@nfdi4plants/arctrl 1.2.0 → 2.0.0-alpha.2

package/Json/Publication.js

@@ -0,0 +1,142 @@
+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, tryIncludeSeq, tryInclude } from "./Encode.js";
+import { OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./OntologyAnnotation.js";
+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 { 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";
+import { context_jsonvalue } from "./context/rocrate/isa_publication_context.js";
+import { fromString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { toString } from "../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
+
+export function Publication_encoder(oa) {
+    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("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_encoder, oa.Comments)]))]);
+}
+
+export const Publication_decoder = object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5;
+    return new Publication(unwrap((objectArg = get$.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", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("title", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("status", OntologyAnnotation_decoder))), unwrap((arg_11 = Decode_resizeArray(Comment_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("comments", arg_11)))));
+});
+
+export function Publication_ROCrate_genID(p) {
+    const matchValue = p.DOI;
+    if (matchValue == null) {
+        const matchValue_1 = p.PubMedID;
+        if (matchValue_1 == null) {
+            const matchValue_2 = p.Title;
+            if (matchValue_2 == null) {
+                return "#EmptyPublication";
+            }
+            else {
+                return "#Pub_" + replace(matchValue_2, " ", "_");
+            }
+        }
+        else {
+            return matchValue_1;
+        }
+    }
+    else {
+        return matchValue;
+    }
+}
+
+export function Publication_ROCrate_encoder(oa) {
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([["@id", new Json(0, [Publication_ROCrate_genID(oa)])], ["@type", new Json(0, ["Publication"])], tryInclude("pubMedID", (value_2) => (new Json(0, [value_2])), oa.PubMedID), tryInclude("doi", (value_4) => (new Json(0, [value_4])), oa.DOI), tryInclude("authorList", Person_ROCrate_encodeAuthorListString, oa.Authors), tryInclude("title", (value_6) => (new Json(0, [value_6])), oa.Title), tryInclude("status", OntologyAnnotation_ROCrate_encoderDefinedTerm, oa.Status), tryIncludeSeq("comments", Comment_ROCrate_encoderDisambiguatingDescription, oa.Comments), ["@context", context_jsonvalue]]))]);
+}
+
+export const Publication_ROCrate_decoder = object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5;
+    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) {
+    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("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)]))]);
+}
+
+export const Publication_ISAJson_allowedFields = ofArray(["pubMedID", "doi", "authorList", "title", "status", "comments"]);
+
+export const Publication_ISAJson_decoder = Decode_noAdditionalProperties(Publication_ISAJson_allowedFields, Publication_decoder);
+
+export function ARCtrl_Publication__Publication_fromJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Publication_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_Publication__Publication_toJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = Publication_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_Publication__Publication_fromROCrateJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Publication_ROCrate_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+/**
+ * exports in json-ld format
+ */
+export function ARCtrl_Publication__Publication_toROCrateJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = Publication_ROCrate_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_Publication__Publication_toISAJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = Publication_ISAJson_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_Publication__Publication_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Publication_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+

package/Json/StringTable.js

@@ -0,0 +1,44 @@
+import { item, map, setItem, fill } from "../fable_modules/fable-library-js.4.16.0/Array.js";
+import { iterate } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { int, string, array as array_1 } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { Dictionary_tryFind } from "../Core/Helper/Collections.js";
+import { addToDict } from "../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { FSharpResult$2 } from "../fable_modules/fable-library-js.4.16.0/Result.js";
+
+export function arrayFromMap(otm) {
+    const a = fill(new Array(otm.size), 0, otm.size, "");
+    iterate((kv) => {
+        setItem(a, kv[1], kv[0]);
+    }, otm);
+    return a;
+}
+
+export function encoder(ot) {
+    return new Json(6, [map((value) => (new Json(0, [value])), ot)]);
+}
+
+export const decoder = array_1(string);
+
+export function encodeString(otm, s) {
+    const matchValue = Dictionary_tryFind(s, otm);
+    if (matchValue == null) {
+        const i_1 = otm.size | 0;
+        addToDict(otm, s, i_1);
+        return new Json(7, [i_1 >>> 0]);
+    }
+    else {
+        const i = matchValue | 0;
+        return new Json(7, [i >>> 0]);
+    }
+}
+
+export function decodeString(ot) {
+    return {
+        Decode(s, json) {
+            const matchValue = int.Decode(s, json);
+            return (matchValue.tag === 1) ? (new FSharpResult$2(1, [matchValue.fields[0]])) : (new FSharpResult$2(0, [item(matchValue.fields[0], ot)]));
+        },
+    };
+}
+

package/Json/Study.js

@@ -0,0 +1,306 @@
+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 { 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";
+import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { defaultSpaces, tryIncludeList, tryIncludeSeq, tryInclude } from "./Encode.js";
+import { Publication_ISAJson_decoder, Publication_ISAJson_encoder, Publication_ROCrate_decoder, Publication_ROCrate_encoder, Publication_decoder, Publication_encoder } from "./Publication.js";
+import { Person_ISAJson_decoder, Person_ISAJson_encoder, Person_ROCrate_decoder, Person_ROCrate_encoder, Person_decoder, Person_encoder } from "./Person.js";
+import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./OntologyAnnotation.js";
+import { ArcTable_decoderCompressed, ArcTable_encoderCompressed, ArcTable_decoder, ArcTable_encoder } from "./Table/ArcTable.js";
+import { Comment_ISAJson_decoder, Comment_ISAJson_encoder, Comment_ROCrate_decoder, Comment_ROCrate_encoder, Comment_decoder, Comment_encoder } from "./Comment.js";
+import { list as list_2, string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { Decode_objectNoAdditionalProperties, Decode_resizeArray } from "./Decode.js";
+import { toFail, printf, toText, replace } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { Assay_fileNameFromIdentifier, createMissingIdentifier, Study_tryIdentifierFromFileName, Study_tryFileNameFromIdentifier } from "../Core/Helper/Identifier.js";
+import { Person_removeSourceAssayComments, Person_getSourceAssayIdentifiersFromComments, Person_setSourceAssayComment, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D, ARCtrl_ArcTables__ArcTables_GetProcesses } from "../Core/Conversion.js";
+import { list as list_1 } from "../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
+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 { Factor_ISAJson_encoder } from "./Process/Factor.js";
+import { MaterialAttribute_ISAJson_encoder } from "./Process/MaterialAttribute.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";
+
+/**
+ * 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);
+    }
+    else {
+        return study.GetRegisteredAssaysOrIdentifier();
+    }
+}
+
+export function Study_encoder(study) {
+    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([["Identifier", new Json(0, [study.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), study.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), study.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), study.PublicReleaseDate), tryIncludeSeq("Publications", Publication_encoder, study.Publications), tryIncludeSeq("Contacts", Person_encoder, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", ArcTable_encoder, study.Tables), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => (new Json(0, [value_9])), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", Comment_encoder, study.Comments)]))]);
+}
+
+export const Study_decoder = object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
+    return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = Decode_resizeArray(Publication_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = Decode_resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = Decode_resizeArray(ArcTable_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((arg_19 = Decode_resizeArray(string), (objectArg_9 = get$.Optional, objectArg_9.Field("RegisteredAssayIdentifiers", arg_19)))), unwrap((arg_21 = Decode_resizeArray(Comment_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("Comments", arg_21)))));
+});
+
+export function Study_encoderCompressed(stringTable, oaTable, cellTable, study) {
+    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([["Identifier", new Json(0, [study.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), study.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), study.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), study.PublicReleaseDate), tryIncludeSeq("Publications", Publication_encoder, study.Publications), tryIncludeSeq("Contacts", Person_encoder, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", (table) => ArcTable_encoderCompressed(stringTable, oaTable, cellTable, table), study.Tables), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => (new Json(0, [value_9])), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", Comment_encoder, study.Comments)]))]);
+}
+
+export function Study_decoderCompressed(stringTable, oaTable, cellTable) {
+    return object((get$) => {
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
+        return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = Decode_resizeArray(Publication_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = Decode_resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = Decode_resizeArray(ArcTable_decoderCompressed(stringTable, oaTable, cellTable)), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((arg_19 = Decode_resizeArray(string), (objectArg_9 = get$.Optional, objectArg_9.Field("RegisteredAssayIdentifiers", arg_19)))), unwrap((arg_21 = Decode_resizeArray(Comment_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("Comments", arg_21)))));
+    });
+}
+
+export function Study_ROCrate_genID(a) {
+    const matchValue = a.Identifier;
+    if (matchValue === "") {
+        return "#EmptyStudy";
+    }
+    else {
+        return `#study/${replace(matchValue, " ", "_")}`;
+    }
+}
+
+export function Study_ROCrate_encoder(assays, s) {
+    let studyName, studyName_1;
+    const fileName = Study_tryFileNameFromIdentifier(s.Identifier);
+    const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(s);
+    const assays_1 = Study_Helper_getAssayInformation(assays, s);
+    return new Json(5, [choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, new Json(3, []))) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([["@id", new Json(0, [Study_ROCrate_genID(s)])], ["@type", list_1(singleton(new Json(0, ["Study"])))], ["additionalType", new Json(0, ["Study"])], ["identifier", new Json(0, [s.Identifier])], tryInclude("filename", (value_4) => (new Json(0, [value_4])), fileName), tryInclude("title", (value_6) => (new Json(0, [value_6])), s.Title), tryInclude("description", (value_8) => (new Json(0, [value_8])), s.Description), tryIncludeSeq("studyDesignDescriptors", OntologyAnnotation_ROCrate_encoderDefinedTerm, s.StudyDesignDescriptors), tryInclude("submissionDate", (value_10) => (new Json(0, [value_10])), s.SubmissionDate), tryInclude("publicReleaseDate", (value_12) => (new Json(0, [value_12])), s.PublicReleaseDate), tryIncludeSeq("publications", Publication_ROCrate_encoder, s.Publications), tryIncludeSeq("people", Person_ROCrate_encoder, s.Contacts), tryIncludeList("processSequence", (studyName = s.Identifier, (oa_3) => Process_ROCrate_encoder(studyName, void 0, oa_3)), processes), tryIncludeSeq("assays", (studyName_1 = s.Identifier, (a_1) => Assay_ROCrate_encoder(studyName_1, a_1)), assays_1), tryIncludeSeq("comments", Comment_ROCrate_encoder, s.Comments), ["@context", context_jsonvalue]]))]);
+}
+
+export const Study_ROCrate_decoder = object((get$) => {
+    let objectArg, arg_6, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, arg_16, objectArg_7, arg_18, objectArg_8, arg_20, objectArg_9, arg_22, objectArg_10;
+    const identifier = defaultArg(bind(Study_tryIdentifierFromFileName, (objectArg = get$.Optional, objectArg.Field("filename", string))), createMissingIdentifier());
+    let assays;
+    const arg_3 = list_2(Assay_ROCrate_decoder);
+    const objectArg_1 = get$.Optional;
+    assays = objectArg_1.Field("assays", arg_3);
+    const assayIdentifiers = map((arg_4) => {
+        const collection = map_1((a) => a.Identifier, arg_4);
+        return Array.from(collection);
+    }, assays);
+    const tables = map((ps) => ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(ps).Tables, (arg_6 = list_2(Process_ROCrate_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("processSequence", arg_6))));
+    return [new ArcStudy(identifier, unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("title", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("description", string))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("submissionDate", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("publicReleaseDate", string))), unwrap((arg_16 = Decode_resizeArray(Publication_ROCrate_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("publications", arg_16)))), unwrap((arg_18 = Decode_resizeArray(Person_ROCrate_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("people", arg_18)))), unwrap((arg_20 = Decode_resizeArray(OntologyAnnotation_ROCrate_decoderDefinedTerm), (objectArg_9 = get$.Optional, objectArg_9.Field("studyDesignDescriptors", arg_20)))), unwrap(tables), unwrap(assayIdentifiers), unwrap((arg_22 = Decode_resizeArray(Comment_ROCrate_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_22))))), defaultArg(assays, empty())];
+});
+
+/**
+ * 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 = Assay_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);
+    }
+    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"]);
+
+export const Study_ISAJson_decoder = Decode_objectNoAdditionalProperties(Study_ISAJson_allowedFields, (get$) => {
+    let objectArg, arg_5, objectArg_2, objectArg_5, objectArg_6, objectArg_7, objectArg_8, arg_21, objectArg_9, arg_23, objectArg_10, arg_25, objectArg_11;
+    const identifier = defaultArgWith((objectArg = get$.Optional, objectArg.Field("identifier", string)), () => {
+        let objectArg_1;
+        return defaultArg(bind(Study_tryIdentifierFromFileName, (objectArg_1 = get$.Optional, objectArg_1.Field("filename", string))), createMissingIdentifier());
+    });
+    const tables = map((arg_6) => {
+        const a = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(arg_6);
+        return a.Tables;
+    }, (arg_5 = list_2(Process_ISAJson_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("processSequence", arg_5))));
+    let assays;
+    const arg_8 = list_2(Assay_ISAJson_decoder);
+    const objectArg_3 = get$.Optional;
+    assays = objectArg_3.Field("assays", arg_8);
+    let personsRaw;
+    const arg_10 = Decode_resizeArray(Person_ISAJson_decoder);
+    const objectArg_4 = get$.Optional;
+    personsRaw = objectArg_4.Field("people", arg_10);
+    const persons = [];
+    if (personsRaw != null) {
+        let enumerator = getEnumerator(value_14(personsRaw));
+        try {
+            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+                const person = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                const sourceAssays = Person_getSourceAssayIdentifiersFromComments(person);
+                const enumerator_1 = getEnumerator(sourceAssays);
+                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));
+                        try {
+                            while (enumerator_2["System.Collections.IEnumerator.MoveNext"]()) {
+                                const assay = enumerator_2["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                                if (assay.Identifier === assayIdentifier) {
+                                    void (assay.Performers.push(person));
+                                }
+                            }
+                        }
+                        finally {
+                            disposeSafe(enumerator_2);
+                        }
+                    }
+                }
+                finally {
+                    disposeSafe(enumerator_1);
+                }
+                person.Comments = Person_removeSourceAssayComments(person);
+                if (isEmpty(sourceAssays)) {
+                    void (persons.push(person));
+                }
+            }
+        }
+        finally {
+            disposeSafe(enumerator);
+        }
+    }
+    const assayIdentifiers = map((arg_11) => {
+        const collection = map_1((a_1) => a_1.Identifier, arg_11);
+        return Array.from(collection);
+    }, assays);
+    return [new ArcStudy(identifier, unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("title", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("description", string))), unwrap((objectArg_7 = get$.Optional, objectArg_7.Field("submissionDate", string))), unwrap((objectArg_8 = get$.Optional, objectArg_8.Field("publicReleaseDate", string))), unwrap((arg_21 = Decode_resizeArray(Publication_ISAJson_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("publications", arg_21)))), unwrap((persons.length === 0) ? void 0 : persons), unwrap((arg_23 = Decode_resizeArray(OntologyAnnotation_ISAJson_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("studyDesignDescriptors", arg_23)))), unwrap(tables), unwrap(assayIdentifiers), unwrap((arg_25 = Decode_resizeArray(Comment_ISAJson_decoder), (objectArg_11 = get$.Optional, objectArg_11.Field("comments", arg_25))))), defaultArg(assays, empty())];
+});
+
+export function ARCtrl_ArcStudy__ArcStudy_fromJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Study_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = Study_encoder(obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5(s) {
+    try {
+        const matchValue = fromString(decode(Study_decoderCompressed), s);
+        if (matchValue.tag === 1) {
+            throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+        }
+        else {
+            return matchValue.fields[0];
+        }
+    }
+    catch (e_1) {
+        const arg_1 = e_1.message;
+        return toFail(printf("Error. Unable to parse json string to ArcStudy: %s"))(arg_1);
+    }
+}
+
+export function ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F(spaces) {
+    return (obj) => toString(defaultArg(spaces, 0), encode(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_fromROCrateJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Study_ROCrate_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_3BA23086(assays, spaces) {
+    return (obj) => {
+        const value = Study_ISAJson_encoder(assays, obj);
+        return toString(defaultSpaces(spaces), value);
+    };
+}
+
+export function ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5(s) {
+    const matchValue = fromString(Study_ISAJson_decoder, s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+