@nfdi4plants/arctrl 3.1.1 → 3.2.0

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

@@ -1,57 +1,58 @@
-import { FileSystem } from './FileSystem/FileSystem.js';
-import { Option } from '@fable-org/fable-library-js/Option.js';
-import { License } from './License.js';
-import { ArcWorkflow, ArcRun, ArcStudy, ArcAssay, ArcInvestigation } from './Core/ArcTypes.js';
-import { Contract } from './Contract/Contract.js';
-import { FSharpResult$2_$union } from '@fable-org/fable-library-js/Result.js';
-import { int32 } from '@fable-org/fable-library-js/Int32.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 { ValidationPackagesConfig } from './ValidationPackages/ValidationPackagesConfig.js';
-import { WorkflowGraphIndex, GraphBuildIssue, WorkflowGraph } from './WorkflowGraph/GraphTypes.js';
-import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { FileSystem } from './FileSystem/FileSystem.ts';
+import { Option } from '@fable-org/fable-library-ts/Option.ts';
+import { License } from './License.ts';
+import { ArcStudy, ArcWorkflow, ArcRun, ArcAssay, ArcInvestigation } from './Core/ArcTypes.ts';
+import { MutableArray } from '@fable-org/fable-library-ts/Util.ts';
+import { Contract } from './Contract/Contract.ts';
+import { FSharpResult$2_$union } from '@fable-org/fable-library-ts/Result.ts';
+import { int32 } from '@fable-org/fable-library-ts/Int32.ts';
+import { Datamap } from './Core/Datamap.ts';
+import { FileSystemTree_$union } from './FileSystem/FileSystemTree.ts';
+import { FSharpList } from '@fable-org/fable-library-ts/List.ts';
+import { FSharpMap } from '@fable-org/fable-library-ts/Map.ts';
+import { CWLProcessingUnit_$union } from './CWL/CWLProcessingUnit.ts';
+import { CWLParameterReference } from './CWL/ParameterReference.ts';
+import { Remark, Comment$ } from './Core/Comment.ts';
+import { Person } from './Core/Person.ts';
+import { Publication } from './Core/Publication.ts';
+import { OntologySourceReference } from './Core/OntologySourceReference.ts';
+import { ValidationPackagesConfig } from './ValidationPackages/ValidationPackagesConfig.ts';
+import { WorkflowGraphIndex, GraphBuildIssue, WorkflowGraph } from './WorkflowGraph/GraphTypes.ts';
+import { TypeInfo } from '@fable-org/fable-library-ts/Reflection.ts';
 export declare class ARC extends ArcInvestigation {
     _license: Option<License>;
     _fs: FileSystem;
-    "init@133": int32;
+    "init@145": 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, fs?: FileSystem, license?: License): ARC;
-    TryWriteAsync(arcPath: string, forceOverwrite?: boolean): Promise<FSharpResult$2_$union<Contract[], string[]>>;
-    TryUpdateAsync(arcPath: string, forceOverwrite?: boolean): Promise<FSharpResult$2_$union<Contract[], string[]>>;
+    TryWriteAsync(arcPath: string, forceOverwrite?: boolean): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
+    TryUpdateAsync(arcPath: string, forceOverwrite?: boolean): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
     SetLicenseFulltext(fulltext: string, path?: string): void;
-    static tryLoadAsync(arcPath: string): Promise<FSharpResult$2_$union<ARC, string[]>>;
-    GetAssayRemoveContracts(assayIdentifier: string): Contract[];
-    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[]>>;
+    static tryLoadAsync(arcPath: string): Promise<FSharpResult$2_$union<ARC, MutableArray<string>>>;
+    GetAssayRemoveContracts(assayIdentifier: string): MutableArray<Contract>;
+    GetRunRemoveContracts(runIdentifier: string): MutableArray<Contract>;
+    GetWorkflowRemoveContracts(workflowIdentifier: string): MutableArray<Contract>;
+    TryRemoveAssayAsync(arcPath: string, assayIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
+    TryRemoveRunAsync(arcPath: string, runIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
+    TryRemoveWorkflowAsync(arcPath: string, workflowIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<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[]>>;
+    TryRenameRunAsync(arcPath: string, oldRunIdentifier: string, newRunIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
+    TryRenameWorkflowAsync(arcPath: string, oldWorkflowIdentifier: string, newWorkflowIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<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(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[]>>;
-    GetStudyRenameContracts(oldStudyIdentifier: string, newStudyIdentifier: string): Contract[];
-    TryRenameStudyAsync(arcPath: string, oldStudyIdentifier: string, newStudyIdentifier: string): Promise<FSharpResult$2_$union<Contract[], string[]>>;
+    GetAssayRenameContracts(oldAssayIdentifier: string, newAssayIdentifier: string): MutableArray<Contract>;
+    GetRunRenameContracts(oldRunIdentifier: string, newRunIdentifier: string): MutableArray<Contract>;
+    GetWorkflowRenameContracts(oldWorkflowIdentifier: string, newWorkflowIdentifier: string): MutableArray<Contract>;
+    TryRenameAssayAsync(arcPath: string, oldAssayIdentifier: string, newAssayIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
+    GetStudyRemoveContracts(studyIdentifier: string): MutableArray<Contract>;
+    TryRemoveStudyAsync(arcPath: string, studyIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
+    GetStudyRenameContracts(oldStudyIdentifier: string, newStudyIdentifier: string): MutableArray<Contract>;
+    TryRenameStudyAsync(arcPath: string, oldStudyIdentifier: string, newStudyIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
     WriteAsync(arcPath: string): Promise<void>;
     UpdateAsync(arcPath: string): Promise<void>;
     RemoveAssayAsync(arcPath: string, assayIdentifier: string): Promise<void>;
@@ -60,55 +61,114 @@ export declare class ARC extends ArcInvestigation {
     RenameStudyAsync(arcPath: string, oldStudyIdentifier: string, newStudyIdentifier: string): Promise<void>;
     static loadAsync(arcPath: string): Promise<ARC>;
     MakeDataFilesAbsolute(): void;
-    static fromFilePaths(filePaths: string[]): ARC;
-    SetFilePaths(filePaths: string[]): void;
-    GetReadContracts(): Contract[];
-    SetISAFromContracts(contracts: Contract[]): void;
+    /**
+     * Add assay folder to the ARC.FileSystem and update the ARC.ISA with the new assay metadata
+     */
+    static fromFilePaths(filePaths: MutableArray<string>): ARC;
+    SetFilePaths(filePaths: MutableArray<string>): void;
+    GetReadContracts(): MutableArray<Contract>;
+    /**
+     * This function creates the ARC-model from fullfilled READ contracts. The necessary READ contracts can be created with `ARC.getReadContracts`.
+     */
+    SetISAFromContracts(contracts: MutableArray<Contract>): void;
     UpdateFileSystem(): void;
-    GetWriteContracts(skipUpdateFS?: boolean): Contract[];
-    GetUpdateContracts(skipUpdateFS?: boolean): Contract[];
-    GetGitInitContracts(branch?: string, repositoryAddress?: string, defaultGitignore?: boolean, defaultGitattributes?: boolean): Contract[];
+    /**
+     * This function returns the all write Contracts for the current state of the ARC. ISA contracts do contain the object data as spreadsheets, while the other contracts only contain the path.
+     *
+     * If datamapFile is set to true, a write contract for the datamap file will be included for each study and assay.
+     */
+    GetWriteContracts(skipUpdateFS?: boolean): MutableArray<Contract>;
+    /**
+     * This function returns the all update Contracts for the current state of the ARC. Only update contracts for those ISA objects that have been changed will be returned.
+     * If an ISA object was added to the ARC, instead a write contract for the complete object folder will be returned.
+     *
+     * An obect is considered changed if its hash code has changed compared with the StaticHash. An object is considered added if its StaticHash code is 0.
+     *
+     * ISA contracts do contain the object data as spreadsheets, while the other contracts only contain the path.
+     */
+    GetUpdateContracts(skipUpdateFS?: boolean): MutableArray<Contract>;
+    GetGitInitContracts(branch?: string, repositoryAddress?: string, defaultGitignore?: boolean, defaultGitattributes?: boolean): MutableArray<Contract>;
     static getCloneContract(remoteUrl: string, merge?: boolean, branch?: string, token?: [string, string], nolfs?: boolean): Contract;
     Copy(): ARC;
+    /**
+     * Returns the FileSystemTree of the ARC with only the registered files and folders included.
+     */
     GetRegisteredPayload(IgnoreHidden?: boolean): FileSystemTree_$union;
+    /**
+     * Returns the FileSystemTree of the ARC with only and folders included that are considered additional payload.
+     */
     GetAdditionalPayload(IgnoreHidden?: boolean): FileSystemTree_$union;
     static get DefaultContracts(): FSharpMap<string, Contract>;
     static fromDeprecatedROCrateJsonString(s: string): ARC;
     static fromROCrateJsonString(s: string): ARC;
     ToROCrateJsonString(spaces?: int32, ignoreBrokenWR?: boolean): string;
+    /**
+     * exports in json-ld format
+     */
     static toROCrateJsonString(spaces?: int32, ignoreBrokenWR?: boolean): ((arg0: ARC) => string);
     GetLicenseWriteContract(): Contract;
+    /**
+     * Returns the write contract for the input ValidationPackagesConfig object.
+     *
+     * This will mutate the ARC file system to include the `.arc/validation_packages.yml` file if it is not already included.
+     */
     GetValidationPackagesConfigWriteContract(vpc: ValidationPackagesConfig): Contract;
+    /**
+     * Returns the delete contract for `.arc/validation_packages.yml`
+     *
+     * If the ARC file system includes the `.arc/validation_packages.yml` file, it is removed.
+     */
     GetValidationPackagesConfigDeleteContract(vpc: ValidationPackagesConfig): Contract;
+    /**
+     * Returns the read contract for `.arc/validation_packages.yml`
+     */
     GetValidationPackagesConfigReadContract(): Contract;
+    /**
+     * Returns the ValidationPackagesConfig object from the given read contract if possible, otherwise returns None/null.
+     */
     GetValidationPackagesConfigFromReadContract(contract: Contract): Option<ValidationPackagesConfig>;
-    ToFilePaths(removeRoot?: boolean, skipUpdateFS?: boolean): string[];
+    ToFilePaths(removeRoot?: boolean, skipUpdateFS?: boolean): MutableArray<string>;
+    /**
+     * Builds workflow graphs for all workflows in this ARC.
+     * Returns a list of workflow identifier and Result pairs, where each Result contains
+     * either a successfully built WorkflowGraph or a GraphBuildIssue describing the failure.
+     */
     BuildWorkflowGraphs(): [string, FSharpResult$2_$union<WorkflowGraph, GraphBuildIssue>][];
+    /**
+     * Builds workflow graphs for all runs in this ARC.
+     * Returns a list of run identifier and Result pairs, where each Result contains
+     * either a successfully built WorkflowGraph or a GraphBuildIssue describing the failure.
+     */
     BuildRunGraphs(): [string, FSharpResult$2_$union<WorkflowGraph, GraphBuildIssue>][];
+    /**
+     * Builds and returns the complete WorkflowGraphIndex containing workflow graphs
+     * for both workflows and runs in this ARC.
+     */
     BuildAllProcessingUnitGraphs(): WorkflowGraphIndex;
 }
 export declare function ARC_$reflection(): TypeInfo;
 export declare function ARC_$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$[], remarks?: Remark[], fs?: FileSystem, license?: License): ARC;
-export declare function ARCAux_getArcAssaysFromContracts(contracts: Contract[]): ArcAssay[];
-export declare function ARCAux_getArcStudiesFromContracts(contracts: Contract[]): [ArcStudy, FSharpList<ArcAssay>][];
-export declare function ARCAux_getArcWorkflowsFromContracts(contracts: Contract[]): ArcWorkflow[];
-export declare function ARCAux_getArcRunsFromContracts(contracts: Contract[]): ArcRun[];
-export declare function ARCAux_getAssayDatamapFromContracts(assayIdentifier: string, contracts: Contract[]): Option<Datamap>;
-export declare function ARCAux_getStudyDatamapFromContracts(studyIdentifier: string, contracts: Contract[]): Option<Datamap>;
-export declare function ARCAux_getWorkflowDatamapFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<Datamap>;
-export declare function ARCAux_getRunDatamapFromContracts(runIdentifier: string, contracts: Contract[]): Option<Datamap>;
-export declare function ARCAux_getWorkflowCWLFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<CWLProcessingUnit_$union>;
-export declare function ARCAux_getRunCWLFromContracts(runIdentifier: string, contracts: Contract[]): Option<CWLProcessingUnit_$union>;
-export declare function ARCAux_getRunYMLFromContracts(runIdentifier: string, contracts: Contract[]): Option<CWLParameterReference[]>;
+export declare function ARCAux_getArcAssaysFromContracts(contracts: MutableArray<Contract>): MutableArray<ArcAssay>;
+export declare function ARCAux_getArcStudiesFromContracts(contracts: MutableArray<Contract>): MutableArray<[ArcStudy, FSharpList<ArcAssay>]>;
+export declare function ARCAux_getArcWorkflowsFromContracts(contracts: MutableArray<Contract>): MutableArray<ArcWorkflow>;
+export declare function ARCAux_getArcRunsFromContracts(contracts: MutableArray<Contract>): MutableArray<ArcRun>;
+export declare function ARCAux_getAssayDatamapFromContracts(assayIdentifier: string, contracts: MutableArray<Contract>): Option<Datamap>;
+export declare function ARCAux_getStudyDatamapFromContracts(studyIdentifier: string, contracts: MutableArray<Contract>): Option<Datamap>;
+export declare function ARCAux_getWorkflowDatamapFromContracts(workflowIdentifier: string, contracts: MutableArray<Contract>): Option<Datamap>;
+export declare function ARCAux_getRunDatamapFromContracts(runIdentifier: string, contracts: MutableArray<Contract>): Option<Datamap>;
+export declare function ARCAux_getWorkflowCWLFromContracts(workflowIdentifier: string, contracts: MutableArray<Contract>): Option<CWLProcessingUnit_$union>;
+export declare function ARCAux_getRunCWLFromContracts(runIdentifier: string, contracts: MutableArray<Contract>): Option<CWLProcessingUnit_$union>;
+export declare function ARCAux_getRunYMLFromContracts(runIdentifier: string, contracts: MutableArray<Contract>): Option<CWLParameterReference[]>;
 /**
  * Builds a lookup map of normalized CWL file paths to decoded CWLProcessingUnit instances from CWL-typed contracts.
  */
-export declare function ARCAux_getCWLByPathFromContracts(contracts: Contract[]): FSharpMap<string, CWLProcessingUnit_$union>;
+export declare function ARCAux_getCWLByPathFromContracts(contracts: MutableArray<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_getArcInvestigationFromContracts(contracts: MutableArray<Contract>): ArcInvestigation;
+export declare function ARCAux_getLicenseFromContracts(contracts: MutableArray<Contract>): Option<License>;
 export declare function ARCAux_updateFSByARC(isa: ArcInvestigation, license: Option<License>, fs: FileSystem): FileSystem;
+export declare const ARCAux_defaultContracts: FSharpMap<string, Contract>;
 //# sourceMappingURL=ARC.d.ts.map

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

@@ -1 +1 @@
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