@nfdi4plants/arctrl 2.5.0 → 3.0.0-alpha.1

package/dist/ts/cjs/ts/ARC.js

@@ -0,0 +1,965 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ARC = void 0;
+exports.ARC_$reflection = ARC_$reflection;
+exports.ARC_$ctor_5BB4A6F7 = ARC_$ctor_5BB4A6F7;
+exports.ARCAux_getArcAssaysFromContracts = ARCAux_getArcAssaysFromContracts;
+exports.ARCAux_getArcStudiesFromContracts = ARCAux_getArcStudiesFromContracts;
+exports.ARCAux_getArcWorkflowsFromContracts = ARCAux_getArcWorkflowsFromContracts;
+exports.ARCAux_getArcRunsFromContracts = ARCAux_getArcRunsFromContracts;
+exports.ARCAux_getAssayDataMapFromContracts = ARCAux_getAssayDataMapFromContracts;
+exports.ARCAux_getStudyDataMapFromContracts = ARCAux_getStudyDataMapFromContracts;
+exports.ARCAux_getWorkflowDataMapFromContracts = ARCAux_getWorkflowDataMapFromContracts;
+exports.ARCAux_getRunDataMapFromContracts = ARCAux_getRunDataMapFromContracts;
+exports.ARCAux_getArcInvestigationFromContracts = ARCAux_getArcInvestigationFromContracts;
+exports.ARCAux_updateFSByISA = ARCAux_updateFSByISA;
+exports.ARCAux_updateFSByCWL = ARCAux_updateFSByCWL;
+const FileSystem_js_1 = require("./FileSystem/FileSystem.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const ArcTypes_js_1 = require("./Core/ArcTypes.js");
+const ContractIO_js_1 = require("./ContractIO/ContractIO.js");
+const Result_js_1 = require("@fable-org/fable-library-js/Result.js");
+const Contract_js_1 = require("./Contract/Contract.js");
+const Promise_fs_js_1 = require("./fable_modules/Fable.Promise.3.2.0/Promise.fs.js");
+const PromiseImpl_fs_js_1 = require("./fable_modules/Fable.Promise.3.2.0/PromiseImpl.fs.js");
+const FileSystemHelper_js_1 = require("./ContractIO/FileSystemHelper.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+const Path_js_1 = require("./FileSystem/Path.js");
+const ArcAssay_js_1 = require("./Contract/ArcAssay.js");
+const ArcInvestigation_js_1 = require("./Contract/ArcInvestigation.js");
+const ArcStudy_js_1 = require("./Contract/ArcStudy.js");
+const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const Identifier_js_1 = require("./Core/Helper/Identifier.js");
+const Set_js_1 = require("@fable-org/fable-library-js/Set.js");
+const DataMap_js_1 = require("./Core/DataMap.js");
+const FileSystemTree_js_1 = require("./FileSystem/FileSystemTree.js");
+const ARC_js_1 = require("./Contract/ARC.js");
+const IdentifierSetters_js_1 = require("./Core/IdentifierSetters.js");
+const ArcTables_js_1 = require("./Core/Table/ArcTables.js");
+const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const ArcInvestigation_js_2 = require("./Spreadsheet/ArcInvestigation.js");
+const ArcStudy_js_2 = require("./Spreadsheet/ArcStudy.js");
+const DataMap_js_2 = require("./Spreadsheet/DataMap.js");
+const ArcAssay_js_2 = require("./Spreadsheet/ArcAssay.js");
+const ArcWorkflow_js_1 = require("./Spreadsheet/ArcWorkflow.js");
+const ArcRun_js_1 = require("./Spreadsheet/ArcRun.js");
+const FsCellsCollection_fs_js_1 = require("./fable_modules/FsSpreadsheet.6.3.1/Cells/FsCellsCollection.fs.js");
+const Datamap_js_1 = require("./Contract/Datamap.js");
+const ArcWorkflow_js_2 = require("./Contract/ArcWorkflow.js");
+const ArcRun_js_2 = require("./Contract/ArcRun.js");
+const Git_js_1 = require("./Contract/Git.js");
+const Collections_js_1 = require("./Core/Helper/Collections.js");
+const Map_js_1 = require("@fable-org/fable-library-js/Map.js");
+const Decode_fs_js_1 = require("./fable_modules/Thoth.Json.JavaScript.0.3.0/Decode.fs.js");
+const ROCrateIO_js_1 = require("./ROCrateIO.js");
+const Encode_fs_js_1 = require("./fable_modules/Thoth.Json.JavaScript.0.3.0/Encode.fs.js");
+const Encode_js_1 = require("./Json/Encode.js");
+const ValidationPackagesConfig_js_1 = require("./Contract/ValidationPackagesConfig.js");
+const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
+const Reflection_js_1 = require("@fable-org/fable-library-js/Reflection.js");
+class ARC extends ArcTypes_js_1.ArcInvestigation {
+    constructor(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, cwl, fs) {
+        super(identifier, (0, Option_js_1.unwrap)(title), (0, Option_js_1.unwrap)(description), (0, Option_js_1.unwrap)(submissionDate), (0, Option_js_1.unwrap)(publicReleaseDate), (0, Option_js_1.unwrap)(ontologySourceReferences), (0, Option_js_1.unwrap)(publications), (0, Option_js_1.unwrap)(contacts), (0, Option_js_1.unwrap)(assays), (0, Option_js_1.unwrap)(studies), (0, Option_js_1.unwrap)(workflows), (0, Option_js_1.unwrap)(runs), (0, Option_js_1.unwrap)(registeredStudyIdentifiers), (0, Option_js_1.unwrap)(comments), (0, Option_js_1.unwrap)(remarks));
+        let fs_1;
+        const this$ = new Types_js_1.FSharpRef((0, Util_js_1.defaultOf)());
+        this$.contents = this;
+        this._cwl = cwl;
+        this._fs = ((fs_1 = (0, Option_js_1.defaultArg)(fs, FileSystem_js_1.FileSystem.create({
+            tree: (0, FileSystemTree_js_1.FileSystemTree_Folder)("", []),
+        })), ARCAux_updateFSByISA(this$.contents, fs_1)));
+        this["init@89"] = 1;
+    }
+    get FileSystem() {
+        const this$ = this;
+        return this$._fs;
+    }
+    set FileSystem(fs) {
+        const this$ = this;
+        this$._fs = fs;
+    }
+    static fromArcInvestigation(isa, cwl, fs) {
+        return new ARC(isa.Identifier, (0, Option_js_1.unwrap)(isa.Title), (0, Option_js_1.unwrap)(isa.Description), (0, Option_js_1.unwrap)(isa.SubmissionDate), (0, Option_js_1.unwrap)(isa.PublicReleaseDate), isa.OntologySourceReferences, isa.Publications, isa.Contacts, isa.Assays, isa.Studies, isa.Workflows, isa.Runs, isa.RegisteredStudyIdentifiers, isa.Comments, isa.Remarks, cwl, (0, Option_js_1.unwrap)(fs));
+    }
+    TryWriteAsync(arcPath) {
+        const this$ = this;
+        return (0, ContractIO_js_1.fullFillContractBatchAsync)(arcPath, this$.GetWriteContracts());
+    }
+    TryUpdateAsync(arcPath) {
+        const this$ = this;
+        return (0, ContractIO_js_1.fullFillContractBatchAsync)(arcPath, this$.GetUpdateContracts());
+    }
+    static tryLoadAsync(arcPath) {
+        return (0, Promise_fs_js_1.PromiseBuilder__Run_212F1D4B)(PromiseImpl_fs_js_1.promise, (0, Promise_fs_js_1.PromiseBuilder__Delay_62FBFDE1)(PromiseImpl_fs_js_1.promise, () => ((0, FileSystemHelper_js_1.getAllFilePathsAsync)(arcPath).then((_arg) => {
+            const arc = ARC.fromFilePaths((0, Seq_js_1.toArray)(_arg));
+            const contracts = arc.GetReadContracts();
+            return (0, ContractIO_js_1.fullFillContractBatchAsync)(arcPath, contracts).then((_arg_1) => {
+                const fulFilledContracts = _arg_1;
+                if (fulFilledContracts.tag === /* Error */ 1) {
+                    const e = fulFilledContracts.fields[0];
+                    return Promise.resolve((0, Result_js_1.FSharpResult$2_Error)(e));
+                }
+                else {
+                    const c = fulFilledContracts.fields[0];
+                    arc.SetISAFromContracts(c);
+                    return Promise.resolve((0, Result_js_1.FSharpResult$2_Ok)(arc));
+                }
+            });
+        }))));
+    }
+    GetAssayRemoveContracts(assayIdentifier) {
+        const this$ = this;
+        if (!(0, Seq_js_1.contains)(assayIdentifier, this$.AssayIdentifiers, {
+            Equals: (x, y) => (x === y),
+            GetHashCode: Util_js_1.stringHash,
+        })) {
+            throw new Error("ARC does not contain assay with given name");
+        }
+        const assay = this$.GetAssay(assayIdentifier);
+        const studies = assay.StudiesRegisteredIn;
+        super.RemoveAssay(assayIdentifier);
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        const assayFolderPath = (0, Path_js_1.getAssayFolderPath)(assayIdentifier);
+        const filteredPaths = paths.filter((p) => !p.startsWith(assayFolderPath));
+        this$.SetFilePaths(filteredPaths);
+        return (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, ArcAssay_js_1.ARCtrl_ArcAssay__ArcAssay_ToDeleteContract)(assay)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, ArcInvestigation_js_1.ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract)(this$)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.map)(ArcStudy_js_1.ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
+    }
+    TryRemoveAssayAsync(arcPath, assayIdentifier) {
+        const this$ = this;
+        return (0, ContractIO_js_1.fullFillContractBatchAsync)(arcPath, this$.GetAssayRemoveContracts(assayIdentifier));
+    }
+    GetAssayRenameContracts(oldAssayIdentifier, newAssayIdentifier) {
+        const this$ = this;
+        if (!(0, Seq_js_1.contains)(oldAssayIdentifier, this$.AssayIdentifiers, {
+            Equals: (x, y) => (x === y),
+            GetHashCode: Util_js_1.stringHash,
+        })) {
+            throw new Error("ARC does not contain assay with given name");
+        }
+        super.RenameAssay(oldAssayIdentifier, newAssayIdentifier);
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        const oldAssayFolderPath = (0, Path_js_1.getAssayFolderPath)(oldAssayIdentifier);
+        const newAssayFolderPath = (0, Path_js_1.getAssayFolderPath)(newAssayIdentifier);
+        const renamedPaths = (0, Array_js_1.map)((p) => (0, String_js_1.replace)(p, oldAssayFolderPath, newAssayFolderPath), paths);
+        this$.SetFilePaths(renamedPaths);
+        return (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(Contract_js_1.Contract.createRename(oldAssayFolderPath, newAssayFolderPath)), (0, Seq_js_1.delay)(() => this$.GetUpdateContracts()))));
+    }
+    TryRenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier) {
+        const this$ = this;
+        return (0, ContractIO_js_1.fullFillContractBatchAsync)(arcPath, this$.GetAssayRenameContracts(oldAssayIdentifier, newAssayIdentifier));
+    }
+    GetStudyRemoveContracts(studyIdentifier) {
+        const this$ = this;
+        super.RemoveStudy(studyIdentifier);
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        const studyFolderPath = (0, Path_js_1.getStudyFolderPath)(studyIdentifier);
+        const filteredPaths = paths.filter((p) => !p.startsWith(studyFolderPath));
+        this$.SetFilePaths(filteredPaths);
+        return [Contract_js_1.Contract.createDelete(studyFolderPath), (0, ArcInvestigation_js_1.ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract)(this$)];
+    }
+    TryRemoveStudyAsync(arcPath, studyIdentifier) {
+        const this$ = this;
+        return (0, ContractIO_js_1.fullFillContractBatchAsync)(arcPath, this$.GetStudyRemoveContracts(studyIdentifier));
+    }
+    GetStudyRenameContracts(oldStudyIdentifier, newStudyIdentifier) {
+        const this$ = this;
+        if (!(0, Seq_js_1.contains)(oldStudyIdentifier, this$.StudyIdentifiers, {
+            Equals: (x, y) => (x === y),
+            GetHashCode: Util_js_1.stringHash,
+        })) {
+            throw new Error("ARC does not contain study with given name");
+        }
+        super.RenameStudy(oldStudyIdentifier, newStudyIdentifier);
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        const oldStudyFolderPath = (0, Path_js_1.getStudyFolderPath)(oldStudyIdentifier);
+        const newStudyFolderPath = (0, Path_js_1.getStudyFolderPath)(newStudyIdentifier);
+        const renamedPaths = (0, Array_js_1.map)((p) => (0, String_js_1.replace)(p, oldStudyFolderPath, newStudyFolderPath), paths);
+        this$.SetFilePaths(renamedPaths);
+        return (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(Contract_js_1.Contract.createRename(oldStudyFolderPath, newStudyFolderPath)), (0, Seq_js_1.delay)(() => this$.GetUpdateContracts()))));
+    }
+    TryRenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier) {
+        const this$ = this;
+        return (0, ContractIO_js_1.fullFillContractBatchAsync)(arcPath, this$.GetStudyRenameContracts(oldStudyIdentifier, newStudyIdentifier));
+    }
+    WriteAsync(arcPath) {
+        const this$ = this;
+        return (0, Promise_fs_js_1.PromiseBuilder__Run_212F1D4B)(PromiseImpl_fs_js_1.promise, (0, Promise_fs_js_1.PromiseBuilder__Delay_62FBFDE1)(PromiseImpl_fs_js_1.promise, () => (this$.TryWriteAsync(arcPath).then((_arg) => {
+            const result = _arg;
+            if (result.tag === /* Error */ 1) {
+                const appended = (0, String_js_1.join)("\n", (0, Array_js_1.map)((e) => e, result.fields[0]));
+                (0, String_js_1.toFail)((0, String_js_1.printf)("Could not write ARC, failed with the following errors %s"))(appended);
+                return Promise.resolve();
+            }
+            else {
+                return Promise.resolve();
+            }
+        }))));
+    }
+    UpdateAsync(arcPath) {
+        const this$ = this;
+        return (0, Promise_fs_js_1.PromiseBuilder__Run_212F1D4B)(PromiseImpl_fs_js_1.promise, (0, Promise_fs_js_1.PromiseBuilder__Delay_62FBFDE1)(PromiseImpl_fs_js_1.promise, () => (this$.TryUpdateAsync(arcPath).then((_arg) => {
+            const result = _arg;
+            if (result.tag === /* Error */ 1) {
+                const appended = (0, String_js_1.join)("\n", (0, Array_js_1.map)((e) => e, result.fields[0]));
+                (0, String_js_1.toFail)((0, String_js_1.printf)("Could not update ARC, failed with the following errors %s"))(appended);
+                return Promise.resolve();
+            }
+            else {
+                return Promise.resolve();
+            }
+        }))));
+    }
+    RemoveAssayAsync(arcPath, assayIdentifier) {
+        const this$ = this;
+        return (0, Promise_fs_js_1.PromiseBuilder__Run_212F1D4B)(PromiseImpl_fs_js_1.promise, (0, Promise_fs_js_1.PromiseBuilder__Delay_62FBFDE1)(PromiseImpl_fs_js_1.promise, () => (this$.TryRemoveAssayAsync(arcPath, assayIdentifier).then((_arg) => {
+            const result = _arg;
+            if (result.tag === /* Error */ 1) {
+                const appended = (0, String_js_1.join)("\n", (0, Array_js_1.map)((e) => e, result.fields[0]));
+                (0, String_js_1.toFail)((0, String_js_1.printf)("Could not remove assay, failed with the following errors %s"))(appended);
+                return Promise.resolve();
+            }
+            else {
+                return Promise.resolve();
+            }
+        }))));
+    }
+    RenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier) {
+        const this$ = this;
+        return (0, Promise_fs_js_1.PromiseBuilder__Run_212F1D4B)(PromiseImpl_fs_js_1.promise, (0, Promise_fs_js_1.PromiseBuilder__Delay_62FBFDE1)(PromiseImpl_fs_js_1.promise, () => (this$.TryRenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier).then((_arg) => {
+            const result = _arg;
+            if (result.tag === /* Error */ 1) {
+                const appended = (0, String_js_1.join)("\n", (0, Array_js_1.map)((e) => e, result.fields[0]));
+                (0, String_js_1.toFail)((0, String_js_1.printf)("Could not rename assay, failed with the following errors %s"))(appended);
+                return Promise.resolve();
+            }
+            else {
+                return Promise.resolve();
+            }
+        }))));
+    }
+    RemoveStudyAsync(arcPath, studyIdentifier) {
+        const this$ = this;
+        return (0, Promise_fs_js_1.PromiseBuilder__Run_212F1D4B)(PromiseImpl_fs_js_1.promise, (0, Promise_fs_js_1.PromiseBuilder__Delay_62FBFDE1)(PromiseImpl_fs_js_1.promise, () => (this$.TryRemoveStudyAsync(arcPath, studyIdentifier).then((_arg) => {
+            const result = _arg;
+            if (result.tag === /* Error */ 1) {
+                const appended = (0, String_js_1.join)("\n", (0, Array_js_1.map)((e) => e, result.fields[0]));
+                (0, String_js_1.toFail)((0, String_js_1.printf)("Could not remove study, failed with the following errors %s"))(appended);
+                return Promise.resolve();
+            }
+            else {
+                return Promise.resolve();
+            }
+        }))));
+    }
+    RenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier) {
+        const this$ = this;
+        return (0, Promise_fs_js_1.PromiseBuilder__Run_212F1D4B)(PromiseImpl_fs_js_1.promise, (0, Promise_fs_js_1.PromiseBuilder__Delay_62FBFDE1)(PromiseImpl_fs_js_1.promise, () => (this$.TryRenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier).then((_arg) => {
+            const result = _arg;
+            if (result.tag === /* Error */ 1) {
+                const appended = (0, String_js_1.join)("\n", (0, Array_js_1.map)((e) => e, result.fields[0]));
+                (0, String_js_1.toFail)((0, String_js_1.printf)("Could not rename study, failed with the following errors %s"))(appended);
+                return Promise.resolve();
+            }
+            else {
+                return Promise.resolve();
+            }
+        }))));
+    }
+    static loadAsync(arcPath) {
+        return (0, Promise_fs_js_1.PromiseBuilder__Run_212F1D4B)(PromiseImpl_fs_js_1.promise, (0, Promise_fs_js_1.PromiseBuilder__Delay_62FBFDE1)(PromiseImpl_fs_js_1.promise, () => (ARC.tryLoadAsync(arcPath).then((_arg) => {
+            const result = _arg;
+            if (result.tag === /* Error */ 1) {
+                const appended = (0, String_js_1.join)("\n", (0, Array_js_1.map)((e) => e, result.fields[0]));
+                (0, String_js_1.toFail)((0, String_js_1.printf)("Could not load ARC, failed with the following errors %s"))(appended);
+                return Promise.resolve(new ARC((0, Identifier_js_1.createMissingIdentifier)()));
+            }
+            else {
+                const arc = result.fields[0];
+                return Promise.resolve(arc);
+            }
+        }))));
+    }
+    MakeDataFilesAbsolute() {
+        const this$ = this;
+        const filesPaths = (0, Set_js_1.ofSeq)(this$.FileSystem.Tree.ToFilePaths(), {
+            Compare: Util_js_1.comparePrimitives,
+        });
+        const checkExistenceFromRoot = (p) => (0, Set_js_1.contains)(p, filesPaths);
+        const updateColumnOption = (dataNameFunction, col) => {
+            let col_1;
+            let matchResult, col_2;
+            if (col != null) {
+                if ((col_1 = (0, Option_js_1.value)(col), col_1.Header.IsDataColumn)) {
+                    matchResult = 0;
+                    col_2 = (0, Option_js_1.value)(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) => {
+            (0, Seq_js_1.iterate)((c_1) => {
+                if (c_1.FilePath != null) {
+                    const newFilePath_1 = dataNameFunction_2(c_1);
+                    c_1.FilePath = newFilePath_1;
+                }
+            }, (0, DataMap_js_1.DataMap__get_DataContexts)(dm));
+        };
+        (0, Seq_js_1.iterate)((s) => {
+            const f = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
+            const source_1 = s.Tables;
+            (0, Seq_js_1.iterate)((0, Util_js_1.curry2)(updateTable)(f), source_1);
+            if (s.DataMap != null) {
+                updateDataMap(f, (0, Option_js_1.value)(s.DataMap));
+            }
+        }, this$.Studies);
+        (0, Seq_js_1.iterate)((a) => {
+            const f_1 = (d_1) => d_1.GetAbsolutePathForAssay(a.Identifier, checkExistenceFromRoot);
+            const source_3 = a.Tables;
+            (0, Seq_js_1.iterate)((0, Util_js_1.curry2)(updateTable)(f_1), source_3);
+            if (a.DataMap != null) {
+                updateDataMap(f_1, (0, Option_js_1.value)(a.DataMap));
+            }
+        }, this$.Assays);
+    }
+    static fromFilePaths(filePaths) {
+        const fs = FileSystem_js_1.FileSystem.fromFilePaths(filePaths);
+        return new ARC((0, Identifier_js_1.createMissingIdentifier)(), undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, undefined, fs);
+    }
+    SetFilePaths(filePaths) {
+        const this$ = this;
+        const tree = FileSystemTree_js_1.FileSystemTree.fromFilePaths(filePaths);
+        this$._fs = (new FileSystem_js_1.FileSystem(tree, this$._fs.History));
+    }
+    GetReadContracts() {
+        const this$ = this;
+        return (0, Array_js_1.choose)(ARC_js_1.tryISAReadContractFromPath, this$._fs.Tree.ToFilePaths());
+    }
+    SetISAFromContracts(contracts) {
+        const this$ = this;
+        const investigation = ARCAux_getArcInvestigationFromContracts(contracts);
+        (0, IdentifierSetters_js_1.setInvestigationIdentifier)(investigation.Identifier, this$);
+        this$.Title = investigation.Title;
+        this$.Description = investigation.Description;
+        this$.SubmissionDate = investigation.SubmissionDate;
+        this$.PublicReleaseDate = investigation.PublicReleaseDate;
+        this$.OntologySourceReferences = investigation.OntologySourceReferences;
+        this$.Publications = investigation.Publications;
+        this$.Contacts = investigation.Contacts;
+        this$.Comments = investigation.Comments;
+        this$.Remarks = investigation.Remarks;
+        this$.RegisteredStudyIdentifiers = investigation.RegisteredStudyIdentifiers;
+        const studies = (0, Array_js_1.map)((tuple) => tuple[0], ARCAux_getArcStudiesFromContracts(contracts));
+        const assays = ARCAux_getArcAssaysFromContracts(contracts);
+        const workflows = ARCAux_getArcWorkflowsFromContracts(contracts);
+        const runs = ARCAux_getArcRunsFromContracts(contracts);
+        const array_2 = this$.AssayIdentifiers;
+        array_2.forEach((ai) => {
+            if (!assays.some((a) => (a.Identifier === ai))) {
+                this$.DeleteAssay(ai);
+            }
+        });
+        const array_4 = this$.StudyIdentifiers;
+        array_4.forEach((si) => {
+            if (!studies.some((s) => (s.Identifier === si))) {
+                this$.DeleteStudy(si);
+            }
+        });
+        studies.forEach((study) => {
+            const registeredStudyOpt = (0, Seq_js_1.tryFind)((s_1) => (s_1.Identifier === study.Identifier), this$.Studies);
+            if (registeredStudyOpt == null) {
+                this$.AddStudy(study);
+            }
+            else {
+                const registeredStudy = (0, Option_js_1.value)(registeredStudyOpt);
+                registeredStudy.UpdateReferenceByStudyFile(study, true);
+            }
+            const datamap = ARCAux_getAssayDataMapFromContracts(study.Identifier, contracts);
+            if (study.DataMap == null) {
+                study.DataMap = datamap;
+            }
+            study.StaticHash = (study.GetLightHashCode() | 0);
+        });
+        assays.forEach((assay) => {
+            const registeredAssayOpt = (0, Seq_js_1.tryFind)((a_1) => (a_1.Identifier === assay.Identifier), this$.Assays);
+            if (registeredAssayOpt == null) {
+                this$.AddAssay(assay);
+            }
+            else {
+                const registeredAssay = (0, Option_js_1.value)(registeredAssayOpt);
+                registeredAssay.UpdateReferenceByAssayFile(assay, true);
+            }
+            const assay_1 = (0, Seq_js_1.find)((a_2) => (a_2.Identifier === assay.Identifier), this$.Assays);
+            let updatedTables;
+            const array_6 = assay_1.StudiesRegisteredIn;
+            updatedTables = (0, Array_js_1.fold)((tables, study_1) => ArcTables_js_1.ArcTables.updateReferenceTablesBySheets(new ArcTables_js_1.ArcTables(study_1.Tables), tables, false), new ArcTables_js_1.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;
+        });
+        workflows.forEach((workflow) => {
+            const datamap_2 = ARCAux_getWorkflowDataMapFromContracts((0, ArcTypes_js_1.ArcWorkflow__get_Identifier)(workflow), contracts);
+            if ((0, ArcTypes_js_1.ArcWorkflow__get_DataMap)(workflow) == null) {
+                (0, ArcTypes_js_1.ArcWorkflow__set_DataMap_51F1E59E)(workflow, datamap_2);
+            }
+            this$.AddWorkflow(workflow);
+            (0, ArcTypes_js_1.ArcWorkflow__set_StaticHash_Z524259A4)(workflow, (0, ArcTypes_js_1.ArcWorkflow__GetLightHashCode)(workflow));
+        });
+        runs.forEach((run) => {
+            const datamap_3 = ARCAux_getRunDataMapFromContracts(run.Identifier, contracts);
+            if (run.DataMap == null) {
+                run.DataMap = datamap_3;
+            }
+            this$.AddRun(run);
+            run.StaticHash = (run.GetLightHashCode() | 0);
+        });
+        (0, Seq_js_1.iterate)((a_3) => {
+            a_3.StaticHash = (a_3.GetLightHashCode() | 0);
+        }, this$.Assays);
+        (0, Seq_js_1.iterate)((s_2) => {
+            s_2.StaticHash = (s_2.GetLightHashCode() | 0);
+        }, this$.Studies);
+        this$.StaticHash = (this$.GetLightHashCode() | 0);
+    }
+    UpdateFileSystem() {
+        const this$ = this;
+        const newFS = ARCAux_updateFSByISA(this$, this$._fs);
+        this$._fs = newFS;
+    }
+    GetWriteContracts(skipUpdateFS) {
+        const this$ = this;
+        if (!(0, Option_js_1.defaultArg)(skipUpdateFS, false)) {
+            this$.UpdateFileSystem();
+        }
+        const workbooks = new Map([]);
+        (0, MapUtil_js_1.addToDict)(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", (0, ArcInvestigation_js_2.ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF)(this$)]);
+        this$.StaticHash = (this$.GetLightHashCode() | 0);
+        (0, Seq_js_1.iterate)((s) => {
+            s.StaticHash = (s.GetLightHashCode() | 0);
+            (0, MapUtil_js_1.addToDict)(workbooks, (0, Identifier_js_1.Study_fileNameFromIdentifier)(s.Identifier), ["ISA_Study", (0, ArcStudy_js_2.ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522)(s)]);
+            if (s.DataMap != null) {
+                const dm = (0, Option_js_1.value)(s.DataMap);
+                (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm, (0, Util_js_1.safeHash)(dm));
+                (0, MapUtil_js_1.addToDict)(workbooks, (0, Identifier_js_1.Study_datamapFileNameFromIdentifier)(s.Identifier), ["ISA_Datamap", (0, DataMap_js_2.toFsWorkbook)(dm)]);
+            }
+        }, this$.Studies);
+        (0, Seq_js_1.iterate)((a) => {
+            a.StaticHash = (a.GetLightHashCode() | 0);
+            (0, MapUtil_js_1.addToDict)(workbooks, (0, Identifier_js_1.Assay_fileNameFromIdentifier)(a.Identifier), ["ISA_Assay", (0, ArcAssay_js_2.ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F)(a)]);
+            if (a.DataMap != null) {
+                const dm_1 = (0, Option_js_1.value)(a.DataMap);
+                (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_1, (0, Util_js_1.safeHash)(dm_1));
+                (0, MapUtil_js_1.addToDict)(workbooks, (0, Identifier_js_1.Assay_datamapFileNameFromIdentifier)(a.Identifier), ["ISA_Datamap", (0, DataMap_js_2.toFsWorkbook)(dm_1)]);
+            }
+        }, this$.Assays);
+        (0, Seq_js_1.iterate)((w) => {
+            (0, ArcTypes_js_1.ArcWorkflow__set_StaticHash_Z524259A4)(w, (0, ArcTypes_js_1.ArcWorkflow__GetLightHashCode)(w));
+            (0, MapUtil_js_1.addToDict)(workbooks, (0, Identifier_js_1.Workflow_fileNameFromIdentifier)((0, ArcTypes_js_1.ArcWorkflow__get_Identifier)(w)), ["ISA_Workflow", (0, ArcWorkflow_js_1.ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E)(w)]);
+            if ((0, ArcTypes_js_1.ArcWorkflow__get_DataMap)(w) != null) {
+                const dm_2 = (0, Option_js_1.value)((0, ArcTypes_js_1.ArcWorkflow__get_DataMap)(w));
+                (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_2, (0, Util_js_1.safeHash)(dm_2));
+                (0, MapUtil_js_1.addToDict)(workbooks, (0, Identifier_js_1.Workflow_datamapFileNameFromIdentifier)((0, ArcTypes_js_1.ArcWorkflow__get_Identifier)(w)), ["ISA_Datamap", (0, DataMap_js_2.toFsWorkbook)(dm_2)]);
+            }
+        }, this$.Workflows);
+        (0, Seq_js_1.iterate)((r) => {
+            r.StaticHash = (r.GetLightHashCode() | 0);
+            (0, MapUtil_js_1.addToDict)(workbooks, (0, Identifier_js_1.Run_fileNameFromIdentifier)(r.Identifier), ["ISA_Run", (0, ArcRun_js_1.ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8)(r)]);
+            if (r.DataMap != null) {
+                const dm_3 = (0, Option_js_1.value)(r.DataMap);
+                (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_3, (0, Util_js_1.safeHash)(dm_3));
+                (0, MapUtil_js_1.addToDict)(workbooks, (0, Identifier_js_1.Run_datamapFileNameFromIdentifier)(r.Identifier), ["ISA_Datamap", (0, DataMap_js_2.toFsWorkbook)(dm_3)]);
+            }
+        }, this$.Runs);
+        return (0, Array_js_1.map)((fp) => {
+            const matchValue = (0, FsCellsCollection_fs_js_1.Dictionary_tryGet)(fp, workbooks);
+            if (matchValue == null) {
+                return Contract_js_1.Contract.createCreate(fp, "PlainText");
+            }
+            else {
+                const wb = (0, Option_js_1.value)(matchValue)[1];
+                const dto = (0, Option_js_1.value)(matchValue)[0];
+                return Contract_js_1.Contract.createCreate(fp, dto, wb);
+            }
+        }, this$._fs.Tree.ToFilePaths(true));
+    }
+    GetUpdateContracts(skipUpdateFS) {
+        const this$ = this;
+        if (this$.StaticHash === 0) {
+            this$.StaticHash = (this$.GetLightHashCode() | 0);
+            return this$.GetWriteContracts((0, Option_js_1.unwrap)(skipUpdateFS));
+        }
+        else {
+            return (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => {
+                const hash = this$.GetLightHashCode() | 0;
+                return (0, Seq_js_1.append)((this$.StaticHash !== hash) ? (0, Seq_js_1.singleton)((0, ArcInvestigation_js_1.ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract)(this$)) : (0, Seq_js_1.empty)(), (0, Seq_js_1.delay)(() => {
+                    this$.StaticHash = (hash | 0);
+                    return (0, Seq_js_1.append)((0, Seq_js_1.collect)((s) => {
+                        const hash_1 = s.GetLightHashCode() | 0;
+                        return (0, Seq_js_1.append)((s.StaticHash === 0) ? (0, ArcStudy_js_1.ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49)(s, true) : ((s.StaticHash !== hash_1) ? (0, Seq_js_1.singleton)((0, ArcStudy_js_1.ARCtrl_ArcStudy__ArcStudy_ToUpdateContract)(s)) : (0, Seq_js_1.empty)()), (0, Seq_js_1.delay)(() => {
+                            let dm_1;
+                            s.StaticHash = (hash_1 | 0);
+                            const matchValue = s.DataMap;
+                            let matchResult, dm_2, dm_3;
+                            if (matchValue != null) {
+                                if ((0, DataMap_js_1.DataMap__get_StaticHash)((0, Option_js_1.value)(matchValue)) === 0) {
+                                    matchResult = 0;
+                                    dm_2 = (0, Option_js_1.value)(matchValue);
+                                }
+                                else if ((dm_1 = (0, Option_js_1.value)(matchValue), (0, DataMap_js_1.DataMap__get_StaticHash)(dm_1) !== (0, Util_js_1.safeHash)(dm_1))) {
+                                    matchResult = 1;
+                                    dm_3 = (0, Option_js_1.value)(matchValue);
+                                }
+                                else {
+                                    matchResult = 2;
+                                }
+                            }
+                            else {
+                                matchResult = 2;
+                            }
+                            switch (matchResult) {
+                                case 0:
+                                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Datamap_js_1.ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5)(dm_2, s.Identifier)), (0, Seq_js_1.delay)(() => {
+                                        (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_2, (0, Util_js_1.safeHash)(dm_2));
+                                        return (0, Seq_js_1.empty)();
+                                    }));
+                                case 1:
+                                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Datamap_js_1.ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5)(dm_3, s.Identifier)), (0, Seq_js_1.delay)(() => {
+                                        (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_3, (0, Util_js_1.safeHash)(dm_3));
+                                        return (0, Seq_js_1.empty)();
+                                    }));
+                                default: {
+                                    return (0, Seq_js_1.empty)();
+                                }
+                            }
+                        }));
+                    }, this$.Studies), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.collect)((a) => {
+                        const hash_2 = a.GetLightHashCode() | 0;
+                        return (0, Seq_js_1.append)((a.StaticHash === 0) ? (0, ArcAssay_js_1.ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49)(a, true) : ((a.StaticHash !== hash_2) ? (0, Seq_js_1.singleton)((0, ArcAssay_js_1.ARCtrl_ArcAssay__ArcAssay_ToUpdateContract)(a)) : (0, Seq_js_1.empty)()), (0, Seq_js_1.delay)(() => {
+                            let dm_5;
+                            a.StaticHash = (hash_2 | 0);
+                            const matchValue_1 = a.DataMap;
+                            let matchResult_1, dm_6, dm_7;
+                            if (matchValue_1 != null) {
+                                if ((0, DataMap_js_1.DataMap__get_StaticHash)((0, Option_js_1.value)(matchValue_1)) === 0) {
+                                    matchResult_1 = 0;
+                                    dm_6 = (0, Option_js_1.value)(matchValue_1);
+                                }
+                                else if ((dm_5 = (0, Option_js_1.value)(matchValue_1), (0, DataMap_js_1.DataMap__get_StaticHash)(dm_5) !== (0, Util_js_1.safeHash)(dm_5))) {
+                                    matchResult_1 = 1;
+                                    dm_7 = (0, Option_js_1.value)(matchValue_1);
+                                }
+                                else {
+                                    matchResult_1 = 2;
+                                }
+                            }
+                            else {
+                                matchResult_1 = 2;
+                            }
+                            switch (matchResult_1) {
+                                case 0:
+                                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Datamap_js_1.ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5)(dm_6, a.Identifier)), (0, Seq_js_1.delay)(() => {
+                                        (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_6, (0, Util_js_1.safeHash)(dm_6));
+                                        return (0, Seq_js_1.empty)();
+                                    }));
+                                case 1:
+                                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Datamap_js_1.ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5)(dm_7, a.Identifier)), (0, Seq_js_1.delay)(() => {
+                                        (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_7, (0, Util_js_1.safeHash)(dm_7));
+                                        return (0, Seq_js_1.empty)();
+                                    }));
+                                default: {
+                                    return (0, Seq_js_1.empty)();
+                                }
+                            }
+                        }));
+                    }, this$.Assays), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.collect)((w) => {
+                        const hash_3 = (0, ArcTypes_js_1.ArcWorkflow__GetLightHashCode)(w) | 0;
+                        return (0, Seq_js_1.append)(((0, ArcTypes_js_1.ArcWorkflow__get_StaticHash)(w) === 0) ? (0, ArcWorkflow_js_2.ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49)(w, true) : (((0, ArcTypes_js_1.ArcWorkflow__get_StaticHash)(w) !== hash_3) ? (0, Seq_js_1.singleton)((0, ArcWorkflow_js_2.ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract)(w)) : (0, Seq_js_1.empty)()), (0, Seq_js_1.delay)(() => {
+                            let dm_9;
+                            (0, ArcTypes_js_1.ArcWorkflow__set_StaticHash_Z524259A4)(w, hash_3);
+                            const matchValue_2 = (0, ArcTypes_js_1.ArcWorkflow__get_DataMap)(w);
+                            let matchResult_2, dm_10, dm_11;
+                            if (matchValue_2 != null) {
+                                if ((0, DataMap_js_1.DataMap__get_StaticHash)((0, Option_js_1.value)(matchValue_2)) === 0) {
+                                    matchResult_2 = 0;
+                                    dm_10 = (0, Option_js_1.value)(matchValue_2);
+                                }
+                                else if ((dm_9 = (0, Option_js_1.value)(matchValue_2), (0, DataMap_js_1.DataMap__get_StaticHash)(dm_9) !== (0, Util_js_1.safeHash)(dm_9))) {
+                                    matchResult_2 = 1;
+                                    dm_11 = (0, Option_js_1.value)(matchValue_2);
+                                }
+                                else {
+                                    matchResult_2 = 2;
+                                }
+                            }
+                            else {
+                                matchResult_2 = 2;
+                            }
+                            switch (matchResult_2) {
+                                case 0:
+                                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Datamap_js_1.ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5)(dm_10, (0, ArcTypes_js_1.ArcWorkflow__get_Identifier)(w))), (0, Seq_js_1.delay)(() => {
+                                        (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_10, (0, Util_js_1.safeHash)(dm_10));
+                                        return (0, Seq_js_1.empty)();
+                                    }));
+                                case 1:
+                                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Datamap_js_1.ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5)(dm_11, (0, ArcTypes_js_1.ArcWorkflow__get_Identifier)(w))), (0, Seq_js_1.delay)(() => {
+                                        (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_11, (0, Util_js_1.safeHash)(dm_11));
+                                        return (0, Seq_js_1.empty)();
+                                    }));
+                                default: {
+                                    return (0, Seq_js_1.empty)();
+                                }
+                            }
+                        }));
+                    }, this$.Workflows), (0, Seq_js_1.delay)(() => (0, Seq_js_1.collect)((r) => {
+                        const hash_4 = r.GetLightHashCode() | 0;
+                        return (0, Seq_js_1.append)((r.StaticHash === 0) ? (0, ArcRun_js_2.ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49)(r, true) : ((r.StaticHash !== hash_4) ? (0, Seq_js_1.singleton)((0, ArcRun_js_2.ARCtrl_ArcRun__ArcRun_ToUpdateContract)(r)) : (0, Seq_js_1.empty)()), (0, Seq_js_1.delay)(() => {
+                            let dm_13;
+                            r.StaticHash = (hash_4 | 0);
+                            const matchValue_3 = r.DataMap;
+                            let matchResult_3, dm_14, dm_15;
+                            if (matchValue_3 != null) {
+                                if ((0, DataMap_js_1.DataMap__get_StaticHash)((0, Option_js_1.value)(matchValue_3)) === 0) {
+                                    matchResult_3 = 0;
+                                    dm_14 = (0, Option_js_1.value)(matchValue_3);
+                                }
+                                else if ((dm_13 = (0, Option_js_1.value)(matchValue_3), (0, DataMap_js_1.DataMap__get_StaticHash)(dm_13) !== (0, Util_js_1.safeHash)(dm_13))) {
+                                    matchResult_3 = 1;
+                                    dm_15 = (0, Option_js_1.value)(matchValue_3);
+                                }
+                                else {
+                                    matchResult_3 = 2;
+                                }
+                            }
+                            else {
+                                matchResult_3 = 2;
+                            }
+                            switch (matchResult_3) {
+                                case 0:
+                                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Datamap_js_1.ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5)(dm_14, r.Identifier)), (0, Seq_js_1.delay)(() => {
+                                        (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_14, (0, Util_js_1.safeHash)(dm_14));
+                                        return (0, Seq_js_1.empty)();
+                                    }));
+                                case 1:
+                                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Datamap_js_1.ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5)(dm_15, r.Identifier)), (0, Seq_js_1.delay)(() => {
+                                        (0, DataMap_js_1.DataMap__set_StaticHash_Z524259A4)(dm_15, (0, Util_js_1.safeHash)(dm_15));
+                                        return (0, Seq_js_1.empty)();
+                                    }));
+                                default: {
+                                    return (0, Seq_js_1.empty)();
+                                }
+                            }
+                        }));
+                    }, this$.Runs)))))));
+                }));
+            }));
+        }
+    }
+    GetGitInitContracts(branch, repositoryAddress, defaultGitignore) {
+        const defaultGitignore_1 = (0, Option_js_1.defaultArg)(defaultGitignore, false);
+        return (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Git_js_1.Init_createInitContract_6DFDD678)((0, Option_js_1.unwrap)(branch))), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(Git_js_1.gitattributesContract), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)(defaultGitignore_1 ? (0, Seq_js_1.singleton)(Git_js_1.gitignoreContract) : (0, Seq_js_1.empty)(), (0, Seq_js_1.delay)(() => ((repositoryAddress != null) ? (0, Seq_js_1.singleton)((0, Git_js_1.Init_createAddRemoteContract_Z721C83C5)((0, Option_js_1.value)(repositoryAddress))) : (0, Seq_js_1.empty)())))))))));
+    }
+    static getCloneContract(remoteUrl, merge, branch, token, nolfs) {
+        return (0, Git_js_1.Clone_createCloneContract_5000466F)(remoteUrl, (0, Option_js_1.unwrap)(merge), (0, Option_js_1.unwrap)(branch), (0, Option_js_1.unwrap)(token), (0, Option_js_1.unwrap)(nolfs));
+    }
+    Copy() {
+        const this$ = this;
+        const nextAssays = [];
+        const nextStudies = [];
+        const nextWorkflows = [];
+        const nextRuns = [];
+        let enumerator = (0, Util_js_1.getEnumerator)(this$.Assays);
+        try {
+            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+                const assay = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                const copy = assay.Copy();
+                void (nextAssays.push(copy));
+            }
+        }
+        finally {
+            (0, Util_js_1.disposeSafe)(enumerator);
+        }
+        let enumerator_1 = (0, Util_js_1.getEnumerator)(this$.Studies);
+        try {
+            while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+                const study = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                const copy_1 = study.Copy();
+                void (nextStudies.push(copy_1));
+            }
+        }
+        finally {
+            (0, Util_js_1.disposeSafe)(enumerator_1);
+        }
+        let enumerator_2 = (0, Util_js_1.getEnumerator)(this$.Workflows);
+        try {
+            while (enumerator_2["System.Collections.IEnumerator.MoveNext"]()) {
+                const workflow = enumerator_2["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                void (nextWorkflows.push((0, ArcTypes_js_1.ArcWorkflow__Copy_6FCE9E49)(workflow)));
+            }
+        }
+        finally {
+            (0, Util_js_1.disposeSafe)(enumerator_2);
+        }
+        let enumerator_3 = (0, Util_js_1.getEnumerator)(this$.Runs);
+        try {
+            while (enumerator_3["System.Collections.IEnumerator.MoveNext"]()) {
+                const run = enumerator_3["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                const copy_3 = run.Copy();
+                void (nextRuns.push(copy_3));
+            }
+        }
+        finally {
+            (0, Util_js_1.disposeSafe)(enumerator_3);
+        }
+        const nextComments = (0, Collections_js_1.ResizeArray_map)((c) => c.Copy(), this$.Comments);
+        const nextRemarks = (0, Collections_js_1.ResizeArray_map)((c_1) => c_1.Copy(), this$.Remarks);
+        const nextContacts = (0, Collections_js_1.ResizeArray_map)((c_2) => c_2.Copy(), this$.Contacts);
+        const nextPublications = (0, Collections_js_1.ResizeArray_map)((c_3) => c_3.Copy(), this$.Publications);
+        const nextOntologySourceReferences = (0, Collections_js_1.ResizeArray_map)((c_4) => c_4.Copy(), this$.OntologySourceReferences);
+        const nextStudyIdentifiers = Array.from(this$.RegisteredStudyIdentifiers);
+        const fsCopy = this$._fs.Copy();
+        return new ARC(this$.Identifier, (0, Option_js_1.unwrap)(this$.Title), (0, Option_js_1.unwrap)(this$.Description), (0, Option_js_1.unwrap)(this$.SubmissionDate), (0, Option_js_1.unwrap)(this$.PublicReleaseDate), nextOntologySourceReferences, nextPublications, nextContacts, nextAssays, nextStudies, nextWorkflows, nextRuns, nextStudyIdentifiers, nextComments, nextRemarks, this$._cwl, fsCopy);
+    }
+    GetRegisteredPayload(IgnoreHidden) {
+        let tree, paths, array_3;
+        const this$ = this;
+        const copy = this$.Copy();
+        const registeredStudies = copy.Studies.slice();
+        const registeredAssays = (0, Array_js_1.concat)((0, Array_js_1.map)((s) => s.RegisteredAssays.slice(), registeredStudies));
+        const includeFiles = (0, Set_js_1.unionMany)([(0, Set_js_1.ofSeq)(["isa.investigation.xlsx", "README.md"], {
+                Compare: Util_js_1.comparePrimitives,
+            }), (0, Set_js_1.unionMany)((0, Array_js_1.map)((s_1) => {
+                const studyFoldername = `${"studies"}/${s_1.Identifier}`;
+                return (0, Set_js_1.ofSeq)((0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(`${studyFoldername}/${"isa.study.xlsx"}`), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(`${studyFoldername}/${"README.md"}`), (0, Seq_js_1.delay)(() => (0, Seq_js_1.collect)((table) => (0, Seq_js_1.collect)((kv) => {
+                    const textValue = kv[1].ToFreeTextCell().AsFreeText;
+                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)(textValue), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(`${studyFoldername}/${"resources"}/${textValue}`), (0, Seq_js_1.delay)(() => (0, Seq_js_1.singleton)(`${studyFoldername}/${"protocols"}/${textValue}`)))));
+                }, table.Values), s_1.Tables))))))), {
+                    Compare: Util_js_1.comparePrimitives,
+                });
+            }, registeredStudies), {
+                Compare: Util_js_1.comparePrimitives,
+            }), (0, Set_js_1.unionMany)((0, Array_js_1.map)((a) => {
+                const assayFoldername = `${"assays"}/${a.Identifier}`;
+                return (0, Set_js_1.ofSeq)((0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(`${assayFoldername}/${"isa.assay.xlsx"}`), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(`${assayFoldername}/${"README.md"}`), (0, Seq_js_1.delay)(() => (0, Seq_js_1.collect)((table_1) => (0, Seq_js_1.collect)((kv_1) => {
+                    const textValue_1 = kv_1[1].ToFreeTextCell().AsFreeText;
+                    return (0, Seq_js_1.append)((0, Seq_js_1.singleton)(textValue_1), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(`${assayFoldername}/${"dataset"}/${textValue_1}`), (0, Seq_js_1.delay)(() => (0, Seq_js_1.singleton)(`${assayFoldername}/${"protocols"}/${textValue_1}`)))));
+                }, table_1.Values), a.Tables))))))), {
+                    Compare: Util_js_1.comparePrimitives,
+                });
+            }, registeredAssays), {
+                Compare: Util_js_1.comparePrimitives,
+            })], {
+            Compare: Util_js_1.comparePrimitives,
+        });
+        const ignoreHidden = (0, Option_js_1.defaultArg)(IgnoreHidden, true);
+        const fsCopy = this$._fs.Copy();
+        return (0, Option_js_1.defaultArg)((0, Option_js_1.bind)((tree_1) => {
+            if (ignoreHidden) {
+                return FileSystemTree_js_1.FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1);
+            }
+            else {
+                return tree_1;
+            }
+        }, (tree = ((paths = ((array_3 = FileSystemTree_js_1.FileSystemTree.toFilePaths()(fsCopy.Tree), array_3.filter((p) => {
+            if (p.startsWith("workflows") ? true : p.startsWith("runs")) {
+                return true;
+            }
+            else {
+                return (0, Set_js_1.FSharpSet__Contains)(includeFiles, p);
+            }
+        }))), FileSystemTree_js_1.FileSystemTree.fromFilePaths(paths))), ignoreHidden ? FileSystemTree_js_1.FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree)), FileSystemTree_js_1.FileSystemTree.fromFilePaths([]));
+    }
+    GetAdditionalPayload(IgnoreHidden) {
+        let tree, paths, array;
+        const this$ = this;
+        const ignoreHidden = (0, Option_js_1.defaultArg)(IgnoreHidden, true);
+        const registeredPayload = (0, Set_js_1.ofSeq)(FileSystemTree_js_1.FileSystemTree.toFilePaths()(this$.GetRegisteredPayload()), {
+            Compare: Util_js_1.comparePrimitives,
+        });
+        return (0, Option_js_1.defaultArg)((0, Option_js_1.bind)((tree_1) => {
+            if (ignoreHidden) {
+                return FileSystemTree_js_1.FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1);
+            }
+            else {
+                return tree_1;
+            }
+        }, (tree = ((paths = ((array = FileSystemTree_js_1.FileSystemTree.toFilePaths()(this$._fs.Copy().Tree), array.filter((p) => !(0, Set_js_1.FSharpSet__Contains)(registeredPayload, p)))), FileSystemTree_js_1.FileSystemTree.fromFilePaths(paths))), ignoreHidden ? FileSystemTree_js_1.FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree)), FileSystemTree_js_1.FileSystemTree.fromFilePaths([]));
+    }
+    static get DefaultContracts() {
+        return (0, Map_js_1.ofSeq)([[".gitignore", Git_js_1.gitignoreContract], [".gitattributes", Git_js_1.gitattributesContract]], {
+            Compare: Util_js_1.comparePrimitives,
+        });
+    }
+    static fromDeprecatedROCrateJsonString(s) {
+        let arg;
+        try {
+            const s_1 = (0, String_js_1.replace)(s, "bio:additionalProperty", "sdo:additionalProperty");
+            let isa;
+            const matchValue = (0, Decode_fs_js_1.fromString)((0, ROCrateIO_js_1.ROCrate_get_decoderDeprecated)(), s_1);
+            if (matchValue.tag === /* Error */ 1) {
+                throw new Error((arg = matchValue.fields[0], (0, String_js_1.toText)((0, String_js_1.printf)("Error decoding string: %O"))(arg)));
+            }
+            else {
+                isa = matchValue.fields[0];
+            }
+            return ARC.fromArcInvestigation(isa);
+        }
+        catch (ex) {
+            const arg_1 = ex.message;
+            return (0, String_js_1.toFail)((0, String_js_1.printf)("Could not parse deprecated ARC-RO-Crate metadata: \n%s"))(arg_1);
+        }
+    }
+    static fromROCrateJsonString(s) {
+        let arg;
+        try {
+            let isa;
+            const matchValue = (0, Decode_fs_js_1.fromString)((0, ROCrateIO_js_1.ROCrate_get_decoder)(), s);
+            if (matchValue.tag === /* Error */ 1) {
+                throw new Error((arg = matchValue.fields[0], (0, String_js_1.toText)((0, String_js_1.printf)("Error decoding string: %O"))(arg)));
+            }
+            else {
+                isa = matchValue.fields[0];
+            }
+            return ARC.fromArcInvestigation(isa);
+        }
+        catch (ex) {
+            const arg_1 = ex.message;
+            return (0, String_js_1.toFail)((0, String_js_1.printf)("Could not parse ARC-RO-Crate metadata: \n%s"))(arg_1);
+        }
+    }
+    ToROCrateJsonString(spaces) {
+        const this$ = this;
+        this$.MakeDataFilesAbsolute();
+        const value = (0, ROCrateIO_js_1.ROCrate_encoder_8A8D439)(this$);
+        return (0, Encode_fs_js_1.toString)((0, Encode_js_1.defaultSpaces)(spaces), value);
+    }
+    static toROCrateJsonString(spaces) {
+        return (obj) => obj.ToROCrateJsonString((0, Option_js_1.unwrap)(spaces));
+    }
+    GetValidationPackagesConfigWriteContract(vpc) {
+        const this$ = this;
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        if (!(0, Array_js_1.contains)(ValidationPackagesConfig_js_1.ValidationPackagesConfigHelper_ConfigFilePath, paths, {
+            Equals: (x, y) => (x === y),
+            GetHashCode: Util_js_1.stringHash,
+        })) {
+            const filePaths = (0, Array_js_1.append)([ValidationPackagesConfig_js_1.ValidationPackagesConfigHelper_ConfigFilePath], paths);
+            this$.SetFilePaths(filePaths);
+        }
+        return (0, ValidationPackagesConfig_js_1.ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toCreateContract_Static_724DAE55)(vpc);
+    }
+    GetValidationPackagesConfigDeleteContract(vpc) {
+        const this$ = this;
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        if ((0, Array_js_1.contains)(ValidationPackagesConfig_js_1.ValidationPackagesConfigHelper_ConfigFilePath, paths, {
+            Equals: (x, y) => (x === y),
+            GetHashCode: Util_js_1.stringHash,
+        })) {
+            const filePaths = paths.filter((p) => !(p === ValidationPackagesConfig_js_1.ValidationPackagesConfigHelper_ConfigFilePath));
+            this$.SetFilePaths(filePaths);
+        }
+        return (0, ValidationPackagesConfig_js_1.ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toDeleteContract_Static_724DAE55)(vpc);
+    }
+    GetValidationPackagesConfigReadContract() {
+        return ValidationPackagesConfig_js_1.ValidationPackagesConfigHelper_ReadContract;
+    }
+    GetValidationPackagesConfigFromReadContract(contract) {
+        return (0, ValidationPackagesConfig_js_1.ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_tryFromReadContract_Static_7570923F)(contract);
+    }
+    ToFilePaths(removeRoot, skipUpdateFS) {
+        const this$ = this;
+        if (!(0, Option_js_1.defaultArg)(skipUpdateFS, false)) {
+            this$.UpdateFileSystem();
+        }
+        return this$.FileSystem.Tree.ToFilePaths((0, Option_js_1.unwrap)(removeRoot));
+    }
+}
+exports.ARC = ARC;
+function ARC_$reflection() {
+    return (0, Reflection_js_1.class_type)("ARCtrl.ARC", undefined, ARC, (0, ArcTypes_js_1.ArcInvestigation_$reflection)());
+}
+function ARC_$ctor_5BB4A6F7(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, cwl, fs) {
+    return new ARC(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, cwl, fs);
+}
+function ARCAux_getArcAssaysFromContracts(contracts) {
+    return (0, Array_js_1.choose)(ArcAssay_js_1.ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, contracts);
+}
+function ARCAux_getArcStudiesFromContracts(contracts) {
+    return (0, Array_js_1.choose)(ArcStudy_js_1.ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, contracts);
+}
+function ARCAux_getArcWorkflowsFromContracts(contracts) {
+    return (0, Array_js_1.choose)(ArcWorkflow_js_2.ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F, contracts);
+}
+function ARCAux_getArcRunsFromContracts(contracts) {
+    return (0, Array_js_1.choose)(ArcRun_js_2.ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, contracts);
+}
+function ARCAux_getAssayDataMapFromContracts(assayIdentifier, contracts) {
+    return (0, Array_js_1.tryPick)((c) => (0, Datamap_js_1.ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static)(assayIdentifier, c), contracts);
+}
+function ARCAux_getStudyDataMapFromContracts(studyIdentifier, contracts) {
+    return (0, Array_js_1.tryPick)((c) => (0, Datamap_js_1.ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static)(studyIdentifier, c), contracts);
+}
+function ARCAux_getWorkflowDataMapFromContracts(workflowIdentifier, contracts) {
+    return (0, Array_js_1.tryPick)((c) => (0, Datamap_js_1.ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static)(workflowIdentifier, c), contracts);
+}
+function ARCAux_getRunDataMapFromContracts(runIdentifier, contracts) {
+    return (0, Array_js_1.tryPick)((c) => (0, Datamap_js_1.ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static)(runIdentifier, c), contracts);
+}
+function ARCAux_getArcInvestigationFromContracts(contracts) {
+    return (0, Array_js_1.exactlyOne)((0, Array_js_1.choose)(ArcInvestigation_js_1.ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts));
+}
+function ARCAux_updateFSByISA(isa, fs) {
+    let assaysFolder;
+    const assays = (0, Array_js_1.map)((a) => FileSystemTree_js_1.FileSystemTree.createAssayFolder(a.Identifier, a.DataMap != null), (0, Seq_js_1.toArray)(isa.Assays));
+    assaysFolder = FileSystemTree_js_1.FileSystemTree.createAssaysFolder(assays);
+    let studiesFolder;
+    const studies = (0, Array_js_1.map)((s) => FileSystemTree_js_1.FileSystemTree.createStudyFolder(s.Identifier, s.DataMap != null), (0, Seq_js_1.toArray)(isa.Studies));
+    studiesFolder = FileSystemTree_js_1.FileSystemTree.createStudiesFolder(studies);
+    let workflowsFolder;
+    const workflows = (0, Array_js_1.map)((w) => FileSystemTree_js_1.FileSystemTree.createWorkflowFolder((0, ArcTypes_js_1.ArcWorkflow__get_Identifier)(w), (0, ArcTypes_js_1.ArcWorkflow__get_DataMap)(w) != null), (0, Seq_js_1.toArray)(isa.Workflows));
+    workflowsFolder = FileSystemTree_js_1.FileSystemTree.createWorkflowsFolder(workflows);
+    let runsFolder;
+    const runs = (0, Array_js_1.map)((r) => FileSystemTree_js_1.FileSystemTree.createRunFolder(r.Identifier, r.DataMap != null), (0, Seq_js_1.toArray)(isa.Runs));
+    runsFolder = FileSystemTree_js_1.FileSystemTree.createRunsFolder(runs);
+    const investigation = FileSystemTree_js_1.FileSystemTree.createInvestigationFile();
+    let tree_1;
+    const tree = FileSystemTree_js_1.FileSystemTree.createRootFolder([investigation, assaysFolder, studiesFolder, workflowsFolder, runsFolder]);
+    tree_1 = FileSystem_js_1.FileSystem.create({
+        tree: tree,
+    });
+    return fs.Union(tree_1);
+}
+function ARCAux_updateFSByCWL(cwl, fs) {
+    const workflows = FileSystemTree_js_1.FileSystemTree.createWorkflowsFolder([]);
+    const runs = FileSystemTree_js_1.FileSystemTree.createRunsFolder([]);
+    let tree_1;
+    const tree = FileSystemTree_js_1.FileSystemTree.createRootFolder([workflows, runs]);
+    tree_1 = FileSystem_js_1.FileSystem.create({
+        tree: tree,
+    });
+    return fs.Union(tree_1);
+}