@nfdi4plants/arctrl 3.0.1 → 3.1.0

package/dist/ts/node_modules/@fable-org/fable-library-js/System.Collections.Generic.js

@@ -0,0 +1,320 @@
+import { compare, equals, structuralHash, getEnumerator, toIterator, defaultOf, disposeSafe } from './Util.js';
+import { class_type } from './Reflection.js';
+import { delay, enumerateWhile, append, singleton, empty, toArray } from './Seq.js';
+import { item, fill, copyTo, initialize, setItem } from './Array.js';
+import { max } from './Double.js';
+
+class Comparer$1 {
+    constructor(comparison) {
+        this.comparison = comparison;
+    }
+    Compare(x, y) {
+        const _ = this;
+        return _.comparison(x, y) | 0;
+    }
+}
+function Comparer$1_$reflection(gen0) {
+    return class_type("System.Collections.Generic.Comparer`1", [gen0], Comparer$1);
+}
+function Comparer$1_$ctor_47C913C(comparison) {
+    return new Comparer$1(comparison);
+}
+function Comparer$1_get_Default() {
+    return Comparer$1_$ctor_47C913C(compare);
+}
+function Comparer$1_Create_47C913C(comparison) {
+    return Comparer$1_$ctor_47C913C(comparison);
+}
+function Comparer$1__Compare_5BDDA0(_, x, y) {
+    return _.comparison(x, y);
+}
+class EqualityComparer$1 {
+    constructor(equals, getHashCode) {
+        this.equals = equals;
+        this.getHashCode = getHashCode;
+    }
+    Equals(x, y) {
+        const _ = this;
+        return _.equals(x, y);
+    }
+    GetHashCode(x) {
+        const _ = this;
+        return _.getHashCode(x) | 0;
+    }
+}
+function EqualityComparer$1_$reflection(gen0) {
+    return class_type("System.Collections.Generic.EqualityComparer`1", [gen0], EqualityComparer$1);
+}
+function EqualityComparer$1_$ctor_Z6EE254AB(equals, getHashCode) {
+    return new EqualityComparer$1(equals, getHashCode);
+}
+function EqualityComparer$1_get_Default() {
+    return EqualityComparer$1_$ctor_Z6EE254AB(equals, structuralHash);
+}
+function EqualityComparer$1_Create_Z6EE254AB(equals, getHashCode) {
+    return EqualityComparer$1_$ctor_Z6EE254AB(equals, getHashCode);
+}
+function EqualityComparer$1__Equals_5BDDA0(_, x, y) {
+    return _.equals(x, y);
+}
+function EqualityComparer$1__GetHashCode_2B595(_, x) {
+    return _.getHashCode(x);
+}
+class Stack$1 {
+    constructor(initialContents, initialCount) {
+        this.contents = initialContents;
+        this.count = (initialCount | 0);
+    }
+    GetEnumerator() {
+        const _ = this;
+        return getEnumerator(delay(() => {
+            let index = _.count - 1;
+            return enumerateWhile(() => (index >= 0), delay(() => append(singleton(item(index, _.contents)), delay(() => {
+                index = ((index - 1) | 0);
+                return empty();
+            }))));
+        }));
+    }
+    [Symbol.iterator]() {
+        return toIterator(getEnumerator(this));
+    }
+    "System.Collections.IEnumerable.GetEnumerator"() {
+        const this$ = this;
+        return getEnumerator(this$);
+    }
+}
+function Stack$1_$reflection(gen0) {
+    return class_type("System.Collections.Generic.Stack`1", [gen0], Stack$1);
+}
+function Stack$1_$ctor_Z3B4C077E(initialContents, initialCount) {
+    return new Stack$1(initialContents, initialCount);
+}
+function Stack$1_$ctor_Z524259A4(initialCapacity) {
+    return Stack$1_$ctor_Z3B4C077E(fill(new Array(initialCapacity), 0, initialCapacity, null), 0);
+}
+function Stack$1_$ctor() {
+    return Stack$1_$ctor_Z524259A4(4);
+}
+function Stack$1_$ctor_BB573A(xs) {
+    const arr = Array.from(xs);
+    return Stack$1_$ctor_Z3B4C077E(arr, arr.length);
+}
+function Stack$1__Ensure_Z524259A4(_, newSize) {
+    const oldSize = _.contents.length | 0;
+    if (newSize > oldSize) {
+        const old = _.contents;
+        _.contents = fill(new Array(max(newSize, oldSize * 2)), 0, max(newSize, oldSize * 2), null);
+        copyTo(old, 0, _.contents, 0, _.count);
+    }
+}
+function Stack$1__get_Count(_) {
+    return _.count;
+}
+function Stack$1__Pop(_) {
+    _.count = ((_.count - 1) | 0);
+    return item(_.count, _.contents);
+}
+function Stack$1__Peek(_) {
+    return item(_.count - 1, _.contents);
+}
+function Stack$1__Contains_2B595(_, x) {
+    let found = false;
+    let i = 0;
+    while ((i < _.count) && !found) {
+        if (equals(x, item(i, _.contents))) {
+            found = true;
+        }
+        else {
+            i = ((i + 1) | 0);
+        }
+    }
+    return found;
+}
+function Stack$1__TryPeek_1F3DB691(this$, result) {
+    if (this$.count > 0) {
+        result.contents = Stack$1__Peek(this$);
+        return true;
+    }
+    else {
+        return false;
+    }
+}
+function Stack$1__TryPop_1F3DB691(this$, result) {
+    if (this$.count > 0) {
+        result.contents = Stack$1__Pop(this$);
+        return true;
+    }
+    else {
+        return false;
+    }
+}
+function Stack$1__Push_2B595(this$, x) {
+    Stack$1__Ensure_Z524259A4(this$, this$.count + 1);
+    this$.contents[this$.count] = x;
+    this$.count = ((this$.count + 1) | 0);
+}
+function Stack$1__Clear(_) {
+    _.count = 0;
+    fill(_.contents, 0, _.contents.length, defaultOf());
+}
+function Stack$1__TrimExcess(this$) {
+    if ((this$.count / this$.contents.length) > 0.9) {
+        Stack$1__Ensure_Z524259A4(this$, this$.count);
+    }
+}
+function Stack$1__ToArray(_) {
+    return initialize(_.count, (i) => item((_.count - 1) - i, _.contents));
+}
+class Queue$1 {
+    constructor(initialContents, initialCount) {
+        this.contents = initialContents;
+        this.count = (initialCount | 0);
+        this.head = 0;
+        this.tail = (((initialCount === this.contents.length) ? 0 : initialCount) | 0);
+    }
+    GetEnumerator() {
+        const _ = this;
+        return getEnumerator(Queue$1__toSeq(_));
+    }
+    [Symbol.iterator]() {
+        return toIterator(getEnumerator(this));
+    }
+    "System.Collections.IEnumerable.GetEnumerator"() {
+        const this$ = this;
+        return getEnumerator(this$);
+    }
+}
+function Queue$1_$reflection(gen0) {
+    return class_type("System.Collections.Generic.Queue`1", [gen0], Queue$1);
+}
+function Queue$1_$ctor_Z3B4C077E(initialContents, initialCount) {
+    return new Queue$1(initialContents, initialCount);
+}
+function Queue$1_$ctor_Z524259A4(initialCapacity) {
+    if (initialCapacity < 0) {
+        throw new Error("capacity is less than 0");
+    }
+    return Queue$1_$ctor_Z3B4C077E(fill(new Array(initialCapacity), 0, initialCapacity, null), 0);
+}
+function Queue$1_$ctor() {
+    return Queue$1_$ctor_Z524259A4(4);
+}
+function Queue$1_$ctor_BB573A(xs) {
+    const arr = Array.from(xs);
+    return Queue$1_$ctor_Z3B4C077E(arr, arr.length);
+}
+function Queue$1__get_Count(_) {
+    return _.count;
+}
+function Queue$1__Enqueue_2B595(_, value) {
+    if (_.count === Queue$1__size(_)) {
+        Queue$1__ensure_Z524259A4(_, _.count + 1);
+    }
+    _.contents[_.tail] = value;
+    _.tail = (((_.tail + 1) % Queue$1__size(_)) | 0);
+    _.count = ((_.count + 1) | 0);
+}
+function Queue$1__Dequeue(_) {
+    if (_.count === 0) {
+        throw new Error("Queue is empty");
+    }
+    const value = item(_.head, _.contents);
+    _.head = (((_.head + 1) % Queue$1__size(_)) | 0);
+    _.count = ((_.count - 1) | 0);
+    return value;
+}
+function Queue$1__Peek(_) {
+    if (_.count === 0) {
+        throw new Error("Queue is empty");
+    }
+    return item(_.head, _.contents);
+}
+function Queue$1__TryDequeue_1F3DB691(this$, result) {
+    if (this$.count === 0) {
+        return false;
+    }
+    else {
+        result.contents = Queue$1__Dequeue(this$);
+        return true;
+    }
+}
+function Queue$1__TryPeek_1F3DB691(this$, result) {
+    if (this$.count === 0) {
+        return false;
+    }
+    else {
+        result.contents = Queue$1__Peek(this$);
+        return true;
+    }
+}
+function Queue$1__Contains_2B595(_, x) {
+    let found = false;
+    let i = 0;
+    while ((i < _.count) && !found) {
+        if (equals(x, item(Queue$1__toIndex_Z524259A4(_, i), _.contents))) {
+            found = true;
+        }
+        else {
+            i = ((i + 1) | 0);
+        }
+    }
+    return found;
+}
+function Queue$1__Clear(_) {
+    _.count = 0;
+    _.head = 0;
+    _.tail = 0;
+    fill(_.contents, 0, Queue$1__size(_), defaultOf());
+}
+function Queue$1__TrimExcess(_) {
+    if ((_.count / _.contents.length) > 0.9) {
+        Queue$1__ensure_Z524259A4(_, _.count);
+    }
+}
+function Queue$1__ToArray(_) {
+    return toArray(Queue$1__toSeq(_));
+}
+function Queue$1__CopyTo_Z3B4C077E(_, target, start) {
+    let i = start;
+    const enumerator = getEnumerator(Queue$1__toSeq(_));
+    try {
+        while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+            const item = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+            setItem(target, i, item);
+            i = ((i + 1) | 0);
+        }
+    }
+    finally {
+        disposeSafe(enumerator);
+    }
+}
+function Queue$1__size(this$) {
+    return this$.contents.length;
+}
+function Queue$1__toIndex_Z524259A4(this$, i) {
+    return (this$.head + i) % Queue$1__size(this$);
+}
+function Queue$1__ensure_Z524259A4(this$, requiredSize) {
+    const newBuffer = fill(new Array(requiredSize), 0, requiredSize, null);
+    if (this$.head < this$.tail) {
+        copyTo(this$.contents, this$.head, newBuffer, 0, this$.count);
+    }
+    else {
+        copyTo(this$.contents, this$.head, newBuffer, 0, Queue$1__size(this$) - this$.head);
+        copyTo(this$.contents, 0, newBuffer, Queue$1__size(this$) - this$.head, this$.tail);
+    }
+    this$.head = 0;
+    this$.contents = newBuffer;
+    this$.tail = (((this$.count === Queue$1__size(this$)) ? 0 : this$.count) | 0);
+}
+function Queue$1__toSeq(this$) {
+    return delay(() => {
+        let i = 0;
+        return enumerateWhile(() => (i < this$.count), delay(() => append(singleton(item(Queue$1__toIndex_Z524259A4(this$, i), this$.contents)), delay(() => {
+            i = ((i + 1) | 0);
+            return empty();
+        }))));
+    });
+}
+
+export { Comparer$1, Comparer$1_$ctor_47C913C, Comparer$1_$reflection, Comparer$1_Create_47C913C, Comparer$1__Compare_5BDDA0, Comparer$1_get_Default, EqualityComparer$1, EqualityComparer$1_$ctor_Z6EE254AB, EqualityComparer$1_$reflection, EqualityComparer$1_Create_Z6EE254AB, EqualityComparer$1__Equals_5BDDA0, EqualityComparer$1__GetHashCode_2B595, EqualityComparer$1_get_Default, Queue$1, Queue$1_$ctor, Queue$1_$ctor_BB573A, Queue$1_$ctor_Z524259A4, Queue$1_$reflection, Queue$1__Clear, Queue$1__Contains_2B595, Queue$1__CopyTo_Z3B4C077E, Queue$1__Dequeue, Queue$1__Enqueue_2B595, Queue$1__Peek, Queue$1__ToArray, Queue$1__TrimExcess, Queue$1__TryDequeue_1F3DB691, Queue$1__TryPeek_1F3DB691, Queue$1__ensure_Z524259A4, Queue$1__get_Count, Queue$1__size, Queue$1__toIndex_Z524259A4, Queue$1__toSeq, Stack$1, Stack$1_$ctor, Stack$1_$ctor_BB573A, Stack$1_$ctor_Z524259A4, Stack$1_$reflection, Stack$1__Clear, Stack$1__Contains_2B595, Stack$1__Ensure_Z524259A4, Stack$1__Peek, Stack$1__Pop, Stack$1__Push_2B595, Stack$1__ToArray, Stack$1__TrimExcess, Stack$1__TryPeek_1F3DB691, Stack$1__TryPop_1F3DB691, Stack$1__get_Count };

package/dist/ts/ts/ARC.d.ts

@@ -2,8 +2,8 @@ import { FileSystem } from './FileSystem/FileSystem.js';
 import { Option } from '@fable-org/fable-library-js/Option.js';
 import { License } from './License.js';
 import { ArcWorkflow, ArcRun, ArcStudy, ArcAssay, ArcInvestigation } from './Core/ArcTypes.js';
-import { FSharpResult$2_$union } from '@fable-org/fable-library-js/Result.js';
 import { Contract } from './Contract/Contract.js';
+import { FSharpResult$2_$union } from '@fable-org/fable-library-js/Result.js';
 import { int32 } from '@fable-org/fable-library-js/Int32.js';
 import { Datamap } from './Core/Datamap.js';
 import { FileSystemTree_$union } from './FileSystem/FileSystemTree.js';
@@ -28,8 +28,8 @@ export declare class ARC extends ArcInvestigation {
     get License(): License | undefined;
     set License(license: Option<License>);
     static fromArcInvestigation(isa: ArcInvestigation, fs?: FileSystem, license?: License): ARC;
-    TryWriteAsync(arcPath: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
-    TryUpdateAsync(arcPath: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
+    TryWriteAsync(arcPath: string, forceOverwrite?: boolean): Promise<FSharpResult$2_$union<Contract[], string[]>>;
+    TryUpdateAsync(arcPath: string, forceOverwrite?: boolean): Promise<FSharpResult$2_$union<Contract[], string[]>>;
     SetLicenseFulltext(fulltext: string, path?: string): void;
     static tryLoadAsync(arcPath: string): Promise<FSharpResult$2_$union<ARC, string[]>>;
     GetAssayRemoveContracts(assayIdentifier: string): Contract[];

package/dist/ts/ts/ARC.d.ts.map

@@ -1 +1 @@
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package/dist/ts/ts/ARC.js

@@ -2,22 +2,22 @@ import { FileSystem } from './FileSystem/FileSystem.js';
 import { unwrap, defaultArg, value, map as map$1, bind, defaultArgWith } from '../node_modules/@fable-org/fable-library-js/Option.js';
 import { License } from './License.js';
 import { ArcInvestigation, ArcInvestigation_$reflection } from './Core/ArcTypes.js';
+import { Contract } from './Contract/Contract.js';
 import { fullFillContractBatchAsync } from './ContractIO/ContractIO.js';
 import { FSharpResult$2_Error, FSharpResult$2_Ok } from '../node_modules/@fable-org/fable-library-js/Result.js';
-import { Contract } from './Contract/Contract.js';
 import { PromiseBuilder__Run_212F1D4B, PromiseBuilder__Delay_62FBFDE1 } 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 { toArray, contains, delay, append, singleton, iterate, tryFind, find, empty, collect, toList } from '../node_modules/@fable-org/fable-library-js/Seq.js';
+import { toArray, contains, delay, append, singleton, iterate, tryFind, find, collect, empty, toList } from '../node_modules/@fable-org/fable-library-js/Seq.js';
 import { defaultOf, stringHash, comparePrimitives, curry2, safeHash, getEnumerator, disposeSafe, equals } from '../node_modules/@fable-org/fable-library-js/Util.js';
-import { getAssayFolderPath, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath, normalizePathKey } from './FileSystem/Path.js';
+import { getAssayFolderPath, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath, combine, normalizePathKey } from './FileSystem/Path.js';
 import { ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from './Contract/ArcAssay.js';
 import { ARCtrl_ArcRun__ArcRun_ToDeleteContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, ARCtrl_ArcRun__ArcRun_tryCWLFromReadContract_Static, ARCtrl_ArcRun__ArcRun_tryYMLFromReadContract_Static } from './Contract/ArcRun.js';
 import { ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F, ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static } from './Contract/ArcWorkflow.js';
 import { join, toFail, printf, replace, toText } from '../node_modules/@fable-org/fable-library-js/String.js';
 import { map, choose, fold, concat, contains as contains$2, append as append$1, tryPick, equalsWith, item } from '../node_modules/@fable-org/fable-library-js/Array.js';
-import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from './Contract/ArcInvestigation.js';
-import { createMissingIdentifier, Workflow_cwlFileNameFromIdentifier, Run_cwlFileNameFromIdentifier, Study_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Assay_datamapFileNameFromIdentifier, Workflow_fileNameFromIdentifier, Workflow_datamapFileNameFromIdentifier, Run_fileNameFromIdentifier, Run_datamapFileNameFromIdentifier } from './Core/Helper/Identifier.js';
+import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from './Contract/ArcInvestigation.js';
+import { createMissingIdentifier, Workflow_cwlFileNameFromIdentifier, Run_cwlFileNameFromIdentifier } from './Core/Helper/Identifier.js';
 import { ofSeq, contains as contains$1, unionMany, FSharpSet__Contains } from '../node_modules/@fable-org/fable-library-js/Set.js';
 import { ResizeArray_iter, ResizeArray_map } from './Core/Helper/Collections.js';
 import { FileSystemTree_Folder, FileSystemTree, FileSystemTree_File } from './FileSystem/FileSystemTree.js';
@@ -26,16 +26,8 @@ import { setInvestigationIdentifier } from './Core/IdentifierSetters.js';
 import { ofSeq as ofSeq$1, ofArray, tryFind as tryFind$1 } from '../node_modules/@fable-org/fable-library-js/Map.js';
 import { ArcTables } from './Core/Table/ArcTables.js';
 import { resolveRunReferencesFromLookup } from './CWLRunResolver.js';
-import { addToDict } from '../node_modules/@fable-org/fable-library-js/MapUtil.js';
-import { ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF } from './Spreadsheet/ArcInvestigation.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 { ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E } from './Spreadsheet/ArcWorkflow.js';
-import { ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8 } from './Spreadsheet/ArcRun.js';
-import { Dictionary_tryGet } from './fable_modules/FsSpreadsheet.7.0.0-alpha.1/Cells/FsCellsCollection.fs.js';
 import { ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from './Contract/ArcStudy.js';
-import { ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static } from './Contract/Datamap.js';
+import { ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static } from './Contract/Datamap.js';
 import { Init_createInitContract_6DFDD678, gitignoreContract, gitattributesContract, Init_createAddRemoteContract_Z721C83C5, Clone_createCloneContract_5000466F } from './Contract/Git.js';
 import { fromString } from './fable_modules/Thoth.Json.JavaScript.0.4.1/Decode.fs.js';
 import { ROCrate_get_decoderDeprecated, ROCrate_get_decoder, ROCrate_encoder_Z7FE34C43 } from './ROCrateIO.js';
@@ -78,13 +70,15 @@ class ARC extends ArcInvestigation {
   static fromArcInvestigation(isa, fs, license) {
     return new ARC(isa.Identifier, unwrap(isa.Title), unwrap(isa.Description), unwrap(isa.SubmissionDate), unwrap(isa.PublicReleaseDate), isa.OntologySourceReferences, isa.Publications, isa.Contacts, isa.Assays, isa.Studies, isa.Workflows, isa.Runs, isa.RegisteredStudyIdentifiers, isa.Comments, isa.Remarks, unwrap(fs), unwrap(license));
   }
-  TryWriteAsync(arcPath) {
+  TryWriteAsync(arcPath, forceOverwrite) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetWriteContracts());
+    const cs = this$.GetWriteContracts();
+    return fullFillContractBatchAsync(defaultArg(forceOverwrite, false), arcPath, cs);
   }
-  TryUpdateAsync(arcPath) {
+  TryUpdateAsync(arcPath, forceOverwrite) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetUpdateContracts());
+    const cs = this$.GetUpdateContracts();
+    return fullFillContractBatchAsync(defaultArg(forceOverwrite, false), arcPath, cs);
   }
   SetLicenseFulltext(fulltext, path) {
     const this$ = this;
@@ -108,7 +102,7 @@ class ARC extends ArcInvestigation {
     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) => {
+      return fullFillContractBatchAsync(false, arcPath, contracts).then((_arg_1) => {
         const fulFilledContracts = _arg_1;
         if (fulFilledContracts.tag === /* Error */
         1) {
@@ -173,15 +167,15 @@ class ARC extends ArcInvestigation {
   }
   TryRemoveAssayAsync(arcPath, assayIdentifier) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetAssayRemoveContracts(assayIdentifier));
+    return fullFillContractBatchAsync(false, arcPath, this$.GetAssayRemoveContracts(assayIdentifier));
   }
   TryRemoveRunAsync(arcPath, runIdentifier) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetRunRemoveContracts(runIdentifier));
+    return fullFillContractBatchAsync(false, arcPath, this$.GetRunRemoveContracts(runIdentifier));
   }
   TryRemoveWorkflowAsync(arcPath, workflowIdentifier) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetWorkflowRemoveContracts(workflowIdentifier));
+    return fullFillContractBatchAsync(false, arcPath, this$.GetWorkflowRemoveContracts(workflowIdentifier));
   }
   RemoveRunAsync(arcPath, runIdentifier) {
     const this$ = this;
@@ -213,11 +207,11 @@ class ARC extends ArcInvestigation {
   }
   TryRenameRunAsync(arcPath, oldRunIdentifier, newRunIdentifier) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetRunRenameContracts(oldRunIdentifier, newRunIdentifier));
+    return fullFillContractBatchAsync(false, arcPath, this$.GetRunRenameContracts(oldRunIdentifier, newRunIdentifier));
   }
   TryRenameWorkflowAsync(arcPath, oldWorkflowIdentifier, newWorkflowIdentifier) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetWorkflowRenameContracts(oldWorkflowIdentifier, newWorkflowIdentifier));
+    return fullFillContractBatchAsync(false, arcPath, this$.GetWorkflowRenameContracts(oldWorkflowIdentifier, newWorkflowIdentifier));
   }
   RenameRunAsync(arcPath, oldRunIdentifier, newRunIdentifier) {
     const this$ = this;
@@ -297,7 +291,7 @@ class ARC extends ArcInvestigation {
   }
   TryRenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetAssayRenameContracts(oldAssayIdentifier, newAssayIdentifier));
+    return fullFillContractBatchAsync(false, arcPath, this$.GetAssayRenameContracts(oldAssayIdentifier, newAssayIdentifier));
   }
   GetStudyRemoveContracts(studyIdentifier) {
     const this$ = this;
@@ -310,7 +304,7 @@ class ARC extends ArcInvestigation {
   }
   TryRemoveStudyAsync(arcPath, studyIdentifier) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetStudyRemoveContracts(studyIdentifier));
+    return fullFillContractBatchAsync(false, arcPath, this$.GetStudyRemoveContracts(studyIdentifier));
   }
   GetStudyRenameContracts(oldStudyIdentifier, newStudyIdentifier) {
     const this$ = this;
@@ -330,7 +324,7 @@ class ARC extends ArcInvestigation {
   }
   TryRenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier) {
     const this$ = this;
-    return fullFillContractBatchAsync(arcPath, this$.GetStudyRenameContracts(oldStudyIdentifier, newStudyIdentifier));
+    return fullFillContractBatchAsync(false, arcPath, this$.GetStudyRenameContracts(oldStudyIdentifier, newStudyIdentifier));
   }
   WriteAsync(arcPath) {
     const this$ = this;
@@ -616,72 +610,57 @@ class ARC extends ArcInvestigation {
     if (!defaultArg(skipUpdateFS, false)) {
       this$.UpdateFileSystem();
     }
-    const filemap = /* @__PURE__ */ new Map([]);
-    addToDict(filemap, "isa.investigation.xlsx", ["ISA_Investigation", ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(this$)]);
-    this$.StaticHash = this$.GetLightHashCode() | 0;
-    iterate((s) => {
-      s.StaticHash = s.GetLightHashCode() | 0;
-      addToDict(filemap, Study_fileNameFromIdentifier(s.Identifier), ["ISA_Study", ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(s)]);
-      if (s.Datamap != null) {
-        const dm = value(s.Datamap);
-        dm.StaticHash = safeHash(dm) | 0;
-        addToDict(filemap, Study_datamapFileNameFromIdentifier(s.Identifier), ["ISA_Datamap", toFsWorkbook(dm)]);
-      }
-    }, this$.Studies);
-    iterate((a) => {
-      a.StaticHash = a.GetLightHashCode() | 0;
-      addToDict(filemap, Assay_fileNameFromIdentifier(a.Identifier), ["ISA_Assay", ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(a)]);
-      if (a.Datamap != null) {
-        const dm_1 = value(a.Datamap);
-        dm_1.StaticHash = safeHash(dm_1) | 0;
-        addToDict(filemap, Assay_datamapFileNameFromIdentifier(a.Identifier), ["ISA_Datamap", toFsWorkbook(dm_1)]);
-      }
-    }, this$.Assays);
-    iterate((w) => {
-      w.StaticHash = w.GetLightHashCode() | 0;
-      addToDict(filemap, Workflow_fileNameFromIdentifier(w.Identifier), ["ISA_Workflow", ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E(w)]);
-      if (w.CWLDescription != null) {
-        throw new Error("Not implemented yet: CWL description in ARC.GetWriteContracts");
-      }
-      if (w.Datamap != null) {
-        const dm_2 = value(w.Datamap);
-        dm_2.StaticHash = safeHash(dm_2) | 0;
-        addToDict(filemap, Workflow_datamapFileNameFromIdentifier(w.Identifier), ["ISA_Datamap", toFsWorkbook(dm_2)]);
-      }
-    }, this$.Workflows);
-    iterate((r) => {
-      r.StaticHash = r.GetLightHashCode() | 0;
-      addToDict(filemap, Run_fileNameFromIdentifier(r.Identifier), ["ISA_Run", ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8(r)]);
-      if (r.CWLDescription != null) {
-        throw new Error("Not implemented yet: CWL description in ARC.GetWriteContracts");
-      }
-      if (r.CWLInput.length > 0) {
-        throw new Error("Not implemented yet: CWL YAML input in ARC.GetWriteContracts");
-      }
-      if (r.Datamap != null) {
-        const dm_3 = value(r.Datamap);
-        dm_3.StaticHash = safeHash(dm_3) | 0;
-        addToDict(filemap, Run_datamapFileNameFromIdentifier(r.Identifier), ["ISA_Datamap", toFsWorkbook(dm_3)]);
-      }
-    }, this$.Runs);
-    const matchValue = this$.License;
-    if (matchValue == null) {
-    } else {
-      const l = value(matchValue);
-      const matchValue_1 = l.Type;
-      l.StaticHash = safeHash(l) | 0;
-      addToDict(filemap, l.Path, ["PlainText", l.Content]);
-    }
-    return map((fp) => {
-      const matchValue_2 = Dictionary_tryGet(fp, filemap);
-      if (matchValue_2 == null) {
-        return Contract.createCreate(fp, "PlainText");
-      } else {
-        const wb = value(matchValue_2)[1];
-        const dto = value(matchValue_2)[0];
-        return Contract.createCreate(fp, dto, wb);
-      }
-    }, this$._fs.Tree.ToFilePaths(true));
+    return toArray(delay(() => {
+      this$.StaticHash = this$.GetLightHashCode() | 0;
+      return append(singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract(this$)), delay(() => append(collect((s) => {
+        s.StaticHash = s.GetLightHashCode() | 0;
+        return append(ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true), delay(() => {
+          if (s.Datamap != null) {
+            const dm = value(s.Datamap);
+            dm.StaticHash = safeHash(dm) | 0;
+            return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5(dm, s.Identifier));
+          } else {
+            return empty();
+          }
+        }));
+      }, this$.Studies), delay(() => append(collect((a) => {
+        a.StaticHash = a.GetLightHashCode() | 0;
+        return append(ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true), delay(() => {
+          if (a.Datamap != null) {
+            const dm_1 = value(a.Datamap);
+            dm_1.StaticHash = safeHash(dm_1) | 0;
+            return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5(dm_1, a.Identifier));
+          } else {
+            return empty();
+          }
+        }));
+      }, this$.Assays), delay(() => append(collect((w) => {
+        w.StaticHash = w.GetLightHashCode() | 0;
+        return append(ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true), delay(() => {
+          if (w.Datamap != null) {
+            const dm_2 = value(w.Datamap);
+            dm_2.StaticHash = safeHash(dm_2) | 0;
+            return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5(dm_2, w.Identifier));
+          } else {
+            return empty();
+          }
+        }));
+      }, this$.Workflows), delay(() => append(collect((r) => {
+        r.StaticHash = r.GetLightHashCode() | 0;
+        return append(ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49(r, true), delay(() => {
+          if (r.Datamap != null) {
+            const dm_3 = value(r.Datamap);
+            dm_3.StaticHash = safeHash(dm_3) | 0;
+            return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5(dm_3, r.Identifier));
+          } else {
+            return empty();
+          }
+        }));
+      }, this$.Runs), delay(() => {
+        let l;
+        return append(this$.License != null ? (l = value(this$.License), l.StaticHash = safeHash(l) | 0, singleton(l.ToCreateContract())) : empty(), delay(() => append(singleton(Contract.createCreate(combine("assays", ".gitkeep"), "PlainText")), delay(() => append(singleton(Contract.createCreate(combine("studies", ".gitkeep"), "PlainText")), delay(() => append(singleton(Contract.createCreate(combine("workflows", ".gitkeep"), "PlainText")), delay(() => singleton(Contract.createCreate(combine("runs", ".gitkeep"), "PlainText"))))))))));
+      }))))))))));
+    }));
   }
   GetUpdateContracts(skipUpdateFS) {
     const this$ = this;