@nfdi4plants/arctrl 2.5.1 → 3.0.0-alpha.2

package/ARC.js

@@ -1,795 +0,0 @@
-import { append as append_1, contains as contains_2, concat, fold, map, exactlyOne, tryPick, choose } from "./fable_modules/fable-library-js.4.24.0/Array.js";
-import { ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from "./Contract/ArcAssay.js";
-import { ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static } from "./Contract/Datamap.js";
-import { ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from "./Contract/ArcStudy.js";
-import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from "./Contract/ArcInvestigation.js";
-import { toList, collect, empty, find, tryFind, iterate, map as map_1, singleton, append, delay, contains, toArray } from "./fable_modules/fable-library-js.4.24.0/Seq.js";
-import { FileSystemTree } from "./FileSystem/FileSystemTree.js";
-import { FileSystem } from "./FileSystem/FileSystem.js";
-import { bind, map as map_2, defaultArg, value as value_2, unwrap } from "./fable_modules/fable-library-js.4.24.0/Option.js";
-import { fullFillContractBatchAsync } from "./ContractIO/ContractIO.js";
-import { PromiseBuilder__Delay_62FBFDE1, PromiseBuilder__Run_212F1D4B } from "./fable_modules/Fable.Promise.3.2.0/Promise.fs.js";
-import { promise } from "./fable_modules/Fable.Promise.3.2.0/PromiseImpl.fs.js";
-import { getAllFilePathsAsync } from "./ContractIO/FileSystemHelper.js";
-import { FSharpResult$2 } from "./fable_modules/fable-library-js.4.24.0/Result.js";
-import { safeHash, curry2, comparePrimitives, stringHash } from "./fable_modules/fable-library-js.4.24.0/Util.js";
-import { getStudyFolderPath, getAssayFolderPath } from "./FileSystem/Path.js";
-import { toText, printf, toFail, join, replace } from "./fable_modules/fable-library-js.4.24.0/String.js";
-import { Contract } from "./Contract/Contract.js";
-import { FSharpSet__Contains, unionMany, contains as contains_1, ofSeq } from "./fable_modules/fable-library-js.4.24.0/Set.js";
-import { DataMap__get_StaticHash, DataMap__set_StaticHash_Z524259A4, DataMap__get_DataContexts } from "./Core/DataMap.js";
-import { tryISAReadContractFromPath } from "./Contract/ARC.js";
-import { ArcTables } from "./Core/Table/ArcTables.js";
-import { addToDict } from "./fable_modules/fable-library-js.4.24.0/MapUtil.js";
-import { ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF } from "./Spreadsheet/ArcInvestigation.js";
-import { ArcInvestigation } from "./Core/ArcTypes.js";
-import { Assay_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Study_fileNameFromIdentifier } from "./Core/Helper/Identifier.js";
-import { ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522 } from "./Spreadsheet/ArcStudy.js";
-import { toFsWorkbook } from "./Spreadsheet/DataMap.js";
-import { ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F } from "./Spreadsheet/ArcAssay.js";
-import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.6.3.1/Cells/FsCellsCollection.fs.js";
-import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, gitattributesContract, Init_createInitContract_6DFDD678 } from "./Contract/Git.js";
-import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library-js.4.24.0/Map.js";
-import { fromString } from "./fable_modules/Thoth.Json.JavaScript.0.3.0/Decode.fs.js";
-import { ROCrate_encoder_8A8D439, ROCrate_get_decoder, ROCrate_get_decoderDeprecated } from "./ROCrateIO.js";
-import { toString } from "./fable_modules/Thoth.Json.JavaScript.0.3.0/Encode.fs.js";
-import { defaultSpaces } from "./Json/Encode.js";
-import { ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_tryFromReadContract_Static_7570923F, ValidationPackagesConfigHelper_ReadContract, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toDeleteContract_Static_724DAE55, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toCreateContract_Static_724DAE55, ValidationPackagesConfigHelper_ConfigFilePath } from "./Contract/ValidationPackagesConfig.js";
-import { class_type } from "./fable_modules/fable-library-js.4.24.0/Reflection.js";
-
-export function ARCAux_getArcAssaysFromContracts(contracts) {
-    return choose(ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, contracts);
-}
-
-export function ARCAux_getAssayDataMapFromContracts(assayIdentifier, contracts) {
-    return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static(assayIdentifier, c), contracts);
-}
-
-export function ARCAux_getArcStudiesFromContracts(contracts) {
-    return choose(ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, contracts);
-}
-
-export function ARCAux_getStudyDataMapFromContracts(studyIdentifier, contracts) {
-    return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static(studyIdentifier, c), contracts);
-}
-
-export function ARCAux_getArcInvestigationFromContracts(contracts) {
-    return exactlyOne(choose(ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts));
-}
-
-export function ARCAux_updateFSByISA(isa, fs) {
-    let patternInput;
-    if (isa == null) {
-        patternInput = [[], []];
-    }
-    else {
-        const inv = isa;
-        patternInput = [toArray(inv.Studies), toArray(inv.Assays)];
-    }
-    let assaysFolder;
-    const assays_1 = map((a) => FileSystemTree.createAssayFolder(a.Identifier, a.DataMap != null), patternInput[1]);
-    assaysFolder = FileSystemTree.createAssaysFolder(assays_1);
-    let studiesFolder;
-    const studies_1 = map((s) => FileSystemTree.createStudyFolder(s.Identifier, s.DataMap != null), patternInput[0]);
-    studiesFolder = FileSystemTree.createStudiesFolder(studies_1);
-    const investigation = FileSystemTree.createInvestigationFile();
-    let tree_1;
-    const tree = FileSystemTree.createRootFolder([investigation, assaysFolder, studiesFolder]);
-    tree_1 = FileSystem.create({
-        tree: tree,
-    });
-    return fs.Union(tree_1);
-}
-
-export function ARCAux_updateFSByCWL(cwl, fs) {
-    const workflows = FileSystemTree.createWorkflowsFolder([]);
-    const runs = FileSystemTree.createRunsFolder([]);
-    let tree_1;
-    const tree = FileSystemTree.createRootFolder([workflows, runs]);
-    tree_1 = FileSystem.create({
-        tree: tree,
-    });
-    return fs.Union(tree_1);
-}
-
-export class ARC {
-    constructor(isa, cwl, fs) {
-        this.cwl = cwl;
-        this._isa = isa;
-        this._cwl = this.cwl;
-        this._fs = ARCAux_updateFSByCWL(this.cwl, ARCAux_updateFSByISA(isa, defaultArg(fs, FileSystem.create({
-            tree: new FileSystemTree(1, ["", []]),
-        }))));
-    }
-    get ISA() {
-        const this$ = this;
-        return unwrap(this$._isa);
-    }
-    set ISA(newISA) {
-        const this$ = this;
-        this$._isa = newISA;
-        this$.UpdateFileSystem();
-    }
-    get CWL() {
-        const this$ = this;
-        return this$.cwl;
-    }
-    get FileSystem() {
-        const this$ = this;
-        return this$._fs;
-    }
-    set FileSystem(fs) {
-        const this$ = this;
-        this$._fs = fs;
-    }
-    TryWriteAsync(arcPath) {
-        const this$ = this;
-        return fullFillContractBatchAsync(arcPath, this$.GetWriteContracts());
-    }
-    TryUpdateAsync(arcPath) {
-        const this$ = this;
-        return fullFillContractBatchAsync(arcPath, this$.GetUpdateContracts());
-    }
-    static tryLoadAsync(arcPath) {
-        return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => (getAllFilePathsAsync(arcPath).then((_arg) => {
-            const arc = ARC.fromFilePaths(toArray(_arg));
-            const contracts = arc.GetReadContracts();
-            return fullFillContractBatchAsync(arcPath, contracts).then((_arg_1) => {
-                const fulFilledContracts = _arg_1;
-                if (fulFilledContracts.tag === 1) {
-                    return Promise.resolve(new FSharpResult$2(1, [fulFilledContracts.fields[0]]));
-                }
-                else {
-                    arc.SetISAFromContracts(fulFilledContracts.fields[0]);
-                    return Promise.resolve(new FSharpResult$2(0, [arc]));
-                }
-            });
-        }))));
-    }
-    GetAssayRemoveContracts(assayIdentifier) {
-        let i;
-        const this$ = this;
-        let isa;
-        const matchValue = this$.ISA;
-        if (matchValue == null) {
-            throw new Error("Cannot remove assay from null ISA value.");
-        }
-        else if ((i = matchValue, contains(assayIdentifier, i.AssayIdentifiers, {
-            Equals: (x, y) => (x === y),
-            GetHashCode: stringHash,
-        }))) {
-            const i_1 = matchValue;
-            isa = i_1;
-        }
-        else {
-            throw new Error("ARC does not contain assay with given name");
-        }
-        const assay = isa.GetAssay(assayIdentifier);
-        const studies = assay.StudiesRegisteredIn;
-        isa.RemoveAssay(assayIdentifier);
-        const paths = this$.FileSystem.Tree.ToFilePaths();
-        const assayFolderPath = getAssayFolderPath(assayIdentifier);
-        const filteredPaths = paths.filter((p) => !p.startsWith(assayFolderPath));
-        this$.SetFilePaths(filteredPaths);
-        return toArray(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append(singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(isa)), delay(() => map_1(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
-    }
-    TryRemoveAssayAsync(arcPath, assayIdentifier) {
-        const this$ = this;
-        return fullFillContractBatchAsync(arcPath, this$.GetAssayRemoveContracts(assayIdentifier));
-    }
-    GetAssayRenameContracts(oldAssayIdentifier, newAssayIdentifier) {
-        let i;
-        const this$ = this;
-        let isa;
-        const matchValue = this$.ISA;
-        if (matchValue == null) {
-            throw new Error("Cannot rename assay in null ISA value.");
-        }
-        else if ((i = matchValue, contains(oldAssayIdentifier, i.AssayIdentifiers, {
-            Equals: (x, y) => (x === y),
-            GetHashCode: stringHash,
-        }))) {
-            const i_1 = matchValue;
-            isa = i_1;
-        }
-        else {
-            throw new Error("ARC does not contain assay with given name");
-        }
-        isa.RenameAssay(oldAssayIdentifier, newAssayIdentifier);
-        const paths = this$.FileSystem.Tree.ToFilePaths();
-        const oldAssayFolderPath = getAssayFolderPath(oldAssayIdentifier);
-        const newAssayFolderPath = getAssayFolderPath(newAssayIdentifier);
-        const renamedPaths = map((p) => replace(p, oldAssayFolderPath, newAssayFolderPath), paths);
-        this$.SetFilePaths(renamedPaths);
-        return toArray(delay(() => append(singleton(Contract.createRename(oldAssayFolderPath, newAssayFolderPath)), delay(() => this$.GetUpdateContracts()))));
-    }
-    TryRenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier) {
-        const this$ = this;
-        return fullFillContractBatchAsync(arcPath, this$.GetAssayRenameContracts(oldAssayIdentifier, newAssayIdentifier));
-    }
-    GetStudyRemoveContracts(studyIdentifier) {
-        const this$ = this;
-        let isa;
-        const matchValue = this$.ISA;
-        if (matchValue == null) {
-            throw new Error("Cannot remove study from null ISA value.");
-        }
-        else {
-            isa = matchValue;
-        }
-        isa.RemoveStudy(studyIdentifier);
-        const paths = this$.FileSystem.Tree.ToFilePaths();
-        const studyFolderPath = getStudyFolderPath(studyIdentifier);
-        const filteredPaths = paths.filter((p) => !p.startsWith(studyFolderPath));
-        this$.SetFilePaths(filteredPaths);
-        return [Contract.createDelete(studyFolderPath), ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(isa)];
-    }
-    TryRemoveStudyAsync(arcPath, studyIdentifier) {
-        const this$ = this;
-        return fullFillContractBatchAsync(arcPath, this$.GetStudyRemoveContracts(studyIdentifier));
-    }
-    GetStudyRenameContracts(oldStudyIdentifier, newStudyIdentifier) {
-        let i;
-        const this$ = this;
-        let isa;
-        const matchValue = this$.ISA;
-        if (matchValue == null) {
-            throw new Error("Cannot rename study in null ISA value.");
-        }
-        else if ((i = matchValue, contains(oldStudyIdentifier, i.StudyIdentifiers, {
-            Equals: (x, y) => (x === y),
-            GetHashCode: stringHash,
-        }))) {
-            const i_1 = matchValue;
-            isa = i_1;
-        }
-        else {
-            throw new Error("ARC does not contain study with given name");
-        }
-        isa.RenameStudy(oldStudyIdentifier, newStudyIdentifier);
-        const paths = this$.FileSystem.Tree.ToFilePaths();
-        const oldStudyFolderPath = getStudyFolderPath(oldStudyIdentifier);
-        const newStudyFolderPath = getStudyFolderPath(newStudyIdentifier);
-        const renamedPaths = map((p) => replace(p, oldStudyFolderPath, newStudyFolderPath), paths);
-        this$.SetFilePaths(renamedPaths);
-        return toArray(delay(() => append(singleton(Contract.createRename(oldStudyFolderPath, newStudyFolderPath)), delay(() => this$.GetUpdateContracts()))));
-    }
-    TryRenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier) {
-        const this$ = this;
-        return fullFillContractBatchAsync(arcPath, this$.GetStudyRenameContracts(oldStudyIdentifier, newStudyIdentifier));
-    }
-    WriteAsync(arcPath) {
-        const this$ = this;
-        return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => (this$.TryWriteAsync(arcPath).then((_arg) => {
-            const result = _arg;
-            if (result.tag === 1) {
-                const appended = join("\n", map((e) => e, result.fields[0]));
-                toFail(printf("Could not write ARC, failed with the following errors %s"))(appended);
-                return Promise.resolve();
-            }
-            else {
-                return Promise.resolve();
-            }
-        }))));
-    }
-    UpdateAsync(arcPath) {
-        const this$ = this;
-        return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => (this$.TryUpdateAsync(arcPath).then((_arg) => {
-            const result = _arg;
-            if (result.tag === 1) {
-                const appended = join("\n", map((e) => e, result.fields[0]));
-                toFail(printf("Could not update ARC, failed with the following errors %s"))(appended);
-                return Promise.resolve();
-            }
-            else {
-                return Promise.resolve();
-            }
-        }))));
-    }
-    RemoveAssayAsync(arcPath, assayIdentifier) {
-        const this$ = this;
-        return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => (this$.TryRemoveAssayAsync(arcPath, assayIdentifier).then((_arg) => {
-            const result = _arg;
-            if (result.tag === 1) {
-                const appended = join("\n", map((e) => e, result.fields[0]));
-                toFail(printf("Could not remove assay, failed with the following errors %s"))(appended);
-                return Promise.resolve();
-            }
-            else {
-                return Promise.resolve();
-            }
-        }))));
-    }
-    RenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier) {
-        const this$ = this;
-        return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => (this$.TryRenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier).then((_arg) => {
-            const result = _arg;
-            if (result.tag === 1) {
-                const appended = join("\n", map((e) => e, result.fields[0]));
-                toFail(printf("Could not rename assay, failed with the following errors %s"))(appended);
-                return Promise.resolve();
-            }
-            else {
-                return Promise.resolve();
-            }
-        }))));
-    }
-    RemoveStudyAsync(arcPath, studyIdentifier) {
-        const this$ = this;
-        return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => (this$.TryRemoveStudyAsync(arcPath, studyIdentifier).then((_arg) => {
-            const result = _arg;
-            if (result.tag === 1) {
-                const appended = join("\n", map((e) => e, result.fields[0]));
-                toFail(printf("Could not remove study, failed with the following errors %s"))(appended);
-                return Promise.resolve();
-            }
-            else {
-                return Promise.resolve();
-            }
-        }))));
-    }
-    RenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier) {
-        const this$ = this;
-        return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => (this$.TryRenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier).then((_arg) => {
-            const result = _arg;
-            if (result.tag === 1) {
-                const appended = join("\n", map((e) => e, result.fields[0]));
-                toFail(printf("Could not rename study, failed with the following errors %s"))(appended);
-                return Promise.resolve();
-            }
-            else {
-                return Promise.resolve();
-            }
-        }))));
-    }
-    static loadAsync(arcPath) {
-        return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => (ARC.tryLoadAsync(arcPath).then((_arg) => {
-            const result = _arg;
-            if (result.tag === 1) {
-                const appended = join("\n", map((e) => e, result.fields[0]));
-                toFail(printf("Could not load ARC, failed with the following errors %s"))(appended);
-                return Promise.resolve(new ARC());
-            }
-            else {
-                return Promise.resolve(result.fields[0]);
-            }
-        }))));
-    }
-    MakeDataFilesAbsolute() {
-        const this$ = this;
-        const filesPaths = ofSeq(this$.FileSystem.Tree.ToFilePaths(), {
-            Compare: comparePrimitives,
-        });
-        const checkExistenceFromRoot = (p) => contains_1(p, filesPaths);
-        const updateColumnOption = (dataNameFunction, col) => {
-            let col_1;
-            let matchResult, col_2;
-            if (col != null) {
-                if ((col_1 = col, col_1.Header.IsDataColumn)) {
-                    matchResult = 0;
-                    col_2 = col;
-                }
-                else {
-                    matchResult = 1;
-                }
-            }
-            else {
-                matchResult = 1;
-            }
-            switch (matchResult) {
-                case 0: {
-                    col_2.Cells.forEach((c) => {
-                        if (c.AsData.FilePath != null) {
-                            const newFilePath = dataNameFunction(c.AsData);
-                            c.AsData.FilePath = newFilePath;
-                        }
-                    });
-                    break;
-                }
-                case 1: {
-                    break;
-                }
-            }
-        };
-        const updateTable = (dataNameFunction_1, t) => {
-            updateColumnOption(dataNameFunction_1, t.TryGetInputColumn());
-            updateColumnOption(dataNameFunction_1, t.TryGetOutputColumn());
-        };
-        const updateDataMap = (dataNameFunction_2, dm) => {
-            iterate((c_1) => {
-                if (c_1.FilePath != null) {
-                    const newFilePath_1 = dataNameFunction_2(c_1);
-                    c_1.FilePath = newFilePath_1;
-                }
-            }, DataMap__get_DataContexts(dm));
-        };
-        const matchValue = this$.ISA;
-        if (matchValue == null) {
-        }
-        else {
-            const inv = matchValue;
-            iterate((s) => {
-                const f = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
-                const source_1 = s.Tables;
-                iterate(curry2(updateTable)(f), source_1);
-                if (s.DataMap != null) {
-                    updateDataMap(f, value_2(s.DataMap));
-                }
-            }, inv.Studies);
-            iterate((a) => {
-                const f_1 = (d_1) => d_1.GetAbsolutePathForAssay(a.Identifier, checkExistenceFromRoot);
-                const source_3 = a.Tables;
-                iterate(curry2(updateTable)(f_1), source_3);
-                if (a.DataMap != null) {
-                    updateDataMap(f_1, value_2(a.DataMap));
-                }
-            }, inv.Assays);
-        }
-    }
-    static fromFilePaths(filePaths) {
-        return new ARC(undefined, undefined, FileSystem.fromFilePaths(filePaths));
-    }
-    SetFilePaths(filePaths) {
-        const this$ = this;
-        const tree = FileSystemTree.fromFilePaths(filePaths);
-        this$._fs = (new FileSystem(tree, this$._fs.History));
-    }
-    GetReadContracts() {
-        const this$ = this;
-        return choose(tryISAReadContractFromPath, this$._fs.Tree.ToFilePaths());
-    }
-    SetISAFromContracts(contracts) {
-        const this$ = this;
-        const investigation = ARCAux_getArcInvestigationFromContracts(contracts);
-        const studies = map((tuple) => tuple[0], ARCAux_getArcStudiesFromContracts(contracts));
-        const assays = ARCAux_getArcAssaysFromContracts(contracts);
-        const array_2 = investigation.AssayIdentifiers;
-        array_2.forEach((ai) => {
-            if (!assays.some((a) => (a.Identifier === ai))) {
-                investigation.DeleteAssay(ai);
-            }
-        });
-        const array_4 = investigation.StudyIdentifiers;
-        array_4.forEach((si) => {
-            if (!studies.some((s) => (s.Identifier === si))) {
-                investigation.DeleteStudy(si);
-            }
-        });
-        studies.forEach((study) => {
-            const registeredStudyOpt = tryFind((s_1) => (s_1.Identifier === study.Identifier), investigation.Studies);
-            if (registeredStudyOpt == null) {
-                investigation.AddStudy(study);
-            }
-            else {
-                const registeredStudy = registeredStudyOpt;
-                registeredStudy.UpdateReferenceByStudyFile(study, true);
-            }
-            const datamap = ARCAux_getAssayDataMapFromContracts(study.Identifier, contracts);
-            if (study.DataMap == null) {
-                study.DataMap = datamap;
-            }
-            study.StaticHash = (study.GetLightHashCode() | 0);
-        });
-        assays.forEach((assay) => {
-            const registeredAssayOpt = tryFind((a_1) => (a_1.Identifier === assay.Identifier), investigation.Assays);
-            if (registeredAssayOpt == null) {
-                investigation.AddAssay(assay);
-            }
-            else {
-                const registeredAssay = registeredAssayOpt;
-                registeredAssay.UpdateReferenceByAssayFile(assay, true);
-            }
-            const assay_1 = find((a_2) => (a_2.Identifier === assay.Identifier), investigation.Assays);
-            let updatedTables;
-            const array_6 = assay_1.StudiesRegisteredIn;
-            updatedTables = fold((tables, study_1) => ArcTables.updateReferenceTablesBySheets(new ArcTables(study_1.Tables), tables, false), new ArcTables(assay_1.Tables), array_6);
-            const datamap_1 = ARCAux_getAssayDataMapFromContracts(assay_1.Identifier, contracts);
-            if (assay_1.DataMap == null) {
-                assay_1.DataMap = datamap_1;
-            }
-            assay_1.Tables = updatedTables.Tables;
-        });
-        iterate((a_3) => {
-            a_3.StaticHash = (a_3.GetLightHashCode() | 0);
-        }, investigation.Assays);
-        iterate((s_2) => {
-            s_2.StaticHash = (s_2.GetLightHashCode() | 0);
-        }, investigation.Studies);
-        investigation.StaticHash = (investigation.GetLightHashCode() | 0);
-        this$.ISA = investigation;
-    }
-    UpdateFileSystem() {
-        const this$ = this;
-        let newFS;
-        const fs = ARCAux_updateFSByISA(this$._isa, this$._fs);
-        newFS = ARCAux_updateFSByCWL(this$._cwl, fs);
-        this$._fs = newFS;
-    }
-    GetWriteContracts() {
-        const this$ = this;
-        const workbooks = new Map([]);
-        const matchValue = this$.ISA;
-        if (matchValue == null) {
-            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(ArcInvestigation.create("MISSING_IDENTIFIER_"))]);
-        }
-        else {
-            const inv = matchValue;
-            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(inv)]);
-            inv.StaticHash = (inv.GetLightHashCode() | 0);
-            iterate((s) => {
-                s.StaticHash = (s.GetLightHashCode() | 0);
-                addToDict(workbooks, Study_fileNameFromIdentifier(s.Identifier), ["ISA_Study", ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(s)]);
-                if (s.DataMap != null) {
-                    const dm = value_2(s.DataMap);
-                    DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
-                    addToDict(workbooks, Study_datamapFileNameFromIdentifier(s.Identifier), ["ISA_Datamap", toFsWorkbook(dm)]);
-                }
-            }, inv.Studies);
-            iterate((a) => {
-                a.StaticHash = (a.GetLightHashCode() | 0);
-                addToDict(workbooks, Assay_fileNameFromIdentifier(a.Identifier), ["ISA_Assay", ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(a)]);
-                if (a.DataMap != null) {
-                    const dm_1 = value_2(a.DataMap);
-                    DataMap__set_StaticHash_Z524259A4(dm_1, safeHash(dm_1));
-                    addToDict(workbooks, Assay_datamapFileNameFromIdentifier(a.Identifier), ["ISA_Datamap", toFsWorkbook(dm_1)]);
-                }
-            }, inv.Assays);
-        }
-        return map((fp) => {
-            const matchValue_1 = Dictionary_tryGet(fp, workbooks);
-            if (matchValue_1 == null) {
-                return Contract.createCreate(fp, "PlainText");
-            }
-            else {
-                const wb = matchValue_1[1];
-                const dto = matchValue_1[0];
-                return Contract.createCreate(fp, dto, wb);
-            }
-        }, this$._fs.Tree.ToFilePaths(true));
-    }
-    GetUpdateContracts() {
-        let inv, inv_1, inv_2;
-        const this$ = this;
-        const matchValue = this$.ISA;
-        return (matchValue != null) ? (((inv = matchValue, inv.StaticHash === 0)) ? ((inv_1 = matchValue, this$.GetWriteContracts())) : ((inv_2 = matchValue, toArray(delay(() => {
-            const hash = inv_2.GetLightHashCode() | 0;
-            return append((inv_2.StaticHash !== hash) ? singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(inv_2)) : empty(), delay(() => {
-                inv_2.StaticHash = (hash | 0);
-                return append(collect((s) => {
-                    const hash_1 = s.GetLightHashCode() | 0;
-                    return append((s.StaticHash === 0) ? ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true) : ((s.StaticHash !== hash_1) ? singleton(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract(s)) : empty()), delay(() => {
-                        let dm_1;
-                        s.StaticHash = (hash_1 | 0);
-                        const matchValue_1 = s.DataMap;
-                        let matchResult, dm_2, dm_3;
-                        if (matchValue_1 != null) {
-                            if (DataMap__get_StaticHash(matchValue_1) === 0) {
-                                matchResult = 0;
-                                dm_2 = matchValue_1;
-                            }
-                            else if ((dm_1 = matchValue_1, DataMap__get_StaticHash(dm_1) !== safeHash(dm_1))) {
-                                matchResult = 1;
-                                dm_3 = matchValue_1;
-                            }
-                            else {
-                                matchResult = 2;
-                            }
-                        }
-                        else {
-                            matchResult = 2;
-                        }
-                        switch (matchResult) {
-                            case 0:
-                                return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
-                                    DataMap__set_StaticHash_Z524259A4(dm_2, safeHash(dm_2));
-                                    return empty();
-                                }));
-                            case 1:
-                                return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
-                                    DataMap__set_StaticHash_Z524259A4(dm_3, safeHash(dm_3));
-                                    return empty();
-                                }));
-                            default: {
-                                return empty();
-                            }
-                        }
-                    }));
-                }, inv_2.Studies), delay(() => collect((a) => {
-                    const hash_2 = a.GetLightHashCode() | 0;
-                    return append((a.StaticHash === 0) ? ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true) : ((a.StaticHash !== hash_2) ? singleton(ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(a)) : empty()), delay(() => {
-                        let dm_5;
-                        a.StaticHash = (hash_2 | 0);
-                        const matchValue_2 = a.DataMap;
-                        let matchResult_1, dm_6, dm_7;
-                        if (matchValue_2 != null) {
-                            if (DataMap__get_StaticHash(matchValue_2) === 0) {
-                                matchResult_1 = 0;
-                                dm_6 = matchValue_2;
-                            }
-                            else if ((dm_5 = matchValue_2, DataMap__get_StaticHash(dm_5) !== safeHash(dm_5))) {
-                                matchResult_1 = 1;
-                                dm_7 = matchValue_2;
-                            }
-                            else {
-                                matchResult_1 = 2;
-                            }
-                        }
-                        else {
-                            matchResult_1 = 2;
-                        }
-                        switch (matchResult_1) {
-                            case 0:
-                                return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
-                                    DataMap__set_StaticHash_Z524259A4(dm_6, safeHash(dm_6));
-                                    return empty();
-                                }));
-                            case 1:
-                                return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
-                                    DataMap__set_StaticHash_Z524259A4(dm_7, safeHash(dm_7));
-                                    return empty();
-                                }));
-                            default: {
-                                return empty();
-                            }
-                        }
-                    }));
-                }, inv_2.Assays)));
-            }));
-        }))))) : this$.GetWriteContracts();
-    }
-    GetGitInitContracts(branch, repositoryAddress, defaultGitignore) {
-        const defaultGitignore_1 = defaultArg(defaultGitignore, false);
-        return toArray(delay(() => append(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append(singleton(gitattributesContract), delay(() => append(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => ((repositoryAddress != null) ? singleton(Init_createAddRemoteContract_Z721C83C5(value_2(repositoryAddress))) : empty())))))))));
-    }
-    static getCloneContract(remoteUrl, merge, branch, token, nolfs) {
-        return Clone_createCloneContract_5000466F(remoteUrl, unwrap(merge), unwrap(branch), unwrap(token), unwrap(nolfs));
-    }
-    Copy() {
-        const this$ = this;
-        const isaCopy = map_2((i) => i.Copy(), this$._isa);
-        const fsCopy = this$._fs.Copy();
-        return new ARC(unwrap(isaCopy), this$._cwl, fsCopy);
-    }
-    GetRegisteredPayload(IgnoreHidden) {
-        let tree, paths, array_3;
-        const this$ = this;
-        const registeredStudies = defaultArg(map_2((isa) => isa.Studies.slice(), map_2((i) => i.Copy(), this$._isa)), []);
-        const registeredAssays = concat(map((s) => s.RegisteredAssays.slice(), registeredStudies));
-        const includeFiles = unionMany([ofSeq(["isa.investigation.xlsx", "README.md"], {
-            Compare: comparePrimitives,
-        }), unionMany(map((s_1) => {
-            const studyFoldername = `${"studies"}/${s_1.Identifier}`;
-            return ofSeq(toList(delay(() => append(singleton(`${studyFoldername}/${"isa.study.xlsx"}`), delay(() => append(singleton(`${studyFoldername}/${"README.md"}`), delay(() => collect((table) => collect((kv) => {
-                const textValue = kv[1].ToFreeTextCell().AsFreeText;
-                return append(singleton(textValue), delay(() => append(singleton(`${studyFoldername}/${"resources"}/${textValue}`), delay(() => singleton(`${studyFoldername}/${"protocols"}/${textValue}`)))));
-            }, table.Values), s_1.Tables))))))), {
-                Compare: comparePrimitives,
-            });
-        }, registeredStudies), {
-            Compare: comparePrimitives,
-        }), unionMany(map((a) => {
-            const assayFoldername = `${"assays"}/${a.Identifier}`;
-            return ofSeq(toList(delay(() => append(singleton(`${assayFoldername}/${"isa.assay.xlsx"}`), delay(() => append(singleton(`${assayFoldername}/${"README.md"}`), delay(() => collect((table_1) => collect((kv_1) => {
-                const textValue_1 = kv_1[1].ToFreeTextCell().AsFreeText;
-                return append(singleton(textValue_1), delay(() => append(singleton(`${assayFoldername}/${"dataset"}/${textValue_1}`), delay(() => singleton(`${assayFoldername}/${"protocols"}/${textValue_1}`)))));
-            }, table_1.Values), a.Tables))))))), {
-                Compare: comparePrimitives,
-            });
-        }, registeredAssays), {
-            Compare: comparePrimitives,
-        })], {
-            Compare: comparePrimitives,
-        });
-        const ignoreHidden = defaultArg(IgnoreHidden, true);
-        const fsCopy = this$._fs.Copy();
-        return defaultArg(bind((tree_1) => {
-            if (ignoreHidden) {
-                return FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1);
-            }
-            else {
-                return tree_1;
-            }
-        }, (tree = ((paths = ((array_3 = FileSystemTree.toFilePaths()(fsCopy.Tree), array_3.filter((p) => {
-            if (p.startsWith("workflows") ? true : p.startsWith("runs")) {
-                return true;
-            }
-            else {
-                return FSharpSet__Contains(includeFiles, p);
-            }
-        }))), FileSystemTree.fromFilePaths(paths))), ignoreHidden ? FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree)), FileSystemTree.fromFilePaths([]));
-    }
-    GetAdditionalPayload(IgnoreHidden) {
-        let tree, paths, array;
-        const this$ = this;
-        const ignoreHidden = defaultArg(IgnoreHidden, true);
-        const registeredPayload = ofSeq(FileSystemTree.toFilePaths()(this$.GetRegisteredPayload()), {
-            Compare: comparePrimitives,
-        });
-        return defaultArg(bind((tree_1) => {
-            if (ignoreHidden) {
-                return FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1);
-            }
-            else {
-                return tree_1;
-            }
-        }, (tree = ((paths = ((array = FileSystemTree.toFilePaths()(this$._fs.Copy().Tree), array.filter((p) => !FSharpSet__Contains(registeredPayload, p)))), FileSystemTree.fromFilePaths(paths))), ignoreHidden ? FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree)), FileSystemTree.fromFilePaths([]));
-    }
-    static get DefaultContracts() {
-        return ofSeq_1([[".gitignore", gitignoreContract], [".gitattributes", gitattributesContract]], {
-            Compare: comparePrimitives,
-        });
-    }
-    static fromDeprecatedROCrateJsonString(s) {
-        let matchValue;
-        try {
-            const s_1 = replace(s, "bio:additionalProperty", "sdo:additionalProperty");
-            return new ARC((matchValue = fromString(ROCrate_get_decoderDeprecated(), s_1), (matchValue.tag === 1) ? (() => {
-                throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-            })() : matchValue.fields[0]));
-        }
-        catch (ex) {
-            const arg_1 = ex.message;
-            return toFail(printf("Could not parse deprecated ARC-RO-Crate metadata: \n%s"))(arg_1);
-        }
-    }
-    static fromROCrateJsonString(s) {
-        let matchValue;
-        try {
-            return new ARC((matchValue = fromString(ROCrate_get_decoder(), s), (matchValue.tag === 1) ? (() => {
-                throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-            })() : matchValue.fields[0]));
-        }
-        catch (ex) {
-            const arg_1 = ex.message;
-            return toFail(printf("Could not parse ARC-RO-Crate metadata: \n%s"))(arg_1);
-        }
-    }
-    ToROCrateJsonString(spaces) {
-        const this$ = this;
-        this$.MakeDataFilesAbsolute();
-        const value = ROCrate_encoder_8A8D439(value_2(this$._isa));
-        return toString(defaultSpaces(spaces), value);
-    }
-    static toROCrateJsonString(spaces) {
-        return (obj) => obj.ToROCrateJsonString(unwrap(spaces));
-    }
-    GetValidationPackagesConfigWriteContract(vpc) {
-        const this$ = this;
-        const paths = this$.FileSystem.Tree.ToFilePaths();
-        if (!contains_2(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
-            Equals: (x, y) => (x === y),
-            GetHashCode: stringHash,
-        })) {
-            const filePaths = append_1([ValidationPackagesConfigHelper_ConfigFilePath], paths);
-            this$.SetFilePaths(filePaths);
-        }
-        return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toCreateContract_Static_724DAE55(vpc);
-    }
-    GetValidationPackagesConfigDeleteContract(vpc) {
-        const this$ = this;
-        const paths = this$.FileSystem.Tree.ToFilePaths();
-        if (contains_2(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
-            Equals: (x, y) => (x === y),
-            GetHashCode: stringHash,
-        })) {
-            const filePaths = paths.filter((p) => !(p === ValidationPackagesConfigHelper_ConfigFilePath));
-            this$.SetFilePaths(filePaths);
-        }
-        return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toDeleteContract_Static_724DAE55(vpc);
-    }
-    GetValidationPackagesConfigReadContract() {
-        return ValidationPackagesConfigHelper_ReadContract;
-    }
-    GetValidationPackagesConfigFromReadContract(contract) {
-        return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_tryFromReadContract_Static_7570923F(contract);
-    }
-}
-
-export function ARC_$reflection() {
-    return class_type("ARCtrl.ARC", undefined, ARC);
-}
-
-export function ARC_$ctor_79978BA1(isa, cwl, fs) {
-    return new ARC(isa, cwl, fs);
-}
-