable_modules/FsSpreadsheet.6.1.2/Ranges/FsRangeAddress.fs.js";
+import { FsRangeBase__Cell_Z3407A44B, FsRangeBase__get_RangeAddress } from "../../fable_modules/FsSpreadsheet.6.1.2/Ranges/FsRangeBase.fs.js";
 import { ArcTable } from "../../Core/Table/ArcTable.js";
 import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.6.1.2/FsWorksheet.fs.js";
 import { comparePrimitives } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
-import { FsRangeAddress_$ctor_7E77A4A0 } from "../../fable_modules/FsSpreadsheet.6.1.2/Ranges/FsRangeAddress.fs.js";
-import { FsAddress_$ctor_Z37302880 } from "../../fable_modules/FsSpreadsheet.6.1.2/FsAddress.fs.js";
-import { Dictionary_tryGet } from "../../fable_modules/FsSpreadsheet.6.1.2/Cells/FsCellsCollection.fs.js";
 import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
-import { FsRangeBase__Cell_Z3407A44B } from "../../fable_modules/FsSpreadsheet.6.1.2/Ranges/FsRangeBase.fs.js";
 
 /**
  * Iterates over elements of the input list and groups adjacent elements.
@@ -64,11 +66,11 @@ export function classifyColumnOrder(column) {
 
 export const helperColumnStrings = ofArray(["Term Source REF", "Term Accession Number", "Unit", "Data Format", "Data Selector Format"]);
 
-export function groupColumnsByHeader(columns) {
-    return Aux_List_groupWhen((c) => {
-        const v = c.Item(1).ValueAsString();
+export function groupColumnsByHeader(stringCellColumns) {
+    return map_1(toArray, toArray(Aux_List_groupWhen((c) => {
+        const v = item(0, c);
         return !exists((s) => (v.indexOf(s) === 0), helperColumnStrings);
-    }, columns);
+    }, ofArray(stringCellColumns))));
 }
 
 /**
@@ -81,8 +83,8 @@ export function tryAnnotationTable(sheet) {
 /**
  * Groups and parses a collection of single columns into the according ISA composite columns
  */
-export function composeColumns(columns) {
-    return toArray(map(fromFsColumns, groupColumnsByHeader(toList(columns))));
+export function composeColumns(stringCellColumns) {
+    return map_1(fromStringCellColumns, groupColumnsByHeader(stringCellColumns));
 }
 
 /**
@@ -96,7 +98,16 @@ export function tryFromFsWorksheet(sheet) {
         }
         else {
             const t = matchValue;
-            const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
+            const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, toArray_1(delay(() => map_2((c) => toArray_1(delay(() => collect((r) => {
+                const matchValue_1 = FsCellsCollection__TryGetCell_Z37302880(sheet.CellCollection, r, c);
+                if (matchValue_1 == null) {
+                    return singleton_1("");
+                }
+                else {
+                    const cell = matchValue_1;
+                    return singleton_1(cell.ValueAsString());
+                }
+            }, rangeDouble(1, 1, FsAddress__get_RowNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(t))))))), rangeDouble(1, 1, FsAddress__get_ColumnNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(t)))))))));
             return ArcTable.addColumns(compositeColumns, void 0, true)(ArcTable.init(sheet.Name));
         }
     }
@@ -114,30 +125,29 @@ export function toFsWorksheet(table) {
         return ws;
     }
     else {
-        const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
+        const columns = collect_1(toStringCellColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
             Compare: comparePrimitives,
         }));
         const maxRow = length(head(columns)) | 0;
         const maxCol = length(columns) | 0;
         const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
         iterateIndexed((colI, col) => {
-            iterateIndexed((rowI, cell) => {
+            iterateIndexed((rowI, stringCell) => {
                 let value;
-                const v = cell.ValueAsString();
                 if (rowI === 0) {
-                    const matchValue = Dictionary_tryGet(v, stringCount);
+                    const matchValue = Dictionary_tryGet(stringCell, stringCount);
                     if (matchValue == null) {
-                        addToDict(stringCount, cell.ValueAsString(), "");
-                        value = v;
+                        addToDict(stringCount, stringCell, "");
+                        value = stringCell;
                     }
                     else {
                         const spaces = matchValue;
-                        stringCount.set(v, spaces + " ");
-                        value = ((v + " ") + spaces);
+                        stringCount.set(stringCell, spaces + " ");
+                        value = ((stringCell + " ") + spaces);
                     }
                 }
                 else {
-                    value = v;
+                    value = stringCell;
                 }
                 const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
                 FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);