@nfdi4plants/arctrl 3.2.3 → 3.3.1

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

@@ -25,6 +25,15 @@ export declare function dynamicPropertiesSnapshotExcept(knownFieldNames: FSharpS
  * Snapshot all dynamic extension properties on an object.
  */
 export declare function dynamicPropertiesSnapshot(dynObj: DynamicObj): FSharpList<[string, any]>;
+/**
+ * The values of two dynamic properties are equal when they are equal objects. A ResizeArray compares references, so
+ * lists compare by their elements, down to the lists inside them.
+ */
+export declare function dynamicValuesEqual(left: any, right: any): boolean;
+/**
+ * A hash of the value of a dynamic property that goes with dynamicValuesEqual.
+ */
+export declare function hashDynamicValue(value: any): int32;
 /**
  * Compare only preserved dynamic extension properties between two CWL objects.
  */

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

@@ -1 +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"}
+{"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,EAA8C,UAAU,EAAE,MAAM,qCAAqC,CAAC;AAI7G;;;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;AAYD;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,GAAG,OAAO,CA4BjE;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,GAAG,GAAG,KAAK,CAQlD;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,UAAU,GAAG,OAAO,CASnF;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,MAAM,EAAE,UAAU,GAAG,KAAK,CAE/D"}

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

@@ -1,9 +1,11 @@
 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 { comparePrimitives, isArrayLike, equals, structuralHash, 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';
+import { collect, delay, append, singleton, filter, toList, sortBy, map, forAll2, fold } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
+import { length, forAll2 as forAll2$1, map as map$1 } from '../../node_modules/@fable-org/fable-library-ts/List.js';
+import { mergeHashes } from './HashHelpers.js';
 
 function toCompilerBackingName(propertyName) {
   const propertyName_1 = isNullOrEmpty(propertyName) ? propertyName : endsWith(propertyName, "_", 4) ? substring(propertyName, 0, propertyName.length - 1) : propertyName;
@@ -47,11 +49,59 @@ function dynamicPropertiesSnapshot(dynObj) {
     Compare: (x, y) => comparePrimitives(x, y) | 0
   }), dynObj);
 }
+function tryItems(value) {
+  if (isArrayLike(value)) {
+    const items = value;
+    return items;
+  } else {
+    return void 0;
+  }
+}
+function dynamicValuesEqual(left, right) {
+  const matchValue = tryItems(left);
+  const matchValue_1 = tryItems(right);
+  let matchResult = void 0, leftItems = void 0, rightItems = void 0;
+  if (matchValue != null) {
+    if (matchValue_1 != null) {
+      matchResult = 0;
+      leftItems = matchValue;
+      rightItems = matchValue_1;
+    } else {
+      matchResult = 1;
+    }
+  } else {
+    matchResult = 1;
+  }
+  switch (matchResult) {
+    case 0:
+      if (leftItems.length === rightItems.length) {
+        return forAll2(dynamicValuesEqual, leftItems, rightItems);
+      } else {
+        return false;
+      }
+    default:
+      return equals(left, right);
+  }
+}
+function hashDynamicValue(value) {
+  const matchValue = tryItems(value);
+  if (matchValue == null) {
+    return structuralHash(value) | 0;
+  } else {
+    return fold((acc, item) => mergeHashes(acc, hashDynamicValue(item)) | 0, 0, matchValue) | 0;
+  }
+}
 function dynamicPropertiesEqual(left, right) {
-  return equals(dynamicPropertiesSnapshot(left), dynamicPropertiesSnapshot(right));
+  const leftProperties = dynamicPropertiesSnapshot(left);
+  const rightProperties = dynamicPropertiesSnapshot(right);
+  if (length(leftProperties) === length(rightProperties)) {
+    return forAll2$1((tupledArg, tupledArg_1) => tupledArg[0] === tupledArg_1[0] && dynamicValuesEqual(tupledArg[1], tupledArg_1[1]), leftProperties, rightProperties);
+  } else {
+    return false;
+  }
 }
 function hashDynamicProperties(dynObj) {
-  return safeHash(dynamicPropertiesSnapshot(dynObj)) | 0;
+  return safeHash(map$1((tupledArg) => [tupledArg[0], hashDynamicValue(tupledArg[1])], dynamicPropertiesSnapshot(dynObj))) | 0;
 }
 
-export { dynamicPropertiesEqual, dynamicPropertiesExcept, dynamicPropertiesSnapshot, dynamicPropertiesSnapshotExcept, hashDynamicProperties, toCompilerBackingName, typedBackingFieldNames };
+export { dynamicPropertiesEqual, dynamicPropertiesExcept, dynamicPropertiesSnapshot, dynamicPropertiesSnapshotExcept, dynamicValuesEqual, hashDynamicProperties, hashDynamicValue, toCompilerBackingName, typedBackingFieldNames };

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

@@ -1,15 +1,15 @@
-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 { int32 } from '@fable-org/fable-library-ts/Int32.ts';
+import { SchemaDefinition_$union, InputRecordField, InputEnumSchema, InputRecordSchema, DirectoryInstance, FileInstance, DocText_$union, FileSize_$union, SchemaSaladBool_$union, SchemaSaladString_$union, ListEntry$1_$union, RawYaml, InputArraySchema, CWLType_$union } from './CWLTypes.ts';
 import { FSharpList } from '@fable-org/fable-library-ts/List.ts';
-import { YAMLElement_$union } from '../fable_modules/YAMLicious.1.0.0/YAMLiciousTypes.fs.js';
+import { Option } from '@fable-org/fable-library-ts/Option.ts';
+import { FSharpChoice$2_$union } from '@fable-org/fable-library-ts/Choice.ts';
+import { YamlNode } from '../fable_modules/YAMLicious.2.0.0/Model.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 { HintEntry_$union, Requirement_$union, LoadListingEnum_$union } from './Requirements.ts';
+import { CWLOutput, OutputSource_$union, OutputBinding, OutputGlob_$union } from './Outputs.ts';
 import { CWLParameterValue_$union } from './ParameterValue.ts';
-import { CWLInput, InputBinding } from './Inputs.ts';
+import { CWLInput, InputFormat_$union, InputBinding, BindingPosition_$union } 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';
@@ -17,6 +17,11 @@ import { CWLWorkflowDescription } from './WorkflowDescription.ts';
 import { CWLExpressionToolDescription } from './ExpressionToolDescription.ts';
 import { CWLOperationDescription } from './OperationDescription.ts';
 import { CWLParameterReference } from './ParameterReference.ts';
+/**
+ * Matches the optional type, the list ["null", X]. Schema Salad reads the shorthand X? as exactly this list. A list
+ * with the null behind X is a plain type list, and X? would reorder it.
+ */
+export declare function $007COptionalOf$007C_$007C(t: CWLType_$union): Option<CWLType_$union>;
 /**
  * Active pattern to classify CWL types as primitive (with shorthand) or complex (requiring full YAML)
  */
@@ -30,192 +35,327 @@ export declare function tryGetArrayShorthand(cwlType: CWLType_$union): Option<st
  * Determine if a type requires full YAML serialization (complex type)
  */
 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.
+ * A string that spans lines is written as a literal block scalar, so a doc text or an expression stays
+ * readable (see multiLineScalar). Any other string goes through Encode.string, which double-quotes text that a core schema
+ * reader takes for a bool, a number or null, and then through ScalarQuoting.keepAsText, which quotes what the loader of
+ * cwltool reads as another type.
+ */
+export declare function encodeString(value: string): YamlNode;
+/**
+ * The text of a doc or a label. The node that the text was read from, when there is one, takes the current text
+ * with YamlNode.withScalarValue. It comes back unchanged while the text is the same, and an edited text keeps the
+ * style of the node and the lines that still fit. withScalarValue and ScalarQuoting.keepAsText quote an edited text that a reader
+ * would take for another type than a string, so the text stays a string. The node of a doc may be a list of
+ * strings, which comes back unchanged while the text is the concatenation of its items and is a string after an
+ * edit. A text without a node is spelled by encodeString.
+ */
+export declare function encodeSourceText(source: Option<YamlNode>, text: string): YamlNode;
+/**
+ * A list of single-line scalars is written inline, as in `baseCommand: [dotnet, fsi]`. Any other list is
+ * a block sequence. An empty list is `[]`.
+ */
+export declare function encodeSequence(items: FSharpList<YamlNode>): YamlNode;
+/**
+ * A mapping of keys and values. The keys are text of a document, such as the id of a port or the name of a field, so a
+ * key that the loader of cwltool reads as another type than a string, such as 1_000, gets quotes.
+ */
+export declare function encodeObject(pairs: FSharpList<[string, YamlNode]>): YamlNode;
+/**
+ * Encode the entries of an id map, such as the step inputs. The map names each entry by its id, and a mapping holds
+ * a key once. Entries with a repeated id are written as a list of objects that carry their ids, so no entry is
+ * lost. The id key names the field that holds the id in such an object, as name does for the fields of a record. The
+ * value key names the field of an entry that is no mapping, as the source of a step input written as its source
+ * alone.
  */
-export declare function yFloat(value: float64): YAMLElement_$union;
-export declare function yMap(pairs: FSharpList<[string, YAMLElement_$union]>): YAMLElement_$union;
+export declare function encodeIdMapOrList(idKey: string, valueKey: string, entries: FSharpList<[string, YamlNode]>): YamlNode;
+/**
+ * The YAML of a raw value that a CWL object keeps. The scalars are in the form that cwltool reads as written (see
+ * ScalarQuoting.normalizeScalar), and RawYaml compares that form.
+ */
+export declare function rawYamlNode(raw: RawYaml): YamlNode;
 /**
  * Encode preserved DynamicObj extension values when they can be represented as YAML.
  */
-export declare function encodeDynamicValue(value: any): Option<YAMLElement_$union>;
+export declare function encodeDynamicValue(value: any): Option<YamlNode>;
 /**
  * Encode all dynamic extension properties on a DynamicObj as a YAML mapping.
  */
-export declare function encodeDynamicObj(dynObj: DynamicObj): YAMLElement_$union;
+export declare function encodeDynamicObj(dynObj: DynamicObj): YamlNode;
 /**
  * Append encodable dynamic extension fields while excluding typed CWL fields.
  */
-export declare function appendDynamicPropertiesExcept(knownFieldNames: FSharpSet<string>, dynObj: DynamicObj, acc: FSharpList<[string, YAMLElement_$union]>): FSharpList<[string, YAMLElement_$union]>;
-export declare function appendDynamicProperties(dynObj: DynamicObj, acc: FSharpList<[string, YAMLElement_$union]>): FSharpList<[string, YAMLElement_$union]>;
+export declare function appendDynamicPropertiesExcept(knownFieldNames: FSharpSet<string>, dynObj: DynamicObj, acc: FSharpList<[string, YamlNode]>): FSharpList<[string, YamlNode]>;
+export declare function appendDynamicProperties(dynObj: DynamicObj, acc: FSharpList<[string, YamlNode]>): FSharpList<[string, YamlNode]>;
 /**
- * Normalize documentation line endings and trim only trailing newline markers.
+ * Normalize documentation line endings. The doc keeps its final line feed, because a block scalar that ends
+ * in one reads back with it.
  */
 export declare function normalizeDocString(doc: string): string;
 /**
  * Encode expression payloads with style-aware scalars.
  * Single-line expressions are double-quoted to protect JS token syntax.
- * Multi-line expressions are emitted as literal block scalars with clip chomping
- * so trailing newlines and blank lines survive decode/encode roundtrips.
+ * Multi-line expressions are literal block scalars (see multiLineScalar), which keep them readable and keep YAML
+ * from reading the punctuation of the JavaScript. The writer picks the chomping, so the trailing line feeds and
+ * blank lines of the expression survive a write and a read.
+ */
+export declare function encodeExpressionScalar(expression: string): YamlNode;
+/**
+ * Encode a Schema Salad directive as a flow mapping, as in {$import: path}. The path is written as it was read.
  */
-export declare function encodeExpressionScalar(expression: string): YAMLElement_$union;
+export declare function directive(key: string, path: string): YamlNode;
+/**
+ * Encode an entry of a list or the one object of a field, with the directive as a mapping in the place of an object.
+ */
+export declare function encodeListEntry<T>(encodeValue: ((arg0: T) => YamlNode), entry: ListEntry$1_$union<T>): YamlNode;
+/**
+ * Encode the entries of an id list, such as the inputs, the outputs, the steps or the fields of a record. Entries
+ * with a distinct id go into a map, as in encodeIdMapOrList. An import has no id to be a key, so a list that holds
+ * one is written as a list in which the import stands in its place. A field that the document wrote as one
+ * directive gets the directive again while the list holds that one import.
+ */
+export declare function encodeIdEntries(idKey: string, valueKey: string, whole: boolean, entries: FSharpList<ListEntry$1_$union<[string, YamlNode]>>): YamlNode;
+/**
+ * Encode schema-salad strings as literals or directive mappings. The function encodes the text of a literal.
+ */
+export declare function encodeSchemaSaladStringWith(encodeLiteral: ((arg0: string) => YamlNode), value: SchemaSaladString_$union): YamlNode;
 /**
  * Encode schema-salad strings as literals or directive mappings.
  */
-export declare function encodeSchemaSaladString(value: SchemaSaladString_$union): YAMLElement_$union;
+export declare function encodeSchemaSaladString(value: SchemaSaladString_$union): YamlNode;
+/**
+ * Encode a boolean field, and a directive as a mapping.
+ */
+export declare function encodeSchemaSaladBool(value: SchemaSaladBool_$union): YamlNode;
+/**
+ * Encode the size of a File, and a directive as a mapping.
+ */
+export declare function encodeFileSize(size: FileSize_$union): YamlNode;
+/**
+ * Encode a loadListing symbol, and a directive as a mapping.
+ */
+export declare function encodeLoadListing(value: LoadListingEnum_$union): YamlNode;
+/**
+ * The value of a field that holds a list of strings. A document that wrote the field as one directive gets the
+ * directive again while the list holds that one directive. Any other list is a sequence.
+ */
+export declare function encodeStringList(whole: boolean, entries: SchemaSaladString_$union[]): YamlNode;
+/**
+ * The label of an object. The node that a literal label was read from keeps its layout, and a directive is written
+ * as a mapping.
+ */
+export declare function encodeLabelValue(source: Option<YamlNode>, label: SchemaSaladString_$union): YamlNode;
+export declare function encodeLabel(label: SchemaSaladString_$union): [string, YamlNode];
+/**
+ * The text of a doc. The line breaks are line feeds, and the node that the text was read from keeps its layout.
+ */
+export declare function encodeDocText(source: Option<YamlNode>, doc: string): YamlNode;
+/**
+ * The doc of a port, a step, a schema or a field, written with the characters of the text.
+ */
+export declare function encodeDocValue(source: Option<YamlNode>, doc: DocText_$union): YamlNode;
+/**
+ * The doc of a process, written with line feeds for the line breaks.
+ */
+export declare function encodeProcessDocValue(source: Option<YamlNode>, doc: DocText_$union): YamlNode;
+export declare function encodeDoc(doc: DocText_$union): [string, YamlNode];
+/**
+ * The value of a field that holds a list of numbers. A document that wrote the field as one directive gets the
+ * directive again while the list holds that one directive. Any other list is a sequence.
+ */
+export declare function encodeIntList(whole: boolean, codes: ListEntry$1_$union<int32>[]): YamlNode;
+/**
+ * The intent of a process. The flag tells that the document wrote the field as one directive.
+ */
+export declare function encodeIntent(whole: boolean, intent: SchemaSaladString_$union[]): [string, YamlNode];
 /**
- * Quote boolean-looking EnvVar values so YAML does not coerce them on decode.
+ * Encode the fields of a File value, led by the supplied discriminator key and value.
  */
-export declare function normalizeEnvValueForEncode(envValue: string): string;
+export declare function encodeFilePairs(discriminatorKey: string, discriminatorValue: string, file: FileInstance): FSharpList<[string, YamlNode]>;
 /**
- * Encode EnvVarRequirement using compact map shorthand (envName -> envValue).
+ * Encode the fields of a Directory value, led by the supplied discriminator key and value.
  */
-export declare function encodeEnvVarRequirementCompactMap(envs: EnvironmentDef[]): YAMLElement_$union;
+export declare function encodeDirectoryPairs(discriminatorKey: string, discriminatorValue: string, directory: DirectoryInstance): FSharpList<[string, YamlNode]>;
 /**
- * Encode SoftwareRequirement using compact map shorthand.
+ * Encode a CWL type for a CWL document. A name, a one-level array of a name and an optional of those are written
+ * as the shorthand (File, File[], File[]?). Every other type is a schema object or a list.
  */
-export declare function encodeSoftwareRequirementCompactMap(packages: SoftwarePackage[]): YAMLElement_$union;
-export declare function encodeLabel(label: string): [string, YAMLElement_$union];
-export declare function encodeDoc(doc: string): [string, YAMLElement_$union];
-export declare function encodeIntent(intent: string[]): [string, YAMLElement_$union];
+export declare function encodeCWLType(t: CWLType_$union): YamlNode;
 /**
- * Encode File fields with the supplied discriminator key (`type` or `class`).
+ * Encode a CWL type as the text of the additional type of an RO-Crate entity. The shorthand nests arrays there
+ * (File[][]), which ARCtrl reads and a CWL document does not.
  */
-export declare function encodeFilePairs(discriminatorKey: string, discriminatorValue: string, file: FileInstance): FSharpList<[string, YAMLElement_$union]>;
+export declare function encodeCWLTypeShorthand(t: CWLType_$union): YamlNode;
 /**
- * Encode Directory fields with the supplied discriminator key (`type` or `class`).
+ * Encode a CWL type, as a CWL document when the flag is set.
  */
-export declare function encodeDirectoryPairs(discriminatorKey: string, discriminatorValue: string, directory: DirectoryInstance): FSharpList<[string, YAMLElement_$union]>;
+export declare function encodeTypeWith(cwlDocument: boolean, t: CWLType_$union): YamlNode;
 /**
- * Encode CWL types using shorthand when possible and full schema objects when required.
+ * Encode the type under items. CWL reads the shorthand File[] and File? as the whole value of a type field and as
+ * a member of a type list, so under items an array is a schema and an optional type is a list.
  */
-export declare function encodeCWLType(t: CWLType_$union): YAMLElement_$union;
+export declare function encodeSchemaType(t: CWLType_$union): YamlNode;
 /**
  * Encode a record field as a map entry keyed by its field name.
  */
-export declare function encodeInputRecordField(field: InputRecordField): [string, YAMLElement_$union];
+export declare function encodeInputRecordField(field: InputRecordField): [string, YamlNode];
 /**
  * Encode record schemas with map-form fields and preserved schema metadata.
  */
-export declare function encodeInputRecordSchema(schema: InputRecordSchema): YAMLElement_$union;
+export declare function encodeInputRecordSchema(schema: InputRecordSchema): YamlNode;
+/**
+ * The entries of a record schema.
+ */
+export declare function inputRecordSchemaPairs(schema: InputRecordSchema): FSharpList<[string, YamlNode]>;
 /**
  * Encode enum schemas while preserving symbol order and schema metadata.
  */
-export declare function encodeInputEnumSchema(schema: InputEnumSchema): YAMLElement_$union;
+export declare function encodeInputEnumSchema(schema: InputEnumSchema): YamlNode;
+/**
+ * The entries of an enum schema.
+ */
+export declare function inputEnumSchemaPairs(schema: InputEnumSchema): FSharpList<[string, YamlNode]>;
 /**
  * Encode array schemas with their item type and preserved schema metadata.
  */
-export declare function encodeInputArraySchema(schema: InputArraySchema): YAMLElement_$union;
+export declare function encodeInputArraySchema(schema: InputArraySchema): YamlNode;
 /**
- * Encode outputBinding fields and preserved extension properties.
+ * The entries of an array schema.
  */
-export declare function encodeOutputBinding(ob: OutputBinding): YAMLElement_$union;
+export declare function inputArraySchemaPairs(schema: InputArraySchema): FSharpList<[string, YamlNode]>;
 /**
- * Encode one source value as a scalar and multiple source values as a sequence.
+ * Encode the glob of an output binding in the form that it holds, so a list of one pattern stays a list.
  */
-export declare function encodeStringArrayOrScalar(values: string[]): YAMLElement_$union;
-export declare function encodeCWLParameterValue(value: CWLParameterValue_$union): YAMLElement_$union;
+export declare function encodeOutputGlob(glob: OutputGlob_$union): YamlNode;
+/**
+ * Encode outputBinding fields and preserved extension properties.
+ */
+export declare function encodeOutputBinding(ob: OutputBinding): YamlNode;
+export declare function encodeCWLParameterValue(value: CWLParameterValue_$union): YamlNode;
 /**
  * Encode a workflow or tool output, choosing shorthand only when type is the sole field.
  */
-export declare function encodeCWLOutput(o: CWLOutput): [string, YAMLElement_$union];
+export declare function encodeCWLOutput(o: CWLOutput): [string, YamlNode];
+/**
+ * Encode the position of an input binding: a number or an expression, and a directive as a mapping.
+ */
+export declare function encodeBindingPosition(position: BindingPosition_$union): YamlNode;
 /**
  * Encode inputBinding fields and preserved extension properties.
  */
-export declare function encodeInputBinding(ib: InputBinding): YAMLElement_$union;
+export declare function encodeInputBinding(ib: InputBinding): YamlNode;
+/**
+ * Encode the format of an input in the form that it holds, so a list of one name stays a list.
+ */
+export declare function encodeInputFormat(format: InputFormat_$union): YamlNode;
 /**
  * Encode a workflow or tool input, choosing shorthand only when type is the sole field.
  */
-export declare function encodeCWLInput(i: CWLInput): [string, YAMLElement_$union];
+export declare function encodeCWLInput(i: CWLInput): [string, YamlNode];
 /**
- * Encode one SchemaDefRequirement type entry and preserved schema extension fields.
+ * Encode one SchemaDefRequirement type entry. CWL defines the entry as the schema itself, with type: record or
+ * enum and the fields of the schema. The name leads when the schema has one, and the extension fields of the
+ * schema follow.
  */
-export declare function encodeSchemaDefRequirementType(s: SchemaDefRequirementType): YAMLElement_$union;
+export declare function encodeSchemaDefinition(definition: SchemaDefinition_$union): YamlNode;
 /**
  * Encode known CWL requirements in extended form while preserving requirement extensions.
  */
-export declare function encodeRequirement(r: Requirement_$union): YAMLElement_$union;
+export declare function encodeRequirement(r: Requirement_$union): YamlNode;
 /**
  * Encode known hints as requirements and unknown hints as their original raw YAML.
  */
-export declare function encodeHintEntry(hint: HintEntry_$union): YAMLElement_$union;
+export declare function encodeHintEntry(hint: HintEntry_$union): YamlNode;
 /**
- * Encode a ResizeArray<string> as either a single string or a sequence
+ * Encode the sources as either a single string or a sequence
  */
-export declare function encodeSourceArray(sources: string[]): YAMLElement_$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;
+export declare function encodeSourceArray(sources: OutputSource_$union): YamlNode;
+export declare function encodeLinkMergeMethod(linkMerge: LinkMergeMethod_$union): YamlNode;
+export declare function encodePickValueMethod(pickValue: PickValueMethod_$union): YamlNode;
+export declare function encodeScatterMethod(scatterMethod: ScatterMethod_$union): YamlNode;
 /**
  * Encode a step input using scalar source shorthand only when no other fields exist.
  */
-export declare function encodeStepInput(si: StepInput): [string, YAMLElement_$union];
+export declare function encodeStepInput(si: StepInput): [string, YamlNode];
 /**
- * Encode all step inputs in map form keyed by step input id.
+ * Encode all step inputs in map form keyed by step input id. A list with an import is written as a list, as in
+ * encodeIdEntries. The flag tells that the document wrote the field as one directive.
  */
-export declare function encodeStepInputs(inputs: StepInput[]): YAMLElement_$union;
+export declare function encodeStepInputs(whole: boolean, inputs: ListEntry$1_$union<StepInput>[]): YamlNode;
 /**
  * Encode record-form step output parameters, including extension fields.
  */
-export declare function encodeStepOutputParameter(so: StepOutputParameter): YAMLElement_$union;
+export declare function encodeStepOutputParameter(so: StepOutputParameter): YamlNode;
 /**
- * Encode step outputs as either scalar ids or record-form output parameters.
+ * Encode step outputs as scalar ids or record-form output parameters. A directive entry stands in its place. A
+ * document that wrote the field as one directive gets the directive again while the list holds that one import.
  */
-export declare function encodeStepOutputs(outputs: StepOutput_$union[]): YAMLElement_$union;
+export declare function encodeStepOutputs(whole: boolean, outputs: StepOutput_$union[]): YamlNode;
 /**
  * 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_$union;
+export declare function encodeScatter(scatter: SchemaSaladString_$union[]): YamlNode;
 /**
  * Encode a CommandLineTool element with ordered sections and preserved metadata.
  */
-export declare function encodeToolDescriptionElement(td: CWLToolDescription): YAMLElement_$union;
+export declare function encodeToolDescriptionElement(td: CWLToolDescription): YamlNode;
 /**
  * Encode an ExpressionTool element with ordered sections and preserved metadata.
  */
-export declare function encodeExpressionToolDescriptionElement(et: CWLExpressionToolDescription): YAMLElement_$union;
+export declare function encodeExpressionToolDescriptionElement(et: CWLExpressionToolDescription): YamlNode;
 /**
  * Encode an Operation element with ordered sections and preserved metadata.
  */
-export declare function encodeOperationDescriptionElement(op: CWLOperationDescription): YAMLElement_$union;
+export declare function encodeOperationDescriptionElement(op: CWLOperationDescription): YamlNode;
+/**
+ * Encode workflow step run targets as paths or inline processing units.
+ */
+export declare function encodeWorkflowStepRun(run: WorkflowStepRun_$union): YamlNode;
 /**
  * Encode a Workflow element with ordered sections and preserved metadata.
  */
-export declare function encodeWorkflowDescriptionElement(wd: CWLWorkflowDescription): YAMLElement_$union;
+export declare function encodeWorkflowDescriptionElement(wd: CWLWorkflowDescription): YamlNode;
 /**
- * Encode one workflow step as a map entry keyed by step id.
+ * Encode the steps of a workflow as the entries of an id list (see encodeIdEntries).
  */
-export declare function encodeWorkflowStep(ws: WorkflowStep): [string, YAMLElement_$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;
+export declare function encodeWorkflowSteps(whole: boolean, steps: ListEntry$1_$union<WorkflowStep>[]): YamlNode;
+/**
+ * Encode one workflow step as a map entry keyed by step id, and without a key when the step has no id.
+ */
+export declare function encodeWorkflowStep(ws: WorkflowStep): [Option<string>, YamlNode];
+export declare function writeYaml(element: YamlNode): string;
 /**
- * Extract object mappings in order, dropping non-mapping presentation nodes.
+ * Encode an entry of a job file as the key and the plain CWL value. The file has no field for a type.
  */
-export declare function getObjectPairs(element: YAMLElement_$union): FSharpList<[string, YAMLElement_$union]>;
+export declare function encodeCWLParameterReference(reference: CWLParameterReference): [string, YamlNode];
+export declare function encodeYAMLParameterFile(references: CWLParameterReference[]): string;
 /**
- * Render top-level CWL sections in a stable order while keeping metadata as a final block.
+ * Render top-level CWL sections in a stable order while keeping metadata as a final block. The document is
+ * one mapping, and a blank line separates the sections, except behind a section that ends in a block scalar
+ * with the chomping Keep. The empty lines behind such a scalar are part of its value, and the writer says
+ * which scalars it writes that way. The writer prints the document once, so only the end of the document
+ * ends a text, and the end of a section is no end of a scalar.
  */
-export declare function renderTopLevelElement(baseKeys: FSharpList<string>, orderedSectionKeys: FSharpList<string>, element: YAMLElement_$union): string;
+export declare function renderTopLevelElement(baseKeys: FSharpList<string>, orderedSectionKeys: FSharpList<string>, element: YamlNode): string;
 export declare function encodeToolDescription(td: CWLToolDescription): string;
 export declare function encodeWorkflowDescription(wd: CWLWorkflowDescription): string;
 export declare function encodeExpressionToolDescription(et: CWLExpressionToolDescription): string;
 export declare function encodeOperationDescription(op: CWLOperationDescription): string;
+/**
+ * Encode a processing unit as its YAML tree, with the runs of its steps and its directives as they were written.
+ */
+export declare function encodeProcessingUnitElement(pu: CWLProcessingUnit_$union): YamlNode;
 export declare function encodeProcessingUnit(pu: CWLProcessingUnit_$union): string;
+/**
+ * Encode a CWLType in flow style, so that the written text has no line break and can be embedded in JSON.
+ * Unions are lists, and schemas are mappings with their fields in the array form.
+ */
+export declare function encodeCWLTypeFlow(t: CWLType_$union): YamlNode;
 /**
  * Encode a CWLType to a single-line YAML string using flow/inline style
  * This produces YAML that doesn't contain newlines and can be embedded in JSON
  */
 export declare function encodeCWLTypeYaml(t: CWLType_$union): string;
-export declare function encodeInputRecordFieldYaml(field: InputRecordField): string;
-export declare function encodeInputRecordSchemaYaml(schema: InputRecordSchema): string;
-export declare function encodeInputEnumSchemaYaml(schema: InputEnumSchema): string;
-export declare function encodeInputArraySchemaYaml(schema: InputArraySchema): string;
 /**
  * Convert a CWLType to a YAML-formatted string for use in serialization
  */

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

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