@nfdi4plants/arctrl 3.2.3 → 3.3.0

package/dist/ts/index.d.ts

@@ -1,13 +1,15 @@
 import { CWLProcessingUnit } from './ts/CWL/CWLProcessingUnit.js';
-import { CWLType, FileInstance, DirectoryInstance, DirentInstance, InputEnumSchema, InputRecordField, InputRecordSchema, InputArraySchema, SchemaDefRequirementType, SoftwarePackage } from './ts/CWL/CWLTypes.js';
+import { CWLType, SchemaSaladString, SchemaSaladBool, FileSize, DocText, ListEntry$1 as ListEntry, FileInstance, DirectoryInstance, DirentInstance, InputEnumSchema, InputRecordField, InputRecordSchema, InputArraySchema, SchemaDefinition, SoftwarePackage } from './ts/CWL/CWLTypes.js';
 import { CWLParameterValue, CWLParameterRecordField } from './ts/CWL/ParameterValue.js';
 import { CWLParameterReference } from './ts/CWL/ParameterReference.js';
-import { CWLInput, InputBinding } from './ts/CWL/Inputs.js';
-import { CWLOutput, OutputBinding } from './ts/CWL/Outputs.js';
+import { CWLInput, InputBinding, InputFormat, BindingPosition } from './ts/CWL/Inputs.js';
+import { CWLOutput, OutputBinding, OutputSource, OutputGlob } from './ts/CWL/Outputs.js';
 import { CWLToolDescription } from './ts/CWL/ToolDescription.js';
 import { CWLWorkflowDescription } from './ts/CWL/WorkflowDescription.js';
-import { WorkflowStep, StepInput, StepOutput } from './ts/CWL/WorkflowSteps.js';
-import { Requirement, DockerRequirement, EnvironmentDef, ResourceRequirementInstance } from './ts/CWL/Requirements.js';
+import { CWLExpressionToolDescription } from './ts/CWL/ExpressionToolDescription.js';
+import { CWLOperationDescription } from './ts/CWL/OperationDescription.js';
+import { WorkflowStep, ResolvedRun, StepInput, StepOutput, StepOutputParameter, WorkflowStepRun, LinkMergeMethod, PickValueMethod, ScatterMethod } from './ts/CWL/WorkflowSteps.js';
+import { Requirement, SchemaDefEntry, DockerRequirement, EnvironmentDef, ResourceRequirementInstance, HintEntry, HintUnknownValue, InitialWorkDirEntry, InlineJavascriptRequirementValue, InplaceUpdateRequirementValue, LoadListingEnum, LoadListingRequirementValue, NetworkAccessRequirementValue, ToolTimeLimitValue, WorkReuseRequirementValue } from './ts/CWL/Requirements.js';
 import { LDNode, LDGraph, LDRef, LDValue } from './ts/ROCrate/LDObject.js';
 import { LDContext } from './ts/ROCrate/LDContext.js';
 import { initV1_1, initV1_2, initBioschemasContext } from './ts/ROCrate/ROCrateContext.js';
@@ -27,8 +29,13 @@ import { LDGraphExtensions_PyJsInterop as LDGraphIO, LDNodeExtensions_PyJsIntero
 import { Conversion as Conversion } from './ts/Conversion.js';
 export { ARC } from './ts/ARC.js';
 export { ArcAssay, ArcStudy, ArcRun, ArcWorkflow, ArcInvestigation } from './ts/Core/ArcTypes.js';
+export { OntologySourceReference } from './ts/Core/OntologySourceReference.js';
 export { Datamap } from './ts/Core/Datamap.js';
 export { DataContext } from './ts/Core/DataContext.js';
+export { Data } from './ts/Core/Data.js';
+export { DataFile } from './ts/Core/DataFile.js';
+export { Component } from './ts/Core/Process/Component.js';
+export { ScalarValue } from './ts/Core/ScalarValue.js';
 export { CompositeCell } from './ts/Core/Table/CompositeCell.js';
 export { CompositeHeader, IOType } from './ts/Core/Table/CompositeHeader.js';
 export { CompositeColumn } from './ts/Core/Table/CompositeColumn.js';
@@ -41,14 +48,21 @@ export { XlsxController } from './ts/Xlsx.js';
 export { Person } from './ts/Core/Person.js';
 export { Publication } from './ts/Core/Publication.js';
 export { OntologyAnnotation } from './ts/Core/OntologyAnnotation.js';
-export { Comment$ as Comment } from './ts/Core/Comment.js';
+export { Comment$ as Comment, Remark } from './ts/Core/Comment.js';
 export { Contract } from './ts/Contract/Contract.js';
 export { WebController } from './ts/Template.Web.js';
 export { FileSystem } from './ts/FileSystem/FileSystem.js';
 export { FileSystemTree } from './ts/FileSystem/FileSystemTree.js';
+export { Commit } from './ts/FileSystem/Commit.js';
+export { License } from './ts/License.js';
 export declare const CWL: {
     CWLProcessingUnit: typeof CWLProcessingUnit;
     CWLType: typeof CWLType;
+    SchemaSaladString: typeof SchemaSaladString;
+    SchemaSaladBool: typeof SchemaSaladBool;
+    FileSize: typeof FileSize;
+    DocText: typeof DocText;
+    ListEntry: typeof ListEntry;
     FileInstance: typeof FileInstance;
     DirectoryInstance: typeof DirectoryInstance;
     DirentInstance: typeof DirentInstance;
@@ -56,24 +70,47 @@ export declare const CWL: {
     InputRecordField: typeof InputRecordField;
     InputRecordSchema: typeof InputRecordSchema;
     InputArraySchema: typeof InputArraySchema;
-    SchemaDefRequirementType: typeof SchemaDefRequirementType;
+    SchemaDefinition: typeof SchemaDefinition;
     SoftwarePackage: typeof SoftwarePackage;
     CWLParameterValue: typeof CWLParameterValue;
     CWLParameterRecordField: typeof CWLParameterRecordField;
     CWLParameterReference: typeof CWLParameterReference;
     CWLInput: typeof CWLInput;
     InputBinding: typeof InputBinding;
+    InputFormat: typeof InputFormat;
+    BindingPosition: typeof BindingPosition;
     CWLOutput: typeof CWLOutput;
     OutputBinding: typeof OutputBinding;
+    OutputSource: typeof OutputSource;
+    OutputGlob: typeof OutputGlob;
     CWLToolDescription: typeof CWLToolDescription;
     CWLWorkflowDescription: typeof CWLWorkflowDescription;
+    CWLExpressionToolDescription: typeof CWLExpressionToolDescription;
+    CWLOperationDescription: typeof CWLOperationDescription;
     WorkflowStep: typeof WorkflowStep;
+    ResolvedRun: typeof ResolvedRun;
     StepInput: typeof StepInput;
     StepOutput: typeof StepOutput;
+    StepOutputParameter: typeof StepOutputParameter;
+    WorkflowStepRun: typeof WorkflowStepRun;
+    LinkMergeMethod: typeof LinkMergeMethod;
+    PickValueMethod: typeof PickValueMethod;
+    ScatterMethod: typeof ScatterMethod;
     Requirement: typeof Requirement;
+    SchemaDefEntry: typeof SchemaDefEntry;
     DockerRequirement: typeof DockerRequirement;
     EnvironmentDef: typeof EnvironmentDef;
     ResourceRequirementInstance: typeof ResourceRequirementInstance;
+    HintEntry: typeof HintEntry;
+    HintUnknownValue: typeof HintUnknownValue;
+    InitialWorkDirEntry: typeof InitialWorkDirEntry;
+    InlineJavascriptRequirementValue: typeof InlineJavascriptRequirementValue;
+    InplaceUpdateRequirementValue: typeof InplaceUpdateRequirementValue;
+    LoadListingEnum: typeof LoadListingEnum;
+    LoadListingRequirementValue: typeof LoadListingRequirementValue;
+    NetworkAccessRequirementValue: typeof NetworkAccessRequirementValue;
+    ToolTimeLimitValue: typeof ToolTimeLimitValue;
+    WorkReuseRequirementValue: typeof WorkReuseRequirementValue;
 };
 export declare const ROCrate: {
     LDNode: typeof LDNode;

package/dist/ts/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/ARCtrl/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,aAAa,CAAA;AACjC,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACjG,OAAO,EAAE,uBAAuB,EAAE,MAAM,sCAAsC,CAAA;AAC9E,OAAO,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAA;AAC9C,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AACtD,OAAO,EAAE,IAAI,EAAE,MAAM,mBAAmB,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,uBAAuB,CAAA;AAChD,OAAO,EAAE,SAAS,EAAE,MAAM,gCAAgC,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AACtD,OAAO,EAAE,aAAa,EAAE,MAAM,kCAAkC,CAAA;AAChE,OAAO,EAAE,eAAe,EAAE,MAAM,EAAE,MAAM,oCAAoC,CAAA;AAC5E,OAAO,EAAE,eAAe,EAAE,MAAM,oCAAoC,CAAA;AACpE,OAAO,EAAE,QAAQ,EAAE,MAAM,6BAA6B,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AAC9D,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAA;AAClD,OAAO,EAAE,cAAc,EAAE,MAAM,cAAc,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,MAAM,cAAc,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,MAAM,cAAc,CAAA;AAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAA;AAC5C,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,iCAAiC,CAAA;AACpE,OAAO,EAAE,QAAQ,IAAI,OAAO,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAA;AAClE,OAAO,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,aAAa,EAAC,MAAM,sBAAsB,CAAA;AACnD,OAAO,EAAE,UAAU,EAAE,MAAM,+BAA+B,CAAA;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,mCAAmC,CAAA;AAClE,OAAO,EAAE,MAAM,EAAE,MAAM,2BAA2B,CAAA;AAClD,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAGzC,OAAO,EAAE,iBAAiB,EAAE,MAAM,+BAA+B,CAAA;AACjE,OAAO,EAAE,OAAO,EAAE,iBAAiB,EAAE,eAAe,EAAE,QAAQ,EAAE,OAAO,EAAE,WAAW,IAAI,SAAS,EAAE,YAAY,EAAE,iBAAiB,EAAE,cAAc,EAAE,eAAe,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AAC3R,OAAO,EAAE,iBAAiB,EAAE,uBAAuB,EAAE,MAAM,4BAA4B,CAAA;AACvF,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAA;AACtE,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,WAAW,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACzF,OAAO,EAAE,SAAS,EAAE,aAAa,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AACxF,OAAO,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAA;AAChE,OAAO,EAAE,sBAAsB,EAAE,MAAM,iCAAiC,CAAA;AACxE,OAAO,EAAE,4BAA4B,EAAE,MAAM,uCAAuC,CAAA;AACpF,OAAO,EAAE,uBAAuB,EAAE,MAAM,kCAAkC,CAAA;AAC1E,OAAO,EAAE,YAAY,EAAE,WAAW,EAAE,SAAS,EAAE,UAAU,EAAE,mBAAmB,EAAE,eAAe,EAAE,eAAe,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,2BAA2B,CAAA;AACnL,OAAO,EACH,WAAW,EAAE,cAAc,EAAE,iBAAiB,EAAE,cAAc,EAAE,2BAA2B,EAC3F,SAAS,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,gCAAgC,EAClF,6BAA6B,EAAE,eAAe,EAAE,2BAA2B,EAC3E,6BAA6B,EAAE,kBAAkB,EAAE,yBAAyB,EAC/E,MAAM,0BAA0B,CAAA;AAEjC,eAAO,MAAM,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAwDf,CAAC;AAGF,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAC,MAAM,0BAA0B,CAAA;AACzE,OAAO,EAAE,SAAS,EAAE,MAAM,2BAA2B,CAAA;AACrD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAA;AAC1F,OAAO,EAAE,SAAS,EAAE,MAAM,iCAAiC,CAAA;AAC3D,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAA;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,oCAAoC,CAAA;AACjE,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,cAAc,EAAE,MAAM,sCAAsC,CAAA;AACrE,OAAO,EAAE,QAAQ,EAAE,MAAM,gCAAgC,CAAA;AACzD,OAAO,EAAE,eAAe,EAAE,MAAM,uCAAuC,CAAA;AACvE,OAAO,EAAE,eAAe,EAAE,MAAM,uCAAuC,CAAA;AACvE,OAAO,EAAE,QAAQ,EAAE,MAAM,gCAAgC,CAAA;AACzD,OAAO,EAAE,kBAAkB,EAAE,MAAM,0CAA0C,CAAA;AAC7E,OAAO,EAAE,SAAS,EAAE,MAAM,iCAAiC,CAAA;AAC3D,OAAO,EAAE,6BAA6B,IAAI,SAAS,EAAE,MAAM,yBAAyB,CAAA;AACpF,OAAO,EAAE,4BAA4B,IAAI,QAAQ,EAAE,MAAM,yBAAyB,CAAA;AAClF,OAAO,EAAE,UAAU,IAAI,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE7D,eAAO,MAAM,OAAO;;;;;;;;;;;;;;;;;;;;;;;;CAwBnB,CAAC"}

package/dist/ts/index.js

@@ -1,7 +1,12 @@
 export { ARC } from './ts/ARC.js';
 export { ArcAssay, ArcInvestigation, ArcRun, ArcStudy, ArcWorkflow } from './ts/Core/ArcTypes.js';
+export { OntologySourceReference } from './ts/Core/OntologySourceReference.js';
 export { Datamap } from './ts/Core/Datamap.js';
 export { DataContext } from './ts/Core/DataContext.js';
+export { Data } from './ts/Core/Data.js';
+export { DataFile } from './ts/Core/DataFile.js';
+export { Component } from './ts/Core/Process/Component.js';
+export { ScalarValue } from './ts/Core/ScalarValue.js';
 export { CompositeCell } from './ts/Core/Table/CompositeCell.js';
 export { CompositeHeader, IOType } from './ts/Core/Table/CompositeHeader.js';
 export { CompositeColumn } from './ts/Core/Table/CompositeColumn.js';
@@ -14,21 +19,25 @@ export { XlsxController } from './ts/Xlsx.js';
 export { Person } from './ts/Core/Person.js';
 export { Publication } from './ts/Core/Publication.js';
 export { OntologyAnnotation } from './ts/Core/OntologyAnnotation.js';
-export { Comment$ as Comment } from './ts/Core/Comment.js';
+export { Comment$ as Comment, Remark } from './ts/Core/Comment.js';
 export { Contract } from './ts/Contract/Contract.js';
 export { WebController } from './ts/Template.Web.js';
 export { FileSystem } from './ts/FileSystem/FileSystem.js';
 export { FileSystemTree } from './ts/FileSystem/FileSystemTree.js';
+export { Commit } from './ts/FileSystem/Commit.js';
+export { License } from './ts/License.js';
 import { CWLProcessingUnit } from './ts/CWL/CWLProcessingUnit.js';
-import { SoftwarePackage, SchemaDefRequirementType, InputArraySchema, InputRecordSchema, InputRecordField, InputEnumSchema, DirentInstance, DirectoryInstance, FileInstance, CWLType } from './ts/CWL/CWLTypes.js';
+import { SoftwarePackage, SchemaDefinition, InputArraySchema, InputRecordSchema, InputRecordField, InputEnumSchema, DirentInstance, DirectoryInstance, FileInstance, ListEntry$1, DocText, FileSize, SchemaSaladBool, SchemaSaladString, CWLType } from './ts/CWL/CWLTypes.js';
 import { CWLParameterRecordField, CWLParameterValue } from './ts/CWL/ParameterValue.js';
 import { CWLParameterReference } from './ts/CWL/ParameterReference.js';
-import { InputBinding, CWLInput } from './ts/CWL/Inputs.js';
-import { OutputBinding, CWLOutput } from './ts/CWL/Outputs.js';
+import { BindingPosition, InputFormat, InputBinding, CWLInput } from './ts/CWL/Inputs.js';
+import { OutputGlob, OutputSource, OutputBinding, CWLOutput } from './ts/CWL/Outputs.js';
 import { CWLToolDescription } from './ts/CWL/ToolDescription.js';
 import { CWLWorkflowDescription } from './ts/CWL/WorkflowDescription.js';
-import { StepOutput, StepInput, WorkflowStep } from './ts/CWL/WorkflowSteps.js';
-import { ResourceRequirementInstance, EnvironmentDef, DockerRequirement, Requirement } from './ts/CWL/Requirements.js';
+import { CWLExpressionToolDescription } from './ts/CWL/ExpressionToolDescription.js';
+import { CWLOperationDescription } from './ts/CWL/OperationDescription.js';
+import { ScatterMethod, PickValueMethod, LinkMergeMethod, WorkflowStepRun, StepOutputParameter, StepOutput, StepInput, ResolvedRun, WorkflowStep } from './ts/CWL/WorkflowSteps.js';
+import { WorkReuseRequirementValue, ToolTimeLimitValue, NetworkAccessRequirementValue, LoadListingRequirementValue, LoadListingEnum, InplaceUpdateRequirementValue, InlineJavascriptRequirementValue, InitialWorkDirEntry, HintUnknownValue, HintEntry, ResourceRequirementInstance, EnvironmentDef, DockerRequirement, SchemaDefEntry, Requirement } from './ts/CWL/Requirements.js';
 import { LDRef, LDValue, LDGraph, LDNode } from './ts/ROCrate/LDObject.js';
 import { LDContext } from './ts/ROCrate/LDContext.js';
 import { initBioschemasContext, initV1_2, initV1_1 } from './ts/ROCrate/ROCrateContext.js';
@@ -50,6 +59,11 @@ import { Conversion } from './ts/Conversion.js';
 const CWL = {
   CWLProcessingUnit,
   CWLType,
+  SchemaSaladString,
+  SchemaSaladBool,
+  FileSize,
+  DocText,
+  ListEntry: ListEntry$1,
   FileInstance,
   DirectoryInstance,
   DirentInstance,
@@ -57,24 +71,47 @@ const CWL = {
   InputRecordField,
   InputRecordSchema,
   InputArraySchema,
-  SchemaDefRequirementType,
+  SchemaDefinition,
   SoftwarePackage,
   CWLParameterValue,
   CWLParameterRecordField,
   CWLParameterReference,
   CWLInput,
   InputBinding,
+  InputFormat,
+  BindingPosition,
   CWLOutput,
   OutputBinding,
+  OutputSource,
+  OutputGlob,
   CWLToolDescription,
   CWLWorkflowDescription,
+  CWLExpressionToolDescription,
+  CWLOperationDescription,
   WorkflowStep,
+  ResolvedRun,
   StepInput,
   StepOutput,
+  StepOutputParameter,
+  WorkflowStepRun,
+  LinkMergeMethod,
+  PickValueMethod,
+  ScatterMethod,
   Requirement,
+  SchemaDefEntry,
   DockerRequirement,
   EnvironmentDef,
-  ResourceRequirementInstance
+  ResourceRequirementInstance,
+  HintEntry,
+  HintUnknownValue,
+  InitialWorkDirEntry,
+  InlineJavascriptRequirementValue,
+  InplaceUpdateRequirementValue,
+  LoadListingEnum,
+  LoadListingRequirementValue,
+  NetworkAccessRequirementValue,
+  ToolTimeLimitValue,
+  WorkReuseRequirementValue
 };
 const ROCrate = {
   LDNode,