@nfdi4plants/arctrl 3.2.2 → 3.3.0

package/dist/ts/ts/Conversion/Workflow.js

@@ -1,43 +1,44 @@
 import { class_type } from '../../node_modules/@fable-org/fable-library-ts/Reflection.js';
-import { isComplexType, cwlTypeToYamlString, writeYaml, encodeCWLType } from '../CWL/Encode.js';
-import { read } from '../fable_modules/YAMLicious.1.0.0/Reader.fs.js';
-import { YAMLElement_Sequence, YAMLElement_Comment$ } from '../fable_modules/YAMLicious.1.0.0/YAMLiciousTypes.fs.js';
-import { object } from '../fable_modules/YAMLicious.1.0.0/Decode.fs.js';
-import { Decode_cwlTypeDecoder$0027, Decode_cwlTypeStringMatcher } from '../CWL/Decode.js';
-import { isEmpty, head, tail } from '../../node_modules/@fable-org/fable-library-ts/List.js';
-import { value, defaultArg, unwrap } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
+import { isComplexType, cwlTypeToYamlString, writeYaml, encodeCWLTypeShorthand, encodeProcessingUnitElement } from '../CWL/Encode.js';
+import { ListEntry$1, SchemaSaladStringModule_tryLiteral, SchemaSaladString_Literal, CWLTypeModule_makeOptional, ListEntry$1_Value, RawYaml__get_MixinPath } from '../CWL/CWLTypes.js';
+import { Decode_cwlTypeFromAdditionalType } from '../CWL/Decode.js';
 import { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
-import { Exception, int32ToString, stringHash } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
+import { unwrap, value, orElse, defaultArg } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
+import { Exception, equals, int32ToString, stringHash, getEnumerator, disposeSafe } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 import { LDFormalParameter } from '../ROCrate/LDTypes/FormalParameter.js';
-import { InputBinding, CWLInput } from '../CWL/Inputs.js';
-import { tryPick, exactlyOne, toArray, find } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
-import { OutputBinding, CWLOutput } from '../CWL/Outputs.js';
+import { InputBinding, BindingPosition_Number$, CWLInput } from '../CWL/Inputs.js';
+import { tryPick, exactlyOne, map, choose, toArray, exists, mapIndexed, filter, find } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
+import { OutputBinding, OutputGlob_Multiple, OutputGlob_Single, CWLOutput } from '../CWL/Outputs.js';
+import { item, tryPick as tryPick$1, append } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
+import { ResizeArray_map, ResizeArray_filter, ResizeArray_singleton, Option_fromSeq, ResizeArray_choose, ResizeArray_appendSingleton, ResizeArray_append, Option_fromValueWithDefault } from '../Core/Helper/Collections.js';
 import { Component_create_Z7A4FC9 } from '../Core/Process/Component.js';
-import { BaseTypes_decomposePropertyValue_Z2F770004, BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
-import { CWLProcessingUnit_getInputs_30922B92, CWLProcessingUnit_Workflow, CWLProcessingUnit_ExpressionTool, CWLProcessingUnit_Operation, CWLProcessingUnit_CommandLineTool } from '../CWL/CWLProcessingUnit.js';
+import { BaseTypes_decomposePropertyValue_Z2F770004, BaseTypes_warnIfTitleEmpty_Z2FC25A28, BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
+import { CWLProcessingUnit, WorkflowStepRunOps_tryGetWorkflow, WorkflowStepRunOps_tryGetProcessingUnit, CWLProcessingUnit_Workflow, CWLProcessingUnit_ExpressionTool, CWLProcessingUnit_Operation, CWLProcessingUnit_CommandLineTool } from '../CWL/CWLProcessingUnit.js';
+import { split, getRelativePathFromFile, normalize, hasUriScheme, splitWithPrefix, normalizeSegments, combine } from '../FileSystem/Path.js';
 import { WorkflowStep, WorkflowStepRun_RunString } from '../CWL/WorkflowSteps.js';
-import { normalize } from '../FileSystem/Path.js';
-import { tryPick as tryPick$1 } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
 import { distinct } from '../../node_modules/@fable-org/fable-library-ts/Seq2.js';
-import { concat, toFail, printf } from '../../node_modules/@fable-org/fable-library-ts/String.js';
+import { concat, isNullOrWhiteSpace, join, toFail, printf } from '../../node_modules/@fable-org/fable-library-ts/String.js';
 import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
 import { LDWorkflowProtocol } from '../ROCrate/LDTypes/WorkflowProtocol.js';
-import { ResizeArray_map, ResizeArray_singleton, Option_fromSeq, ResizeArray_choose, ResizeArray_appendSingleton, Option_fromValueWithDefault } from '../Core/Helper/Collections.js';
+import { YamlNodeModule_isMissingValue } from '../fable_modules/YAMLicious.2.0.0/Node.fs.js';
+import { tryPick as tryPick$2 } from '../../node_modules/@fable-org/fable-library-ts/List.js';
+import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.js';
+import { addToSet } from '../../node_modules/@fable-org/fable-library-ts/MapUtil.js';
+import { LDFile } from '../ROCrate/LDTypes/File.js';
 import { LDComputerLanguage } from '../ROCrate/LDTypes/ComputerLanguage.js';
 import { CWLToolDescription } from '../CWL/ToolDescription.js';
 import { LDComputationalWorkflow } from '../ROCrate/LDTypes/ComputationalWorkflow.js';
 import { LDLabProtocol } from '../ROCrate/LDTypes/LabProtocol.js';
 import { CWLExpressionToolDescription } from '../CWL/ExpressionToolDescription.js';
 import { CWLOperationDescription } from '../CWL/OperationDescription.js';
-import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.js';
-import { resolveWorkflowStepRunFromLookup } from '../CWLRunResolver.js';
+import { resolveWorkflowStepFromLookup } from '../CWLRunResolver.js';
 import { Workflow_cwlFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
 import { LDOrganization } from '../ROCrate/LDTypes/Organization.js';
 import { ArcWorkflow } from '../Core/ArcTypes.js';
 import { PersonConversion_composePerson_2B0BECCC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
-import { utcNow } from '../../node_modules/@fable-org/fable-library-ts/Date.js';
-import { DatamapConversion_composeFragmentDescriptors_Z892BFC3, DatamapConversion_decomposeFragmentDescriptors_Z6E59645F } from './Datamap.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';
 
 class WorkflowConversion {
   constructor() {
@@ -50,88 +51,82 @@ function WorkflowConversion_composeAdditionalType_Z5C31A0F9(t) {
   if (isComplexType(t)) {
     return cwlTypeToYamlString(t);
   } else {
-    const s = writeYaml(encodeCWLType(t));
+    const s = writeYaml(encodeCWLTypeShorthand(t));
     return s.trim();
   }
 }
 function WorkflowConversion_decomposeAdditionalType_Z721C83C5(t) {
-  const yamlElement = read(t);
-  let matchResult = void 0, items = void 0;
-  switch (yamlElement.tag) {
-    case /* Value */
-    1: {
-      matchResult = 0;
-      break;
-    }
-    case /* Object */
-    3: {
-      if (!isEmpty(yamlElement.fields[0])) {
-        if (head(yamlElement.fields[0]).tag === /* Sequence */
-        2) {
-          if (isEmpty(tail(yamlElement.fields[0]))) {
-            matchResult = 1;
-            items = head(yamlElement.fields[0]).fields[0];
-          } else {
-            matchResult = 2;
-          }
-        } else {
-          matchResult = 2;
-        }
-      } else {
-        matchResult = 2;
-      }
-      break;
-    }
-    default:
-      matchResult = 2;
-  }
-  switch (matchResult) {
-    case 0:
-      return object((get$) => Decode_cwlTypeStringMatcher(t, get$), YAMLElement_Comment$("unused-shorthand-context"))[0];
-    case 1:
-      return Decode_cwlTypeDecoder$0027(YAMLElement_Sequence(items));
-    default:
-      return Decode_cwlTypeDecoder$0027(yamlElement);
-  }
+  return Decode_cwlTypeFromAdditionalType(t);
 }
 function WorkflowConversion_composeFormalParamInputIdentifiers(prefix, position) {
   if (prefix == null) {
     if (position == null) {
       return void 0;
     } else {
-      const po_1 = value(position) | 0;
+      const po_1 = position | 0;
       return [LDPropertyValue.createPosition(po_1)];
     }
   } else if (position == null) {
-    const pr_1 = value(prefix);
+    const pr_1 = prefix;
     return [LDPropertyValue.createPrefix(pr_1)];
   } else {
-    const po = value(position) | 0;
-    const pr = value(prefix);
+    const po = position | 0;
+    const pr = prefix;
     return [LDPropertyValue.createPosition(po), LDPropertyValue.createPrefix(pr)];
   }
 }
 function WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(inp, workflowName, runName) {
+  let option_5 = void 0;
   let additionalType;
   const matchValue = inp.Type_;
   if (matchValue == null) {
     throw new Exception("Input must have a type");
   } else {
-    additionalType = WorkflowConversion_composeAdditionalType_Z5C31A0F9(value(matchValue));
+    additionalType = WorkflowConversion_composeAdditionalType_Z5C31A0F9(matchValue);
   }
-  const valueRequired = !defaultArg(inp.Optional, false);
+  const valueRequired = !inp.Optional;
   const id = LDFormalParameter.genID(inp.Name, unwrap(workflowName), unwrap(runName));
   let identifiers;
-  const option_2 = inp.InputBinding;
-  if (option_2 != null) {
-    const ib = value(option_2);
-    identifiers = WorkflowConversion_composeFormalParamInputIdentifiers(ib.Prefix, ib._position);
+  let option_7;
+  const option_1 = inp.InputBinding;
+  if (option_1 != null) {
+    const entry = option_1;
+    option_7 = ListEntry$1.tryValue(entry);
+  } else {
+    option_7 = void 0;
+  }
+  if (option_7 != null) {
+    const ib = option_7;
+    let position;
+    const option_3 = ib._position;
+    if (option_3 != null) {
+      const _arg = option_3;
+      switch (_arg.tag) {
+        case /* Expression */
+        1:
+        case /* Imported */
+        2:
+        case /* Included */
+        3:
+        case /* Mixed */
+        4: {
+          position = void 0;
+          break;
+        }
+        default:
+          position = _arg.fields[0];
+      }
+    } else {
+      position = void 0;
+    }
+    identifiers = WorkflowConversion_composeFormalParamInputIdentifiers((option_5 = ib.Prefix, option_5 != null ? SchemaSaladStringModule_tryLiteral(option_5) : void 0), position);
   } else {
     identifiers = void 0;
   }
   return LDFormalParameter.create(additionalType, id, void 0, inp.Name, void 0, void 0, void 0, void 0, valueRequired, unwrap(identifiers));
 }
 function WorkflowConversion_decomposeInputBindings_1AAAE9A5(identifiers, context) {
+  let option_1 = void 0, option_3 = void 0;
   const prefix = tryPick((n) => LDPropertyValue.tryGetAsPrefix(n, unwrap(context)), identifiers);
   const position = tryPick((n_1) => LDPropertyValue.tryGetAsPosition(n_1, unwrap(context)), identifiers);
   let matchResult = void 0;
@@ -148,40 +143,23 @@ function WorkflowConversion_decomposeInputBindings_1AAAE9A5(identifiers, context
     case 0:
       return void 0;
     default:
-      return InputBinding.create(unwrap(prefix), unwrap(position));
+      return InputBinding.create(unwrap((option_1 = prefix, option_1 != null ? SchemaSaladString_Literal(option_1) : void 0)), unwrap((option_3 = position, option_3 != null ? BindingPosition_Number$(option_3) : void 0)));
   }
 }
 function WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(inp, context, graph) {
+  let option_1 = void 0;
   const t_1 = WorkflowConversion_decomposeAdditionalType_Z721C83C5(exactlyOne(inp.AdditionalType));
   const binding = WorkflowConversion_decomposeInputBindings_1AAAE9A5(LDFormalParameter.getIdentifiers(inp, unwrap(graph), unwrap(context)), unwrap(context));
-  let optional;
-  const matchValue = LDFormalParameter.tryGetValueRequiredAsBoolean(inp, unwrap(context));
-  let matchResult = void 0;
-  if (matchValue != null) {
-    if (value(matchValue)) {
-      matchResult = 0;
-    } else {
-      matchResult = 1;
-    }
-  } else {
-    matchResult = 1;
-  }
-  switch (matchResult) {
-    case 0: {
-      optional = void 0;
-      break;
-    }
-    default:
-      optional = true;
-  }
-  return new CWLInput(LDFormalParameter.getNameAsString(inp, unwrap(context)), t_1, unwrap(binding), unwrap(optional));
+  const required = equals(LDFormalParameter.tryGetValueRequiredAsBoolean(inp, unwrap(context)), true);
+  return new CWLInput(LDFormalParameter.getNameAsString(inp, unwrap(context)), required ? t_1 : CWLTypeModule_makeOptional(t_1), unwrap((option_1 = binding, option_1 != null ? ListEntry$1_Value(option_1) : void 0)));
 }
-function WorkflowConversion_composeFormalParameterOutputIdentifiers_6DFDD678(glob) {
+function WorkflowConversion_composeFormalParameterOutputIdentifiers_A254C9D(glob) {
+  let collection = void 0;
   if (glob == null) {
     return void 0;
   } else {
-    const g = value(glob);
-    return [LDPropertyValue.createGlob(g)];
+    const globs = glob;
+    return collection = map((g) => LDPropertyValue.createGlob(g), choose(SchemaSaladStringModule_tryLiteral, globs.AsValues())), Array.from(collection);
   }
 }
 function WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(out, workflowName, runName) {
@@ -190,30 +168,48 @@ function WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(out, work
   if (matchValue == null) {
     throw new Exception("Output must have a type");
   } else {
-    additionalType = WorkflowConversion_composeAdditionalType_Z5C31A0F9(value(matchValue));
+    additionalType = WorkflowConversion_composeAdditionalType_Z5C31A0F9(matchValue);
   }
   const id = LDFormalParameter.genID(out.Name, unwrap(workflowName), unwrap(runName));
   let identifiers;
+  let option_3;
   const option_1 = out.OutputBinding;
   if (option_1 != null) {
-    const ob = value(option_1);
-    identifiers = WorkflowConversion_composeFormalParameterOutputIdentifiers_6DFDD678(ob.Glob);
+    const entry = option_1;
+    option_3 = ListEntry$1.tryValue(entry);
+  } else {
+    option_3 = void 0;
+  }
+  if (option_3 != null) {
+    const ob = option_3;
+    identifiers = WorkflowConversion_composeFormalParameterOutputIdentifiers_A254C9D(ob.Glob);
   } else {
     identifiers = void 0;
   }
   return LDFormalParameter.create(additionalType, id, void 0, out.Name, void 0, void 0, void 0, void 0, true, unwrap(identifiers));
 }
 function WorkflowConversion_decomposeOutputBindings_1AAAE9A5(identifiers, context) {
-  return OutputBinding.create(unwrap(tryPick((n) => LDPropertyValue.tryGetAsGlob(n, unwrap(context)), identifiers)));
+  let globs;
+  const collection = choose((n) => LDPropertyValue.tryGetAsGlob(n, unwrap(context)), identifiers);
+  globs = Array.from(collection);
+  const matchValue = globs.length | 0;
+  switch (matchValue) {
+    case 0:
+      return OutputBinding.create();
+    case 1:
+      return OutputBinding.create(OutputGlob_Single(SchemaSaladString_Literal(item(0, globs))));
+    default:
+      return OutputBinding.create(OutputGlob_Multiple(ResizeArray_map(SchemaSaladString_Literal, globs)));
+  }
 }
 function WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(outp, context, graph) {
   const t_1 = WorkflowConversion_decomposeAdditionalType_Z721C83C5(exactlyOne(outp.AdditionalType));
   const binding = WorkflowConversion_decomposeOutputBindings_1AAAE9A5(LDFormalParameter.getIdentifiers(outp, unwrap(graph), unwrap(context)), unwrap(context));
   const option_1 = LDFormalParameter.tryGetValueRequiredAsBoolean(outp, unwrap(context));
   if (option_1 != null) {
-    !value(option_1);
+    !option_1;
   }
-  return new CWLOutput(LDFormalParameter.getNameAsString(outp, unwrap(context)), t_1, binding);
+  return new CWLOutput(LDFormalParameter.getNameAsString(outp, unwrap(context)), t_1, ListEntry$1_Value(binding));
 }
 function WorkflowConversion_composeComputationalTool_Z685B8F25(tool) {
   let c = void 0, f = void 0, i = void 0, oa = void 0, s = void 0;
@@ -221,9 +217,9 @@ function WorkflowConversion_composeComputationalTool_Z685B8F25(tool) {
   const matchValue = tool.ComponentType;
   let matchResult = void 0, c_1 = void 0;
   if (matchValue != null) {
-    if (c = value(matchValue), c.Name != null) {
+    if (c = matchValue, c.Name != null) {
       matchResult = 0;
-      c_1 = value(matchValue);
+      c_1 = matchValue;
     } else {
       matchResult = 1;
     }
@@ -240,16 +236,16 @@ function WorkflowConversion_composeComputationalTool_Z685B8F25(tool) {
   }
   let patternInput_1;
   const matchValue_1 = tool.ComponentValue;
-  patternInput_1 = matchValue_1 == null ? [void 0, void 0] : value(matchValue_1).tag === /* Float */
-  2 ? (f = value(matchValue_1).fields[0], [f.toString(), void 0]) : value(matchValue_1).tag === /* Int */
-  1 ? (i = value(matchValue_1).fields[0] | 0, [int32ToString(i), void 0]) : value(matchValue_1).tag === /* Ontology */
-  0 ? (oa = value(matchValue_1).fields[0], [oa.Name, oa.TermAccessionNumber]) : (s = value(matchValue_1).fields[0], [s, void 0]);
+  patternInput_1 = matchValue_1 == null ? [void 0, void 0] : matchValue_1.tag === /* Float */
+  2 ? (f = matchValue_1.fields[0], [f.toString(), void 0]) : matchValue_1.tag === /* Int */
+  1 ? (i = matchValue_1.fields[0] | 0, [int32ToString(i), void 0]) : matchValue_1.tag === /* Ontology */
+  0 ? (oa = matchValue_1.fields[0], [oa.Name, oa.TermAccessionNumber]) : (s = matchValue_1.fields[0], [s, void 0]);
   let patternInput_2;
   const matchValue_2 = tool.ComponentUnit;
   if (matchValue_2 == null) {
     patternInput_2 = [void 0, void 0];
   } else {
-    const oa_1 = value(matchValue_2);
+    const oa_1 = matchValue_2;
     patternInput_2 = [oa_1.Name, oa_1.TermAccessionNumber];
   }
   return LDPropertyValue.createComponent(patternInput[0], unwrap(patternInput_1[0]), void 0, unwrap(patternInput[1]), unwrap(patternInput_2[1]), unwrap(patternInput_2[0]), unwrap(patternInput_1[1]));
@@ -259,7 +255,7 @@ function WorkflowConversion_decomposeComputationalTool_Z6839B9E8(tool, graph, co
   return Component_create_Z7A4FC9(unwrap(patternInput[1]), unwrap(patternInput[2]), patternInput[0]);
 }
 function WorkflowConversion_getInputParametersFromProcessingUnit_30922B92(pu) {
-  return CWLProcessingUnit_getInputs_30922B92(pu);
+  return CWLProcessingUnit.getInputValues(pu);
 }
 function WorkflowConversion_get_toolDescriptionTypeName() {
   return "ToolDescription";
@@ -273,22 +269,104 @@ function WorkflowConversion_get_expressionToolDescriptionTypeName() {
 function WorkflowConversion_get_operationDescriptionTypeName() {
   return "OperationDescription";
 }
-function WorkflowConversion_runToIdentifier_Z4EBA8CB1(run) {
+function WorkflowConversion_isInArcFolder_Z721C83C5(path) {
+  const segments = split(path);
+  if (segments.length > 1) {
+    if ((item(0, segments) === "assays" ? true : item(0, segments) === "studies") ? true : item(0, segments) === "workflows") {
+      return true;
+    } else {
+      return item(0, segments) === "runs";
+    }
+  } else {
+    return false;
+  }
+}
+function WorkflowConversion_runToIdentifier_Z4E98F2C(cwlFilePath, run) {
+  const ofPath = (runPath) => {
+    const matchValue = WorkflowConversion_tryResolveFileReference(cwlFilePath, runPath);
+    let matchResult = void 0, path_1 = void 0;
+    if (matchValue != null) {
+      if (WorkflowConversion_isInArcFolder_Z721C83C5(matchValue)) {
+        matchResult = 0;
+        path_1 = matchValue;
+      } else {
+        matchResult = 1;
+      }
+    } else {
+      matchResult = 1;
+    }
+    switch (matchResult) {
+      case 0:
+        return "./" + path_1;
+      default:
+        return runPath;
+    }
+  };
+  let matchResult_1 = void 0, runPath_1 = void 0;
   switch (run.tag) {
+    case /* RunImport */
+    1: {
+      matchResult_1 = 0;
+      runPath_1 = run.fields[0];
+      break;
+    }
+    case /* RunMixed */
+    2: {
+      matchResult_1 = 1;
+      break;
+    }
+    case /* RunRaw */
+    3: {
+      matchResult_1 = 2;
+      break;
+    }
     case /* RunCommandLineTool */
-    1:
-      return "inline:CommandLineTool";
+    4: {
+      matchResult_1 = 3;
+      break;
+    }
     case /* RunWorkflow */
-    2:
-      return "inline:Workflow";
+    5: {
+      matchResult_1 = 4;
+      break;
+    }
     case /* RunExpressionTool */
-    3:
-      return "inline:ExpressionTool";
+    6: {
+      matchResult_1 = 5;
+      break;
+    }
     case /* RunOperation */
-    4:
-      return "inline:Operation";
+    7: {
+      matchResult_1 = 6;
+      break;
+    }
+    default: {
+      matchResult_1 = 0;
+      runPath_1 = run.fields[0];
+    }
+  }
+  switch (matchResult_1) {
+    case 0:
+      return ofPath(runPath_1);
+    case 1:
+      return ofPath(RawYaml__get_MixinPath(run.fields[0]));
+    case 2:
+      return void 0;
+    case 3:
+      return "inline:CommandLineTool";
+    case 4:
+      return "inline:Workflow";
+    case 5:
+      return "inline:ExpressionTool";
     default:
-      return run.fields[0];
+      return "inline:Operation";
+  }
+}
+function WorkflowConversion_identifierToRun_Z384F8060(cwlFilePath, identifier) {
+  if (identifier.startsWith("./") && WorkflowConversion_isInArcFolder_Z721C83C5(identifier)) {
+    return getRelativePathFromFile(cwlFilePath, identifier);
+  } else {
+    return identifier;
   }
 }
 function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedRunPath, graph, context) {
@@ -301,7 +379,7 @@ function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedR
     }
   };
   if (graph != null) {
-    const graph_1 = value(graph);
+    const graph_1 = graph;
     const normalizedResolvedRunPath = normalize(resolvedRunPath);
     const candidateNode = tryPick$1((id) => graph_1.TryGetNode(id), toArray(distinct([resolvedRunPath, normalizedResolvedRunPath, concat("./", normalizedResolvedRunPath)], {
       Equals: (x, y) => x === y,
@@ -309,15 +387,15 @@ function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedR
     })));
     let matchResult = void 0, node_3 = void 0, node_4 = void 0, node_5 = void 0;
     if (candidateNode != null) {
-      if (node = value(candidateNode), LDWorkflowProtocol.validate(node, unwrap(context))) {
+      if (node = candidateNode, LDWorkflowProtocol.validate(node, unwrap(context))) {
         matchResult = 0;
-        node_3 = value(candidateNode);
-      } else if (node_1 = value(candidateNode), LDDataset.validateARCWorkflow(node_1, graph_1, unwrap(context))) {
+        node_3 = candidateNode;
+      } else if (node_1 = candidateNode, LDDataset.validateARCWorkflow(node_1, graph_1, unwrap(context))) {
         matchResult = 1;
-        node_4 = value(candidateNode);
-      } else if (node_2 = value(candidateNode), LDDataset.validateARCRun(node_2, unwrap(context))) {
+        node_4 = candidateNode;
+      } else if (node_2 = candidateNode, LDDataset.validateARCRun(node_2, unwrap(context))) {
         matchResult = 2;
-        node_5 = value(candidateNode);
+        node_5 = candidateNode;
       } else {
         matchResult = 3;
       }
@@ -330,7 +408,7 @@ function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedR
       case 1: {
         const option_1 = LDDataset.tryGetMainEntityAsWorkflowProtocol(node_4, graph_1, unwrap(context));
         if (option_1 != null) {
-          return tryDecodeWorkflowProtocol(value(option_1));
+          return tryDecodeWorkflowProtocol(option_1);
         } else {
           return void 0;
         }
@@ -338,7 +416,7 @@ function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedR
       case 2: {
         const option_3 = LDDataset.tryGetMainEntityAsWorkflowProtocol(node_5, graph_1, unwrap(context));
         if (option_3 != null) {
-          return tryDecodeWorkflowProtocol(value(option_3));
+          return tryDecodeWorkflowProtocol(option_3);
         } else {
           return void 0;
         }
@@ -350,60 +428,459 @@ function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedR
     return void 0;
   }
 }
+function WorkflowConversion_isRelativeFileReference_Z721C83C5(reference) {
+  if (!isNullOrWhiteSpace(reference) && !hasUriScheme(reference)) {
+    return splitWithPrefix(reference)[0] == null;
+  } else {
+    return false;
+  }
+}
+function WorkflowConversion_tryResolveFileReference(cwlFilePath, reference) {
+  if (WorkflowConversion_isRelativeFileReference_Z721C83C5(reference)) {
+    const fileSegments = split(cwlFilePath);
+    const segments_1 = normalizeSegments(append(fileSegments.slice(void 0, fileSegments.length - 2 + 1), split(reference)));
+    if (segments_1.length === 0 ? true : item(0, segments_1) === "..") {
+      return void 0;
+    } else {
+      return join("/", segments_1);
+    }
+  } else {
+    return void 0;
+  }
+}
+function WorkflowConversion_fileReferencesOfYaml_51084C1(root) {
+  const references = [];
+  const tryScalarText = (node) => {
+    const matchValue = node.Kind;
+    let matchResult = void 0, scalar_1 = void 0;
+    if (matchValue.tag === /* Scalar */
+    0) {
+      if (matchValue.fields[0], !YamlNodeModule_isMissingValue(node)) {
+        matchResult = 0;
+        scalar_1 = matchValue.fields[0];
+      } else {
+        matchResult = 1;
+      }
+    } else {
+      matchResult = 1;
+    }
+    switch (matchResult) {
+      case 0:
+        return scalar_1.Value;
+      default:
+        return void 0;
+    }
+  };
+  const isDirective = (key) => {
+    if (key === "$import" ? true : key === "$include") {
+      return true;
+    } else {
+      return key === "$mixin";
+    }
+  };
+  const visit = (isStep) => (node_1) => {
+    let literalClass = void 0;
+    const matchValue_1 = node_1.Kind;
+    switch (matchValue_1.tag) {
+      case /* Mapping */
+      1: {
+        const collection = matchValue_1.fields[0];
+        const fieldText = (name) => tryPick$2((entry) => {
+          if (equals(tryScalarText(entry.Key), name)) {
+            return tryScalarText(entry.Value);
+          } else {
+            return void 0;
+          }
+        }, collection.Items);
+        const matchValue_2 = fieldText("class");
+        let matchResult_1 = void 0, literalClass_1 = void 0;
+        if (matchValue_2 != null) {
+          if (literalClass = matchValue_2, literalClass === "File" ? true : literalClass === "Directory") {
+            matchResult_1 = 0;
+            literalClass_1 = matchValue_2;
+          } else {
+            matchResult_1 = 1;
+          }
+        } else {
+          matchResult_1 = 1;
+        }
+        switch (matchResult_1) {
+          case 0: {
+            const option_2 = orElse(fieldText("location"), fieldText("path"));
+            if (option_2 != null) {
+              const path = option_2;
+              void references.push([path, literalClass_1 === "Directory"]);
+            }
+            break;
+          }
+        }
+        const isWorkflow = equals(fieldText("class"), "Workflow");
+        const enumerator = getEnumerator(collection.Items);
+        try {
+          while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+            const entry_1 = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+            const key_1 = defaultArg(tryScalarText(entry_1.Key), "");
+            const matchValue_3 = tryScalarText(entry_1.Value);
+            let matchResult_2 = void 0, path_2 = void 0;
+            if (matchValue_3 != null) {
+              if (matchValue_3, isDirective(key_1) ? true : isStep && key_1 === "run") {
+                matchResult_2 = 0;
+                path_2 = matchValue_3;
+              } else if (isWorkflow && key_1 === "steps") {
+                matchResult_2 = 1;
+              } else {
+                matchResult_2 = 2;
+              }
+            } else if (isWorkflow && key_1 === "steps") {
+              matchResult_2 = 1;
+            } else {
+              matchResult_2 = 2;
+            }
+            switch (matchResult_2) {
+              case 0: {
+                void references.push([path_2, false]);
+                break;
+              }
+              case 1: {
+                visitSteps(entry_1.Value);
+                break;
+              }
+              case 2: {
+                visit(false)(entry_1.Value);
+                break;
+              }
+            }
+          }
+        } finally {
+          disposeSafe(enumerator);
+        }
+        break;
+      }
+      case /* Sequence */
+      2: {
+        const enumerator_1 = getEnumerator(matchValue_1.fields[0].Items);
+        try {
+          while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+            visit(false)(enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]().Node);
+          }
+        } finally {
+          disposeSafe(enumerator_1);
+        }
+        break;
+      }
+      default:
+    }
+  };
+  const visitSteps = (node_2) => {
+    const matchValue_4 = node_2.Kind;
+    switch (matchValue_4.tag) {
+      case /* Mapping */
+      1: {
+        const enumerator_2 = getEnumerator(matchValue_4.fields[0].Items);
+        try {
+          while (enumerator_2["System.Collections.IEnumerator.MoveNext"]()) {
+            const entry_2 = enumerator_2["System.Collections.Generic.IEnumerator`1.get_Current"]();
+            const key_2 = defaultArg(tryScalarText(entry_2.Key), "");
+            const matchValue_5 = tryScalarText(entry_2.Value);
+            let matchResult_3 = void 0, path_4 = void 0;
+            if (matchValue_5 != null) {
+              if (matchValue_5, isDirective(key_2)) {
+                matchResult_3 = 0;
+                path_4 = matchValue_5;
+              } else {
+                matchResult_3 = 1;
+              }
+            } else {
+              matchResult_3 = 1;
+            }
+            switch (matchResult_3) {
+              case 0: {
+                void references.push([path_4, false]);
+                break;
+              }
+              case 1: {
+                visit(true)(entry_2.Value);
+                break;
+              }
+            }
+          }
+        } finally {
+          disposeSafe(enumerator_2);
+        }
+        break;
+      }
+      case /* Sequence */
+      2: {
+        const enumerator_3 = getEnumerator(matchValue_4.fields[0].Items);
+        try {
+          while (enumerator_3["System.Collections.IEnumerator.MoveNext"]()) {
+            visit(true)(enumerator_3["System.Collections.Generic.IEnumerator`1.get_Current"]().Node);
+          }
+        } finally {
+          disposeSafe(enumerator_3);
+        }
+        break;
+      }
+      default:
+    }
+  };
+  visit(false)(root);
+  return references;
+}
+function WorkflowConversion_resolvedRunsOf_30922B92(processingUnit) {
+  const resolved = [];
+  const entered = [];
+  const visit = (workflow) => {
+    if (!exists((other) => other === workflow, entered)) {
+      void entered.push(workflow);
+      let enumerator = getEnumerator(CWLWorkflowDescription.getStepValues(workflow));
+      try {
+        while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+          const step = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+          const matchValue = step.Run;
+          let matchResult = void 0, runPath = void 0;
+          switch (matchValue.tag) {
+            case /* RunString */
+            0: {
+              matchResult = 0;
+              runPath = matchValue.fields[0];
+              break;
+            }
+            case /* RunImport */
+            1: {
+              matchResult = 0;
+              runPath = matchValue.fields[0];
+              break;
+            }
+            case /* RunWorkflow */
+            5: {
+              matchResult = 1;
+              break;
+            }
+            default:
+              matchResult = 2;
+          }
+          switch (matchResult) {
+            case 0: {
+              let option_3;
+              const option_1 = step.ResolvedRun.Run;
+              option_3 = option_1 != null ? WorkflowStepRunOps_tryGetProcessingUnit(option_1) : void 0;
+              if (option_3 != null) {
+                const target = option_3;
+                void resolved.push([runPath, target]);
+              }
+              break;
+            }
+            case 1: {
+              const option_5 = WorkflowStepRunOps_tryGetWorkflow(step.Run);
+              if (option_5 != null) {
+                visit(option_5);
+              }
+              break;
+            }
+          }
+        }
+      } finally {
+        disposeSafe(enumerator);
+      }
+    }
+  };
+  if (processingUnit.tag === /* Workflow */
+  1) {
+    visit(processingUnit.fields[0]);
+  }
+  return resolved;
+}
+function WorkflowConversion_getReferencedFilePaths_589B7F6(cwlFilePath, processingUnit, fs) {
+  const mainPath = normalize(cwlFilePath);
+  const paths = [];
+  const added = /* @__PURE__ */ new Set([]);
+  const visited = /* @__PURE__ */ new Set([]);
+  const add = (path_1) => {
+    if (path_1 !== mainPath && addToSet(path_1, added)) {
+      void paths.push(path_1);
+    }
+  };
+  const visit = (filePath, processingUnit_1) => {
+    if (addToSet(filePath, visited)) {
+      let enumerator = getEnumerator(WorkflowConversion_fileReferencesOfYaml_51084C1(encodeProcessingUnitElement(processingUnit_1)));
+      try {
+        while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+          let path = void 0, matchValue = void 0;
+          const forLoopVar = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+          const matchValue_1 = WorkflowConversion_tryResolveFileReference(filePath, forLoopVar[0]);
+          let matchResult = void 0, path_4 = void 0, path_5 = void 0;
+          if (matchValue_1 != null) {
+            if (matchValue_1, forLoopVar[1]) {
+              matchResult = 0;
+              path_4 = matchValue_1;
+            } else if (path = matchValue_1, matchValue = fs.Tree.TryGetPath(path), matchValue != null && matchValue.tag === /* File */
+            0) {
+              matchResult = 1;
+              path_5 = matchValue_1;
+            } else {
+              matchResult = 2;
+            }
+          } else {
+            matchResult = 2;
+          }
+          switch (matchResult) {
+            case 0: {
+              const matchValue_2 = fs.Tree.TryGetPath(path_4);
+              let matchResult_1 = void 0, folder = void 0;
+              if (matchValue_2 != null) {
+                if (matchValue_2.tag === /* Folder */
+                1) {
+                  matchResult_1 = 0;
+                  folder = matchValue_2;
+                } else {
+                  matchResult_1 = 1;
+                }
+              } else {
+                matchResult_1 = 1;
+              }
+              switch (matchResult_1) {
+                case 0: {
+                  const arr = folder.ToFilePaths(true);
+                  for (let idx = 0; idx <= arr.length - 1; idx++) {
+                    add(combine(path_4, item(idx, arr)));
+                  }
+                  break;
+                }
+              }
+              break;
+            }
+            case 1: {
+              add(path_5);
+              break;
+            }
+          }
+        }
+      } finally {
+        disposeSafe(enumerator);
+      }
+      let enumerator_1 = getEnumerator(WorkflowConversion_resolvedRunsOf_30922B92(processingUnit_1));
+      try {
+        while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+          const forLoopVar_1 = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
+          const option_1 = WorkflowConversion_tryResolveFileReference(filePath, forLoopVar_1[0]);
+          if (option_1 != null) {
+            visit(option_1, forLoopVar_1[1]);
+          }
+        }
+      } finally {
+        disposeSafe(enumerator_1);
+      }
+    }
+  };
+  visit(mainPath, processingUnit);
+  return paths;
+}
+function WorkflowConversion_composeReferencedFiles_Z7F3BB4EE(cwlFilePath, processingUnit, fs, parts) {
+  const partPaths = /* @__PURE__ */ new Set([]);
+  const enumerator = getEnumerator(parts);
+  try {
+    while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+      const part = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+      addToSet(normalize(part.Id), partPaths);
+    }
+  } finally {
+    disposeSafe(enumerator);
+  }
+  return ResizeArray_map((path_1) => LDFile.create(path_1), ResizeArray_filter((path) => !partPaths.has(path), WorkflowConversion_getReferencedFilePaths_589B7F6(cwlFilePath, processingUnit, fs)));
+}
 function WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA(filePath, workflow, workflowName, runName) {
+  let arg = void 0;
   let inputs;
   const option_1 = workflow.Inputs;
-  inputs = option_1 != null ? ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), value(option_1)) : void 0;
-  const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), workflow.Outputs);
+  inputs = option_1 != null ? (arg = option_1, ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), ListEntry$1.values(arg))) : void 0;
+  const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), ListEntry$1.values(workflow.Outputs));
   return LDWorkflowProtocol.create(filePath, unwrap(inputs), outputs, void 0, void 0, void 0, filePath, ResizeArray_singleton(LDComputerLanguage.createCWL()), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, [WorkflowConversion_get_toolDescriptionTypeName()]);
 }
 function WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8(protocol, context, graph) {
   const inputs = ResizeArray_map((i) => WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(i, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getInputsAsFormalParameters(protocol, unwrap(graph), unwrap(context)));
-  return new CWLToolDescription(ResizeArray_map((o) => WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(o, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getOutputsAsFormalParameter(protocol, unwrap(graph), unwrap(context))), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, inputs);
+  const outputs = ResizeArray_map((o) => WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(o, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getOutputsAsFormalParameter(protocol, unwrap(graph), unwrap(context)));
+  return new CWLToolDescription(ListEntry$1.ofValues(outputs), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, ListEntry$1.ofValues(inputs));
 }
 function WorkflowConversion_composeWorkflowProtocolFromExpressionToolDescription_Z7BEB6658(filePath, expressionTool, workflowName, runName) {
+  let arg = void 0;
   let inputs;
   const option_1 = expressionTool.Inputs;
-  inputs = option_1 != null ? ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), value(option_1)) : void 0;
-  const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), expressionTool.Outputs);
+  inputs = option_1 != null ? (arg = option_1, ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), ListEntry$1.values(arg))) : void 0;
+  const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), ListEntry$1.values(expressionTool.Outputs));
   const protocol = LDWorkflowProtocol.create(filePath, unwrap(inputs), outputs, void 0, void 0, void 0, filePath, ResizeArray_singleton(LDComputerLanguage.createCWL()), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, [WorkflowConversion_get_expressionToolDescriptionTypeName()]);
-  LDLabProtocol.setDescriptionAsString(protocol, expressionTool.Expression);
+  LDLabProtocol.setDescriptionAsString(protocol, expressionTool.Expression.AsDirectiveString);
   return protocol;
 }
 function WorkflowConversion_decomposeWorkflowProtocolToExpressionToolDescription_2664C4B8(protocol, context, graph) {
   const inputs = ResizeArray_map((i) => WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(i, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getInputsAsFormalParameters(protocol, unwrap(graph), unwrap(context)));
-  return new CWLExpressionToolDescription(ResizeArray_map((o) => WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(o, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getOutputsAsFormalParameter(protocol, unwrap(graph), unwrap(context))), defaultArg(LDLabProtocol.tryGetDescriptionAsString(protocol, unwrap(context)), "$(null)"), void 0, void 0, void 0, void 0, inputs);
+  const outputs = ResizeArray_map((o) => WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(o, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getOutputsAsFormalParameter(protocol, unwrap(graph), unwrap(context)));
+  const expression = defaultArg(LDLabProtocol.tryGetDescriptionAsString(protocol, unwrap(context)), "$(null)");
+  return new CWLExpressionToolDescription(ListEntry$1.ofValues(outputs), SchemaSaladString_Literal(expression), void 0, void 0, void 0, void 0, ListEntry$1.ofValues(inputs));
 }
 function WorkflowConversion_composeWorkflowProtocolFromOperationDescription_Z75DE0D49(filePath, operation, workflowName, runName) {
-  const inputs = ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), operation.Inputs);
-  const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), operation.Outputs);
+  const inputs = ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), ListEntry$1.values(operation.Inputs));
+  const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), ListEntry$1.values(operation.Outputs));
   return LDWorkflowProtocol.create(filePath, inputs, outputs, void 0, void 0, void 0, filePath, ResizeArray_singleton(LDComputerLanguage.createCWL()), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, [WorkflowConversion_get_operationDescriptionTypeName()]);
 }
 function WorkflowConversion_decomposeWorkflowProtocolToOperationDescription_2664C4B8(protocol, context, graph) {
-  return new CWLOperationDescription(ResizeArray_map((i) => WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(i, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getInputsAsFormalParameters(protocol, unwrap(graph), unwrap(context))), ResizeArray_map((o) => WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(o, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getOutputsAsFormalParameter(protocol, unwrap(graph), unwrap(context))));
-}
-function WorkflowConversion_composeWorkflowStep_Z35AB9E5D(step, workflowID) {
-  const id = `WorkflowStep_${workflowID}_${step.Id}`;
-  const cw = LDComputationalWorkflow.create(id, void 0, void 0, void 0, void 0, void 0, step.Id);
-  LDDataset.setIdentifierAsString(cw, WorkflowConversion_runToIdentifier_Z4EBA8CB1(step.Run));
+  const inputs = ResizeArray_map((i) => WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(i, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getInputsAsFormalParameters(protocol, unwrap(graph), unwrap(context)));
+  const outputs = ResizeArray_map((o) => WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(o, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getOutputsAsFormalParameter(protocol, unwrap(graph), unwrap(context)));
+  return new CWLOperationDescription(ListEntry$1.ofValues(inputs), ListEntry$1.ofValues(outputs));
+}
+function WorkflowConversion_composeWorkflowStep_4F8B7302(step, filePath, position) {
+  let id;
+  const matchValue = step.Id;
+  id = matchValue == null ? position == null ? void 0 : `WorkflowStep_${filePath}?position=${position}` : concat("WorkflowStep_", filePath, "_", matchValue);
+  const cw = LDComputationalWorkflow.create(unwrap(id), void 0, void 0, void 0, void 0, void 0, unwrap(step.Id));
+  const option_1 = WorkflowConversion_runToIdentifier_Z4E98F2C(filePath, step.Run);
+  if (option_1 != null) {
+    const identifier = option_1;
+    LDDataset.setIdentifierAsString(cw, identifier);
+  }
   return cw;
 }
 function WorkflowConversion_composeWorkflowProtocolFromWorkflow_Z6FBB852F(filePath, workflow, workflowName, runName) {
-  const inputs = ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), workflow.Inputs);
-  const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), workflow.Outputs);
-  const steps = ResizeArray_map((s) => WorkflowConversion_composeWorkflowStep_Z35AB9E5D(s, filePath), workflow.Steps);
+  const inputs = ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), ListEntry$1.values(workflow.Inputs));
+  const outputs = ResizeArray_map((o) => WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(o, unwrap(workflowName), unwrap(runName)), ListEntry$1.values(workflow.Outputs));
+  let steps;
+  const collection = mapIndexed((position, s) => WorkflowConversion_composeWorkflowStep_4F8B7302(s, filePath, position), ListEntry$1.values(workflow.Steps));
+  steps = Array.from(collection);
   return LDWorkflowProtocol.create(filePath, inputs, outputs, void 0, void 0, void 0, filePath, ResizeArray_singleton(LDComputerLanguage.createCWL()), void 0, void 0, void 0, void 0, steps, void 0, void 0, void 0, [WorkflowConversion_get_workflowDescriptionTypeName()]);
 }
 function WorkflowConversion_decomposeWorkflowStep_77DD0449(step, workflowFilePath, resolveRunReferences, context, graph) {
-  let initialRun = void 0;
-  return new WorkflowStep(LDComputationalWorkflow.getNameAsString(step, unwrap(context)), [], [], (initialRun = WorkflowStepRun_RunString(LDDataset.getIdentifierAsString(step, unwrap(context))), !defaultArg(resolveRunReferences, true) ? initialRun : workflowFilePath == null ? initialRun : resolveWorkflowStepRunFromLookup(value(workflowFilePath), initialRun, (runPath) => WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(runPath, unwrap(graph), unwrap(context)))));
+  const name = LDComputationalWorkflow.tryGetNameAsString(step, unwrap(context));
+  const identifier = LDDataset.getIdentifierAsString(step, unwrap(context));
+  const runString = workflowFilePath == null ? identifier : WorkflowConversion_identifierToRun_Z384F8060(workflowFilePath, identifier);
+  const shouldResolveRunReferences = defaultArg(resolveRunReferences, true);
+  const workflowStep = new WorkflowStep(name, [], [], WorkflowStepRun_RunString(runString));
+  let matchResult = void 0, path_2 = void 0;
+  if (workflowFilePath != null) {
+    if (workflowFilePath, shouldResolveRunReferences) {
+      matchResult = 0;
+      path_2 = workflowFilePath;
+    } else {
+      matchResult = 1;
+    }
+  } else {
+    matchResult = 1;
+  }
+  switch (matchResult) {
+    case 0: {
+      resolveWorkflowStepFromLookup(path_2, workflowStep, (runPath) => WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(runPath, unwrap(graph), unwrap(context)));
+      break;
+    }
+  }
+  return workflowStep;
 }
 function WorkflowConversion_decomposeWorkflowProtocolToWorkflow_ZB11202F(protocol, resolveRunReferences, context, graph) {
+  let collection = void 0;
   const workflowFilePath = defaultArg(LDDataset.tryGetIdentifierAsString(protocol, unwrap(context)), protocol.Id);
   const shouldResolveRunReferences = defaultArg(resolveRunReferences, true);
   const inputs = ResizeArray_map((i) => WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(i, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getInputsAsFormalParameters(protocol, unwrap(graph), unwrap(context)));
   const outputs = ResizeArray_map((o) => WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(o, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getOutputsAsFormalParameter(protocol, unwrap(graph), unwrap(context)));
-  return new CWLWorkflowDescription(ResizeArray_map((s) => WorkflowConversion_decomposeWorkflowStep_77DD0449(s, workflowFilePath, shouldResolveRunReferences, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getHasPart(protocol, unwrap(graph), unwrap(context))), inputs, outputs);
+  const steps = ResizeArray_map((s_1) => WorkflowConversion_decomposeWorkflowStep_77DD0449(s_1, workflowFilePath, shouldResolveRunReferences, unwrap(context), unwrap(graph)), (collection = filter((s) => LDDataset.tryGetIdentifierAsString(s, unwrap(context)) != null, LDComputationalWorkflow.getHasPart(protocol, unwrap(graph), unwrap(context))), Array.from(collection)));
+  return new CWLWorkflowDescription(ListEntry$1.ofValues(steps), ListEntry$1.ofValues(inputs), ListEntry$1.ofValues(outputs));
 }
 function WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(filePath, pu, workflowName, runName) {
   switch (pu.tag) {
@@ -416,6 +893,9 @@ function WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(
     case /* Operation */
     3:
       return WorkflowConversion_composeWorkflowProtocolFromOperationDescription_Z75DE0D49(filePath, pu.fields[0], unwrap(workflowName), unwrap(runName));
+    case /* RawProcess */
+    4:
+      return WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA(filePath, new CWLToolDescription([]), unwrap(workflowName), unwrap(runName));
     default:
       return WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA(filePath, pu.fields[0], unwrap(workflowName), unwrap(runName));
   }
@@ -433,28 +913,31 @@ function WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(p
     return CWLProcessingUnit_CommandLineTool(WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8(protocol, unwrap(context), unwrap(graph)));
   }
 }
-function WorkflowConversion_composeWorkflow_42450E6E(workflow, fs) {
-  let inv = void 0, option_3 = void 0;
-  let workflowProtocol;
+function WorkflowConversion_composeWorkflow_38B68F62(workflow, fs, dateCreated) {
+  let inv = void 0, option_6 = void 0, fs_1 = void 0;
+  BaseTypes_warnIfTitleEmpty_Z2FC25A28("Workflow", workflow.Identifier, workflow.Title);
   const workflowFilePath = Workflow_cwlFileNameFromIdentifier(workflow.Identifier);
+  let workflowProtocol;
   const matchValue = workflow.CWLDescription;
   if (matchValue == null) {
     const arg = workflow.Identifier;
     workflowProtocol = toFail(printf("Workflow %s must have a CWL description"))(arg);
   } else {
-    workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, value(matchValue), workflow.Identifier);
+    workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, matchValue, workflow.Identifier);
   }
   const publisher = LDOrganization.create("DataPLANT");
   let persons;
   const option_1 = workflow.Investigation;
-  persons = option_1 != null ? (inv = value(option_1), inv.GetAllPersons()) : void 0;
+  persons = option_1 != null ? (inv = option_1, inv.GetAllPersons()) : void 0;
   const creators = Option_fromSeq(ResizeArray_map((c) => PersonConversion_composePerson_2B0BECCC(c, unwrap(persons)), workflow.Contacts));
-  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);
   if (workflow.Version != null) {
     LDLabProtocol.setVersionAsString(workflowProtocol, value(workflow.Version));
   }
@@ -465,30 +948,39 @@ function WorkflowConversion_composeWorkflow_42450E6E(workflow, fs) {
     const intendedUse = BaseTypes_composeDefinedTerm_ZDED3A0F(value(workflow.WorkflowType));
     LDLabProtocol.setIntendedUseAsDefinedTerm(workflowProtocol, intendedUse);
   }
-  const dataFiles = ResizeArray_choose((df) => LDPropertyValue.tryGetSubjectOf(df), defaultArg((option_3 = workflow.Datamap, option_3 != null ? DatamapConversion_composeFragmentDescriptors_Z892BFC3(value(option_3)) : void 0), []));
+  let fragmentDescriptors;
+  const option_3 = workflow.Datamap;
+  fragmentDescriptors = option_3 != null ? DatamapConversion_composeFragmentDescriptors_Z892BFC3(option_3) : void 0;
+  const dataFiles = ResizeArray_choose((df) => LDPropertyValue.tryGetSubjectOf(df), defaultArg(fragmentDescriptors, []));
   if (workflow.Components.length > 0) {
     const softwareTools = ResizeArray_map(WorkflowConversion_composeComputationalTool_Z685B8F25, workflow.Components);
     LDLabProtocol.setComputationalTools(workflowProtocol, softwareTools);
   }
-  const hasParts = dataFiles.length === 0 ? ResizeArray_singleton(workflowProtocol) : ResizeArray_appendSingleton(workflowProtocol, dataFiles);
+  const ownParts = dataFiles.length === 0 ? ResizeArray_singleton(workflowProtocol) : ResizeArray_appendSingleton(workflowProtocol, dataFiles);
+  const hasParts = ResizeArray_append(ownParts, defaultArg((option_6 = fs, option_6 != null ? (fs_1 = option_6, WorkflowConversion_composeReferencedFiles_Z7F3BB4EE(workflowFilePath, value(workflow.CWLDescription), fs_1, ownParts)) : void 0), []));
   const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, workflow.Comments));
-  return LDDataset.createARCWorkflow(workflow.Identifier, ResizeArray_singleton(workflowProtocol), void 0, unwrap(workflow.Title), unwrap(workflow.Description), unwrap(creators), unwrap(hasParts), unwrap(comments));
+  const arcWorkflow = LDDataset.createARCWorkflow(workflow.Identifier, ResizeArray_singleton(workflowProtocol), void 0, unwrap(workflow.Title), unwrap(workflow.Description), unwrap(creators), unwrap(hasParts), unwrap(comments));
+  const option_9 = fragmentDescriptors;
+  if (option_9 != null) {
+    const fds = option_9;
+    LDDataset.setVariableMeasuredAsPropertyValues(arcWorkflow, fds);
+  }
+  return arcWorkflow;
 }
 function WorkflowConversion_decomposeWorkflow_Z6839B9E8(workflow, graph, context) {
   const workflowProtocol = find((me) => LDComputationalWorkflow.validate(me, unwrap(context)), LDDataset.getMainEntities(workflow, unwrap(graph), unwrap(context)));
-  const cwlDescription = WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(workflowProtocol, void 0, unwrap(context), unwrap(graph));
   const version = LDLabProtocol.tryGetVersionAsString(workflowProtocol, unwrap(context));
   const uri = LDLabProtocol.tryGetUrl(workflowProtocol, unwrap(context));
   let workflowType;
   const option_1 = LDLabProtocol.tryGetIntendedUseAsDefinedTerm(workflowProtocol, unwrap(graph), unwrap(context));
-  workflowType = option_1 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(value(option_1), unwrap(context)) : void 0;
+  workflowType = option_1 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(option_1, unwrap(context)) : void 0;
   const components = ResizeArray_map((ct) => WorkflowConversion_decomposeComputationalTool_Z6839B9E8(ct, unwrap(graph), unwrap(context)), LDLabProtocol.getComputationalTools(workflowProtocol, unwrap(graph), unwrap(context)));
   const contacts = ResizeArray_map((c) => PersonConversion_decomposePerson_Z6839B9E8(c, unwrap(graph), unwrap(context)), LDDataset.getCreators(workflow, unwrap(graph), unwrap(context)));
   const comments = ResizeArray_map((c_1) => BaseTypes_decomposeComment_Z2F770004(c_1, unwrap(context)), LDDataset.getComments(workflow, unwrap(graph), unwrap(context)));
   let datamap;
   const v = DatamapConversion_decomposeFragmentDescriptors_Z6E59645F(LDDataset.getVariableMeasuredAsFragmentDescriptors(workflow, unwrap(graph), unwrap(context)), unwrap(graph), unwrap(context));
   datamap = Option_fromValueWithDefault(Datamap.init(), v);
-  return ArcWorkflow.create(LDDataset.getIdentifierAsString(workflow, unwrap(context)), unwrap(LDDataset.tryGetNameAsString(workflow, unwrap(context))), unwrap(LDDataset.tryGetDescriptionAsString(workflow, unwrap(context))), unwrap(workflowType), unwrap(uri), unwrap(version), void 0, void 0, components, unwrap(datamap), contacts, cwlDescription, comments);
+  return ArcWorkflow.create(LDDataset.getIdentifierAsString(workflow, unwrap(context)), unwrap(LDDataset.tryGetNameAsString(workflow, unwrap(context))), unwrap(LDDataset.tryGetDescriptionAsString(workflow, unwrap(context))), unwrap(workflowType), unwrap(uri), unwrap(version), void 0, void 0, components, unwrap(datamap), contacts, void 0, comments);
 }
 
-export { WorkflowConversion, WorkflowConversion_$reflection, WorkflowConversion_composeAdditionalType_Z5C31A0F9, WorkflowConversion_composeComputationalTool_Z685B8F25, WorkflowConversion_composeFormalParamInputIdentifiers, WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7, WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80, WorkflowConversion_composeFormalParameterOutputIdentifiers_6DFDD678, WorkflowConversion_composeWorkflowProtocolFromExpressionToolDescription_Z7BEB6658, WorkflowConversion_composeWorkflowProtocolFromOperationDescription_Z75DE0D49, WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7, WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA, WorkflowConversion_composeWorkflowProtocolFromWorkflow_Z6FBB852F, WorkflowConversion_composeWorkflowStep_Z35AB9E5D, WorkflowConversion_composeWorkflow_42450E6E, WorkflowConversion_decomposeAdditionalType_Z721C83C5, WorkflowConversion_decomposeComputationalTool_Z6839B9E8, WorkflowConversion_decomposeInputBindings_1AAAE9A5, WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8, WorkflowConversion_decomposeOutputBindings_1AAAE9A5, WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToExpressionToolDescription_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToOperationDescription_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F, WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToWorkflow_ZB11202F, WorkflowConversion_decomposeWorkflowStep_77DD0449, WorkflowConversion_decomposeWorkflow_Z6839B9E8, WorkflowConversion_getInputParametersFromProcessingUnit_30922B92, WorkflowConversion_get_expressionToolDescriptionTypeName, WorkflowConversion_get_operationDescriptionTypeName, WorkflowConversion_get_toolDescriptionTypeName, WorkflowConversion_get_workflowDescriptionTypeName, WorkflowConversion_runToIdentifier_Z4EBA8CB1, WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418 };
+export { WorkflowConversion, WorkflowConversion_$reflection, WorkflowConversion_composeAdditionalType_Z5C31A0F9, WorkflowConversion_composeComputationalTool_Z685B8F25, WorkflowConversion_composeFormalParamInputIdentifiers, WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7, WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80, WorkflowConversion_composeFormalParameterOutputIdentifiers_A254C9D, WorkflowConversion_composeReferencedFiles_Z7F3BB4EE, WorkflowConversion_composeWorkflowProtocolFromExpressionToolDescription_Z7BEB6658, WorkflowConversion_composeWorkflowProtocolFromOperationDescription_Z75DE0D49, WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7, WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA, WorkflowConversion_composeWorkflowProtocolFromWorkflow_Z6FBB852F, WorkflowConversion_composeWorkflowStep_4F8B7302, WorkflowConversion_composeWorkflow_38B68F62, WorkflowConversion_decomposeAdditionalType_Z721C83C5, WorkflowConversion_decomposeComputationalTool_Z6839B9E8, WorkflowConversion_decomposeInputBindings_1AAAE9A5, WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8, WorkflowConversion_decomposeOutputBindings_1AAAE9A5, WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToExpressionToolDescription_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToOperationDescription_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F, WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToWorkflow_ZB11202F, WorkflowConversion_decomposeWorkflowStep_77DD0449, WorkflowConversion_decomposeWorkflow_Z6839B9E8, WorkflowConversion_getInputParametersFromProcessingUnit_30922B92, WorkflowConversion_getReferencedFilePaths_589B7F6, WorkflowConversion_get_expressionToolDescriptionTypeName, WorkflowConversion_get_operationDescriptionTypeName, WorkflowConversion_get_toolDescriptionTypeName, WorkflowConversion_get_workflowDescriptionTypeName, WorkflowConversion_identifierToRun_Z384F8060, WorkflowConversion_runToIdentifier_Z4E98F2C, WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418 };