@nfdi4plants/arctrl 1.2.0 → 2.0.0-alpha.2

package/ISA/ISA.Json/ArcTypes/ArcStudy.js

@@ -1,203 +0,0 @@
-import { map, empty, singleton, append, delay, toList } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { map as map_1, defaultArg, value as value_7 } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { JsonHelper_tryGetComments, JsonHelper_tryGetFactors, JsonHelper_tryGetStringResizeArray, JsonHelper_tryGetTables, JsonHelper_tryGetOAs, JsonHelper_tryGetPersons, JsonHelper_tryGetPublications, JsonHelper_EncoderComments, JsonHelper_EncoderFactors, JsonHelper_EncoderTables, JsonHelper_EncoderOAs, JsonHelper_EncoderPersons, JsonHelper_EncoderPublications } from "./ArcAssay.js";
-import { seq } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
-import { array, string, object } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { ArcStudy } from "../../ISA/ArcTypes/ArcTypes.js";
-import { ArcTable_compressedDecoder, ArcTable_compressedEncoder } from "./ArcTable.js";
-import { toString } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { Study_decoder, Study_encoder } from "../Study.js";
-import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor } from "../ConverterOptions.js";
-import { fromString } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
-import { toFail, printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { StringTable_arrayFromMap, StringTable_encoder, StringTable_decoder } from "../StringTable.js";
-import { OATable_arrayFromMap, OATable_encoder, OATable_decoder } from "./OATable.js";
-import { CellTable_arrayFromMap, CellTable_encoder, CellTable_decoder } from "./CellTable.js";
-import { Dictionary } from "../../../fable_modules/fable-library-js.4.13.0/MutableMap.js";
-import { safeHash, equals } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-
-export function ArcStudy_encoder(study) {
-    return new Json(5, [toList(delay(() => append(singleton(["Identifier", new Json(0, [study.Identifier])]), delay(() => append((study.Title != null) ? singleton(["Title", new Json(0, [value_7(study.Title)])]) : empty(), delay(() => append((study.Description != null) ? singleton(["Description", new Json(0, [value_7(study.Description)])]) : empty(), delay(() => append((study.SubmissionDate != null) ? singleton(["SubmissionDate", new Json(0, [value_7(study.SubmissionDate)])]) : empty(), delay(() => append((study.PublicReleaseDate != null) ? singleton(["PublicReleaseDate", new Json(0, [value_7(study.PublicReleaseDate)])]) : empty(), delay(() => append((study.Publications.length !== 0) ? singleton(["Publications", JsonHelper_EncoderPublications(study.Publications)]) : empty(), delay(() => append((study.Contacts.length !== 0) ? singleton(["Contacts", JsonHelper_EncoderPersons(study.Contacts)]) : empty(), delay(() => append((study.StudyDesignDescriptors.length !== 0) ? singleton(["StudyDesignDescriptors", JsonHelper_EncoderOAs(study.StudyDesignDescriptors)]) : empty(), delay(() => append((study.TableCount !== 0) ? singleton(["Tables", JsonHelper_EncoderTables(study.Tables)]) : empty(), delay(() => append((study.RegisteredAssayIdentifiers.length !== 0) ? singleton(["RegisteredAssayIdentifiers", seq(map((value_5) => (new Json(0, [value_5])), study.RegisteredAssayIdentifiers))]) : empty(), delay(() => append((study.Factors.length !== 0) ? singleton(["Factors", JsonHelper_EncoderFactors(study.Factors)]) : empty(), delay(() => ((study.Comments.length !== 0) ? singleton(["Comments", JsonHelper_EncoderComments(study.Comments)]) : empty())))))))))))))))))))))))))]);
-}
-
-export const ArcStudy_decoder = object((get$) => {
-    let identifier;
-    const objectArg = get$.Required;
-    identifier = objectArg.Field("Identifier", string);
-    let title;
-    const objectArg_1 = get$.Optional;
-    title = objectArg_1.Field("Title", string);
-    let description;
-    const objectArg_2 = get$.Optional;
-    description = objectArg_2.Field("Description", string);
-    let submissionDate;
-    const objectArg_3 = get$.Optional;
-    submissionDate = objectArg_3.Field("SubmissionDate", string);
-    let publicReleaseDate;
-    const objectArg_4 = get$.Optional;
-    publicReleaseDate = objectArg_4.Field("PublicReleaseDate", string);
-    const publications = JsonHelper_tryGetPublications(get$, "Publications");
-    const contacts = JsonHelper_tryGetPersons(get$, "Contacts");
-    const studyDesignDescriptors = JsonHelper_tryGetOAs(get$, "StudyDesignDescriptors");
-    const tables = JsonHelper_tryGetTables(get$, "Tables");
-    const registeredAssayIdentifiers = JsonHelper_tryGetStringResizeArray(get$, "RegisteredAssayIdentifiers");
-    const factors = JsonHelper_tryGetFactors(get$, "Factors");
-    const comments = JsonHelper_tryGetComments(get$, "Comments");
-    return ArcStudy.make(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors, comments);
-});
-
-export function ArcStudy_compressedEncoder(stringTable, oaTable, cellTable, study) {
-    return new Json(5, [toList(delay(() => append(singleton(["Identifier", new Json(0, [study.Identifier])]), delay(() => append((study.Title != null) ? singleton(["Title", new Json(0, [value_7(study.Title)])]) : empty(), delay(() => append((study.Description != null) ? singleton(["Description", new Json(0, [value_7(study.Description)])]) : empty(), delay(() => append((study.SubmissionDate != null) ? singleton(["SubmissionDate", new Json(0, [value_7(study.SubmissionDate)])]) : empty(), delay(() => append((study.PublicReleaseDate != null) ? singleton(["PublicReleaseDate", new Json(0, [value_7(study.PublicReleaseDate)])]) : empty(), delay(() => append((study.Publications.length !== 0) ? singleton(["Publications", JsonHelper_EncoderPublications(study.Publications)]) : empty(), delay(() => append((study.Contacts.length !== 0) ? singleton(["Contacts", JsonHelper_EncoderPersons(study.Contacts)]) : empty(), delay(() => append((study.StudyDesignDescriptors.length !== 0) ? singleton(["StudyDesignDescriptors", JsonHelper_EncoderOAs(study.StudyDesignDescriptors)]) : empty(), delay(() => append((study.TableCount !== 0) ? singleton(["Tables", seq(map((table) => ArcTable_compressedEncoder(stringTable, oaTable, cellTable, table), study.Tables))]) : empty(), delay(() => append((study.RegisteredAssayIdentifiers.length !== 0) ? singleton(["RegisteredAssayIdentifiers", seq(map((value_5) => (new Json(0, [value_5])), study.RegisteredAssayIdentifiers))]) : empty(), delay(() => append((study.Factors.length !== 0) ? singleton(["Factors", JsonHelper_EncoderFactors(study.Factors)]) : empty(), delay(() => ((study.Comments.length !== 0) ? singleton(["Comments", JsonHelper_EncoderComments(study.Comments)]) : empty())))))))))))))))))))))))))]);
-}
-
-export function ArcStudy_compressedDecoder(stringTable, oaTable, cellTable) {
-    return object((get$) => {
-        let arg_1, objectArg;
-        const tables = defaultArg(map_1((collection) => Array.from(collection), (arg_1 = array(ArcTable_compressedDecoder(stringTable, oaTable, cellTable)), (objectArg = get$.Optional, objectArg.Field("Tables", arg_1)))), []);
-        let identifier;
-        const objectArg_1 = get$.Required;
-        identifier = objectArg_1.Field("Identifier", string);
-        let title;
-        const objectArg_2 = get$.Optional;
-        title = objectArg_2.Field("Title", string);
-        let description;
-        const objectArg_3 = get$.Optional;
-        description = objectArg_3.Field("Description", string);
-        let submissionDate;
-        const objectArg_4 = get$.Optional;
-        submissionDate = objectArg_4.Field("SubmissionDate", string);
-        let publicReleaseDate;
-        const objectArg_5 = get$.Optional;
-        publicReleaseDate = objectArg_5.Field("PublicReleaseDate", string);
-        const publications = JsonHelper_tryGetPublications(get$, "Publications");
-        const contacts = JsonHelper_tryGetPersons(get$, "Contacts");
-        const studyDesignDescriptors = JsonHelper_tryGetOAs(get$, "StudyDesignDescriptors");
-        const registeredAssayIdentifiers = JsonHelper_tryGetStringResizeArray(get$, "RegisteredAssayIdentifiers");
-        const factors = JsonHelper_tryGetFactors(get$, "Factors");
-        const comments = JsonHelper_tryGetComments(get$, "Comments");
-        return ArcStudy.make(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors, comments);
-    });
-}
-
-/**
- * exports in json-ld format
- */
-export function ArcStudy_toJsonldString(a, assays) {
-    let returnVal;
-    return toString(2, Study_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), a.ToStudy(assays)));
-}
-
-export function ArcStudy_toJsonldStringWithContext(a, assays) {
-    let returnVal;
-    return toString(2, Study_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a.ToStudy(assays)));
-}
-
-export function ArcStudy_fromJsonString(s) {
-    let s_2;
-    const matchValue = fromString(Study_decoder(ConverterOptions_$ctor()), s);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        s_2 = matchValue.fields[0];
-    }
-    return ArcStudy.fromStudy(s_2);
-}
-
-export function ArcStudy_toJsonString(a, assays) {
-    return toString(2, Study_encoder(ConverterOptions_$ctor(), a.ToStudy(assays)));
-}
-
-export function ArcStudy_toArcJsonString(a) {
-    return toString(0, ArcStudy_encoder(a));
-}
-
-export function ArcStudy_fromArcJsonString(jsonString) {
-    try {
-        const matchValue = fromString(ArcStudy_decoder, jsonString);
-        if (matchValue.tag === 1) {
-            throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-        }
-        else {
-            return matchValue.fields[0];
-        }
-    }
-    catch (e_1) {
-        const arg_1 = e_1.message;
-        return toFail(printf("Error. Unable to parse json string to ArcStudy: %s"))(arg_1);
-    }
-}
-
-export function ARCtrl_ISA_ArcStudy__ArcStudy_fromArcJsonString_Static_Z721C83C5(jsonString) {
-    try {
-        const matchValue = fromString(ArcStudy_decoder, jsonString);
-        if (matchValue.tag === 1) {
-            throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-        }
-        else {
-            return matchValue.fields[0];
-        }
-    }
-    catch (e_1) {
-        const arg_1 = e_1.message;
-        return toFail(printf("Error. Unable to parse json string to ArcStudy: %s"))(arg_1);
-    }
-}
-
-export function ARCtrl_ISA_ArcStudy__ArcStudy_ToArcJsonString_71136F3F(this$, spaces) {
-    return toString(defaultArg(spaces, 0), ArcStudy_encoder(this$));
-}
-
-export function ARCtrl_ISA_ArcStudy__ArcStudy_toArcJsonString_Static_1B3D5E9B(a) {
-    return ARCtrl_ISA_ArcStudy__ArcStudy_ToArcJsonString_71136F3F(a);
-}
-
-export function ARCtrl_ISA_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5(jsonString) {
-    const decoder = object((get$) => {
-        let arg_5, objectArg_2;
-        let stringTable;
-        const objectArg = get$.Required;
-        stringTable = objectArg.Field("stringTable", StringTable_decoder);
-        let oaTable;
-        const arg_3 = OATable_decoder(stringTable);
-        const objectArg_1 = get$.Required;
-        oaTable = objectArg_1.Field("oaTable", arg_3);
-        const arg_7 = ArcStudy_compressedDecoder(stringTable, oaTable, (arg_5 = CellTable_decoder(stringTable, oaTable), (objectArg_2 = get$.Required, objectArg_2.Field("cellTable", arg_5))));
-        const objectArg_3 = get$.Required;
-        return objectArg_3.Field("study", arg_7);
-    });
-    try {
-        const matchValue = fromString(decoder, jsonString);
-        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_9 = e_1.message;
-        return toFail(printf("Error. Unable to parse json string to ArcAssay: %s"))(arg_9);
-    }
-}
-
-export function ARCtrl_ISA_ArcStudy__ArcStudy_ToCompressedJsonString_71136F3F(this$, spaces) {
-    const spaces_1 = defaultArg(spaces, 0) | 0;
-    const stringTable = new Map([]);
-    const oaTable = new Dictionary([], {
-        Equals: equals,
-        GetHashCode: safeHash,
-    });
-    const cellTable = new Dictionary([], {
-        Equals: equals,
-        GetHashCode: safeHash,
-    });
-    const arcStudy = ArcStudy_compressedEncoder(stringTable, oaTable, cellTable, this$);
-    return toString(spaces_1, new Json(5, [[["cellTable", CellTable_encoder(stringTable, oaTable, CellTable_arrayFromMap(cellTable))], ["oaTable", OATable_encoder(stringTable, OATable_arrayFromMap(oaTable))], ["stringTable", StringTable_encoder(StringTable_arrayFromMap(stringTable))], ["study", arcStudy]]]));
-}
-
-export function ARCtrl_ISA_ArcStudy__ArcStudy_toCompressedJsonString_Static_1B3D5E9B(s) {
-    return ARCtrl_ISA_ArcStudy__ArcStudy_ToCompressedJsonString_71136F3F(s);
-}
-

package/ISA/ISA.Json/ArcTypes/CellTable.js

@@ -1,40 +0,0 @@
-import { sortBy, map, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { comparePrimitives } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { item, map as map_1 } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
-import { CompositeCell_compressedDecoder, CompositeCell_compressedEncoder } from "./CompositeCell.js";
-import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { int, object, array as array_1 } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { Dict_tryFind } from "../../ISA/Helper.js";
-import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-
-export function CellTable_arrayFromMap(otm) {
-    return toArray(map((kv_1) => kv_1[0], sortBy((kv) => kv[1], otm, {
-        Compare: comparePrimitives,
-    })));
-}
-
-export function CellTable_encoder(stringTable, oaTable, ot) {
-    return new Json(6, [map_1((cc) => CompositeCell_compressedEncoder(stringTable, oaTable, cc), ot)]);
-}
-
-export function CellTable_decoder(stringTable, oaTable) {
-    return array_1(CompositeCell_compressedDecoder(stringTable, oaTable));
-}
-
-export function CellTable_encodeCell(otm, cc) {
-    const matchValue = Dict_tryFind(cc, otm);
-    if (matchValue == null) {
-        const i_1 = otm.size | 0;
-        addToDict(otm, cc, i_1);
-        return new Json(7, [i_1 >>> 0]);
-    }
-    else {
-        const i = matchValue | 0;
-        return new Json(7, [i >>> 0]);
-    }
-}
-
-export function CellTable_decodeCell(ot) {
-    return object((get$) => item(get$.Required.Raw(int), ot));
-}
-

package/ISA/ISA.Json/ArcTypes/CompositeCell.js

@@ -1,62 +0,0 @@
-import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "../Ontology.js";
-import { ConverterOptions_$ctor } from "../ConverterOptions.js";
-import { ofArray, singleton } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { list } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
-import { index, string, object } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { CompositeCell } from "../../ISA/ArcTypes/CompositeCell.js";
-import { toText, printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { OATable_decodeOA, OATable_encodeOA } from "./OATable.js";
-import { StringTable_decodeString, StringTable_encodeString } from "../StringTable.js";
-import { fromString } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
-import { toString } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-
-export function CompositeCell_encoder(cc) {
-    const oaToJsonString = (oa) => OntologyAnnotation_encoder(ConverterOptions_$ctor(), oa);
-    const patternInput = (cc.tag === 0) ? ["Term", singleton(oaToJsonString(cc.fields[0]))] : ((cc.tag === 2) ? ["Unitized", ofArray([new Json(0, [cc.fields[0]]), oaToJsonString(cc.fields[1])])] : ["FreeText", singleton(new Json(0, [cc.fields[0]]))]);
-    return new Json(5, [[["celltype", new Json(0, [patternInput[0]])], ["values", list(patternInput[1])]]]);
-}
-
-export const CompositeCell_decoder = object((get$) => {
-    let arg_3, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, arg_9, objectArg_4;
-    let matchValue;
-    const objectArg = get$.Required;
-    matchValue = objectArg.Field("celltype", string);
-    return (matchValue === "FreeText") ? (new CompositeCell(1, [(arg_3 = index(0, string), (objectArg_1 = get$.Required, objectArg_1.Field("values", arg_3)))])) : ((matchValue === "Term") ? (new CompositeCell(0, [(arg_5 = index(0, OntologyAnnotation_decoder(ConverterOptions_$ctor())), (objectArg_2 = get$.Required, objectArg_2.Field("values", arg_5)))])) : ((matchValue === "Unitized") ? (new CompositeCell(2, [(arg_7 = index(0, string), (objectArg_3 = get$.Required, objectArg_3.Field("values", arg_7))), (arg_9 = index(1, OntologyAnnotation_decoder(ConverterOptions_$ctor())), (objectArg_4 = get$.Required, objectArg_4.Field("values", arg_9)))])) : toFail(printf("Error reading CompositeCell from json string: %A"))(matchValue)));
-});
-
-export function CompositeCell_compressedEncoder(stringTable, oaTable, cc) {
-    const patternInput = (cc.tag === 0) ? ["Term", singleton(OATable_encodeOA(oaTable, cc.fields[0]))] : ((cc.tag === 2) ? ["Unitized", ofArray([StringTable_encodeString(stringTable, cc.fields[0]), OATable_encodeOA(oaTable, cc.fields[1])])] : ["FreeText", singleton(StringTable_encodeString(stringTable, cc.fields[0]))]);
-    return new Json(5, [[["t", StringTable_encodeString(stringTable, patternInput[0])], ["v", list(patternInput[1])]]]);
-}
-
-export function CompositeCell_compressedDecoder(stringTable, oaTable) {
-    return object((get$) => {
-        let arg_3, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, arg_9, objectArg_4;
-        let matchValue;
-        const arg_1 = StringTable_decodeString(stringTable);
-        const objectArg = get$.Required;
-        matchValue = objectArg.Field("t", arg_1);
-        return (matchValue === "FreeText") ? (new CompositeCell(1, [(arg_3 = index(0, StringTable_decodeString(stringTable)), (objectArg_1 = get$.Required, objectArg_1.Field("v", arg_3)))])) : ((matchValue === "Term") ? (new CompositeCell(0, [(arg_5 = index(0, OATable_decodeOA(oaTable)), (objectArg_2 = get$.Required, objectArg_2.Field("v", arg_5)))])) : ((matchValue === "Unitized") ? (new CompositeCell(2, [(arg_7 = index(0, StringTable_decodeString(stringTable)), (objectArg_3 = get$.Required, objectArg_3.Field("v", arg_7))), (arg_9 = index(1, OATable_decodeOA(oaTable)), (objectArg_4 = get$.Required, objectArg_4.Field("v", arg_9)))])) : toFail(printf("Error reading CompositeCell from json string: %A"))(matchValue)));
-    });
-}
-
-export function ARCtrl_ISA_CompositeCell__CompositeCell_fromJsonString_Static_Z721C83C5(jsonString) {
-    const matchValue = fromString(CompositeCell_decoder, jsonString);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function ARCtrl_ISA_CompositeCell__CompositeCell_ToJsonString_71136F3F(this$, spaces) {
-    return toString(defaultArg(spaces, 0), CompositeCell_encoder(this$));
-}
-
-export function ARCtrl_ISA_CompositeCell__CompositeCell_toJsonString_Static_1B703D57(a) {
-    return ARCtrl_ISA_CompositeCell__CompositeCell_ToJsonString_71136F3F(a);
-}
-

package/ISA/ISA.Json/ArcTypes/IOType.js

@@ -1,33 +0,0 @@
-import { toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
-import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { string, succeed, andThen } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { IOType } from "../../ISA/ArcTypes/CompositeHeader.js";
-import { fromString } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
-import { printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { toString as toString_1 } from "../../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-
-export function IOType_encoder(io) {
-    return new Json(0, [toString(io)]);
-}
-
-export const IOType_decoder = andThen((s) => succeed(IOType.ofString(s)), string);
-
-export function ARCtrl_ISA_IOType__IOType_fromJsonString_Static_Z721C83C5(jsonString) {
-    const matchValue = fromString(IOType_decoder, jsonString);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function ARCtrl_ISA_IOType__IOType_ToJsonString_71136F3F(this$, spaces) {
-    return toString_1(defaultArg(spaces, 0), IOType_encoder(this$));
-}
-
-export function ARCtrl_ISA_IOType__IOType_toJsonString_Static_Z359DBB26(a) {
-    return ARCtrl_ISA_IOType__IOType_ToJsonString_71136F3F(a);
-}
-

package/ISA/ISA.Json/ArcTypes/OATable.js

@@ -1,42 +0,0 @@
-import { sortBy, map, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { comparePrimitives } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { item, map as map_1 } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
-import { ConverterOptions_$ctor } from "../ConverterOptions.js";
-import { OntologyAnnotation_compressedDecoder, OntologyAnnotation_compressedEncoder } from "../Ontology.js";
-import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { int, object, array as array_1 } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { Dict_tryFind } from "../../ISA/Helper.js";
-import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-
-export function OATable_arrayFromMap(otm) {
-    return toArray(map((kv_1) => kv_1[0], sortBy((kv) => kv[1], otm, {
-        Compare: comparePrimitives,
-    })));
-}
-
-export function OATable_encoder(stringTable, ot) {
-    let options;
-    return new Json(6, [map_1((options = ConverterOptions_$ctor(), (oa) => OntologyAnnotation_compressedEncoder(stringTable, options, oa)), ot)]);
-}
-
-export function OATable_decoder(stringTable) {
-    return array_1(OntologyAnnotation_compressedDecoder(stringTable, ConverterOptions_$ctor()));
-}
-
-export function OATable_encodeOA(otm, oa) {
-    const matchValue = Dict_tryFind(oa, otm);
-    if (matchValue == null) {
-        const i_1 = otm.size | 0;
-        addToDict(otm, oa, i_1);
-        return new Json(7, [i_1 >>> 0]);
-    }
-    else {
-        const i = matchValue | 0;
-        return new Json(7, [i >>> 0]);
-    }
-}
-
-export function OATable_decodeOA(ot) {
-    return object((get$) => item(get$.Required.Raw(int), ot));
-}
-

package/ISA/ISA.Json/Assay.js

@@ -1,129 +0,0 @@
-import { ofArray, choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
-import { equals } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { tryInclude, tryIncludeList } from "./GEncode.js";
-import { Data_decoder, Data_encoder, Sample_decoder, Sample_encoder } from "./Data.js";
-import { MaterialAttribute_decoder, MaterialAttribute_encoder, Material_decoder, Material_encoder } from "./Material.js";
-import { uri, object } from "./Decode.js";
-import { string, list as list_1 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { AssayMaterials } from "../ISA/JsonTypes/AssayMaterials.js";
-import { printf, toText, replace, remove } from "../../fable_modules/fable-library-js.4.13.0/String.js";
-import { max } from "../../fable_modules/fable-library-js.4.13.0/Double.js";
-import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { Operators_FailurePattern } from "../../fable_modules/fable-library-js.4.13.0/FSharp.Core.js";
-import { Assay_identifierFromFileName } from "../ISA/Identifier.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeContext, ConverterOptions__get_IsRoCrate, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
-import { list as list_2 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
-import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
-import { Process_decoder, Process_encoder } from "./Process.js";
-import { decoder as decoder_1, encoder } from "./Comment.js";
-import { context_jsonvalue } from "./context/rocrate/isa_assay_context.js";
-import { Assay } from "../ISA/JsonTypes/Assay.js";
-import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
-import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
-
-export function AssayMaterials_encoder(options, oa) {
-    return new Json(5, [choose((tupledArg) => {
-        const v = tupledArg[1];
-        if (equals(v, new Json(3, []))) {
-            return void 0;
-        }
-        else {
-            return [tupledArg[0], v];
-        }
-    }, ofArray([tryIncludeList("samples", (oa_1) => Sample_encoder(options, oa_1), oa.Samples), tryIncludeList("otherMaterials", (oa_2) => Material_encoder(options, oa_2), oa.OtherMaterials)]))]);
-}
-
-export const AssayMaterials_allowedFields = ofArray(["samples", "otherMaterials"]);
-
-export function AssayMaterials_decoder(options) {
-    return object(AssayMaterials_allowedFields, (get$) => {
-        let arg_1, objectArg, arg_3, objectArg_1;
-        return new AssayMaterials((arg_1 = list_1(Sample_decoder(options)), (objectArg = get$.Optional, objectArg.Field("samples", arg_1))), (arg_3 = list_1(Material_decoder(options)), (objectArg_1 = get$.Optional, objectArg_1.Field("otherMaterials", arg_3))));
-    });
-}
-
-export function Assay_genID(a) {
-    const matchValue = a.ID;
-    if (matchValue == null) {
-        const matchValue_1 = a.FileName;
-        if (matchValue_1 == null) {
-            return "#EmptyAssay";
-        }
-        else {
-            const n = matchValue_1;
-            return remove(replace(n, " ", "_"), 0, 1 + max(n.lastIndexOf("/"), n.lastIndexOf("\\")));
-        }
-    }
-    else {
-        return URIModule_toString(matchValue);
-    }
-}
-
-export function Assay_encoder(options, studyName, oa) {
-    let assayName;
-    try {
-        const matchValue = oa.FileName;
-        assayName = ((matchValue == null) ? void 0 : Assay_identifierFromFileName(matchValue));
-    }
-    catch (matchValue_1) {
-        const activePatternResult = Operators_FailurePattern(matchValue_1);
-        if (activePatternResult != null) {
-            const msg = activePatternResult;
-            assayName = void 0;
-        }
-        else {
-            throw matchValue_1;
-        }
-    }
-    return new Json(5, [choose((tupledArg) => {
-        const v = tupledArg[1];
-        if (equals(v, new Json(3, []))) {
-            return void 0;
-        }
-        else {
-            return [tupledArg[0], v];
-        }
-    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [Assay_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_2(ofArray([new Json(0, ["Assay"]), new Json(0, ["ArcAssay"])]))]) : empty(), delay(() => append(singleton(tryInclude("filename", (value_5) => (new Json(0, [value_5])), oa.FileName)), delay(() => append(singleton(tryInclude("measurementType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa.MeasurementType)), delay(() => append(singleton(tryInclude("technologyType", (oa_2) => OntologyAnnotation_encoder(options, oa_2), oa.TechnologyType)), delay(() => append(singleton(tryInclude("technologyPlatform", (value_7) => (new Json(0, [value_7])), oa.TechnologyPlatform)), delay(() => append(singleton(tryIncludeList("dataFiles", (oa_3) => Data_encoder(options, oa_3), oa.DataFiles)), delay(() => {
-        let matchValue_2, m;
-        return append(ConverterOptions__get_IsRoCrate(options) ? ((matchValue_2 = oa.Materials, (matchValue_2 == null) ? (empty()) : ((m = matchValue_2, append(singleton(tryIncludeList("samples", (oa_4) => Sample_encoder(options, oa_4), m.Samples)), delay(() => singleton(tryIncludeList("materials", (oa_5) => Material_encoder(options, oa_5), m.OtherMaterials)))))))) : empty(), delay(() => append(!ConverterOptions__get_IsRoCrate(options) ? singleton(tryInclude("materials", (oa_6) => AssayMaterials_encoder(options, oa_6), oa.Materials)) : empty(), delay(() => append(singleton(tryIncludeList("characteristicCategories", (oa_7) => MaterialAttribute_encoder(options, oa_7), oa.CharacteristicCategories)), delay(() => append(singleton(tryIncludeList("unitCategories", (oa_8) => OntologyAnnotation_encoder(options, oa_8), oa.UnitCategories)), delay(() => append(singleton(tryIncludeList("processSequence", (oa_9) => Process_encoder(options, studyName, assayName, oa_9), oa.ProcessSequence)), delay(() => append(singleton(tryIncludeList("comments", (comment) => encoder(options, comment), oa.Comments)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty())))))))))))));
-    })))))))))))))))))]);
-}
-
-export const Assay_allowedFields = ofArray(["@id", "filename", "measurementType", "technologyType", "technologyPlatform", "dataFiles", "materials", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
-
-export function Assay_decoder(options) {
-    return object(Assay_allowedFields, (get$) => {
-        let objectArg, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
-        return new Assay((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("filename", string)), (arg_5 = OntologyAnnotation_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", arg_5))), (arg_7 = OntologyAnnotation_decoder(options), (objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", arg_7))), (objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", string)), (arg_11 = list_1(Data_decoder(options)), (objectArg_5 = get$.Optional, objectArg_5.Field("dataFiles", arg_11))), (arg_13 = AssayMaterials_decoder(options), (objectArg_6 = get$.Optional, objectArg_6.Field("materials", arg_13))), (arg_15 = list_1(MaterialAttribute_decoder(options)), (objectArg_7 = get$.Optional, objectArg_7.Field("characteristicCategories", arg_15))), (arg_17 = list_1(OntologyAnnotation_decoder(options)), (objectArg_8 = get$.Optional, objectArg_8.Field("unitCategories", arg_17))), (arg_19 = list_1(Process_decoder(options)), (objectArg_9 = get$.Optional, objectArg_9.Field("processSequence", arg_19))), (arg_21 = list_1(decoder_1(options)), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_21))));
-    });
-}
-
-export function Assay_fromJsonString(s) {
-    const matchValue = fromString(Assay_decoder(ConverterOptions_$ctor()), s);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function Assay_toJsonString(p) {
-    return toString(2, Assay_encoder(ConverterOptions_$ctor(), void 0, p));
-}
-
-/**
- * exports in json-ld format
- */
-export function Assay_toJsonldString(a) {
-    let returnVal;
-    return toString(2, Assay_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), void 0, a));
-}
-
-export function Assay_toJsonldStringWithContext(a) {
-    let returnVal;
-    return toString(2, Assay_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), void 0, a));
-}
-

package/ISA/ISA.Json/Comment.js

@@ -1,80 +0,0 @@
-import { printf, toText, replace } from "../../fable_modules/fable-library-js.4.13.0/String.js";
-import { value as value_8 } from "../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
-import { equals } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeContext, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
-import { tryInclude } from "./GEncode.js";
-import { context_jsonvalue } from "./context/rocrate/isa_comment_context.js";
-import { string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { uri } from "./Decode.js";
-import { Comment$ } from "../ISA/JsonTypes/Comment.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 genID(c) {
-    const matchValue = c.ID;
-    if (matchValue == null) {
-        const matchValue_1 = c.Name;
-        if (matchValue_1 == null) {
-            return "#EmptyComment";
-        }
-        else {
-            const n = matchValue_1;
-            const v = (c.Value != null) ? ("_" + replace(value_8(c.Value), " ", "_")) : "";
-            return ("#Comment_" + replace(n, " ", "_")) + v;
-        }
-    }
-    else {
-        return URIModule_toString(matchValue);
-    }
-}
-
-export function encoder(options, comment) {
-    return new Json(5, [choose((tupledArg) => {
-        const v = tupledArg[1];
-        if (equals(v, new Json(3, []))) {
-            return void 0;
-        }
-        else {
-            return [tupledArg[0], v];
-        }
-    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [genID(comment)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), comment.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["Comment"])]) : empty(), delay(() => append(singleton(tryInclude("name", (value_4) => (new Json(0, [value_4])), comment.Name)), delay(() => append(singleton(tryInclude("value", (value_6) => (new Json(0, [value_6])), comment.Value)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty()))))))))))))]);
-}
-
-export function decoder(options) {
-    return object((get$) => {
-        let objectArg, objectArg_1, objectArg_2;
-        return new Comment$((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("value", string)));
-    });
-}
-
-export function fromJsonString(s) {
-    const matchValue = fromString(decoder(ConverterOptions_$ctor()), s);
-    if (matchValue.tag === 1) {
-        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-    }
-    else {
-        return matchValue.fields[0];
-    }
-}
-
-export function toJsonString(c) {
-    return toString(2, encoder(ConverterOptions_$ctor(), c));
-}
-
-/**
- * exports in json-ld format
- */
-export function toJsonldString(c) {
-    let returnVal;
-    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), c));
-}
-
-export function toJsonldStringWithContext(a) {
-    let returnVal;
-    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
-}
-

package/ISA/ISA.Json/ConverterOptions.js

@@ -1,51 +0,0 @@
-import { class_type } from "../../fable_modules/fable-library-js.4.13.0/Reflection.js";
-
-export class ConverterOptions {
-    constructor() {
-        this.setID = false;
-        this.includeType = false;
-        this.includeContext = false;
-        this.isRoCrate = false;
-    }
-}
-
-export function ConverterOptions_$reflection() {
-    return class_type("ARCtrl.ISA.Json.ConverterOptions", void 0, ConverterOptions);
-}
-
-export function ConverterOptions_$ctor() {
-    return new ConverterOptions();
-}
-
-export function ConverterOptions__get_SetID(this$) {
-    return this$.setID;
-}
-
-export function ConverterOptions__set_SetID_Z1FBCCD16(this$, setId) {
-    this$.setID = setId;
-}
-
-export function ConverterOptions__get_IncludeType(this$) {
-    return this$.includeType;
-}
-
-export function ConverterOptions__set_IncludeType_Z1FBCCD16(this$, iT) {
-    this$.includeType = iT;
-}
-
-export function ConverterOptions__get_IncludeContext(this$) {
-    return this$.includeContext;
-}
-
-export function ConverterOptions__set_IncludeContext_Z1FBCCD16(this$, iC) {
-    this$.includeContext = iC;
-}
-
-export function ConverterOptions__get_IsRoCrate(this$) {
-    return this$.isRoCrate;
-}
-
-export function ConverterOptions__set_IsRoCrate_Z1FBCCD16(this$, iR) {
-    this$.isRoCrate = iR;
-}
-