@nfdi4plants/arctrl 3.1.0 → 3.2.0

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

@@ -1,24 +1,25 @@
-import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+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-alpha.7/Reader.fs.js';
-import { YAMLElement_Sequence, YAMLElement_Comment } from '../fable_modules/YAMLicious.1.0.0-alpha.7/YAMLiciousTypes.fs.js';
-import { object } from '../fable_modules/YAMLicious.1.0.0-alpha.7/Decode.fs.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-js/List.js';
-import { value, defaultArg, unwrap, bind, map } from '../../node_modules/@fable-org/fable-library-js/Option.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 { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
+import { Exception, int32ToString, stringHash } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 import { LDFormalParameter } from '../ROCrate/LDTypes/FormalParameter.js';
-import { InputBinding_create_ZAC0108A, CWLInput } from '../CWL/Inputs.js';
-import { tryPick, exactlyOne, toArray, find } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
-import { OutputBinding_create_6DFDD678, CWLOutput } from '../CWL/Outputs.js';
-import { int32ToString, stringHash } from '../../node_modules/@fable-org/fable-library-js/Util.js';
-import { Component_create_Z2F0B38C7 } from '../Core/Process/Component.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 { 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 { 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-js/Array.js';
-import { distinct } from '../../node_modules/@fable-org/fable-library-js/Seq2.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 { 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';
@@ -31,13 +32,12 @@ import { CWLOperationDescription } from '../CWL/OperationDescription.js';
 import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.js';
 import { resolveWorkflowStepRunFromLookup } from '../CWLRunResolver.js';
 import { Workflow_cwlFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
-import { toFail, printf } from '../../node_modules/@fable-org/fable-library-js/String.js';
 import { LDOrganization } from '../ROCrate/LDTypes/Organization.js';
-import { PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
-import { utcNow } from '../../node_modules/@fable-org/fable-library-js/Date.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 { Datamap } from '../Core/Datamap.js';
-import { ArcWorkflow } from '../Core/ArcTypes.js';
 
 class WorkflowConversion {
   constructor() {
@@ -56,7 +56,7 @@ function WorkflowConversion_composeAdditionalType_Z5C31A0F9(t) {
 }
 function WorkflowConversion_decomposeAdditionalType_Z721C83C5(t) {
   const yamlElement = read(t);
-  let matchResult, items;
+  let matchResult = void 0, items = void 0;
   switch (yamlElement.tag) {
     case /* Value */
     1: {
@@ -87,7 +87,7 @@ function WorkflowConversion_decomposeAdditionalType_Z721C83C5(t) {
   }
   switch (matchResult) {
     case 0:
-      return object((get$) => Decode_cwlTypeStringMatcher(t, get$), YAMLElement_Comment("unused-shorthand-context"))[0];
+      return object((get$) => Decode_cwlTypeStringMatcher(t, get$), YAMLElement_Comment$("unused-shorthand-context"))[0];
     case 1:
       return Decode_cwlTypeDecoder$0027(YAMLElement_Sequence(items));
     default:
@@ -115,19 +115,26 @@ function WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(inp, workf
   let additionalType;
   const matchValue = inp.Type_;
   if (matchValue == null) {
-    throw new Error("Input must have a type");
+    throw new Exception("Input must have a type");
   } else {
     additionalType = WorkflowConversion_composeAdditionalType_Z5C31A0F9(value(matchValue));
   }
   const valueRequired = !defaultArg(inp.Optional, false);
   const id = LDFormalParameter.genID(inp.Name, unwrap(workflowName), unwrap(runName));
-  const identifiers = bind((ib) => WorkflowConversion_composeFormalParamInputIdentifiers(ib.Prefix, ib.Position), inp.InputBinding);
+  let identifiers;
+  const option_2 = inp.InputBinding;
+  if (option_2 != null) {
+    const ib = value(option_2);
+    identifiers = WorkflowConversion_composeFormalParamInputIdentifiers(ib.Prefix, ib._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) {
   const prefix = tryPick((n) => LDPropertyValue.tryGetAsPrefix(n, unwrap(context)), identifiers);
   const position = tryPick((n_1) => LDPropertyValue.tryGetAsPosition(n_1, unwrap(context)), identifiers);
-  let matchResult;
+  let matchResult = void 0;
   if (prefix == null) {
     if (position == null) {
       matchResult = 0;
@@ -141,7 +148,7 @@ function WorkflowConversion_decomposeInputBindings_1AAAE9A5(identifiers, context
     case 0:
       return void 0;
     default:
-      return InputBinding_create_ZAC0108A(unwrap(prefix), unwrap(position));
+      return InputBinding.create(unwrap(prefix), unwrap(position));
   }
 }
 function WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(inp, context, graph) {
@@ -149,7 +156,7 @@ function WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(inp, cont
   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;
+  let matchResult = void 0;
   if (matchValue != null) {
     if (value(matchValue)) {
       matchResult = 0;
@@ -181,28 +188,38 @@ function WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(out, work
   let additionalType;
   const matchValue = out.Type_;
   if (matchValue == null) {
-    throw new Error("Output must have a type");
+    throw new Exception("Output must have a type");
   } else {
     additionalType = WorkflowConversion_composeAdditionalType_Z5C31A0F9(value(matchValue));
   }
   const id = LDFormalParameter.genID(out.Name, unwrap(workflowName), unwrap(runName));
-  const identifiers = bind((ob) => WorkflowConversion_composeFormalParameterOutputIdentifiers_6DFDD678(ob.Glob), out.OutputBinding);
+  let identifiers;
+  const option_1 = out.OutputBinding;
+  if (option_1 != null) {
+    const ob = value(option_1);
+    identifiers = WorkflowConversion_composeFormalParameterOutputIdentifiers_6DFDD678(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_6DFDD678(unwrap(tryPick((n) => LDPropertyValue.tryGetAsGlob(n, unwrap(context)), identifiers)));
+  return OutputBinding.create(unwrap(tryPick((n) => LDPropertyValue.tryGetAsGlob(n, unwrap(context)), identifiers)));
 }
 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 optional = map((value) => !value, LDFormalParameter.tryGetValueRequiredAsBoolean(outp, unwrap(context)));
+  const option_1 = LDFormalParameter.tryGetValueRequiredAsBoolean(outp, unwrap(context));
+  if (option_1 != null) {
+    !value(option_1);
+  }
   return new CWLOutput(LDFormalParameter.getNameAsString(outp, unwrap(context)), t_1, binding);
 }
 function WorkflowConversion_composeComputationalTool_Z685B8F25(tool) {
-  let c, f, i, oa, s;
+  let c = void 0, f = void 0, i = void 0, oa = void 0, s = void 0;
   let patternInput;
   const matchValue = tool.ComponentType;
-  let matchResult, c_1;
+  let matchResult = void 0, c_1 = void 0;
   if (matchValue != null) {
     if (c = value(matchValue), c.Name != null) {
       matchResult = 0;
@@ -219,7 +236,7 @@ function WorkflowConversion_composeComputationalTool_Z685B8F25(tool) {
       break;
     }
     default:
-      throw new Error("Component must have a type");
+      throw new Exception("Component must have a type");
   }
   let patternInput_1;
   const matchValue_1 = tool.ComponentValue;
@@ -239,7 +256,7 @@ function WorkflowConversion_composeComputationalTool_Z685B8F25(tool) {
 }
 function WorkflowConversion_decomposeComputationalTool_Z6839B9E8(tool, graph, context) {
   const patternInput = BaseTypes_decomposePropertyValue_Z2F770004(tool, unwrap(context));
-  return Component_create_Z2F0B38C7(unwrap(patternInput[1]), unwrap(patternInput[2]), patternInput[0]);
+  return Component_create_Z7A4FC9(unwrap(patternInput[1]), unwrap(patternInput[2]), patternInput[0]);
 }
 function WorkflowConversion_getInputParametersFromProcessingUnit_30922B92(pu) {
   return CWLProcessingUnit_getInputs_30922B92(pu);
@@ -275,7 +292,7 @@ function WorkflowConversion_runToIdentifier_Z4EBA8CB1(run) {
   }
 }
 function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedRunPath, graph, context) {
-  let node, node_1, node_2;
+  let node = void 0, node_1 = void 0, node_2 = void 0;
   const tryDecodeWorkflowProtocol = (protocol) => {
     try {
       return WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(protocol, false, unwrap(context), unwrap(graph));
@@ -286,11 +303,11 @@ function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedR
   if (graph != null) {
     const graph_1 = value(graph);
     const normalizedResolvedRunPath = normalize(resolvedRunPath);
-    const candidateNode = tryPick$1((id) => graph_1.TryGetNode(id), toArray(distinct([resolvedRunPath, normalizedResolvedRunPath, `./${normalizedResolvedRunPath}`], {
+    const candidateNode = tryPick$1((id) => graph_1.TryGetNode(id), toArray(distinct([resolvedRunPath, normalizedResolvedRunPath, concat("./", normalizedResolvedRunPath)], {
       Equals: (x, y) => x === y,
-      GetHashCode: stringHash
+      GetHashCode: (x) => stringHash(x) | 0
     })));
-    let matchResult, node_3, node_4, node_5;
+    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))) {
         matchResult = 0;
@@ -310,10 +327,22 @@ function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedR
     switch (matchResult) {
       case 0:
         return tryDecodeWorkflowProtocol(node_3);
-      case 1:
-        return bind(tryDecodeWorkflowProtocol, LDDataset.tryGetMainEntityAsWorkflowProtocol(node_4, graph_1, unwrap(context)));
-      case 2:
-        return bind(tryDecodeWorkflowProtocol, LDDataset.tryGetMainEntityAsWorkflowProtocol(node_5, graph_1, unwrap(context)));
+      case 1: {
+        const option_1 = LDDataset.tryGetMainEntityAsWorkflowProtocol(node_4, graph_1, unwrap(context));
+        if (option_1 != null) {
+          return tryDecodeWorkflowProtocol(value(option_1));
+        } else {
+          return void 0;
+        }
+      }
+      case 2: {
+        const option_3 = LDDataset.tryGetMainEntityAsWorkflowProtocol(node_5, graph_1, unwrap(context));
+        if (option_3 != null) {
+          return tryDecodeWorkflowProtocol(value(option_3));
+        } else {
+          return void 0;
+        }
+      }
       default:
         return void 0;
     }
@@ -322,16 +351,20 @@ function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedR
   }
 }
 function WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA(filePath, workflow, workflowName, runName) {
-  const inputs = map((a) => ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), a), workflow.Inputs);
+  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);
   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, inputs);
+  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);
 }
 function WorkflowConversion_composeWorkflowProtocolFromExpressionToolDescription_Z7BEB6658(filePath, expressionTool, workflowName, runName) {
-  const inputs = map((a) => ResizeArray_map((i) => WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(i, unwrap(workflowName), unwrap(runName)), a), expressionTool.Inputs);
+  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);
   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);
@@ -362,7 +395,7 @@ function WorkflowConversion_composeWorkflowProtocolFromWorkflow_Z6FBB852F(filePa
   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;
+  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)))));
 }
 function WorkflowConversion_decomposeWorkflowProtocolToWorkflow_ZB11202F(protocol, resolveRunReferences, context, graph) {
@@ -401,6 +434,7 @@ function WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(p
   }
 }
 function WorkflowConversion_composeWorkflow_42450E6E(workflow, fs) {
+  let inv = void 0, option_3 = void 0;
   let workflowProtocol;
   const workflowFilePath = Workflow_cwlFileNameFromIdentifier(workflow.Identifier);
   const matchValue = workflow.CWLDescription;
@@ -411,7 +445,10 @@ function WorkflowConversion_composeWorkflow_42450E6E(workflow, fs) {
     workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, value(matchValue), workflow.Identifier);
   }
   const publisher = LDOrganization.create("DataPLANT");
-  const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, workflow.Contacts));
+  let persons;
+  const option_1 = workflow.Investigation;
+  persons = option_1 != null ? (inv = value(option_1), inv.GetAllPersons()) : void 0;
+  const creators = Option_fromSeq(ResizeArray_map((c) => PersonConversion_composePerson_2B0BECCC(c, unwrap(persons)), workflow.Contacts));
   const dateCreated = utcNow();
   if (creators != null) {
     LDComputationalWorkflow.setCreators(workflowProtocol, value(creators));
@@ -428,7 +465,7 @@ 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(map(DatamapConversion_composeFragmentDescriptors_Z892BFC3, workflow.Datamap), []));
+  const dataFiles = ResizeArray_choose((df) => LDPropertyValue.tryGetSubjectOf(df), defaultArg((option_3 = workflow.Datamap, option_3 != null ? DatamapConversion_composeFragmentDescriptors_Z892BFC3(value(option_3)) : void 0), []));
   if (workflow.Components.length > 0) {
     const softwareTools = ResizeArray_map(WorkflowConversion_composeComputationalTool_Z685B8F25, workflow.Components);
     LDLabProtocol.setComputationalTools(workflowProtocol, softwareTools);
@@ -442,7 +479,9 @@ function WorkflowConversion_decomposeWorkflow_Z6839B9E8(workflow, graph, 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));
-  const workflowType = map((iu) => BaseTypes_decomposeDefinedTerm_Z2F770004(iu, unwrap(context)), LDLabProtocol.tryGetIntendedUseAsDefinedTerm(workflowProtocol, unwrap(graph), 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;
   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)));

package/dist/ts/ts/Conversion.d.ts

@@ -1,29 +1,32 @@
-import { Option } from '@fable-org/fable-library-js/Option.js';
-import { ArcInvestigation, ArcRun, ArcWorkflow, ArcStudy, ArcAssay } from './Core/ArcTypes.js';
-import { FileSystem } from './FileSystem/FileSystem.js';
-import { LDGraph, LDNode } from './ROCrate/LDObject.js';
-import { LDContext } from './ROCrate/LDContext.js';
-import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
-export declare function ARCtrl_ArcAssay__ArcAssay_ToROCrateAssay_1695DD5C(this$: ArcAssay, fs: Option<FileSystem>): LDNode;
+import { ArcInvestigation, ArcRun, ArcWorkflow, ArcStudy, ArcAssay } from './Core/ArcTypes.ts';
+import { FileSystem } from './FileSystem/FileSystem.ts';
+import { LDGraph, LDNode } from './ROCrate/LDObject.ts';
+import { LDContext } from './ROCrate/LDContext.ts';
+import { TypeInfo } from '@fable-org/fable-library-ts/Reflection.ts';
+export declare function ARCtrl_ArcAssay__ArcAssay_ToROCrateAssay_1695DD5C(this$: ArcAssay, fs?: FileSystem): LDNode;
 export declare function ARCtrl_ArcAssay__ArcAssay_fromROCrateAssay_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcAssay;
-export declare function ARCtrl_ArcStudy__ArcStudy_ToROCrateStudy_1695DD5C(this$: ArcStudy, fs: Option<FileSystem>): LDNode;
+export declare function ARCtrl_ArcStudy__ArcStudy_ToROCrateStudy_1695DD5C(this$: ArcStudy, fs?: FileSystem): LDNode;
 export declare function ARCtrl_ArcStudy__ArcStudy_fromROCrateStudy_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcStudy;
-export declare function ARCtrl_ArcWorkflow__ArcWorkflow_ToROCrateWorkflow_1695DD5C(this$: ArcWorkflow, fs: Option<FileSystem>): LDNode;
+export declare function ARCtrl_ArcWorkflow__ArcWorkflow_ToROCrateWorkflow_1695DD5C(this$: ArcWorkflow, fs?: FileSystem): LDNode;
 export declare function ARCtrl_ArcWorkflow__ArcWorkflow_fromROCrateWorkflow_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcWorkflow;
-export declare function ARCtrl_ArcRun__ArcRun_ToROCrateRun_1695DD5C(this$: ArcRun, fs: Option<FileSystem>): LDNode;
+export declare function ARCtrl_ArcRun__ArcRun_ToROCrateRun_1695DD5C(this$: ArcRun, fs?: FileSystem): LDNode;
 export declare function ARCtrl_ArcRun__ArcRun_fromROCrateRun_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcRun;
-export declare function ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_Z7960E96B(this$: ArcInvestigation, fs: Option<FileSystem>, ignoreBrokenWR: Option<boolean>): LDNode;
+export declare function ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_Z7960E96B(this$: ArcInvestigation, fs?: FileSystem, ignoreBrokenWR?: boolean): LDNode;
 export declare function ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcInvestigation;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_toArcAssay_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcAssay;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_fromArcAssay_Static_1501C0F8(a: ArcAssay): LDNode;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_toArcStudy_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcStudy;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_fromArcStudy_Static_1680536E(a: ArcStudy): LDNode;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_toArcWorkflow_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcWorkflow;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_fromArcWorkflow_Static_Z1C75CB0E(a: ArcWorkflow): LDNode;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_toArcRun_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcRun;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_fromArcRun_Static_Z3EFAF6F8(a: ArcRun): LDNode;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_toArcInvestigation_Static_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcInvestigation;
-export declare function ARCtrl_ROCrate_Dataset__Dataset_fromArcInvestigation_Static_Z720BD3FF(a: ArcInvestigation): LDNode;
+export declare class Dataset {
+    constructor();
+}
+export declare function Dataset_$reflection(): TypeInfo;
+export declare function Dataset_toArcAssay_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcAssay;
+export declare function Dataset_fromArcAssay_1501C0F8(a: ArcAssay): LDNode;
+export declare function Dataset_toArcStudy_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcStudy;
+export declare function Dataset_fromArcStudy_1680536E(a: ArcStudy): LDNode;
+export declare function Dataset_toArcWorkflow_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcWorkflow;
+export declare function Dataset_fromArcWorkflow_Z1C75CB0E(a: ArcWorkflow): LDNode;
+export declare function Dataset_toArcRun_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcRun;
+export declare function Dataset_fromArcRun_Z3EFAF6F8(a: ArcRun): LDNode;
+export declare function Dataset_toArcInvestigation_Z6839B9E8(a: LDNode, graph?: LDGraph, context?: LDContext): ArcInvestigation;
+export declare function Dataset_fromArcInvestigation_Z720BD3FF(a: ArcInvestigation): LDNode;
 export declare class Conversion {
     constructor();
     static arcAssayToDataset(a: ArcAssay, fs?: FileSystem): LDNode;

package/dist/ts/ts/Conversion.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"Conversion.d.ts","sourceRoot":"","sources":["../../../src/ARCtrl/ts/Conversion.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AAC/F,OAAO,EAAE,UAAU,EAAE,MAAM,4BAA4B,CAAC;AACxD,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,uBAAuB,CAAC;AACxD,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAKnD,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAEjF,wBAAgB,iDAAiD,CAAC,KAAK,EAAE,QAAQ,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CAE1G;AAED,wBAAgB,2DAA2D,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,QAAQ,CAErI;AAED,wBAAgB,iDAAiD,CAAC,KAAK,EAAE,QAAQ,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CAE1G;AAED,wBAAgB,2DAA2D,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,QAAQ,CAErI;AAED,wBAAgB,0DAA0D,CAAC,KAAK,EAAE,WAAW,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CAEtH;AAED,wBAAgB,oEAAoE,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,WAAW,CAEjJ;AAED,wBAAgB,2CAA2C,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CAElG;AAED,wBAAgB,qDAAqD,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAE7H;AAED,wBAAgB,0EAA0E,CAAC,KAAK,EAAE,gBAAgB,EAAE,EAAE,CAAC,EAAE,UAAU,EAAE,cAAc,CAAC,EAAE,OAAO,GAAG,MAAM,CAErK;AAED,wBAAgB,mFAAmF,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,gBAAgB,CAErK;AAED,qBAAa,OAAO;;CAGnB;AAED,wBAAgB,mBAAmB,IAAI,QAAQ,CAE9C;AAED,wBAAgB,4BAA4B,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,QAAQ,CAEtG;AAED,wBAAgB,6BAA6B,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM,CAEjE;AAED,wBAAgB,4BAA4B,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,QAAQ,CAEtG;AAED,wBAAgB,6BAA6B,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM,CAEjE;AAED,wBAAgB,+BAA+B,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,WAAW,CAE5G;AAED,wBAAgB,iCAAiC,CAAC,CAAC,EAAE,WAAW,GAAG,MAAM,CAExE;AAED,wBAAgB,0BAA0B,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAElG;AAED,wBAAgB,4BAA4B,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE9D;AAED,wBAAgB,oCAAoC,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,gBAAgB,CAEtH;AAED,wBAAgB,sCAAsC,CAAC,CAAC,EAAE,gBAAgB,GAAG,MAAM,CAElF;AAED,qBAAa,UAAU;;IAGnB,MAAM,CAAC,iBAAiB,CAAC,CAAC,EAAE,QAAQ,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM;IAG9D,MAAM,CAAC,iBAAiB,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,QAAQ;IAGnF,MAAM,CAAC,iBAAiB,CAAC,CAAC,EAAE,QAAQ,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM;IAG9D,MAAM,CAAC,iBAAiB,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,QAAQ;IAGnF,MAAM,CAAC,oBAAoB,CAAC,CAAC,EAAE,WAAW,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM;IAGpE,MAAM,CAAC,oBAAoB,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,WAAW;IAGzF,MAAM,CAAC,eAAe,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM;IAG1D,MAAM,CAAC,eAAe,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM;IAG/E,MAAM,CAAC,yBAAyB,CAAC,CAAC,EAAE,gBAAgB,EAAE,EAAE,CAAC,EAAE,UAAU,EAAE,cAAc,CAAC,EAAE,OAAO,GAAG,MAAM;IAGxG,MAAM,CAAC,yBAAyB,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,gBAAgB;CAGtG;AAED,wBAAgB,sBAAsB,IAAI,QAAQ,CAEjD"}

package/dist/ts/ts/Conversion.js

@@ -1,10 +1,10 @@
 import { AssayConversion_composeAssay_Z5C53FD5C, AssayConversion_decomposeAssay_Z6839B9E8 } from './Conversion/Assay.js';
-import { unwrap } from '../node_modules/@fable-org/fable-library-js/Option.js';
+import { unwrap } from '../node_modules/@fable-org/fable-library-ts/Option.js';
 import { StudyConversion_composeStudy_ZFE0E38E, StudyConversion_decomposeStudy_Z6839B9E8 } from './Conversion/Study.js';
 import { WorkflowConversion_composeWorkflow_42450E6E, WorkflowConversion_decomposeWorkflow_Z6839B9E8 } from './Conversion/Workflow.js';
 import { RunConversion_composeRun_Z8CC08AC, RunConversion_decomposeRun_Z6839B9E8 } from './Conversion/Run.js';
 import { InvestigationConversion_composeInvestigation_Z284BC0AC, InvestigationConversion_decomposeInvestigation_Z6839B9E8 } from './Conversion/Investigation.js';
-import { class_type } from '../node_modules/@fable-org/fable-library-js/Reflection.js';
+import { class_type } from '../node_modules/@fable-org/fable-library-ts/Reflection.js';
 
 function ARCtrl_ArcAssay__ArcAssay_ToROCrateAssay_1695DD5C(this$, fs) {
   return AssayConversion_composeAssay_Z5C53FD5C(this$, unwrap(fs));
@@ -36,34 +36,41 @@ function ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_Z7960E
 function ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(a, graph, context) {
   return InvestigationConversion_decomposeInvestigation_Z6839B9E8(a, unwrap(graph), unwrap(context));
 }
-function ARCtrl_ROCrate_Dataset__Dataset_toArcAssay_Static_Z6839B9E8(a, graph, context) {
+class Dataset {
+  constructor() {
+  }
+}
+function Dataset_$reflection() {
+  return class_type("ARCtrl.Conversion.TypeExtensions.Dataset", void 0, Dataset);
+}
+function Dataset_toArcAssay_Z6839B9E8(a, graph, context) {
   return AssayConversion_decomposeAssay_Z6839B9E8(a, unwrap(graph), unwrap(context));
 }
-function ARCtrl_ROCrate_Dataset__Dataset_fromArcAssay_Static_1501C0F8(a) {
+function Dataset_fromArcAssay_1501C0F8(a) {
   return AssayConversion_composeAssay_Z5C53FD5C(a);
 }
-function ARCtrl_ROCrate_Dataset__Dataset_toArcStudy_Static_Z6839B9E8(a, graph, context) {
+function Dataset_toArcStudy_Z6839B9E8(a, graph, context) {
   return StudyConversion_decomposeStudy_Z6839B9E8(a, unwrap(graph), unwrap(context));
 }
-function ARCtrl_ROCrate_Dataset__Dataset_fromArcStudy_Static_1680536E(a) {
+function Dataset_fromArcStudy_1680536E(a) {
   return StudyConversion_composeStudy_ZFE0E38E(a);
 }
-function ARCtrl_ROCrate_Dataset__Dataset_toArcWorkflow_Static_Z6839B9E8(a, graph, context) {
+function Dataset_toArcWorkflow_Z6839B9E8(a, graph, context) {
   return WorkflowConversion_decomposeWorkflow_Z6839B9E8(a, unwrap(graph), unwrap(context));
 }
-function ARCtrl_ROCrate_Dataset__Dataset_fromArcWorkflow_Static_Z1C75CB0E(a) {
+function Dataset_fromArcWorkflow_Z1C75CB0E(a) {
   return WorkflowConversion_composeWorkflow_42450E6E(a);
 }
-function ARCtrl_ROCrate_Dataset__Dataset_toArcRun_Static_Z6839B9E8(a, graph, context) {
+function Dataset_toArcRun_Z6839B9E8(a, graph, context) {
   return RunConversion_decomposeRun_Z6839B9E8(a, unwrap(graph), unwrap(context));
 }
-function ARCtrl_ROCrate_Dataset__Dataset_fromArcRun_Static_Z3EFAF6F8(a) {
+function Dataset_fromArcRun_Z3EFAF6F8(a) {
   return RunConversion_composeRun_Z8CC08AC(a);
 }
-function ARCtrl_ROCrate_Dataset__Dataset_toArcInvestigation_Static_Z6839B9E8(a, graph, context) {
+function Dataset_toArcInvestigation_Z6839B9E8(a, graph, context) {
   return InvestigationConversion_decomposeInvestigation_Z6839B9E8(a, unwrap(graph), unwrap(context));
 }
-function ARCtrl_ROCrate_Dataset__Dataset_fromArcInvestigation_Static_Z720BD3FF(a) {
+function Dataset_fromArcInvestigation_Z720BD3FF(a) {
   return InvestigationConversion_composeInvestigation_Z284BC0AC(a);
 }
 class Conversion {
@@ -104,4 +111,4 @@ function Conversion_$reflection() {
   return class_type("ARCtrl.Conversion.TypeExtensions.Conversion", void 0, Conversion);
 }
 
-export { ARCtrl_ArcAssay__ArcAssay_ToROCrateAssay_1695DD5C, ARCtrl_ArcAssay__ArcAssay_fromROCrateAssay_Static_Z6839B9E8, ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_Z7960E96B, ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8, ARCtrl_ArcRun__ArcRun_ToROCrateRun_1695DD5C, ARCtrl_ArcRun__ArcRun_fromROCrateRun_Static_Z6839B9E8, ARCtrl_ArcStudy__ArcStudy_ToROCrateStudy_1695DD5C, ARCtrl_ArcStudy__ArcStudy_fromROCrateStudy_Static_Z6839B9E8, ARCtrl_ArcWorkflow__ArcWorkflow_ToROCrateWorkflow_1695DD5C, ARCtrl_ArcWorkflow__ArcWorkflow_fromROCrateWorkflow_Static_Z6839B9E8, ARCtrl_ROCrate_Dataset__Dataset_fromArcAssay_Static_1501C0F8, ARCtrl_ROCrate_Dataset__Dataset_fromArcInvestigation_Static_Z720BD3FF, ARCtrl_ROCrate_Dataset__Dataset_fromArcRun_Static_Z3EFAF6F8, ARCtrl_ROCrate_Dataset__Dataset_fromArcStudy_Static_1680536E, ARCtrl_ROCrate_Dataset__Dataset_fromArcWorkflow_Static_Z1C75CB0E, ARCtrl_ROCrate_Dataset__Dataset_toArcAssay_Static_Z6839B9E8, ARCtrl_ROCrate_Dataset__Dataset_toArcInvestigation_Static_Z6839B9E8, ARCtrl_ROCrate_Dataset__Dataset_toArcRun_Static_Z6839B9E8, ARCtrl_ROCrate_Dataset__Dataset_toArcStudy_Static_Z6839B9E8, ARCtrl_ROCrate_Dataset__Dataset_toArcWorkflow_Static_Z6839B9E8, Conversion, Conversion_$reflection };
+export { ARCtrl_ArcAssay__ArcAssay_ToROCrateAssay_1695DD5C, ARCtrl_ArcAssay__ArcAssay_fromROCrateAssay_Static_Z6839B9E8, ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_Z7960E96B, ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8, ARCtrl_ArcRun__ArcRun_ToROCrateRun_1695DD5C, ARCtrl_ArcRun__ArcRun_fromROCrateRun_Static_Z6839B9E8, ARCtrl_ArcStudy__ArcStudy_ToROCrateStudy_1695DD5C, ARCtrl_ArcStudy__ArcStudy_fromROCrateStudy_Static_Z6839B9E8, ARCtrl_ArcWorkflow__ArcWorkflow_ToROCrateWorkflow_1695DD5C, ARCtrl_ArcWorkflow__ArcWorkflow_fromROCrateWorkflow_Static_Z6839B9E8, Conversion, Conversion_$reflection, Dataset, Dataset_$reflection, Dataset_fromArcAssay_1501C0F8, Dataset_fromArcInvestigation_Z720BD3FF, Dataset_fromArcRun_Z3EFAF6F8, Dataset_fromArcStudy_1680536E, Dataset_fromArcWorkflow_Z1C75CB0E, Dataset_toArcAssay_Z6839B9E8, Dataset_toArcInvestigation_Z6839B9E8, Dataset_toArcRun_Z6839B9E8, Dataset_toArcStudy_Z6839B9E8, Dataset_toArcWorkflow_Z6839B9E8 };