@nfdi4plants/arctrl 3.0.0-beta.4 → 3.0.0-beta.6

package/dist/ts/ts/ARC.js

@@ -1,25 +1,26 @@
 import { FileSystem } from './FileSystem/FileSystem.js';
-import { unwrap, defaultArg, value, bind } from '../node_modules/@fable-org/fable-library-js/Option.js';
-import { ArcInvestigation, ArcWorkflow__get_Identifier, ArcWorkflow__get_DataMap, ArcWorkflow__set_DataMap_51F1E59E, ArcWorkflow__set_StaticHash_Z524259A4, ArcWorkflow__GetLightHashCode, ArcWorkflow__Copy_6FCE9E49, ArcWorkflow__get_StaticHash } from './Core/ArcTypes.js';
+import { unwrap, defaultArg, value, map as map$2, bind, defaultArgWith } from '../node_modules/@fable-org/fable-library-js/Option.js';
+import { License } from './License.js';
+import { ArcInvestigation, ArcWorkflow__get_Identifier, ArcWorkflow__get_DataMap, ArcWorkflow__set_DataMap_51F1E59E, ArcWorkflow__set_StaticHash_Z524259A4, ArcWorkflow__GetLightHashCode, ArcWorkflow__get_StaticHash, ArcWorkflow__Copy_6FCE9E49, ArcInvestigation_$reflection } from './Core/ArcTypes.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 { contains, toArray, delay, iterate, tryFind, find, toList, append as append$1, singleton, empty, map as map$1, collect } from '../node_modules/@fable-org/fable-library-js/Seq.js';
-import { stringHash, curry2, safeHash, getEnumerator, disposeSafe, comparePrimitives, defaultOf, equals } from '../node_modules/@fable-org/fable-library-js/Util.js';
+import { toArray, contains, delay, append, singleton, map, iterate, tryFind, find, empty, collect, 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, getStudyFolderPath } from './FileSystem/Path.js';
-import { ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToUpdateContract } from './Contract/ArcAssay.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_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from './Contract/ArcInvestigation.js';
-import { ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49 } from './Contract/ArcStudy.js';
-import { map, choose, fold, concat, contains as contains$1, append, equalsWith, item, tryPick } from '../node_modules/@fable-org/fable-library-js/Array.js';
-import { replace, toText, printf, toFail, join } from '../node_modules/@fable-org/fable-library-js/String.js';
+import { ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from './Contract/ArcStudy.js';
+import { map as map$1, 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 { replace, join, toFail, printf, toText } from '../node_modules/@fable-org/fable-library-js/String.js';
 import { createMissingIdentifier, Study_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Assay_datamapFileNameFromIdentifier, Workflow_fileNameFromIdentifier, Workflow_datamapFileNameFromIdentifier, Run_fileNameFromIdentifier, Run_datamapFileNameFromIdentifier } from './Core/Helper/Identifier.js';
-import { ofSeq, unionMany, FSharpSet__Contains, contains as contains$2 } from '../node_modules/@fable-org/fable-library-js/Set.js';
-import { ResizeArray_map, ResizeArray_iter } from './Core/Helper/Collections.js';
-import { DataMap__set_StaticHash_Z524259A4, DataMap__get_DataContexts, DataMap__get_StaticHash } from './Core/DataMap.js';
-import { FileSystemTree_Folder, FileSystemTree } from './FileSystem/FileSystemTree.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 { DataMap__get_DataContexts, DataMap__set_StaticHash_Z524259A4, DataMap__get_StaticHash } from './Core/DataMap.js';
+import { FileSystemTree_Folder, FileSystemTree, FileSystemTree_File } from './FileSystem/FileSystemTree.js';
 import { tryISAReadContractFromPath } from './Contract/ARC.js';
 import { setInvestigationIdentifier } from './Core/IdentifierSetters.js';
 import { ArcTables } from './Core/Table/ArcTables.js';
@@ -31,29 +32,31 @@ import { ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F } from './Sprea
 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_DataMap__DataMap_tryFromReadContractForAssay_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static, 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 } from './Contract/Datamap.js';
-import { ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract } from './Contract/ArcWorkflow.js';
-import { ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract } from './Contract/ArcRun.js';
-import { Clone_createCloneContract_5000466F, gitignoreContract, gitattributesContract, Init_createInitContract_6DFDD678, Init_createAddRemoteContract_Z721C83C5 } from './Contract/Git.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_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F } from './Contract/ArcWorkflow.js';
+import { ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F } from './Contract/ArcRun.js';
+import { Init_createInitContract_6DFDD678, gitignoreContract, gitattributesContract, Init_createAddRemoteContract_Z721C83C5, Clone_createCloneContract_5000466F } from './Contract/Git.js';
 import { ofSeq as ofSeq$1 } from '../node_modules/@fable-org/fable-library-js/Map.js';
 import { fromString } from './fable_modules/Thoth.Json.JavaScript.0.4.1/Decode.fs.js';
-import { ROCrate_get_decoderDeprecated, ROCrate_get_decoder, ROCrate_encoder_B568605 } from './ROCrateIO.js';
+import { ROCrate_get_decoderDeprecated, ROCrate_get_decoder, ROCrate_encoder_1E8A3F74 } from './ROCrateIO.js';
 import { toString } from './fable_modules/Thoth.Json.JavaScript.0.4.1/Encode.fs.js';
 import { defaultSpaces } from './Json/Encode.js';
 import { ValidationPackagesConfigHelper_ConfigFilePath, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toCreateContract_Static_724DAE55, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toDeleteContract_Static_724DAE55, ValidationPackagesConfigHelper_ReadContract, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_tryFromReadContract_Static_7570923F } from './Contract/ValidationPackagesConfig.js';
 import { FSharpRef } from '../node_modules/@fable-org/fable-library-js/Types.js';
+import { class_type } from '../node_modules/@fable-org/fable-library-js/Reflection.js';
 
 class ARC extends ArcInvestigation {
-  constructor(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, cwl, fs) {
+  constructor(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, cwl, fs, license) {
     super(identifier, unwrap(title), unwrap(description), unwrap(submissionDate), unwrap(publicReleaseDate), unwrap(ontologySourceReferences), unwrap(publications), unwrap(contacts), unwrap(assays), unwrap(studies), unwrap(workflows), unwrap(runs), unwrap(registeredStudyIdentifiers), unwrap(comments), unwrap(remarks));
     let fs_1;
     const this$ = new FSharpRef(defaultOf());
     this$.contents = this;
     this._cwl = cwl;
+    this._license = license;
     this._fs = (fs_1 = defaultArg(fs, FileSystem.create({
       tree: FileSystemTree_Folder("", [])
-    })), ARCAux_updateFSByISA(this$.contents, fs_1));
-    this["init@90"] = 1;
+    })), ARCAux_updateFSByARC(this$.contents, license, fs_1));
+    this["init@104"] = 1;
   }
   get FileSystem() {
     const this$ = this;
@@ -63,8 +66,16 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     this$._fs = fs;
   }
-  static fromArcInvestigation(isa, cwl, fs) {
-    return new ARC(isa.Identifier, unwrap(isa.Title), unwrap(isa.Description), unwrap(isa.SubmissionDate), unwrap(isa.PublicReleaseDate), isa.OntologySourceReferences, isa.Publications, isa.Contacts, isa.Assays, isa.Studies, isa.Workflows, isa.Runs, isa.RegisteredStudyIdentifiers, isa.Comments, isa.Remarks, cwl, unwrap(fs));
+  get License() {
+    const this$ = this;
+    return unwrap(this$._license);
+  }
+  set License(license) {
+    const this$ = this;
+    this$._license = license;
+  }
+  static fromArcInvestigation(isa, cwl, fs, license) {
+    return new ARC(isa.Identifier, unwrap(isa.Title), unwrap(isa.Description), unwrap(isa.SubmissionDate), unwrap(isa.PublicReleaseDate), isa.OntologySourceReferences, isa.Publications, isa.Contacts, isa.Assays, isa.Studies, isa.Workflows, isa.Runs, isa.RegisteredStudyIdentifiers, isa.Comments, isa.Remarks, cwl, unwrap(fs), unwrap(license));
   }
   TryWriteAsync(arcPath) {
     const this$ = this;
@@ -74,6 +85,24 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     return fullFillContractBatchAsync(arcPath, this$.GetUpdateContracts());
   }
+  SetLicenseFulltext(fulltext, path) {
+    const this$ = this;
+    const matchValue = this$.License;
+    if (matchValue == null) {
+      const license_1 = new License("fulltext", fulltext);
+      this$.License = license_1;
+      if (path != null) {
+        license_1.Path = value(path);
+      }
+    } else {
+      const license = value(matchValue);
+      license.Type = "fulltext";
+      license.Content = fulltext;
+      if (path != null) {
+        license.Path = value(path);
+      }
+    }
+  }
   static tryLoadAsync(arcPath) {
     return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => getAllFilePathsAsync(arcPath).then((_arg) => {
       const arc = ARC.fromFilePaths(toArray(_arg));
@@ -107,7 +136,7 @@ class ARC extends ArcInvestigation {
     const assayFolderPath = getAssayFolderPath(assayIdentifier);
     const filteredPaths = paths.filter((p) => !p.startsWith(assayFolderPath));
     this$.SetFilePaths(filteredPaths);
-    return toArray(delay(() => append$1(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append$1(singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$)), delay(() => map$1(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
+    return toArray(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append(singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$)), delay(() => map(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
   }
   TryRemoveAssayAsync(arcPath, assayIdentifier) {
     const this$ = this;
@@ -125,9 +154,9 @@ class ARC extends ArcInvestigation {
     const paths = this$.FileSystem.Tree.ToFilePaths();
     const oldAssayFolderPath = getAssayFolderPath(oldAssayIdentifier);
     const newAssayFolderPath = getAssayFolderPath(newAssayIdentifier);
-    const renamedPaths = map((p) => replace(p, oldAssayFolderPath, newAssayFolderPath), paths);
+    const renamedPaths = map$1((p) => replace(p, oldAssayFolderPath, newAssayFolderPath), paths);
     this$.SetFilePaths(renamedPaths);
-    return toArray(delay(() => append$1(singleton(Contract.createRename(oldAssayFolderPath, newAssayFolderPath)), delay(() => this$.GetUpdateContracts()))));
+    return toArray(delay(() => append(singleton(Contract.createRename(oldAssayFolderPath, newAssayFolderPath)), delay(() => this$.GetUpdateContracts()))));
   }
   TryRenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier) {
     const this$ = this;
@@ -158,9 +187,9 @@ class ARC extends ArcInvestigation {
     const paths = this$.FileSystem.Tree.ToFilePaths();
     const oldStudyFolderPath = getStudyFolderPath(oldStudyIdentifier);
     const newStudyFolderPath = getStudyFolderPath(newStudyIdentifier);
-    const renamedPaths = map((p) => replace(p, oldStudyFolderPath, newStudyFolderPath), paths);
+    const renamedPaths = map$1((p) => replace(p, oldStudyFolderPath, newStudyFolderPath), paths);
     this$.SetFilePaths(renamedPaths);
-    return toArray(delay(() => append$1(singleton(Contract.createRename(oldStudyFolderPath, newStudyFolderPath)), delay(() => this$.GetUpdateContracts()))));
+    return toArray(delay(() => append(singleton(Contract.createRename(oldStudyFolderPath, newStudyFolderPath)), delay(() => this$.GetUpdateContracts()))));
   }
   TryRenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier) {
     const this$ = this;
@@ -172,7 +201,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map((e) => e, result.fields[0]));
+        const appended = join("\n", map$1((e) => e, result.fields[0]));
         toFail(printf("Could not write ARC, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -186,7 +215,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map((e) => e, result.fields[0]));
+        const appended = join("\n", map$1((e) => e, result.fields[0]));
         toFail(printf("Could not update ARC, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -200,7 +229,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map((e) => e, result.fields[0]));
+        const appended = join("\n", map$1((e) => e, result.fields[0]));
         toFail(printf("Could not remove assay, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -214,7 +243,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map((e) => e, result.fields[0]));
+        const appended = join("\n", map$1((e) => e, result.fields[0]));
         toFail(printf("Could not rename assay, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -228,7 +257,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map((e) => e, result.fields[0]));
+        const appended = join("\n", map$1((e) => e, result.fields[0]));
         toFail(printf("Could not remove study, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -242,7 +271,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map((e) => e, result.fields[0]));
+        const appended = join("\n", map$1((e) => e, result.fields[0]));
         toFail(printf("Could not rename study, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -255,7 +284,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map((e) => e, result.fields[0]));
+        const appended = join("\n", map$1((e) => e, result.fields[0]));
         toFail(printf("Could not load ARC, failed with the following errors %s"))(appended);
         return Promise.resolve(new ARC(createMissingIdentifier()));
       } else {
@@ -269,7 +298,7 @@ class ARC extends ArcInvestigation {
     const filesPaths = ofSeq(this$.FileSystem.Tree.ToFilePaths(), {
       Compare: comparePrimitives
     });
-    const checkExistenceFromRoot = (p) => contains$2(p, filesPaths);
+    const checkExistenceFromRoot = (p) => contains$1(p, filesPaths);
     const updateColumnOption = (dataNameFunction, col) => {
       let col_1;
       let matchResult, col_2;
@@ -293,6 +322,9 @@ class ARC extends ArcInvestigation {
           }, col_2.Cells);
           break;
         }
+        case 1: {
+          break;
+        }
       }
     };
     const updateTable = (dataNameFunction_1, t) => {
@@ -351,10 +383,11 @@ class ARC extends ArcInvestigation {
     this$.Comments = investigation.Comments;
     this$.Remarks = investigation.Remarks;
     this$.RegisteredStudyIdentifiers = investigation.RegisteredStudyIdentifiers;
-    const studies = map((tuple) => tuple[0], ARCAux_getArcStudiesFromContracts(contracts));
+    const studies = map$1((tuple) => tuple[0], ARCAux_getArcStudiesFromContracts(contracts));
     const assays = ARCAux_getArcAssaysFromContracts(contracts);
     const workflows = ARCAux_getArcWorkflowsFromContracts(contracts);
     const runs = ARCAux_getArcRunsFromContracts(contracts);
+    const license = ARCAux_getLicenseFromContracts(contracts);
     const array_2 = this$.AssayIdentifiers;
     array_2.forEach((ai) => {
       if (!assays.some((a) => a.Identifier === ai)) {
@@ -421,11 +454,12 @@ class ARC extends ArcInvestigation {
     iterate((s_2) => {
       s_2.StaticHash = s_2.GetLightHashCode() | 0;
     }, this$.Studies);
+    this$.License = license;
     this$.StaticHash = this$.GetLightHashCode() | 0;
   }
   UpdateFileSystem() {
     const this$ = this;
-    const newFS = ARCAux_updateFSByISA(this$, this$._fs);
+    const newFS = ARCAux_updateFSByARC(this$, this$._license, this$._fs);
     this$._fs = newFS;
   }
   GetWriteContracts(skipUpdateFS) {
@@ -433,52 +467,60 @@ class ARC extends ArcInvestigation {
     if (!defaultArg(skipUpdateFS, false)) {
       this$.UpdateFileSystem();
     }
-    const workbooks = /* @__PURE__ */ new Map([]);
-    addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(this$)]);
+    const filemap = /* @__PURE__ */ new Map([]);
+    addToDict(filemap, "isa.investigation.xlsx", ["ISA_Investigation", ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(this$)]);
     this$.StaticHash = this$.GetLightHashCode() | 0;
     iterate((s) => {
       s.StaticHash = s.GetLightHashCode() | 0;
-      addToDict(workbooks, Study_fileNameFromIdentifier(s.Identifier), ["ISA_Study", ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(s)]);
+      addToDict(filemap, Study_fileNameFromIdentifier(s.Identifier), ["ISA_Study", ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(s)]);
       if (s.DataMap != null) {
         const dm = value(s.DataMap);
         DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
-        addToDict(workbooks, Study_datamapFileNameFromIdentifier(s.Identifier), ["ISA_Datamap", toFsWorkbook(dm)]);
+        addToDict(filemap, Study_datamapFileNameFromIdentifier(s.Identifier), ["ISA_Datamap", toFsWorkbook(dm)]);
       }
     }, this$.Studies);
     iterate((a) => {
       a.StaticHash = a.GetLightHashCode() | 0;
-      addToDict(workbooks, Assay_fileNameFromIdentifier(a.Identifier), ["ISA_Assay", ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(a)]);
+      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);
         DataMap__set_StaticHash_Z524259A4(dm_1, safeHash(dm_1));
-        addToDict(workbooks, Assay_datamapFileNameFromIdentifier(a.Identifier), ["ISA_Datamap", toFsWorkbook(dm_1)]);
+        addToDict(filemap, Assay_datamapFileNameFromIdentifier(a.Identifier), ["ISA_Datamap", toFsWorkbook(dm_1)]);
       }
     }, this$.Assays);
     iterate((w) => {
       ArcWorkflow__set_StaticHash_Z524259A4(w, ArcWorkflow__GetLightHashCode(w));
-      addToDict(workbooks, Workflow_fileNameFromIdentifier(ArcWorkflow__get_Identifier(w)), ["ISA_Workflow", ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E(w)]);
+      addToDict(filemap, Workflow_fileNameFromIdentifier(ArcWorkflow__get_Identifier(w)), ["ISA_Workflow", ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E(w)]);
       if (ArcWorkflow__get_DataMap(w) != null) {
         const dm_2 = value(ArcWorkflow__get_DataMap(w));
         DataMap__set_StaticHash_Z524259A4(dm_2, safeHash(dm_2));
-        addToDict(workbooks, Workflow_datamapFileNameFromIdentifier(ArcWorkflow__get_Identifier(w)), ["ISA_Datamap", toFsWorkbook(dm_2)]);
+        addToDict(filemap, Workflow_datamapFileNameFromIdentifier(ArcWorkflow__get_Identifier(w)), ["ISA_Datamap", toFsWorkbook(dm_2)]);
       }
     }, this$.Workflows);
     iterate((r) => {
       r.StaticHash = r.GetLightHashCode() | 0;
-      addToDict(workbooks, Run_fileNameFromIdentifier(r.Identifier), ["ISA_Run", ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8(r)]);
+      addToDict(filemap, Run_fileNameFromIdentifier(r.Identifier), ["ISA_Run", ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8(r)]);
       if (r.DataMap != null) {
         const dm_3 = value(r.DataMap);
         DataMap__set_StaticHash_Z524259A4(dm_3, safeHash(dm_3));
-        addToDict(workbooks, Run_datamapFileNameFromIdentifier(r.Identifier), ["ISA_Datamap", toFsWorkbook(dm_3)]);
+        addToDict(filemap, Run_datamapFileNameFromIdentifier(r.Identifier), ["ISA_Datamap", toFsWorkbook(dm_3)]);
       }
     }, this$.Runs);
-    return map((fp) => {
-      const matchValue = Dictionary_tryGet(fp, workbooks);
-      if (matchValue == null) {
+    const matchValue = this$.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$1((fp) => {
+      const matchValue_2 = Dictionary_tryGet(fp, filemap);
+      if (matchValue_2 == null) {
         return Contract.createCreate(fp, "PlainText");
       } else {
-        const wb = value(matchValue)[1];
-        const dto = value(matchValue)[0];
+        const wb = value(matchValue_2)[1];
+        const dto = value(matchValue_2)[0];
         return Contract.createCreate(fp, dto, wb);
       }
     }, this$._fs.Tree.ToFilePaths(true));
@@ -491,11 +533,11 @@ class ARC extends ArcInvestigation {
     } else {
       return toArray(delay(() => {
         const hash = this$.GetLightHashCode() | 0;
-        return append$1(this$.StaticHash !== hash ? singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$)) : empty(), delay(() => {
+        return append(this$.StaticHash !== hash ? singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$)) : empty(), delay(() => {
           this$.StaticHash = hash | 0;
-          return append$1(collect((s) => {
+          return append(collect((s) => {
             const hash_1 = s.GetLightHashCode() | 0;
-            return append$1(s.StaticHash === 0 ? ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true) : s.StaticHash !== hash_1 ? singleton(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract(s)) : empty(), delay(() => {
+            return append(s.StaticHash === 0 ? ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true) : s.StaticHash !== hash_1 ? singleton(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract(s)) : empty(), delay(() => {
               let dm_1;
               s.StaticHash = hash_1 | 0;
               const matchValue = s.DataMap;
@@ -515,12 +557,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult) {
                 case 0:
-                  return append$1(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
                     DataMap__set_StaticHash_Z524259A4(dm_2, safeHash(dm_2));
                     return empty();
                   }));
                 case 1:
-                  return append$1(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
                     DataMap__set_StaticHash_Z524259A4(dm_3, safeHash(dm_3));
                     return empty();
                   }));
@@ -529,9 +571,9 @@ class ARC extends ArcInvestigation {
                 }
               }
             }));
-          }, this$.Studies), delay(() => append$1(collect((a) => {
+          }, this$.Studies), delay(() => append(collect((a) => {
             const hash_2 = a.GetLightHashCode() | 0;
-            return append$1(a.StaticHash === 0 ? ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true) : a.StaticHash !== hash_2 ? singleton(ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(a)) : empty(), delay(() => {
+            return append(a.StaticHash === 0 ? ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true) : a.StaticHash !== hash_2 ? singleton(ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(a)) : empty(), delay(() => {
               let dm_5;
               a.StaticHash = hash_2 | 0;
               const matchValue_1 = a.DataMap;
@@ -551,12 +593,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_1) {
                 case 0:
-                  return append$1(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
                     DataMap__set_StaticHash_Z524259A4(dm_6, safeHash(dm_6));
                     return empty();
                   }));
                 case 1:
-                  return append$1(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
                     DataMap__set_StaticHash_Z524259A4(dm_7, safeHash(dm_7));
                     return empty();
                   }));
@@ -565,9 +607,9 @@ class ARC extends ArcInvestigation {
                 }
               }
             }));
-          }, this$.Assays), delay(() => append$1(collect((w) => {
+          }, this$.Assays), delay(() => append(collect((w) => {
             const hash_3 = ArcWorkflow__GetLightHashCode(w) | 0;
-            return append$1(ArcWorkflow__get_StaticHash(w) === 0 ? ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true) : ArcWorkflow__get_StaticHash(w) !== hash_3 ? singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract(w)) : empty(), delay(() => {
+            return append(ArcWorkflow__get_StaticHash(w) === 0 ? ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true) : ArcWorkflow__get_StaticHash(w) !== hash_3 ? singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract(w)) : empty(), delay(() => {
               let dm_9;
               ArcWorkflow__set_StaticHash_Z524259A4(w, hash_3);
               const matchValue_2 = ArcWorkflow__get_DataMap(w);
@@ -587,12 +629,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_2) {
                 case 0:
-                  return append$1(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5(dm_10, ArcWorkflow__get_Identifier(w))), delay(() => {
+                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5(dm_10, ArcWorkflow__get_Identifier(w))), delay(() => {
                     DataMap__set_StaticHash_Z524259A4(dm_10, safeHash(dm_10));
                     return empty();
                   }));
                 case 1:
-                  return append$1(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, ArcWorkflow__get_Identifier(w))), delay(() => {
+                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, ArcWorkflow__get_Identifier(w))), delay(() => {
                     DataMap__set_StaticHash_Z524259A4(dm_11, safeHash(dm_11));
                     return empty();
                   }));
@@ -601,9 +643,9 @@ class ARC extends ArcInvestigation {
                 }
               }
             }));
-          }, this$.Workflows), delay(() => collect((r) => {
+          }, this$.Workflows), delay(() => append(collect((r) => {
             const hash_4 = r.GetLightHashCode() | 0;
-            return append$1(r.StaticHash === 0 ? ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49(r, true) : r.StaticHash !== hash_4 ? singleton(ARCtrl_ArcRun__ArcRun_ToUpdateContract(r)) : empty(), delay(() => {
+            return append(r.StaticHash === 0 ? ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49(r, true) : r.StaticHash !== hash_4 ? singleton(ARCtrl_ArcRun__ArcRun_ToUpdateContract(r)) : empty(), delay(() => {
               let dm_13;
               r.StaticHash = hash_4 | 0;
               const matchValue_3 = r.DataMap;
@@ -623,12 +665,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_3) {
                 case 0:
-                  return append$1(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
                     DataMap__set_StaticHash_Z524259A4(dm_14, safeHash(dm_14));
                     return empty();
                   }));
                 case 1:
-                  return append$1(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
                     DataMap__set_StaticHash_Z524259A4(dm_15, safeHash(dm_15));
                     return empty();
                   }));
@@ -637,7 +679,19 @@ class ARC extends ArcInvestigation {
                 }
               }
             }));
-          }, this$.Runs)))))));
+          }, this$.Runs), delay(() => {
+            const matchValue_4 = this$.License;
+            if (matchValue_4 == null) {
+              return empty();
+            } else {
+              const l = value(matchValue_4);
+              const hash_5 = safeHash(l) | 0;
+              return append(l.StaticHash === 0 ? singleton(l.ToCreateContract()) : l.StaticHash !== hash_5 ? singleton(l.ToUpdateContract()) : empty(), delay(() => {
+                l.StaticHash = hash_5 | 0;
+                return empty();
+              }));
+            }
+          }))))))));
         }));
       }));
     }
@@ -645,7 +699,7 @@ class ARC extends ArcInvestigation {
   GetGitInitContracts(branch, repositoryAddress, defaultGitignore, defaultGitattributes) {
     const defaultGitignore_1 = defaultArg(defaultGitignore, false);
     const defaultGitattributes_1 = defaultArg(defaultGitattributes, false);
-    return toArray(delay(() => append$1(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append$1(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => append$1(defaultGitattributes_1 ? singleton(gitattributesContract) : empty(), delay(() => repositoryAddress != null ? singleton(Init_createAddRemoteContract_Z721C83C5(value(repositoryAddress))) : empty()))))))));
+    return toArray(delay(() => append(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => append(defaultGitattributes_1 ? singleton(gitattributesContract) : empty(), delay(() => repositoryAddress != null ? singleton(Init_createAddRemoteContract_Z721C83C5(value(repositoryAddress))) : empty()))))))));
   }
   static getCloneContract(remoteUrl, merge, branch, token, nolfs) {
     return Clone_createCloneContract_5000466F(remoteUrl, unwrap(merge), unwrap(branch), unwrap(token), unwrap(nolfs));
@@ -701,32 +755,33 @@ class ARC extends ArcInvestigation {
     const nextPublications = ResizeArray_map((c_3) => c_3.Copy(), this$.Publications);
     const nextOntologySourceReferences = ResizeArray_map((c_4) => c_4.Copy(), this$.OntologySourceReferences);
     const nextStudyIdentifiers = Array.from(this$.RegisteredStudyIdentifiers);
+    const nextLicense = map$2((_arg) => _arg.Copy(), this$.License);
     const fsCopy = this$._fs.Copy();
-    return new ARC(this$.Identifier, unwrap(this$.Title), unwrap(this$.Description), unwrap(this$.SubmissionDate), unwrap(this$.PublicReleaseDate), nextOntologySourceReferences, nextPublications, nextContacts, nextAssays, nextStudies, nextWorkflows, nextRuns, nextStudyIdentifiers, nextComments, nextRemarks, this$._cwl, fsCopy);
+    return new ARC(this$.Identifier, unwrap(this$.Title), unwrap(this$.Description), unwrap(this$.SubmissionDate), unwrap(this$.PublicReleaseDate), nextOntologySourceReferences, nextPublications, nextContacts, nextAssays, nextStudies, nextWorkflows, nextRuns, nextStudyIdentifiers, nextComments, nextRemarks, this$._cwl, fsCopy, unwrap(nextLicense));
   }
   GetRegisteredPayload(IgnoreHidden) {
     let tree, paths, array_3;
     const this$ = this;
     const copy = this$.Copy();
     const registeredStudies = copy.Studies.slice();
-    const registeredAssays = concat(map((s) => s.RegisteredAssays.slice(), registeredStudies));
-    const includeFiles = unionMany([ofSeq(["isa.investigation.xlsx", "README.md"], {
+    const registeredAssays = concat(map$1((s) => s.RegisteredAssays.slice(), registeredStudies));
+    const includeFiles = unionMany([ofSeq(toList(delay(() => append(singleton("isa.investigation.xlsx"), delay(() => append(singleton("README.md"), delay(() => this$.License != null ? singleton(value(this$.License).Path) : empty())))))), {
       Compare: comparePrimitives
-    }), unionMany(map((s_1) => {
+    }), unionMany(map$1((s_1) => {
       const studyFoldername = `${"studies"}/${s_1.Identifier}`;
-      return ofSeq(toList(delay(() => append$1(singleton(`${studyFoldername}/${"isa.study.xlsx"}`), delay(() => append$1(singleton(`${studyFoldername}/${"README.md"}`), delay(() => collect((table) => collect((kv) => {
+      return ofSeq(toList(delay(() => append(singleton(`${studyFoldername}/${"isa.study.xlsx"}`), delay(() => append(singleton(`${studyFoldername}/${"README.md"}`), delay(() => collect((table) => collect((kv) => {
         const textValue = kv[1].ToFreeTextCell().AsFreeText;
-        return append$1(singleton(textValue), delay(() => append$1(singleton(`${studyFoldername}/${"resources"}/${textValue}`), delay(() => singleton(`${studyFoldername}/${"protocols"}/${textValue}`)))));
+        return append(singleton(textValue), delay(() => append(singleton(`${studyFoldername}/${"resources"}/${textValue}`), delay(() => singleton(`${studyFoldername}/${"protocols"}/${textValue}`)))));
       }, table.Values), s_1.Tables))))))), {
         Compare: comparePrimitives
       });
     }, registeredStudies), {
       Compare: comparePrimitives
-    }), unionMany(map((a) => {
+    }), unionMany(map$1((a) => {
       const assayFoldername = `${"assays"}/${a.Identifier}`;
-      return ofSeq(toList(delay(() => append$1(singleton(`${assayFoldername}/${"isa.assay.xlsx"}`), delay(() => append$1(singleton(`${assayFoldername}/${"README.md"}`), delay(() => collect((table_1) => collect((kv_1) => {
+      return ofSeq(toList(delay(() => append(singleton(`${assayFoldername}/${"isa.assay.xlsx"}`), delay(() => append(singleton(`${assayFoldername}/${"README.md"}`), delay(() => collect((table_1) => collect((kv_1) => {
         const textValue_1 = kv_1[1].ToFreeTextCell().AsFreeText;
-        return append$1(singleton(textValue_1), delay(() => append$1(singleton(`${assayFoldername}/${"dataset"}/${textValue_1}`), delay(() => singleton(`${assayFoldername}/${"protocols"}/${textValue_1}`)))));
+        return append(singleton(textValue_1), delay(() => append(singleton(`${assayFoldername}/${"dataset"}/${textValue_1}`), delay(() => singleton(`${assayFoldername}/${"protocols"}/${textValue_1}`)))));
       }, table_1.Values), a.Tables))))))), {
         Compare: comparePrimitives
       });
@@ -803,7 +858,7 @@ class ARC extends ArcInvestigation {
       let fileSystem;
       const paths = Array.from(patternInput[1]);
       fileSystem = FileSystem.fromFilePaths(paths);
-      return ARC.fromArcInvestigation(patternInput[0], void 0, fileSystem);
+      return ARC.fromArcInvestigation(patternInput[0], void 0, fileSystem, unwrap(patternInput[2]));
     } catch (ex) {
       const arg_1 = ex.message;
       return toFail(printf("Could not parse ARC-RO-Crate metadata: \n%s"))(arg_1);
@@ -812,20 +867,25 @@ class ARC extends ArcInvestigation {
   ToROCrateJsonString(spaces) {
     const this$ = this;
     this$.MakeDataFilesAbsolute();
-    const value = ROCrate_encoder_B568605(this$, void 0, this$._fs);
+    const value = ROCrate_encoder_1E8A3F74(this$, unwrap(this$._license), this$._fs);
     return toString(defaultSpaces(spaces), value);
   }
   static toROCrateJsonString(spaces) {
     return (obj) => obj.ToROCrateJsonString(unwrap(spaces));
   }
+  GetLicenseWriteContract() {
+    const this$ = this;
+    const _arg = defaultArgWith(this$.License, () => License.GetDefaultLicense());
+    return _arg.ToCreateContract();
+  }
   GetValidationPackagesConfigWriteContract(vpc) {
     const this$ = this;
     const paths = this$.FileSystem.Tree.ToFilePaths();
-    if (!contains$1(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
+    if (!contains$2(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
       Equals: (x, y) => x === y,
       GetHashCode: stringHash
     })) {
-      const filePaths = append([ValidationPackagesConfigHelper_ConfigFilePath], paths);
+      const filePaths = append$1([ValidationPackagesConfigHelper_ConfigFilePath], paths);
       this$.SetFilePaths(filePaths);
     }
     return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toCreateContract_Static_724DAE55(vpc);
@@ -833,14 +893,14 @@ class ARC extends ArcInvestigation {
   GetValidationPackagesConfigDeleteContract(vpc) {
     const this$ = this;
     const paths = this$.FileSystem.Tree.ToFilePaths();
-    if (contains$1(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
+    if (contains$2(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
       Equals: (x, y) => x === y,
       GetHashCode: stringHash
     })) {
       const filePaths = paths.filter((p) => !(p === ValidationPackagesConfigHelper_ConfigFilePath));
       this$.SetFilePaths(filePaths);
     }
-    return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toDeleteContract_Static_724DAE55();
+    return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toDeleteContract_Static_724DAE55(vpc);
   }
   GetValidationPackagesConfigReadContract() {
     return ValidationPackagesConfigHelper_ReadContract;
@@ -856,6 +916,12 @@ class ARC extends ArcInvestigation {
     return this$.FileSystem.Tree.ToFilePaths(unwrap(removeRoot));
   }
 }
+function ARC_$reflection() {
+  return class_type("ARCtrl.ARC", void 0, ARC, ArcInvestigation_$reflection());
+}
+function ARC_$ctor_Z4D7EB22(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, cwl, fs, license) {
+  return new ARC(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, cwl, fs, license);
+}
 function ARCAux_getArcAssaysFromContracts(contracts) {
   return choose(ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, contracts);
 }
@@ -889,26 +955,39 @@ function ARCAux_getArcInvestigationFromContracts(contracts) {
     return toFail(printf("Could not find investigation in contracts. Expected exactly one investigation, but found %d."))(arg);
   }
 }
-function ARCAux_updateFSByISA(isa, fs) {
+function ARCAux_getLicenseFromContracts(contracts) {
+  return tryPick((c) => License.tryFromReadContract(c), contracts);
+}
+function ARCAux_updateFSByARC(isa, license, fs) {
   let assaysFolder;
-  const assays = map((a) => FileSystemTree.createAssayFolder(a.Identifier, a.DataMap != null), toArray(isa.Assays));
+  const assays = map$1((a) => FileSystemTree.createAssayFolder(a.Identifier, a.DataMap != null), toArray(isa.Assays));
   assaysFolder = FileSystemTree.createAssaysFolder(assays);
   let studiesFolder;
-  const studies = map((s) => FileSystemTree.createStudyFolder(s.Identifier, s.DataMap != null), toArray(isa.Studies));
+  const studies = map$1((s) => FileSystemTree.createStudyFolder(s.Identifier, s.DataMap != null), toArray(isa.Studies));
   studiesFolder = FileSystemTree.createStudiesFolder(studies);
   let workflowsFolder;
-  const workflows = map((w) => FileSystemTree.createWorkflowFolder(ArcWorkflow__get_Identifier(w), ArcWorkflow__get_DataMap(w) != null), toArray(isa.Workflows));
+  const workflows = map$1((w) => FileSystemTree.createWorkflowFolder(ArcWorkflow__get_Identifier(w), ArcWorkflow__get_DataMap(w) != null), toArray(isa.Workflows));
   workflowsFolder = FileSystemTree.createWorkflowsFolder(workflows);
   let runsFolder;
-  const runs = map((r) => FileSystemTree.createRunFolder(r.Identifier, r.DataMap != null), toArray(isa.Runs));
+  const runs = map$1((r) => FileSystemTree.createRunFolder(r.Identifier, r.DataMap != null), toArray(isa.Runs));
   runsFolder = FileSystemTree.createRunsFolder(runs);
   const investigation = FileSystemTree.createInvestigationFile();
   let tree_1;
-  const tree = FileSystemTree.createRootFolder([investigation, assaysFolder, studiesFolder, workflowsFolder, runsFolder]);
+  const tree = FileSystemTree.createRootFolder(toArray(delay(() => append(singleton(investigation), delay(() => append(singleton(assaysFolder), delay(() => append(singleton(studiesFolder), delay(() => append(singleton(workflowsFolder), delay(() => append(singleton(runsFolder), delay(() => license != null ? singleton(FileSystemTree_File(value(license).Path)) : empty())))))))))))));
+  tree_1 = FileSystem.create({
+    tree
+  });
+  return fs.Union(tree_1);
+}
+function ARCAux_updateFSByCWL(cwl, fs) {
+  const workflows = FileSystemTree.createWorkflowsFolder([]);
+  const runs = FileSystemTree.createRunsFolder([]);
+  let tree_1;
+  const tree = FileSystemTree.createRootFolder([workflows, runs]);
   tree_1 = FileSystem.create({
     tree
   });
   return fs.Union(tree_1);
 }
 
-export { ARC, ARCAux_getArcAssaysFromContracts, ARCAux_getArcInvestigationFromContracts, ARCAux_getArcRunsFromContracts, ARCAux_getArcStudiesFromContracts, ARCAux_getArcWorkflowsFromContracts, ARCAux_getAssayDataMapFromContracts, ARCAux_getRunDataMapFromContracts, ARCAux_getStudyDataMapFromContracts, ARCAux_getWorkflowDataMapFromContracts, ARCAux_updateFSByISA };
+export { ARC, ARCAux_getArcAssaysFromContracts, ARCAux_getArcInvestigationFromContracts, ARCAux_getArcRunsFromContracts, ARCAux_getArcStudiesFromContracts, ARCAux_getArcWorkflowsFromContracts, ARCAux_getAssayDataMapFromContracts, ARCAux_getLicenseFromContracts, ARCAux_getRunDataMapFromContracts, ARCAux_getStudyDataMapFromContracts, ARCAux_getWorkflowDataMapFromContracts, ARCAux_updateFSByARC, ARCAux_updateFSByCWL, ARC_$ctor_Z4D7EB22, ARC_$reflection };