@nfdi4plants/arctrl 3.0.0-beta.11 → 3.0.0-beta.13

package/dist/ts/ts/Conversion/Table.js

@@ -0,0 +1,203 @@
+import { fold, zip, toList, delay, map as map$1 } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { LDLabProtocol } from '../ROCrate/LDTypes/LabProtocol.js';
+import { BaseTypes_composeComponent, BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_decomposeComponent_Z2F770004 } from './Basic.js';
+import { ResizeArray_appendSingleton, ResizeArray_singleton } from '../Core/Helper/Collections.js';
+import { unwrap, map } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { ArcTable } from '../Core/Table/ArcTable.js';
+import { getEnumerator, disposeSafe, safeHash, equals } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { ARCtrl_ROCrate_LDNode__LDNode_TryGetColumnIndex } from './ColumnIndex.js';
+import { ProcessConversion_tryGetProtocolType_Z6839B9E8, ProcessConversion_getProcessGetter, ProcessConversion_processToRows_Z6839B9E8, ProcessConversion_groupProcesses_Z27F0B586 } from './Process.js';
+import { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
+import { createMissingIdentifier } from '../Core/Helper/Identifier.js';
+import { singleton, initialize, collect, ofSeq, map as map$2 } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { List_distinct } from '../../node_modules/@fable-org/fable-library-js/Seq2.js';
+import { LDLabProcess } from '../ROCrate/LDTypes/LabProcess.js';
+import { rangeDouble } from '../../node_modules/@fable-org/fable-library-js/Range.js';
+import { Unchecked_alignByHeaders } from '../Core/Table/ArcTableAux.js';
+import { ArcTables } from '../Core/Table/ArcTables.js';
+
+function CompositeRow_toProtocol(tableName, row) {
+  return fold((p, hc) => {
+    let matchResult, oa, v, v_1, v_2, v_3;
+    switch (hc[0].tag) {
+      case /* ProtocolType */
+      4: {
+        if (hc[1].tag === /* Term */
+        0) {
+          matchResult = 0;
+          oa = hc[1].fields[0];
+        } else {
+          matchResult = 6;
+        }
+        break;
+      }
+      case /* ProtocolVersion */
+      7: {
+        if (hc[1].tag === /* FreeText */
+        1) {
+          matchResult = 1;
+          v = hc[1].fields[0];
+        } else {
+          matchResult = 6;
+        }
+        break;
+      }
+      case /* ProtocolUri */
+      6: {
+        if (hc[1].tag === /* FreeText */
+        1) {
+          matchResult = 2;
+          v_1 = hc[1].fields[0];
+        } else {
+          matchResult = 6;
+        }
+        break;
+      }
+      case /* ProtocolDescription */
+      5: {
+        if (hc[1].tag === /* FreeText */
+        1) {
+          matchResult = 3;
+          v_2 = hc[1].fields[0];
+        } else {
+          matchResult = 6;
+        }
+        break;
+      }
+      case /* ProtocolREF */
+      8: {
+        if (hc[1].tag === /* FreeText */
+        1) {
+          matchResult = 4;
+          v_3 = hc[1].fields[0];
+        } else {
+          matchResult = 6;
+        }
+        break;
+      }
+      case /* Component */
+      0: {
+        switch (hc[1].tag) {
+          case /* Term */
+          0:
+          case /* Unitized */
+          2: {
+            matchResult = 5;
+            break;
+          }
+          default:
+            matchResult = 6;
+        }
+        break;
+      }
+      default:
+        matchResult = 6;
+    }
+    switch (matchResult) {
+      case 0: {
+        LDLabProtocol.setIntendedUseAsDefinedTerm(p, BaseTypes_composeDefinedTerm_ZDED3A0F(oa));
+        break;
+      }
+      case 1: {
+        LDLabProtocol.setVersionAsString(p, v);
+        break;
+      }
+      case 2: {
+        LDLabProtocol.setUrl(p, v_1);
+        break;
+      }
+      case 3: {
+        LDLabProtocol.setDescriptionAsString(p, v_2);
+        break;
+      }
+      case 4: {
+        LDLabProtocol.setNameAsString(p, v_3);
+        break;
+      }
+      case 5: {
+        const newC = ResizeArray_appendSingleton(BaseTypes_composeComponent(hc[0], hc[1]), LDLabProtocol.getLabEquipments(p));
+        LDLabProtocol.setLabEquipments(p, newC);
+        break;
+      }
+    }
+    return p;
+  }, LDLabProtocol.create(tableName, tableName), row);
+}
+function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_Z6839B9E8(p, graph, context) {
+  const name = LDLabProtocol.getNameAsString(p, unwrap(context));
+  const t = ArcTable.init(name);
+  let enumerator = getEnumerator(LDLabProtocol.getComponents(p, unwrap(graph), unwrap(context)));
+  try {
+    while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+      const c = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+      const patternInput = BaseTypes_decomposeComponent_Z2F770004(c, unwrap(context));
+      t.AddColumn(patternInput[0], ResizeArray_singleton(patternInput[1]), unwrap(ARCtrl_ROCrate_LDNode__LDNode_TryGetColumnIndex(c)));
+    }
+  } finally {
+    disposeSafe(enumerator);
+  }
+  map((d) => {
+    t.AddProtocolDescriptionColumn(ResizeArray_singleton(d));
+  }, LDLabProtocol.tryGetDescriptionAsString(p, unwrap(context)));
+  map((d_1) => {
+    t.AddProtocolVersionColumn(ResizeArray_singleton(d_1));
+  }, LDLabProtocol.tryGetVersionAsString(p, unwrap(context)));
+  map((d_2) => {
+    t.AddProtocolTypeColumn(ResizeArray_singleton(d_2));
+  }, ProcessConversion_tryGetProtocolType_Z6839B9E8(p, void 0, unwrap(context)));
+  map((d_3) => {
+    t.AddProtocolUriColumn(ResizeArray_singleton(d_3));
+  }, LDLabProtocol.tryGetUrl(p, unwrap(context)));
+  t.AddProtocolNameColumn(ResizeArray_singleton(name));
+  return t;
+}
+function ARCtrl_ArcTable__ArcTable_GetProtocols(this$) {
+  let source;
+  if (this$.RowCount === 0) {
+    return singleton((source = this$.Headers, fold((p, h) => {
+      if (h.tag === /* Component */
+      0) {
+        const oa = h.fields[0];
+        const matchValue = oa.NameText;
+        const matchValue_1 = oa.TermAccessionOntobeeUrl;
+        const newC = ResizeArray_appendSingleton(LDPropertyValue.createComponent(matchValue, "Empty Component Value", void 0, matchValue_1), LDLabProtocol.getLabEquipments(p));
+        LDLabProtocol.setLabEquipments(p, newC);
+      }
+      return p;
+    }, LDLabProtocol.create(createMissingIdentifier(), this$.Name), source)));
+  } else {
+    return List_distinct(initialize(this$.RowCount, (i) => {
+      let row;
+      const source_2 = this$.GetRow(i, true);
+      row = zip(this$.Headers, source_2);
+      return CompositeRow_toProtocol(this$.Name, row);
+    }), {
+      Equals: equals,
+      GetHashCode: safeHash
+    });
+  }
+}
+function ARCtrl_ArcTable__ArcTable_GetProcesses_5E660E5C(this$, assayName, studyName, fs) {
+  if (this$.RowCount === 0) {
+    return singleton(LDLabProcess.create(this$.Name));
+  } else {
+    const getter = ProcessConversion_getProcessGetter(assayName, studyName, this$.Name, this$.Headers, fs);
+    return toList(delay(() => map$1((i) => getter(this$)(i), rangeDouble(0, 1, this$.RowCount - 1))));
+  }
+}
+function ARCtrl_ArcTable__ArcTable_fromProcesses_Static_Z3575FB5F(name, ps, graph, context) {
+  const tupledArg = Unchecked_alignByHeaders(true, collect((p) => ofSeq(ProcessConversion_processToRows_Z6839B9E8(p, unwrap(graph), unwrap(context))), ps));
+  return ArcTable.fromArcTableValues(name, tupledArg[0], tupledArg[1]);
+}
+function ARCtrl_ArcTables__ArcTables_GetProcesses_5E660E5C(this$, assayName, studyName, fs) {
+  return collect((t) => ARCtrl_ArcTable__ArcTable_GetProcesses_5E660E5C(t, unwrap(assayName), unwrap(studyName), unwrap(fs)), toList(this$.Tables));
+}
+function ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586(ps, graph, context) {
+  let collection;
+  return new ArcTables((collection = map$2((tupledArg) => {
+    const tupledArg_1 = Unchecked_alignByHeaders(true, collect((p) => ofSeq(ProcessConversion_processToRows_Z6839B9E8(p, unwrap(graph), unwrap(context))), tupledArg[1]));
+    return ArcTable.fromArcTableValues(tupledArg[0], tupledArg_1[0], tupledArg_1[1]);
+  }, ProcessConversion_groupProcesses_Z27F0B586(ps, unwrap(graph), unwrap(context))), Array.from(collection)));
+}
+
+export { ARCtrl_ArcTable__ArcTable_GetProcesses_5E660E5C, ARCtrl_ArcTable__ArcTable_GetProtocols, ARCtrl_ArcTable__ArcTable_fromProcesses_Static_Z3575FB5F, ARCtrl_ArcTable__ArcTable_fromProtocol_Static_Z6839B9E8, ARCtrl_ArcTables__ArcTables_GetProcesses_5E660E5C, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586, CompositeRow_toProtocol };

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

@@ -0,0 +1,45 @@
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { CWLType_$union } from '../CWL/CWLTypes.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.js';
+import { CWLInput, InputBinding } from '../CWL/Inputs.js';
+import { LDContext } from '../ROCrate/LDContext.js';
+import { CWLOutput, OutputBinding } from '../CWL/Outputs.js';
+import { Component } from '../Core/Process/Component.js';
+import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.js';
+import { CWLToolDescription } from '../CWL/ToolDescription.js';
+import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.js';
+import { WorkflowStep } from '../CWL/WorkflowSteps.js';
+import { ArcWorkflow } from '../Core/ArcTypes.js';
+import { FileSystem } from '../FileSystem/FileSystem.js';
+export declare class WorkflowConversion {
+    constructor();
+}
+export declare function WorkflowConversion_$reflection(): TypeInfo;
+export declare function WorkflowConversion_composeAdditionalType_Z5C31A0F9(t: CWLType_$union): string;
+export declare function WorkflowConversion_decomposeAdditionalType_Z721C83C5(t: string): CWLType_$union;
+export declare function WorkflowConversion_composeFormalParamInputIdentifiers(prefix: Option<string>, position: Option<int32>): Option<LDNode[]>;
+export declare function WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(inp: CWLInput, workflowName?: string, runName?: string): LDNode;
+export declare function WorkflowConversion_decomposeInputBindings_1AAAE9A5(identifiers: LDNode[], context?: LDContext): Option<InputBinding>;
+export declare function WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(inp: LDNode, context?: LDContext, graph?: LDGraph): CWLInput;
+export declare function WorkflowConversion_composeFormalParameterOutputIdentifiers_6DFDD678(glob: Option<string>): Option<LDNode[]>;
+export declare function WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(out: CWLOutput, workflowName?: string, runName?: string): LDNode;
+export declare function WorkflowConversion_decomposeOutputBindings_1AAAE9A5(identifiers: LDNode[], context?: LDContext): OutputBinding;
+export declare function WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(inp: LDNode, context?: LDContext, graph?: LDGraph): CWLOutput;
+export declare function WorkflowConversion_composeComputationalTool_Z685B8F25(tool: Component): LDNode;
+export declare function WorkflowConversion_decomposeComputationalTool_Z6839B9E8(tool: LDNode, graph?: LDGraph, context?: LDContext): Component;
+export declare function WorkflowConversion_getInputParametersFromProcessingUnit_30922B92(pu: CWLProcessingUnit_$union): CWLInput[];
+export declare function WorkflowConversion_get_toolDescriptionTypeName(): string;
+export declare function WorkflowConversion_get_workflowDescriptionTypeName(): string;
+export declare function WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA(filePath: string, workflow: CWLToolDescription, workflowName?: string, runName?: string): LDNode;
+export declare function WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8(protocol: LDNode, context?: LDContext, graph?: LDGraph): CWLToolDescription;
+export declare function WorkflowConversion_composeWorkflowStep_Z35AB9E5D<$a>(step: WorkflowStep, workflowID: $a): LDNode;
+export declare function WorkflowConversion_composeWorkflowProtocolFromWorkflow_Z6FBB852F(filePath: string, workflow: CWLWorkflowDescription, workflowName?: string, runName?: string): LDNode;
+export declare function WorkflowConversion_decomposeWorkflowStep_2664C4B8(step: LDNode, context?: LDContext, graph?: LDGraph): WorkflowStep;
+export declare function WorkflowConversion_decomposeWorkflowProtocolToWorkflow_2664C4B8(protocol: LDNode, context?: LDContext, graph?: LDGraph): CWLWorkflowDescription;
+export declare function WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(filePath: string, pu: CWLProcessingUnit_$union, workflowName?: string, runName?: string): LDNode;
+export declare function WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_2664C4B8(protocol: LDNode, context?: LDContext, graph?: LDGraph): CWLProcessingUnit_$union;
+export declare function WorkflowConversion_composeWorkflow_42450E6E(workflow: ArcWorkflow, fs?: FileSystem): LDNode;
+export declare function WorkflowConversion_decomposeWorkflow_Z6839B9E8(workflow: LDNode, graph?: LDGraph, context?: LDContext): ArcWorkflow;
+//# sourceMappingURL=Workflow.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"Workflow.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Workflow.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAEjF,OAAO,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAIpD,OAAO,EAAiC,MAAM,EAAoB,MAAM,uCAAuC,CAAC;AAChH,OAAO,EAAW,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAEtE,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,EAAgC,QAAQ,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAExF,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AACpD,OAAO,EAAiC,SAAS,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAI5F,OAAO,EAA8B,SAAS,EAAE,MAAM,8BAA8B,CAAC;AAErF,OAAO,EAAE,sBAAsB,EAAE,MAAM,+BAA+B,CAAC;AAEvE,OAAO,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAiE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AAKtI,OAAO,EAAc,YAAY,EAAE,MAAM,yBAAyB,CAAC;AASnE,OAAO,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAClD,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,qBAAa,kBAAkB;;CAG9B;AAED,wBAAgB,8BAA8B,IAAI,QAAQ,CAEzD;AAED,wBAAgB,kDAAkD,CAAC,CAAC,EAAE,cAAc,GAAG,MAAM,CAG5F;AAED,wBAAgB,oDAAoD,CAAC,CAAC,EAAE,MAAM,GAAG,cAAc,CAE9F;AAED,wBAAgB,qDAAqD,CAAC,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,KAAK,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,CAmBvI;AAED,wBAAgB,4DAA4D,CAAC,GAAG,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAa3I;AAED,wBAAgB,kDAAkD,CAAC,WAAW,EAAE,MAAM,EAAE,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAAC,YAAY,CAAC,CAqBnI;AAED,wBAAgB,6DAA6D,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,QAAQ,CA0BzI;AAED,wBAAgB,mEAAmE,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,CAQ1H;AAED,wBAAgB,6DAA6D,CAAC,GAAG,EAAE,SAAS,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAY7I;AAED,wBAAgB,mDAAmD,CAAC,WAAW,EAAE,MAAM,EAAE,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,aAAa,CAE7H;AAED,wBAAgB,8DAA8D,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAK3I;AAED,wBAAgB,qDAAqD,CAAC,IAAI,EAAE,SAAS,GAAG,MAAM,CAsC7F;AAED,wBAAgB,uDAAuD,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,SAAS,CAGrI;AAED,wBAAgB,gEAAgE,CAAC,EAAE,EAAE,wBAAwB,GAAG,QAAQ,EAAE,CAezH;AAED,wBAAgB,8CAA8C,IAAI,MAAM,CAEvE;AAED,wBAAgB,kDAAkD,IAAI,MAAM,CAE3E;AAED,wBAAgB,sEAAsE,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,kBAAkB,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAItL;AAED,wBAAgB,sEAAsE,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,kBAAkB,CAGjK;AAED,wBAAgB,gDAAgD,CAAC,EAAE,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,EAAE,GAAG,MAAM,CAK/G;AAED,wBAAgB,gEAAgE,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,sBAAsB,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAKpL;AAED,wBAAgB,iDAAiD,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,YAAY,CAIlI;AAED,wBAAgB,+DAA+D,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,sBAAsB,CAI9J;AAED,wBAAgB,sEAAsE,CAAC,QAAQ,EAAE,MAAM,EAAE,EAAE,EAAE,wBAAwB,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAOtL;AAED,wBAAgB,qEAAqE,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,wBAAwB,CAOtK;AAED,wBAAgB,2CAA2C,CAAC,QAAQ,EAAE,WAAW,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CA8B1G;AAED,wBAAgB,8CAA8C,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,WAAW,CAalI"}

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

@@ -0,0 +1,305 @@
+import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+import { writeYaml, encodeCWLType } from '../CWL/Encode.js';
+import { object } from '../fable_modules/YAMLicious.0.0.3/Decode.fs.js';
+import { Decode_cwlTypeStringMatcher } from '../CWL/Decode.js';
+import { YAMLElement_Comment } from '../fable_modules/YAMLicious.0.0.3/YAMLiciousTypes.fs.js';
+import { value, defaultArg, unwrap, bind, map } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
+import { LDFormalParameter } from '../ROCrate/LDTypes/FormalParameter.js';
+import { InputBinding_create_ZAC0108A, CWLInput } from '../CWL/Inputs.js';
+import { tryPick, exactlyOne, find } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { OutputBinding_create_6DFDD678, CWLOutput } from '../CWL/Outputs.js';
+import { int32ToString } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { Component_create_Z2F0B38C7 } 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 { CWLWorkflowDescription } from '../CWL/WorkflowDescription.js';
+import { ResizeArray_map, ResizeArray_singleton, ResizeArray_choose, Option_fromSeq, Option_fromValueWithDefault } from '../Core/Helper/Collections.js';
+import { CWLToolDescription } from '../CWL/ToolDescription.js';
+import { CWLProcessingUnit_Workflow, CWLProcessingUnit_CommandLineTool } from '../CWL/CWLProcessingUnit.js';
+import { LDWorkflowProtocol } from '../ROCrate/LDTypes/WorkflowProtocol.js';
+import { LDComputerLanguage } from '../ROCrate/LDTypes/ComputerLanguage.js';
+import { LDComputationalWorkflow } from '../ROCrate/LDTypes/ComputationalWorkflow.js';
+import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
+import { WorkflowStep, StepOutput } from '../CWL/WorkflowSteps.js';
+import { Workflow_cwlFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
+import { toFail, printf } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { LDLabProtocol } from '../ROCrate/LDTypes/LabProtocol.js';
+import { DatamapConversion_composeFragmentDescriptors_Z8923FA3, DatamapConversion_decomposeFragmentDescriptors_Z6E59645F } from './Datamap.js';
+import { DataMap } from '../Core/DataMap.js';
+import { PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
+import { ArcWorkflow } from '../Core/ArcTypes.js';
+
+class WorkflowConversion {
+  constructor() {
+  }
+}
+function WorkflowConversion_$reflection() {
+  return class_type("ARCtrl.Conversion.WorkflowConversion", void 0, WorkflowConversion);
+}
+function WorkflowConversion_composeAdditionalType_Z5C31A0F9(t) {
+  const s = writeYaml(encodeCWLType(t));
+  return s.trim();
+}
+function WorkflowConversion_decomposeAdditionalType_Z721C83C5(t) {
+  return object((get$) => Decode_cwlTypeStringMatcher(t, get$), YAMLElement_Comment("dawd"))[0];
+}
+function WorkflowConversion_composeFormalParamInputIdentifiers(prefix, position) {
+  if (prefix == null) {
+    if (position == null) {
+      return void 0;
+    } else {
+      const po_1 = value(position) | 0;
+      return [LDPropertyValue.createPosition(po_1)];
+    }
+  } else if (position == null) {
+    const pr_1 = value(prefix);
+    return [LDPropertyValue.createPrefix(pr_1)];
+  } else {
+    const po = value(position) | 0;
+    const pr = value(prefix);
+    return [LDPropertyValue.createPosition(po), LDPropertyValue.createPrefix(pr)];
+  }
+}
+function WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(inp, workflowName, runName) {
+  let additionalType;
+  const matchValue = inp.Type_;
+  if (matchValue == null) {
+    throw new Error("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);
+  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;
+  if (prefix == null) {
+    if (position == null) {
+      matchResult = 0;
+    } else {
+      matchResult = 1;
+    }
+  } else {
+    matchResult = 1;
+  }
+  switch (matchResult) {
+    case 0:
+      return void 0;
+    default:
+      return InputBinding_create_ZAC0108A(unwrap(prefix), unwrap(position));
+  }
+}
+function WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(inp, context, graph) {
+  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;
+  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));
+}
+function WorkflowConversion_composeFormalParameterOutputIdentifiers_6DFDD678(glob) {
+  if (glob == null) {
+    return void 0;
+  } else {
+    const g = value(glob);
+    return [LDPropertyValue.createGlob(g)];
+  }
+}
+function WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(out, workflowName, runName) {
+  let additionalType;
+  const matchValue = out.Type_;
+  if (matchValue == null) {
+    throw new Error("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);
+  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)));
+}
+function WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(inp, context, graph) {
+  const t_1 = WorkflowConversion_decomposeAdditionalType_Z721C83C5(exactlyOne(inp.AdditionalType));
+  const binding = WorkflowConversion_decomposeOutputBindings_1AAAE9A5(LDFormalParameter.getIdentifiers(inp, unwrap(graph), unwrap(context)), unwrap(context));
+  const optional = map((value) => !value, LDFormalParameter.tryGetValueRequiredAsBoolean(inp, unwrap(context)));
+  return new CWLOutput(LDFormalParameter.getNameAsString(inp, unwrap(context)), t_1, binding);
+}
+function WorkflowConversion_composeComputationalTool_Z685B8F25(tool) {
+  let c, f, i, oa, s;
+  let patternInput;
+  const matchValue = tool.ComponentType;
+  let matchResult, c_1;
+  if (matchValue != null) {
+    if (c = value(matchValue), c.Name != null) {
+      matchResult = 0;
+      c_1 = value(matchValue);
+    } else {
+      matchResult = 1;
+    }
+  } else {
+    matchResult = 1;
+  }
+  switch (matchResult) {
+    case 0: {
+      patternInput = [value(c_1.Name), c_1.TermAccessionNumber];
+      break;
+    }
+    default:
+      throw new Error("Component must have a type");
+  }
+  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]);
+  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);
+    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]));
+}
+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]);
+}
+function WorkflowConversion_getInputParametersFromProcessingUnit_30922B92(pu) {
+  if (pu.tag === /* Workflow */
+  1) {
+    const wf = pu.fields[0];
+    return ResizeArray_map((i_1) => i_1, wf.Inputs);
+  } else {
+    const tool = pu.fields[0];
+    const matchValue = tool.Inputs;
+    if (matchValue == null) {
+      return [];
+    } else {
+      return ResizeArray_map((i) => i, value(matchValue));
+    }
+  }
+}
+function WorkflowConversion_get_toolDescriptionTypeName() {
+  return "ToolDescription";
+}
+function WorkflowConversion_get_workflowDescriptionTypeName() {
+  return "WorkflowDescription";
+}
+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);
+  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, void 0, 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, inputs);
+}
+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, step.Run);
+  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);
+  return LDWorkflowProtocol.create(filePath, inputs, outputs, void 0, void 0, void 0, void 0, 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_2664C4B8(step, context, graph) {
+  const name = LDComputationalWorkflow.getNameAsString(step, unwrap(context));
+  const run = LDDataset.getIdentifierAsString(step, unwrap(context));
+  return new WorkflowStep(name, [], StepOutput.create([]), run);
+}
+function WorkflowConversion_decomposeWorkflowProtocolToWorkflow_2664C4B8(protocol, context, graph) {
+  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_2664C4B8(s, unwrap(context), unwrap(graph)), LDComputationalWorkflow.getHasPart(protocol, unwrap(graph), unwrap(context))), inputs, outputs);
+}
+function WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(filePath, pu, workflowName, runName) {
+  if (pu.tag === /* Workflow */
+  1) {
+    return WorkflowConversion_composeWorkflowProtocolFromWorkflow_Z6FBB852F(filePath, pu.fields[0], unwrap(workflowName), unwrap(runName));
+  } else {
+    return WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA(filePath, pu.fields[0], unwrap(workflowName), unwrap(runName));
+  }
+}
+function WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_2664C4B8(protocol, context, graph) {
+  if (LDComputationalWorkflow.getAdditionalTypeAsString(protocol, unwrap(context)) === WorkflowConversion_get_workflowDescriptionTypeName()) {
+    return CWLProcessingUnit_Workflow(WorkflowConversion_decomposeWorkflowProtocolToWorkflow_2664C4B8(protocol, unwrap(context), unwrap(graph)));
+  } else {
+    return CWLProcessingUnit_CommandLineTool(WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8(protocol, unwrap(context), unwrap(graph)));
+  }
+}
+function WorkflowConversion_composeWorkflow_42450E6E(workflow, fs) {
+  let workflowProtocol;
+  const workflowFilePath = Workflow_cwlFileNameFromIdentifier(workflow.Identifier);
+  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);
+  }
+  if (workflow.Version != null) {
+    LDLabProtocol.setVersionAsString(workflowProtocol, value(workflow.Version));
+  }
+  if (workflow.URI != null) {
+    LDLabProtocol.setUrl(workflowProtocol, value(workflow.URI));
+  }
+  if (workflow.WorkflowType != null) {
+    const intendedUse = BaseTypes_composeDefinedTerm_ZDED3A0F(value(workflow.WorkflowType));
+    LDLabProtocol.setIntendedUseAsDefinedTerm(workflowProtocol, intendedUse);
+  }
+  const dataFiles = ResizeArray_choose((df) => LDPropertyValue.tryGetSubjectOf(df), defaultArg(map(DatamapConversion_composeFragmentDescriptors_Z8923FA3, workflow.DataMap), []));
+  if (workflow.Components.length > 0) {
+    const softwareTools = ResizeArray_map(WorkflowConversion_composeComputationalTool_Z685B8F25, workflow.Components);
+    LDLabProtocol.setComputationalTools(workflowProtocol, softwareTools);
+  }
+  const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, workflow.Contacts));
+  const hasParts = Option_fromSeq(dataFiles);
+  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));
+}
+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_2664C4B8(workflowProtocol, 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)));
+  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);
+}
+
+export { WorkflowConversion, WorkflowConversion_$reflection, WorkflowConversion_composeAdditionalType_Z5C31A0F9, WorkflowConversion_composeComputationalTool_Z685B8F25, WorkflowConversion_composeFormalParamInputIdentifiers, WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7, WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80, WorkflowConversion_composeFormalParameterOutputIdentifiers_6DFDD678, 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_decomposeWorkflowProtocolToProcessingUnit_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8, WorkflowConversion_decomposeWorkflowProtocolToWorkflow_2664C4B8, WorkflowConversion_decomposeWorkflowStep_2664C4B8, WorkflowConversion_decomposeWorkflow_Z6839B9E8, WorkflowConversion_getInputParametersFromProcessingUnit_30922B92, WorkflowConversion_get_toolDescriptionTypeName, WorkflowConversion_get_workflowDescriptionTypeName };