@galaxy-tool-util/schema 0.2.0 → 0.4.0

package/dist/workflow/raw/native.effect.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/raw/native.effect.js

@@ -358,9 +358,9 @@ export const NativeGalaxyWorkflowSchema = Schema.Struct({
     name: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
     class: Schema.Literal("NativeGalaxyWorkflow"),
     /** Format marker. Always the string ``"true"``. */
-    a_galaxy_workflow: Schema.String,
+    a_galaxy_workflow: Schema.Literal("true"),
     /** Format version. Always ``"0.1"`` currently. In the JSON document this field is written as ``format-version``. */
-    "format-version": Schema.String,
+    "format-version": Schema.Literal("0.1"),
     /** Human-readable workflow description. */
     annotation: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
     /** Classification tags for the workflow. */
@@ -457,9 +457,7 @@ export const NativeStepSchema = Schema.Struct({
     /** Post-job actions applied to outputs after tool execution. Keys are compound strings of the form ``{ActionType}{OutputName}``. Values are NativePostJobAction objects. */
     post_job_actions: Schema.optional(Schema.Union(Schema.Record({ key: Schema.String, value: NativePostJobActionSchema }), Schema.Null)),
     /** Embedded subworkflow definition. A complete native workflow document (with ``a_galaxy_workflow``, ``format-version``, ``steps``, etc.) nested inside this step. */
-    subworkflow: Schema.optional(Schema.Union(Schema.suspend(() => NativeGalaxyWorkflowSchema).annotations({
-        identifier: "NativeGalaxyWorkflowSchema",
-    }), Schema.Null)),
+    subworkflow: Schema.optional(Schema.Union(NativeGalaxyWorkflowSchema, Schema.Null)),
     /** Embedded tool definition for user-defined (dynamic) tools. Present when the step uses a ``GalaxyUserTool`` instead of a registered tool. Contains the full tool definition including ``class: GalaxyU... */
     tool_representation: Schema.optional(Schema.Union(Schema.Record({ key: Schema.String, value: Schema.Unknown }), Schema.Null)),
     /** Default values for step inputs. Keys are parameter names, values are objects with a ``default`` key. */

package/dist/workflow/raw/native.effect.js.map

@@ -1 +1 @@
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package/dist/workflow/report-models.d.ts

@@ -0,0 +1,412 @@
+/**
+ * Structured report models for CLI and API output.
+ *
+ * These types mirror Python's `galaxy.tool_util.workflow_state._report_models`
+ * exactly — field names are snake_case, status literals match, and JSON shape
+ * is identical so that the same frontend rendering code works for both.
+ *
+ * Hierarchy:
+ *   Step-level  →  Single-workflow wrappers  →  Tree-level reports
+ */
+export type StepStatus = "ok" | "fail" | "skip_tool_not_found" | "skip_replacement_params";
+export declare const SKIP_STATUSES: ReadonlySet<StepStatus>;
+export interface ValidationStepResult {
+    step: string;
+    tool_id: string | null;
+    version: string | null;
+    status: StepStatus;
+    errors: string[];
+}
+export interface CleanStepResult {
+    step: string;
+    tool_id: string | null;
+    version: string | null;
+    removed_keys: string[];
+    skipped: boolean;
+    skip_reason: string;
+    display_label: string;
+}
+export interface ResolvedOutputType {
+    name: string;
+    collection_type: string | null;
+}
+export interface ConnectionResult {
+    source_step: string;
+    source_output: string;
+    target_step: string;
+    target_input: string;
+    status: "ok" | "invalid" | "skip";
+    mapping: string | null;
+    errors: string[];
+}
+export interface ConnectionStepResult {
+    step: string;
+    tool_id: string | null;
+    version: string | null;
+    step_type: string;
+    map_over: string | null;
+    connections: ConnectionResult[];
+    resolved_outputs: ResolvedOutputType[];
+    errors: string[];
+}
+export interface ConnectionValidationReport {
+    valid: boolean;
+    step_results: ConnectionStepResult[];
+    summary: Record<string, number>;
+    has_details: boolean;
+}
+export interface WorkflowEntry {
+    relative_path: string;
+    format: string;
+    category: string;
+}
+export interface WorkflowIndex {
+    directory: string;
+    workflows: WorkflowEntry[];
+}
+export interface SingleValidationReport {
+    workflow: string;
+    results: ValidationStepResult[];
+    connection_report: ConnectionValidationReport | null;
+    skipped_reason: SkipWorkflowReason | null;
+    structure_errors: string[];
+    encoding_errors: string[];
+    summary: {
+        ok: number;
+        fail: number;
+        skip: number;
+    };
+    clean_report?: SingleCleanReport | null;
+}
+export interface SingleLintReport {
+    workflow: string;
+    lint_errors: number;
+    lint_warnings: number;
+    results: ValidationStepResult[];
+    structure_errors: string[];
+    encoding_errors: string[];
+    summary: {
+        lint_errors: number;
+        lint_warnings: number;
+        state_ok: number;
+        state_fail: number;
+        state_skip: number;
+    };
+}
+export interface SingleCleanReport {
+    workflow: string;
+    results: CleanStepResult[];
+    total_removed: number;
+    steps_with_removals: number;
+    before_content?: string | null;
+    after_content?: string | null;
+}
+export type DiffType = "value_mismatch" | "missing_in_roundtrip" | "missing_in_original" | "connection_mismatch" | "position_mismatch" | "label_mismatch" | "annotation_mismatch" | "comment_mismatch" | "step_missing";
+export type DiffSeverity = "error" | "benign";
+export interface BenignArtifact {
+    reason: string;
+    proven_by: string[];
+}
+export interface StepDiff {
+    step_path: string;
+    key_path: string;
+    diff_type: DiffType;
+    severity: DiffSeverity;
+    description: string;
+    original_value: unknown;
+    roundtrip_value: unknown;
+    benign_artifact: BenignArtifact | null;
+}
+export type SkipWorkflowReason = "legacy_encoding";
+export type FailureClass = "tool_not_found" | "native_validation" | "conversion_error" | "type_not_handled" | "format2_validation" | "reimport_error" | "roundtrip_mismatch" | "subworkflow" | "parse_error" | "other";
+export interface StepResult {
+    step_id: string;
+    tool_id: string | null;
+    success: boolean;
+    failure_class: FailureClass | null;
+    error: string | null;
+    diffs: StepDiff[];
+    format2_state: Record<string, unknown> | null;
+    format2_connections: Record<string, unknown> | null;
+}
+export interface RoundTripResult {
+    workflow_name: string;
+    direction: string;
+    step_results: StepResult[];
+}
+export interface StepIdMappingResult {
+    mapping: Record<string, string | null>;
+    match_methods: Record<string, string>;
+}
+export interface RoundTripValidationResult {
+    workflow_path: string;
+    category: string;
+    conversion_result: RoundTripResult | null;
+    diffs: StepDiff[] | null;
+    step_id_mapping: StepIdMappingResult | null;
+    stale_clean_results: CleanStepResult[] | null;
+    error: string | null;
+    skipped_reason: SkipWorkflowReason | null;
+    structure_errors: string[];
+    encoding_errors: string[];
+    readonly error_diffs: StepDiff[];
+    readonly benign_diffs: StepDiff[];
+    readonly ok: boolean;
+    readonly status: string;
+    readonly conversion_failure_lines: string[];
+    readonly summary_line: string;
+}
+export interface SingleRoundTripReport {
+    workflow: string;
+    result: RoundTripValidationResult;
+    before_content?: string | null;
+    after_content?: string | null;
+}
+export interface SingleExportReport {
+    workflow: string;
+    ok: boolean;
+    steps_converted: number;
+    steps_fallback: number;
+    readonly summary: Record<string, number>;
+}
+export interface StepEncodeStatus {
+    step_id: string;
+    step_label: string | null;
+    tool_id: string | null;
+    encoded: boolean;
+    error: string | null;
+}
+export interface ToNativeResult {
+    native_dict: Record<string, unknown>;
+    steps: StepEncodeStatus[];
+    readonly all_encoded: boolean;
+    readonly summary: string;
+}
+export type WorkflowSourceFormat = "native" | "format2";
+export interface ExportResult {
+    source_path: string;
+    output_path: string;
+    source_format: WorkflowSourceFormat;
+    target_format: WorkflowSourceFormat;
+    report: SingleExportReport | ToNativeResult;
+    dry_run: boolean;
+    content: string | null;
+}
+export interface ConvertResult extends ExportResult {
+    removed_path: string;
+}
+export interface WorkflowValidationResult {
+    path: string;
+    category: string;
+    name: string;
+    error: string | null;
+    skipped_reason: SkipWorkflowReason | null;
+    results: ValidationStepResult[];
+    connection_report: null;
+    summary: {
+        ok: number;
+        fail: number;
+        skip: number;
+    } | null;
+    failures: {
+        step: string;
+        tool_id: string | null;
+        message: string;
+    }[] | null;
+}
+export interface LintWorkflowResult {
+    path: string;
+    category: string;
+    name: string;
+    error: string | null;
+    skipped_reason: SkipWorkflowReason | null;
+    lint_errors: number;
+    lint_warnings: number;
+    results: ValidationStepResult[];
+    step_counts: {
+        ok: number;
+        fail: number;
+        skip: number;
+    } | null;
+}
+export interface WorkflowCleanResult {
+    path: string;
+    category: string;
+    name: string;
+    error: string | null;
+    skipped_reason: SkipWorkflowReason | null;
+    results: CleanStepResult[];
+    total_removed: number;
+    steps_affected: number;
+}
+export interface CategoryGroup<T> {
+    name: string;
+    results: T[];
+}
+export interface TreeValidationReport {
+    root: string;
+    workflows: WorkflowValidationResult[];
+    categories: CategoryGroup<WorkflowValidationResult>[];
+    all_failures: {
+        workflow: string;
+        step: string;
+        tool_id: string | null;
+        message: string;
+    }[];
+    summary: {
+        ok: number;
+        fail: number;
+        skip: number;
+        error: number;
+        skipped: number;
+    };
+}
+export interface LintTreeReport {
+    root: string;
+    workflows: LintWorkflowResult[];
+    categories: CategoryGroup<LintWorkflowResult>[];
+    summary: {
+        lint_errors: number;
+        lint_warnings: number;
+        state_ok: number;
+        state_fail: number;
+        state_skip: number;
+        errors: number;
+        skipped: number;
+    };
+}
+export interface TreeCleanReport {
+    root: string;
+    workflows: WorkflowCleanResult[];
+    categories: CategoryGroup<WorkflowCleanResult>[];
+    summary: {
+        total_keys: number;
+        affected: number;
+        clean: number;
+        errors: number;
+        skipped: number;
+    };
+}
+/** Compute summary counts for a list of step results. */
+export declare function validationSummary(results: ValidationStepResult[]): {
+    ok: number;
+    fail: number;
+    skip: number;
+};
+/** Build flat failure list from step results (for template rendering). */
+export declare function validationFailures(results: ValidationStepResult[]): {
+    step: string;
+    tool_id: string | null;
+    message: string;
+}[];
+/** Compute display_label matching Python's CleanStepResult. */
+export declare function cleanDisplayLabel(tool_id: string | null, version: string | null): string;
+/** Compute category from a relative path (directory portion, or "(root)"). */
+export declare function categoryOf(relativePath: string): string;
+/** Group results by category, sorted by name. */
+export declare function groupByCategory<T extends {
+    category: string;
+}>(results: T[]): CategoryGroup<T>[];
+export declare function buildSingleValidationReport(workflow: string, results: ValidationStepResult[], opts?: {
+    skipped_reason?: SkipWorkflowReason | null;
+    structure_errors?: string[];
+    encoding_errors?: string[];
+}): SingleValidationReport;
+export declare function buildSingleLintReport(workflow: string, lint_errors: number, lint_warnings: number, results: ValidationStepResult[], opts?: {
+    structure_errors?: string[];
+    encoding_errors?: string[];
+}): SingleLintReport;
+export declare function buildSingleCleanReport(workflow: string, results: CleanStepResult[]): SingleCleanReport;
+export declare function buildWorkflowValidationResult(relativePath: string, stepResults: ValidationStepResult[], opts?: {
+    error?: string | null;
+    skipped_reason?: SkipWorkflowReason | null;
+}): WorkflowValidationResult;
+export declare function buildLintWorkflowResult(relativePath: string, lint_errors: number, lint_warnings: number, stepResults: ValidationStepResult[], opts?: {
+    error?: string | null;
+    skipped_reason?: SkipWorkflowReason | null;
+}): LintWorkflowResult;
+export declare function buildWorkflowCleanResult(relativePath: string, stepResults: CleanStepResult[], opts?: {
+    error?: string | null;
+    skipped_reason?: SkipWorkflowReason | null;
+}): WorkflowCleanResult;
+export interface WorkflowExportResult {
+    path: string;
+    category: string;
+    name: string;
+    error: string | null;
+    skipped_reason: string | null;
+    ok: boolean;
+    steps_converted: number;
+    steps_fallback: number;
+    readonly status: "ok" | "partial" | "error" | "skipped";
+}
+export interface ExportTreeReport {
+    root: string;
+    output_dir: string;
+    workflows: WorkflowExportResult[];
+    readonly summary: {
+        ok: number;
+        fail: number;
+        skipped: number;
+    };
+}
+export interface WorkflowToNativeResult {
+    path: string;
+    category: string;
+    name: string;
+    error: string | null;
+    skipped_reason: string | null;
+    ok: boolean;
+    steps_encoded: number;
+    steps_fallback: number;
+    readonly status: "ok" | "partial" | "error" | "skipped";
+}
+export interface ToNativeTreeReport {
+    root: string;
+    output_dir: string;
+    workflows: WorkflowToNativeResult[];
+    readonly summary: {
+        ok: number;
+        fail: number;
+        skipped: number;
+    };
+}
+export interface ToolFailureMode {
+    tool_id: string | null;
+    failure_class: string;
+    count: number;
+}
+export interface RoundTripTreeReport {
+    root: string;
+    workflows: RoundTripValidationResult[];
+    readonly total: number;
+    readonly summary: {
+        clean: number;
+        benign_only: number;
+        fail: number;
+        error: number;
+        skipped: number;
+    };
+    readonly tool_failure_modes: ToolFailureMode[];
+}
+export declare function buildTreeValidationReport(root: string, workflows: WorkflowValidationResult[]): TreeValidationReport;
+export declare function buildLintTreeReport(root: string, workflows: LintWorkflowResult[]): LintTreeReport;
+export declare function buildWorkflowExportResult(relativePath: string, opts?: {
+    ok?: boolean;
+    steps_converted?: number;
+    steps_fallback?: number;
+    error?: string | null;
+    skipped_reason?: SkipWorkflowReason | null;
+}): WorkflowExportResult;
+export declare function buildExportTreeReport(root: string, output_dir: string, workflows: WorkflowExportResult[]): ExportTreeReport;
+export declare function buildWorkflowToNativeResult(relativePath: string, opts?: {
+    ok?: boolean;
+    steps_encoded?: number;
+    steps_fallback?: number;
+    error?: string | null;
+    skipped_reason?: SkipWorkflowReason | null;
+}): WorkflowToNativeResult;
+export declare function buildToNativeTreeReport(root: string, output_dir: string, workflows: WorkflowToNativeResult[]): ToNativeTreeReport;
+export declare function buildRoundTripTreeReport(root: string, workflows: RoundTripValidationResult[]): RoundTripTreeReport;
+export declare function buildTreeCleanReport(root: string, workflows: WorkflowCleanResult[]): TreeCleanReport;
+//# sourceMappingURL=report-models.d.ts.map

package/dist/workflow/report-models.d.ts.map

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