@nfdi4plants/arctrl 3.0.0-beta.8 → 3.0.0

package/README.md

@@ -19,7 +19,7 @@
 
 ```fsharp
 #r "nuget: ARCtrl"
-``` 
+```
 
 ```bash
 <PackageReference Include="ARCtrl" Version="1.1.0" />
@@ -55,6 +55,8 @@ Documentation can be found [here](https://nfdi4plants.github.io/nfdi4plants.know
 
 #### Local Setup
 
+##### Windows
+
 On windows you can use the `setup.cmd` to run the following steps automatically!
 
 1. Setup dotnet tools
@@ -63,11 +65,11 @@ On windows you can use the `setup.cmd` to run the following steps automatically!
 
 
 2. Install NPM dependencies
-   
+
     `npm install`
 
 3. Setup python environment
-    
+
     `py -m venv .venv`
 
 4. Install [uv](https://docs.astral.sh/uv/) and dependencies
@@ -78,6 +80,31 @@ On windows you can use the `setup.cmd` to run the following steps automatically!
 
 Verify correct setup with `./build.cmd runtests` ✨
 
+##### Linux / macOS
+
+On unix you can use the `setup.sh` to run the following steps automatically!
+
+1. Setup dotnet tools
+
+   `dotnet tool restore`
+
+
+2. Install NPM dependencies
+
+    `npm install`
+
+3. Setup python environment
+
+    `python -m venv .venv`
+
+4. Install [uv](https://docs.astral.sh/uv/) and dependencies
+
+   1. `.venv/bin/python -m pip install -U pip setuptools`
+   2. `.venv/bin/python -m pip install uv`
+   3. `.venv/bin/python -m uv pip install -r pyproject.toml --group dev`
+
+Verify correct setup with `bash build.sh runtests` ✨
+
 ## Branding
 
 Feel free to reference `ARCtrl` on slides or elsewhere using our logos:

package/dist/ts/index.d.ts

@@ -1,23 +1,33 @@
+import { CWLProcessingUnit } from './ts/CWL/CWLProcessingUnit.js';
+import { CWLType, FileInstance, DirectoryInstance, DirentInstance, InputEnumSchema, InputRecordField, InputRecordSchema, InputArraySchema, SchemaDefRequirementType, SoftwarePackage } from './ts/CWL/CWLTypes.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 { 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 { LDNode, LDGraph, LDRef, LDValue } from './ts/ROCrate/LDObject.js';
 import { LDContext } from './ts/ROCrate/LDContext.js';
-import { initV1_1, initV1_2DRAFT, initBioschemasContext } from './ts/ROCrate/ROCrateContext.js';
-import { LDComment } from './ts/ROCrate/Generic/Comment.js';
-import { LDDefinedTerm } from './ts/ROCrate/Generic/DefinedTerm.js';
-import { LDFile } from './ts/ROCrate/Generic/File.js';
-import { LDLabProcess } from './ts/ROCrate/Generic/LabProcess.js';
-import { LDLabProtocol } from './ts/ROCrate/Generic/LabProtocol.js';
-import { LDOrganization } from './ts/ROCrate/Generic/Organization.js';
-import { LDPerson } from './ts/ROCrate/Generic/Person.js';
-import { LDPostalAddress } from './ts/ROCrate/Generic/PostalAddress.js';
-import { LDPropertyValue } from './ts/ROCrate/Generic/PropertyValue.js';
-import { LDSample } from './ts/ROCrate/Generic/Sample.js';
-import { LDScholarlyArticle } from './ts/ROCrate/Generic/ScholarlyArticle.js';
-import { LDDataset } from './ts/ROCrate/Generic/Dataset.js';
+import { initV1_1, initV1_2, initBioschemasContext } from './ts/ROCrate/ROCrateContext.js';
+import { LDComment } from './ts/ROCrate/LDTypes/Comment.js';
+import { LDDefinedTerm } from './ts/ROCrate/LDTypes/DefinedTerm.js';
+import { LDFile } from './ts/ROCrate/LDTypes/File.js';
+import { LDLabProcess } from './ts/ROCrate/LDTypes/LabProcess.js';
+import { LDLabProtocol } from './ts/ROCrate/LDTypes/LabProtocol.js';
+import { LDOrganization } from './ts/ROCrate/LDTypes/Organization.js';
+import { LDPerson } from './ts/ROCrate/LDTypes/Person.js';
+import { LDPostalAddress } from './ts/ROCrate/LDTypes/PostalAddress.js';
+import { LDPropertyValue } from './ts/ROCrate/LDTypes/PropertyValue.js';
+import { LDSample } from './ts/ROCrate/LDTypes/Sample.js';
+import { LDScholarlyArticle } from './ts/ROCrate/LDTypes/ScholarlyArticle.js';
+import { LDDataset } from './ts/ROCrate/LDTypes/Dataset.js';
 import { LDGraphExtensions_PyJsInterop as LDGraphIO, LDNodeExtensions_PyJsInterop as LDNodeIO } from './ts/JsonIO/LDObject.js';
-import { TypeExtensions_Conversion as Conversion } from './ts/Conversion.js';
+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 { DataMap } from './ts/Core/DataMap.js';
+export { Datamap } from './ts/Core/Datamap.js';
+export { DataContext } from './ts/Core/DataContext.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';
@@ -25,6 +35,7 @@ export { ArcTable } from './ts/Core/Table/ArcTable.js';
 export { Template, Organisation } from './ts/Core/Template.js';
 export { Templates } from './ts/Core/Templates.js';
 export { JsonController } from './ts/Json.js';
+export { YamlController } from './ts/Yaml.js';
 export { XlsxController } from './ts/Xlsx.js';
 export { Person } from './ts/Core/Person.js';
 export { Publication } from './ts/Core/Publication.js';
@@ -34,6 +45,33 @@ 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 declare const CWL: {
+    CWLProcessingUnit: typeof CWLProcessingUnit;
+    CWLType: typeof CWLType;
+    FileInstance: typeof FileInstance;
+    DirectoryInstance: typeof DirectoryInstance;
+    DirentInstance: typeof DirentInstance;
+    InputEnumSchema: typeof InputEnumSchema;
+    InputRecordField: typeof InputRecordField;
+    InputRecordSchema: typeof InputRecordSchema;
+    InputArraySchema: typeof InputArraySchema;
+    SchemaDefRequirementType: typeof SchemaDefRequirementType;
+    SoftwarePackage: typeof SoftwarePackage;
+    CWLParameterReference: typeof CWLParameterReference;
+    CWLInput: typeof CWLInput;
+    InputBinding: typeof InputBinding;
+    CWLOutput: typeof CWLOutput;
+    OutputBinding: typeof OutputBinding;
+    CWLToolDescription: typeof CWLToolDescription;
+    CWLWorkflowDescription: typeof CWLWorkflowDescription;
+    WorkflowStep: typeof WorkflowStep;
+    StepInput: typeof StepInput;
+    StepOutput: typeof StepOutput;
+    Requirement: typeof Requirement;
+    DockerRequirement: typeof DockerRequirement;
+    EnvironmentDef: typeof EnvironmentDef;
+    ResourceRequirementInstance: typeof ResourceRequirementInstance;
+};
 export declare const ROCrate: {
     LDNode: typeof LDNode;
     LDGraph: typeof LDGraph;
@@ -41,7 +79,7 @@ export declare const ROCrate: {
     LDRef: typeof LDRef;
     LDContext: typeof LDContext;
     initV1_1: typeof initV1_1;
-    initV1_2DRAFT: typeof initV1_2DRAFT;
+    initV1_2: typeof initV1_2;
     initBioschemasContext: typeof initBioschemasContext;
     LDComment: typeof LDComment;
     LDDefinedTerm: typeof LDDefinedTerm;

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,OAAO,EAAE,MAAM,sBAAsB,CAAA;AAC9C,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,sBAAsB,CAAA;AAC1D,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;AAGlE,OAAO,EAAE,iBAAiB,EAAE,MAAM,+BAA+B,CAAA;AACjE,OAAO,EAAE,OAAO,EAAE,YAAY,EAAE,iBAAiB,EAAE,cAAc,EAAE,eAAe,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,gBAAgB,EAAE,wBAAwB,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AAClN,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAA;AACtE,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAC3D,OAAO,EAAE,SAAS,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAA;AAC9D,OAAO,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAA;AAChE,OAAO,EAAE,sBAAsB,EAAE,MAAM,iCAAiC,CAAA;AACxE,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,2BAA2B,CAAA;AAC/E,OAAO,EAAE,WAAW,EAAE,iBAAiB,EAAE,cAAc,EAAE,2BAA2B,EAAE,MAAM,0BAA0B,CAAA;AAEtH,eAAO,MAAM,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;CA0Bf,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

@@ -1,6 +1,7 @@
 export { ARC } from './ts/ARC.js';
 export { ArcAssay, ArcInvestigation, ArcRun, ArcStudy, ArcWorkflow } from './ts/Core/ArcTypes.js';
-export { DataMap } from './ts/Core/DataMap.js';
+export { Datamap } from './ts/Core/Datamap.js';
+export { DataContext } from './ts/Core/DataContext.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';
@@ -8,6 +9,7 @@ export { ArcTable } from './ts/Core/Table/ArcTable.js';
 export { Organisation, Template } from './ts/Core/Template.js';
 export { Templates } from './ts/Core/Templates.js';
 export { JsonController } from './ts/Json.js';
+export { YamlController } from './ts/Yaml.js';
 export { XlsxController } from './ts/Xlsx.js';
 export { Person } from './ts/Core/Person.js';
 export { Publication } from './ts/Core/Publication.js';
@@ -17,24 +19,60 @@ 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';
+import { CWLProcessingUnit } from './ts/CWL/CWLProcessingUnit.js';
+import { SoftwarePackage, SchemaDefRequirementType, InputArraySchema, InputRecordSchema, InputRecordField, InputEnumSchema, DirentInstance, DirectoryInstance, FileInstance, CWLType } from './ts/CWL/CWLTypes.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 { 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 { LDRef, LDValue, LDGraph, LDNode } from './ts/ROCrate/LDObject.js';
 import { LDContext } from './ts/ROCrate/LDContext.js';
-import { initBioschemasContext, initV1_2DRAFT, initV1_1 } from './ts/ROCrate/ROCrateContext.js';
-import { LDComment } from './ts/ROCrate/Generic/Comment.js';
-import { LDDefinedTerm } from './ts/ROCrate/Generic/DefinedTerm.js';
-import { LDFile } from './ts/ROCrate/Generic/File.js';
-import { LDLabProcess } from './ts/ROCrate/Generic/LabProcess.js';
-import { LDLabProtocol } from './ts/ROCrate/Generic/LabProtocol.js';
-import { LDOrganization } from './ts/ROCrate/Generic/Organization.js';
-import { LDPerson } from './ts/ROCrate/Generic/Person.js';
-import { LDPostalAddress } from './ts/ROCrate/Generic/PostalAddress.js';
-import { LDPropertyValue } from './ts/ROCrate/Generic/PropertyValue.js';
-import { LDSample } from './ts/ROCrate/Generic/Sample.js';
-import { LDScholarlyArticle } from './ts/ROCrate/Generic/ScholarlyArticle.js';
-import { LDDataset } from './ts/ROCrate/Generic/Dataset.js';
+import { initBioschemasContext, initV1_2, initV1_1 } from './ts/ROCrate/ROCrateContext.js';
+import { LDComment } from './ts/ROCrate/LDTypes/Comment.js';
+import { LDDefinedTerm } from './ts/ROCrate/LDTypes/DefinedTerm.js';
+import { LDFile } from './ts/ROCrate/LDTypes/File.js';
+import { LDLabProcess } from './ts/ROCrate/LDTypes/LabProcess.js';
+import { LDLabProtocol } from './ts/ROCrate/LDTypes/LabProtocol.js';
+import { LDOrganization } from './ts/ROCrate/LDTypes/Organization.js';
+import { LDPerson } from './ts/ROCrate/LDTypes/Person.js';
+import { LDPostalAddress } from './ts/ROCrate/LDTypes/PostalAddress.js';
+import { LDPropertyValue } from './ts/ROCrate/LDTypes/PropertyValue.js';
+import { LDSample } from './ts/ROCrate/LDTypes/Sample.js';
+import { LDScholarlyArticle } from './ts/ROCrate/LDTypes/ScholarlyArticle.js';
+import { LDDataset } from './ts/ROCrate/LDTypes/Dataset.js';
 import { LDNodeExtensions_PyJsInterop, LDGraphExtensions_PyJsInterop } from './ts/JsonIO/LDObject.js';
-import { TypeExtensions_Conversion } from './ts/Conversion.js';
+import { Conversion } from './ts/Conversion.js';
 
+const CWL = {
+  CWLProcessingUnit,
+  CWLType,
+  FileInstance,
+  DirectoryInstance,
+  DirentInstance,
+  InputEnumSchema,
+  InputRecordField,
+  InputRecordSchema,
+  InputArraySchema,
+  SchemaDefRequirementType,
+  SoftwarePackage,
+  CWLParameterReference,
+  CWLInput,
+  InputBinding,
+  CWLOutput,
+  OutputBinding,
+  CWLToolDescription,
+  CWLWorkflowDescription,
+  WorkflowStep,
+  StepInput,
+  StepOutput,
+  Requirement,
+  DockerRequirement,
+  EnvironmentDef,
+  ResourceRequirementInstance
+};
 const ROCrate = {
   LDNode,
   LDGraph,
@@ -42,7 +80,7 @@ const ROCrate = {
   LDRef,
   LDContext,
   initV1_1,
-  initV1_2DRAFT,
+  initV1_2,
   initBioschemasContext,
   LDComment,
   LDDefinedTerm,
@@ -58,7 +96,7 @@ const ROCrate = {
   LDDataset,
   LDGraphIO: LDGraphExtensions_PyJsInterop,
   LDNodeIO: LDNodeExtensions_PyJsInterop,
-  Conversion: TypeExtensions_Conversion
+  Conversion
 };
 
-export { ROCrate };
+export { CWL, ROCrate };

package/dist/ts/ts/ARC.d.ts

@@ -5,27 +5,29 @@ import { ArcWorkflow, ArcRun, ArcStudy, ArcAssay, ArcInvestigation } from './Cor
 import { FSharpResult$2_$union } from '@fable-org/fable-library-js/Result.js';
 import { Contract } from './Contract/Contract.js';
 import { int32 } from '@fable-org/fable-library-js/Int32.js';
-import { DataMap } from './Core/DataMap.js';
+import { Datamap } from './Core/Datamap.js';
 import { FileSystemTree_$union } from './FileSystem/FileSystemTree.js';
 import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { FSharpMap } from '@fable-org/fable-library-js/Map.js';
+import { CWLProcessingUnit_$union } from './CWL/CWLProcessingUnit.js';
+import { CWLParameterReference } from './CWL/ParameterReference.js';
 import { Remark, Comment$ } from './Core/Comment.js';
 import { Person } from './Core/Person.js';
 import { Publication } from './Core/Publication.js';
 import { OntologySourceReference } from './Core/OntologySourceReference.js';
-import { FSharpMap } from '@fable-org/fable-library-js/Map.js';
 import { ValidationPackagesConfig } from './ValidationPackages/ValidationPackagesConfig.js';
+import { WorkflowGraphIndex, GraphBuildIssue, WorkflowGraph } from './WorkflowGraph/GraphTypes.js';
 import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
 export declare class ARC extends ArcInvestigation {
-    _cwl: Option<void>;
     _license: Option<License>;
     _fs: FileSystem;
-    "init@104": int32;
-    constructor(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, ontologySourceReferences?: OntologySourceReference[], publications?: Publication[], contacts?: Person[], assays?: ArcAssay[], studies?: ArcStudy[], workflows?: ArcWorkflow[], runs?: ArcRun[], registeredStudyIdentifiers?: string[], comments?: Comment$[], remarks?: Remark[], cwl?: Option<void>, fs?: FileSystem, license?: License);
+    "init@133": int32;
+    constructor(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, ontologySourceReferences?: OntologySourceReference[], publications?: Publication[], contacts?: Person[], assays?: ArcAssay[], studies?: ArcStudy[], workflows?: ArcWorkflow[], runs?: ArcRun[], registeredStudyIdentifiers?: string[], comments?: Comment$[], remarks?: Remark[], fs?: FileSystem, license?: License);
     get FileSystem(): FileSystem;
     set FileSystem(fs: FileSystem);
     get License(): License | undefined;
     set License(license: Option<License>);
-    static fromArcInvestigation(isa: ArcInvestigation, cwl?: Option<void>, fs?: FileSystem, license?: License): ARC;
+    static fromArcInvestigation(isa: ArcInvestigation, fs?: FileSystem, license?: License): ARC;
     TryWriteAsync(arcPath: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
     TryUpdateAsync(arcPath: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
     SetLicenseFulltext(fulltext: string, path?: string): void;
@@ -34,9 +36,17 @@ export declare class ARC extends ArcInvestigation {
     GetRunRemoveContracts(runIdentifier: string): Contract[];
     GetWorkflowRemoveContracts(workflowIdentifier: string): Contract[];
     TryRemoveAssayAsync(arcPath: string, assayIdentifier: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
+    TryRemoveRunAsync(arcPath: string, runIdentifier: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
+    TryRemoveWorkflowAsync(arcPath: string, workflowIdentifier: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
+    RemoveRunAsync(arcPath: string, runIdentifier: string): Promise<void>;
+    RemoveWorkflowAsync(arcPath: string, workflowIdentifier: string): Promise<void>;
+    TryRenameRunAsync(arcPath: string, oldRunIdentifier: string, newRunIdentifier: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
+    TryRenameWorkflowAsync(arcPath: string, oldWorkflowIdentifier: string, newWorkflowIdentifier: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
+    RenameRunAsync(arcPath: string, oldRunIdentifier: string, newRunIdentifier: string): Promise<void>;
+    RenameWorkflowAsync(arcPath: string, oldWorkflowIdentifier: string, newWorkflowIdentifier: string): Promise<void>;
     GetAssayRenameContracts(oldAssayIdentifier: string, newAssayIdentifier: string): Contract[];
     GetRunRenameContracts(oldRunIdentifier: string, newRunIdentifier: string): Contract[];
-    GetWorkflowRenameContracts(oldRunIdentifier: string, newRunIdentifier: string): Contract[];
+    GetWorkflowRenameContracts(oldWorkflowIdentifier: string, newWorkflowIdentifier: string): Contract[];
     TryRenameAssayAsync(arcPath: string, oldAssayIdentifier: string, newAssayIdentifier: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
     GetStudyRemoveContracts(studyIdentifier: string): Contract[];
     TryRemoveStudyAsync(arcPath: string, studyIdentifier: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
@@ -65,27 +75,40 @@ export declare class ARC extends ArcInvestigation {
     static get DefaultContracts(): FSharpMap<string, Contract>;
     static fromDeprecatedROCrateJsonString(s: string): ARC;
     static fromROCrateJsonString(s: string): ARC;
-    ToROCrateJsonString(spaces?: int32): string;
-    static toROCrateJsonString(spaces?: int32): ((arg0: ARC) => string);
+    ToROCrateJsonString(spaces?: int32, ignoreBrokenWR?: boolean): string;
+    static toROCrateJsonString(spaces?: int32, ignoreBrokenWR?: boolean): ((arg0: ARC) => string);
     GetLicenseWriteContract(): Contract;
     GetValidationPackagesConfigWriteContract(vpc: ValidationPackagesConfig): Contract;
     GetValidationPackagesConfigDeleteContract(vpc: ValidationPackagesConfig): Contract;
     GetValidationPackagesConfigReadContract(): Contract;
     GetValidationPackagesConfigFromReadContract(contract: Contract): Option<ValidationPackagesConfig>;
     ToFilePaths(removeRoot?: boolean, skipUpdateFS?: boolean): string[];
+    BuildWorkflowGraphs(): [string, FSharpResult$2_$union<WorkflowGraph, GraphBuildIssue>][];
+    BuildRunGraphs(): [string, FSharpResult$2_$union<WorkflowGraph, GraphBuildIssue>][];
+    BuildAllProcessingUnitGraphs(): WorkflowGraphIndex;
 }
 export declare function ARC_$reflection(): TypeInfo;
-export declare function ARC_$ctor_Z4D7EB22(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, ontologySourceReferences?: OntologySourceReference[], publications?: Publication[], contacts?: Person[], assays?: ArcAssay[], studies?: ArcStudy[], workflows?: ArcWorkflow[], runs?: ArcRun[], registeredStudyIdentifiers?: string[], comments?: Comment$[], remarks?: Remark[], cwl?: Option<void>, fs?: FileSystem, license?: License): ARC;
+export declare function ARC_$ctor_Z443FB9BF(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, ontologySourceReferences?: OntologySourceReference[], publications?: Publication[], contacts?: Person[], assays?: ArcAssay[], studies?: ArcStudy[], workflows?: ArcWorkflow[], runs?: ArcRun[], registeredStudyIdentifiers?: string[], comments?: Comment$[], remarks?: Remark[], fs?: FileSystem, license?: License): ARC;
 export declare function ARCAux_getArcAssaysFromContracts(contracts: Contract[]): ArcAssay[];
 export declare function ARCAux_getArcStudiesFromContracts(contracts: Contract[]): [ArcStudy, FSharpList<ArcAssay>][];
 export declare function ARCAux_getArcWorkflowsFromContracts(contracts: Contract[]): ArcWorkflow[];
 export declare function ARCAux_getArcRunsFromContracts(contracts: Contract[]): ArcRun[];
-export declare function ARCAux_getAssayDataMapFromContracts(assayIdentifier: string, contracts: Contract[]): Option<DataMap>;
-export declare function ARCAux_getStudyDataMapFromContracts(studyIdentifier: string, contracts: Contract[]): Option<DataMap>;
-export declare function ARCAux_getWorkflowDataMapFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<DataMap>;
-export declare function ARCAux_getRunDataMapFromContracts(runIdentifier: string, contracts: Contract[]): Option<DataMap>;
+export declare function ARCAux_getAssayDatamapFromContracts(assayIdentifier: string, contracts: Contract[]): Option<Datamap>;
+export declare function ARCAux_getStudyDatamapFromContracts(studyIdentifier: string, contracts: Contract[]): Option<Datamap>;
+export declare function ARCAux_getWorkflowDatamapFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<Datamap>;
+export declare function ARCAux_getRunDatamapFromContracts(runIdentifier: string, contracts: Contract[]): Option<Datamap>;
+export declare function ARCAux_getWorkflowCWLFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<CWLProcessingUnit_$union>;
+export declare function ARCAux_getRunCWLFromContracts(runIdentifier: string, contracts: Contract[]): Option<CWLProcessingUnit_$union>;
+export declare function ARCAux_getRunYMLFromContracts(runIdentifier: string, contracts: Contract[]): Option<CWLParameterReference[]>;
+/**
+ * Builds a lookup map of normalized CWL file paths to decoded CWLProcessingUnit instances from CWL-typed contracts.
+ */
+export declare function ARCAux_getCWLByPathFromContracts(contracts: Contract[]): FSharpMap<string, CWLProcessingUnit_$union>;
+/**
+ * Looks up a CWLProcessingUnit by normalized path in the given lookup map.
+ */
+export declare function ARCAux_tryGetCWLByPath(cwlByPath: FSharpMap<string, CWLProcessingUnit_$union>, path: string): Option<CWLProcessingUnit_$union>;
 export declare function ARCAux_getArcInvestigationFromContracts(contracts: Contract[]): ArcInvestigation;
 export declare function ARCAux_getLicenseFromContracts(contracts: Contract[]): Option<License>;
 export declare function ARCAux_updateFSByARC(isa: ArcInvestigation, license: Option<License>, fs: FileSystem): FileSystem;
-export declare function ARCAux_updateFSByCWL(cwl: Option<void>, fs: FileSystem): FileSystem;
 //# sourceMappingURL=ARC.d.ts.map

package/dist/ts/ts/ARC.d.ts.map

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