@nfdi4plants/arctrl 3.2.3 → 3.3.0

package/dist/ts/ts/Conversion/Run.js

@@ -1,27 +1,29 @@
 import { class_type } from '../../node_modules/@fable-org/fable-library-ts/Reflection.js';
-import { replace, trimStart, toFail, printf, concat } from '../../node_modules/@fable-org/fable-library-ts/String.js';
-import { combineMany, combine } from '../FileSystem/Path.js';
-import { FileInstanceModule_pathOrLocation, DirectoryInstanceModule_pathOrLocation, CWLTypeModule_typesEqual, CWLTypeModule_isArrayType, CWLTypeModule_tryGetNonNullUnionType, FileInstance, InputRecordSchemaModule_tryGetFieldType, DirectoryInstance, CWLType_file } from '../CWL/CWLTypes.js';
+import { hasUriScheme, normalize, combineMany, split, combine } from '../FileSystem/Path.js';
+import { defaultOf, Exception, equals, isIterable, getEnumerator, isDisposable, disposeSafe } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
+import { mapIndexed, item, map } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
+import { join, toFail, printf, replace, concat } from '../../node_modules/@fable-org/fable-library-ts/String.js';
+import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
+import { unwrap, value, defaultArg, some, orElse } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
+import { LDRef, LDNode } from '../ROCrate/LDObject.js';
+import { Option_fromSeq, ResizeArray_map, ResizeArray_choose, ResizeArray_zip, ResizeArray_singleton, ResizeArray_appendSingleton, ResizeArray_append, Option_fromValueWithDefault, ResizeArray_filter } from '../Core/Helper/Collections.js';
 import { LDFile } from '../ROCrate/LDTypes/File.js';
-import { unwrap, value, defaultArg, some } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
-import { ResizeArray_map, ResizeArray_zip, ResizeArray_singleton, ResizeArray_appendSingleton, Option_fromSeq, Option_fromValueWithDefault, ResizeArray_filter } from '../Core/Helper/Collections.js';
-import { CWLParameterValue_Array$, CWLParameterValue_String$, CWLParameterValue_Record, CWLParameterRecordField, CWLParameterValue_File, CWLParameterValue_Boolean$, CWLParameterValue_Float, CWLParameterValue_Int, CWLParameterValue, CWLParameterValueModule_tryParseFloat, CWLParameterValueModule_tryParseInt64, CWLParameterValue_Directory } from '../CWL/ParameterValue.js';
+import { FileInstanceModule_pathOrLocation, SchemaSaladStringModule_tryLiteral, DirectoryInstanceModule_pathOrLocation, CWLTypeModule_admits, CWLTypeModule_isArrayType, CWLTypeModule_tryGetNonNullUnionType, DirectoryInstance, SchemaSaladString_Literal, FileInstance, InputRecordSchemaModule_tryGetFieldType } from '../CWL/CWLTypes.js';
+import { CWLParameterValue_Array$, CWLParameterValue_String$, CWLParameterValue_Record, CWLParameterRecordField, CWLParameterValue_Directory, CWLParameterValue_File, CWLParameterValue_Boolean$, CWLParameterValue_Float, CWLParameterValue_Int, CWLParameterValue, CWLParameterValueModule_tryParseFloat, CWLParameterValueModule_tryParseInt64 } from '../CWL/ParameterValue.js';
 import { DynamicObj } from '../fable_modules/DynamicObj.8.0.0/DynamicObj.fs.js';
-import { iterate, map, tryPick, find } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
+import { iterate, map as map$1, tryPick, append, find } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
 import { setProperty } from '../fable_modules/DynamicObj.8.0.0/DynObj.fs.js';
 import { toInt64_unchecked, fromInt32 } from '../../node_modules/@fable-org/fable-library-ts/BigInt.js';
-import { defaultOf, Exception, equals, isIterable } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 import { CWLParameterReference } from '../CWL/ParameterReference.js';
 import { formatCWLType } from '../CWL/Encode.js';
-import { item } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
-import { LDRef, LDNode } from '../ROCrate/LDObject.js';
 import { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
 import { toString, FSharpRef } from '../../node_modules/@fable-org/fable-library-ts/Types.js';
 import { tryParse } from '../../node_modules/@fable-org/fable-library-ts/Boolean.js';
 import { toFloat64 } from '../../node_modules/@fable-org/fable-library-ts/Decimal.js';
-import { WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8, WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7, WorkflowConversion_getInputParametersFromProcessingUnit_30922B92, WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F } from './Workflow.js';
+import { WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8, WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7, WorkflowConversion_getInputParametersFromProcessingUnit_30922B92, WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F, WorkflowConversion_composeReferencedFiles_Z7F3BB4EE } from './Workflow.js';
 import { LDFormalParameter } from '../ROCrate/LDTypes/FormalParameter.js';
 import { Run_cwlFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
+import { DecodeParameters_decodeParameterValue } from '../CWL/Decode.js';
 import { LDComputationalWorkflow } from '../ROCrate/LDTypes/ComputationalWorkflow.js';
 import { ARCtrl_ArcTables__ArcTables_GetProcesses_5E660E5C, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586 } from './Table.js';
 import { ArcTables } from '../Core/Table/ArcTables.js';
@@ -29,14 +31,14 @@ import { ofSeq } from '../../node_modules/@fable-org/fable-library-ts/List.js';
 import { LDWorkflowInvocation } from '../ROCrate/LDTypes/WorkflowInvocation.js';
 import { LDLabProcess } from '../ROCrate/LDTypes/LabProcess.js';
 import { ArcRun } from '../Core/ArcTypes.js';
-import { BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composePropertyValueFromOA_ZDED3A0F, BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_decomposePropertyValueToOA_Z2F770004, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
+import { addToSet } from '../../node_modules/@fable-org/fable-library-ts/MapUtil.js';
+import { BaseTypes_warnIfTitleEmpty_Z2FC25A28, BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composePropertyValueFromOA_ZDED3A0F, BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_decomposePropertyValueToOA_Z2F770004, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
 import { PersonConversion_composePerson_2B0BECCC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
 import { LDOrganization } from '../ROCrate/LDTypes/Organization.js';
-import { utcNow } from '../../node_modules/@fable-org/fable-library-ts/Date.js';
+import { utcNow, toUniversalTime } from '../../node_modules/@fable-org/fable-library-ts/Date.js';
 import { Datamap } from '../Core/Datamap.js';
 import { DatamapConversion_composeFragmentDescriptors_Z892BFC3, DatamapConversion_decomposeFragmentDescriptors_Z6E59645F } from './Datamap.js';
 import { AssayConversion_getDataFilesFromProcesses_6BABD1B0 } from './Assay.js';
-import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
 import { LDWorkflowProtocol } from '../ROCrate/LDTypes/WorkflowProtocol.js';
 import { Big } from '../../node_modules/@fable-org/fable-library-ts/lib/big.js';
 
@@ -48,36 +50,92 @@ function RunConversion_$reflection() {
   return class_type("ARCtrl.Conversion.RunConversion", void 0, RunConversion);
 }
 function RunConversion_composeCWLInputFilePath_Z384F8060(path, runName) {
-  if (path.startsWith("../..")) {
-    return replace(replace(path, "../../", ""), "../..", "");
+  if (hasUriScheme(path)) {
+    return path;
   } else {
-    return combineMany(["runs", runName, path]);
+    return normalize(combineMany(["runs", runName, path]));
   }
 }
 function RunConversion_decomposeCWLInputFilePath_Z384F8060(path, runName) {
-  const prefix = combineMany(["runs", runName]);
-  if (path.startsWith(prefix)) {
-    return trimStart(replace(path, prefix, ""), "/");
+  if (hasUriScheme(path)) {
+    return path;
   } else {
-    return combine("../..", path);
+    const runFolder = split(combineMany(["runs", runName]));
+    const segments = split(path);
+    let isInRunFolder;
+    if (segments.length >= runFolder.length) {
+      const array_1 = mapIndexed((index, segment) => item(index, segments) === segment, runFolder);
+      isInRunFolder = array_1.every((x) => x);
+    } else {
+      isInRunFolder = false;
+    }
+    if (isInRunFolder && segments.length === runFolder.length) {
+      return ".";
+    } else if (isInRunFolder) {
+      return join("/", segments.slice(runFolder.length, segments.length));
+    } else {
+      return combine("../..", join("/", segments));
+    }
   }
 }
-function RunConversion_composeCWLParameterValue_6CF93391(value, runName, context) {
+function RunConversion_composeDirectoryDataset_111D9870(path, fs, context) {
+  let collection = void 0;
+  if (hasUriScheme(path)) {
+    return LDDataset.create(path, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(context));
+  } else {
+    const id = path.endsWith("/") ? path : path + "/";
+    let files;
+    let matchValue;
+    const option_1 = fs;
+    if (option_1 != null) {
+      const fs_1 = option_1;
+      matchValue = fs_1.Tree.TryGetPath(path);
+    } else {
+      matchValue = void 0;
+    }
+    let matchResult = void 0, folder = void 0;
+    if (matchValue != null) {
+      if (matchValue.tag === /* Folder */
+      1) {
+        matchResult = 0;
+        folder = matchValue;
+      } else {
+        matchResult = 1;
+      }
+    } else {
+      matchResult = 1;
+    }
+    switch (matchResult) {
+      case 0: {
+        files = Option_fromSeq((collection = map((file) => LDFile.create(combine(path, file), void 0, void 0, void 0, void 0, void 0, unwrap(context)), folder.ToFilePaths(true)), Array.from(collection)));
+        break;
+      }
+      default:
+        files = void 0;
+    }
+    return LDDataset.create(id, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(files), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(context));
+  }
+}
+function RunConversion_composeCWLParameterValue_1A8A78ED(value, runName, context, fs) {
   switch (value.tag) {
     case /* Directory */
     6: {
       const path_3 = RunConversion_composeCWLInputFilePath_Z384F8060(DirectoryInstanceModule_pathOrLocation(value.fields[0]), runName);
-      return LDFile.create(path_3, void 0, void 0, void 0, void 0, void 0, unwrap(context));
+      if (path_3 === ".") {
+        return new LDRef(LDDataset.genIDInvesigation());
+      } else {
+        return RunConversion_composeDirectoryDataset_111D9870(path_3, unwrap(fs), unwrap(context));
+      }
     }
     case /* Array */
     7:
-      return ResizeArray_map((value_3) => RunConversion_composeCWLParameterValue_6CF93391(value_3, runName, unwrap(context)), value.fields[0]);
+      return ResizeArray_map((value_3) => RunConversion_composeCWLParameterValue_1A8A78ED(value_3, runName, unwrap(context), unwrap(fs)), value.fields[0]);
     case /* Record */
     8: {
       const fields = value.fields[0];
       const record = new DynamicObj();
       iterate((field) => {
-        setProperty(field.Name, RunConversion_composeCWLParameterValue_6CF93391(field.Value, runName, unwrap(context)), record);
+        setProperty(field.Name, RunConversion_composeCWLParameterValue_1A8A78ED(field.Value, runName, unwrap(context), unwrap(fs)), record);
       }, fields);
       return record;
     }
@@ -99,7 +157,9 @@ function RunConversion_composeCWLParameterValue_6CF93391(value, runName, context
     default: {
       const file = value.fields[0];
       const path_1 = RunConversion_composeCWLInputFilePath_Z384F8060(FileInstanceModule_pathOrLocation(file), runName);
-      const encodingFormat = file.Format;
+      let encodingFormat;
+      const option_1 = file.Format;
+      encodingFormat = option_1 != null ? SchemaSaladStringModule_tryLiteral(option_1) : void 0;
       return LDFile.create(path_1, void 0, void 0, void 0, unwrap(encodingFormat), void 0, unwrap(context));
     }
   }
@@ -108,20 +168,22 @@ function RunConversion_composeLegacyValue_Z62BDCFA3(inputValue) {
   let collection = void 0;
   const option_1 = inputValue.Value;
   if (option_1 != null) {
-    return value(option_1);
+    return option_1;
   } else {
-    return CWLParameterValue_Array$((collection = map(CWLParameterValue_String$, inputValue.Values), Array.from(collection)));
+    return CWLParameterValue_Array$((collection = map$1(CWLParameterValue_String$, inputValue.Values), Array.from(collection)));
   }
 }
-function RunConversion_composeCWLInputValue_70DD9184(inputValue, exampleOfWork, inputParam, runName) {
-  let option_4 = void 0, matchValue_1 = void 0;
+function RunConversion_composeCWLInputValue_Z65E5E0A8(inputValue, exampleOfWork, inputParam, runName, fs) {
+  let option_8 = void 0, matchValue_1 = void 0;
   if (inputParam.Type_ == null) {
     throw new Exception(`Cannot convert param values "${inputValue.Values}" as Input parameter "${inputParam.Name}" has no type.`);
   }
   const type_ = value(inputParam.Type_);
-  if (inputValue.Type != null) {
-    if (!CWLTypeModule_typesEqual(value(inputValue.Type), type_)) {
-      throw new Exception(`Type (${formatCWLType(value(inputValue.Type))}) of yml input value "${inputValue.Key}" does not match type of workflow input parameter (${formatCWLType(type_)}).`);
+  const option_1 = inputValue.Type;
+  if (option_1 != null) {
+    const valueType = option_1;
+    if (!CWLTypeModule_admits(type_, valueType)) {
+      throw new Exception(`Could not create workflow invocation for run "${runName}": Type (${formatCWLType(valueType)}) of yml input value "${inputValue.Key}" does not match type of workflow input parameter (${formatCWLType(type_)}).`);
     }
   }
   let matchResult = void 0;
@@ -146,10 +208,10 @@ function RunConversion_composeCWLInputValue_70DD9184(inputValue, exampleOfWork,
       const matchValue = inputValue.Value;
       let matchResult_1 = void 0, fileValue = void 0;
       if (matchValue != null) {
-        if (value(matchValue).tag === /* File */
+        if (matchValue.tag === /* File */
         5) {
           matchResult_1 = 0;
-          fileValue = value(matchValue).fields[0];
+          fileValue = matchValue.fields[0];
         } else {
           matchResult_1 = 1;
         }
@@ -158,9 +220,11 @@ function RunConversion_composeCWLInputValue_70DD9184(inputValue, exampleOfWork,
       }
       switch (matchResult_1) {
         case 0: {
-          const option_1 = fileValue.Format;
-          if (option_1 != null) {
-            const format = value(option_1);
+          let option_5;
+          const option_3 = fileValue.Format;
+          option_5 = option_3 != null ? SchemaSaladStringModule_tryLiteral(option_3) : void 0;
+          if (option_5 != null) {
+            const format = option_5;
             LDFile.setEncodingFormatAsString(file, format);
           }
           break;
@@ -170,13 +234,13 @@ function RunConversion_composeCWLInputValue_70DD9184(inputValue, exampleOfWork,
     }
     case 1: {
       const pv = LDPropertyValue.createCWLParameter(exampleOfWork, inputValue.Key, []);
-      const value_2 = RunConversion_composeCWLParameterValue_6CF93391(defaultArg(inputValue.Value, RunConversion_composeLegacyValue_Z62BDCFA3(inputValue)), runName);
+      const value_2 = RunConversion_composeCWLParameterValue_1A8A78ED(defaultArg(inputValue.Value, RunConversion_composeLegacyValue_Z62BDCFA3(inputValue)), runName, void 0, unwrap(fs));
       LDPropertyValue.setValueObjects(pv, value_2);
       return pv;
     }
     default: {
       const pv_1 = LDPropertyValue.createCWLParameter(exampleOfWork, inputValue.Key, []);
-      const value_4 = RunConversion_composeCWLParameterValue_6CF93391((option_4 = inputValue.Value, option_4 != null ? value(option_4) : (matchValue_1 = inputValue.Values.length | 0, matchValue_1 === 0 ? CWLParameterValue_Array$([]) : matchValue_1 === 1 ? CWLParameterValue_String$(item(0, inputValue.Values)) : CWLParameterValue_Array$(ResizeArray_map(CWLParameterValue_String$, inputValue.Values)))), runName);
+      const value_4 = RunConversion_composeCWLParameterValue_1A8A78ED((option_8 = inputValue.Value, option_8 != null ? option_8 : (matchValue_1 = inputValue.Values.length | 0, matchValue_1 === 0 ? CWLParameterValue_Array$([]) : matchValue_1 === 1 ? CWLParameterValue_String$(item(0, inputValue.Values)) : CWLParameterValue_Array$(ResizeArray_map(CWLParameterValue_String$, inputValue.Values)))), runName, void 0, unwrap(fs));
       LDPropertyValue.setValueObjects(pv_1, value_4);
       return pv_1;
     }
@@ -197,20 +261,24 @@ function RunConversion_resolveLDValue_Z224E8241(value$1, graph) {
   }
   switch (matchResult) {
     case 0:
-      return defaultArg((option_1 = value(graph).TryGetNode(ref_1.Id), option_1 != null ? some(value(option_1)) : void 0), value$1);
+      return defaultArg((option_1 = value(graph).TryGetNode(ref_1.Id), option_1 != null ? some(option_1) : void 0), value$1);
     default:
       return value$1;
   }
 }
-function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, expectedType, graph) {
-  let collection = void 0, node = void 0, node_2 = void 0, collection_1 = void 0, collection_2 = void 0, collection_3 = void 0, node_4 = void 0;
-  const value_1 = RunConversion_resolveLDValue_Z224E8241(value$1, unwrap(graph));
+function RunConversion_decomposeCWLParameterValue_Z3524B680(value, runName, expectedType, graph) {
+  let collection = void 0, option_5 = void 0, node_1 = void 0, node_3 = void 0, collection_1 = void 0, option_15 = void 0, collection_2 = void 0, collection_3 = void 0, node_5 = void 0;
+  const value_1 = RunConversion_resolveLDValue_Z224E8241(value, unwrap(graph));
+  const isDirectory = (node) => {
+    let option_1 = void 0, graph_1 = void 0;
+    return LDDataset.validate(node, unwrap((option_1 = graph, option_1 != null ? (graph_1 = option_1, graph_1.TryGetContext()) : void 0)));
+  };
   let expectedType_1;
-  const option_1 = expectedType;
-  expectedType_1 = option_1 != null ? CWLTypeModule_tryGetNonNullUnionType(value(option_1)) : void 0;
+  const option_3 = expectedType;
+  expectedType_1 = option_3 != null ? CWLTypeModule_tryGetNonNullUnionType(option_3) : void 0;
   let matchResult = void 0, arraySchema = void 0, recordSchema = void 0;
   if (expectedType_1 != null) {
-    switch (value(expectedType_1).tag) {
+    switch (expectedType_1.tag) {
       case /* File */
       0: {
         matchResult = 1;
@@ -222,49 +290,49 @@ function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, ex
         break;
       }
       case /* String */
-      3: {
+      2: {
         matchResult = 3;
         break;
       }
       case /* Int */
-      4:
+      3:
       case /* Long */
-      5: {
+      4: {
         matchResult = 4;
         break;
       }
       case /* Float */
-      6:
+      5:
       case /* Double */
-      7: {
+      6: {
         matchResult = 5;
         break;
       }
       case /* Boolean */
-      8: {
+      7: {
         matchResult = 6;
         break;
       }
       case /* Null */
-      10: {
+      17: {
         matchResult = 7;
         break;
       }
       case /* Enum */
-      13: {
+      20: {
         matchResult = 8;
         break;
       }
       case /* Array */
-      11: {
+      18: {
         matchResult = 0;
-        arraySchema = value(expectedType_1).fields[0];
+        arraySchema = expectedType_1.fields[0];
         break;
       }
       case /* Record */
-      12: {
+      19: {
         matchResult = 9;
-        recordSchema = value(expectedType_1).fields[0];
+        recordSchema = expectedType_1.fields[0];
         break;
       }
       default:
@@ -278,30 +346,36 @@ function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, ex
       if (typeof value_1 === "string") {
         return CWLParameterValue_Array$([CWLParameterValue_String$(value_1)]);
       } else if (isIterable(value_1)) {
-        return CWLParameterValue_Array$((collection = map((value_3) => RunConversion_decomposeCWLParameterValue_Z3524B680(value_3, runName, arraySchema.Items, unwrap(graph)), value_1), Array.from(collection)));
+        return CWLParameterValue_Array$((collection = map$1((value_3) => RunConversion_decomposeCWLParameterValue_Z3524B680(value_3, runName, arraySchema.Items, unwrap(graph)), value_1), Array.from(collection)));
       } else {
         return CWLParameterValue_Array$([RunConversion_decomposeCWLParameterValue_Z3524B680(value_1, runName, arraySchema.Items, unwrap(graph))]);
       }
     case 1: {
       let matchResult_1 = void 0;
       if (value_1 instanceof LDNode) {
-        if (node = value_1, LDFile.validate(node)) {
+        if (node_1 = value_1, LDFile.validate(node_1)) {
           matchResult_1 = 0;
         } else {
-          matchResult_1 = 2;
+          matchResult_1 = 3;
         }
-      } else if (typeof value_1 === "string") {
+      } else if (value_1 instanceof LDRef) {
         matchResult_1 = 1;
-      } else {
+      } else if (typeof value_1 === "string") {
         matchResult_1 = 2;
+      } else {
+        matchResult_1 = 3;
       }
       switch (matchResult_1) {
         case 0: {
-          const node_1 = value_1;
-          return CWLParameterValue_File(new FileInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(node_1.Id, runName), void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(LDFile.tryGetEncodingFormatAsString(node_1))));
+          const node_2 = value_1;
+          return CWLParameterValue_File(new FileInstance(void 0, SchemaSaladString_Literal(RunConversion_decomposeCWLInputFilePath_Z384F8060(node_2.Id, runName)), void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap((option_5 = LDFile.tryGetEncodingFormatAsString(node_2), option_5 != null ? SchemaSaladString_Literal(option_5) : void 0))));
         }
-        case 1:
-          return CWLParameterValue_File(new FileInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(value_1, runName)));
+        case 1: {
+          const reference = value_1;
+          return CWLParameterValue_File(new FileInstance(void 0, SchemaSaladString_Literal(RunConversion_decomposeCWLInputFilePath_Z384F8060(reference.Id, runName))));
+        }
+        case 2:
+          return CWLParameterValue_File(new FileInstance(void 0, SchemaSaladString_Literal(RunConversion_decomposeCWLInputFilePath_Z384F8060(value_1, runName))));
         default:
           return CWLParameterValue_String$(toString(value_1));
       }
@@ -309,23 +383,29 @@ function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, ex
     case 2: {
       let matchResult_2 = void 0;
       if (value_1 instanceof LDNode) {
-        if (node_2 = value_1, LDFile.validate(node_2)) {
+        if (node_3 = value_1, isDirectory(node_3) ? true : LDFile.validate(node_3)) {
           matchResult_2 = 0;
         } else {
-          matchResult_2 = 2;
+          matchResult_2 = 3;
         }
-      } else if (typeof value_1 === "string") {
+      } else if (value_1 instanceof LDRef) {
         matchResult_2 = 1;
-      } else {
+      } else if (typeof value_1 === "string") {
         matchResult_2 = 2;
+      } else {
+        matchResult_2 = 3;
       }
       switch (matchResult_2) {
         case 0: {
-          const node_3 = value_1;
-          return CWLParameterValue_Directory(new DirectoryInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(node_3.Id, runName)));
+          const node_4 = value_1;
+          return CWLParameterValue_Directory(new DirectoryInstance(void 0, SchemaSaladString_Literal(RunConversion_decomposeCWLInputFilePath_Z384F8060(node_4.Id, runName))));
         }
-        case 1:
-          return CWLParameterValue_Directory(new DirectoryInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(value_1, runName)));
+        case 1: {
+          const reference_1 = value_1;
+          return CWLParameterValue_Directory(new DirectoryInstance(void 0, SchemaSaladString_Literal(RunConversion_decomposeCWLInputFilePath_Z384F8060(reference_1.Id, runName))));
+        }
+        case 2:
+          return CWLParameterValue_Directory(new DirectoryInstance(void 0, SchemaSaladString_Literal(RunConversion_decomposeCWLInputFilePath_Z384F8060(value_1, runName))));
         default:
           return CWLParameterValue_String$(toString(value_1));
       }
@@ -339,21 +419,21 @@ function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, ex
         return CWLParameterValue_String$(toString(value_1));
       }
     case 4: {
-      let option_5;
-      const option_3 = CWLParameterValueModule_tryParseInt64(value_1);
-      option_5 = option_3 != null ? CWLParameterValue_Int(value(option_3)) : void 0;
-      if (option_5 != null) {
-        return value(option_5);
+      let option_9;
+      const option_7 = CWLParameterValueModule_tryParseInt64(value_1);
+      option_9 = option_7 != null ? CWLParameterValue_Int(option_7) : void 0;
+      if (option_9 != null) {
+        return option_9;
       } else {
         return CWLParameterValue_String$(toString(value_1));
       }
     }
     case 5: {
-      let option_9;
-      const option_7 = CWLParameterValueModule_tryParseFloat(value_1);
-      option_9 = option_7 != null ? CWLParameterValue_Float(value(option_7)) : void 0;
-      if (option_9 != null) {
-        return value(option_9);
+      let option_13;
+      const option_11 = CWLParameterValueModule_tryParseFloat(value_1);
+      option_13 = option_11 != null ? CWLParameterValue_Float(option_11) : void 0;
+      if (option_13 != null) {
+        return option_13;
       } else {
         return CWLParameterValue_String$(toString(value_1));
       }
@@ -364,10 +444,8 @@ function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, ex
       } else if (typeof value_1 === "string") {
         const value_6 = value_1;
         let matchValue;
-        let outArg = false;
-        matchValue = [tryParse(value_6, new FSharpRef(() => outArg, (v) => {
-          outArg = v;
-        })), outArg];
+        const cell = new FSharpRef(false);
+        matchValue = [tryParse(value_6, cell), cell.contents];
         if (matchValue[0]) {
           return CWLParameterValue_Boolean$(matchValue[1]);
         } else {
@@ -389,12 +467,12 @@ function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, ex
     case 9:
       if (value_1 instanceof DynamicObj) {
         const record = value_1;
-        return CWLParameterValue_Record((collection_1 = map((kvp) => new CWLParameterRecordField(kvp[0], RunConversion_decomposeCWLParameterValue_Z3524B680(kvp[1], runName, unwrap(InputRecordSchemaModule_tryGetFieldType(kvp[0], recordSchema)), unwrap(graph))), record.GetProperties(false)), Array.from(collection_1)));
+        return CWLParameterValue_Record((collection_1 = map$1((kvp) => new CWLParameterRecordField(kvp[0], RunConversion_decomposeCWLParameterValue_Z3524B680(kvp[1], runName, unwrap(InputRecordSchemaModule_tryGetFieldType(kvp[0], recordSchema)), unwrap(graph))), record.GetProperties(false)), Array.from(collection_1)));
       } else {
         return CWLParameterValue_String$(toString(value_1));
       }
     default: {
-      let matchResult_3 = void 0, value_8 = void 0, value_9 = void 0, value_10 = void 0, value_11 = void 0, value_12 = void 0, value_13 = void 0, node_5 = void 0, values_1 = void 0, record_1 = void 0;
+      let matchResult_3 = void 0, value_8 = void 0, value_9 = void 0, value_10 = void 0, value_11 = void 0, value_12 = void 0, value_13 = void 0, node_7 = void 0, node_8 = void 0, values_1 = void 0, record_1 = void 0;
       if (equals(value_1, defaultOf())) {
         matchResult_3 = 0;
       } else if (typeof value_1 === "string") {
@@ -416,29 +494,32 @@ function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, ex
         matchResult_3 = 6;
         value_13 = value_1;
       } else if (value_1 instanceof LDNode) {
-        if (node_4 = value_1, LDFile.validate(node_4)) {
+        if (node_5 = value_1, LDFile.validate(node_5)) {
           matchResult_3 = 7;
-          node_5 = value_1;
-        } else if (isIterable(value_1)) {
+          node_7 = value_1;
+        } else if (isDirectory(value_1)) {
           matchResult_3 = 8;
+          node_8 = value_1;
+        } else if (isIterable(value_1)) {
+          matchResult_3 = 9;
           values_1 = value_1;
         } else {
-          matchResult_3 = 9;
+          matchResult_3 = 10;
           record_1 = value_1;
         }
       } else if (value_1 instanceof DynamicObj) {
         if (isIterable(value_1)) {
-          matchResult_3 = 8;
+          matchResult_3 = 9;
           values_1 = value_1;
         } else {
-          matchResult_3 = 9;
+          matchResult_3 = 10;
           record_1 = value_1;
         }
       } else if (isIterable(value_1)) {
-        matchResult_3 = 8;
+        matchResult_3 = 9;
         values_1 = value_1;
       } else {
-        matchResult_3 = 10;
+        matchResult_3 = 11;
       }
       switch (matchResult_3) {
         case 0:
@@ -456,11 +537,13 @@ function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, ex
         case 6:
           return CWLParameterValue_Boolean$(value_13);
         case 7:
-          return CWLParameterValue_File(new FileInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(node_5.Id, runName), void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(LDFile.tryGetEncodingFormatAsString(node_5))));
+          return CWLParameterValue_File(new FileInstance(void 0, SchemaSaladString_Literal(RunConversion_decomposeCWLInputFilePath_Z384F8060(node_7.Id, runName)), void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap((option_15 = LDFile.tryGetEncodingFormatAsString(node_7), option_15 != null ? SchemaSaladString_Literal(option_15) : void 0))));
         case 8:
-          return CWLParameterValue_Array$((collection_2 = map((value_14) => RunConversion_decomposeCWLParameterValue_Z3524B680(value_14, runName, void 0, unwrap(graph)), values_1), Array.from(collection_2)));
+          return CWLParameterValue_Directory(new DirectoryInstance(void 0, SchemaSaladString_Literal(RunConversion_decomposeCWLInputFilePath_Z384F8060(node_8.Id, runName))));
         case 9:
-          return CWLParameterValue_Record((collection_3 = map((kvp_1) => new CWLParameterRecordField(kvp_1[0], RunConversion_decomposeCWLParameterValue_Z3524B680(kvp_1[1], runName, void 0, unwrap(graph))), record_1.GetProperties(false)), Array.from(collection_3)));
+          return CWLParameterValue_Array$((collection_2 = map$1((value_14) => RunConversion_decomposeCWLParameterValue_Z3524B680(value_14, runName, void 0, unwrap(graph)), values_1), Array.from(collection_2)));
+        case 10:
+          return CWLParameterValue_Record((collection_3 = map$1((kvp_1) => new CWLParameterRecordField(kvp_1[0], RunConversion_decomposeCWLParameterValue_Z3524B680(kvp_1[1], runName, void 0, unwrap(graph))), record_1.GetProperties(false)), Array.from(collection_3)));
         default:
           return CWLParameterValue_String$(toString(value_1));
       }
@@ -482,11 +565,11 @@ function RunConversion_decomposeCWLInputValue_Z1346FE9D(inputValue, runName, con
     const arg = inputValue.Id;
     exampleOfWork = toFail(printf("Input value %s of run %s must have an exampleOfWork property pointing to a CWL formal parameter."))(arg)(runName);
   } else {
-    exampleOfWork = value(matchValue);
+    exampleOfWork = matchValue;
   }
   const key = LDFormalParameter.getNameAsString(exampleOfWork, unwrap(context));
   if (LDFile.validateCWLParameter(inputValue, unwrap(context))) {
-    return new CWLParameterReference(key, [RunConversion_decomposeCWLInputFilePath_Z384F8060(inputValue.Id, runName)], void 0, CWLType_file());
+    return new CWLParameterReference(key, void 0, CWLParameterValue_File(new FileInstance(void 0, SchemaSaladString_Literal(RunConversion_decomposeCWLInputFilePath_Z384F8060(inputValue.Id, runName)))));
   } else if (LDPropertyValue.validateCWLParameter(inputValue, unwrap(context))) {
     return new CWLParameterReference(key, void 0, RunConversion_decomposeCWLParameterValue_Z3524B680(LDPropertyValue.getValueObject(inputValue, unwrap(context)), runName, unwrap(RunConversion_tryGetExpectedTypeFromFormalParameter_2664C4B8(exampleOfWork, unwrap(context), unwrap(graph))), unwrap(graph)));
   } else {
@@ -503,22 +586,30 @@ function RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run, fs) {
     const arg = run.Identifier;
     workflowProtocol = toFail(printf("Run %s must have a CWL description"))(arg);
   } else {
-    workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, value(matchValue), void 0, run.Identifier);
+    workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, matchValue, void 0, run.Identifier);
   }
-  const inputParams = ResizeArray_map((tupledArg) => {
+  const inputParams = ResizeArray_choose((tupledArg) => {
+    let matchValue_1 = void 0, option_1 = void 0, reference = void 0, option_3 = void 0;
+    const i = tupledArg[0];
     const ldI = tupledArg[1];
     const name = LDFormalParameter.getNameAsString(ldI, unwrap(workflowProtocol.TryGetContext()));
-    const paramRef = tryPick((i_1) => {
+    const given = tryPick((i_1) => {
       if (i_1.Key === name) {
         return i_1;
       } else {
         return void 0;
       }
     }, run.CWLInput);
+    const paramRef = (matchValue_1 = (option_1 = given, option_1 != null ? (reference = option_1, reference.Value) : void 0), matchValue_1 != null && !(matchValue_1.tag === /* Null */
+    0)) ? given : orElse((option_3 = i.DefaultValue, option_3 != null ? new CWLParameterReference(name, void 0, DecodeParameters_decodeParameterValue(option_3.Node)) : void 0), given);
     if (paramRef == null) {
-      throw new Exception(`Could not create workflow invocation for run "${run.Identifier}": Workflow parameter "${name}" had no assigned value.`);
+      if (i.Optional ? true : i.DefaultValue != null) {
+        return void 0;
+      } else {
+        throw new Exception(`Could not create workflow invocation for run "${run.Identifier}": Workflow parameter "${name}" had no assigned value.`);
+      }
     } else {
-      return RunConversion_composeCWLInputValue_70DD9184(value(paramRef), ldI, tupledArg[0], run.Identifier);
+      return RunConversion_composeCWLInputValue_Z65E5E0A8(paramRef, ldI, i, run.Identifier, unwrap(fs));
     }
   }, (b = LDComputationalWorkflow.getInputsAsFormalParameters(workflowProtocol, void 0, unwrap(workflowProtocol.TryGetContext())), ResizeArray_zip(WorkflowConversion_getInputParametersFromProcessingUnit_30922B92(value(run.CWLDescription)), b)));
   let processSequence;
@@ -536,8 +627,8 @@ function RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run, fs) {
       const protocol = LDLabProcess.tryGetExecutesLabProtocol(p);
       const parameterValues = Option_fromSeq(LDLabProcess.getParameterValues(p));
       let agents;
-      const option_1 = LDLabProcess.tryGetAgent(p);
-      agents = option_1 != null ? ResizeArray_singleton(value(option_1)) : void 0;
+      const option_6 = LDLabProcess.tryGetAgent(p);
+      agents = option_6 != null ? ResizeArray_singleton(option_6) : void 0;
       const disambiguatingDescriptions = Option_fromSeq(LDLabProcess.getDisambiguatingDescriptionsAsString(p));
       return LDWorkflowInvocation.create(name_1, workflowProtocol, inputs, unwrap(results), void 0, unwrap(agents), id, void 0, unwrap(disambiguatingDescriptions), unwrap(protocol), unwrap(parameterValues));
     }, processSequence));
@@ -547,61 +638,155 @@ function RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(workflowInvocat
   let matchValue = void 0;
   return [(matchValue = LDLabProcess.tryGetExecutesLabProtocol(workflowInvocation, unwrap(graph), unwrap(context)), matchValue == null ? (() => {
     throw new Exception(concat('Could not decompose workflow invocation for run "', runName, '": Workflow parameter "name" had no assigned value.'));
-  })() : WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(value(matchValue), void 0, unwrap(context), unwrap(graph))), ResizeArray_map((iv) => RunConversion_decomposeCWLInputValue_Z1346FE9D(iv, runName, unwrap(context), unwrap(graph)), LDLabProcess.getObjects(workflowInvocation, unwrap(graph), unwrap(context)))];
+  })() : WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(matchValue, void 0, unwrap(context), unwrap(graph))), ResizeArray_map((iv) => RunConversion_decomposeCWLInputValue_Z1346FE9D(iv, runName, unwrap(context), unwrap(graph)), LDLabProcess.getObjects(workflowInvocation, unwrap(graph), unwrap(context)))];
 }
-function RunConversion_composeRun_Z8CC08AC(run, fs) {
-  let i = void 0, fds_1 = void 0, vm_1 = void 0, fds = void 0, vm = void 0;
-  let workflowProtocol;
+function RunConversion_getDataEntitiesOfParameterValues_Z5C8C9A1A(invocations, knownIds) {
+  const entities = [];
+  const ids = new Set(knownIds);
+  const collect = (value) => {
+    let node = void 0;
+    let matchResult = void 0, node_1 = void 0, record = void 0, values = void 0;
+    if (value instanceof LDNode) {
+      if (node = value, LDDataset.validate(node) ? true : LDFile.validate(node)) {
+        matchResult = 0;
+        node_1 = value;
+      } else {
+        matchResult = 1;
+      }
+    } else if (typeof value === "string") {
+      matchResult = 1;
+    } else if (value instanceof DynamicObj) {
+      matchResult = 2;
+      record = value;
+    } else if (isIterable(value)) {
+      matchResult = 3;
+      values = value;
+    } else {
+      matchResult = 4;
+    }
+    switch (matchResult) {
+      case 0: {
+        if (addToSet(node_1.Id, ids)) {
+          void entities.push(node_1);
+        }
+        break;
+      }
+      case 1: {
+        break;
+      }
+      case 2: {
+        const enumerator = getEnumerator(record.GetProperties(false));
+        try {
+          while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+            collect(enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]()[1]);
+          }
+        } finally {
+          disposeSafe(enumerator);
+        }
+        break;
+      }
+      case 3: {
+        const enumerator_1 = getEnumerator(values);
+        try {
+          while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+            collect(enumerator_1["System.Collections.IEnumerator.get_Current"]());
+          }
+        } finally {
+          if (isDisposable(enumerator_1)) {
+            disposeSafe(enumerator_1);
+          }
+        }
+        break;
+      }
+      case 4: {
+        break;
+      }
+    }
+  };
+  let enumerator_2 = getEnumerator(invocations);
+  try {
+    while (enumerator_2["System.Collections.IEnumerator.MoveNext"]()) {
+      const invocation = enumerator_2["System.Collections.Generic.IEnumerator`1.get_Current"]();
+      let enumerator_3 = getEnumerator(LDLabProcess.getObjects(invocation));
+      try {
+        while (enumerator_3["System.Collections.IEnumerator.MoveNext"]()) {
+          const parameter = enumerator_3["System.Collections.Generic.IEnumerator`1.get_Current"]();
+          const option_1 = LDPropertyValue.tryGetValueObject(parameter);
+          if (option_1 != null) {
+            collect(value(option_1));
+          }
+        }
+      } finally {
+        disposeSafe(enumerator_3);
+      }
+    }
+  } finally {
+    disposeSafe(enumerator_2);
+  }
+  return entities;
+}
+function RunConversion_composeRun_3F79BD1(run, fs, dateCreated, isCrateRoot) {
+  let i = void 0, option_14 = void 0, option_17 = void 0, fs_1 = void 0, fds_1 = void 0, vm_1 = void 0, fds = void 0, vm = void 0;
+  const isCrateRoot_1 = defaultArg(isCrateRoot, false);
+  BaseTypes_warnIfTitleEmpty_Z2FC25A28("Run", run.Identifier, run.Title);
   const workflowFilePath = Run_cwlFileNameFromIdentifier(run.Identifier);
+  let workflowProtocol;
   const matchValue = run.CWLDescription;
   if (matchValue == null) {
     const arg = run.Identifier;
     workflowProtocol = toFail(printf("Run %s must have a CWL description"))(arg);
   } else {
-    workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, value(matchValue), void 0, run.Identifier);
+    workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, matchValue, void 0, run.Identifier);
   }
   const workflowInvocations = Option_fromSeq(RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run, unwrap(fs)));
   let measurementMethod;
   const option_1 = run.TechnologyType;
-  measurementMethod = option_1 != null ? BaseTypes_composeDefinedTerm_ZDED3A0F(value(option_1)) : void 0;
+  measurementMethod = option_1 != null ? BaseTypes_composeDefinedTerm_ZDED3A0F(option_1) : void 0;
   let measurementTechnique;
   const option_3 = run.TechnologyPlatform;
-  measurementTechnique = option_3 != null ? BaseTypes_composeDefinedTerm_ZDED3A0F(value(option_3)) : void 0;
+  measurementTechnique = option_3 != null ? BaseTypes_composeDefinedTerm_ZDED3A0F(option_3) : void 0;
   let variableMeasured;
   const option_5 = run.MeasurementType;
-  variableMeasured = option_5 != null ? BaseTypes_composePropertyValueFromOA_ZDED3A0F(value(option_5)) : void 0;
+  variableMeasured = option_5 != null ? BaseTypes_composePropertyValueFromOA_ZDED3A0F(option_5) : void 0;
   let persons;
   const option_7 = run.Investigation;
-  persons = option_7 != null ? (i = value(option_7), i.GetAllPersons()) : void 0;
+  persons = option_7 != null ? (i = option_7, i.GetAllPersons()) : void 0;
   const creators = Option_fromSeq(ResizeArray_map((c) => PersonConversion_composePerson_2B0BECCC(c, unwrap(persons)), run.Performers));
   const publisher = LDOrganization.create("DataPLANT");
-  const dateCreated = utcNow();
+  let dateCreated_1;
+  let copyOfStruct = defaultArg(dateCreated, utcNow());
+  dateCreated_1 = toUniversalTime(copyOfStruct);
   if (creators != null) {
     LDComputationalWorkflow.setCreators(workflowProtocol, value(creators));
   }
   LDComputationalWorkflow.setSdPublisher(workflowProtocol, publisher);
-  LDComputationalWorkflow.setDateCreatedAsDateTime(workflowProtocol, dateCreated);
+  LDComputationalWorkflow.setDateCreatedAsDateTime(workflowProtocol, dateCreated_1);
   let fragmentDescriptors;
   const option_9 = run.Datamap;
-  fragmentDescriptors = option_9 != null ? DatamapConversion_composeFragmentDescriptors_Z892BFC3(value(option_9)) : void 0;
+  fragmentDescriptors = option_9 != null ? DatamapConversion_composeFragmentDescriptors_Z892BFC3(option_9) : void 0;
   let dataFiles;
   const option_11 = workflowInvocations;
-  dataFiles = option_11 != null ? AssayConversion_getDataFilesFromProcesses_6BABD1B0(value(option_11), unwrap(fragmentDescriptors)) : void 0;
-  const hasParts = dataFiles == null ? ResizeArray_singleton(workflowProtocol) : ResizeArray_appendSingleton(workflowProtocol, value(dataFiles));
-  const variableMeasureds = variableMeasured == null ? fragmentDescriptors == null ? void 0 : (fds_1 = value(fragmentDescriptors), fds_1) : fragmentDescriptors == null ? (vm_1 = value(variableMeasured), ResizeArray_singleton(vm_1)) : (fds = value(fragmentDescriptors), vm = value(variableMeasured), ResizeArray_appendSingleton(vm, fds));
+  dataFiles = option_11 != null ? AssayConversion_getDataFilesFromProcesses_6BABD1B0(option_11, unwrap(fragmentDescriptors)) : void 0;
+  let parameterValueData;
+  let knownIds;
+  const ids = map$1((file) => file.Id, defaultArg(dataFiles, []));
+  knownIds = isCrateRoot_1 ? ids : append([LDDataset.genIDARCRun(run.Identifier)], ids);
+  parameterValueData = defaultArg((option_14 = workflowInvocations, option_14 != null ? RunConversion_getDataEntitiesOfParameterValues_Z5C8C9A1A(option_14, knownIds) : void 0), []);
+  const ownParts = ResizeArray_append(dataFiles == null ? ResizeArray_singleton(workflowProtocol) : ResizeArray_appendSingleton(workflowProtocol, dataFiles), parameterValueData);
+  const hasParts = ResizeArray_append(ownParts, defaultArg((option_17 = fs, option_17 != null ? (fs_1 = option_17, WorkflowConversion_composeReferencedFiles_Z7F3BB4EE(workflowFilePath, value(run.CWLDescription), fs_1, ownParts)) : void 0), []));
+  const variableMeasureds = variableMeasured == null ? fragmentDescriptors == null ? void 0 : (fds_1 = fragmentDescriptors, fds_1) : fragmentDescriptors == null ? (vm_1 = variableMeasured, ResizeArray_singleton(vm_1)) : (fds = fragmentDescriptors, vm = variableMeasured, ResizeArray_appendSingleton(vm, fds));
   const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, run.Comments));
   return LDDataset.createARCRun(run.Identifier, ResizeArray_singleton(workflowProtocol), void 0, unwrap(run.Title), unwrap(run.Description), unwrap(creators), unwrap(hasParts), unwrap(measurementMethod), unwrap(measurementTechnique), unwrap(variableMeasureds), unwrap(workflowInvocations), unwrap(workflowInvocations), unwrap(comments));
 }
 function RunConversion_decomposeRun_Z6839B9E8(run, graph, context) {
-  const workflowProtocol = LDDataset.tryGetMainEntityAsWorkflowProtocol(run, unwrap(graph), unwrap(context));
   const mainWorkflowInvocation = find((wi) => {
     let lp = void 0;
     const matchValue = LDLabProcess.tryGetExecutesLabProtocol(wi, unwrap(graph), unwrap(context));
     let matchResult = void 0, lp_1 = void 0;
     if (matchValue != null) {
-      if (lp = value(matchValue), LDWorkflowProtocol.validate(lp, unwrap(context))) {
+      if (lp = matchValue, LDWorkflowProtocol.validate(lp, unwrap(context))) {
         matchResult = 0;
-        lp_1 = value(matchValue);
+        lp_1 = matchValue;
       } else {
         matchResult = 1;
       }
@@ -615,23 +800,22 @@ function RunConversion_decomposeRun_Z6839B9E8(run, graph, context) {
         return false;
     }
   }, LDDataset.getAboutsAsWorkflowInvocation(run, unwrap(graph), unwrap(context)));
-  const patternInput = workflowProtocol == null ? RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(mainWorkflowInvocation, LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(context), unwrap(graph)) : [WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(value(workflowProtocol), void 0, unwrap(context), unwrap(graph)), ResizeArray_map((iv) => RunConversion_decomposeCWLInputValue_Z1346FE9D(iv, LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(context), unwrap(graph)), LDLabProcess.getObjects(mainWorkflowInvocation, unwrap(graph), unwrap(context)))];
   let measurementMethod;
   const option_1 = LDDataset.tryGetMeasurementMethodAsDefinedTerm(run, unwrap(graph), unwrap(context));
-  measurementMethod = option_1 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(value(option_1), unwrap(context)) : void 0;
+  measurementMethod = option_1 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(option_1, unwrap(context)) : void 0;
   let measurementTechnique;
   const option_3 = LDDataset.tryGetMeasurementTechniqueAsDefinedTerm(run, unwrap(graph), unwrap(context));
-  measurementTechnique = option_3 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(value(option_3), unwrap(context)) : void 0;
+  measurementTechnique = option_3 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(option_3, unwrap(context)) : void 0;
   let variableMeasured;
   const option_5 = LDDataset.tryGetVariableMeasuredAsMeasurementType(run, unwrap(graph), unwrap(context));
-  variableMeasured = option_5 != null ? BaseTypes_decomposePropertyValueToOA_Z2F770004(value(option_5), unwrap(context)) : void 0;
+  variableMeasured = option_5 != null ? BaseTypes_decomposePropertyValueToOA_Z2F770004(option_5, unwrap(context)) : void 0;
   const contacts = ResizeArray_map((c) => PersonConversion_decomposePerson_Z6839B9E8(c, unwrap(graph), unwrap(context)), LDDataset.getCreators(run, unwrap(graph), unwrap(context)));
   const comments = ResizeArray_map((c_1) => BaseTypes_decomposeComment_Z2F770004(c_1, unwrap(context)), LDDataset.getComments(run, unwrap(graph), unwrap(context)));
   let datamap;
   const v_1 = DatamapConversion_decomposeFragmentDescriptors_Z6E59645F(LDDataset.getVariableMeasuredAsFragmentDescriptors(run, unwrap(graph), unwrap(context)), unwrap(graph), unwrap(context));
   datamap = Option_fromValueWithDefault(Datamap.init(), v_1);
   const tables = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586(ofSeq(ResizeArray_filter((wi_1) => wi_1.Id !== mainWorkflowInvocation.Id, LDDataset.getAboutsAsLabProcess(run, unwrap(graph), unwrap(context)))), unwrap(graph), unwrap(context));
-  return ArcRun.create(LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(LDDataset.tryGetNameAsString(run, unwrap(context))), unwrap(LDDataset.tryGetDescriptionAsString(run, unwrap(context))), unwrap(variableMeasured), unwrap(measurementMethod), unwrap(measurementTechnique), void 0, tables.Tables, unwrap(datamap), contacts, patternInput[0], patternInput[1], comments);
+  return ArcRun.create(LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(LDDataset.tryGetNameAsString(run, unwrap(context))), unwrap(LDDataset.tryGetDescriptionAsString(run, unwrap(context))), unwrap(variableMeasured), unwrap(measurementMethod), unwrap(measurementTechnique), void 0, tables.Tables, unwrap(datamap), contacts, void 0, void 0, comments);
 }
 
-export { RunConversion, RunConversion_$reflection, RunConversion_composeCWLInputFilePath_Z384F8060, RunConversion_composeCWLInputValue_70DD9184, RunConversion_composeCWLParameterValue_6CF93391, RunConversion_composeRun_Z8CC08AC, RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC, RunConversion_decomposeCWLInputFilePath_Z384F8060, RunConversion_decomposeCWLInputValue_Z1346FE9D, RunConversion_decomposeCWLParameterValue_Z3524B680, RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D, RunConversion_decomposeRun_Z6839B9E8 };
+export { RunConversion, RunConversion_$reflection, RunConversion_composeCWLInputFilePath_Z384F8060, RunConversion_composeCWLInputValue_Z65E5E0A8, RunConversion_composeCWLParameterValue_1A8A78ED, RunConversion_composeDirectoryDataset_111D9870, RunConversion_composeRun_3F79BD1, RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC, RunConversion_decomposeCWLInputFilePath_Z384F8060, RunConversion_decomposeCWLInputValue_Z1346FE9D, RunConversion_decomposeCWLParameterValue_Z3524B680, RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D, RunConversion_decomposeRun_Z6839B9E8 };