@nfdi4plants/arctrl 3.0.0-beta.8 → 3.0.0

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

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+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { CWLType_$union } from '../CWL/CWLTypes.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.js';
+import { CWLInput, InputBinding } from '../CWL/Inputs.js';
+import { LDContext } from '../ROCrate/LDContext.js';
+import { CWLOutput, OutputBinding } from '../CWL/Outputs.js';
+import { Component } from '../Core/Process/Component.js';
+import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.js';
+import { WorkflowStep, WorkflowStepRun_$union } from '../CWL/WorkflowSteps.js';
+import { CWLToolDescription } from '../CWL/ToolDescription.js';
+import { CWLExpressionToolDescription } from '../CWL/ExpressionToolDescription.js';
+import { CWLOperationDescription } from '../CWL/OperationDescription.js';
+import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.js';
+import { ArcWorkflow } from '../Core/ArcTypes.js';
+import { FileSystem } from '../FileSystem/FileSystem.js';
+export declare class WorkflowConversion {
+    constructor();
+}
+export declare function WorkflowConversion_$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(outp: 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;
+/**
+ * Returns the normalized input parameters for a CWL processing unit.
+ * Supports CommandLineTool, Workflow, and ExpressionTool variants.
+ */
+export declare function WorkflowConversion_getInputParametersFromProcessingUnit_30922B92(pu: CWLProcessingUnit_$union): CWLInput[];
+export declare function WorkflowConversion_get_toolDescriptionTypeName(): string;
+export declare function WorkflowConversion_get_workflowDescriptionTypeName(): string;
+export declare function WorkflowConversion_get_expressionToolDescriptionTypeName(): string;
+export declare function WorkflowConversion_get_operationDescriptionTypeName(): string;
+/**
+ * Converts a workflow step run payload to a storable dataset identifier.
+ * String runs preserve the path, while inline runs are mapped to stable inline markers.
+ */
+export declare function WorkflowConversion_runToIdentifier_Z4EBA8CB1(run: WorkflowStepRun_$union): string;
+/**
+ * Attempts to decode a CWL processing unit from an LDGraph node addressed by a resolved run path.
+ * Supports direct WorkflowProtocol nodes and ARC Workflow/Run datasets that reference a main workflow protocol.
+ */
+export declare function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedRunPath: string, graph?: LDGraph, context?: LDContext): Option<CWLProcessingUnit_$union>;
+export declare function WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA(filePath: string, workflow: CWLToolDescription, workflowName?: string, runName?: string): LDNode;
+export declare function WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8(protocol: LDNode, context?: LDContext, graph?: LDGraph): CWLToolDescription;
+/**
+ * Converts an ExpressionTool CWL description into an LD workflow protocol node.
+ * Persists the expression text in schema:description to keep roundtrip fidelity in the current RO-Crate projection.
+ */
+export declare function WorkflowConversion_composeWorkflowProtocolFromExpressionToolDescription_Z7BEB6658(filePath: string, expressionTool: CWLExpressionToolDescription, workflowName?: string, runName?: string): LDNode;
+/**
+ * Converts an LD workflow protocol node into an ExpressionTool CWL description.
+ * Falls back to <c>$(null)</c> if no expression text is stored.
+ */
+export declare function WorkflowConversion_decomposeWorkflowProtocolToExpressionToolDescription_2664C4B8(protocol: LDNode, context?: LDContext, graph?: LDGraph): CWLExpressionToolDescription;
+export declare function WorkflowConversion_composeWorkflowProtocolFromOperationDescription_Z75DE0D49(filePath: string, operation: CWLOperationDescription, workflowName?: string, runName?: string): LDNode;
+export declare function WorkflowConversion_decomposeWorkflowProtocolToOperationDescription_2664C4B8(protocol: LDNode, context?: LDContext, graph?: LDGraph): CWLOperationDescription;
+export declare function WorkflowConversion_composeWorkflowStep_Z35AB9E5D<$a>(step: WorkflowStep, workflowID: $a): LDNode;
+export declare function WorkflowConversion_composeWorkflowProtocolFromWorkflow_Z6FBB852F(filePath: string, workflow: CWLWorkflowDescription, workflowName?: string, runName?: string): LDNode;
+/**
+ * Converts a workflow-step LD node into a CWL WorkflowStep.
+ * Can optionally resolve run string references into inline CWL processing units via the graph.
+ */
+export declare function WorkflowConversion_decomposeWorkflowStep_77DD0449(step: LDNode, workflowFilePath?: string, resolveRunReferences?: boolean, context?: LDContext, graph?: LDGraph): WorkflowStep;
+/**
+ * Converts an LD workflow protocol node to a CWL workflow description.
+ * Optionally resolves step run references using the containing graph.
+ */
+export declare function WorkflowConversion_decomposeWorkflowProtocolToWorkflow_ZB11202F(protocol: LDNode, resolveRunReferences?: boolean, context?: LDContext, graph?: LDGraph): CWLWorkflowDescription;
+/**
+ * Converts a generic CWL processing unit into a workflow protocol representation.
+ * Dispatches by processing-unit variant.
+ */
+export declare function WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7(filePath: string, pu: CWLProcessingUnit_$union, workflowName?: string, runName?: string): LDNode;
+/**
+ * Converts a workflow protocol node back into the appropriate CWL processing unit variant.
+ * Uses <c>additionalType</c> to discriminate Workflow, ExpressionTool, and Operation descriptions.
+ */
+export declare function WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(protocol: LDNode, resolveRunReferences?: boolean, 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

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