@nfdi4plants/arctrl 3.0.0-beta.9 → 3.0.0

package/dist/ts/ts/ARC.js

@@ -10,39 +10,42 @@ import { promise } from './fable_modules/Fable.Promise.3.2.0/PromiseImpl.fs.js';
 import { getAllFilePathsAsync } from './ContractIO/FileSystemHelper.js';
 import { toArray, contains, delay, append, singleton, iterate, tryFind, find, empty, collect, toList } from '../node_modules/@fable-org/fable-library-js/Seq.js';
 import { defaultOf, stringHash, comparePrimitives, curry2, safeHash, getEnumerator, disposeSafe, equals } from '../node_modules/@fable-org/fable-library-js/Util.js';
-import { getAssayFolderPath, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath } from './FileSystem/Path.js';
+import { getAssayFolderPath, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath, normalizePathKey } from './FileSystem/Path.js';
 import { ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from './Contract/ArcAssay.js';
-import { ARCtrl_ArcRun__ArcRun_ToDeleteContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F } from './Contract/ArcRun.js';
-import { ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F } from './Contract/ArcWorkflow.js';
+import { ARCtrl_ArcRun__ArcRun_ToDeleteContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, ARCtrl_ArcRun__ArcRun_tryCWLFromReadContract_Static, ARCtrl_ArcRun__ArcRun_tryYMLFromReadContract_Static } from './Contract/ArcRun.js';
+import { ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F, ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static } from './Contract/ArcWorkflow.js';
 import { join, toFail, printf, replace, toText } from '../node_modules/@fable-org/fable-library-js/String.js';
 import { map, choose, fold, concat, contains as contains$2, append as append$1, tryPick, equalsWith, item } from '../node_modules/@fable-org/fable-library-js/Array.js';
 import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from './Contract/ArcInvestigation.js';
-import { createMissingIdentifier, Study_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Assay_datamapFileNameFromIdentifier, Workflow_fileNameFromIdentifier, Workflow_datamapFileNameFromIdentifier, Run_fileNameFromIdentifier, Run_datamapFileNameFromIdentifier } from './Core/Helper/Identifier.js';
+import { createMissingIdentifier, Workflow_cwlFileNameFromIdentifier, Run_cwlFileNameFromIdentifier, Study_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Assay_datamapFileNameFromIdentifier, Workflow_fileNameFromIdentifier, Workflow_datamapFileNameFromIdentifier, Run_fileNameFromIdentifier, Run_datamapFileNameFromIdentifier } from './Core/Helper/Identifier.js';
 import { ofSeq, contains as contains$1, unionMany, FSharpSet__Contains } from '../node_modules/@fable-org/fable-library-js/Set.js';
 import { ResizeArray_iter, ResizeArray_map } from './Core/Helper/Collections.js';
 import { FileSystemTree_Folder, FileSystemTree, FileSystemTree_File } from './FileSystem/FileSystemTree.js';
 import { tryISAReadContractFromPath } from './Contract/ARC.js';
 import { setInvestigationIdentifier } from './Core/IdentifierSetters.js';
+import { ofSeq as ofSeq$1, ofArray, tryFind as tryFind$1 } from '../node_modules/@fable-org/fable-library-js/Map.js';
 import { ArcTables } from './Core/Table/ArcTables.js';
+import { resolveRunReferencesFromLookup } from './CWLRunResolver.js';
 import { addToDict } from '../node_modules/@fable-org/fable-library-js/MapUtil.js';
 import { ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF } from './Spreadsheet/ArcInvestigation.js';
 import { ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522 } from './Spreadsheet/ArcStudy.js';
-import { toFsWorkbook } from './Spreadsheet/DataMap.js';
+import { toFsWorkbook } from './Spreadsheet/Datamap.js';
 import { ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F } from './Spreadsheet/ArcAssay.js';
 import { ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E } from './Spreadsheet/ArcWorkflow.js';
 import { ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8 } from './Spreadsheet/ArcRun.js';
 import { Dictionary_tryGet } from './fable_modules/FsSpreadsheet.7.0.0-alpha.1/Cells/FsCellsCollection.fs.js';
 import { ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from './Contract/ArcStudy.js';
-import { ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static } from './Contract/Datamap.js';
+import { ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static } from './Contract/Datamap.js';
 import { Init_createInitContract_6DFDD678, gitignoreContract, gitattributesContract, Init_createAddRemoteContract_Z721C83C5, Clone_createCloneContract_5000466F } from './Contract/Git.js';
-import { ofSeq as ofSeq$1 } from '../node_modules/@fable-org/fable-library-js/Map.js';
 import { fromString } from './fable_modules/Thoth.Json.JavaScript.0.4.1/Decode.fs.js';
-import { ROCrate_get_decoderDeprecated, ROCrate_get_decoder, ROCrate_encoder_1E8A3F74 } from './ROCrateIO.js';
+import { ROCrate_get_decoderDeprecated, ROCrate_get_decoder, ROCrate_encoder_Z7FE34C43 } from './ROCrateIO.js';
 import { toString } from './fable_modules/Thoth.Json.JavaScript.0.4.1/Encode.fs.js';
 import { defaultSpaces } from './Json/Encode.js';
 import { ValidationPackagesConfigHelper_ConfigFilePath, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toCreateContract_Static_724DAE55, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toDeleteContract_Static_724DAE55, ValidationPackagesConfigHelper_ReadContract, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_tryFromReadContract_Static_7570923F } from './Contract/ValidationPackagesConfig.js';
+import { ofInvestigation } from './WorkflowGraph/Adapters.js';
 import { FSharpRef } from '../node_modules/@fable-org/fable-library-js/Types.js';
 import { class_type } from '../node_modules/@fable-org/fable-library-js/Reflection.js';
+import { Decode_decodeCWLProcessingUnit } from './CWL/Decode.js';
 
 class ARC extends ArcInvestigation {
   constructor(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, fs, license) {
@@ -54,7 +57,7 @@ class ARC extends ArcInvestigation {
     this._fs = (fs_1 = defaultArg(fs, FileSystem.create({
       tree: FileSystemTree_Folder("", [])
     })), ARCAux_updateFSByARC(this$.contents, license, fs_1));
-    this["init@96"] = 1;
+    this["init@133"] = 1;
   }
   get FileSystem() {
     const this$ = this;
@@ -465,7 +468,7 @@ class ARC extends ArcInvestigation {
       updateColumnOption(dataNameFunction_1, t.TryGetInputColumn());
       updateColumnOption(dataNameFunction_1, t.TryGetOutputColumn());
     };
-    const updateDataMap = (dataNameFunction_2, dm) => {
+    const updateDatamap = (dataNameFunction_2, dm) => {
       iterate((c_1) => {
         if (c_1.FilePath != null) {
           const newFilePath_1 = dataNameFunction_2(c_1);
@@ -477,16 +480,16 @@ class ARC extends ArcInvestigation {
       const f_1 = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
       const source_1 = s.Tables;
       iterate(curry2(updateTable)(f_1), source_1);
-      if (s.DataMap != null) {
-        updateDataMap(f_1, value(s.DataMap));
+      if (s.Datamap != null) {
+        updateDatamap(f_1, value(s.Datamap));
       }
     }, this$.Studies);
     iterate((a_1) => {
       const f_2 = (d_1) => d_1.GetAbsolutePathForAssay(a_1.Identifier, checkExistenceFromRoot);
       const source_3 = a_1.Tables;
       iterate(curry2(updateTable)(f_2), source_3);
-      if (a_1.DataMap != null) {
-        updateDataMap(f_2, value(a_1.DataMap));
+      if (a_1.Datamap != null) {
+        updateDatamap(f_2, value(a_1.Datamap));
       }
     }, this$.Assays);
   }
@@ -522,6 +525,8 @@ class ARC extends ArcInvestigation {
     const workflows = ARCAux_getArcWorkflowsFromContracts(contracts);
     const runs = ARCAux_getArcRunsFromContracts(contracts);
     const license = ARCAux_getLicenseFromContracts(contracts);
+    const cwlByPath = ARCAux_getCWLByPathFromContracts(contracts);
+    const tryGetCWLByPath = (path) => ARCAux_tryGetCWLByPath(cwlByPath, path);
     const array_2 = this$.AssayIdentifiers;
     array_2.forEach((ai) => {
       if (!assays.some((a) => a.Identifier === ai)) {
@@ -542,9 +547,9 @@ class ARC extends ArcInvestigation {
         const registeredStudy = value(registeredStudyOpt);
         registeredStudy.UpdateReferenceByStudyFile(study, true);
       }
-      const datamap = ARCAux_getStudyDataMapFromContracts(study.Identifier, contracts);
-      if (study.DataMap == null) {
-        study.DataMap = datamap;
+      const datamap = ARCAux_getStudyDatamapFromContracts(study.Identifier, contracts);
+      if (study.Datamap == null) {
+        study.Datamap = datamap;
       }
       study.StaticHash = study.GetLightHashCode() | 0;
     });
@@ -560,25 +565,35 @@ class ARC extends ArcInvestigation {
       let updatedTables;
       const array_6 = assay_1.StudiesRegisteredIn;
       updatedTables = fold((tables, study_1) => ArcTables.updateReferenceTablesBySheets(new ArcTables(study_1.Tables), tables, false), new ArcTables(assay_1.Tables), array_6);
-      const datamap_1 = ARCAux_getAssayDataMapFromContracts(assay_1.Identifier, contracts);
-      if (assay_1.DataMap == null) {
-        assay_1.DataMap = datamap_1;
+      const datamap_1 = ARCAux_getAssayDatamapFromContracts(assay_1.Identifier, contracts);
+      if (assay_1.Datamap == null) {
+        assay_1.Datamap = datamap_1;
       }
       assay_1.Tables = updatedTables.Tables;
     });
     workflows.forEach((workflow) => {
-      const datamap_2 = ARCAux_getWorkflowDataMapFromContracts(workflow.Identifier, contracts);
-      if (workflow.DataMap == null) {
-        workflow.DataMap = datamap_2;
+      const datamap_2 = ARCAux_getWorkflowDatamapFromContracts(workflow.Identifier, contracts);
+      const cwl = ARCAux_getWorkflowCWLFromContracts(workflow.Identifier, contracts);
+      const cwlFilePath = Workflow_cwlFileNameFromIdentifier(workflow.Identifier);
+      const resolvedCwl = map$1((processingUnit) => resolveRunReferencesFromLookup(cwlFilePath, processingUnit, tryGetCWLByPath), cwl);
+      if (workflow.Datamap == null) {
+        workflow.Datamap = datamap_2;
       }
+      workflow.CWLDescription = resolvedCwl;
       this$.AddWorkflow(workflow);
       workflow.StaticHash = workflow.GetLightHashCode() | 0;
     });
     runs.forEach((run) => {
-      const datamap_3 = ARCAux_getRunDataMapFromContracts(run.Identifier, contracts);
-      if (run.DataMap == null) {
-        run.DataMap = datamap_3;
+      const datamap_3 = ARCAux_getRunDatamapFromContracts(run.Identifier, contracts);
+      const cwl_1 = ARCAux_getRunCWLFromContracts(run.Identifier, contracts);
+      const yml = ARCAux_getRunYMLFromContracts(run.Identifier, contracts);
+      const cwlFilePath_1 = Run_cwlFileNameFromIdentifier(run.Identifier);
+      const resolvedCwl_1 = map$1((processingUnit_1) => resolveRunReferencesFromLookup(cwlFilePath_1, processingUnit_1, tryGetCWLByPath), cwl_1);
+      if (run.Datamap == null) {
+        run.Datamap = datamap_3;
       }
+      run.CWLInput = defaultArg(yml, []);
+      run.CWLDescription = resolvedCwl_1;
       this$.AddRun(run);
       run.StaticHash = run.GetLightHashCode() | 0;
     });
@@ -607,8 +622,8 @@ class ARC extends ArcInvestigation {
     iterate((s) => {
       s.StaticHash = s.GetLightHashCode() | 0;
       addToDict(filemap, Study_fileNameFromIdentifier(s.Identifier), ["ISA_Study", ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(s)]);
-      if (s.DataMap != null) {
-        const dm = value(s.DataMap);
+      if (s.Datamap != null) {
+        const dm = value(s.Datamap);
         dm.StaticHash = safeHash(dm) | 0;
         addToDict(filemap, Study_datamapFileNameFromIdentifier(s.Identifier), ["ISA_Datamap", toFsWorkbook(dm)]);
       }
@@ -616,8 +631,8 @@ class ARC extends ArcInvestigation {
     iterate((a) => {
       a.StaticHash = a.GetLightHashCode() | 0;
       addToDict(filemap, Assay_fileNameFromIdentifier(a.Identifier), ["ISA_Assay", ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(a)]);
-      if (a.DataMap != null) {
-        const dm_1 = value(a.DataMap);
+      if (a.Datamap != null) {
+        const dm_1 = value(a.Datamap);
         dm_1.StaticHash = safeHash(dm_1) | 0;
         addToDict(filemap, Assay_datamapFileNameFromIdentifier(a.Identifier), ["ISA_Datamap", toFsWorkbook(dm_1)]);
       }
@@ -625,8 +640,11 @@ class ARC extends ArcInvestigation {
     iterate((w) => {
       w.StaticHash = w.GetLightHashCode() | 0;
       addToDict(filemap, Workflow_fileNameFromIdentifier(w.Identifier), ["ISA_Workflow", ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E(w)]);
-      if (w.DataMap != null) {
-        const dm_2 = value(w.DataMap);
+      if (w.CWLDescription != null) {
+        throw new Error("Not implemented yet: CWL description in ARC.GetWriteContracts");
+      }
+      if (w.Datamap != null) {
+        const dm_2 = value(w.Datamap);
         dm_2.StaticHash = safeHash(dm_2) | 0;
         addToDict(filemap, Workflow_datamapFileNameFromIdentifier(w.Identifier), ["ISA_Datamap", toFsWorkbook(dm_2)]);
       }
@@ -634,8 +652,14 @@ class ARC extends ArcInvestigation {
     iterate((r) => {
       r.StaticHash = r.GetLightHashCode() | 0;
       addToDict(filemap, Run_fileNameFromIdentifier(r.Identifier), ["ISA_Run", ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8(r)]);
-      if (r.DataMap != null) {
-        const dm_3 = value(r.DataMap);
+      if (r.CWLDescription != null) {
+        throw new Error("Not implemented yet: CWL description in ARC.GetWriteContracts");
+      }
+      if (r.CWLInput.length > 0) {
+        throw new Error("Not implemented yet: CWL YAML input in ARC.GetWriteContracts");
+      }
+      if (r.Datamap != null) {
+        const dm_3 = value(r.Datamap);
         dm_3.StaticHash = safeHash(dm_3) | 0;
         addToDict(filemap, Run_datamapFileNameFromIdentifier(r.Identifier), ["ISA_Datamap", toFsWorkbook(dm_3)]);
       }
@@ -674,7 +698,7 @@ class ARC extends ArcInvestigation {
             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;
               s.StaticHash = hash_1 | 0;
-              const matchValue = s.DataMap;
+              const matchValue = s.Datamap;
               let matchResult, dm_2, dm_3;
               if (matchValue != null) {
                 if (dm = value(matchValue), dm.StaticHash === 0) {
@@ -691,12 +715,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
                     dm_2.StaticHash = safeHash(dm_2) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
                     dm_3.StaticHash = safeHash(dm_3) | 0;
                     return empty();
                   }));
@@ -710,7 +734,7 @@ class ARC extends ArcInvestigation {
             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;
               a.StaticHash = hash_2 | 0;
-              const matchValue_1 = a.DataMap;
+              const matchValue_1 = a.Datamap;
               let matchResult_1, dm_6, dm_7;
               if (matchValue_1 != null) {
                 if (dm_4 = value(matchValue_1), dm_4.StaticHash === 0) {
@@ -727,12 +751,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_1) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
+                  return append(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(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
                     dm_7.StaticHash = safeHash(dm_7) | 0;
                     return empty();
                   }));
@@ -746,7 +770,7 @@ class ARC extends ArcInvestigation {
             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;
               w.StaticHash = hash_3 | 0;
-              const matchValue_2 = w.DataMap;
+              const matchValue_2 = w.Datamap;
               let matchResult_2, dm_10, dm_11;
               if (matchValue_2 != null) {
                 if (dm_8 = value(matchValue_2), dm_8.StaticHash === 0) {
@@ -763,12 +787,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_2) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5(dm_10, w.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5(dm_10, w.Identifier)), delay(() => {
                     dm_10.StaticHash = safeHash(dm_10) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, w.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, w.Identifier)), delay(() => {
                     dm_11.StaticHash = safeHash(dm_11) | 0;
                     return empty();
                   }));
@@ -782,7 +806,7 @@ class ARC extends ArcInvestigation {
             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;
               r.StaticHash = hash_4 | 0;
-              const matchValue_3 = r.DataMap;
+              const matchValue_3 = r.Datamap;
               let matchResult_3, dm_14, dm_15;
               if (matchValue_3 != null) {
                 if (dm_12 = value(matchValue_3), dm_12.StaticHash === 0) {
@@ -799,12 +823,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_3) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
                     dm_14.StaticHash = safeHash(dm_14) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
                     dm_15.StaticHash = safeHash(dm_15) | 0;
                     return empty();
                   }));
@@ -999,14 +1023,14 @@ class ARC extends ArcInvestigation {
       return toFail(printf("Could not parse ARC-RO-Crate metadata: \n%s"))(arg_1);
     }
   }
-  ToROCrateJsonString(spaces) {
+  ToROCrateJsonString(spaces, ignoreBrokenWR) {
     const this$ = this;
     this$.MakeDataFilesAbsolute();
-    const value = ROCrate_encoder_1E8A3F74(this$, unwrap(this$._license), this$._fs);
+    const value = ROCrate_encoder_Z7FE34C43(this$, unwrap(this$._license), this$._fs, unwrap(ignoreBrokenWR));
     return toString(defaultSpaces(spaces), value);
   }
-  static toROCrateJsonString(spaces) {
-    return (obj) => obj.ToROCrateJsonString(unwrap(spaces));
+  static toROCrateJsonString(spaces, ignoreBrokenWR) {
+    return (obj) => obj.ToROCrateJsonString(unwrap(spaces), unwrap(ignoreBrokenWR));
   }
   GetLicenseWriteContract() {
     const this$ = this;
@@ -1050,6 +1074,18 @@ class ARC extends ArcInvestigation {
     }
     return this$.FileSystem.Tree.ToFilePaths(unwrap(removeRoot));
   }
+  BuildWorkflowGraphs() {
+    const this$ = this;
+    return ofInvestigation(this$).WorkflowGraphs;
+  }
+  BuildRunGraphs() {
+    const this$ = this;
+    return ofInvestigation(this$).RunGraphs;
+  }
+  BuildAllProcessingUnitGraphs() {
+    const this$ = this;
+    return ofInvestigation(this$);
+  }
 }
 function ARC_$reflection() {
   return class_type("ARCtrl.ARC", void 0, ARC, ArcInvestigation_$reflection());
@@ -1069,17 +1105,66 @@ function ARCAux_getArcWorkflowsFromContracts(contracts) {
 function ARCAux_getArcRunsFromContracts(contracts) {
   return choose(ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, contracts);
 }
-function ARCAux_getAssayDataMapFromContracts(assayIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static(assayIdentifier, c), contracts);
+function ARCAux_getAssayDatamapFromContracts(assayIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static(assayIdentifier, c), contracts);
+}
+function ARCAux_getStudyDatamapFromContracts(studyIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static(studyIdentifier, c), contracts);
+}
+function ARCAux_getWorkflowDatamapFromContracts(workflowIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static(workflowIdentifier, c), contracts);
+}
+function ARCAux_getRunDatamapFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static(runIdentifier, c), contracts);
+}
+function ARCAux_getWorkflowCWLFromContracts(workflowIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static(workflowIdentifier, c), contracts);
+}
+function ARCAux_getRunCWLFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcRun__ArcRun_tryCWLFromReadContract_Static(runIdentifier, c), contracts);
 }
-function ARCAux_getStudyDataMapFromContracts(studyIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static(studyIdentifier, c), contracts);
+function ARCAux_getRunYMLFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcRun__ArcRun_tryYMLFromReadContract_Static(runIdentifier, c), contracts);
 }
-function ARCAux_getWorkflowDataMapFromContracts(workflowIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static(workflowIdentifier, c), contracts);
+function ARCAux_getCWLByPathFromContracts(contracts) {
+  return ofArray(choose((c) => {
+    let matchResult, text;
+    if (c.Operation === "READ") {
+      if (c.DTOType != null) {
+        if (value(c.DTOType) === "CWL") {
+          if (c.DTO != null) {
+            if (typeof value(c.DTO) === "string") {
+              matchResult = 0;
+              text = value(c.DTO);
+            } else {
+              matchResult = 1;
+            }
+          } else {
+            matchResult = 1;
+          }
+        } else {
+          matchResult = 1;
+        }
+      } else {
+        matchResult = 1;
+      }
+    } else {
+      matchResult = 1;
+    }
+    switch (matchResult) {
+      case 0: {
+        const cwl = Decode_decodeCWLProcessingUnit(text);
+        return [normalizePathKey(c.Path), cwl];
+      }
+      default:
+        return void 0;
+    }
+  }, contracts), {
+    Compare: comparePrimitives
+  });
 }
-function ARCAux_getRunDataMapFromContracts(runIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static(runIdentifier, c), contracts);
+function ARCAux_tryGetCWLByPath(cwlByPath, path) {
+  return tryFind$1(normalizePathKey(path), cwlByPath);
 }
 function ARCAux_getArcInvestigationFromContracts(contracts) {
   const matchValue = choose(ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts);
@@ -1095,16 +1180,16 @@ function ARCAux_getLicenseFromContracts(contracts) {
 }
 function ARCAux_updateFSByARC(isa, license, fs) {
   let assaysFolder;
-  const assays = map((a) => FileSystemTree.createAssayFolder(a.Identifier, a.DataMap != null), toArray(isa.Assays));
+  const assays = map((a) => FileSystemTree.createAssayFolder(a.Identifier, a.Datamap != null), toArray(isa.Assays));
   assaysFolder = FileSystemTree.createAssaysFolder(assays);
   let studiesFolder;
-  const studies = map((s) => FileSystemTree.createStudyFolder(s.Identifier, s.DataMap != null), toArray(isa.Studies));
+  const studies = map((s) => FileSystemTree.createStudyFolder(s.Identifier, s.Datamap != null), toArray(isa.Studies));
   studiesFolder = FileSystemTree.createStudiesFolder(studies);
   let workflowsFolder;
-  const workflows = map((w) => FileSystemTree.createWorkflowFolder(w.Identifier, w.DataMap != null), toArray(isa.Workflows));
+  const workflows = map((w) => FileSystemTree.createWorkflowFolder(w.Identifier, w.CWLDescription != null, w.Datamap != null), toArray(isa.Workflows));
   workflowsFolder = FileSystemTree.createWorkflowsFolder(workflows);
   let runsFolder;
-  const runs = map((r) => FileSystemTree.createRunFolder(r.Identifier, r.DataMap != null), toArray(isa.Runs));
+  const runs = map((r) => FileSystemTree.createRunFolder(r.Identifier, r.CWLDescription != null, r.CWLInput.length > 0, r.Datamap != null), toArray(isa.Runs));
   runsFolder = FileSystemTree.createRunsFolder(runs);
   const investigation = FileSystemTree.createInvestigationFile();
   let tree_1;
@@ -1115,4 +1200,4 @@ function ARCAux_updateFSByARC(isa, license, fs) {
   return fs.Union(tree_1);
 }
 
-export { ARC, ARCAux_getArcAssaysFromContracts, ARCAux_getArcInvestigationFromContracts, ARCAux_getArcRunsFromContracts, ARCAux_getArcStudiesFromContracts, ARCAux_getArcWorkflowsFromContracts, ARCAux_getAssayDataMapFromContracts, ARCAux_getLicenseFromContracts, ARCAux_getRunDataMapFromContracts, ARCAux_getStudyDataMapFromContracts, ARCAux_getWorkflowDataMapFromContracts, ARCAux_updateFSByARC, ARC_$ctor_Z443FB9BF, ARC_$reflection };
+export { ARC, ARCAux_getArcAssaysFromContracts, ARCAux_getArcInvestigationFromContracts, ARCAux_getArcRunsFromContracts, ARCAux_getArcStudiesFromContracts, ARCAux_getArcWorkflowsFromContracts, ARCAux_getAssayDatamapFromContracts, ARCAux_getCWLByPathFromContracts, ARCAux_getLicenseFromContracts, ARCAux_getRunCWLFromContracts, ARCAux_getRunDatamapFromContracts, ARCAux_getRunYMLFromContracts, ARCAux_getStudyDatamapFromContracts, ARCAux_getWorkflowCWLFromContracts, ARCAux_getWorkflowDatamapFromContracts, ARCAux_tryGetCWLByPath, ARCAux_updateFSByARC, ARC_$ctor_Z443FB9BF, ARC_$reflection };

package/dist/ts/ts/CWL/CWLProcessingUnit.d.ts

@@ -0,0 +1,62 @@
+import { Union } from '@fable-org/fable-library-js/Types.js';
+import { CWLToolDescription } from './ToolDescription.js';
+import { CWLWorkflowDescription } from './WorkflowDescription.js';
+import { CWLExpressionToolDescription } from './ExpressionToolDescription.js';
+import { CWLOperationDescription } from './OperationDescription.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { CWLInput } from './Inputs.js';
+import { CWLOutput } from './Outputs.js';
+import { HintEntry_$union, Requirement_$union } from './Requirements.js';
+import { WorkflowStepRun_$union } from './WorkflowSteps.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+export type CWLProcessingUnit_$union = CWLProcessingUnit<0> | CWLProcessingUnit<1> | CWLProcessingUnit<2> | CWLProcessingUnit<3>;
+export type CWLProcessingUnit_$cases = {
+    0: ["CommandLineTool", [CWLToolDescription]];
+    1: ["Workflow", [CWLWorkflowDescription]];
+    2: ["ExpressionTool", [CWLExpressionToolDescription]];
+    3: ["Operation", [CWLOperationDescription]];
+};
+export declare function CWLProcessingUnit_CommandLineTool(Item: CWLToolDescription): CWLProcessingUnit<0>;
+export declare function CWLProcessingUnit_Workflow(Item: CWLWorkflowDescription): CWLProcessingUnit<1>;
+export declare function CWLProcessingUnit_ExpressionTool(Item: CWLExpressionToolDescription): CWLProcessingUnit<2>;
+export declare function CWLProcessingUnit_Operation(Item: CWLOperationDescription): CWLProcessingUnit<3>;
+export declare class CWLProcessingUnit<Tag extends keyof CWLProcessingUnit_$cases> extends Union<Tag, CWLProcessingUnit_$cases[Tag][0]> {
+    readonly tag: Tag;
+    readonly fields: CWLProcessingUnit_$cases[Tag][1];
+    constructor(tag: Tag, fields: CWLProcessingUnit_$cases[Tag][1]);
+    cases(): string[];
+}
+export declare function CWLProcessingUnit_$reflection(): TypeInfo;
+/**
+ * Returns normalized inputs for all CWL processing unit variants.
+ */
+export declare function CWLProcessingUnit_getInputs_30922B92(processingUnit: CWLProcessingUnit_$union): CWLInput[];
+/**
+ * Returns outputs for all CWL processing unit variants.
+ */
+export declare function CWLProcessingUnit_getOutputs_30922B92(processingUnit: CWLProcessingUnit_$union): CWLOutput[];
+/**
+ * Returns requirements for all CWL processing unit variants.
+ */
+export declare function CWLProcessingUnit_getRequirements_30922B92(processingUnit: CWLProcessingUnit_$union): Requirement_$union[];
+/**
+ * Returns hints for all CWL processing unit variants.
+ */
+export declare function CWLProcessingUnit_getHints_30922B92(processingUnit: CWLProcessingUnit_$union): HintEntry_$union[];
+/**
+ * Returns intent for all CWL processing unit variants.
+ */
+export declare function CWLProcessingUnit_getIntent_30922B92(processingUnit: CWLProcessingUnit_$union): string[];
+/**
+ * Returns known requirement hints only, dropping unknown extension hints.
+ */
+export declare function CWLProcessingUnit_getKnownHints_30922B92(processingUnit: CWLProcessingUnit_$union): Requirement_$union[];
+export declare function WorkflowStepRunOps_fromTool(tool: CWLToolDescription): WorkflowStepRun_$union;
+export declare function WorkflowStepRunOps_fromWorkflow(workflow: CWLWorkflowDescription): WorkflowStepRun_$union;
+export declare function WorkflowStepRunOps_fromExpressionTool(expressionTool: CWLExpressionToolDescription): WorkflowStepRun_$union;
+export declare function WorkflowStepRunOps_fromOperation(operation: CWLOperationDescription): WorkflowStepRun_$union;
+export declare function WorkflowStepRunOps_tryGetTool(run: WorkflowStepRun_$union): Option<CWLToolDescription>;
+export declare function WorkflowStepRunOps_tryGetWorkflow(run: WorkflowStepRun_$union): Option<CWLWorkflowDescription>;
+export declare function WorkflowStepRunOps_tryGetExpressionTool(run: WorkflowStepRun_$union): Option<CWLExpressionToolDescription>;
+export declare function WorkflowStepRunOps_tryGetOperation(run: WorkflowStepRun_$union): Option<CWLOperationDescription>;
+//# sourceMappingURL=CWLProcessingUnit.d.ts.map

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

@@ -0,0 +1 @@
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