@nfdi4plants/arctrl 3.2.2 → 3.3.0

package/dist/ts/ts/ARC.js

@@ -1,23 +1,24 @@
 import { FileSystem } from './FileSystem/FileSystem.js';
-import { unwrap, defaultArg, value } from '../node_modules/@fable-org/fable-library-ts/Option.js';
+import { unwrap, defaultArg, value, toArray as toArray$1 } from '../node_modules/@fable-org/fable-library-ts/Option.js';
 import { License } from './License.js';
 import { ArcInvestigation, ArcInvestigation_$reflection } from './Core/ArcTypes.js';
+import { append, map, choose, item, fold, concat, contains as contains$2, tryPick, equalsWith } from '../node_modules/@fable-org/fable-library-ts/Array.js';
 import { defaultOf, stringHash, Exception, comparePrimitives, curry2, safeHash, getEnumerator, disposeSafe, equals } from '../node_modules/@fable-org/fable-library-ts/Util.js';
 import { Contract } from './Contract/Contract.js';
-import { fullFillContractBatchAsync } from './ContractIO/ContractIO.js';
+import { fullFillContractBatchAsync, tryFulfillEmptyEntityContractAsync } from './ContractIO/ContractIO.js';
 import { FSharpResult$2_Error$, FSharpResult$2_Ok } from '../node_modules/@fable-org/fable-library-ts/Result.js';
 import { PromiseBuilder__Run_212F1D4B, PromiseBuilder__Delay_62FBFDE1 } from './fable_modules/Fable.Promise.3.2.0/Promise.fs.js';
 import { promise } from './fable_modules/Fable.Promise.3.2.0/PromiseImpl.fs.js';
 import { getAllFilePathsAsync } from './ContractIO/FileSystemHelper.js';
-import { toArray, contains, delay, append, singleton, iterate, tryFind, find, collect, empty, toList } from '../node_modules/@fable-org/fable-library-ts/Seq.js';
-import { getAssayFolderPath, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath, combine, normalizePathKey } from './FileSystem/Path.js';
+import { toArray, contains, delay, append as append$1, singleton, iterate, tryFind, find, collect, empty, toList } from '../node_modules/@fable-org/fable-library-ts/Seq.js';
+import { all } from './CrossAsync.js';
+import { split, getAssayFolderPath, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath, combine, normalizePathKey } from './FileSystem/Path.js';
 import { ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from './Contract/ArcAssay.js';
-import { ARCtrl_ArcRun__ArcRun_ToDeleteContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, ARCtrl_ArcRun__ArcRun_tryCWLFromReadContract_Static, ARCtrl_ArcRun__ArcRun_tryYMLFromReadContract_Static } from './Contract/ArcRun.js';
-import { ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F, ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static } from './Contract/ArcWorkflow.js';
+import { ARCtrl_ArcRun__ArcRun_ToDeleteContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_TryToCWLContract_Z2D283928, ARCtrl_ArcRun__ArcRun_TryToYMLContract_Z2D283928, 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_TryToCWLContract_Z2D283928, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F, ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static, CWLFileReading_decodeCWLFile } from './Contract/ArcWorkflow.js';
 import { join, toFail, printf, replace, concat as concat$1, toText } from '../node_modules/@fable-org/fable-library-ts/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-ts/Array.js';
 import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from './Contract/ArcInvestigation.js';
-import { createMissingIdentifier, Workflow_cwlFileNameFromIdentifier, Run_cwlFileNameFromIdentifier } from './Core/Helper/Identifier.js';
+import { createMissingIdentifier, Workflow_cwlFileNameFromIdentifier, Run_cwlFileNameFromIdentifier, Run_ymlFileNameFromIdentifier } from './Core/Helper/Identifier.js';
 import { ofSeq, contains as contains$1, unionMany, FSharpSet__Contains } from '../node_modules/@fable-org/fable-library-ts/Set.js';
 import { ResizeArray_iter, ResizeArray_map } from './Core/Helper/Collections.js';
 import { FileSystemTree_Folder, FileSystemTree, FileSystemTree_File } from './FileSystem/FileSystemTree.js';
@@ -37,7 +38,6 @@ import { ValidationPackagesConfigHelper_ConfigFilePath, ARCtrl_ValidationPackage
 import { ofInvestigation } from './WorkflowGraph/Adapters.js';
 import { FSharpRef } from '../node_modules/@fable-org/fable-library-ts/Types.js';
 import { class_type } from '../node_modules/@fable-org/fable-library-ts/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, fs, license) {
@@ -49,7 +49,7 @@ class ARC extends ArcInvestigation {
     this._fs = (fs_1 = defaultArg(fs, FileSystem.create({
       tree: FileSystemTree_Folder("", [])
     })), ARCAux_updateFSByARC(this$.contents, license, fs_1));
-    this["init@145"] = 1;
+    this["init@179"] = 1;
   }
   get FileSystem() {
     const this$ = this;
@@ -70,9 +70,9 @@ class ARC extends ArcInvestigation {
   static fromArcInvestigation(isa, fs, license) {
     return new ARC(isa.Identifier, unwrap(isa.Title), unwrap(isa.Description), unwrap(isa.SubmissionDate), unwrap(isa.PublicReleaseDate), isa.OntologySourceReferences, isa.Publications, isa.Contacts, isa.Assays, isa.Studies, isa.Workflows, isa.Runs, isa.RegisteredStudyIdentifiers, isa.Comments, isa.Remarks, unwrap(fs), unwrap(license));
   }
-  TryWriteAsync(arcPath, forceOverwrite) {
+  TryWriteAsync(arcPath, forceOverwrite, additionalContracts) {
     const this$ = this;
-    const cs = this$.GetWriteContracts();
+    const cs = append(this$.GetWriteContracts(), defaultArg(additionalContracts, []));
     return fullFillContractBatchAsync(defaultArg(forceOverwrite, false), arcPath, cs);
   }
   TryUpdateAsync(arcPath, forceOverwrite) {
@@ -90,7 +90,7 @@ class ARC extends ArcInvestigation {
         license_1.Path = value(path);
       }
     } else {
-      const license = value(matchValue);
+      const license = matchValue;
       license.Type = "fulltext";
       license.Content = fulltext;
       if (path != null) {
@@ -102,17 +102,75 @@ class ARC extends ArcInvestigation {
     return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => getAllFilePathsAsync(arcPath).then((_arg) => {
       const arc = ARC.fromFilePaths(toArray(_arg));
       const contracts = arc.GetReadContracts();
-      return fullFillContractBatchAsync(false, arcPath, contracts).then((_arg_1) => {
-        const fulFilledContracts = _arg_1;
-        if (fulFilledContracts.tag === /* Error */
-        1) {
-          const e = fulFilledContracts.fields[0];
-          return Promise.resolve(FSharpResult$2_Error$(e));
-        } else {
-          const c = fulFilledContracts.fields[0];
-          arc.SetISAFromContracts(c);
-          return Promise.resolve(FSharpResult$2_Ok(arc));
-        }
+      return all(map((c) => tryFulfillEmptyEntityContractAsync(arcPath, c), contracts)).then((_arg_1) => {
+        const recoveredContracts_1 = choose((x) => x, _arg_1);
+        const contracts_1 = contracts.filter((c_1) => !recoveredContracts_1.some((rc) => rc.Path === c_1.Path));
+        return fullFillContractBatchAsync(false, arcPath, contracts_1).then((_arg_2) => {
+          const fulFilledContracts = _arg_2;
+          if (fulFilledContracts.tag === /* Error */
+          1) {
+            const e = fulFilledContracts.fields[0];
+            return Promise.resolve(FSharpResult$2_Error$(e));
+          } else {
+            const c_2 = fulFilledContracts.fields[0];
+            arc.SetISAFromContracts(append(c_2, recoveredContracts_1));
+            recoveredContracts_1.forEach((rc_1) => {
+              const identifier = item(1, split(rc_1.Path));
+              const matchValue = rc_1.DTOType;
+              let matchResult = void 0;
+              if (matchValue != null) {
+                switch (matchValue) {
+                  case "ISA_Assay": {
+                    matchResult = 0;
+                    break;
+                  }
+                  case "ISA_Study": {
+                    matchResult = 1;
+                    break;
+                  }
+                  case "ISA_Workflow": {
+                    matchResult = 2;
+                    break;
+                  }
+                  case "ISA_Run": {
+                    matchResult = 3;
+                    break;
+                  }
+                  default:
+                    matchResult = 4;
+                }
+              } else {
+                matchResult = 4;
+              }
+              switch (matchResult) {
+                case 0: {
+                  const a = arc.GetAssay(identifier);
+                  a.StaticHash = a.GetLightHashCode() + 1 | 0;
+                  break;
+                }
+                case 1: {
+                  const s = arc.GetStudy(identifier);
+                  s.StaticHash = s.GetLightHashCode() + 1 | 0;
+                  break;
+                }
+                case 2: {
+                  const w = arc.GetWorkflow(identifier);
+                  w.StaticHash = w.GetLightHashCode() + 1 | 0;
+                  break;
+                }
+                case 3: {
+                  const r = arc.GetRun(identifier);
+                  r.StaticHash = r.GetLightHashCode() + 1 | 0;
+                  break;
+                }
+                case 4: {
+                  break;
+                }
+              }
+            });
+            return Promise.resolve(FSharpResult$2_Ok(arc));
+          }
+        });
       });
     })));
   }
@@ -131,7 +189,7 @@ class ARC extends ArcInvestigation {
     const assayFolderPath = getAssayFolderPath(assayIdentifier);
     const filteredPaths = paths.filter((p) => !p.startsWith(assayFolderPath));
     this$.SetFilePaths(filteredPaths);
-    return toArray(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => this$.GetUpdateContracts()))));
+    return toArray(delay(() => append$1(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => this$.GetUpdateContracts()))));
   }
   GetRunRemoveContracts(runIdentifier) {
     const this$ = this;
@@ -147,7 +205,7 @@ class ARC extends ArcInvestigation {
     const runFolderPath = getRunFolderPath(runIdentifier);
     const filteredPaths = paths.filter((p) => !p.startsWith(runFolderPath));
     this$.SetFilePaths(filteredPaths);
-    return toArray(delay(() => append(singleton(ARCtrl_ArcRun__ArcRun_ToDeleteContract(run)), delay(() => this$.GetUpdateContracts()))));
+    return toArray(delay(() => append$1(singleton(ARCtrl_ArcRun__ArcRun_ToDeleteContract(run)), delay(() => this$.GetUpdateContracts()))));
   }
   GetWorkflowRemoveContracts(workflowIdentifier) {
     const this$ = this;
@@ -163,7 +221,7 @@ class ARC extends ArcInvestigation {
     const workflowFolderPath = getWorkflowFolderPath(workflowIdentifier);
     const filteredPaths = paths.filter((p) => !p.startsWith(workflowFolderPath));
     this$.SetFilePaths(filteredPaths);
-    return toArray(delay(() => append(singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract(workflow)), delay(() => this$.GetUpdateContracts()))));
+    return toArray(delay(() => append$1(singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract(workflow)), delay(() => this$.GetUpdateContracts()))));
   }
   TryRemoveAssayAsync(arcPath, assayIdentifier) {
     const this$ = this;
@@ -255,7 +313,7 @@ class ARC extends ArcInvestigation {
     const newAssayFolderPath = getAssayFolderPath(newAssayIdentifier);
     const renamedPaths = map((p) => replace(p, oldAssayFolderPath, newAssayFolderPath), paths);
     this$.SetFilePaths(renamedPaths);
-    return toArray(delay(() => append(singleton(Contract.createRename(oldAssayFolderPath, newAssayFolderPath)), delay(() => this$.GetUpdateContracts()))));
+    return toArray(delay(() => append$1(singleton(Contract.createRename(oldAssayFolderPath, newAssayFolderPath)), delay(() => this$.GetUpdateContracts()))));
   }
   GetRunRenameContracts(oldRunIdentifier, newRunIdentifier) {
     const this$ = this;
@@ -271,7 +329,7 @@ class ARC extends ArcInvestigation {
     const newPath = getRunFolderPath(newRunIdentifier);
     const renamedPaths = map((p) => replace(p, oldPath, newPath), paths);
     this$.SetFilePaths(renamedPaths);
-    return toArray(delay(() => append(singleton(Contract.createRename(oldPath, newPath)), delay(() => this$.GetUpdateContracts()))));
+    return toArray(delay(() => append$1(singleton(Contract.createRename(oldPath, newPath)), delay(() => this$.GetUpdateContracts()))));
   }
   GetWorkflowRenameContracts(oldWorkflowIdentifier, newWorkflowIdentifier) {
     const this$ = this;
@@ -287,7 +345,7 @@ class ARC extends ArcInvestigation {
     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()))));
+    return toArray(delay(() => append$1(singleton(Contract.createRename(oldPath, newPath)), delay(() => this$.GetUpdateContracts()))));
   }
   TryRenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier) {
     const this$ = this;
@@ -320,15 +378,15 @@ class ARC extends ArcInvestigation {
     const newStudyFolderPath = getStudyFolderPath(newStudyIdentifier);
     const renamedPaths = map((p) => replace(p, oldStudyFolderPath, newStudyFolderPath), paths);
     this$.SetFilePaths(renamedPaths);
-    return toArray(delay(() => append(singleton(Contract.createRename(oldStudyFolderPath, newStudyFolderPath)), delay(() => this$.GetUpdateContracts()))));
+    return toArray(delay(() => append$1(singleton(Contract.createRename(oldStudyFolderPath, newStudyFolderPath)), delay(() => this$.GetUpdateContracts()))));
   }
   TryRenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier) {
     const this$ = this;
     return fullFillContractBatchAsync(false, arcPath, this$.GetStudyRenameContracts(oldStudyIdentifier, newStudyIdentifier));
   }
-  WriteAsync(arcPath) {
+  WriteAsync(arcPath, additionalContracts) {
     const this$ = this;
-    return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryWriteAsync(arcPath).then((_arg) => {
+    return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryWriteAsync(arcPath, void 0, unwrap(additionalContracts)).then((_arg) => {
       const result = _arg;
       if (result.tag === /* Error */
       1) {
@@ -434,9 +492,9 @@ class ARC extends ArcInvestigation {
       let col_1 = void 0;
       let matchResult = void 0, col_2 = void 0;
       if (col != null) {
-        if (col_1 = value(col), col_1.Header.IsDataColumn) {
+        if (col_1 = col, col_1.Header.IsDataColumn) {
           matchResult = 0;
-          col_2 = value(col);
+          col_2 = col;
         } else {
           matchResult = 1;
         }
@@ -544,7 +602,7 @@ class ARC extends ArcInvestigation {
       if (registeredStudyOpt == null) {
         this$.AddStudy(study);
       } else {
-        const registeredStudy = value(registeredStudyOpt);
+        const registeredStudy = registeredStudyOpt;
         registeredStudy.UpdateReferenceByStudyFile(study, true);
       }
       const datamap = ARCAux_getStudyDatamapFromContracts(study.Identifier, contracts);
@@ -558,7 +616,7 @@ class ARC extends ArcInvestigation {
       if (registeredAssayOpt == null) {
         this$.AddAssay(assay);
       } else {
-        const registeredAssay = value(registeredAssayOpt);
+        const registeredAssay = registeredAssayOpt;
         registeredAssay.UpdateReferenceByAssayFile(assay, true);
       }
       const assay_1 = find((a_2) => a_2.Identifier === assay.Identifier, this$.Assays);
@@ -577,13 +635,14 @@ class ARC extends ArcInvestigation {
       const cwlFilePath = Workflow_cwlFileNameFromIdentifier(workflow.Identifier);
       let resolvedCwl;
       const option_1 = cwl;
-      resolvedCwl = option_1 != null ? resolveRunReferencesFromLookup(cwlFilePath, value(option_1), tryGetCWLByPath) : void 0;
+      resolvedCwl = option_1 != null ? resolveRunReferencesFromLookup(cwlFilePath, option_1, tryGetCWLByPath) : void 0;
       if (workflow.Datamap == null) {
         workflow.Datamap = datamap_2;
       }
       workflow.CWLDescription = resolvedCwl;
       this$.AddWorkflow(workflow);
       workflow.StaticHash = workflow.GetLightHashCode() | 0;
+      workflow.CWLStaticHash = workflow.GetCWLHashCode() | 0;
     });
     runs.forEach((run) => {
       const datamap_3 = ARCAux_getRunDatamapFromContracts(run.Identifier, contracts);
@@ -592,7 +651,7 @@ class ARC extends ArcInvestigation {
       const cwlFilePath_1 = Run_cwlFileNameFromIdentifier(run.Identifier);
       let resolvedCwl_1;
       const option_3 = cwl_1;
-      resolvedCwl_1 = option_3 != null ? resolveRunReferencesFromLookup(cwlFilePath_1, value(option_3), tryGetCWLByPath) : void 0;
+      resolvedCwl_1 = option_3 != null ? resolveRunReferencesFromLookup(cwlFilePath_1, option_3, tryGetCWLByPath) : void 0;
       if (run.Datamap == null) {
         run.Datamap = datamap_3;
       }
@@ -600,6 +659,8 @@ class ARC extends ArcInvestigation {
       run.CWLDescription = resolvedCwl_1;
       this$.AddRun(run);
       run.StaticHash = run.GetLightHashCode() | 0;
+      run.CWLStaticHash = run.GetCWLHashCode() | 0;
+      run.CWLInputStaticHash = run.GetCWLInputHashCode() | 0;
     });
     iterate((a_3) => {
       a_3.StaticHash = a_3.GetLightHashCode() | 0;
@@ -625,57 +686,59 @@ class ARC extends ArcInvestigation {
     if (!defaultArg(skipUpdateFS, false)) {
       this$.UpdateFileSystem();
     }
-    return toArray(delay(() => {
-      this$.StaticHash = this$.GetLightHashCode() | 0;
-      return append(singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract(this$)), delay(() => append(collect((s) => {
-        s.StaticHash = s.GetLightHashCode() | 0;
-        return append(ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true), delay(() => {
-          if (s.Datamap != null) {
-            const dm = value(s.Datamap);
-            dm.StaticHash = safeHash(dm) | 0;
-            return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5(dm, s.Identifier));
-          } else {
-            return empty();
-          }
-        }));
-      }, this$.Studies), delay(() => append(collect((a) => {
-        a.StaticHash = a.GetLightHashCode() | 0;
-        return append(ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true), delay(() => {
-          if (a.Datamap != null) {
-            const dm_1 = value(a.Datamap);
-            dm_1.StaticHash = safeHash(dm_1) | 0;
-            return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5(dm_1, a.Identifier));
-          } else {
-            return empty();
-          }
-        }));
-      }, this$.Assays), delay(() => append(collect((w) => {
-        w.StaticHash = w.GetLightHashCode() | 0;
-        return append(ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true), delay(() => {
-          if (w.Datamap != null) {
-            const dm_2 = value(w.Datamap);
-            dm_2.StaticHash = safeHash(dm_2) | 0;
-            return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5(dm_2, w.Identifier));
-          } else {
-            return empty();
-          }
-        }));
-      }, this$.Workflows), delay(() => append(collect((r) => {
-        r.StaticHash = r.GetLightHashCode() | 0;
-        return append(ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49(r, true), delay(() => {
-          if (r.Datamap != null) {
-            const dm_3 = value(r.Datamap);
-            dm_3.StaticHash = safeHash(dm_3) | 0;
-            return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5(dm_3, r.Identifier));
-          } else {
-            return empty();
-          }
-        }));
-      }, this$.Runs), delay(() => {
-        let l = void 0;
-        return append(this$.License != null ? (l = value(this$.License), l.StaticHash = safeHash(l) | 0, singleton(l.ToCreateContract())) : empty(), delay(() => append(singleton(Contract.createCreate(combine("assays", ".gitkeep"), "PlainText")), delay(() => append(singleton(Contract.createCreate(combine("studies", ".gitkeep"), "PlainText")), delay(() => append(singleton(Contract.createCreate(combine("workflows", ".gitkeep"), "PlainText")), delay(() => singleton(Contract.createCreate(combine("runs", ".gitkeep"), "PlainText"))))))))));
-      }))))))))));
-    }));
+    this$.StaticHash = this$.GetLightHashCode() | 0;
+    const investigationContract = ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract(this$);
+    return toArray(delay(() => append$1(singleton(investigationContract), delay(() => append$1(collect((s) => {
+      s.StaticHash = s.GetLightHashCode() | 0;
+      return append$1(ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true), delay(() => {
+        if (s.Datamap != null) {
+          const dm = value(s.Datamap);
+          dm.StaticHash = safeHash(dm) | 0;
+          return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5(dm, s.Identifier));
+        } else {
+          return empty();
+        }
+      }));
+    }, this$.Studies), delay(() => append$1(collect((a) => {
+      a.StaticHash = a.GetLightHashCode() | 0;
+      return append$1(ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true), delay(() => {
+        if (a.Datamap != null) {
+          const dm_1 = value(a.Datamap);
+          dm_1.StaticHash = safeHash(dm_1) | 0;
+          return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5(dm_1, a.Identifier));
+        } else {
+          return empty();
+        }
+      }));
+    }, this$.Assays), delay(() => append$1(collect((w) => {
+      w.StaticHash = w.GetLightHashCode() | 0;
+      w.CWLStaticHash = w.GetCWLHashCode() | 0;
+      return append$1(ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true), delay(() => {
+        if (w.Datamap != null) {
+          const dm_2 = value(w.Datamap);
+          dm_2.StaticHash = safeHash(dm_2) | 0;
+          return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5(dm_2, w.Identifier));
+        } else {
+          return empty();
+        }
+      }));
+    }, this$.Workflows), delay(() => append$1(collect((r) => {
+      r.StaticHash = r.GetLightHashCode() | 0;
+      r.CWLStaticHash = r.GetCWLHashCode() | 0;
+      r.CWLInputStaticHash = r.GetCWLInputHashCode() | 0;
+      return append$1(ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49(r, true), delay(() => {
+        if (r.Datamap != null) {
+          const dm_3 = value(r.Datamap);
+          dm_3.StaticHash = safeHash(dm_3) | 0;
+          return singleton(ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5(dm_3, r.Identifier));
+        } else {
+          return empty();
+        }
+      }));
+    }, this$.Runs), delay(() => {
+      let l = void 0;
+      return append$1(this$.License != null ? (l = value(this$.License), l.StaticHash = safeHash(l) | 0, singleton(l.ToCreateContract())) : empty(), delay(() => append$1(singleton(Contract.createCreate(combine("assays", ".gitkeep"), "PlainText")), delay(() => append$1(singleton(Contract.createCreate(combine("studies", ".gitkeep"), "PlainText")), delay(() => append$1(singleton(Contract.createCreate(combine("workflows", ".gitkeep"), "PlainText")), delay(() => singleton(Contract.createCreate(combine("runs", ".gitkeep"), "PlainText"))))))))));
+    }))))))))))));
   }
   /**
    * This function returns the all update Contracts for the current state of the ARC. Only update contracts for those ISA objects that have been changed will be returned.
@@ -693,22 +756,22 @@ class ARC extends ArcInvestigation {
     } else {
       return toArray(delay(() => {
         const hash = this$.GetLightHashCode() | 0;
-        return append(this$.StaticHash !== hash ? singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$)) : empty(), delay(() => {
+        return append$1(this$.StaticHash !== hash ? singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$)) : empty(), delay(() => {
           this$.StaticHash = hash | 0;
-          return append(collect((s) => {
+          return append$1(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(() => {
+            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(() => {
               let dm = void 0, dm_1 = void 0;
               s.StaticHash = hash_1 | 0;
               const matchValue = s.Datamap;
               let matchResult = void 0, dm_2 = void 0, dm_3 = void 0;
               if (matchValue != null) {
-                if (dm = value(matchValue), dm.StaticHash === 0) {
+                if (dm = matchValue, dm.StaticHash === 0) {
                   matchResult = 0;
-                  dm_2 = value(matchValue);
-                } else if (dm_1 = value(matchValue), dm_1.StaticHash !== safeHash(dm_1)) {
+                  dm_2 = matchValue;
+                } else if (dm_1 = matchValue, dm_1.StaticHash !== safeHash(dm_1)) {
                   matchResult = 1;
-                  dm_3 = value(matchValue);
+                  dm_3 = matchValue;
                 } else {
                   matchResult = 2;
                 }
@@ -717,12 +780,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult) {
                 case 0:
-                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
+                  return append$1(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(() => {
+                  return append$1(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
                     dm_3.StaticHash = safeHash(dm_3) | 0;
                     return empty();
                   }));
@@ -731,20 +794,20 @@ class ARC extends ArcInvestigation {
                 }
               }
             }));
-          }, this$.Studies), delay(() => append(collect((a) => {
+          }, this$.Studies), delay(() => append$1(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(() => {
+            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(() => {
               let dm_4 = void 0, dm_5 = void 0;
               a.StaticHash = hash_2 | 0;
               const matchValue_1 = a.Datamap;
               let matchResult_1 = void 0, dm_6 = void 0, dm_7 = void 0;
               if (matchValue_1 != null) {
-                if (dm_4 = value(matchValue_1), dm_4.StaticHash === 0) {
+                if (dm_4 = matchValue_1, dm_4.StaticHash === 0) {
                   matchResult_1 = 0;
-                  dm_6 = value(matchValue_1);
-                } else if (dm_5 = value(matchValue_1), dm_5.StaticHash !== safeHash(dm_5)) {
+                  dm_6 = matchValue_1;
+                } else if (dm_5 = matchValue_1, dm_5.StaticHash !== safeHash(dm_5)) {
                   matchResult_1 = 1;
-                  dm_7 = value(matchValue_1);
+                  dm_7 = matchValue_1;
                 } else {
                   matchResult_1 = 2;
                 }
@@ -753,12 +816,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_1) {
                 case 0:
-                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
+                  return append$1(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(() => {
+                  return append$1(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
                     dm_7.StaticHash = safeHash(dm_7) | 0;
                     return empty();
                   }));
@@ -767,86 +830,97 @@ class ARC extends ArcInvestigation {
                 }
               }
             }));
-          }, this$.Assays), delay(() => append(collect((w) => {
+          }, this$.Assays), delay(() => append$1(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_8 = void 0, dm_9 = void 0;
+            return append$1(w.StaticHash === 0 ? append$1(ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true), delay(() => {
+              w.CWLStaticHash = w.GetCWLHashCode() | 0;
+              return empty();
+            })) : w.StaticHash !== hash_3 ? singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract(w)) : empty(), delay(() => {
               w.StaticHash = hash_3 | 0;
-              const matchValue_2 = w.Datamap;
-              let matchResult_2 = void 0, dm_10 = void 0, dm_11 = void 0;
-              if (matchValue_2 != null) {
-                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), dm_9.StaticHash !== safeHash(dm_9)) {
-                  matchResult_2 = 1;
-                  dm_11 = value(matchValue_2);
+              return append$1(ARCAux_workflowFileContracts(w), delay(() => {
+                let dm_8 = void 0, dm_9 = void 0;
+                const matchValue_2 = w.Datamap;
+                let matchResult_2 = void 0, dm_10 = void 0, dm_11 = void 0;
+                if (matchValue_2 != null) {
+                  if (dm_8 = matchValue_2, dm_8.StaticHash === 0) {
+                    matchResult_2 = 0;
+                    dm_10 = matchValue_2;
+                  } else if (dm_9 = matchValue_2, dm_9.StaticHash !== safeHash(dm_9)) {
+                    matchResult_2 = 1;
+                    dm_11 = matchValue_2;
+                  } else {
+                    matchResult_2 = 2;
+                  }
                 } else {
                   matchResult_2 = 2;
                 }
-              } else {
-                matchResult_2 = 2;
-              }
-              switch (matchResult_2) {
-                case 0:
-                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5(dm_10, w.Identifier)), delay(() => {
-                    dm_10.StaticHash = safeHash(dm_10) | 0;
+                switch (matchResult_2) {
+                  case 0:
+                    return append$1(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5(dm_10, w.Identifier)), delay(() => {
+                      dm_10.StaticHash = safeHash(dm_10) | 0;
+                      return empty();
+                    }));
+                  case 1:
+                    return append$1(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, w.Identifier)), delay(() => {
+                      dm_11.StaticHash = safeHash(dm_11) | 0;
+                      return empty();
+                    }));
+                  default: {
                     return empty();
-                  }));
-                case 1:
-                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, w.Identifier)), delay(() => {
-                    dm_11.StaticHash = safeHash(dm_11) | 0;
-                    return empty();
-                  }));
-                default: {
-                  return empty();
+                  }
                 }
-              }
+              }));
             }));
-          }, this$.Workflows), delay(() => append(collect((r) => {
+          }, this$.Workflows), delay(() => append$1(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_12 = void 0, dm_13 = void 0;
+            return append$1(r.StaticHash === 0 ? append$1(ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49(r, true), delay(() => {
+              r.CWLStaticHash = r.GetCWLHashCode() | 0;
+              r.CWLInputStaticHash = r.GetCWLInputHashCode() | 0;
+              return empty();
+            })) : r.StaticHash !== hash_4 ? singleton(ARCtrl_ArcRun__ArcRun_ToUpdateContract(r)) : empty(), delay(() => {
               r.StaticHash = hash_4 | 0;
-              const matchValue_3 = r.Datamap;
-              let matchResult_3 = void 0, dm_14 = void 0, dm_15 = void 0;
-              if (matchValue_3 != null) {
-                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), dm_13.StaticHash !== safeHash(dm_13)) {
-                  matchResult_3 = 1;
-                  dm_15 = value(matchValue_3);
+              return append$1(ARCAux_runFileContracts(r), delay(() => {
+                let dm_12 = void 0, dm_13 = void 0;
+                const matchValue_3 = r.Datamap;
+                let matchResult_3 = void 0, dm_14 = void 0, dm_15 = void 0;
+                if (matchValue_3 != null) {
+                  if (dm_12 = matchValue_3, dm_12.StaticHash === 0) {
+                    matchResult_3 = 0;
+                    dm_14 = matchValue_3;
+                  } else if (dm_13 = matchValue_3, dm_13.StaticHash !== safeHash(dm_13)) {
+                    matchResult_3 = 1;
+                    dm_15 = matchValue_3;
+                  } else {
+                    matchResult_3 = 2;
+                  }
                 } else {
                   matchResult_3 = 2;
                 }
-              } else {
-                matchResult_3 = 2;
-              }
-              switch (matchResult_3) {
-                case 0:
-                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
-                    dm_14.StaticHash = safeHash(dm_14) | 0;
+                switch (matchResult_3) {
+                  case 0:
+                    return append$1(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
+                      dm_14.StaticHash = safeHash(dm_14) | 0;
+                      return empty();
+                    }));
+                  case 1:
+                    return append$1(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
+                      dm_15.StaticHash = safeHash(dm_15) | 0;
+                      return empty();
+                    }));
+                  default: {
                     return empty();
-                  }));
-                case 1:
-                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
-                    dm_15.StaticHash = safeHash(dm_15) | 0;
-                    return empty();
-                  }));
-                default: {
-                  return empty();
+                  }
                 }
-              }
+              }));
             }));
           }, this$.Runs), delay(() => {
             const matchValue_4 = this$.License;
             if (matchValue_4 == null) {
               return empty();
             } else {
-              const l = value(matchValue_4);
+              const l = 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(() => {
+              return append$1(l.StaticHash === 0 ? singleton(l.ToCreateContract()) : l.StaticHash !== hash_5 ? singleton(l.ToUpdateContract()) : empty(), delay(() => {
                 l.StaticHash = hash_5 | 0;
                 return empty();
               }));
@@ -859,7 +933,7 @@ 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(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()))))))));
+    return toArray(delay(() => append$1(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append$1(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => append$1(defaultGitattributes_1 ? singleton(gitattributesContract) : empty(), delay(() => repositoryAddress != null ? singleton(Init_createAddRemoteContract_Z721C83C5(value(repositoryAddress))) : empty()))))))));
   }
   static getCloneContract(remoteUrl, merge, branch, token, nolfs) {
     return Clone_createCloneContract_5000466F(remoteUrl, unwrap(merge), unwrap(branch), unwrap(token), unwrap(nolfs));
@@ -919,7 +993,7 @@ class ARC extends ArcInvestigation {
     const nextStudyIdentifiers = Array.from(this$.RegisteredStudyIdentifiers);
     let nextLicense;
     const option_1 = this$.License;
-    nextLicense = option_1 != null ? (_arg = value(option_1), _arg.Copy()) : void 0;
+    nextLicense = option_1 != null ? (_arg = option_1, _arg.Copy()) : void 0;
     const fsCopy = this$._fs.Copy();
     return new ARC(this$.Identifier, unwrap(this$.Title), unwrap(this$.Description), unwrap(this$.SubmissionDate), unwrap(this$.PublicReleaseDate), nextOntologySourceReferences, nextPublications, nextContacts, nextAssays, nextStudies, nextWorkflows, nextRuns, nextStudyIdentifiers, nextComments, nextRemarks, fsCopy, unwrap(nextLicense));
   }
@@ -932,13 +1006,13 @@ class ARC extends ArcInvestigation {
     const copy = this$.Copy();
     const registeredStudies = copy.Studies.slice();
     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())))))), {
+    const includeFiles = unionMany([ofSeq(toList(delay(() => append$1(singleton("isa.investigation.xlsx"), delay(() => append$1(singleton("README.md"), delay(() => this$.License != null ? singleton(value(this$.License).Path) : empty())))))), {
       Compare: (x, y) => comparePrimitives(x, y) | 0
     }), unionMany(map((s_1) => {
       const studyFoldername = concat$1("studies", "/", s_1.Identifier);
-      return ofSeq(toList(delay(() => append(singleton(concat$1(studyFoldername, "/", "isa.study.xlsx")), delay(() => append(singleton(concat$1(studyFoldername, "/", "README.md")), delay(() => collect((table) => collect((kv) => {
+      return ofSeq(toList(delay(() => append$1(singleton(concat$1(studyFoldername, "/", "isa.study.xlsx")), delay(() => append$1(singleton(concat$1(studyFoldername, "/", "README.md")), delay(() => collect((table) => collect((kv) => {
         const textValue = kv[1].ToFreeTextCell().AsFreeText;
-        return append(singleton(textValue), delay(() => append(singleton(`${studyFoldername}/${"resources"}/${textValue}`), delay(() => singleton(`${studyFoldername}/${"protocols"}/${textValue}`)))));
+        return append$1(singleton(textValue), delay(() => append$1(singleton(`${studyFoldername}/${"resources"}/${textValue}`), delay(() => singleton(`${studyFoldername}/${"protocols"}/${textValue}`)))));
       }, table.Values), s_1.Tables))))))), {
         Compare: (x_1, y_1) => comparePrimitives(x_1, y_1) | 0
       });
@@ -946,9 +1020,9 @@ class ARC extends ArcInvestigation {
       Compare: (x_2, y_2) => comparePrimitives(x_2, y_2) | 0
     }), unionMany(map((a) => {
       const assayFoldername = concat$1("assays", "/", a.Identifier);
-      return ofSeq(toList(delay(() => append(singleton(concat$1(assayFoldername, "/", "isa.assay.xlsx")), delay(() => append(singleton(concat$1(assayFoldername, "/", "README.md")), delay(() => collect((table_1) => collect((kv_1) => {
+      return ofSeq(toList(delay(() => append$1(singleton(concat$1(assayFoldername, "/", "isa.assay.xlsx")), delay(() => append$1(singleton(concat$1(assayFoldername, "/", "README.md")), delay(() => collect((table_1) => collect((kv_1) => {
         const textValue_1 = kv_1[1].ToFreeTextCell().AsFreeText;
-        return append(singleton(textValue_1), delay(() => append(singleton(`${assayFoldername}/${"dataset"}/${textValue_1}`), delay(() => singleton(`${assayFoldername}/${"protocols"}/${textValue_1}`)))));
+        return append$1(singleton(textValue_1), delay(() => append$1(singleton(`${assayFoldername}/${"dataset"}/${textValue_1}`), delay(() => singleton(`${assayFoldername}/${"protocols"}/${textValue_1}`)))));
       }, table_1.Values), a.Tables))))))), {
         Compare: (x_3, y_3) => comparePrimitives(x_3, y_3) | 0
       });
@@ -965,7 +1039,7 @@ class ARC extends ArcInvestigation {
       } else {
         return FSharpSet__Contains(includeFiles, p);
       }
-    })), FileSystemTree.fromFilePaths(paths)), ignoreHidden ? FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree), option_1 != null ? (tree_1 = value(option_1), ignoreHidden ? FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1) : tree_1) : void 0), FileSystemTree.fromFilePaths([]));
+    })), FileSystemTree.fromFilePaths(paths)), ignoreHidden ? FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree), option_1 != null ? (tree_1 = option_1, ignoreHidden ? FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1) : tree_1) : void 0), FileSystemTree.fromFilePaths([]));
   }
   /**
    * Returns the FileSystemTree of the ARC with only and folders included that are considered additional payload.
@@ -977,7 +1051,7 @@ class ARC extends ArcInvestigation {
     const registeredPayload = ofSeq(FileSystemTree.toFilePaths()(this$.GetRegisteredPayload()), {
       Compare: (x, y) => comparePrimitives(x, y) | 0
     });
-    return defaultArg((option_1 = (tree = (paths = (array = FileSystemTree.toFilePaths()(this$._fs.Copy().Tree), array.filter((p) => !FSharpSet__Contains(registeredPayload, p))), FileSystemTree.fromFilePaths(paths)), ignoreHidden ? FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree), option_1 != null ? (tree_1 = value(option_1), ignoreHidden ? FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1) : tree_1) : void 0), FileSystemTree.fromFilePaths([]));
+    return defaultArg((option_1 = (tree = (paths = (array = FileSystemTree.toFilePaths()(this$._fs.Copy().Tree), array.filter((p) => !FSharpSet__Contains(registeredPayload, p))), FileSystemTree.fromFilePaths(paths)), ignoreHidden ? FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree), option_1 != null ? (tree_1 = option_1, ignoreHidden ? FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1) : tree_1) : void 0), FileSystemTree.fromFilePaths([]));
   }
   static get DefaultContracts() {
     return ARCAux_defaultContracts;
@@ -1036,7 +1110,7 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     let _arg;
     const option_1 = this$.License;
-    _arg = option_1 != null ? value(option_1) : License.GetDefaultLicense();
+    _arg = option_1 != null ? option_1 : License.GetDefaultLicense();
     return _arg.ToCreateContract();
   }
   /**
@@ -1051,7 +1125,7 @@ class ARC extends ArcInvestigation {
       Equals: (x, y) => x === y,
       GetHashCode: (x) => stringHash(x) | 0
     })) {
-      const filePaths = append$1([ValidationPackagesConfigHelper_ConfigFilePath], paths);
+      const filePaths = append([ValidationPackagesConfigHelper_ConfigFilePath], paths);
       this$.SetFilePaths(filePaths);
     }
     return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toCreateContract_Static_724DAE55(vpc);
@@ -1125,6 +1199,31 @@ function ARC_$reflection() {
 function ARC_$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_fileContract(path, staticHash, hash, contractOf) {
+  if (staticHash === hash) {
+    return void 0;
+  } else if (hash === 0) {
+    return Contract.createDelete(path);
+  } else if (staticHash === 0) {
+    return contractOf("CREATE");
+  } else {
+    return contractOf("UPDATE");
+  }
+}
+function ARCAux_runFileContracts(run) {
+  const cwlHash = run.GetCWLHashCode() | 0;
+  const ymlHash = run.GetCWLInputHashCode() | 0;
+  const contracts = choose((x) => x, [ARCAux_fileContract(Run_cwlFileNameFromIdentifier(run.Identifier), run.CWLStaticHash, cwlHash, (operation) => ARCtrl_ArcRun__ArcRun_TryToCWLContract_Z2D283928(run, operation)), ARCAux_fileContract(Run_ymlFileNameFromIdentifier(run.Identifier), run.CWLInputStaticHash, ymlHash, (operation_1) => ARCtrl_ArcRun__ArcRun_TryToYMLContract_Z2D283928(run, operation_1))]);
+  run.CWLStaticHash = cwlHash | 0;
+  run.CWLInputStaticHash = ymlHash | 0;
+  return contracts;
+}
+function ARCAux_workflowFileContracts(workflow) {
+  const cwlHash = workflow.GetCWLHashCode() | 0;
+  const contracts = toArray$1(ARCAux_fileContract(Workflow_cwlFileNameFromIdentifier(workflow.Identifier), workflow.CWLStaticHash, cwlHash, (operation) => ARCtrl_ArcWorkflow__ArcWorkflow_TryToCWLContract_Z2D283928(workflow, operation)));
+  workflow.CWLStaticHash = cwlHash | 0;
+  return contracts;
+}
 function ARCAux_getArcAssaysFromContracts(contracts) {
   return choose(ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, contracts);
 }
@@ -1163,11 +1262,11 @@ function ARCAux_getCWLByPathFromContracts(contracts) {
     let matchResult = void 0, text = void 0;
     if (c.Operation === "READ") {
       if (c.DTOType != null) {
-        if (value(c.DTOType) === "CWL") {
+        if (c.DTOType === "CWL") {
           if (c.DTO != null) {
-            if (typeof value(c.DTO) === "string") {
+            if (typeof c.DTO === "string") {
               matchResult = 0;
-              text = value(c.DTO);
+              text = c.DTO;
             } else {
               matchResult = 1;
             }
@@ -1184,10 +1283,8 @@ function ARCAux_getCWLByPathFromContracts(contracts) {
       matchResult = 1;
     }
     switch (matchResult) {
-      case 0: {
-        const cwl = Decode_decodeCWLProcessingUnit(text);
-        return [normalizePathKey(c.Path), cwl];
-      }
+      case 0:
+        return [normalizePathKey(c.Path), CWLFileReading_decodeCWLFile(c.Path, text)];
       default:
         return void 0;
     }
@@ -1225,7 +1322,7 @@ function ARCAux_updateFSByARC(isa, license, fs) {
   runsFolder = FileSystemTree.createRunsFolder(runs);
   const investigation = FileSystemTree.createInvestigationFile();
   let tree_1;
-  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())))))))))))));
+  const tree = FileSystemTree.createRootFolder(toArray(delay(() => append$1(singleton(investigation), delay(() => append$1(singleton(assaysFolder), delay(() => append$1(singleton(studiesFolder), delay(() => append$1(singleton(workflowsFolder), delay(() => append$1(singleton(runsFolder), delay(() => license != null ? singleton(FileSystemTree_File(value(license).Path)) : empty())))))))))))));
   tree_1 = FileSystem.create({
     tree
   });
@@ -1235,4 +1332,4 @@ const ARCAux_defaultContracts = ofSeq$1([[".gitignore", gitignoreContract], [".g
   Compare: (x, y) => comparePrimitives(x, y) | 0
 });
 
-export { ARC, ARCAux_defaultContracts, 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 };
+export { ARC, ARCAux_defaultContracts, ARCAux_fileContract, 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_runFileContracts, ARCAux_tryGetCWLByPath, ARCAux_updateFSByARC, ARCAux_workflowFileContracts, ARC_$ctor_Z443FB9BF, ARC_$reflection };