@galaxy-tool-util/schema 0.1.0 → 0.4.0

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

@@ -29,12 +29,6 @@ export const DocumentedSchema = Schema.Struct({
     /** A documentation string for this object, or an array of strings which should be concatenated. */
     doc: Schema.optional(Schema.Union(Schema.Null, Schema.String, Schema.Array(Schema.String))),
 });
-export const RecordSchemaSchema = Schema.Struct({
-    /** Defines the fields of the record. */
-    fields: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.suspend(() => RecordFieldSchema)))),
-    /** Must be `record` */
-    type: Schema.Literal("record"),
-});
 /**
  * Define an enumerated type.
  */
@@ -44,9 +38,21 @@ export const EnumSchemaSchema = Schema.Struct({
     /** Must be `enum` */
     type: Schema.Literal("enum"),
 });
+export const RecordSchemaSchema = Schema.Struct({
+    /** Defines the fields of the record. */
+    fields: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.suspend(() => RecordFieldSchema).annotations({
+        identifier: "RecordFieldSchema",
+    })))),
+    /** Must be `record` */
+    type: Schema.Literal("record"),
+});
 export const ArraySchemaSchema = Schema.Struct({
     /** Defines the type of the array elements. */
-    items: Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema), Schema.String, Schema.Array(Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema), Schema.String))),
+    items: Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema).annotations({
+        identifier: "ArraySchemaSchema",
+    }), Schema.String, Schema.Array(Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema).annotations({
+        identifier: "ArraySchemaSchema",
+    }), Schema.String))),
     /** Must be `array` */
     type: Schema.Literal("array"),
 });
@@ -255,27 +261,6 @@ export const NativeFreehandCommentSchema = Schema.Struct({
     /** Freehand content data: ``line``, ``thickness``. */
     data: Schema.optional(Schema.Union(Schema.Null, NativeFreehandCommentDataSchema)),
 });
-/**
- * Provenance tracking for workflows imported from external sources.
-Contains either a direct URL or TRS (Tool Registry Service) metadata,
-depending on how the workflow was imported.
-
-For URL imports, only ``url`` is set. For TRS imports (Dockstore,
-WorkflowHub), ``trs_tool_id``, ``trs_version_id``, and ``trs_url``
-are set, with ``trs_server`` optionally identifying the server.
- */
-export const NativeSourceMetadataSchema = Schema.Struct({
-    /** URL from which the workflow was directly imported. */
-    url: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** Tool identifier in the Tool Registry Service (e.g. ``"#workflow/github.com/user/repo/workflow"`` or ``"109"``). */
-    trs_tool_id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** Version identifier in the TRS (e.g. ``"master"``, ``"5"``). */
-    trs_version_id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** TRS server name (e.g. ``"dockstore"``, ``"workflowhub"``). Optional even for TRS imports. */
-    trs_server: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** Complete TRS API endpoint URL for this workflow version. */
-    trs_url: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-});
 /**
  * Workflow invocation report template.
  */
@@ -326,6 +311,27 @@ export const NativeCreatorPersonSchema = Schema.Struct({
     /** Job title or role. */
     jobTitle: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
 });
+/**
+ * Provenance tracking for workflows imported from external sources.
+Contains either a direct URL or TRS (Tool Registry Service) metadata,
+depending on how the workflow was imported.
+
+For URL imports, only ``url`` is set. For TRS imports (Dockstore,
+WorkflowHub), ``trs_tool_id``, ``trs_version_id``, and ``trs_url``
+are set, with ``trs_server`` optionally identifying the server.
+ */
+export const NativeSourceMetadataSchema = Schema.Struct({
+    /** URL from which the workflow was directly imported. */
+    url: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** Tool identifier in the Tool Registry Service (e.g. ``"#workflow/github.com/user/repo/workflow"`` or ``"109"``). */
+    trs_tool_id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** Version identifier in the TRS (e.g. ``"master"``, ``"5"``). */
+    trs_version_id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** TRS server name (e.g. ``"dockstore"``, ``"workflowhub"``). Optional even for TRS imports. */
+    trs_server: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** Complete TRS API endpoint URL for this workflow version. */
+    trs_url: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+});
 /**
  * An organization that created or contributed to the workflow.
 Corresponds to a `schema.org Organization <https://schema.org/Organization>`_.
@@ -352,9 +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. */
@@ -384,12 +390,16 @@ export const NativeGalaxyWorkflowSchema = Schema.Struct({
     /** Step dictionary keyed by string integers (``"0"``, ``"1"``, ...). Values are NativeStep objects. Steps are processed in sorted numeric order during import. */
     steps: Schema.optional(Schema.Union(Schema.Record({
         key: Schema.String,
-        value: Schema.suspend(() => NativeStepSchema),
+        value: Schema.suspend(() => NativeStepSchema).annotations({
+            identifier: "NativeStepSchema",
+        }),
     }), Schema.Null)),
     /** Map of locally-defined subworkflow dicts, used during format conversion. */
     subworkflows: Schema.optional(Schema.Union(Schema.Record({
         key: Schema.String,
-        value: Schema.suspend(() => NativeGalaxyWorkflowSchema),
+        value: Schema.suspend(() => NativeGalaxyWorkflowSchema).annotations({
+            identifier: "NativeGalaxyWorkflowSchema",
+        }),
     }), Schema.Null)),
 });
 /**

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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