@nfdi4plants/arctrl 3.0.0-beta.9 → 3.0.1

package/dist/ts/ts/WorkflowGraph/Adapters.js

@@ -0,0 +1,94 @@
+import { value } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { ofSeq, empty as empty$1, isEmpty, tryFind } from '../../node_modules/@fable-org/fable-library-js/Map.js';
+import { map, delay, append, collect, empty, singleton } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { normalizePathKey } from '../FileSystem/Path.js';
+import { Workflow_cwlFileNameFromIdentifier, Run_cwlFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
+import { comparePrimitives, getEnumerator, disposeSafe } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { GraphBuildIssue_create_Z2F3B511A, GraphIssueKind_MissingCwlDescription, WorkflowGraphIndex_create_56E060E0 } from './GraphTypes.js';
+import { buildWith } from './Builder.js';
+import { WorkflowGraphBuildOptionsModule_withRootWorkflowFilePath, WorkflowGraphBuildOptionsModule_withRootScope, WorkflowGraphBuildOptionsModule_defaultOptions, WorkflowGraphBuildOptionsModule_withTryResolveRunPath } from './BuildOptions.js';
+import { FSharpResult$2_Ok, FSharpResult$2_Error } from '../../node_modules/@fable-org/fable-library-js/Result.js';
+
+function createCwlLookupFromInvestigation(investigation) {
+  if (investigation != null) {
+    const inv = value(investigation);
+    return ofSeq(map((tupledArg) => [normalizePathKey(tupledArg[0]), tupledArg[1]], delay(() => append(collect((workflow) => {
+      const matchValue = workflow.CWLDescription;
+      if (matchValue == null) {
+        return empty();
+      } else {
+        const cwl = value(matchValue);
+        return singleton([Workflow_cwlFileNameFromIdentifier(workflow.Identifier), cwl]);
+      }
+    }, inv.Workflows), delay(() => collect((run) => {
+      const matchValue_1 = run.CWLDescription;
+      if (matchValue_1 == null) {
+        return empty();
+      } else {
+        const cwl_1 = value(matchValue_1);
+        return singleton([Run_cwlFileNameFromIdentifier(run.Identifier), cwl_1]);
+      }
+    }, inv.Runs))))), {
+      Compare: comparePrimitives
+    });
+  } else {
+    return empty$1({
+      Compare: comparePrimitives
+    });
+  }
+}
+function createResolver(lookup) {
+  if (isEmpty(lookup)) {
+    return void 0;
+  } else {
+    return (path) => tryFind(normalizePathKey(path), lookup);
+  }
+}
+function createMissingDescriptionError(identifier, scopeType) {
+  return GraphBuildIssue_create_Z2F3B511A(GraphIssueKind_MissingCwlDescription(), `No CWLDescription available for ${scopeType} '${identifier}'.`, identifier);
+}
+function ofWorkflow(workflow) {
+  let options_2, options_1;
+  const matchValue = workflow.CWLDescription;
+  if (matchValue != null) {
+    const processingUnit = value(matchValue);
+    return FSharpResult$2_Ok(buildWith((options_2 = (options_1 = WorkflowGraphBuildOptionsModule_withRootScope(workflow.Identifier, WorkflowGraphBuildOptionsModule_defaultOptions), WorkflowGraphBuildOptionsModule_withRootWorkflowFilePath(Workflow_cwlFileNameFromIdentifier(workflow.Identifier), options_1)), WorkflowGraphBuildOptionsModule_withTryResolveRunPath(createResolver(createCwlLookupFromInvestigation(workflow.Investigation)), options_2)), processingUnit));
+  } else {
+    return FSharpResult$2_Error(createMissingDescriptionError(workflow.Identifier, "workflow"));
+  }
+}
+function ofRun(run) {
+  let options_2, options_1;
+  const matchValue = run.CWLDescription;
+  if (matchValue != null) {
+    const processingUnit = value(matchValue);
+    return FSharpResult$2_Ok(buildWith((options_2 = (options_1 = WorkflowGraphBuildOptionsModule_withRootScope(run.Identifier, WorkflowGraphBuildOptionsModule_defaultOptions), WorkflowGraphBuildOptionsModule_withRootWorkflowFilePath(Run_cwlFileNameFromIdentifier(run.Identifier), options_1)), WorkflowGraphBuildOptionsModule_withTryResolveRunPath(createResolver(createCwlLookupFromInvestigation(run.Investigation)), options_2)), processingUnit));
+  } else {
+    return FSharpResult$2_Error(createMissingDescriptionError(run.Identifier, "run"));
+  }
+}
+function ofInvestigation(investigation) {
+  const workflowGraphs = [];
+  const runGraphs = [];
+  let enumerator = getEnumerator(investigation.Workflows);
+  try {
+    while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+      const workflow = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+      void workflowGraphs.push([workflow.Identifier, ofWorkflow(workflow)]);
+    }
+  } finally {
+    disposeSafe(enumerator);
+  }
+  let enumerator_1 = getEnumerator(investigation.Runs);
+  try {
+    while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+      const run = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
+      void runGraphs.push([run.Identifier, ofRun(run)]);
+    }
+  } finally {
+    disposeSafe(enumerator_1);
+  }
+  return WorkflowGraphIndex_create_56E060E0(workflowGraphs, runGraphs);
+}
+
+export { createCwlLookupFromInvestigation, createMissingDescriptionError, createResolver, ofInvestigation, ofRun, ofWorkflow };

package/dist/ts/ts/WorkflowGraph/BuildOptions.d.ts

@@ -0,0 +1,37 @@
+import { Record } from '@fable-org/fable-library-js/Types.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+export declare class WorkflowGraphBuildOptions extends Record {
+    readonly RootScope: string;
+    readonly RootWorkflowFilePath: Option<string>;
+    readonly TryResolveRunPath: Option<((arg0: string) => Option<CWLProcessingUnit_$union>)>;
+    readonly StrictUnresolvedRunReferences: boolean;
+    readonly ExpandNestedWorkflows: boolean;
+    constructor(RootScope: string, RootWorkflowFilePath: Option<string>, TryResolveRunPath: Option<((arg0: string) => Option<CWLProcessingUnit_$union>)>, StrictUnresolvedRunReferences: boolean, ExpandNestedWorkflows: boolean);
+}
+export declare function WorkflowGraphBuildOptions_$reflection(): TypeInfo;
+export declare const WorkflowGraphBuildOptionsModule_defaultOptions: WorkflowGraphBuildOptions;
+/**
+ * Sets the root scope name used as the top-level graph identifier.
+ */
+export declare function WorkflowGraphBuildOptionsModule_withRootScope(rootScope: string, options: WorkflowGraphBuildOptions): WorkflowGraphBuildOptions;
+/**
+ * Sets the file path of the root workflow CWL file, used for resolving relative run references.
+ */
+export declare function WorkflowGraphBuildOptionsModule_withRootWorkflowFilePath(rootWorkflowFilePath: Option<string>, options: WorkflowGraphBuildOptions): WorkflowGraphBuildOptions;
+/**
+ * Sets the optional function used to resolve CWL run path references to CWLProcessingUnit instances.
+ */
+export declare function WorkflowGraphBuildOptionsModule_withTryResolveRunPath(tryResolveRunPath: Option<((arg0: string) => Option<CWLProcessingUnit_$union>)>, options: WorkflowGraphBuildOptions): WorkflowGraphBuildOptions;
+/**
+ * Sets whether unresolved run references should produce diagnostic warnings.
+ * When true, a missing resolver or unresolvable path generates a diagnostic issue.
+ */
+export declare function WorkflowGraphBuildOptionsModule_withStrictUnresolvedRunReferences(strict: boolean, options: WorkflowGraphBuildOptions): WorkflowGraphBuildOptions;
+/**
+ * Sets whether nested workflows should be fully expanded in the graph.
+ * When true, steps in nested workflows are recursively built.
+ */
+export declare function WorkflowGraphBuildOptionsModule_withExpandNestedWorkflows(expandNestedWorkflows: boolean, options: WorkflowGraphBuildOptions): WorkflowGraphBuildOptions;
+//# sourceMappingURL=BuildOptions.d.ts.map

package/dist/ts/ts/WorkflowGraph/BuildOptions.d.ts.map

@@ -0,0 +1 @@
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package/dist/ts/ts/WorkflowGraph/BuildOptions.js

@@ -0,0 +1,35 @@
+import { Record } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+import { CWLProcessingUnit_$reflection } from '../CWL/CWLProcessingUnit.js';
+import { record_type, string_type, option_type, bool_type, lambda_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+
+class WorkflowGraphBuildOptions extends Record {
+  constructor(RootScope, RootWorkflowFilePath, TryResolveRunPath, StrictUnresolvedRunReferences, ExpandNestedWorkflows) {
+    super();
+    this.RootScope = RootScope;
+    this.RootWorkflowFilePath = RootWorkflowFilePath;
+    this.TryResolveRunPath = TryResolveRunPath;
+    this.StrictUnresolvedRunReferences = StrictUnresolvedRunReferences;
+    this.ExpandNestedWorkflows = ExpandNestedWorkflows;
+  }
+}
+function WorkflowGraphBuildOptions_$reflection() {
+  return record_type("ARCtrl.WorkflowGraph.WorkflowGraphBuildOptions", [], WorkflowGraphBuildOptions, () => [["RootScope", string_type], ["RootWorkflowFilePath", option_type(string_type)], ["TryResolveRunPath", option_type(lambda_type(string_type, option_type(CWLProcessingUnit_$reflection())))], ["StrictUnresolvedRunReferences", bool_type], ["ExpandNestedWorkflows", bool_type]]);
+}
+const WorkflowGraphBuildOptionsModule_defaultOptions = new WorkflowGraphBuildOptions("root", void 0, void 0, false, true);
+function WorkflowGraphBuildOptionsModule_withRootScope(rootScope, options) {
+  return new WorkflowGraphBuildOptions(rootScope, options.RootWorkflowFilePath, options.TryResolveRunPath, options.StrictUnresolvedRunReferences, options.ExpandNestedWorkflows);
+}
+function WorkflowGraphBuildOptionsModule_withRootWorkflowFilePath(rootWorkflowFilePath, options) {
+  return new WorkflowGraphBuildOptions(options.RootScope, rootWorkflowFilePath, options.TryResolveRunPath, options.StrictUnresolvedRunReferences, options.ExpandNestedWorkflows);
+}
+function WorkflowGraphBuildOptionsModule_withTryResolveRunPath(tryResolveRunPath, options) {
+  return new WorkflowGraphBuildOptions(options.RootScope, options.RootWorkflowFilePath, tryResolveRunPath, options.StrictUnresolvedRunReferences, options.ExpandNestedWorkflows);
+}
+function WorkflowGraphBuildOptionsModule_withStrictUnresolvedRunReferences(strict, options) {
+  return new WorkflowGraphBuildOptions(options.RootScope, options.RootWorkflowFilePath, options.TryResolveRunPath, strict, options.ExpandNestedWorkflows);
+}
+function WorkflowGraphBuildOptionsModule_withExpandNestedWorkflows(expandNestedWorkflows, options) {
+  return new WorkflowGraphBuildOptions(options.RootScope, options.RootWorkflowFilePath, options.TryResolveRunPath, options.StrictUnresolvedRunReferences, expandNestedWorkflows);
+}
+
+export { WorkflowGraphBuildOptions, WorkflowGraphBuildOptionsModule_defaultOptions, WorkflowGraphBuildOptionsModule_withExpandNestedWorkflows, WorkflowGraphBuildOptionsModule_withRootScope, WorkflowGraphBuildOptionsModule_withRootWorkflowFilePath, WorkflowGraphBuildOptionsModule_withStrictUnresolvedRunReferences, WorkflowGraphBuildOptionsModule_withTryResolveRunPath, WorkflowGraphBuildOptions_$reflection };

package/dist/ts/ts/WorkflowGraph/Builder.d.ts

@@ -0,0 +1,160 @@
+import { Record } from '@fable-org/fable-library-js/Types.js';
+import { PortDirection_$union, ProcessingUnitKind_$union, EdgeKind_$union, WorkflowGraphEdge, WorkflowGraphNode, GraphIssueKind_$union, WorkflowGraph } from './GraphTypes.js';
+import { FSharpSet } from '@fable-org/fable-library-js/Set.js';
+import { FSharpMap } from '@fable-org/fable-library-js/Map.js';
+import { WorkflowStep, WorkflowStepRun_$union } from '../CWL/WorkflowSteps.js';
+import { WorkflowGraphBuildOptions } from './BuildOptions.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { IEquatable } from '@fable-org/fable-library-js/Util.js';
+import { DynamicObj } from '../fable_modules/DynamicObj.7.1.0/DynamicObj.fs.js';
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.js';
+import { CWLToolDescription } from '../CWL/ToolDescription.js';
+import { CWLExpressionToolDescription } from '../CWL/ExpressionToolDescription.js';
+import { CWLOperationDescription } from '../CWL/OperationDescription.js';
+import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.js';
+export declare class BuildState extends Record {
+    readonly Graph: WorkflowGraph;
+    NodeIds: FSharpSet<string>;
+    EdgeIds: FSharpSet<string>;
+    RunResolutionStack: FSharpSet<string>;
+    RunResolutionCache: FSharpMap<string, WorkflowStepRun_$union>;
+    RunNodeCache: FSharpMap<string, string>;
+    readonly Options: WorkflowGraphBuildOptions;
+    constructor(Graph: WorkflowGraph, NodeIds: FSharpSet<string>, EdgeIds: FSharpSet<string>, RunResolutionStack: FSharpSet<string>, RunResolutionCache: FSharpMap<string, WorkflowStepRun_$union>, RunNodeCache: FSharpMap<string, string>, Options: WorkflowGraphBuildOptions);
+}
+export declare function BuildState_$reflection(): TypeInfo;
+export declare class RunResolutionResult extends Record implements IEquatable<RunResolutionResult> {
+    readonly ResolvedRun: WorkflowStepRun_$union;
+    readonly ResolvedFromPath: Option<string>;
+    readonly AttemptedLookup: boolean;
+    readonly ResolutionPathKeys: string[];
+    constructor(ResolvedRun: WorkflowStepRun_$union, ResolvedFromPath: Option<string>, AttemptedLookup: boolean, ResolutionPathKeys: string[]);
+}
+export declare function RunResolutionResult_$reflection(): TypeInfo;
+/**
+ * Creates an empty WorkflowGraph with the given root node ID.
+ */
+export declare function createGraph(rootNodeId: string): WorkflowGraph;
+/**
+ * Creates initial build state from options and root node ID.
+ */
+export declare function createState(options: WorkflowGraphBuildOptions, rootNodeId: string): BuildState;
+/**
+ * Appends a diagnostic issue to the graph's diagnostics list.
+ */
+export declare function addDiagnostic(state: BuildState, kind: GraphIssueKind_$union, message: string, scope: Option<string>, reference: Option<string>): void;
+/**
+ * Checks if a node ID is already registered in the build state.
+ */
+export declare function hasNode(state: BuildState, nodeId: string): boolean;
+/**
+ * Adds a node to the graph if not already present.
+ */
+export declare function addNode(state: BuildState, node: WorkflowGraphNode): void;
+/**
+ * Adds an edge to the graph if not already present.
+ */
+export declare function addEdge(state: BuildState, edge: WorkflowGraphEdge): void;
+/**
+ * Creates and adds an edge with a given kind, source, target, and optional label.
+ */
+export declare function addEdgeByType(state: BuildState, kind: EdgeKind_$union, sourceNodeId: string, targetNodeId: string, label: Option<string>): void;
+/**
+ * Builds a DynamicObj metadata instance from key-value pairs where values are present.
+ */
+export declare function createMetadata(pairs: FSharpList<[string, Option<any>]>): Option<DynamicObj>;
+/**
+ * Creates and adds a processing unit node to the graph. Returns the node ID.
+ */
+export declare function addProcessingUnitNode(state: BuildState, scope: string, kind: ProcessingUnitKind_$union, label: string, ownerNodeId: Option<string>, reference: Option<string>, metadata: Option<DynamicObj>): string;
+/**
+ * Creates and adds a port node (input or output) owned by a given node. Returns the node ID.
+ */
+export declare function addPortNode(state: BuildState, ownerNodeId: string, direction: PortDirection_$union, portId: string, label: string): string;
+/**
+ * Creates a step node for a CWL workflow step, adds a Contains edge from the workflow. Returns the step node ID.
+ */
+export declare function addStepNode(state: BuildState, scope: string, workflowNodeId: string, step: WorkflowStep): string;
+/**
+ * Adds all input and output port nodes for a CWL workflow.
+ */
+export declare function addWorkflowPorts(state: BuildState, workflowNodeId: string, workflow: CWLWorkflowDescription): void;
+/**
+ * Adds all input and output port nodes for a CWL CommandLineTool.
+ */
+export declare function addToolPorts(state: BuildState, toolNodeId: string, tool: CWLToolDescription): void;
+/**
+ * Adds all input and output port nodes for a CWL ExpressionTool.
+ */
+export declare function addExpressionToolPorts(state: BuildState, toolNodeId: string, tool: CWLExpressionToolDescription): void;
+/**
+ * Adds all input and output port nodes for a CWL Operation.
+ */
+export declare function addOperationPorts(state: BuildState, operationNodeId: string, operation: CWLOperationDescription): void;
+/**
+ * Adds all input and output port nodes for a workflow step.
+ */
+export declare function addStepPorts(state: BuildState, stepNodeId: string, step: WorkflowStep): void;
+/**
+ * Strips '#' prefixes, query strings, and fragment identifiers from a reference string.
+ */
+export declare function trimToNameCandidate(value: string): string;
+/**
+ * Returns true if a run path ends in '.cwl'.
+ */
+export declare function isCwlReference(runPath: string): boolean;
+/**
+ * Extracts the basename of a path and strips the '.cwl' extension.
+ */
+export declare function tryBasenameNoCwlExtension(value: string): Option<string>;
+/**
+ * Selects the first available processing unit display name from dynamic metadata:
+ * `name` first, then `id`; each value is normalized to a CWL basename.
+ */
+export declare function tryGetProcessingUnitName<$a extends DynamicObj>(processingUnit: $a): Option<string>;
+/**
+ * Picks the first non-None candidate label, or falls back to a default.
+ */
+export declare function chooseLabel(fallback: string, candidates: FSharpList<Option<string>>): string;
+/**
+ * Generates multiple path candidates to try when resolving a run reference.
+ */
+export declare function getRunPathCandidates(workflowFilePath: Option<string>, runPath: string): string[];
+/**
+ * Attempts to resolve a CWL run string reference to an actual CWLProcessingUnit via the configured resolver.
+ */
+export declare function resolveRunString(state: BuildState, workflowFilePath: Option<string>, runPath: string): RunResolutionResult;
+/**
+ * Recursively builds graph nodes and edges for a CWLProcessingUnit (CommandLineTool, ExpressionTool, Operation, or Workflow).
+ */
+export declare function buildProcessingUnit(state: BuildState, scope: string, workflowFilePath: Option<string>, ownerNodeId: Option<string>, isRoot: boolean, processingUnit: CWLProcessingUnit_$union): string;
+/**
+ * Resolves and builds the graph representation of a workflow step's run field.
+ */
+export declare function buildRunNode(state: BuildState, runScope: string, stepNodeId: string, workflowFilePath: Option<string>, run: WorkflowStepRun_$union): [WorkflowStepRun_$union, string];
+/**
+ * Connects step input ports to their sources (workflow inputs or other step outputs).
+ */
+export declare function wireStepInputs(state: BuildState, scope: string, workflowNodeId: string, step: WorkflowStep): void;
+/**
+ * Connects workflow output ports to their sources (step outputs or workflow inputs).
+ */
+export declare function wireWorkflowOutputs(state: BuildState, scope: string, workflowNodeId: string, workflow: CWLWorkflowDescription): void;
+/**
+ * Iterates over all workflow steps, creating nodes, resolving run targets, and wiring data flows.
+ */
+export declare function buildWorkflowSteps(state: BuildState, scope: string, workflowFilePath: Option<string>, workflowNodeId: string, workflow: CWLWorkflowDescription): void;
+/**
+ * Builds a WorkflowGraph from a CWLProcessingUnit using the specified build options.
+ * This is the primary entry point for graph construction with full control over scope,
+ * run resolution, nested workflow expansion, and strictness.
+ */
+export declare function buildWith(options: WorkflowGraphBuildOptions, processingUnit: CWLProcessingUnit_$union): WorkflowGraph;
+/**
+ * Builds a WorkflowGraph from a CWLProcessingUnit using default build options.
+ * Convenience wrapper around buildWith with WorkflowGraphBuildOptions.defaultOptions.
+ */
+export declare function build(processingUnit: CWLProcessingUnit_$union): WorkflowGraph;
+//# sourceMappingURL=Builder.d.ts.map

package/dist/ts/ts/WorkflowGraph/Builder.d.ts.map

@@ -0,0 +1 @@
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