@nfdi4plants/arctrl 3.1.1 → 3.2.0

package/dist/ts/ts/ARC.js

@@ -1,55 +1,55 @@
 import { FileSystem } from './FileSystem/FileSystem.js';
-import { unwrap, defaultArg, value, map as map$1, bind, defaultArgWith } from '../node_modules/@fable-org/fable-library-js/Option.js';
+import { unwrap, defaultArg, value } from '../node_modules/@fable-org/fable-library-ts/Option.js';
 import { License } from './License.js';
 import { ArcInvestigation, ArcInvestigation_$reflection } from './Core/ArcTypes.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 { FSharpResult$2_Error, FSharpResult$2_Ok } from '../node_modules/@fable-org/fable-library-js/Result.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-js/Seq.js';
-import { defaultOf, stringHash, comparePrimitives, curry2, safeHash, getEnumerator, disposeSafe, equals } from '../node_modules/@fable-org/fable-library-js/Util.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 { 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 { 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 { ofSeq, contains as contains$1, unionMany, FSharpSet__Contains } from '../node_modules/@fable-org/fable-library-js/Set.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';
 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 { ofSeq as ofSeq$1, ofArray, tryFind as tryFind$1 } from '../node_modules/@fable-org/fable-library-ts/Map.js';
 import { ArcTables } from './Core/Table/ArcTables.js';
 import { resolveRunReferencesFromLookup } from './CWLRunResolver.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_ToCreateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static } from './Contract/Datamap.js';
 import { Init_createInitContract_6DFDD678, gitignoreContract, gitattributesContract, Init_createAddRemoteContract_Z721C83C5, Clone_createCloneContract_5000466F } from './Contract/Git.js';
-import { fromString } from './fable_modules/Thoth.Json.JavaScript.0.4.1/Decode.fs.js';
+import { fromString } from './fable_modules/Thoth.Json.JavaScript.0.5.0/Decode.fs.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 { toString } from './fable_modules/Thoth.Json.JavaScript.0.5.0/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 { 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) {
     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;
+    let fs_1 = void 0;
     const this$ = new FSharpRef(defaultOf());
     this$.contents = this;
     this._license = license;
     this._fs = (fs_1 = defaultArg(fs, FileSystem.create({
       tree: FileSystemTree_Folder("", [])
     })), ARCAux_updateFSByARC(this$.contents, license, fs_1));
-    this["init@133"] = 1;
+    this["init@145"] = 1;
   }
   get FileSystem() {
     const this$ = this;
@@ -107,7 +107,7 @@ class ARC extends ArcInvestigation {
         if (fulFilledContracts.tag === /* Error */
         1) {
           const e = fulFilledContracts.fields[0];
-          return Promise.resolve(FSharpResult$2_Error(e));
+          return Promise.resolve(FSharpResult$2_Error$(e));
         } else {
           const c = fulFilledContracts.fields[0];
           arc.SetISAFromContracts(c);
@@ -120,12 +120,12 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     if (!contains(assayIdentifier, this$.AssayIdentifiers, {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })) {
-      throw new Error("ARC does not contain assay with given name");
+      throw new Exception("ARC does not contain assay with given name");
     }
     const assay = this$.GetAssay(assayIdentifier);
-    const studies = assay.StudiesRegisteredIn;
+    assay.StudiesRegisteredIn;
     super.RemoveAssay(assayIdentifier);
     const paths = this$.FileSystem.Tree.ToFilePaths();
     const assayFolderPath = getAssayFolderPath(assayIdentifier);
@@ -137,9 +137,9 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     if (!contains(runIdentifier, this$.RunIdentifiers, {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })) {
-      throw new Error("ARC does not contain run with given name");
+      throw new Exception("ARC does not contain run with given name");
     }
     const run = this$.GetRun(runIdentifier);
     this$.DeleteRun(runIdentifier);
@@ -153,9 +153,9 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     if (!contains(workflowIdentifier, this$.WorkflowIdentifiers, {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })) {
-      throw new Error("ARC does not contain workflow with given name");
+      throw new Exception("ARC does not contain workflow with given name");
     }
     const workflow = this$.GetWorkflow(workflowIdentifier);
     this$.DeleteWorkflow(workflowIdentifier);
@@ -245,9 +245,9 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     if (!contains(oldAssayIdentifier, this$.AssayIdentifiers, {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })) {
-      throw new Error("ARC does not contain assay with given name");
+      throw new Exception("ARC does not contain assay with given name");
     }
     super.RenameAssay(oldAssayIdentifier, newAssayIdentifier);
     const paths = this$.FileSystem.Tree.ToFilePaths();
@@ -261,9 +261,9 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     if (!contains(oldRunIdentifier, this$.RunIdentifiers, {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })) {
-      throw new Error("ARC does not contain run with given name");
+      throw new Exception("ARC does not contain run with given name");
     }
     super.RenameRun(oldRunIdentifier, newRunIdentifier);
     const paths = this$.FileSystem.Tree.ToFilePaths();
@@ -277,9 +277,9 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     if (!contains(oldWorkflowIdentifier, this$.WorkflowIdentifiers, {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })) {
-      throw new Error("ARC does not contain workflow with given name");
+      throw new Exception("ARC does not contain workflow with given name");
     }
     super.RenameWorkflow(oldWorkflowIdentifier, newWorkflowIdentifier);
     const paths = this$.FileSystem.Tree.ToFilePaths();
@@ -310,9 +310,9 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     if (!contains(oldStudyIdentifier, this$.StudyIdentifiers, {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })) {
-      throw new Error("ARC does not contain study with given name");
+      throw new Exception("ARC does not contain study with given name");
     }
     super.RenameStudy(oldStudyIdentifier, newStudyIdentifier);
     const paths = this$.FileSystem.Tree.ToFilePaths();
@@ -427,12 +427,12 @@ class ARC extends ArcInvestigation {
   MakeDataFilesAbsolute() {
     const this$ = this;
     const filesPaths = ofSeq(this$.FileSystem.Tree.ToFilePaths(), {
-      Compare: comparePrimitives
+      Compare: (x, y) => comparePrimitives(x, y) | 0
     });
     const checkExistenceFromRoot = (p) => contains$1(p, filesPaths);
     const updateColumnOption = (dataNameFunction, col) => {
-      let col_1;
-      let matchResult, col_2;
+      let col_1 = void 0;
+      let matchResult = void 0, col_2 = void 0;
       if (col != null) {
         if (col_1 = value(col), col_1.Header.IsDataColumn) {
           matchResult = 0;
@@ -487,6 +487,9 @@ class ARC extends ArcInvestigation {
       }
     }, this$.Assays);
   }
+  /**
+   * Add assay folder to the ARC.FileSystem and update the ARC.ISA with the new assay metadata
+   */
   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, fs);
@@ -500,6 +503,9 @@ class ARC extends ArcInvestigation {
     const this$ = this;
     return choose(tryISAReadContractFromPath, this$._fs.Tree.ToFilePaths());
   }
+  /**
+   * This function creates the ARC-model from fullfilled READ contracts. The necessary READ contracts can be created with `ARC.getReadContracts`.
+   */
   SetISAFromContracts(contracts) {
     const this$ = this;
     const investigation = ARCAux_getArcInvestigationFromContracts(contracts);
@@ -569,7 +575,9 @@ class ARC extends ArcInvestigation {
       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);
+      let resolvedCwl;
+      const option_1 = cwl;
+      resolvedCwl = option_1 != null ? resolveRunReferencesFromLookup(cwlFilePath, value(option_1), tryGetCWLByPath) : void 0;
       if (workflow.Datamap == null) {
         workflow.Datamap = datamap_2;
       }
@@ -582,7 +590,9 @@ class ARC extends ArcInvestigation {
       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$1((processingUnit_1) => resolveRunReferencesFromLookup(cwlFilePath_1, processingUnit_1, tryGetCWLByPath), cwl_1);
+      let resolvedCwl_1;
+      const option_3 = cwl_1;
+      resolvedCwl_1 = option_3 != null ? resolveRunReferencesFromLookup(cwlFilePath_1, value(option_3), tryGetCWLByPath) : void 0;
       if (run.Datamap == null) {
         run.Datamap = datamap_3;
       }
@@ -605,6 +615,11 @@ class ARC extends ArcInvestigation {
     const newFS = ARCAux_updateFSByARC(this$, this$._license, this$._fs);
     this$._fs = newFS;
   }
+  /**
+   * This function returns the all write Contracts for the current state of the ARC. ISA contracts do contain the object data as spreadsheets, while the other contracts only contain the path.
+   * 
+   * If datamapFile is set to true, a write contract for the datamap file will be included for each study and assay.
+   */
   GetWriteContracts(skipUpdateFS) {
     const this$ = this;
     if (!defaultArg(skipUpdateFS, false)) {
@@ -657,11 +672,19 @@ class ARC extends ArcInvestigation {
           }
         }));
       }, this$.Runs), delay(() => {
-        let l;
+        let l = void 0;
         return append(this$.License != null ? (l = value(this$.License), l.StaticHash = safeHash(l) | 0, singleton(l.ToCreateContract())) : empty(), delay(() => append(singleton(Contract.createCreate(combine("assays", ".gitkeep"), "PlainText")), delay(() => append(singleton(Contract.createCreate(combine("studies", ".gitkeep"), "PlainText")), delay(() => append(singleton(Contract.createCreate(combine("workflows", ".gitkeep"), "PlainText")), delay(() => singleton(Contract.createCreate(combine("runs", ".gitkeep"), "PlainText"))))))))));
       }))))))))));
     }));
   }
+  /**
+   * This function returns the all update Contracts for the current state of the ARC. Only update contracts for those ISA objects that have been changed will be returned.
+   * If an ISA object was added to the ARC, instead a write contract for the complete object folder will be returned.
+   * 
+   * An obect is considered changed if its hash code has changed compared with the StaticHash. An object is considered added if its StaticHash code is 0.
+   * 
+   * ISA contracts do contain the object data as spreadsheets, while the other contracts only contain the path.
+   */
   GetUpdateContracts(skipUpdateFS) {
     const this$ = this;
     if (this$.StaticHash === 0) {
@@ -675,10 +698,10 @@ class ARC extends ArcInvestigation {
           return append(collect((s) => {
             const hash_1 = s.GetLightHashCode() | 0;
             return append(s.StaticHash === 0 ? ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true) : s.StaticHash !== hash_1 ? singleton(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract(s)) : empty(), delay(() => {
-              let dm, dm_1;
+              let dm = void 0, dm_1 = void 0;
               s.StaticHash = hash_1 | 0;
               const matchValue = s.Datamap;
-              let matchResult, dm_2, dm_3;
+              let matchResult = void 0, dm_2 = void 0, dm_3 = void 0;
               if (matchValue != null) {
                 if (dm = value(matchValue), dm.StaticHash === 0) {
                   matchResult = 0;
@@ -711,10 +734,10 @@ class ARC extends ArcInvestigation {
           }, this$.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_4, dm_5;
+              let dm_4 = void 0, dm_5 = void 0;
               a.StaticHash = hash_2 | 0;
               const matchValue_1 = a.Datamap;
-              let matchResult_1, dm_6, dm_7;
+              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) {
                   matchResult_1 = 0;
@@ -747,10 +770,10 @@ class ARC extends ArcInvestigation {
           }, this$.Assays), delay(() => append(collect((w) => {
             const hash_3 = w.GetLightHashCode() | 0;
             return append(w.StaticHash === 0 ? ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true) : w.StaticHash !== hash_3 ? singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract(w)) : empty(), delay(() => {
-              let dm_8, dm_9;
+              let dm_8 = void 0, dm_9 = void 0;
               w.StaticHash = hash_3 | 0;
               const matchValue_2 = w.Datamap;
-              let matchResult_2, dm_10, dm_11;
+              let matchResult_2 = void 0, dm_10 = void 0, dm_11 = void 0;
               if (matchValue_2 != null) {
                 if (dm_8 = value(matchValue_2), dm_8.StaticHash === 0) {
                   matchResult_2 = 0;
@@ -783,10 +806,10 @@ class ARC extends ArcInvestigation {
           }, this$.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_12, dm_13;
+              let dm_12 = void 0, dm_13 = void 0;
               r.StaticHash = hash_4 | 0;
               const matchValue_3 = r.Datamap;
-              let matchResult_3, dm_14, dm_15;
+              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;
@@ -842,6 +865,7 @@ class ARC extends ArcInvestigation {
     return Clone_createCloneContract_5000466F(remoteUrl, unwrap(merge), unwrap(branch), unwrap(token), unwrap(nolfs));
   }
   Copy() {
+    let _arg = void 0;
     const this$ = this;
     const nextAssays = [];
     const nextStudies = [];
@@ -893,86 +917,80 @@ 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$1((_arg) => _arg.Copy(), this$.License);
+    let nextLicense;
+    const option_1 = this$.License;
+    nextLicense = option_1 != null ? (_arg = value(option_1), _arg.Copy()) : void 0;
     const fsCopy = this$._fs.Copy();
     return new ARC(this$.Identifier, unwrap(this$.Title), unwrap(this$.Description), unwrap(this$.SubmissionDate), unwrap(this$.PublicReleaseDate), nextOntologySourceReferences, nextPublications, nextContacts, nextAssays, nextStudies, nextWorkflows, nextRuns, nextStudyIdentifiers, nextComments, nextRemarks, fsCopy, unwrap(nextLicense));
   }
+  /**
+   * Returns the FileSystemTree of the ARC with only the registered files and folders included.
+   */
   GetRegisteredPayload(IgnoreHidden) {
-    let tree, paths, array_3;
+    let option_1 = void 0, tree = void 0, paths = void 0, array_3 = void 0, tree_1 = void 0;
     const this$ = this;
     const copy = this$.Copy();
     const registeredStudies = copy.Studies.slice();
     const registeredAssays = concat(map((s) => s.RegisteredAssays.slice(), registeredStudies));
     const includeFiles = unionMany([ofSeq(toList(delay(() => append(singleton("isa.investigation.xlsx"), delay(() => append(singleton("README.md"), delay(() => this$.License != null ? singleton(value(this$.License).Path) : empty())))))), {
-      Compare: comparePrimitives
+      Compare: (x, y) => comparePrimitives(x, y) | 0
     }), unionMany(map((s_1) => {
-      const studyFoldername = `${"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 studyFoldername = concat$1("studies", "/", s_1.Identifier);
+      return ofSeq(toList(delay(() => append(singleton(concat$1(studyFoldername, "/", "isa.study.xlsx")), delay(() => append(singleton(concat$1(studyFoldername, "/", "README.md")), delay(() => collect((table) => collect((kv) => {
         const textValue = kv[1].ToFreeTextCell().AsFreeText;
         return append(singleton(textValue), delay(() => append(singleton(`${studyFoldername}/${"resources"}/${textValue}`), delay(() => singleton(`${studyFoldername}/${"protocols"}/${textValue}`)))));
       }, table.Values), s_1.Tables))))))), {
-        Compare: comparePrimitives
+        Compare: (x_1, y_1) => comparePrimitives(x_1, y_1) | 0
       });
     }, registeredStudies), {
-      Compare: comparePrimitives
+      Compare: (x_2, y_2) => comparePrimitives(x_2, y_2) | 0
     }), unionMany(map((a) => {
-      const assayFoldername = `${"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 assayFoldername = concat$1("assays", "/", a.Identifier);
+      return ofSeq(toList(delay(() => append(singleton(concat$1(assayFoldername, "/", "isa.assay.xlsx")), delay(() => append(singleton(concat$1(assayFoldername, "/", "README.md")), delay(() => collect((table_1) => collect((kv_1) => {
         const textValue_1 = kv_1[1].ToFreeTextCell().AsFreeText;
         return append(singleton(textValue_1), delay(() => append(singleton(`${assayFoldername}/${"dataset"}/${textValue_1}`), delay(() => singleton(`${assayFoldername}/${"protocols"}/${textValue_1}`)))));
       }, table_1.Values), a.Tables))))))), {
-        Compare: comparePrimitives
+        Compare: (x_3, y_3) => comparePrimitives(x_3, y_3) | 0
       });
     }, registeredAssays), {
-      Compare: comparePrimitives
+      Compare: (x_4, y_4) => comparePrimitives(x_4, y_4) | 0
     })], {
-      Compare: comparePrimitives
+      Compare: (x_5, y_5) => comparePrimitives(x_5, y_5) | 0
     });
     const ignoreHidden = defaultArg(IgnoreHidden, true);
     const fsCopy = this$._fs.Copy();
-    return defaultArg(bind((tree_1) => {
-      if (ignoreHidden) {
-        return FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1);
-      } else {
-        return tree_1;
-      }
-    }, (tree = (paths = (array_3 = FileSystemTree.toFilePaths()(fsCopy.Tree), array_3.filter((p) => {
+    return defaultArg((option_1 = (tree = (paths = (array_3 = FileSystemTree.toFilePaths()(fsCopy.Tree), array_3.filter((p) => {
       if (p.startsWith("workflows") ? true : p.startsWith("runs")) {
         return true;
       } else {
         return FSharpSet__Contains(includeFiles, p);
       }
-    })), FileSystemTree.fromFilePaths(paths)), ignoreHidden ? FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree)), FileSystemTree.fromFilePaths([]));
+    })), 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([]));
   }
+  /**
+   * Returns the FileSystemTree of the ARC with only and folders included that are considered additional payload.
+   */
   GetAdditionalPayload(IgnoreHidden) {
-    let tree, paths, array;
+    let option_1 = void 0, tree = void 0, paths = void 0, array = void 0, tree_1 = void 0;
     const this$ = this;
     const ignoreHidden = defaultArg(IgnoreHidden, true);
     const registeredPayload = ofSeq(FileSystemTree.toFilePaths()(this$.GetRegisteredPayload()), {
-      Compare: comparePrimitives
+      Compare: (x, y) => comparePrimitives(x, y) | 0
     });
-    return defaultArg(bind((tree_1) => {
-      if (ignoreHidden) {
-        return FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1);
-      } else {
-        return tree_1;
-      }
-    }, (tree = (paths = (array = FileSystemTree.toFilePaths()(this$._fs.Copy().Tree), array.filter((p) => !FSharpSet__Contains(registeredPayload, p))), FileSystemTree.fromFilePaths(paths)), ignoreHidden ? FileSystemTree.filterFiles((n) => !n.startsWith("."))(tree) : tree)), 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 = value(option_1), ignoreHidden ? FileSystemTree.filterFolders((n_1) => !n_1.startsWith("."))(tree_1) : tree_1) : void 0), FileSystemTree.fromFilePaths([]));
   }
   static get DefaultContracts() {
-    return ofSeq$1([[".gitignore", gitignoreContract], [".gitattributes", gitattributesContract]], {
-      Compare: comparePrimitives
-    });
+    return ARCAux_defaultContracts;
   }
   static fromDeprecatedROCrateJsonString(s) {
-    let arg;
+    let arg = void 0;
     try {
       const s_1 = replace(s, "bio:additionalProperty", "sdo:additionalProperty");
       let isa;
       const matchValue = fromString(ROCrate_get_decoderDeprecated(), s_1);
       if (matchValue.tag === /* Error */
       1) {
-        throw new Error((arg = matchValue.fields[0], toText(printf("Error decoding string: %O"))(arg)));
+        throw new Exception((arg = matchValue.fields[0], toText(printf("Error decoding string: %O"))(arg)));
       } else {
         isa = matchValue.fields[0];
       }
@@ -983,13 +1001,13 @@ class ARC extends ArcInvestigation {
     }
   }
   static fromROCrateJsonString(s) {
-    let arg;
+    let arg = void 0;
     try {
       let patternInput;
       const matchValue = fromString(ROCrate_get_decoder(), s);
       if (matchValue.tag === /* Error */
       1) {
-        throw new Error((arg = matchValue.fields[0], toText(printf("Error decoding string: %O"))(arg)));
+        throw new Exception((arg = matchValue.fields[0], toText(printf("Error decoding string: %O"))(arg)));
       } else {
         patternInput = matchValue.fields[0];
       }
@@ -1008,41 +1026,62 @@ class ARC extends ArcInvestigation {
     const value = ROCrate_encoder_Z7FE34C43(this$, unwrap(this$._license), this$._fs, unwrap(ignoreBrokenWR));
     return toString(defaultSpaces(spaces), value);
   }
+  /**
+   * exports in json-ld format
+   */
   static toROCrateJsonString(spaces, ignoreBrokenWR) {
     return (obj) => obj.ToROCrateJsonString(unwrap(spaces), unwrap(ignoreBrokenWR));
   }
   GetLicenseWriteContract() {
     const this$ = this;
-    const _arg = defaultArgWith(this$.License, () => License.GetDefaultLicense());
+    let _arg;
+    const option_1 = this$.License;
+    _arg = option_1 != null ? value(option_1) : License.GetDefaultLicense();
     return _arg.ToCreateContract();
   }
+  /**
+   * Returns the write contract for the input ValidationPackagesConfig object.
+   * 
+   * This will mutate the ARC file system to include the `.arc/validation_packages.yml` file if it is not already included.
+   */
   GetValidationPackagesConfigWriteContract(vpc) {
     const this$ = this;
     const paths = this$.FileSystem.Tree.ToFilePaths();
     if (!contains$2(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })) {
       const filePaths = append$1([ValidationPackagesConfigHelper_ConfigFilePath], paths);
       this$.SetFilePaths(filePaths);
     }
     return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toCreateContract_Static_724DAE55(vpc);
   }
+  /**
+   * Returns the delete contract for `.arc/validation_packages.yml`
+   * 
+   * If the ARC file system includes the `.arc/validation_packages.yml` file, it is removed.
+   */
   GetValidationPackagesConfigDeleteContract(vpc) {
     const this$ = this;
     const paths = this$.FileSystem.Tree.ToFilePaths();
     if (contains$2(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })) {
       const filePaths = paths.filter((p) => !(p === ValidationPackagesConfigHelper_ConfigFilePath));
       this$.SetFilePaths(filePaths);
     }
     return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toDeleteContract_Static_724DAE55(vpc);
   }
+  /**
+   * Returns the read contract for `.arc/validation_packages.yml`
+   */
   GetValidationPackagesConfigReadContract() {
     return ValidationPackagesConfigHelper_ReadContract;
   }
+  /**
+   * Returns the ValidationPackagesConfig object from the given read contract if possible, otherwise returns None/null.
+   */
   GetValidationPackagesConfigFromReadContract(contract) {
     return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_tryFromReadContract_Static_7570923F(contract);
   }
@@ -1053,14 +1092,28 @@ class ARC extends ArcInvestigation {
     }
     return this$.FileSystem.Tree.ToFilePaths(unwrap(removeRoot));
   }
+  /**
+   * Builds workflow graphs for all workflows in this ARC.
+   * Returns a list of workflow identifier and Result pairs, where each Result contains
+   * either a successfully built WorkflowGraph or a GraphBuildIssue describing the failure.
+   */
   BuildWorkflowGraphs() {
     const this$ = this;
     return ofInvestigation(this$).WorkflowGraphs;
   }
+  /**
+   * Builds workflow graphs for all runs in this ARC.
+   * Returns a list of run identifier and Result pairs, where each Result contains
+   * either a successfully built WorkflowGraph or a GraphBuildIssue describing the failure.
+   */
   BuildRunGraphs() {
     const this$ = this;
     return ofInvestigation(this$).RunGraphs;
   }
+  /**
+   * Builds and returns the complete WorkflowGraphIndex containing workflow graphs
+   * for both workflows and runs in this ARC.
+   */
   BuildAllProcessingUnitGraphs() {
     const this$ = this;
     return ofInvestigation(this$);
@@ -1107,7 +1160,7 @@ function ARCAux_getRunYMLFromContracts(runIdentifier, contracts) {
 }
 function ARCAux_getCWLByPathFromContracts(contracts) {
   return ofArray(choose((c) => {
-    let matchResult, text;
+    let matchResult = void 0, text = void 0;
     if (c.Operation === "READ") {
       if (c.DTOType != null) {
         if (value(c.DTOType) === "CWL") {
@@ -1139,7 +1192,7 @@ function ARCAux_getCWLByPathFromContracts(contracts) {
         return void 0;
     }
   }, contracts), {
-    Compare: comparePrimitives
+    Compare: (x, y) => comparePrimitives(x, y) | 0
   });
 }
 function ARCAux_tryGetCWLByPath(cwlByPath, path) {
@@ -1178,5 +1231,8 @@ function ARCAux_updateFSByARC(isa, license, fs) {
   });
   return fs.Union(tree_1);
 }
+const ARCAux_defaultContracts = ofSeq$1([[".gitignore", gitignoreContract], [".gitattributes", gitattributesContract]], {
+  Compare: (x, y) => comparePrimitives(x, y) | 0
+});
 
-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 };
+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 };

package/dist/ts/ts/CWL/CWLKnownFieldNames.d.ts

@@ -0,0 +1,32 @@
+import { FSharpSet } from '@fable-org/fable-library-ts/Set.ts';
+export declare const fileInstance: FSharpSet<string>;
+export declare const directoryInstance: FSharpSet<string>;
+export declare const direntInstance: FSharpSet<string>;
+export declare const inputEnumSchema: FSharpSet<string>;
+export declare const inputRecordField: FSharpSet<string>;
+export declare const inputRecordSchema: FSharpSet<string>;
+export declare const inputArraySchema: FSharpSet<string>;
+export declare const schemaDefRequirementType: FSharpSet<string>;
+export declare const softwarePackage: FSharpSet<string>;
+export declare const inputBinding: FSharpSet<string>;
+export declare const cwlInput: FSharpSet<string>;
+export declare const outputBinding: FSharpSet<string>;
+export declare const cwlOutput: FSharpSet<string>;
+export declare const dockerRequirement: FSharpSet<string>;
+export declare const environmentDef: FSharpSet<string>;
+export declare const loadListingRequirementValue: FSharpSet<string>;
+export declare const workReuseRequirementValue: FSharpSet<string>;
+export declare const networkAccessRequirementValue: FSharpSet<string>;
+export declare const inplaceUpdateRequirementValue: FSharpSet<string>;
+export declare const resourceRequirementInstance: FSharpSet<string>;
+export declare const inlineJavascriptRequirementValue: FSharpSet<string>;
+export declare const hintUnknownValue: FSharpSet<string>;
+export declare const toolDescription: FSharpSet<string>;
+export declare const expressionToolDescription: FSharpSet<string>;
+export declare const operationDescription: FSharpSet<string>;
+export declare const workflowDescription: FSharpSet<string>;
+export declare const stepInput: FSharpSet<string>;
+export declare const stepOutputParameter: FSharpSet<string>;
+export declare const workflowStep: FSharpSet<string>;
+export declare const parameterReference: FSharpSet<string>;
+//# sourceMappingURL=CWLKnownFieldNames.d.ts.map

package/dist/ts/ts/CWL/CWLKnownFieldNames.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"CWLKnownFieldNames.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/CWL/CWLKnownFieldNames.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAS,MAAM,oCAAoC,CAAC;AAItE,eAAO,MAAM,YAAY,EAAE,SAAS,CAAC,MAAM,CAEzC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,SAAS,CAAC,MAAM,CAE9C,CAAC;AAEH,eAAO,MAAM,cAAc,EAAE,SAAS,CAAC,MAAM,CAE3C,CAAC;AAEH,eAAO,MAAM,eAAe,EAAE,SAAS,CAAC,MAAM,CAE5C,CAAC;AAEH,eAAO,MAAM,gBAAgB,EAAE,SAAS,CAAC,MAAM,CAE7C,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,SAAS,CAAC,MAAM,CAE9C,CAAC;AAEH,eAAO,MAAM,gBAAgB,EAAE,SAAS,CAAC,MAAM,CAE7C,CAAC;AAEH,eAAO,MAAM,wBAAwB,EAAE,SAAS,CAAC,MAAM,CAErD,CAAC;AAEH,eAAO,MAAM,eAAe,EAAE,SAAS,CAAC,MAAM,CAE5C,CAAC;AAEH,eAAO,MAAM,YAAY,EAAE,SAAS,CAAC,MAAM,CAEzC,CAAC;AAEH,eAAO,MAAM,QAAQ,EAAE,SAAS,CAAC,MAAM,CAErC,CAAC;AAEH,eAAO,MAAM,aAAa,EAAE,SAAS,CAAC,MAAM,CAE1C,CAAC;AAEH,eAAO,MAAM,SAAS,EAAE,SAAS,CAAC,MAAM,CAEtC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,SAAS,CAAC,MAAM,CAE9C,CAAC;AAEH,eAAO,MAAM,cAAc,EAAE,SAAS,CAAC,MAAM,CAE3C,CAAC;AAEH,eAAO,MAAM,2BAA2B,EAAE,SAAS,CAAC,MAAM,CAExD,CAAC;AAEH,eAAO,MAAM,yBAAyB,EAAE,SAAS,CAAC,MAAM,CAEtD,CAAC;AAEH,eAAO,MAAM,6BAA6B,EAAE,SAAS,CAAC,MAAM,CAE1D,CAAC;AAEH,eAAO,MAAM,6BAA6B,EAAE,SAAS,CAAC,MAAM,CAE1D,CAAC;AAEH,eAAO,MAAM,2BAA2B,EAAE,SAAS,CAAC,MAAM,CAExD,CAAC;AAEH,eAAO,MAAM,gCAAgC,EAAE,SAAS,CAAC,MAAM,CAE7D,CAAC;AAEH,eAAO,MAAM,gBAAgB,EAAE,SAAS,CAAC,MAAM,CAE7C,CAAC;AAEH,eAAO,MAAM,eAAe,EAAE,SAAS,CAAC,MAAM,CAE5C,CAAC;AAEH,eAAO,MAAM,yBAAyB,EAAE,SAAS,CAAC,MAAM,CAEtD,CAAC;AAEH,eAAO,MAAM,oBAAoB,EAAE,SAAS,CAAC,MAAM,CAEjD,CAAC;AAEH,eAAO,MAAM,mBAAmB,EAAE,SAAS,CAAC,MAAM,CAEhD,CAAC;AAEH,eAAO,MAAM,SAAS,EAAE,SAAS,CAAC,MAAM,CAEtC,CAAC;AAEH,eAAO,MAAM,mBAAmB,EAAE,SAAS,CAAC,MAAM,CAEhD,CAAC;AAEH,eAAO,MAAM,YAAY,EAAE,SAAS,CAAC,MAAM,CAEzC,CAAC;AAEH,eAAO,MAAM,kBAAkB,EAAE,SAAS,CAAC,MAAM,CAE/C,CAAC"}