@nfdi4plants/arctrl 2.5.1 → 3.0.0-alpha.2

package/Json/StringTable.js

@@ -1,61 +0,0 @@
-import { item, map, setItem, fill } from "../fable_modules/fable-library-js.4.24.0/Array.js";
-import { iterate } from "../fable_modules/fable-library-js.4.24.0/Seq.js";
-import { int, string, array as array_2 } from "../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
-import { Dictionary_tryFind } from "../Core/Helper/Collections.js";
-import { addToDict } from "../fable_modules/fable-library-js.4.24.0/MapUtil.js";
-import { FSharpResult$2 } from "../fable_modules/fable-library-js.4.24.0/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) {
-    const values = map((value) => ({
-        Encode(helpers) {
-            return helpers.encodeString(value);
-        },
-    }), ot);
-    return {
-        Encode(helpers_1) {
-            const arg = map((v) => v.Encode(helpers_1), values);
-            return helpers_1.encodeArray(arg);
-        },
-    };
-}
-
-export const decoder = array_2(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 {
-            Encode(helpers_1) {
-                return helpers_1.encodeSignedIntegralNumber(i_1);
-            },
-        };
-    }
-    else {
-        const i = matchValue | 0;
-        return {
-            Encode(helpers) {
-                return helpers.encodeSignedIntegralNumber(i);
-            },
-        };
-    }
-}
-
-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

@@ -1,349 +0,0 @@
-import { Option_fromValueWithDefault, ResizeArray_map } from "../Core/Helper/Collections.js";
-import { defaultArgWith, bind, unwrap, map, value as value_17, defaultArg } from "../fable_modules/fable-library-js.4.24.0/Option.js";
-import { empty, map as map_2, singleton, ofArray, choose, tryFind } from "../fable_modules/fable-library-js.4.24.0/List.js";
-import { ArcStudy, ArcAssay } from "../Core/ArcTypes.js";
-import { tryIncludeList, tryIncludeSeq, tryInclude } from "./Encode.js";
-import { ISAJson_decoder as ISAJson_decoder_4, ISAJson_encoder as ISAJson_encoder_2, ROCrate_decoder as ROCrate_decoder_3, ROCrate_encoder as ROCrate_encoder_1, decoder as decoder_2, encoder as encoder_5 } from "./Publication.js";
-import { ISAJson_decoder as ISAJson_decoder_3, ISAJson_encoder as ISAJson_encoder_3, ROCrate_decoder as ROCrate_decoder_4, ROCrate_encoder as ROCrate_encoder_2, decoder as decoder_3, encoder as encoder_6 } from "./Person.js";
-import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./OntologyAnnotation.js";
-import { decoderCompressed as decoderCompressed_1, encoderCompressed as encoderCompressed_1, decoder as decoder_4, encoder as encoder_7 } from "./Table/ArcTable.js";
-import { decoderCompressed as decoderCompressed_2, encoderCompressed as encoderCompressed_2, decoder as decoder_5, encoder as encoder_8 } from "./DataMap/DataMap.js";
-import { ISAJson_decoder as ISAJson_decoder_5, ISAJson_encoder as ISAJson_encoder_6, ROCrate_decoder as ROCrate_decoder_5, ROCrate_encoder as ROCrate_encoder_6, decoder as decoder_6, encoder as encoder_9 } from "./Comment.js";
-import { isEmpty, map as map_1 } from "../fable_modules/fable-library-js.4.24.0/Seq.js";
-import { list as list_2, resizeArray, string, object } from "../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
-import { replace } from "../fable_modules/fable-library-js.4.24.0/String.js";
-import { Study_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.0.4.0/Encode.fs.js";
-import { ISAJson_decoder as ISAJson_decoder_1, ISAJson_encoder as ISAJson_encoder_4, ROCrate_decoder as ROCrate_decoder_2, ROCrate_encoder as ROCrate_encoder_3 } from "./Process/Process.js";
-import { ISAJson_decoder as ISAJson_decoder_2, ISAJson_encoder as ISAJson_encoder_5, ROCrate_decoder as ROCrate_decoder_1, ROCrate_encoder as ROCrate_encoder_4 } from "./Assay.js";
-import { ROCrate_encoder as ROCrate_encoder_5 } from "./Data.js";
-import { getProtocols, getCharacteristics, getFactors, getUnits, getData } from "../Core/Process/ProcessSequence.js";
-import { context_jsonvalue } from "./context/rocrate/isa_study_context.js";
-import { disposeSafe, getEnumerator } from "../fable_modules/fable-library-js.4.24.0/Util.js";
-import { encoder as encoder_10 } from "./Process/Factor.js";
-import { encoder as encoder_11 } from "./Process/MaterialAttribute.js";
-import { encoder as encoder_12 } from "./Process/StudyMaterials.js";
-import { ISAJson_encoder as ISAJson_encoder_1 } from "./Process/Protocol.js";
-import { encode } from "./IDTable.js";
-import { Decode_objectNoAdditionalProperties } from "./Decode.js";
-
-/**
- * Get registered assays or get assays from `assays` if IsSome
- */
-export function Helper_getAssayInformation(assays, study) {
-    if (assays != null) {
-        return ResizeArray_map((assayId) => defaultArg(tryFind((a) => (a.Identifier === assayId), value_17(assays)), ArcAssay.init(assayId)), study.RegisteredAssayIdentifiers);
-    }
-    else {
-        return study.GetRegisteredAssaysOrIdentifier();
-    }
-}
-
-export function encoder(study) {
-    let value;
-    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = study.Identifier, {
-        Encode(helpers) {
-            return helpers.encodeString(value);
-        },
-    })], tryInclude("Title", (value_1) => ({
-        Encode(helpers_1) {
-            return helpers_1.encodeString(value_1);
-        },
-    }), study.Title), tryInclude("Description", (value_3) => ({
-        Encode(helpers_2) {
-            return helpers_2.encodeString(value_3);
-        },
-    }), study.Description), tryInclude("SubmissionDate", (value_5) => ({
-        Encode(helpers_3) {
-            return helpers_3.encodeString(value_5);
-        },
-    }), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => ({
-        Encode(helpers_4) {
-            return helpers_4.encodeString(value_7);
-        },
-    }), study.PublicReleaseDate), tryIncludeSeq("Publications", encoder_5, study.Publications), tryIncludeSeq("Contacts", encoder_6, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", encoder_7, study.Tables), tryInclude("DataMap", encoder_8, study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => ({
-        Encode(helpers_5) {
-            return helpers_5.encodeString(value_9);
-        },
-    }), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", encoder_9, study.Comments)]));
-    return {
-        Encode(helpers_6) {
-            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values);
-            return helpers_6.encodeObject(arg);
-        },
-    };
-}
-
-export const decoder = object((get$) => {
-    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
-    return new ArcStudy((objectArg = get$.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 = resizeArray(decoder_2), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = resizeArray(decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = resizeArray(decoder_4), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", decoder_5))), unwrap((arg_21 = resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21)))), unwrap((arg_23 = resizeArray(decoder_6), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23)))));
-});
-
-export function encoderCompressed(stringTable, oaTable, cellTable, study) {
-    let value;
-    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = study.Identifier, {
-        Encode(helpers) {
-            return helpers.encodeString(value);
-        },
-    })], tryInclude("Title", (value_1) => ({
-        Encode(helpers_1) {
-            return helpers_1.encodeString(value_1);
-        },
-    }), study.Title), tryInclude("Description", (value_3) => ({
-        Encode(helpers_2) {
-            return helpers_2.encodeString(value_3);
-        },
-    }), study.Description), tryInclude("SubmissionDate", (value_5) => ({
-        Encode(helpers_3) {
-            return helpers_3.encodeString(value_5);
-        },
-    }), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => ({
-        Encode(helpers_4) {
-            return helpers_4.encodeString(value_7);
-        },
-    }), study.PublicReleaseDate), tryIncludeSeq("Publications", encoder_5, study.Publications), tryIncludeSeq("Contacts", encoder_6, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", (table) => encoderCompressed_1(stringTable, oaTable, cellTable, table), study.Tables), tryInclude("DataMap", (dm) => encoderCompressed_2(stringTable, oaTable, cellTable, dm), study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => ({
-        Encode(helpers_5) {
-            return helpers_5.encodeString(value_9);
-        },
-    }), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", encoder_9, study.Comments)]));
-    return {
-        Encode(helpers_6) {
-            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values);
-            return helpers_6.encodeObject(arg);
-        },
-    };
-}
-
-export function 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, arg_23, objectArg_11;
-        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$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = resizeArray(decoder_2), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = resizeArray(decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = resizeArray(decoderCompressed_1(stringTable, oaTable, cellTable)), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((arg_19 = decoderCompressed_2(stringTable, oaTable, cellTable), (objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", arg_19)))), unwrap((arg_21 = resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21)))), unwrap((arg_23 = resizeArray(decoder_6), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23)))));
-    });
-}
-
-export function ROCrate_genID(a) {
-    const matchValue = a.Identifier;
-    if (matchValue === "") {
-        return "#EmptyStudy";
-    }
-    else {
-        return `studies/${replace(matchValue, " ", "_")}/`;
-    }
-}
-
-export function ROCrate_encoder(assays, s) {
-    let value, value_3, studyName, studyName_1;
-    const fileName = Study_tryFileNameFromIdentifier(s.Identifier);
-    const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(s);
-    const assays_1 = Helper_getAssayInformation(assays, s);
-    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = ROCrate_genID(s), {
-        Encode(helpers) {
-            return helpers.encodeString(value);
-        },
-    })], ["@type", list_1(singleton({
-        Encode(helpers_1) {
-            return helpers_1.encodeString("Study");
-        },
-    }))], ["additionalType", {
-        Encode(helpers_2) {
-            return helpers_2.encodeString("Study");
-        },
-    }], ["identifier", (value_3 = s.Identifier, {
-        Encode(helpers_3) {
-            return helpers_3.encodeString(value_3);
-        },
-    })], tryInclude("filename", (value_4) => ({
-        Encode(helpers_4) {
-            return helpers_4.encodeString(value_4);
-        },
-    }), fileName), tryInclude("title", (value_6) => ({
-        Encode(helpers_5) {
-            return helpers_5.encodeString(value_6);
-        },
-    }), s.Title), tryInclude("description", (value_8) => ({
-        Encode(helpers_6) {
-            return helpers_6.encodeString(value_8);
-        },
-    }), s.Description), tryIncludeSeq("studyDesignDescriptors", OntologyAnnotation_ROCrate_encoderDefinedTerm, s.StudyDesignDescriptors), tryInclude("submissionDate", (value_10) => ({
-        Encode(helpers_7) {
-            return helpers_7.encodeString(value_10);
-        },
-    }), s.SubmissionDate), tryInclude("publicReleaseDate", (value_12) => ({
-        Encode(helpers_8) {
-            return helpers_8.encodeString(value_12);
-        },
-    }), s.PublicReleaseDate), tryIncludeSeq("publications", ROCrate_encoder_1, s.Publications), tryIncludeSeq("people", ROCrate_encoder_2, s.Contacts), tryIncludeList("processSequence", (studyName = s.Identifier, (oa_3) => ROCrate_encoder_3(studyName, undefined, oa_3)), processes), tryIncludeSeq("assays", (studyName_1 = s.Identifier, (a_1) => ROCrate_encoder_4(studyName_1, a_1)), assays_1), tryIncludeList("dataFiles", ROCrate_encoder_5, getData(processes)), tryIncludeSeq("comments", ROCrate_encoder_6, s.Comments), ["@context", context_jsonvalue]]));
-    return {
-        Encode(helpers_9) {
-            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_9)], values);
-            return helpers_9.encodeObject(arg);
-        },
-    };
-}
-
-export const 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$.Optional, objectArg.Field("filename", string))), createMissingIdentifier());
-    let assays;
-    const arg_3 = list_2(ROCrate_decoder_1);
-    const objectArg_1 = get$.Optional;
-    assays = objectArg_1.Field("assays", arg_3);
-    const assayIdentifiers = map((arg_4) => {
-        const collection = map_2((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(ROCrate_decoder_2), (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$.Optional, objectArg_6.Field("publicReleaseDate", string))), unwrap((arg_16 = resizeArray(ROCrate_decoder_3), (objectArg_7 = get$.Optional, objectArg_7.Field("publications", arg_16)))), unwrap((arg_18 = resizeArray(ROCrate_decoder_4), (objectArg_8 = get$.Optional, objectArg_8.Field("people", arg_18)))), unwrap((arg_20 = resizeArray(OntologyAnnotation_ROCrate_decoderDefinedTerm), (objectArg_9 = get$.Optional, objectArg_9.Field("studyDesignDescriptors", arg_20)))), unwrap(tables), undefined, unwrap(assayIdentifiers), unwrap((arg_22 = resizeArray(ROCrate_decoder_5), (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 ISAJson_encoder(idMap, assays, s) {
-    const f = (s_1) => {
-        let studyName, value_6, value_8, studyName_1, studyName_2;
-        const study = s_1.Copy(true);
-        const fileName = Study_fileNameFromIdentifier(study.Identifier);
-        let assays_1;
-        const n = [];
-        let enumerator = getEnumerator(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 encodedUnits = tryIncludeList("unitCategories", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), getUnits(processes));
-        const encodedFactors = tryIncludeList("factors", (value_1) => encoder_10(idMap, value_1), getFactors(processes));
-        const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_3) => encoder_11(idMap, value_3), getCharacteristics(processes));
-        const encodedMaterials = tryInclude("materials", (ps) => encoder_12(idMap, ps), Option_fromValueWithDefault(empty(), processes));
-        let encodedProtocols;
-        const value_5 = getProtocols(processes);
-        encodedProtocols = tryIncludeList("protocols", (studyName = s_1.Identifier, (oa_1) => ISAJson_encoder_1(studyName, undefined, undefined, idMap, oa_1)), value_5);
-        const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value_6 = ROCrate_genID(study), {
-            Encode(helpers) {
-                return helpers.encodeString(value_6);
-            },
-        })], ["filename", {
-            Encode(helpers_1) {
-                return helpers_1.encodeString(fileName);
-            },
-        }], ["identifier", (value_8 = study.Identifier, {
-            Encode(helpers_2) {
-                return helpers_2.encodeString(value_8);
-            },
-        })], tryInclude("title", (value_9) => ({
-            Encode(helpers_3) {
-                return helpers_3.encodeString(value_9);
-            },
-        }), study.Title), tryInclude("description", (value_11) => ({
-            Encode(helpers_4) {
-                return helpers_4.encodeString(value_11);
-            },
-        }), study.Description), tryInclude("submissionDate", (value_13) => ({
-            Encode(helpers_5) {
-                return helpers_5.encodeString(value_13);
-            },
-        }), study.SubmissionDate), tryInclude("publicReleaseDate", (value_15) => ({
-            Encode(helpers_6) {
-                return helpers_6.encodeString(value_15);
-            },
-        }), study.PublicReleaseDate), tryIncludeSeq("publications", (oa_2) => ISAJson_encoder_2(idMap, oa_2), study.Publications), tryIncludeSeq("people", (person_2) => ISAJson_encoder_3(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) => ISAJson_encoder_4(studyName_1, undefined, idMap, oa_4)), processes), tryIncludeSeq("assays", (studyName_2 = s_1.Identifier, (a_2) => ISAJson_encoder_5(studyName_2, idMap, a_2)), assays_1), encodedFactors, encodedCharacteristics, encodedUnits, tryIncludeSeq("comments", (comment) => ISAJson_encoder_6(idMap, comment), study.Comments)]));
-        return {
-            Encode(helpers_7) {
-                const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_7)], values);
-                return helpers_7.encodeObject(arg);
-            },
-        };
-    };
-    if (idMap != null) {
-        return encode(ROCrate_genID, f, s, idMap);
-    }
-    else {
-        return f(s);
-    }
-}
-
-export const 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 ISAJson_decoder = Decode_objectNoAdditionalProperties(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(ISAJson_decoder_1), (objectArg_2 = get$.Optional, objectArg_2.Field("processSequence", arg_5))));
-    let assays;
-    const arg_8 = list_2(ISAJson_decoder_2);
-    const objectArg_3 = get$.Optional;
-    assays = objectArg_3.Field("assays", arg_8);
-    let personsRaw;
-    const arg_10 = resizeArray(ISAJson_decoder_3);
-    const objectArg_4 = get$.Optional;
-    personsRaw = objectArg_4.Field("people", arg_10);
-    const persons = [];
-    if (personsRaw != null) {
-        let enumerator = getEnumerator(value_17(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_17(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_2((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$.Optional, objectArg_8.Field("publicReleaseDate", string))), unwrap((arg_21 = resizeArray(ISAJson_decoder_4), (objectArg_9 = get$.Optional, objectArg_9.Field("publications", arg_21)))), unwrap((persons.length === 0) ? undefined : persons), unwrap((arg_23 = resizeArray(OntologyAnnotation_ISAJson_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("studyDesignDescriptors", arg_23)))), unwrap(tables), undefined, unwrap(assayIdentifiers), unwrap((arg_25 = resizeArray(ISAJson_decoder_5), (objectArg_11 = get$.Optional, objectArg_11.Field("comments", arg_25))))), defaultArg(assays, empty())];
-});
-

package/Json/Table/ArcTable.js

@@ -1,227 +0,0 @@
-import { toArray, collect, empty, map, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.24.0/Seq.js";
-import { tuple2, map as map_1, list } from "../../fable_modules/Thoth.Json.Core.0.4.0/Encode.fs.js";
-import { decoder as decoder_1, encoder as encoder_1 } from "./CompositeHeader.js";
-import { decoder as decoder_2, encoder as encoder_2 } from "./CompositeCell.js";
-import { empty as empty_2, ofSeq } from "../../fable_modules/fable-library-js.4.24.0/Map.js";
-import { int32ToString, equals, arrayHash, equalArrays, compareArrays } from "../../fable_modules/fable-library-js.4.24.0/Util.js";
-import { Helpers_prependPath, array as array_2, string, int, tuple2 as tuple2_1, map$0027, list as list_1, object } from "../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
-import { defaultArg } from "../../fable_modules/fable-library-js.4.24.0/Option.js";
-import { empty as empty_1 } from "../../fable_modules/fable-library-js.4.24.0/List.js";
-import { Dictionary } from "../../fable_modules/fable-library-js.4.24.0/MutableMap.js";
-import { ArcTable } from "../../Core/Table/ArcTable.js";
-import { decodeCell, encodeCell } from "./CellTable.js";
-import { addToDict, getItemFromDict } from "../../fable_modules/fable-library-js.4.24.0/MapUtil.js";
-import { rangeDouble } from "../../fable_modules/fable-library-js.4.24.0/Range.js";
-import { fill, setItem, fold, iterateIndexed, map as map_2 } from "../../fable_modules/fable-library-js.4.24.0/Array.js";
-import { FSharpResult$2 } from "../../fable_modules/fable-library-js.4.24.0/Result.js";
-import { ErrorReason$1 } from "../../fable_modules/Thoth.Json.Core.0.4.0/Types.fs.js";
-import { decodeString, encodeString } from "../StringTable.js";
-
-export function encoder(table) {
-    const values = toList(delay(() => {
-        let value_4;
-        return append(singleton(["name", (value_4 = table.Name, {
-            Encode(helpers_2) {
-                return helpers_2.encodeString(value_4);
-            },
-        })]), delay(() => append((table.Headers.length !== 0) ? singleton(["header", list(toList(delay(() => map(encoder_1, table.Headers))))]) : empty(), delay(() => ((table.Values.size !== 0) ? singleton(["values", map_1((tupledArg) => tuple2((value) => ({
-            Encode(helpers) {
-                return helpers.encodeSignedIntegralNumber(value);
-            },
-        }), (value_2) => ({
-            Encode(helpers_1) {
-                return helpers_1.encodeSignedIntegralNumber(value_2);
-            },
-        }), tupledArg[0], tupledArg[1]), encoder_2, ofSeq(toList(delay(() => collect((matchValue) => {
-            const activePatternResult = matchValue;
-            return singleton([activePatternResult[0], activePatternResult[1]]);
-        }, table.Values))), {
-            Compare: compareArrays,
-        }))]) : empty())))));
-    }));
-    return {
-        Encode(helpers_3) {
-            const arg = map((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_3)], values);
-            return helpers_3.encodeObject(arg);
-        },
-    };
-}
-
-export const decoder = object((get$) => {
-    let arg_1, objectArg, arg_3, objectArg_1, objectArg_2;
-    let decodedHeader;
-    const collection = defaultArg((arg_1 = list_1(decoder_1), (objectArg = get$.Optional, objectArg.Field("header", arg_1))), empty_1());
-    decodedHeader = Array.from(collection);
-    const decodedValues = new Dictionary(defaultArg((arg_3 = map$0027(tuple2_1(int, int), decoder_2), (objectArg_1 = get$.Optional, objectArg_1.Field("values", arg_3))), empty_2({
-        Compare: compareArrays,
-    })), {
-        Equals: equalArrays,
-        GetHashCode: arrayHash,
-    });
-    return ArcTable.create((objectArg_2 = get$.Required, objectArg_2.Field("name", string)), decodedHeader, decodedValues);
-});
-
-export function encoderCompressedColumn(columnIndex, rowCount, cellTable, table) {
-    if (table.Headers[columnIndex].IsIOType ? true : (rowCount < 100)) {
-        const values = toArray(delay(() => map((r) => encodeCell(cellTable, getItemFromDict(table.Values, [columnIndex, r])), rangeDouble(0, 1, rowCount - 1))));
-        return {
-            Encode(helpers) {
-                const arg = map_2((v) => v.Encode(helpers), values);
-                return helpers.encodeArray(arg);
-            },
-        };
-    }
-    else {
-        let current = getItemFromDict(table.Values, [columnIndex, 0]);
-        let from = 0;
-        const values_3 = toArray(delay(() => append(collect((i) => {
-            let values_1, value, value_1;
-            const next = getItemFromDict(table.Values, [columnIndex, i]);
-            return !equals(next, current) ? append(singleton((values_1 = [["f", (value = (from | 0), {
-                Encode(helpers_1) {
-                    return helpers_1.encodeSignedIntegralNumber(value);
-                },
-            })], ["t", (value_1 = ((i - 1) | 0), {
-                Encode(helpers_2) {
-                    return helpers_2.encodeSignedIntegralNumber(value_1);
-                },
-            })], ["v", encodeCell(cellTable, current)]], {
-                Encode(helpers_3) {
-                    const arg_1 = map((tupledArg) => [tupledArg[0], tupledArg[1].Encode(helpers_3)], values_1);
-                    return helpers_3.encodeObject(arg_1);
-                },
-            })), delay(() => {
-                current = next;
-                from = (i | 0);
-                return empty();
-            })) : empty();
-        }, rangeDouble(1, 1, rowCount - 1)), delay(() => {
-            let values_2, value_2, value_3;
-            return singleton((values_2 = [["f", (value_2 = (from | 0), {
-                Encode(helpers_4) {
-                    return helpers_4.encodeSignedIntegralNumber(value_2);
-                },
-            })], ["t", (value_3 = ((rowCount - 1) | 0), {
-                Encode(helpers_5) {
-                    return helpers_5.encodeSignedIntegralNumber(value_3);
-                },
-            })], ["v", encodeCell(cellTable, current)]], {
-                Encode(helpers_6) {
-                    const arg_2 = map((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values_2);
-                    return helpers_6.encodeObject(arg_2);
-                },
-            }));
-        }))));
-        return {
-            Encode(helpers_7) {
-                const arg_3 = map_2((v_3) => v_3.Encode(helpers_7), values_3);
-                return helpers_7.encodeArray(arg_3);
-            },
-        };
-    }
-}
-
-export function decoderCompressedColumn(cellTable, table, columnIndex) {
-    return {
-        Decode(helper, column) {
-            const matchValue = array_2(decodeCell(cellTable)).Decode(helper, column);
-            if (matchValue.tag === 1) {
-                const rangeDecoder = object((get$) => {
-                    let from;
-                    const objectArg = get$.Required;
-                    from = objectArg.Field("f", int);
-                    let to_;
-                    const objectArg_1 = get$.Required;
-                    to_ = objectArg_1.Field("t", int);
-                    let value;
-                    const arg_5 = decodeCell(cellTable);
-                    const objectArg_2 = get$.Required;
-                    value = objectArg_2.Field("v", arg_5);
-                    for (let i = from; i <= to_; i++) {
-                        addToDict(table.Values, [columnIndex, i], value);
-                    }
-                });
-                const matchValue_1 = array_2(rangeDecoder).Decode(helper, column);
-                return (matchValue_1.tag === 1) ? (new FSharpResult$2(1, [matchValue_1.fields[0]])) : (new FSharpResult$2(0, [undefined]));
-            }
-            else {
-                iterateIndexed((r, cell) => {
-                    addToDict(table.Values, [columnIndex, r], cell);
-                }, matchValue.fields[0]);
-                return new FSharpResult$2(0, [undefined]);
-            }
-        },
-    };
-}
-
-export function arrayi(decoderi) {
-    return {
-        Decode(helpers, value) {
-            if (helpers.isArray(value)) {
-                let i = -1;
-                const tokens = helpers.asArray(value);
-                return fold((acc, value_1) => {
-                    let tupledArg;
-                    i = ((i + 1) | 0);
-                    if (acc.tag === 0) {
-                        const acc_1 = acc.fields[0];
-                        const matchValue = decoderi(i).Decode(helpers, value_1);
-                        if (matchValue.tag === 0) {
-                            setItem(acc_1, i, matchValue.fields[0]);
-                            return new FSharpResult$2(0, [acc_1]);
-                        }
-                        else {
-                            return new FSharpResult$2(1, [(tupledArg = matchValue.fields[0], Helpers_prependPath((".[" + int32ToString(i)) + "]", tupledArg[0], tupledArg[1]))]);
-                        }
-                    }
-                    else {
-                        return acc;
-                    }
-                }, new FSharpResult$2(0, [fill(new Array(tokens.length), 0, tokens.length, null)]), tokens);
-            }
-            else {
-                return new FSharpResult$2(1, [["", new ErrorReason$1(0, ["an array", value])]]);
-            }
-        },
-    };
-}
-
-export function encoderCompressed(stringTable, oaTable, cellTable, table) {
-    const values_1 = toList(delay(() => append(singleton(["n", encodeString(stringTable, table.Name)]), delay(() => append((table.Headers.length !== 0) ? singleton(["h", list(toList(delay(() => map(encoder_1, table.Headers))))]) : empty(), delay(() => {
-        if (table.Values.size !== 0) {
-            const rowCount = table.RowCount | 0;
-            const columns = toArray(delay(() => map((c) => encoderCompressedColumn(c, rowCount, cellTable, table), rangeDouble(0, 1, table.ColumnCount - 1))));
-            return singleton(["c", {
-                Encode(helpers) {
-                    const arg = map_2((v) => v.Encode(helpers), columns);
-                    return helpers.encodeArray(arg);
-                },
-            }]);
-        }
-        else {
-            return empty();
-        }
-    }))))));
-    return {
-        Encode(helpers_1) {
-            const arg_1 = map((tupledArg) => [tupledArg[0], tupledArg[1].Encode(helpers_1)], values_1);
-            return helpers_1.encodeObject(arg_1);
-        },
-    };
-}
-
-export function decoderCompressed(stringTable, oaTable, cellTable) {
-    return object((get$) => {
-        let arg_1, objectArg, arg_3, objectArg_1, arg_5, objectArg_2;
-        let decodedHeader;
-        const collection = defaultArg((arg_1 = list_1(decoder_1), (objectArg = get$.Optional, objectArg.Field("h", arg_1))), empty_1());
-        decodedHeader = Array.from(collection);
-        const table = ArcTable.create((arg_3 = decodeString(stringTable), (objectArg_1 = get$.Required, objectArg_1.Field("n", arg_3))), decodedHeader, new Dictionary([], {
-            Equals: equalArrays,
-            GetHashCode: arrayHash,
-        }));
-        (arg_5 = arrayi((columnIndex) => decoderCompressedColumn(cellTable, table, columnIndex)), (objectArg_2 = get$.Optional, objectArg_2.Field("c", arg_5)));
-        return table;
-    });
-}
-