@nfdi4plants/arctrl 3.1.0 → 3.2.0

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

@@ -1,34 +1,44 @@
-import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
-import { writeYaml, encodeCWLType } from '../CWL/Encode.js';
-import { CWLType_file } from '../CWL/CWLTypes.js';
-import { exists, tryPick, find } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
-import { replace, trimStart, join, toFail, printf } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { class_type } from '../../node_modules/@fable-org/fable-library-ts/Reflection.js';
+import { replace, trimStart, toFail, printf, concat } from '../../node_modules/@fable-org/fable-library-ts/String.js';
 import { combineMany, combine } from '../FileSystem/Path.js';
-import { value, defaultArg, bind, unwrap, map } from '../../node_modules/@fable-org/fable-library-js/Option.js';
-import { equals } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { FileInstanceModule_pathOrLocation, DirectoryInstanceModule_pathOrLocation, CWLTypeModule_typesEqual, CWLTypeModule_isArrayType, CWLTypeModule_tryGetNonNullUnionType, FileInstance, InputRecordSchemaModule_tryGetFieldType, DirectoryInstance, CWLType_file } from '../CWL/CWLTypes.js';
 import { LDFile } from '../ROCrate/LDTypes/File.js';
-import { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
-import { ResizeArray_singleton, ResizeArray_map, ResizeArray_zip, ResizeArray_appendSingleton, Option_fromSeq, Option_fromValueWithDefault, ResizeArray_filter } from '../Core/Helper/Collections.js';
+import { unwrap, value, defaultArg, some } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
+import { ResizeArray_map, ResizeArray_zip, ResizeArray_singleton, ResizeArray_appendSingleton, Option_fromSeq, Option_fromValueWithDefault, ResizeArray_filter } from '../Core/Helper/Collections.js';
+import { CWLParameterValue_Array$, CWLParameterValue_String$, CWLParameterValue_Record, CWLParameterRecordField, CWLParameterValue_File, CWLParameterValue_Boolean$, CWLParameterValue_Float, CWLParameterValue_Int, CWLParameterValue, CWLParameterValueModule_tryParseFloat, CWLParameterValueModule_tryParseInt64, CWLParameterValue_Directory } from '../CWL/ParameterValue.js';
+import { DynamicObj } from '../fable_modules/DynamicObj.8.0.0/DynamicObj.fs.js';
+import { iterate, map, tryPick, find } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
+import { setProperty } from '../fable_modules/DynamicObj.8.0.0/DynObj.fs.js';
+import { toInt64_unchecked, fromInt32 } from '../../node_modules/@fable-org/fable-library-ts/BigInt.js';
+import { defaultOf, Exception, equals, isIterable } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 import { CWLParameterReference } from '../CWL/ParameterReference.js';
+import { formatCWLType } from '../CWL/Encode.js';
+import { item } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
+import { LDRef, LDNode } from '../ROCrate/LDObject.js';
+import { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
+import { toString, FSharpRef } from '../../node_modules/@fable-org/fable-library-ts/Types.js';
+import { tryParse } from '../../node_modules/@fable-org/fable-library-ts/Boolean.js';
+import { toFloat64 } from '../../node_modules/@fable-org/fable-library-ts/Decimal.js';
+import { WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8, WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7, WorkflowConversion_getInputParametersFromProcessingUnit_30922B92, WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F } from './Workflow.js';
 import { LDFormalParameter } from '../ROCrate/LDTypes/FormalParameter.js';
 import { Run_cwlFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
-import { WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7, WorkflowConversion_getInputParametersFromProcessingUnit_30922B92, WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F } from './Workflow.js';
 import { LDComputationalWorkflow } from '../ROCrate/LDTypes/ComputationalWorkflow.js';
 import { ARCtrl_ArcTables__ArcTables_GetProcesses_5E660E5C, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586 } from './Table.js';
 import { ArcTables } from '../Core/Table/ArcTables.js';
-import { ofSeq } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { ofSeq } from '../../node_modules/@fable-org/fable-library-ts/List.js';
 import { LDWorkflowInvocation } from '../ROCrate/LDTypes/WorkflowInvocation.js';
 import { LDLabProcess } from '../ROCrate/LDTypes/LabProcess.js';
 import { ArcRun } from '../Core/ArcTypes.js';
 import { BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composePropertyValueFromOA_ZDED3A0F, BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_decomposePropertyValueToOA_Z2F770004, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
-import { PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
+import { PersonConversion_composePerson_2B0BECCC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
 import { LDOrganization } from '../ROCrate/LDTypes/Organization.js';
-import { utcNow } from '../../node_modules/@fable-org/fable-library-js/Date.js';
-import { DatamapConversion_composeFragmentDescriptors_Z892BFC3, DatamapConversion_decomposeFragmentDescriptors_Z6E59645F } from './Datamap.js';
+import { utcNow } from '../../node_modules/@fable-org/fable-library-ts/Date.js';
 import { Datamap } from '../Core/Datamap.js';
+import { DatamapConversion_composeFragmentDescriptors_Z892BFC3, DatamapConversion_decomposeFragmentDescriptors_Z6E59645F } from './Datamap.js';
 import { AssayConversion_getDataFilesFromProcesses_6BABD1B0 } from './Assay.js';
 import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
 import { LDWorkflowProtocol } from '../ROCrate/LDTypes/WorkflowProtocol.js';
+import { Big } from '../../node_modules/@fable-org/fable-library-ts/lib/big.js';
 
 class RunConversion {
   constructor() {
@@ -37,29 +47,6 @@ class RunConversion {
 function RunConversion_$reflection() {
   return class_type("ARCtrl.Conversion.RunConversion", void 0, RunConversion);
 }
-function RunConversion_formatCWLType_Z5C31A0F9(type_) {
-  const s = writeYaml(encodeCWLType(type_));
-  return s.trim();
-}
-function RunConversion_isArrayType_Z5C31A0F9(type_) {
-  switch (type_.tag) {
-    case /* Array */
-    11:
-      return true;
-    case /* Union */
-    14:
-      return exists((_arg) => {
-        if (_arg.tag === /* Array */
-        11) {
-          return true;
-        } else {
-          return false;
-        }
-      }, type_.fields[0]);
-    default:
-      return false;
-  }
-}
 function RunConversion_composeCWLInputFilePath_Z384F8060(path, runName) {
   if (path.startsWith("../..")) {
     return replace(replace(path, "../../", ""), "../..", "");
@@ -75,42 +62,417 @@ function RunConversion_decomposeCWLInputFilePath_Z384F8060(path, runName) {
     return combine("../..", path);
   }
 }
+function RunConversion_composeCWLParameterValue_6CF93391(value, runName, context) {
+  switch (value.tag) {
+    case /* Directory */
+    6: {
+      const path_3 = RunConversion_composeCWLInputFilePath_Z384F8060(DirectoryInstanceModule_pathOrLocation(value.fields[0]), runName);
+      return LDFile.create(path_3, void 0, void 0, void 0, void 0, void 0, unwrap(context));
+    }
+    case /* Array */
+    7:
+      return ResizeArray_map((value_3) => RunConversion_composeCWLParameterValue_6CF93391(value_3, runName, unwrap(context)), value.fields[0]);
+    case /* Record */
+    8: {
+      const fields = value.fields[0];
+      const record = new DynamicObj();
+      iterate((field) => {
+        setProperty(field.Name, RunConversion_composeCWLParameterValue_6CF93391(field.Value, runName, unwrap(context)), record);
+      }, fields);
+      return record;
+    }
+    case /* String */
+    1:
+      return value.fields[0];
+    case /* Int */
+    2:
+      return value.fields[0];
+    case /* Float */
+    3:
+      return value.fields[0];
+    case /* Boolean */
+    4:
+      return value.fields[0];
+    case /* Null */
+    0:
+      return defaultOf();
+    default: {
+      const file = value.fields[0];
+      const path_1 = RunConversion_composeCWLInputFilePath_Z384F8060(FileInstanceModule_pathOrLocation(file), runName);
+      const encodingFormat = file.Format;
+      return LDFile.create(path_1, void 0, void 0, void 0, unwrap(encodingFormat), void 0, unwrap(context));
+    }
+  }
+}
+function RunConversion_composeLegacyValue_Z62BDCFA3(inputValue) {
+  let collection = void 0;
+  const option_1 = inputValue.Value;
+  if (option_1 != null) {
+    return value(option_1);
+  } else {
+    return CWLParameterValue_Array$((collection = map(CWLParameterValue_String$, inputValue.Values), Array.from(collection)));
+  }
+}
 function RunConversion_composeCWLInputValue_70DD9184(inputValue, exampleOfWork, inputParam, runName) {
+  let option_4 = void 0, matchValue_1 = void 0;
   if (inputParam.Type_ == null) {
-    throw new Error(`Cannot convert param values "${inputValue.Values}" as Input parameter "${inputParam.Name}" has no type.`);
+    throw new Exception(`Cannot convert param values "${inputValue.Values}" as Input parameter "${inputParam.Name}" has no type.`);
   }
   const type_ = value(inputParam.Type_);
   if (inputValue.Type != null) {
-    if (!equals(value(inputValue.Type), type_)) {
-      throw new Error(`Type (${RunConversion_formatCWLType_Z5C31A0F9(value(inputValue.Type))}) of yml input value "${inputValue.Key}" does not match type of workflow input parameter (${RunConversion_formatCWLType_Z5C31A0F9(type_)}).`);
+    if (!CWLTypeModule_typesEqual(value(inputValue.Type), type_)) {
+      throw new Exception(`Type (${formatCWLType(value(inputValue.Type))}) of yml input value "${inputValue.Key}" does not match type of workflow input parameter (${formatCWLType(type_)}).`);
     }
   }
-  let matchResult;
+  let matchResult = void 0;
   if (type_.tag === /* File */
   0) {
     if (inputValue.Values.length === 1) {
       matchResult = 0;
-    } else if (RunConversion_isArrayType_Z5C31A0F9(type_)) {
+    } else if (CWLTypeModule_isArrayType(type_)) {
       matchResult = 1;
     } else {
       matchResult = 2;
     }
-  } else if (RunConversion_isArrayType_Z5C31A0F9(type_)) {
+  } else if (CWLTypeModule_isArrayType(type_)) {
     matchResult = 1;
   } else {
     matchResult = 2;
   }
   switch (matchResult) {
     case 0: {
-      const path = RunConversion_composeCWLInputFilePath_Z384F8060(inputValue.Values[0], runName);
-      return LDFile.createCWLParameter(path, exampleOfWork);
+      const path = RunConversion_composeCWLInputFilePath_Z384F8060(item(0, inputValue.Values), runName);
+      const file = LDFile.createCWLParameter(path, exampleOfWork);
+      const matchValue = inputValue.Value;
+      let matchResult_1 = void 0, fileValue = void 0;
+      if (matchValue != null) {
+        if (value(matchValue).tag === /* File */
+        5) {
+          matchResult_1 = 0;
+          fileValue = value(matchValue).fields[0];
+        } else {
+          matchResult_1 = 1;
+        }
+      } else {
+        matchResult_1 = 1;
+      }
+      switch (matchResult_1) {
+        case 0: {
+          const option_1 = fileValue.Format;
+          if (option_1 != null) {
+            const format = value(option_1);
+            LDFile.setEncodingFormatAsString(file, format);
+          }
+          break;
+        }
+      }
+      return file;
     }
     case 1: {
-      const values = join(defaultArg(bind((ib) => ib.ItemSeparator, inputParam.InputBinding), ","), inputValue.Values);
-      return LDPropertyValue.createCWLParameter(exampleOfWork, inputValue.Key, ResizeArray_singleton(values));
+      const pv = LDPropertyValue.createCWLParameter(exampleOfWork, inputValue.Key, []);
+      const value_2 = RunConversion_composeCWLParameterValue_6CF93391(defaultArg(inputValue.Value, RunConversion_composeLegacyValue_Z62BDCFA3(inputValue)), runName);
+      LDPropertyValue.setValueObjects(pv, value_2);
+      return pv;
+    }
+    default: {
+      const pv_1 = LDPropertyValue.createCWLParameter(exampleOfWork, inputValue.Key, []);
+      const value_4 = RunConversion_composeCWLParameterValue_6CF93391((option_4 = inputValue.Value, option_4 != null ? value(option_4) : (matchValue_1 = inputValue.Values.length | 0, matchValue_1 === 0 ? CWLParameterValue_Array$([]) : matchValue_1 === 1 ? CWLParameterValue_String$(item(0, inputValue.Values)) : CWLParameterValue_Array$(ResizeArray_map(CWLParameterValue_String$, inputValue.Values)))), runName);
+      LDPropertyValue.setValueObjects(pv_1, value_4);
+      return pv_1;
     }
+  }
+}
+function RunConversion_resolveLDValue_Z224E8241(value$1, graph) {
+  let option_1 = void 0;
+  let matchResult = void 0, ref_1 = void 0;
+  if (value$1 instanceof LDRef) {
+    if (value$1, graph != null) {
+      matchResult = 0;
+      ref_1 = value$1;
+    } else {
+      matchResult = 1;
+    }
+  } else {
+    matchResult = 1;
+  }
+  switch (matchResult) {
+    case 0:
+      return defaultArg((option_1 = value(graph).TryGetNode(ref_1.Id), option_1 != null ? some(value(option_1)) : void 0), value$1);
     default:
-      return LDPropertyValue.createCWLParameter(exampleOfWork, inputValue.Key, inputValue.Values);
+      return value$1;
+  }
+}
+function RunConversion_decomposeCWLParameterValue_Z3524B680(value$1, runName, expectedType, graph) {
+  let collection = void 0, node = void 0, node_2 = void 0, collection_1 = void 0, collection_2 = void 0, collection_3 = void 0, node_4 = void 0;
+  const value_1 = RunConversion_resolveLDValue_Z224E8241(value$1, unwrap(graph));
+  let expectedType_1;
+  const option_1 = expectedType;
+  expectedType_1 = option_1 != null ? CWLTypeModule_tryGetNonNullUnionType(value(option_1)) : void 0;
+  let matchResult = void 0, arraySchema = void 0, recordSchema = void 0;
+  if (expectedType_1 != null) {
+    switch (value(expectedType_1).tag) {
+      case /* File */
+      0: {
+        matchResult = 1;
+        break;
+      }
+      case /* Directory */
+      1: {
+        matchResult = 2;
+        break;
+      }
+      case /* String */
+      3: {
+        matchResult = 3;
+        break;
+      }
+      case /* Int */
+      4:
+      case /* Long */
+      5: {
+        matchResult = 4;
+        break;
+      }
+      case /* Float */
+      6:
+      case /* Double */
+      7: {
+        matchResult = 5;
+        break;
+      }
+      case /* Boolean */
+      8: {
+        matchResult = 6;
+        break;
+      }
+      case /* Null */
+      10: {
+        matchResult = 7;
+        break;
+      }
+      case /* Enum */
+      13: {
+        matchResult = 8;
+        break;
+      }
+      case /* Array */
+      11: {
+        matchResult = 0;
+        arraySchema = value(expectedType_1).fields[0];
+        break;
+      }
+      case /* Record */
+      12: {
+        matchResult = 9;
+        recordSchema = value(expectedType_1).fields[0];
+        break;
+      }
+      default:
+        matchResult = 10;
+    }
+  } else {
+    matchResult = 10;
+  }
+  switch (matchResult) {
+    case 0:
+      if (typeof value_1 === "string") {
+        return CWLParameterValue_Array$([CWLParameterValue_String$(value_1)]);
+      } else if (isIterable(value_1)) {
+        return CWLParameterValue_Array$((collection = map((value_3) => RunConversion_decomposeCWLParameterValue_Z3524B680(value_3, runName, arraySchema.Items, unwrap(graph)), value_1), Array.from(collection)));
+      } else {
+        return CWLParameterValue_Array$([RunConversion_decomposeCWLParameterValue_Z3524B680(value_1, runName, arraySchema.Items, unwrap(graph))]);
+      }
+    case 1: {
+      let matchResult_1 = void 0;
+      if (value_1 instanceof LDNode) {
+        if (node = value_1, LDFile.validate(node)) {
+          matchResult_1 = 0;
+        } else {
+          matchResult_1 = 2;
+        }
+      } else if (typeof value_1 === "string") {
+        matchResult_1 = 1;
+      } else {
+        matchResult_1 = 2;
+      }
+      switch (matchResult_1) {
+        case 0: {
+          const node_1 = value_1;
+          return CWLParameterValue_File(new FileInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(node_1.Id, runName), void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(LDFile.tryGetEncodingFormatAsString(node_1))));
+        }
+        case 1:
+          return CWLParameterValue_File(new FileInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(value_1, runName)));
+        default:
+          return CWLParameterValue_String$(toString(value_1));
+      }
+    }
+    case 2: {
+      let matchResult_2 = void 0;
+      if (value_1 instanceof LDNode) {
+        if (node_2 = value_1, LDFile.validate(node_2)) {
+          matchResult_2 = 0;
+        } else {
+          matchResult_2 = 2;
+        }
+      } else if (typeof value_1 === "string") {
+        matchResult_2 = 1;
+      } else {
+        matchResult_2 = 2;
+      }
+      switch (matchResult_2) {
+        case 0: {
+          const node_3 = value_1;
+          return CWLParameterValue_Directory(new DirectoryInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(node_3.Id, runName)));
+        }
+        case 1:
+          return CWLParameterValue_Directory(new DirectoryInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(value_1, runName)));
+        default:
+          return CWLParameterValue_String$(toString(value_1));
+      }
+    }
+    case 3:
+      if (equals(value_1, defaultOf())) {
+        return CWLParameterValue.Null;
+      } else if (typeof value_1 === "string") {
+        return CWLParameterValue_String$(value_1);
+      } else {
+        return CWLParameterValue_String$(toString(value_1));
+      }
+    case 4: {
+      let option_5;
+      const option_3 = CWLParameterValueModule_tryParseInt64(value_1);
+      option_5 = option_3 != null ? CWLParameterValue_Int(value(option_3)) : void 0;
+      if (option_5 != null) {
+        return value(option_5);
+      } else {
+        return CWLParameterValue_String$(toString(value_1));
+      }
+    }
+    case 5: {
+      let option_9;
+      const option_7 = CWLParameterValueModule_tryParseFloat(value_1);
+      option_9 = option_7 != null ? CWLParameterValue_Float(value(option_7)) : void 0;
+      if (option_9 != null) {
+        return value(option_9);
+      } else {
+        return CWLParameterValue_String$(toString(value_1));
+      }
+    }
+    case 6:
+      if (typeof value_1 === "boolean") {
+        return CWLParameterValue_Boolean$(value_1);
+      } else if (typeof value_1 === "string") {
+        const value_6 = value_1;
+        let matchValue;
+        let outArg = false;
+        matchValue = [tryParse(value_6, new FSharpRef(() => outArg, (v) => {
+          outArg = v;
+        })), outArg];
+        if (matchValue[0]) {
+          return CWLParameterValue_Boolean$(matchValue[1]);
+        } else {
+          return CWLParameterValue_String$(value_6);
+        }
+      } else {
+        return CWLParameterValue_String$(toString(value_1));
+      }
+    case 7:
+      return CWLParameterValue.Null;
+    case 8:
+      if (equals(value_1, defaultOf())) {
+        return CWLParameterValue.Null;
+      } else if (typeof value_1 === "string") {
+        return CWLParameterValue_String$(value_1);
+      } else {
+        return CWLParameterValue_String$(toString(value_1));
+      }
+    case 9:
+      if (value_1 instanceof DynamicObj) {
+        const record = value_1;
+        return CWLParameterValue_Record((collection_1 = map((kvp) => new CWLParameterRecordField(kvp[0], RunConversion_decomposeCWLParameterValue_Z3524B680(kvp[1], runName, unwrap(InputRecordSchemaModule_tryGetFieldType(kvp[0], recordSchema)), unwrap(graph))), record.GetProperties(false)), Array.from(collection_1)));
+      } else {
+        return CWLParameterValue_String$(toString(value_1));
+      }
+    default: {
+      let matchResult_3 = void 0, value_8 = void 0, value_9 = void 0, value_10 = void 0, value_11 = void 0, value_12 = void 0, value_13 = void 0, node_5 = void 0, values_1 = void 0, record_1 = void 0;
+      if (equals(value_1, defaultOf())) {
+        matchResult_3 = 0;
+      } else if (typeof value_1 === "string") {
+        matchResult_3 = 1;
+        value_8 = value_1;
+      } else if (typeof value_1 === "number") {
+        matchResult_3 = 2;
+        value_9 = value_1;
+      } else if (typeof value_1 === "bigint") {
+        matchResult_3 = 3;
+        value_10 = value_1;
+      } else if (value_1 instanceof Big) {
+        matchResult_3 = 4;
+        value_11 = value_1;
+      } else if (typeof value_1 === "number") {
+        matchResult_3 = 5;
+        value_12 = value_1;
+      } else if (typeof value_1 === "boolean") {
+        matchResult_3 = 6;
+        value_13 = value_1;
+      } else if (value_1 instanceof LDNode) {
+        if (node_4 = value_1, LDFile.validate(node_4)) {
+          matchResult_3 = 7;
+          node_5 = value_1;
+        } else if (isIterable(value_1)) {
+          matchResult_3 = 8;
+          values_1 = value_1;
+        } else {
+          matchResult_3 = 9;
+          record_1 = value_1;
+        }
+      } else if (value_1 instanceof DynamicObj) {
+        if (isIterable(value_1)) {
+          matchResult_3 = 8;
+          values_1 = value_1;
+        } else {
+          matchResult_3 = 9;
+          record_1 = value_1;
+        }
+      } else if (isIterable(value_1)) {
+        matchResult_3 = 8;
+        values_1 = value_1;
+      } else {
+        matchResult_3 = 10;
+      }
+      switch (matchResult_3) {
+        case 0:
+          return CWLParameterValue.Null;
+        case 1:
+          return CWLParameterValue_String$(value_8);
+        case 2:
+          return CWLParameterValue_Int(toInt64_unchecked(fromInt32(value_9)));
+        case 3:
+          return CWLParameterValue_Int(value_10);
+        case 4:
+          return CWLParameterValue_Float(toFloat64(value_11));
+        case 5:
+          return CWLParameterValue_Float(value_12);
+        case 6:
+          return CWLParameterValue_Boolean$(value_13);
+        case 7:
+          return CWLParameterValue_File(new FileInstance(void 0, RunConversion_decomposeCWLInputFilePath_Z384F8060(node_5.Id, runName), void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(LDFile.tryGetEncodingFormatAsString(node_5))));
+        case 8:
+          return CWLParameterValue_Array$((collection_2 = map((value_14) => RunConversion_decomposeCWLParameterValue_Z3524B680(value_14, runName, void 0, unwrap(graph)), values_1), Array.from(collection_2)));
+        case 9:
+          return CWLParameterValue_Record((collection_3 = map((kvp_1) => new CWLParameterRecordField(kvp_1[0], RunConversion_decomposeCWLParameterValue_Z3524B680(kvp_1[1], runName, void 0, unwrap(graph))), record_1.GetProperties(false)), Array.from(collection_3)));
+        default:
+          return CWLParameterValue_String$(toString(value_1));
+      }
+    }
+  }
+}
+function RunConversion_tryGetExpectedTypeFromFormalParameter_2664C4B8(exampleOfWork, context, graph) {
+  try {
+    const input = WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(exampleOfWork, unwrap(context), unwrap(graph));
+    return input.Type_;
+  } catch (matchValue) {
+    return void 0;
   }
 }
 function RunConversion_decomposeCWLInputValue_Z1346FE9D(inputValue, runName, context, graph) {
@@ -124,16 +486,16 @@ function RunConversion_decomposeCWLInputValue_Z1346FE9D(inputValue, runName, con
   }
   const key = LDFormalParameter.getNameAsString(exampleOfWork, unwrap(context));
   if (LDFile.validateCWLParameter(inputValue, unwrap(context))) {
-    return new CWLParameterReference(key, [RunConversion_decomposeCWLInputFilePath_Z384F8060(inputValue.Id, runName)], CWLType_file());
+    return new CWLParameterReference(key, [RunConversion_decomposeCWLInputFilePath_Z384F8060(inputValue.Id, runName)], void 0, CWLType_file());
   } else if (LDPropertyValue.validateCWLParameter(inputValue, unwrap(context))) {
-    return new CWLParameterReference(key, LDPropertyValue.getValuesAsString(inputValue, unwrap(context)));
+    return new CWLParameterReference(key, void 0, RunConversion_decomposeCWLParameterValue_Z3524B680(LDPropertyValue.getValueObject(inputValue, unwrap(context)), runName, unwrap(RunConversion_tryGetExpectedTypeFromFormalParameter_2664C4B8(exampleOfWork, unwrap(context), unwrap(graph))), unwrap(graph)));
   } else {
     const arg_2 = inputValue.Id;
     return toFail(printf("Input value %s of run %s is neither a CWL File nor a CWL Parameter."))(arg_2)(runName);
   }
 }
 function RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run, fs) {
-  let b;
+  let b = void 0;
   let workflowProtocol;
   const workflowFilePath = Run_cwlFileNameFromIdentifier(run.Identifier);
   const matchValue = run.CWLDescription;
@@ -154,7 +516,7 @@ function RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run, fs) {
       }
     }, run.CWLInput);
     if (paramRef == null) {
-      throw new Error(`Could not create workflow invocation for run "${run.Identifier}": Workflow parameter "${name}" had no assigned value.`);
+      throw new Exception(`Could not create workflow invocation for run "${run.Identifier}": Workflow parameter "${name}" had no assigned value.`);
     } else {
       return RunConversion_composeCWLInputValue_70DD9184(value(paramRef), ldI, tupledArg[0], run.Identifier);
     }
@@ -167,26 +529,28 @@ function RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run, fs) {
     return ResizeArray_singleton(mainInvocation);
   } else {
     return ResizeArray_appendSingleton(mainInvocation, ResizeArray_map((p) => {
-      const id = replace(p.Id, "Process", `WorkflowInvocation_${run.Identifier}`);
+      const id = replace(p.Id, "Process", concat("WorkflowInvocation_", run.Identifier));
       const name_1 = LDLabProcess.getNameAsString(p, unwrap(p.TryGetContext()));
       const inputs = LDLabProcess.getObjects(p);
       const results = Option_fromSeq(LDLabProcess.getResults(p));
       const protocol = LDLabProcess.tryGetExecutesLabProtocol(p);
       const parameterValues = Option_fromSeq(LDLabProcess.getParameterValues(p));
-      const agents = map(ResizeArray_singleton, LDLabProcess.tryGetAgent(p));
+      let agents;
+      const option_1 = LDLabProcess.tryGetAgent(p);
+      agents = option_1 != null ? ResizeArray_singleton(value(option_1)) : void 0;
       const disambiguatingDescriptions = Option_fromSeq(LDLabProcess.getDisambiguatingDescriptionsAsString(p));
       return LDWorkflowInvocation.create(name_1, workflowProtocol, inputs, unwrap(results), void 0, unwrap(agents), id, void 0, unwrap(disambiguatingDescriptions), unwrap(protocol), unwrap(parameterValues));
     }, processSequence));
   }
 }
 function RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(workflowInvocation, runName, context, graph) {
-  let matchValue;
+  let matchValue = void 0;
   return [(matchValue = LDLabProcess.tryGetExecutesLabProtocol(workflowInvocation, unwrap(graph), unwrap(context)), matchValue == null ? (() => {
-    throw new Error(`Could not decompose workflow invocation for run "${runName}": Workflow parameter "name" had no assigned value.`);
+    throw new Exception(concat('Could not decompose workflow invocation for run "', runName, '": Workflow parameter "name" had no assigned value.'));
   })() : WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(value(matchValue), void 0, unwrap(context), unwrap(graph))), ResizeArray_map((iv) => RunConversion_decomposeCWLInputValue_Z1346FE9D(iv, runName, unwrap(context), unwrap(graph)), LDLabProcess.getObjects(workflowInvocation, unwrap(graph), unwrap(context)))];
 }
 function RunConversion_composeRun_Z8CC08AC(run, fs) {
-  let fds_1, vm_1, fds, vm;
+  let i = void 0, fds_1 = void 0, vm_1 = void 0, fds = void 0, vm = void 0;
   let workflowProtocol;
   const workflowFilePath = Run_cwlFileNameFromIdentifier(run.Identifier);
   const matchValue = run.CWLDescription;
@@ -197,10 +561,19 @@ function RunConversion_composeRun_Z8CC08AC(run, fs) {
     workflowProtocol = WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(workflowFilePath, value(matchValue), void 0, run.Identifier);
   }
   const workflowInvocations = Option_fromSeq(RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run, unwrap(fs)));
-  const measurementMethod = map(BaseTypes_composeDefinedTerm_ZDED3A0F, run.TechnologyType);
-  const measurementTechnique = map(BaseTypes_composeDefinedTerm_ZDED3A0F, run.TechnologyPlatform);
-  const variableMeasured = map(BaseTypes_composePropertyValueFromOA_ZDED3A0F, run.MeasurementType);
-  const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, run.Performers));
+  let measurementMethod;
+  const option_1 = run.TechnologyType;
+  measurementMethod = option_1 != null ? BaseTypes_composeDefinedTerm_ZDED3A0F(value(option_1)) : void 0;
+  let measurementTechnique;
+  const option_3 = run.TechnologyPlatform;
+  measurementTechnique = option_3 != null ? BaseTypes_composeDefinedTerm_ZDED3A0F(value(option_3)) : void 0;
+  let variableMeasured;
+  const option_5 = run.MeasurementType;
+  variableMeasured = option_5 != null ? BaseTypes_composePropertyValueFromOA_ZDED3A0F(value(option_5)) : void 0;
+  let persons;
+  const option_7 = run.Investigation;
+  persons = option_7 != null ? (i = value(option_7), i.GetAllPersons()) : void 0;
+  const creators = Option_fromSeq(ResizeArray_map((c) => PersonConversion_composePerson_2B0BECCC(c, unwrap(persons)), run.Performers));
   const publisher = LDOrganization.create("DataPLANT");
   const dateCreated = utcNow();
   if (creators != null) {
@@ -208,8 +581,12 @@ function RunConversion_composeRun_Z8CC08AC(run, fs) {
   }
   LDComputationalWorkflow.setSdPublisher(workflowProtocol, publisher);
   LDComputationalWorkflow.setDateCreatedAsDateTime(workflowProtocol, dateCreated);
-  const fragmentDescriptors = map(DatamapConversion_composeFragmentDescriptors_Z892BFC3, run.Datamap);
-  const dataFiles = map((ps) => AssayConversion_getDataFilesFromProcesses_6BABD1B0(ps, unwrap(fragmentDescriptors)), workflowInvocations);
+  let fragmentDescriptors;
+  const option_9 = run.Datamap;
+  fragmentDescriptors = option_9 != null ? DatamapConversion_composeFragmentDescriptors_Z892BFC3(value(option_9)) : void 0;
+  let dataFiles;
+  const option_11 = workflowInvocations;
+  dataFiles = option_11 != null ? AssayConversion_getDataFilesFromProcesses_6BABD1B0(value(option_11), unwrap(fragmentDescriptors)) : void 0;
   const hasParts = dataFiles == null ? ResizeArray_singleton(workflowProtocol) : ResizeArray_appendSingleton(workflowProtocol, value(dataFiles));
   const variableMeasureds = variableMeasured == null ? fragmentDescriptors == null ? void 0 : (fds_1 = value(fragmentDescriptors), fds_1) : fragmentDescriptors == null ? (vm_1 = value(variableMeasured), ResizeArray_singleton(vm_1)) : (fds = value(fragmentDescriptors), vm = value(variableMeasured), ResizeArray_appendSingleton(vm, fds));
   const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, run.Comments));
@@ -218,9 +595,9 @@ function RunConversion_composeRun_Z8CC08AC(run, fs) {
 function RunConversion_decomposeRun_Z6839B9E8(run, graph, context) {
   const workflowProtocol = LDDataset.tryGetMainEntityAsWorkflowProtocol(run, unwrap(graph), unwrap(context));
   const mainWorkflowInvocation = find((wi) => {
-    let lp;
+    let lp = void 0;
     const matchValue = LDLabProcess.tryGetExecutesLabProtocol(wi, unwrap(graph), unwrap(context));
-    let matchResult, lp_1;
+    let matchResult = void 0, lp_1 = void 0;
     if (matchValue != null) {
       if (lp = value(matchValue), LDWorkflowProtocol.validate(lp, unwrap(context))) {
         matchResult = 0;
@@ -239,9 +616,15 @@ function RunConversion_decomposeRun_Z6839B9E8(run, graph, context) {
     }
   }, LDDataset.getAboutsAsWorkflowInvocation(run, unwrap(graph), unwrap(context)));
   const patternInput = workflowProtocol == null ? RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(mainWorkflowInvocation, LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(context), unwrap(graph)) : [WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(value(workflowProtocol), void 0, unwrap(context), unwrap(graph)), ResizeArray_map((iv) => RunConversion_decomposeCWLInputValue_Z1346FE9D(iv, LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(context), unwrap(graph)), LDLabProcess.getObjects(mainWorkflowInvocation, unwrap(graph), unwrap(context)))];
-  const measurementMethod = map((m) => BaseTypes_decomposeDefinedTerm_Z2F770004(m, unwrap(context)), LDDataset.tryGetMeasurementMethodAsDefinedTerm(run, unwrap(graph), unwrap(context)));
-  const measurementTechnique = map((m_1) => BaseTypes_decomposeDefinedTerm_Z2F770004(m_1, unwrap(context)), LDDataset.tryGetMeasurementTechniqueAsDefinedTerm(run, unwrap(graph), unwrap(context)));
-  const variableMeasured = map((v) => BaseTypes_decomposePropertyValueToOA_Z2F770004(v, unwrap(context)), LDDataset.tryGetVariableMeasuredAsMeasurementType(run, unwrap(graph), unwrap(context)));
+  let measurementMethod;
+  const option_1 = LDDataset.tryGetMeasurementMethodAsDefinedTerm(run, unwrap(graph), unwrap(context));
+  measurementMethod = option_1 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(value(option_1), unwrap(context)) : void 0;
+  let measurementTechnique;
+  const option_3 = LDDataset.tryGetMeasurementTechniqueAsDefinedTerm(run, unwrap(graph), unwrap(context));
+  measurementTechnique = option_3 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(value(option_3), unwrap(context)) : void 0;
+  let variableMeasured;
+  const option_5 = LDDataset.tryGetVariableMeasuredAsMeasurementType(run, unwrap(graph), unwrap(context));
+  variableMeasured = option_5 != null ? BaseTypes_decomposePropertyValueToOA_Z2F770004(value(option_5), unwrap(context)) : void 0;
   const contacts = ResizeArray_map((c) => PersonConversion_decomposePerson_Z6839B9E8(c, unwrap(graph), unwrap(context)), LDDataset.getCreators(run, unwrap(graph), unwrap(context)));
   const comments = ResizeArray_map((c_1) => BaseTypes_decomposeComment_Z2F770004(c_1, unwrap(context)), LDDataset.getComments(run, unwrap(graph), unwrap(context)));
   let datamap;
@@ -251,4 +634,4 @@ function RunConversion_decomposeRun_Z6839B9E8(run, graph, context) {
   return ArcRun.create(LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(LDDataset.tryGetNameAsString(run, unwrap(context))), unwrap(LDDataset.tryGetDescriptionAsString(run, unwrap(context))), unwrap(variableMeasured), unwrap(measurementMethod), unwrap(measurementTechnique), void 0, tables.Tables, unwrap(datamap), contacts, patternInput[0], patternInput[1], comments);
 }
 
-export { RunConversion, RunConversion_$reflection, RunConversion_composeCWLInputFilePath_Z384F8060, RunConversion_composeCWLInputValue_70DD9184, RunConversion_composeRun_Z8CC08AC, RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC, RunConversion_decomposeCWLInputFilePath_Z384F8060, RunConversion_decomposeCWLInputValue_Z1346FE9D, RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D, RunConversion_decomposeRun_Z6839B9E8, RunConversion_formatCWLType_Z5C31A0F9, RunConversion_isArrayType_Z5C31A0F9 };
+export { RunConversion, RunConversion_$reflection, RunConversion_composeCWLInputFilePath_Z384F8060, RunConversion_composeCWLInputValue_70DD9184, RunConversion_composeCWLParameterValue_6CF93391, RunConversion_composeRun_Z8CC08AC, RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC, RunConversion_decomposeCWLInputFilePath_Z384F8060, RunConversion_decomposeCWLInputValue_Z1346FE9D, RunConversion_decomposeCWLParameterValue_Z3524B680, RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D, RunConversion_decomposeRun_Z6839B9E8 };

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

@@ -1,7 +1,7 @@
-import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
-import { LDGraph, LDNode } from '../ROCrate/LDObject.js';
-import { LDContext } from '../ROCrate/LDContext.js';
-import { Publication } from '../Core/Publication.js';
+import { TypeInfo } from '@fable-org/fable-library-ts/Reflection.ts';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.ts';
+import { LDContext } from '../ROCrate/LDContext.ts';
+import { Publication } from '../Core/Publication.ts';
 export declare class ScholarlyArticleConversion {
     constructor();
 }