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

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"]();
@@ -247,6 +260,10 @@ export function ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F(spaces) {
     };
 }
 
+export function ARCtrl_ArcStudy__ArcStudy_ToJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5(s) {
     try {
         const matchValue = fromString(decode(Study_decoderCompressed), s);
@@ -264,17 +281,11 @@ 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));
 }
 
-/**
- * exports in json-ld format
- */
-export function ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086(assays, spaces) {
-    return (obj) => {
-        const value = Study_ROCrate_encoder(assays, obj);
-        return toString(defaultSpaces(spaces), value);
-    };
+export function ARCtrl_ArcStudy__ArcStudy_ToCompressedJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(this$);
 }
 
 export function ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5(s) {
@@ -287,13 +298,20 @@ export function ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5
     }
 }
 
-export function ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_3BA23086(assays, spaces) {
+/**
+ * exports in json-ld format
+ */
+export function ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086(assays, spaces) {
     return (obj) => {
-        const value = Study_ISAJson_encoder(assays, obj);
+        const value = Study_ROCrate_encoder(assays, obj);
         return toString(defaultSpaces(spaces), value);
     };
 }
 
+export function ARCtrl_ArcStudy__ArcStudy_ToROCrateJsonString_3BA23086(this$, assays, spaces) {
+    return ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086(unwrap(assays), unwrap(spaces))(this$);
+}
+
 export function ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5(s) {
     const matchValue = fromString(Study_ISAJson_decoder, s);
     if (matchValue.tag === 1) {
@@ -304,3 +322,15 @@ export function ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5(s)
     }
 }
 
+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(idMap, assays, obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+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/Table/CellTable.js

@@ -35,6 +35,9 @@ export function encodeCell(otm, cc) {
 }
 
 export function decodeCell(ot) {
-    return object((get$) => item(get$.Required.Raw(int), ot));
+    return object((get$) => {
+        const i = get$.Required.Raw(int) | 0;
+        return item(i, ot).Copy();
+    });
 }
 

package/Json/Table/Templates.js

@@ -1,6 +1,6 @@
 import { toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
 import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { dict, datetimeUtc, guid, object, string, succeed, andThen } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { array as array_1, datetimeUtc, guid, object, string, succeed, andThen } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { Template, Organisation } from "../../Core/Template.js";
 import { ArcTable_decoderCompressed, ArcTable_encoderCompressed, ArcTable_decoder, ArcTable_encoder } from "./ArcTable.js";
 import { defaultSpaces, dateTime, tryIncludeSeq } from "../Encode.js";
@@ -45,7 +45,7 @@ export function Templates_encoder(templates) {
     return new Json(6, [map(Template_encoder, templates)]);
 }
 
-export const Templates_decoder = dict(Template_decoder);
+export const Templates_decoder = array_1(Template_decoder);
 
 export function Templates_fromJsonString(jsonString) {
     try {
@@ -85,6 +85,10 @@ export function ARCtrl_Template__Template_toJsonString_Static_71136F3F(spaces) {
     return (template) => toString_2(defaultSpaces(spaces), Template_encoder(template));
 }
 
+export function ARCtrl_Template__Template_toJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_Template__Template_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_Template__Template_fromCompressedJsonString_Static_Z721C83C5(s) {
     try {
         const matchValue = fromString(decode(Template_decoderCompressed), s);
@@ -105,3 +109,7 @@ export function ARCtrl_Template__Template_toCompressedJsonString_Static_71136F3F
     return (obj) => toString_2(defaultArg(spaces, 0), encode(Template_encoderCompressed, obj));
 }
 
+export function ARCtrl_Template__Template_toCompressedJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_Template__Template_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+

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/DataMapTable/DataMapColumn.js

@@ -1,36 +1,42 @@
 import { toFsCells, fromFsCells } from "./DataMapHeader.js";
-import { singleton as singleton_1, ofArray, item, map } from "../../fable_modules/fable-library-js.4.16.0/List.js";
-import { FsAddress__get_RowNumber } from "../../fable_modules/FsSpreadsheet.6.1.2/FsAddress.fs.js";
-import { FsRangeAddress__get_LastAddress } from "../../fable_modules/FsSpreadsheet.6.1.2/Ranges/FsRangeAddress.fs.js";
-import { FsRangeBase__get_RangeAddress } from "../../fable_modules/FsSpreadsheet.6.1.2/Ranges/FsRangeBase.fs.js";
-import { empty, exists, singleton, append, toList, map as map_1, delay, toArray } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
-import { rangeDouble } from "../../fable_modules/fable-library-js.4.16.0/Range.js";
-import { CompositeColumn } from "../../Core/Table/CompositeColumn.js";
-import { item as item_1, map as map_2 } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
-import { toFsCells as toFsCells_1 } from "../AnnotationTable/CompositeCell.js";
+import { transpose, singleton, ofArray, map } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { tryFind, singleton as singleton_1, append, delay, map as map_1, collect, toList } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { distinct } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { bind, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { stringHash } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+import { FsCell } from "../../fable_modules/FsSpreadsheet.6.1.2/Cells/FsCell.fs.js";
+import { DataContext__get_GeneratedBy, DataContext__get_Description, DataContext__get_ObjectType, DataContext__get_Unit, DataContext__get_Explication } from "../../Core/DataContext.js";
 
-export function fromFsColumns(columns) {
-    const patternInput = fromFsCells(map((c) => c.Item(1), columns));
-    const l = FsAddress__get_RowNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(item(0, columns)))) | 0;
-    const cells_1 = toArray(delay(() => map_1((i) => patternInput[1](map((c_1) => c_1.Item(i), columns)), rangeDouble(2, 1, l))));
-    return CompositeColumn.create(patternInput[0], cells_1);
+export function setFromFsColumns(dc, columns) {
+    const cellParser = fromFsCells(map((c) => c.Item(1), columns));
+    for (let i = 0; i <= (dc.length - 1); i++) {
+        cellParser(dc[i])(map((c_1) => c_1.Item(i + 2), columns));
+    }
+    return dc;
 }
 
-export function toFsColumns(column) {
-    const isTerm = column.Header.IsTermColumn;
-    const isData = column.Header.IsDataColumn;
-    const header = toFsCells(column.Header);
-    const cells = map_2((cell) => toFsCells_1(isTerm, false, cell), column.Cells);
-    if (isTerm) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i) => item(0, item_1(i, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_1) => item(1, item_1(i_1, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_2) => item(2, item_1(i_2, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))]);
-    }
-    else if (isData) {
-        const hasFormat = exists((c) => (c.AsData.Format != null), column.Cells);
-        const hasSelectorFormat = exists((c_1) => (c_1.AsData.SelectorFormat != null), column.Cells);
-        return toList(delay(() => append(singleton(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_3) => item(0, item_1(i_3, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))), delay(() => append(hasFormat ? singleton(toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_4) => item(1, item_1(i_4, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))) : empty(), delay(() => (hasSelectorFormat ? singleton(toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_5) => item(2, item_1(i_5, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))) : empty())))))));
-    }
-    else {
-        return singleton_1(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_6) => item(0, item_1(i_6, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))));
-    }
+export function toFsColumns(dc) {
+    const commentKeys = toList(distinct(collect((dc_1) => map_1((c) => defaultArg(c.Name, ""), dc_1.Comments), dc), {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    }));
+    const headers = toFsCells(commentKeys);
+    const createTerm = (oa) => {
+        if (oa == null) {
+            return ofArray([new FsCell(""), new FsCell(""), new FsCell("")]);
+        }
+        else {
+            const oa_1 = oa;
+            return ofArray([new FsCell(defaultArg(oa_1.Name, "")), new FsCell(defaultArg(oa_1.TermSourceREF, "")), new FsCell(defaultArg(oa_1.TermAccessionNumber, ""))]);
+        }
+    };
+    const createText = (s) => singleton(new FsCell(defaultArg(s, "")));
+    return transpose(toList(delay(() => append(singleton_1(headers), delay(() => map_1((dc_4) => {
+        const dc_3 = dc_4;
+        return toList(delay(() => {
+            let dc_2;
+            return append((dc_2 = dc_3, ofArray([new FsCell(defaultArg(dc_2.Name, "")), new FsCell(defaultArg(dc_2.Format, "")), new FsCell(defaultArg(dc_2.SelectorFormat, ""))])), delay(() => append(createTerm(DataContext__get_Explication(dc_3)), delay(() => append(createTerm(DataContext__get_Unit(dc_3)), delay(() => append(createTerm(DataContext__get_ObjectType(dc_3)), delay(() => append(createText(DataContext__get_Description(dc_3)), delay(() => append(createText(DataContext__get_GeneratedBy(dc_3)), delay(() => map((key) => (new FsCell(defaultArg(bind((c_2) => c_2.Value, tryFind((c_1) => (defaultArg(c_1.Name, "") === key), dc_3.Comments)), ""))), commentKeys)))))))))))));
+        }));
+    }, dc))))));
 }