@nfdi4plants/arctrl 3.0.0-beta.8 → 3.0.0

package/dist/ts/ts/ARC.js

@@ -1,5 +1,5 @@
 import { FileSystem } from './FileSystem/FileSystem.js';
-import { unwrap, defaultArg, value, map as map$2, bind, defaultArgWith } from '../node_modules/@fable-org/fable-library-js/Option.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 { fullFillContractBatchAsync } from './ContractIO/ContractIO.js';
@@ -8,55 +8,56 @@ 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, map, 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, 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, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath } from './FileSystem/Path.js';
+import { getAssayFolderPath, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath, 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 { ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from './Contract/ArcStudy.js';
-import { ARCtrl_ArcRun__ArcRun_ToDeleteContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F } from './Contract/ArcRun.js';
-import { ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F } from './Contract/ArcWorkflow.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 { 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 { 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 { 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 { 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_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_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 { 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_1E8A3F74 } from './ROCrateIO.js';
+import { ROCrate_get_decoderDeprecated, ROCrate_get_decoder, ROCrate_encoder_Z7FE34C43 } 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 { ofInvestigation } from './WorkflowGraph/Adapters.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';
+import { Decode_decodeCWLProcessingUnit } from './CWL/Decode.js';
 
 class ARC extends ArcInvestigation {
-  constructor(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, cwl, fs, license) {
+  constructor(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, 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$.contents = this;
-    this._cwl = cwl;
     this._license = license;
     this._fs = (fs_1 = defaultArg(fs, FileSystem.create({
       tree: FileSystemTree_Folder("", [])
     })), ARCAux_updateFSByARC(this$.contents, license, fs_1));
-    this["init@104"] = 1;
+    this["init@133"] = 1;
   }
   get FileSystem() {
     const this$ = this;
@@ -74,8 +75,8 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     this$._license = license;
   }
-  static fromArcInvestigation(isa, cwl, fs, license) {
-    return new ARC(isa.Identifier, unwrap(isa.Title), unwrap(isa.Description), unwrap(isa.SubmissionDate), unwrap(isa.PublicReleaseDate), isa.OntologySourceReferences, isa.Publications, isa.Contacts, isa.Assays, isa.Studies, isa.Workflows, isa.Runs, isa.RegisteredStudyIdentifiers, isa.Comments, isa.Remarks, cwl, unwrap(fs), unwrap(license));
+  static fromArcInvestigation(isa, fs, license) {
+    return new ARC(isa.Identifier, unwrap(isa.Title), unwrap(isa.Description), unwrap(isa.SubmissionDate), unwrap(isa.PublicReleaseDate), isa.OntologySourceReferences, isa.Publications, isa.Contacts, isa.Assays, isa.Studies, isa.Workflows, isa.Runs, isa.RegisteredStudyIdentifiers, isa.Comments, isa.Remarks, unwrap(fs), unwrap(license));
   }
   TryWriteAsync(arcPath) {
     const this$ = this;
@@ -136,7 +137,7 @@ class ARC extends ArcInvestigation {
     const assayFolderPath = getAssayFolderPath(assayIdentifier);
     const filteredPaths = paths.filter((p) => !p.startsWith(assayFolderPath));
     this$.SetFilePaths(filteredPaths);
-    return toArray(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append(singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$)), delay(() => map(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
+    return toArray(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => this$.GetUpdateContracts()))));
   }
   GetRunRemoveContracts(runIdentifier) {
     const this$ = this;
@@ -152,7 +153,7 @@ class ARC extends ArcInvestigation {
     const runFolderPath = getRunFolderPath(runIdentifier);
     const filteredPaths = paths.filter((p) => !p.startsWith(runFolderPath));
     this$.SetFilePaths(filteredPaths);
-    return [ARCtrl_ArcRun__ArcRun_ToDeleteContract(run), ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$)];
+    return toArray(delay(() => append(singleton(ARCtrl_ArcRun__ArcRun_ToDeleteContract(run)), delay(() => this$.GetUpdateContracts()))));
   }
   GetWorkflowRemoveContracts(workflowIdentifier) {
     const this$ = this;
@@ -168,12 +169,84 @@ class ARC extends ArcInvestigation {
     const workflowFolderPath = getWorkflowFolderPath(workflowIdentifier);
     const filteredPaths = paths.filter((p) => !p.startsWith(workflowFolderPath));
     this$.SetFilePaths(filteredPaths);
-    return [ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract(workflow), ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$)];
+    return toArray(delay(() => append(singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract(workflow)), delay(() => this$.GetUpdateContracts()))));
   }
   TryRemoveAssayAsync(arcPath, assayIdentifier) {
     const this$ = this;
     return fullFillContractBatchAsync(arcPath, this$.GetAssayRemoveContracts(assayIdentifier));
   }
+  TryRemoveRunAsync(arcPath, runIdentifier) {
+    const this$ = this;
+    return fullFillContractBatchAsync(arcPath, this$.GetRunRemoveContracts(runIdentifier));
+  }
+  TryRemoveWorkflowAsync(arcPath, workflowIdentifier) {
+    const this$ = this;
+    return fullFillContractBatchAsync(arcPath, this$.GetWorkflowRemoveContracts(workflowIdentifier));
+  }
+  RemoveRunAsync(arcPath, runIdentifier) {
+    const this$ = this;
+    return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryRemoveRunAsync(arcPath, runIdentifier).then((_arg) => {
+      const result = _arg;
+      if (result.tag === /* Error */
+      1) {
+        const appended = join("\n", map((e) => e, result.fields[0]));
+        toFail(printf("Could not remove run, failed with the following errors %s"))(appended);
+        return Promise.resolve();
+      } else {
+        return Promise.resolve();
+      }
+    })));
+  }
+  RemoveWorkflowAsync(arcPath, workflowIdentifier) {
+    const this$ = this;
+    return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryRemoveWorkflowAsync(arcPath, workflowIdentifier).then((_arg) => {
+      const result = _arg;
+      if (result.tag === /* Error */
+      1) {
+        const appended = join("\n", map((e) => e, result.fields[0]));
+        toFail(printf("Could not remove workflow, failed with the following errors %s"))(appended);
+        return Promise.resolve();
+      } else {
+        return Promise.resolve();
+      }
+    })));
+  }
+  TryRenameRunAsync(arcPath, oldRunIdentifier, newRunIdentifier) {
+    const this$ = this;
+    return fullFillContractBatchAsync(arcPath, this$.GetRunRenameContracts(oldRunIdentifier, newRunIdentifier));
+  }
+  TryRenameWorkflowAsync(arcPath, oldWorkflowIdentifier, newWorkflowIdentifier) {
+    const this$ = this;
+    return fullFillContractBatchAsync(arcPath, this$.GetWorkflowRenameContracts(oldWorkflowIdentifier, newWorkflowIdentifier));
+  }
+  RenameRunAsync(arcPath, oldRunIdentifier, newRunIdentifier) {
+    const this$ = this;
+    return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryRenameRunAsync(arcPath, oldRunIdentifier, newRunIdentifier).then((_arg) => {
+      const result = _arg;
+      if (result.tag === /* Error */
+      1) {
+        const appended = join("\n", map((e) => e, result.fields[0]));
+        toFail(printf("Could not rename run, failed with the following errors %s"))(appended);
+        return Promise.resolve();
+      } else {
+        return Promise.resolve();
+      }
+    })));
+  }
+  RenameWorkflowAsync(arcPath, oldWorkflowIdentifier, newWorkflowIdentifier) {
+    const this$ = this;
+    return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryRenameWorkflowAsync(arcPath, oldWorkflowIdentifier, newWorkflowIdentifier).then((_arg) => {
+      const result = _arg;
+      if (result.tag === /* Error */
+      1) {
+        const appended = join("\n", map((e) => e, result.fields[0]));
+        toFail(printf("Could not rename workflow, failed with the following errors %s"))(appended);
+        return Promise.resolve();
+      } else {
+        return Promise.resolve();
+      }
+    })));
+  }
   GetAssayRenameContracts(oldAssayIdentifier, newAssayIdentifier) {
     const this$ = this;
     if (!contains(oldAssayIdentifier, this$.AssayIdentifiers, {
@@ -186,7 +259,7 @@ class ARC extends ArcInvestigation {
     const paths = this$.FileSystem.Tree.ToFilePaths();
     const oldAssayFolderPath = getAssayFolderPath(oldAssayIdentifier);
     const newAssayFolderPath = getAssayFolderPath(newAssayIdentifier);
-    const renamedPaths = map$1((p) => replace(p, oldAssayFolderPath, newAssayFolderPath), paths);
+    const renamedPaths = map((p) => replace(p, oldAssayFolderPath, newAssayFolderPath), paths);
     this$.SetFilePaths(renamedPaths);
     return toArray(delay(() => append(singleton(Contract.createRename(oldAssayFolderPath, newAssayFolderPath)), delay(() => this$.GetUpdateContracts()))));
   }
@@ -198,27 +271,27 @@ class ARC extends ArcInvestigation {
     })) {
       throw new Error("ARC does not contain run with given name");
     }
-    this$.RenameRun(oldRunIdentifier, newRunIdentifier);
+    super.RenameRun(oldRunIdentifier, newRunIdentifier);
     const paths = this$.FileSystem.Tree.ToFilePaths();
     const oldPath = getRunFolderPath(oldRunIdentifier);
     const newPath = getRunFolderPath(newRunIdentifier);
-    const renamedPaths = map$1((p) => replace(p, oldPath, newPath), paths);
+    const renamedPaths = map((p) => replace(p, oldPath, newPath), paths);
     this$.SetFilePaths(renamedPaths);
     return toArray(delay(() => append(singleton(Contract.createRename(oldPath, newPath)), delay(() => this$.GetUpdateContracts()))));
   }
-  GetWorkflowRenameContracts(oldRunIdentifier, newRunIdentifier) {
+  GetWorkflowRenameContracts(oldWorkflowIdentifier, newWorkflowIdentifier) {
     const this$ = this;
-    if (!contains(oldRunIdentifier, this$.WorkflowIdentifiers, {
+    if (!contains(oldWorkflowIdentifier, this$.WorkflowIdentifiers, {
       Equals: (x, y) => x === y,
       GetHashCode: stringHash
     })) {
-      throw new Error("ARC does not contain run with given name");
+      throw new Error("ARC does not contain workflow with given name");
     }
-    this$.RenameWorkflow(oldRunIdentifier, newRunIdentifier);
+    super.RenameWorkflow(oldWorkflowIdentifier, newWorkflowIdentifier);
     const paths = this$.FileSystem.Tree.ToFilePaths();
-    const oldPath = getWorkflowFolderPath(oldRunIdentifier);
-    const newPath = getWorkflowFolderPath(newRunIdentifier);
-    const renamedPaths = map$1((p) => replace(p, oldPath, newPath), paths);
+    const oldPath = getWorkflowFolderPath(oldWorkflowIdentifier);
+    const newPath = getWorkflowFolderPath(newWorkflowIdentifier);
+    const renamedPaths = map((p) => replace(p, oldPath, newPath), paths);
     this$.SetFilePaths(renamedPaths);
     return toArray(delay(() => append(singleton(Contract.createRename(oldPath, newPath)), delay(() => this$.GetUpdateContracts()))));
   }
@@ -251,7 +324,7 @@ class ARC extends ArcInvestigation {
     const paths = this$.FileSystem.Tree.ToFilePaths();
     const oldStudyFolderPath = getStudyFolderPath(oldStudyIdentifier);
     const newStudyFolderPath = getStudyFolderPath(newStudyIdentifier);
-    const renamedPaths = map$1((p) => replace(p, oldStudyFolderPath, newStudyFolderPath), paths);
+    const renamedPaths = map((p) => replace(p, oldStudyFolderPath, newStudyFolderPath), paths);
     this$.SetFilePaths(renamedPaths);
     return toArray(delay(() => append(singleton(Contract.createRename(oldStudyFolderPath, newStudyFolderPath)), delay(() => this$.GetUpdateContracts()))));
   }
@@ -265,7 +338,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map$1((e) => e, result.fields[0]));
+        const appended = join("\n", map((e) => e, result.fields[0]));
         toFail(printf("Could not write ARC, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -279,7 +352,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map$1((e) => e, result.fields[0]));
+        const appended = join("\n", map((e) => e, result.fields[0]));
         toFail(printf("Could not update ARC, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -293,7 +366,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map$1((e) => e, result.fields[0]));
+        const appended = join("\n", map((e) => e, result.fields[0]));
         toFail(printf("Could not remove assay, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -307,7 +380,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map$1((e) => e, result.fields[0]));
+        const appended = join("\n", map((e) => e, result.fields[0]));
         toFail(printf("Could not rename assay, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -321,7 +394,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map$1((e) => e, result.fields[0]));
+        const appended = join("\n", map((e) => e, result.fields[0]));
         toFail(printf("Could not remove study, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -335,7 +408,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map$1((e) => e, result.fields[0]));
+        const appended = join("\n", map((e) => e, result.fields[0]));
         toFail(printf("Could not rename study, failed with the following errors %s"))(appended);
         return Promise.resolve();
       } else {
@@ -348,7 +421,7 @@ class ARC extends ArcInvestigation {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
-        const appended = join("\n", map$1((e) => e, result.fields[0]));
+        const appended = join("\n", map((e) => e, result.fields[0]));
         toFail(printf("Could not load ARC, failed with the following errors %s"))(appended);
         return Promise.resolve(new ARC(createMissingIdentifier()));
       } else {
@@ -395,34 +468,34 @@ class ARC extends ArcInvestigation {
       updateColumnOption(dataNameFunction_1, t.TryGetInputColumn());
       updateColumnOption(dataNameFunction_1, t.TryGetOutputColumn());
     };
-    const updateDataMap = (dataNameFunction_2, dm) => {
+    const updateDatamap = (dataNameFunction_2, dm) => {
       iterate((c_1) => {
         if (c_1.FilePath != null) {
           const newFilePath_1 = dataNameFunction_2(c_1);
           c_1.FilePath = newFilePath_1;
         }
-      }, DataMap__get_DataContexts(dm));
+      }, dm.DataContexts);
     };
     iterate((s) => {
       const f_1 = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
       const source_1 = s.Tables;
       iterate(curry2(updateTable)(f_1), source_1);
-      if (s.DataMap != null) {
-        updateDataMap(f_1, value(s.DataMap));
+      if (s.Datamap != null) {
+        updateDatamap(f_1, value(s.Datamap));
       }
     }, this$.Studies);
     iterate((a_1) => {
       const f_2 = (d_1) => d_1.GetAbsolutePathForAssay(a_1.Identifier, checkExistenceFromRoot);
       const source_3 = a_1.Tables;
       iterate(curry2(updateTable)(f_2), source_3);
-      if (a_1.DataMap != null) {
-        updateDataMap(f_2, value(a_1.DataMap));
+      if (a_1.Datamap != null) {
+        updateDatamap(f_2, value(a_1.Datamap));
       }
     }, this$.Assays);
   }
   static fromFilePaths(filePaths) {
     const fs = FileSystem.fromFilePaths(filePaths);
-    return new ARC(createMissingIdentifier(), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, fs);
+    return new ARC(createMissingIdentifier(), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, fs);
   }
   SetFilePaths(filePaths) {
     const this$ = this;
@@ -447,11 +520,13 @@ class ARC extends ArcInvestigation {
     this$.Comments = investigation.Comments;
     this$.Remarks = investigation.Remarks;
     this$.RegisteredStudyIdentifiers = investigation.RegisteredStudyIdentifiers;
-    const studies = map$1((tuple) => tuple[0], ARCAux_getArcStudiesFromContracts(contracts));
+    const studies = map((tuple) => tuple[0], ARCAux_getArcStudiesFromContracts(contracts));
     const assays = ARCAux_getArcAssaysFromContracts(contracts);
     const workflows = ARCAux_getArcWorkflowsFromContracts(contracts);
     const runs = ARCAux_getArcRunsFromContracts(contracts);
     const license = ARCAux_getLicenseFromContracts(contracts);
+    const cwlByPath = ARCAux_getCWLByPathFromContracts(contracts);
+    const tryGetCWLByPath = (path) => ARCAux_tryGetCWLByPath(cwlByPath, path);
     const array_2 = this$.AssayIdentifiers;
     array_2.forEach((ai) => {
       if (!assays.some((a) => a.Identifier === ai)) {
@@ -472,9 +547,9 @@ class ARC extends ArcInvestigation {
         const registeredStudy = value(registeredStudyOpt);
         registeredStudy.UpdateReferenceByStudyFile(study, true);
       }
-      const datamap = ARCAux_getStudyDataMapFromContracts(study.Identifier, contracts);
-      if (study.DataMap == null) {
-        study.DataMap = datamap;
+      const datamap = ARCAux_getStudyDatamapFromContracts(study.Identifier, contracts);
+      if (study.Datamap == null) {
+        study.Datamap = datamap;
       }
       study.StaticHash = study.GetLightHashCode() | 0;
     });
@@ -490,25 +565,35 @@ class ARC extends ArcInvestigation {
       let updatedTables;
       const array_6 = assay_1.StudiesRegisteredIn;
       updatedTables = fold((tables, study_1) => ArcTables.updateReferenceTablesBySheets(new ArcTables(study_1.Tables), tables, false), new ArcTables(assay_1.Tables), array_6);
-      const datamap_1 = ARCAux_getAssayDataMapFromContracts(assay_1.Identifier, contracts);
-      if (assay_1.DataMap == null) {
-        assay_1.DataMap = datamap_1;
+      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(workflow.Identifier, contracts);
-      if (workflow.DataMap == null) {
-        workflow.DataMap = datamap_2;
+      const datamap_2 = ARCAux_getWorkflowDatamapFromContracts(workflow.Identifier, contracts);
+      const cwl = ARCAux_getWorkflowCWLFromContracts(workflow.Identifier, contracts);
+      const cwlFilePath = Workflow_cwlFileNameFromIdentifier(workflow.Identifier);
+      const resolvedCwl = map$1((processingUnit) => resolveRunReferencesFromLookup(cwlFilePath, processingUnit, tryGetCWLByPath), cwl);
+      if (workflow.Datamap == null) {
+        workflow.Datamap = datamap_2;
       }
+      workflow.CWLDescription = resolvedCwl;
       this$.AddWorkflow(workflow);
       workflow.StaticHash = workflow.GetLightHashCode() | 0;
     });
     runs.forEach((run) => {
-      const datamap_3 = ARCAux_getRunDataMapFromContracts(run.Identifier, contracts);
-      if (run.DataMap == null) {
-        run.DataMap = datamap_3;
+      const datamap_3 = ARCAux_getRunDatamapFromContracts(run.Identifier, contracts);
+      const cwl_1 = ARCAux_getRunCWLFromContracts(run.Identifier, contracts);
+      const yml = ARCAux_getRunYMLFromContracts(run.Identifier, contracts);
+      const cwlFilePath_1 = Run_cwlFileNameFromIdentifier(run.Identifier);
+      const resolvedCwl_1 = map$1((processingUnit_1) => resolveRunReferencesFromLookup(cwlFilePath_1, processingUnit_1, tryGetCWLByPath), cwl_1);
+      if (run.Datamap == null) {
+        run.Datamap = datamap_3;
       }
+      run.CWLInput = defaultArg(yml, []);
+      run.CWLDescription = resolvedCwl_1;
       this$.AddRun(run);
       run.StaticHash = run.GetLightHashCode() | 0;
     });
@@ -537,36 +622,45 @@ class ARC extends ArcInvestigation {
     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);
-        DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
+      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$.Studies);
     iterate((a) => {
       a.StaticHash = a.GetLightHashCode() | 0;
       addToDict(filemap, Assay_fileNameFromIdentifier(a.Identifier), ["ISA_Assay", ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(a)]);
-      if (a.DataMap != null) {
-        const dm_1 = value(a.DataMap);
-        DataMap__set_StaticHash_Z524259A4(dm_1, safeHash(dm_1));
+      if (a.Datamap != null) {
+        const dm_1 = value(a.Datamap);
+        dm_1.StaticHash = safeHash(dm_1) | 0;
         addToDict(filemap, Assay_datamapFileNameFromIdentifier(a.Identifier), ["ISA_Datamap", toFsWorkbook(dm_1)]);
       }
     }, this$.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.DataMap != null) {
-        const dm_2 = value(w.DataMap);
-        DataMap__set_StaticHash_Z524259A4(dm_2, safeHash(dm_2));
+      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$.Workflows);
     iterate((r) => {
       r.StaticHash = r.GetLightHashCode() | 0;
       addToDict(filemap, Run_fileNameFromIdentifier(r.Identifier), ["ISA_Run", ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8(r)]);
-      if (r.DataMap != null) {
-        const dm_3 = value(r.DataMap);
-        DataMap__set_StaticHash_Z524259A4(dm_3, safeHash(dm_3));
+      if (r.CWLDescription != null) {
+        throw new Error("Not implemented yet: CWL description in ARC.GetWriteContracts");
+      }
+      if (r.CWLInput.length > 0) {
+        throw new Error("Not implemented yet: CWL YAML input in ARC.GetWriteContracts");
+      }
+      if (r.Datamap != null) {
+        const dm_3 = value(r.Datamap);
+        dm_3.StaticHash = safeHash(dm_3) | 0;
         addToDict(filemap, Run_datamapFileNameFromIdentifier(r.Identifier), ["ISA_Datamap", toFsWorkbook(dm_3)]);
       }
     }, this$.Runs);
@@ -578,7 +672,7 @@ class ARC extends ArcInvestigation {
       l.StaticHash = safeHash(l) | 0;
       addToDict(filemap, l.Path, ["PlainText", l.Content]);
     }
-    return map$1((fp) => {
+    return map((fp) => {
       const matchValue_2 = Dictionary_tryGet(fp, filemap);
       if (matchValue_2 == null) {
         return Contract.createCreate(fp, "PlainText");
@@ -602,15 +696,15 @@ class ARC extends ArcInvestigation {
           return append(collect((s) => {
             const hash_1 = s.GetLightHashCode() | 0;
             return append(s.StaticHash === 0 ? ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true) : s.StaticHash !== hash_1 ? singleton(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract(s)) : empty(), delay(() => {
-              let dm_1;
+              let dm, dm_1;
               s.StaticHash = hash_1 | 0;
-              const matchValue = s.DataMap;
+              const matchValue = s.Datamap;
               let matchResult, dm_2, dm_3;
               if (matchValue != null) {
-                if (DataMap__get_StaticHash(value(matchValue)) === 0) {
+                if (dm = value(matchValue), dm.StaticHash === 0) {
                   matchResult = 0;
                   dm_2 = value(matchValue);
-                } else if (dm_1 = value(matchValue), DataMap__get_StaticHash(dm_1) !== safeHash(dm_1)) {
+                } else if (dm_1 = value(matchValue), dm_1.StaticHash !== safeHash(dm_1)) {
                   matchResult = 1;
                   dm_3 = value(matchValue);
                 } else {
@@ -621,13 +715,13 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
-                    DataMap__set_StaticHash_Z524259A4(dm_2, safeHash(dm_2));
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
+                    dm_2.StaticHash = safeHash(dm_2) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
-                    DataMap__set_StaticHash_Z524259A4(dm_3, safeHash(dm_3));
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
+                    dm_3.StaticHash = safeHash(dm_3) | 0;
                     return empty();
                   }));
                 default: {
@@ -638,15 +732,15 @@ class ARC extends ArcInvestigation {
           }, this$.Studies), delay(() => append(collect((a) => {
             const hash_2 = a.GetLightHashCode() | 0;
             return append(a.StaticHash === 0 ? ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true) : a.StaticHash !== hash_2 ? singleton(ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(a)) : empty(), delay(() => {
-              let dm_5;
+              let dm_4, dm_5;
               a.StaticHash = hash_2 | 0;
-              const matchValue_1 = a.DataMap;
+              const matchValue_1 = a.Datamap;
               let matchResult_1, dm_6, dm_7;
               if (matchValue_1 != null) {
-                if (DataMap__get_StaticHash(value(matchValue_1)) === 0) {
+                if (dm_4 = value(matchValue_1), dm_4.StaticHash === 0) {
                   matchResult_1 = 0;
                   dm_6 = value(matchValue_1);
-                } else if (dm_5 = value(matchValue_1), DataMap__get_StaticHash(dm_5) !== safeHash(dm_5)) {
+                } else if (dm_5 = value(matchValue_1), dm_5.StaticHash !== safeHash(dm_5)) {
                   matchResult_1 = 1;
                   dm_7 = value(matchValue_1);
                 } else {
@@ -657,13 +751,13 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_1) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
-                    DataMap__set_StaticHash_Z524259A4(dm_6, safeHash(dm_6));
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
+                    dm_6.StaticHash = safeHash(dm_6) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
-                    DataMap__set_StaticHash_Z524259A4(dm_7, safeHash(dm_7));
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
+                    dm_7.StaticHash = safeHash(dm_7) | 0;
                     return empty();
                   }));
                 default: {
@@ -674,15 +768,15 @@ class ARC extends ArcInvestigation {
           }, this$.Assays), delay(() => append(collect((w) => {
             const hash_3 = w.GetLightHashCode() | 0;
             return append(w.StaticHash === 0 ? ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true) : w.StaticHash !== hash_3 ? singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract(w)) : empty(), delay(() => {
-              let dm_9;
+              let dm_8, dm_9;
               w.StaticHash = hash_3 | 0;
-              const matchValue_2 = w.DataMap;
+              const matchValue_2 = w.Datamap;
               let matchResult_2, dm_10, dm_11;
               if (matchValue_2 != null) {
-                if (DataMap__get_StaticHash(value(matchValue_2)) === 0) {
+                if (dm_8 = value(matchValue_2), dm_8.StaticHash === 0) {
                   matchResult_2 = 0;
                   dm_10 = value(matchValue_2);
-                } else if (dm_9 = value(matchValue_2), DataMap__get_StaticHash(dm_9) !== safeHash(dm_9)) {
+                } else if (dm_9 = value(matchValue_2), dm_9.StaticHash !== safeHash(dm_9)) {
                   matchResult_2 = 1;
                   dm_11 = value(matchValue_2);
                 } else {
@@ -693,13 +787,13 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_2) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5(dm_10, w.Identifier)), delay(() => {
-                    DataMap__set_StaticHash_Z524259A4(dm_10, safeHash(dm_10));
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5(dm_10, w.Identifier)), delay(() => {
+                    dm_10.StaticHash = safeHash(dm_10) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, w.Identifier)), delay(() => {
-                    DataMap__set_StaticHash_Z524259A4(dm_11, safeHash(dm_11));
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, w.Identifier)), delay(() => {
+                    dm_11.StaticHash = safeHash(dm_11) | 0;
                     return empty();
                   }));
                 default: {
@@ -710,15 +804,15 @@ class ARC extends ArcInvestigation {
           }, this$.Workflows), delay(() => append(collect((r) => {
             const hash_4 = r.GetLightHashCode() | 0;
             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;
+              let dm_12, dm_13;
               r.StaticHash = hash_4 | 0;
-              const matchValue_3 = r.DataMap;
+              const matchValue_3 = r.Datamap;
               let matchResult_3, dm_14, dm_15;
               if (matchValue_3 != null) {
-                if (DataMap__get_StaticHash(value(matchValue_3)) === 0) {
+                if (dm_12 = value(matchValue_3), dm_12.StaticHash === 0) {
                   matchResult_3 = 0;
                   dm_14 = value(matchValue_3);
-                } else if (dm_13 = value(matchValue_3), DataMap__get_StaticHash(dm_13) !== safeHash(dm_13)) {
+                } else if (dm_13 = value(matchValue_3), dm_13.StaticHash !== safeHash(dm_13)) {
                   matchResult_3 = 1;
                   dm_15 = value(matchValue_3);
                 } else {
@@ -729,13 +823,13 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_3) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
-                    DataMap__set_StaticHash_Z524259A4(dm_14, safeHash(dm_14));
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
+                    dm_14.StaticHash = safeHash(dm_14) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
-                    DataMap__set_StaticHash_Z524259A4(dm_15, safeHash(dm_15));
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
+                    dm_15.StaticHash = safeHash(dm_15) | 0;
                     return empty();
                   }));
                 default: {
@@ -820,19 +914,19 @@ 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 nextLicense = map$1((_arg) => _arg.Copy(), this$.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$._cwl, fsCopy, unwrap(nextLicense));
+    return new ARC(this$.Identifier, unwrap(this$.Title), unwrap(this$.Description), unwrap(this$.SubmissionDate), unwrap(this$.PublicReleaseDate), nextOntologySourceReferences, nextPublications, nextContacts, nextAssays, nextStudies, nextWorkflows, nextRuns, nextStudyIdentifiers, nextComments, nextRemarks, 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$1((s) => s.RegisteredAssays.slice(), registeredStudies));
+    const registeredAssays = concat(map((s) => s.RegisteredAssays.slice(), registeredStudies));
     const includeFiles = unionMany([ofSeq(toList(delay(() => append(singleton("isa.investigation.xlsx"), delay(() => append(singleton("README.md"), delay(() => this$.License != null ? singleton(value(this$.License).Path) : empty())))))), {
       Compare: comparePrimitives
-    }), unionMany(map$1((s_1) => {
+    }), unionMany(map((s_1) => {
       const studyFoldername = `${"studies"}/${s_1.Identifier}`;
       return ofSeq(toList(delay(() => append(singleton(`${studyFoldername}/${"isa.study.xlsx"}`), delay(() => append(singleton(`${studyFoldername}/${"README.md"}`), delay(() => collect((table) => collect((kv) => {
         const textValue = kv[1].ToFreeTextCell().AsFreeText;
@@ -842,7 +936,7 @@ class ARC extends ArcInvestigation {
       });
     }, registeredStudies), {
       Compare: comparePrimitives
-    }), unionMany(map$1((a) => {
+    }), unionMany(map((a) => {
       const assayFoldername = `${"assays"}/${a.Identifier}`;
       return ofSeq(toList(delay(() => append(singleton(`${assayFoldername}/${"isa.assay.xlsx"}`), delay(() => append(singleton(`${assayFoldername}/${"README.md"}`), delay(() => collect((table_1) => collect((kv_1) => {
         const textValue_1 = kv_1[1].ToFreeTextCell().AsFreeText;
@@ -923,20 +1017,20 @@ class ARC extends ArcInvestigation {
       let fileSystem;
       const paths = Array.from(patternInput[1]);
       fileSystem = FileSystem.fromFilePaths(paths);
-      return ARC.fromArcInvestigation(patternInput[0], void 0, fileSystem, unwrap(patternInput[2]));
+      return ARC.fromArcInvestigation(patternInput[0], fileSystem, unwrap(patternInput[2]));
     } catch (ex) {
       const arg_1 = ex.message;
       return toFail(printf("Could not parse ARC-RO-Crate metadata: \n%s"))(arg_1);
     }
   }
-  ToROCrateJsonString(spaces) {
+  ToROCrateJsonString(spaces, ignoreBrokenWR) {
     const this$ = this;
     this$.MakeDataFilesAbsolute();
-    const value = ROCrate_encoder_1E8A3F74(this$, unwrap(this$._license), this$._fs);
+    const value = ROCrate_encoder_Z7FE34C43(this$, unwrap(this$._license), this$._fs, unwrap(ignoreBrokenWR));
     return toString(defaultSpaces(spaces), value);
   }
-  static toROCrateJsonString(spaces) {
-    return (obj) => obj.ToROCrateJsonString(unwrap(spaces));
+  static toROCrateJsonString(spaces, ignoreBrokenWR) {
+    return (obj) => obj.ToROCrateJsonString(unwrap(spaces), unwrap(ignoreBrokenWR));
   }
   GetLicenseWriteContract() {
     const this$ = this;
@@ -980,12 +1074,24 @@ class ARC extends ArcInvestigation {
     }
     return this$.FileSystem.Tree.ToFilePaths(unwrap(removeRoot));
   }
+  BuildWorkflowGraphs() {
+    const this$ = this;
+    return ofInvestigation(this$).WorkflowGraphs;
+  }
+  BuildRunGraphs() {
+    const this$ = this;
+    return ofInvestigation(this$).RunGraphs;
+  }
+  BuildAllProcessingUnitGraphs() {
+    const this$ = this;
+    return ofInvestigation(this$);
+  }
 }
 function ARC_$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 ARC_$ctor_Z443FB9BF(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, fs, license) {
+  return new ARC(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, fs, license);
 }
 function ARCAux_getArcAssaysFromContracts(contracts) {
   return choose(ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, contracts);
@@ -999,17 +1105,66 @@ function ARCAux_getArcWorkflowsFromContracts(contracts) {
 function ARCAux_getArcRunsFromContracts(contracts) {
   return choose(ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, contracts);
 }
-function ARCAux_getAssayDataMapFromContracts(assayIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static(assayIdentifier, c), contracts);
+function ARCAux_getAssayDatamapFromContracts(assayIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static(assayIdentifier, c), contracts);
+}
+function ARCAux_getStudyDatamapFromContracts(studyIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static(studyIdentifier, c), contracts);
+}
+function ARCAux_getWorkflowDatamapFromContracts(workflowIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static(workflowIdentifier, c), contracts);
 }
-function ARCAux_getStudyDataMapFromContracts(studyIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static(studyIdentifier, c), contracts);
+function ARCAux_getRunDatamapFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static(runIdentifier, c), contracts);
 }
-function ARCAux_getWorkflowDataMapFromContracts(workflowIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static(workflowIdentifier, c), contracts);
+function ARCAux_getWorkflowCWLFromContracts(workflowIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static(workflowIdentifier, c), contracts);
 }
-function ARCAux_getRunDataMapFromContracts(runIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static(runIdentifier, c), contracts);
+function ARCAux_getRunCWLFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcRun__ArcRun_tryCWLFromReadContract_Static(runIdentifier, c), contracts);
+}
+function ARCAux_getRunYMLFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcRun__ArcRun_tryYMLFromReadContract_Static(runIdentifier, c), contracts);
+}
+function ARCAux_getCWLByPathFromContracts(contracts) {
+  return ofArray(choose((c) => {
+    let matchResult, text;
+    if (c.Operation === "READ") {
+      if (c.DTOType != null) {
+        if (value(c.DTOType) === "CWL") {
+          if (c.DTO != null) {
+            if (typeof value(c.DTO) === "string") {
+              matchResult = 0;
+              text = value(c.DTO);
+            } else {
+              matchResult = 1;
+            }
+          } else {
+            matchResult = 1;
+          }
+        } else {
+          matchResult = 1;
+        }
+      } else {
+        matchResult = 1;
+      }
+    } else {
+      matchResult = 1;
+    }
+    switch (matchResult) {
+      case 0: {
+        const cwl = Decode_decodeCWLProcessingUnit(text);
+        return [normalizePathKey(c.Path), cwl];
+      }
+      default:
+        return void 0;
+    }
+  }, contracts), {
+    Compare: comparePrimitives
+  });
+}
+function ARCAux_tryGetCWLByPath(cwlByPath, path) {
+  return tryFind$1(normalizePathKey(path), cwlByPath);
 }
 function ARCAux_getArcInvestigationFromContracts(contracts) {
   const matchValue = choose(ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts);
@@ -1025,16 +1180,16 @@ function ARCAux_getLicenseFromContracts(contracts) {
 }
 function ARCAux_updateFSByARC(isa, license, fs) {
   let assaysFolder;
-  const assays = map$1((a) => FileSystemTree.createAssayFolder(a.Identifier, a.DataMap != null), toArray(isa.Assays));
+  const assays = map((a) => FileSystemTree.createAssayFolder(a.Identifier, a.Datamap != null), toArray(isa.Assays));
   assaysFolder = FileSystemTree.createAssaysFolder(assays);
   let studiesFolder;
-  const studies = map$1((s) => FileSystemTree.createStudyFolder(s.Identifier, s.DataMap != null), toArray(isa.Studies));
+  const studies = map((s) => FileSystemTree.createStudyFolder(s.Identifier, s.Datamap != null), toArray(isa.Studies));
   studiesFolder = FileSystemTree.createStudiesFolder(studies);
   let workflowsFolder;
-  const workflows = map$1((w) => FileSystemTree.createWorkflowFolder(w.Identifier, w.DataMap != null), toArray(isa.Workflows));
+  const workflows = map((w) => FileSystemTree.createWorkflowFolder(w.Identifier, w.CWLDescription != null, w.Datamap != null), toArray(isa.Workflows));
   workflowsFolder = FileSystemTree.createWorkflowsFolder(workflows);
   let runsFolder;
-  const runs = map$1((r) => FileSystemTree.createRunFolder(r.Identifier, r.DataMap != null), toArray(isa.Runs));
+  const runs = map((r) => FileSystemTree.createRunFolder(r.Identifier, r.CWLDescription != null, r.CWLInput.length > 0, r.Datamap != null), toArray(isa.Runs));
   runsFolder = FileSystemTree.createRunsFolder(runs);
   const investigation = FileSystemTree.createInvestigationFile();
   let tree_1;
@@ -1044,15 +1199,5 @@ function ARCAux_updateFSByARC(isa, license, fs) {
   });
   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_getLicenseFromContracts, ARCAux_getRunDataMapFromContracts, ARCAux_getStudyDataMapFromContracts, ARCAux_getWorkflowDataMapFromContracts, ARCAux_updateFSByARC, ARCAux_updateFSByCWL, ARC_$ctor_Z4D7EB22, ARC_$reflection };
+export { ARC, ARCAux_getArcAssaysFromContracts, ARCAux_getArcInvestigationFromContracts, ARCAux_getArcRunsFromContracts, ARCAux_getArcStudiesFromContracts, ARCAux_getArcWorkflowsFromContracts, ARCAux_getAssayDatamapFromContracts, ARCAux_getCWLByPathFromContracts, ARCAux_getLicenseFromContracts, ARCAux_getRunCWLFromContracts, ARCAux_getRunDatamapFromContracts, ARCAux_getRunYMLFromContracts, ARCAux_getStudyDatamapFromContracts, ARCAux_getWorkflowCWLFromContracts, ARCAux_getWorkflowDatamapFromContracts, ARCAux_tryGetCWLByPath, ARCAux_updateFSByARC, ARC_$ctor_Z443FB9BF, ARC_$reflection };