@nfdi4plants/arctrl 3.1.0 → 3.2.0

package/dist/ts/ts/CWL/DynamicObjHelpers.d.ts

@@ -0,0 +1,37 @@
+import { FSharpSet } from '@fable-org/fable-library-ts/Set.ts';
+import { int32 } from '@fable-org/fable-library-ts/Int32.ts';
+import { DynamicObj } from '../fable_modules/DynamicObj.8.0.0/DynamicObj.fs.js';
+import { FSharpList } from '@fable-org/fable-library-ts/List.ts';
+/**
+ * Convert a public F# property name to the private backing-field name that
+ * DynamicObj exposes for typed members compiled by Fable or .NET.
+ */
+export declare function toCompilerBackingName(propertyName: string): string;
+/**
+ * Return both common backing-field spellings for all typed properties so they
+ * can be excluded from dynamic CWL extension fields.
+ */
+export declare function typedBackingFieldNames(dynObj: DynamicObj): FSharpSet<string>;
+/**
+ * Enumerate only true dynamic properties, excluding known CWL fields and
+ * compiler-generated storage for typed members.
+ */
+export declare function dynamicPropertiesExcept(knownFieldNames: FSharpSet<string>, dynObj: DynamicObj): Iterable<[string, any]>;
+/**
+ * Create a stable, sorted dynamic-property snapshot for equality and hashing.
+ */
+export declare function dynamicPropertiesSnapshotExcept(knownFieldNames: FSharpSet<string>, dynObj: DynamicObj): FSharpList<[string, any]>;
+/**
+ * Snapshot all dynamic extension properties on an object.
+ */
+export declare function dynamicPropertiesSnapshot(dynObj: DynamicObj): FSharpList<[string, any]>;
+/**
+ * Compare only preserved dynamic extension properties between two CWL objects.
+ */
+export declare function dynamicPropertiesEqual(left: DynamicObj, right: DynamicObj): boolean;
+/**
+ * Hash preserved dynamic extension properties in the same stable order used
+ * by dynamicPropertiesEqual.
+ */
+export declare function hashDynamicProperties(dynObj: DynamicObj): int32;
+//# sourceMappingURL=DynamicObjHelpers.d.ts.map

package/dist/ts/ts/CWL/DynamicObjHelpers.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DynamicObjHelpers.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/CWL/DynamicObjHelpers.ts"],"names":[],"mappings":"AAKA,OAAO,EAAmB,SAAS,EAAS,MAAM,oCAAoC,CAAC;AAGvF,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAC7D,OAAO,EAAE,UAAU,EAAE,MAAM,oDAAoD,CAAC;AAChF,OAAO,EAAE,UAAU,EAAE,MAAM,qCAAqC,CAAC;AAEjE;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,YAAY,EAAE,MAAM,GAAG,MAAM,CAiBlE;AAED;;;GAGG;AACH,wBAAgB,sBAAsB,CAAC,MAAM,EAAE,UAAU,GAAG,SAAS,CAAC,MAAM,CAAC,CAI5E;AAED;;;GAGG;AACH,wBAAgB,uBAAuB,CAAC,eAAe,EAAE,SAAS,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,UAAU,GAAG,QAAQ,CAAC,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,CAUvH;AAED;;GAEG;AACH,wBAAgB,+BAA+B,CAAC,eAAe,EAAE,SAAS,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,UAAU,GAAG,UAAU,CAAC,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,CAIjI;AAED;;GAEG;AACH,wBAAgB,yBAAyB,CAAC,MAAM,EAAE,UAAU,GAAG,UAAU,CAAC,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,CAIvF;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,UAAU,GAAG,OAAO,CAEnF;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,MAAM,EAAE,UAAU,GAAG,KAAK,CAE/D"}

package/dist/ts/ts/CWL/DynamicObjHelpers.js

@@ -0,0 +1,57 @@
+import { isNullOrEmpty, endsWith, substring } from '../../node_modules/@fable-org/fable-library-ts/String.js';
+import { comparePrimitives, equals, safeHash } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
+import { isUpper } from '../../node_modules/@fable-org/fable-library-ts/Char.js';
+import { item, setItem } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
+import { ofSeq, contains, empty } from '../../node_modules/@fable-org/fable-library-ts/Set.js';
+import { collect, delay, append, singleton, filter, toList, sortBy, map } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
+
+function toCompilerBackingName(propertyName) {
+  const propertyName_1 = isNullOrEmpty(propertyName) ? propertyName : endsWith(propertyName, "_", 4) ? substring(propertyName, 0, propertyName.length - 1) : propertyName;
+  const chars = propertyName_1.split("");
+  let index = 0;
+  let keepLowering = true;
+  while (keepLowering && index < chars.length && isUpper(item(index, chars))) {
+    const nextIsEnd = index + 1 === chars.length;
+    const nextIsUpper = !nextIsEnd && isUpper(item(index + 1, chars));
+    if ((index === 0 ? true : nextIsEnd) ? true : nextIsUpper) {
+      setItem(chars, index, item(index, chars).toLowerCase());
+      index = index + 1 | 0;
+    } else {
+      keepLowering = false;
+    }
+  }
+  return "_" + chars.join("");
+}
+function typedBackingFieldNames(dynObj) {
+  return ofSeq(collect((property_1) => delay(() => append(singleton("_" + property_1.Name), delay(() => singleton(toCompilerBackingName(property_1.Name))))), filter((property) => !property.IsDynamic, dynObj.GetPropertyHelpers(true))), {
+    Compare: (x, y) => comparePrimitives(x, y) | 0
+  });
+}
+function dynamicPropertiesExcept(knownFieldNames, dynObj) {
+  const typedBackingFields = typedBackingFieldNames(dynObj);
+  return filter((kv) => {
+    if (!contains(kv[0], knownFieldNames)) {
+      return !contains(kv[0], typedBackingFields);
+    } else {
+      return false;
+    }
+  }, dynObj.GetProperties(false));
+}
+function dynamicPropertiesSnapshotExcept(knownFieldNames, dynObj) {
+  return toList(sortBy((tuple) => tuple[0], map((kv) => [kv[0], kv[1]], dynamicPropertiesExcept(knownFieldNames, dynObj)), {
+    Compare: (x, y) => comparePrimitives(x, y) | 0
+  }));
+}
+function dynamicPropertiesSnapshot(dynObj) {
+  return dynamicPropertiesSnapshotExcept(empty({
+    Compare: (x, y) => comparePrimitives(x, y) | 0
+  }), dynObj);
+}
+function dynamicPropertiesEqual(left, right) {
+  return equals(dynamicPropertiesSnapshot(left), dynamicPropertiesSnapshot(right));
+}
+function hashDynamicProperties(dynObj) {
+  return safeHash(dynamicPropertiesSnapshot(dynObj)) | 0;
+}
+
+export { dynamicPropertiesEqual, dynamicPropertiesExcept, dynamicPropertiesSnapshot, dynamicPropertiesSnapshotExcept, hashDynamicProperties, toCompilerBackingName, typedBackingFieldNames };

package/dist/ts/ts/CWL/Encode.d.ts

@@ -1,17 +1,22 @@
-import { FSharpChoice$2_$union } from '@fable-org/fable-library-js/Choice.js';
-import { SchemaDefRequirementType, InputEnumSchema, InputRecordSchema, InputRecordField, SoftwarePackage, SchemaSaladString_$union, CWLType_$union, InputArraySchema } from './CWLTypes.js';
-import { Option } from '@fable-org/fable-library-js/Option.js';
-import { FSharpList } from '@fable-org/fable-library-js/List.js';
-import { YAMLElement_$union } from '../fable_modules/YAMLicious.1.0.0-alpha.7/YAMLiciousTypes.fs.js';
-import { HintEntry_$union, Requirement_$union, EnvironmentDef } from './Requirements.js';
-import { CWLOutput, OutputBinding } from './Outputs.js';
-import { CWLInput, InputBinding } from './Inputs.js';
-import { WorkflowStep, WorkflowStepRun_$union, StepOutput_$union, StepOutputParameter, StepInput, ScatterMethod_$union, PickValueMethod_$union, LinkMergeMethod_$union } from './WorkflowSteps.js';
-import { CWLProcessingUnit_$union } from './CWLProcessingUnit.js';
-import { CWLToolDescription } from './ToolDescription.js';
-import { CWLWorkflowDescription } from './WorkflowDescription.js';
-import { CWLExpressionToolDescription } from './ExpressionToolDescription.js';
-import { CWLOperationDescription } from './OperationDescription.js';
+import { FSharpChoice$2_$union } from '@fable-org/fable-library-ts/Choice.ts';
+import { SchemaDefRequirementType, InputRecordField, InputEnumSchema, InputRecordSchema, DirectoryInstance, FileInstance, SoftwarePackage, SchemaSaladString_$union, CWLType_$union, InputArraySchema } from './CWLTypes.ts';
+import { float64 } from '@fable-org/fable-library-ts/Int32.ts';
+import { Option } from '@fable-org/fable-library-ts/Option.ts';
+import { FSharpList } from '@fable-org/fable-library-ts/List.ts';
+import { YAMLElement_$union } from '../fable_modules/YAMLicious.1.0.0/YAMLiciousTypes.fs.js';
+import { DynamicObj } from '../fable_modules/DynamicObj.8.0.0/DynamicObj.fs.js';
+import { FSharpSet } from '@fable-org/fable-library-ts/Set.ts';
+import { HintEntry_$union, Requirement_$union, EnvironmentDef } from './Requirements.ts';
+import { CWLOutput, OutputBinding } from './Outputs.ts';
+import { CWLParameterValue_$union } from './ParameterValue.ts';
+import { CWLInput, InputBinding } from './Inputs.ts';
+import { WorkflowStep, WorkflowStepRun_$union, StepOutput_$union, StepOutputParameter, StepInput, ScatterMethod_$union, PickValueMethod_$union, LinkMergeMethod_$union } from './WorkflowSteps.ts';
+import { CWLProcessingUnit_$union } from './CWLProcessingUnit.ts';
+import { CWLToolDescription } from './ToolDescription.ts';
+import { CWLWorkflowDescription } from './WorkflowDescription.ts';
+import { CWLExpressionToolDescription } from './ExpressionToolDescription.ts';
+import { CWLOperationDescription } from './OperationDescription.ts';
+import { CWLParameterReference } from './ParameterReference.ts';
 /**
  * Active pattern to classify CWL types as primitive (with shorthand) or complex (requiring full YAML)
  */
@@ -26,7 +31,27 @@ export declare function tryGetArrayShorthand(cwlType: CWLType_$union): Option<st
  */
 export declare function isComplexType(t_mut: CWLType_$union): boolean;
 export declare function yBool(b: boolean): YAMLElement_$union;
+/**
+ * Encode floats with round-trip formatting on .NET while keeping Fable output usable.
+ */
+export declare function yFloat(value: float64): YAMLElement_$union;
 export declare function yMap(pairs: FSharpList<[string, YAMLElement_$union]>): YAMLElement_$union;
+/**
+ * Encode preserved DynamicObj extension values when they can be represented as YAML.
+ */
+export declare function encodeDynamicValue(value: any): Option<YAMLElement_$union>;
+/**
+ * Encode all dynamic extension properties on a DynamicObj as a YAML mapping.
+ */
+export declare function encodeDynamicObj(dynObj: DynamicObj): YAMLElement_$union;
+/**
+ * Append encodable dynamic extension fields while excluding typed CWL fields.
+ */
+export declare function appendDynamicPropertiesExcept(knownFieldNames: FSharpSet<string>, dynObj: DynamicObj, acc: FSharpList<[string, YAMLElement_$union]>): FSharpList<[string, YAMLElement_$union]>;
+export declare function appendDynamicProperties(dynObj: DynamicObj, acc: FSharpList<[string, YAMLElement_$union]>): FSharpList<[string, YAMLElement_$union]>;
+/**
+ * Normalize documentation line endings and trim only trailing newline markers.
+ */
 export declare function normalizeDocString(doc: string): string;
 /**
  * Encode expression payloads with style-aware scalars.
@@ -35,7 +60,13 @@ export declare function normalizeDocString(doc: string): string;
  * so trailing newlines and blank lines survive decode/encode roundtrips.
  */
 export declare function encodeExpressionScalar(expression: string): YAMLElement_$union;
+/**
+ * Encode schema-salad strings as literals or directive mappings.
+ */
 export declare function encodeSchemaSaladString(value: SchemaSaladString_$union): YAMLElement_$union;
+/**
+ * Quote boolean-looking EnvVar values so YAML does not coerce them on decode.
+ */
 export declare function normalizeEnvValueForEncode(envValue: string): string;
 /**
  * Encode EnvVarRequirement using compact map shorthand (envName -> envValue).
@@ -48,18 +79,66 @@ export declare function encodeSoftwareRequirementCompactMap(packages: SoftwarePa
 export declare function encodeLabel(label: string): [string, YAMLElement_$union];
 export declare function encodeDoc(doc: string): [string, YAMLElement_$union];
 export declare function encodeIntent(intent: string[]): [string, YAMLElement_$union];
+/**
+ * Encode File fields with the supplied discriminator key (`type` or `class`).
+ */
+export declare function encodeFilePairs(discriminatorKey: string, discriminatorValue: string, file: FileInstance): FSharpList<[string, YAMLElement_$union]>;
+/**
+ * Encode Directory fields with the supplied discriminator key (`type` or `class`).
+ */
+export declare function encodeDirectoryPairs(discriminatorKey: string, discriminatorValue: string, directory: DirectoryInstance): FSharpList<[string, YAMLElement_$union]>;
+/**
+ * Encode CWL types using shorthand when possible and full schema objects when required.
+ */
 export declare function encodeCWLType(t: CWLType_$union): YAMLElement_$union;
+/**
+ * Encode a record field as a map entry keyed by its field name.
+ */
 export declare function encodeInputRecordField(field: InputRecordField): [string, YAMLElement_$union];
+/**
+ * Encode record schemas with map-form fields and preserved schema metadata.
+ */
 export declare function encodeInputRecordSchema(schema: InputRecordSchema): YAMLElement_$union;
+/**
+ * Encode enum schemas while preserving symbol order and schema metadata.
+ */
 export declare function encodeInputEnumSchema(schema: InputEnumSchema): YAMLElement_$union;
+/**
+ * Encode array schemas with their item type and preserved schema metadata.
+ */
 export declare function encodeInputArraySchema(schema: InputArraySchema): YAMLElement_$union;
+/**
+ * Encode outputBinding fields and preserved extension properties.
+ */
 export declare function encodeOutputBinding(ob: OutputBinding): YAMLElement_$union;
+/**
+ * Encode one source value as a scalar and multiple source values as a sequence.
+ */
 export declare function encodeStringArrayOrScalar(values: string[]): YAMLElement_$union;
+export declare function encodeCWLParameterValue(value: CWLParameterValue_$union): YAMLElement_$union;
+/**
+ * Encode a workflow or tool output, choosing shorthand only when type is the sole field.
+ */
 export declare function encodeCWLOutput(o: CWLOutput): [string, YAMLElement_$union];
+/**
+ * Encode inputBinding fields and preserved extension properties.
+ */
 export declare function encodeInputBinding(ib: InputBinding): YAMLElement_$union;
+/**
+ * Encode a workflow or tool input, choosing shorthand only when type is the sole field.
+ */
 export declare function encodeCWLInput(i: CWLInput): [string, YAMLElement_$union];
+/**
+ * Encode one SchemaDefRequirement type entry and preserved schema extension fields.
+ */
 export declare function encodeSchemaDefRequirementType(s: SchemaDefRequirementType): YAMLElement_$union;
+/**
+ * Encode known CWL requirements in extended form while preserving requirement extensions.
+ */
 export declare function encodeRequirement(r: Requirement_$union): YAMLElement_$union;
+/**
+ * Encode known hints as requirements and unknown hints as their original raw YAML.
+ */
 export declare function encodeHintEntry(hint: HintEntry_$union): YAMLElement_$union;
 /**
  * Encode a ResizeArray<string> as either a single string or a sequence
@@ -68,19 +147,60 @@ export declare function encodeSourceArray(sources: string[]): YAMLElement_$union
 export declare function encodeLinkMergeMethod(linkMerge: LinkMergeMethod_$union): YAMLElement_$union;
 export declare function encodePickValueMethod(pickValue: PickValueMethod_$union): YAMLElement_$union;
 export declare function encodeScatterMethod(scatterMethod: ScatterMethod_$union): YAMLElement_$union;
+/**
+ * Encode a step input using scalar source shorthand only when no other fields exist.
+ */
 export declare function encodeStepInput(si: StepInput): [string, YAMLElement_$union];
+/**
+ * Encode all step inputs in map form keyed by step input id.
+ */
 export declare function encodeStepInputs(inputs: StepInput[]): YAMLElement_$union;
+/**
+ * Encode record-form step output parameters, including extension fields.
+ */
 export declare function encodeStepOutputParameter(so: StepOutputParameter): YAMLElement_$union;
+/**
+ * Encode step outputs as either scalar ids or record-form output parameters.
+ */
 export declare function encodeStepOutputs(outputs: StepOutput_$union[]): YAMLElement_$union;
+/**
+ * Encode scatter as scalar shorthand for one item or a sequence for multiple items.
+ */
 export declare function encodeScatter(scatter: string[]): YAMLElement_$union;
+/**
+ * Encode workflow step run targets as paths or inline processing units.
+ */
 export declare function encodeWorkflowStepRun(run: WorkflowStepRun_$union): YAMLElement_$union;
+/**
+ * Encode a CommandLineTool element with ordered sections and preserved metadata.
+ */
 export declare function encodeToolDescriptionElement(td: CWLToolDescription): YAMLElement_$union;
+/**
+ * Encode an ExpressionTool element with ordered sections and preserved metadata.
+ */
 export declare function encodeExpressionToolDescriptionElement(et: CWLExpressionToolDescription): YAMLElement_$union;
+/**
+ * Encode an Operation element with ordered sections and preserved metadata.
+ */
 export declare function encodeOperationDescriptionElement(op: CWLOperationDescription): YAMLElement_$union;
+/**
+ * Encode a Workflow element with ordered sections and preserved metadata.
+ */
 export declare function encodeWorkflowDescriptionElement(wd: CWLWorkflowDescription): YAMLElement_$union;
+/**
+ * Encode one workflow step as a map entry keyed by step id.
+ */
 export declare function encodeWorkflowStep(ws: WorkflowStep): [string, YAMLElement_$union];
 export declare function writeYaml(element: YAMLElement_$union): string;
+export declare function encodeCWLParameterReference(reference: CWLParameterReference): [string, YAMLElement_$union];
+export declare function encodeYAMLParameterFile(references: CWLParameterReference[]): string;
+/**
+ * Extract object mappings in order, dropping non-mapping presentation nodes.
+ */
 export declare function getObjectPairs(element: YAMLElement_$union): FSharpList<[string, YAMLElement_$union]>;
+/**
+ * Render top-level CWL sections in a stable order while keeping metadata as a final block.
+ */
 export declare function renderTopLevelElement(baseKeys: FSharpList<string>, orderedSectionKeys: FSharpList<string>, element: YAMLElement_$union): string;
 export declare function encodeToolDescription(td: CWLToolDescription): string;
 export declare function encodeWorkflowDescription(wd: CWLWorkflowDescription): string;
@@ -100,4 +220,8 @@ export declare function encodeInputArraySchemaYaml(schema: InputArraySchema): st
  * Convert a CWLType to a YAML-formatted string for use in serialization
  */
 export declare function cwlTypeToYamlString(t: CWLType_$union): string;
+/**
+ * Helper function to format CWLType for display in error messages
+ */
+export declare function formatCWLType(type_: CWLType_$union): string;
 //# sourceMappingURL=Encode.d.ts.map

package/dist/ts/ts/CWL/Encode.d.ts.map

@@ -1 +1 @@
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