@galaxy-tool-util/gxwf-web 0.0.0

package/dist/workflows.d.ts

@@ -0,0 +1,126 @@
+/**
+ * Workflow discovery and per-workflow operations for the gxwf-web HTTP server.
+ *
+ * Discovery mirrors Python's `discover_workflows` in workflow_tree.py:
+ *   - scans for .ga, .gxwf.yml, .gxwf.yaml files
+ *   - validates content (a_galaxy_workflow / class: GalaxyWorkflow)
+ *   - category = first parent directory of relative path, or "" for root
+ *
+ * Operations delegate to @galaxy-tool-util/schema and @galaxy-tool-util/cli.
+ *
+ * All six operation endpoints are POST. clean/export/convert are mutating by
+ * default — dry_run=true returns the would-be content without touching disk.
+ * validate/lint/roundtrip are read-only regardless.
+ *
+ * ## Parity status vs Python server
+ *
+ * | Endpoint  | Python params                          | TS status                                |
+ * |-----------|----------------------------------------|------------------------------------------|
+ * | validate  | strict, connections, mode, allow, deny | strict wired; rest accepted (no-op)      |
+ * | lint      | strict, allow, deny                    | strict wired; allow/deny accepted (no-op)|
+ * | clean     | preserve, strip, dry_run               | writes back; dry_run wired; preserve/strip no-op |
+ * | export    | dry_run                                | full parity                              |
+ * | convert   | dry_run                                | full parity                              |
+ * | roundtrip | strict_structure, strict_encoding, strict_state, include_content | full parity |
+ *
+ * TS extension not in Python spec: GET /api/schemas/structural?format=...
+ * mode=pydantic (Python default) maps to effect (TS default); mode=json-schema accepted (no-op).
+ * allow/deny/preserve/strip require StaleKeyPolicy — tracked as future work in stale-keys.ts.
+ */
+import type { ToolCache } from "@galaxy-tool-util/core";
+import { type WorkflowFormat, type WorkflowIndex, type SingleValidationReport, type SingleLintReport, type SingleCleanReport, type SingleRoundTripReport } from "@galaxy-tool-util/schema";
+import type { ConvertResult, ExportResult } from "./models.js";
+/** Scan directory for workflow files, returning a WorkflowIndex (matches Python's discover_workflows). */
+export declare function discoverWorkflows(directory: string): WorkflowIndex;
+export interface WorkflowFile {
+    absPath: string;
+    data: Record<string, unknown>;
+    format: WorkflowFormat;
+}
+/**
+ * Resolve a relative workflow path within a directory and load its data.
+ * Throws HttpError 404 if not found, 400 if unreadable.
+ */
+export declare function loadWorkflowFile(directory: string, relPath: string): WorkflowFile;
+export interface ValidateOptions {
+    /** Reject unknown keys at envelope/step level (mirrors Python strict_structure). */
+    strict_structure?: boolean;
+    /** Reject JSON-string tool_state and format2 field misuse (mirrors Python strict_encoding). */
+    strict_encoding?: boolean;
+    /**
+     * Validate connections between steps. Not yet implemented in TS — accepted
+     * for API parity but silently ignored.
+     */
+    connections?: boolean;
+    /**
+     * Validation mode: "effect" (default) uses Effect Schema decode;
+     * "json-schema" uses AJV against the generated JSON Schema (mirrors Python --mode json-schema).
+     * Python default "pydantic" is treated as "effect".
+     */
+    mode?: string;
+    /**
+     * Run clean in-memory before validating. Results are embedded in the
+     * returned report as clean_report.
+     */
+    clean_first?: boolean;
+    /**
+     * Tool IDs whose stale keys are allowed. Accepted for API parity; requires
+     * StaleKeyPolicy (future work) — currently ignored.
+     */
+    allow?: string[];
+    /**
+     * Tool IDs whose stale keys are denied. Accepted for API parity; requires
+     * StaleKeyPolicy (future work) — currently ignored.
+     */
+    deny?: string[];
+}
+/** Validate a workflow's tool state. */
+export declare function operateValidate(wf: WorkflowFile, cache: ToolCache, opts?: ValidateOptions): Promise<SingleValidationReport>;
+export interface LintOptions {
+    strict_structure?: boolean;
+    strict_encoding?: boolean;
+    /**
+     * Tool IDs whose stale keys are allowed. Accepted for API parity; requires
+     * StaleKeyPolicy (future work) — currently ignored.
+     */
+    allow?: string[];
+    /**
+     * Tool IDs whose stale keys are denied. Accepted for API parity; requires
+     * StaleKeyPolicy (future work) — currently ignored.
+     */
+    deny?: string[];
+}
+/** Lint a workflow — structural checks, best practices, tool state validation. */
+export declare function operateLint(wf: WorkflowFile, cache: ToolCache, opts?: LintOptions): Promise<SingleLintReport>;
+export interface CleanOptions {
+    /**
+     * Keys to preserve (not strip). Accepted for API parity; requires
+     * StaleKeyPolicy (future work) — currently ignored.
+     */
+    preserve?: string[];
+    /**
+     * Keys to always strip. Accepted for API parity; requires
+     * StaleKeyPolicy (future work) — currently ignored.
+     */
+    strip?: string[];
+    /** When true, return the cleaned content without writing it back to disk. */
+    dry_run?: boolean;
+}
+/** Clean stale tool state keys in a workflow; writes back to disk unless dry_run. */
+export declare function operateClean(wf: WorkflowFile, opts?: CleanOptions): Promise<SingleCleanReport>;
+export interface ExportConvertOptions {
+    dry_run?: boolean;
+}
+/** Export: write converted workflow alongside the original (or return content on dry_run). */
+export declare function operateExport(wf: WorkflowFile, cache: ToolCache, opts?: ExportConvertOptions): Promise<ExportResult>;
+/** Convert: like export, but also removes the original file. */
+export declare function operateConvert(wf: WorkflowFile, cache: ToolCache, opts?: ExportConvertOptions): Promise<ConvertResult>;
+export interface RoundtripOptions {
+    strict_structure?: boolean;
+    strict_encoding?: boolean;
+    strict_state?: boolean;
+    include_content?: boolean;
+}
+/** Run roundtrip validation (native → format2 → native). */
+export declare function operateRoundtrip(wf: WorkflowFile, cache: ToolCache, opts?: RoundtripOptions): Promise<SingleRoundTripReport>;
+//# sourceMappingURL=workflows.d.ts.map

package/dist/workflows.d.ts.map

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package/dist/workflows.js

@@ -0,0 +1,462 @@
+/**
+ * Workflow discovery and per-workflow operations for the gxwf-web HTTP server.
+ *
+ * Discovery mirrors Python's `discover_workflows` in workflow_tree.py:
+ *   - scans for .ga, .gxwf.yml, .gxwf.yaml files
+ *   - validates content (a_galaxy_workflow / class: GalaxyWorkflow)
+ *   - category = first parent directory of relative path, or "" for root
+ *
+ * Operations delegate to @galaxy-tool-util/schema and @galaxy-tool-util/cli.
+ *
+ * All six operation endpoints are POST. clean/export/convert are mutating by
+ * default — dry_run=true returns the would-be content without touching disk.
+ * validate/lint/roundtrip are read-only regardless.
+ *
+ * ## Parity status vs Python server
+ *
+ * | Endpoint  | Python params                          | TS status                                |
+ * |-----------|----------------------------------------|------------------------------------------|
+ * | validate  | strict, connections, mode, allow, deny | strict wired; rest accepted (no-op)      |
+ * | lint      | strict, allow, deny                    | strict wired; allow/deny accepted (no-op)|
+ * | clean     | preserve, strip, dry_run               | writes back; dry_run wired; preserve/strip no-op |
+ * | export    | dry_run                                | full parity                              |
+ * | convert   | dry_run                                | full parity                              |
+ * | roundtrip | strict_structure, strict_encoding, strict_state, include_content | full parity |
+ *
+ * TS extension not in Python spec: GET /api/schemas/structural?format=...
+ * mode=pydantic (Python default) maps to effect (TS default); mode=json-schema accepted (no-op).
+ * allow/deny/preserve/strip require StaleKeyPolicy — tracked as future work in stale-keys.ts.
+ */
+import * as fs from "node:fs";
+import * as path from "node:path";
+import { parse as parseYaml } from "yaml";
+import { cleanWorkflow, roundtripValidate, toFormat2Stateful, toNativeStateful, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, detectFormat, serializeWorkflow, } from "@galaxy-tool-util/schema";
+import { validateNativeSteps, validateFormat2Steps, decodeStructureErrors, detectEncodingErrors, loadToolInputsForWorkflow, createDefaultResolver, lintWorkflowReport, validateNativeStepsJsonSchema, validateFormat2StepsJsonSchema, decodeStructureErrorsJsonSchema, } from "@galaxy-tool-util/cli";
+import { HttpError } from "./contents.js";
+// ── Discovery ────────────────────────────────────────────────────────────────
+const EXCLUDE_DIRS = new Set([
+    ".git",
+    ".hg",
+    ".venv",
+    "node_modules",
+    "__pycache__",
+    ".snakemake",
+    ".checkpoints",
+    ".pytest_cache",
+    ".mypy_cache",
+    ".tox",
+    ".ruff_cache",
+]);
+function classifyFilename(filename) {
+    if (filename.endsWith(".gxwf.yml") || filename.endsWith(".gxwf.yaml"))
+        return "format2";
+    if (filename.endsWith(".ga"))
+        return "native";
+    return null;
+}
+function isWorkflowContent(filePath, format) {
+    try {
+        const content = fs.readFileSync(filePath, "utf-8");
+        if (format === "native") {
+            const data = JSON.parse(content);
+            return data?.a_galaxy_workflow === "true";
+        }
+        else {
+            const data = parseYaml(content);
+            return data?.class === "GalaxyWorkflow";
+        }
+    }
+    catch {
+        return false;
+    }
+}
+function categoryOf(relPath) {
+    const sep = "/";
+    const idx = relPath.indexOf(sep);
+    return idx > 0 ? relPath.slice(0, idx) : "";
+}
+function walkDir(dirPath, root, entries) {
+    let names;
+    try {
+        names = fs.readdirSync(dirPath);
+    }
+    catch {
+        return;
+    }
+    for (const name of names) {
+        if (EXCLUDE_DIRS.has(name))
+            continue;
+        const fullPath = path.join(dirPath, name);
+        let stat;
+        try {
+            stat = fs.statSync(fullPath);
+        }
+        catch {
+            continue;
+        }
+        if (stat.isDirectory()) {
+            walkDir(fullPath, root, entries);
+        }
+        else if (stat.isFile()) {
+            const format = classifyFilename(name);
+            if (!format)
+                continue;
+            if (!isWorkflowContent(fullPath, format))
+                continue;
+            // Always use forward slashes in relative paths
+            const relPath = path.relative(root, fullPath).split(path.sep).join("/");
+            entries.push({
+                relative_path: relPath,
+                format,
+                category: categoryOf(relPath),
+            });
+        }
+    }
+}
+/** Scan directory for workflow files, returning a WorkflowIndex (matches Python's discover_workflows). */
+export function discoverWorkflows(directory) {
+    const root = path.resolve(directory);
+    const entries = [];
+    walkDir(root, root, entries);
+    entries.sort((a, b) => a.relative_path.localeCompare(b.relative_path));
+    return { directory: root, workflows: entries };
+}
+/**
+ * Resolve a relative workflow path within a directory and load its data.
+ * Throws HttpError 404 if not found, 400 if unreadable.
+ */
+export function loadWorkflowFile(directory, relPath) {
+    const root = path.resolve(directory);
+    const abs = path.resolve(root, relPath);
+    // Prevent path traversal
+    if (abs !== root && !abs.startsWith(root + path.sep)) {
+        throw new HttpError(403, "Path escapes configured directory");
+    }
+    if (!fs.existsSync(abs)) {
+        throw new HttpError(404, `Workflow not found: ${relPath}`);
+    }
+    let data;
+    try {
+        const content = fs.readFileSync(abs, "utf-8");
+        if (abs.endsWith(".ga")) {
+            data = JSON.parse(content);
+        }
+        else {
+            data = parseYaml(content);
+        }
+    }
+    catch (e) {
+        throw new HttpError(400, `Cannot read workflow file: ${String(e)}`);
+    }
+    const format = detectFormat(data);
+    if (!format) {
+        throw new HttpError(422, `Cannot detect workflow format for: ${relPath}`);
+    }
+    return { absPath: abs, data, format };
+}
+/** Validate a workflow's tool state. */
+export async function operateValidate(wf, cache, opts = {}) {
+    const { absPath, format } = wf;
+    let { data } = wf;
+    const useJsonSchema = opts.mode === "json-schema";
+    const expansionOpts = {
+        resolver: createDefaultResolver({ workflowDirectory: path.dirname(absPath) }),
+    };
+    // Optional clean-first pass: run clean in-memory, validate on cleaned dict
+    let clean_report = null;
+    if (opts.clean_first) {
+        const cleanResult = await cleanWorkflow(data);
+        const cleanResults = cleanResult.results;
+        clean_report = buildSingleCleanReport(absPath, cleanResults);
+        data = cleanResult.workflow;
+    }
+    // Structural validation
+    const structureErrors = useJsonSchema
+        ? decodeStructureErrorsJsonSchema(data, format)
+        : opts.strict_structure
+            ? decodeStructureErrors(data, format)
+            : [];
+    // Encoding errors (only in strict_encoding mode via Effect path)
+    const encodingErrors = [];
+    if (opts.strict_encoding && !useJsonSchema) {
+        // decodeStructureErrors covers encoding signals; encoding errors surfaced via detectEncodingErrors
+        if ((await cache.index.listAll()).length > 0) {
+            const encErrors = await detectEncodingErrors(data, cache, format, expansionOpts);
+            encodingErrors.push(...encErrors);
+        }
+    }
+    let results = [];
+    try {
+        if (useJsonSchema) {
+            if (format === "native") {
+                results = await validateNativeStepsJsonSchema(data, cache, undefined, "", expansionOpts);
+            }
+            else {
+                results = await validateFormat2StepsJsonSchema(data, cache, undefined, "", expansionOpts);
+            }
+        }
+        else {
+            if (format === "native") {
+                results = await validateNativeSteps(data, cache, "", expansionOpts);
+            }
+            else {
+                results = await validateFormat2Steps(data, cache, "", expansionOpts);
+            }
+        }
+    }
+    catch (e) {
+        if (e instanceof Error && e.message.includes("legacy parameter encoding")) {
+            encodingErrors.push(e.message);
+        }
+        else {
+            throw e;
+        }
+    }
+    const report = buildSingleValidationReport(absPath, results, {
+        structure_errors: structureErrors,
+        encoding_errors: encodingErrors,
+    });
+    if (clean_report !== null) {
+        report.clean_report = clean_report;
+    }
+    return report;
+}
+/** Lint a workflow — structural checks, best practices, tool state validation. */
+export async function operateLint(wf, cache, opts = {}) {
+    const { absPath, data, format } = wf;
+    const strict = {
+        strictEncoding: opts.strict_encoding ?? false,
+        strictStructure: opts.strict_structure ?? false,
+        strictState: false,
+    };
+    const report = await lintWorkflowReport(absPath, data, format, { cache, strict });
+    const lintErrors = report.structural.error_count + (report.bestPractices?.error_count ?? 0);
+    const lintWarnings = report.structural.warn_count + (report.bestPractices?.warn_count ?? 0);
+    // Always compute structure_errors from Effect Schema decode (matches CLI JSON mode)
+    const structureErrors = decodeStructureErrors(data, format);
+    // Detect legacy encoding errors (when cache is available)
+    let encodingErrors = [];
+    if ((await cache.index.listAll()).length > 0) {
+        const expansionOpts = {
+            resolver: createDefaultResolver({ workflowDirectory: path.dirname(absPath) }),
+        };
+        encodingErrors = await detectEncodingErrors(data, cache, format, expansionOpts);
+    }
+    return buildSingleLintReport(absPath, lintErrors, lintWarnings, report.stateValidation ?? [], {
+        structure_errors: structureErrors,
+        encoding_errors: encodingErrors,
+    });
+}
+/** Clean stale tool state keys in a workflow; writes back to disk unless dry_run. */
+export async function operateClean(wf, opts = {}) {
+    const { absPath, data, format } = wf;
+    const before_content = fs.readFileSync(absPath, "utf-8");
+    const cleanResult = await cleanWorkflow(data);
+    // Match Python clean_single's after_content: indent=2, no trailing newline.
+    const after_content = serializeWorkflow(cleanResult.workflow, format, {
+        indent: 2,
+        trailingNewline: false,
+    });
+    if (!opts.dry_run) {
+        fs.writeFileSync(absPath, after_content);
+    }
+    const base = buildSingleCleanReport(absPath, cleanResult.results);
+    return {
+        ...base,
+        before_content,
+        after_content,
+    };
+}
+/**
+ * Compute the output path for an export/convert.
+ * Native `.ga` → `.gxwf.yml`; format2 `.gxwf.yml`/`.gxwf.yaml` → `.ga`.
+ */
+function computeOutputPath(absPath, sourceFormat) {
+    if (sourceFormat === "native") {
+        // foo.ga → foo.gxwf.yml
+        const base = absPath.endsWith(".ga") ? absPath.slice(0, -".ga".length) : absPath;
+        return `${base}.gxwf.yml`;
+    }
+    // foo.gxwf.yml / foo.gxwf.yaml → foo.ga
+    const dir = path.dirname(absPath);
+    const name = path.basename(absPath);
+    const stem = name.endsWith(".gxwf.yml")
+        ? name.slice(0, -".gxwf.yml".length)
+        : name.endsWith(".gxwf.yaml")
+            ? name.slice(0, -".gxwf.yaml".length)
+            : name.replace(/\.[^.]+$/, "");
+    return path.join(dir, `${stem}.ga`);
+}
+async function performExport(wf, cache) {
+    const { absPath, data, format } = wf;
+    const expansionOpts = {
+        resolver: createDefaultResolver({ workflowDirectory: path.dirname(absPath) }),
+    };
+    if (format === "native") {
+        const { resolver } = await loadToolInputsForWorkflow(data, "native", cache, expansionOpts);
+        const result = toFormat2Stateful(data, resolver);
+        const converted = result.steps.filter((s) => s.converted).length;
+        const fallback = result.steps.length - converted;
+        const report = {
+            workflow: absPath,
+            ok: fallback === 0,
+            steps_converted: converted,
+            steps_fallback: fallback,
+            summary: { converted, fallback },
+        };
+        return {
+            output_path: computeOutputPath(absPath, "native"),
+            content: serializeWorkflow(result.workflow, "format2"),
+            report,
+            source_format: "native",
+            target_format: "format2",
+        };
+    }
+    const { resolver } = await loadToolInputsForWorkflow(data, "format2", cache, expansionOpts);
+    const result = toNativeStateful(data, resolver);
+    const steps = result.steps.map((s) => ({
+        step_id: s.stepId,
+        step_label: null,
+        tool_id: s.toolId ?? null,
+        encoded: s.converted,
+        error: s.error ?? null,
+    }));
+    const allEncoded = steps.every((s) => s.encoded);
+    const encodedCount = steps.filter((s) => s.encoded).length;
+    const nativeDict = result.workflow;
+    const report = {
+        native_dict: nativeDict,
+        steps,
+        all_encoded: allEncoded,
+        summary: `${encodedCount}/${steps.length} steps encoded`,
+    };
+    return {
+        output_path: computeOutputPath(absPath, "format2"),
+        // Match Python format_native_json: JSON indent=4 + trailing newline.
+        content: serializeWorkflow(nativeDict, "native", { indent: 4 }),
+        report,
+        source_format: "format2",
+        target_format: "native",
+    };
+}
+/** Export: write converted workflow alongside the original (or return content on dry_run). */
+export async function operateExport(wf, cache, opts = {}) {
+    const outcome = await performExport(wf, cache);
+    if (!opts.dry_run) {
+        fs.writeFileSync(outcome.output_path, outcome.content);
+    }
+    return {
+        source_path: wf.absPath,
+        output_path: outcome.output_path,
+        source_format: outcome.source_format,
+        target_format: outcome.target_format,
+        report: outcome.report,
+        dry_run: !!opts.dry_run,
+        content: opts.dry_run ? outcome.content : null,
+    };
+}
+/** Convert: like export, but also removes the original file. */
+export async function operateConvert(wf, cache, opts = {}) {
+    const outcome = await performExport(wf, cache);
+    if (!opts.dry_run) {
+        fs.writeFileSync(outcome.output_path, outcome.content);
+        fs.unlinkSync(wf.absPath);
+    }
+    return {
+        source_path: wf.absPath,
+        output_path: outcome.output_path,
+        removed_path: wf.absPath,
+        source_format: outcome.source_format,
+        target_format: outcome.target_format,
+        report: outcome.report,
+        dry_run: !!opts.dry_run,
+        content: opts.dry_run ? outcome.content : null,
+    };
+}
+/** Run roundtrip validation (native → format2 → native). */
+export async function operateRoundtrip(wf, cache, opts = {}) {
+    const { absPath, data, format } = wf;
+    if (format !== "native") {
+        throw new HttpError(422, "roundtrip requires a native (.ga) workflow");
+    }
+    const expansionOpts = {
+        resolver: createDefaultResolver({ workflowDirectory: path.dirname(absPath) }),
+    };
+    const { resolver } = await loadToolInputsForWorkflow(data, "native", cache, expansionOpts);
+    const result = roundtripValidate(data, resolver, {
+        strictStructure: opts.strict_structure,
+        strictEncoding: opts.strict_encoding,
+        strictState: opts.strict_state,
+    });
+    // Convert TS-internal RoundtripResult → Python-API RoundTripValidationResult
+    const allDiffs = result.stepResults.flatMap((s) => s.diffs);
+    const errorDiffs = allDiffs.filter((d) => d.severity === "error");
+    const benignDiffs = allDiffs.filter((d) => d.severity === "benign");
+    // Build a Python-shape RoundTripResult for conversion_result.
+    // Direction "forward+reverse" covers the full TS roundtrip.
+    const conversionStepResults = result.stepResults.map((s) => ({
+        step_id: s.stepId,
+        tool_id: s.toolId ?? null,
+        success: s.success,
+        failure_class: _mapRoundtripFailureClass(s.failureClass ?? null),
+        error: s.error ?? null,
+        diffs: s.diffs,
+        format2_state: null,
+        format2_connections: null,
+    }));
+    // Build conversion failure lines from forward/reverse step statuses
+    const conversionFailureLines = [
+        ...result.forwardSteps
+            .filter((s) => !s.converted)
+            .map((s) => `forward step ${s.stepId}: ${s.error ?? s.failureClass ?? "unknown"}`),
+        ...result.reverseSteps
+            .filter((s) => !s.converted)
+            .map((s) => `reverse step ${s.stepId}: ${s.error ?? s.failureClass ?? "unknown"}`),
+    ];
+    const ok = result.success && result.clean;
+    const status = ok ? "ok" : errorDiffs.length > 0 ? "error" : "benign";
+    const summaryLine = `${ok ? "ok" : "fail"}: ${errorDiffs.length} error diff(s), ${benignDiffs.length} benign diff(s)`;
+    const validationResult = {
+        workflow_path: absPath,
+        category: "",
+        conversion_result: {
+            workflow_name: result.workflowName ?? absPath,
+            direction: "forward+reverse",
+            step_results: conversionStepResults,
+        },
+        diffs: allDiffs,
+        step_id_mapping: { mapping: {}, match_methods: {} },
+        stale_clean_results: null,
+        error: null,
+        skipped_reason: null,
+        structure_errors: result.structureErrors,
+        encoding_errors: result.encodingErrors,
+        error_diffs: errorDiffs,
+        benign_diffs: benignDiffs,
+        ok,
+        status,
+        conversion_failure_lines: conversionFailureLines,
+        summary_line: summaryLine,
+    };
+    const before_content = opts.include_content ? JSON.stringify(data, null, 2) : undefined;
+    const after_content = opts.include_content && result.reimportedWorkflow != null
+        ? JSON.stringify(result.reimportedWorkflow, null, 2)
+        : undefined;
+    return {
+        workflow: absPath,
+        result: validationResult,
+        before_content: before_content ?? null,
+        after_content: after_content ?? null,
+    };
+}
+// ── Internal helpers ─────────────────────────────────────────────────────────
+function _mapRoundtripFailureClass(cls) {
+    if (cls === null)
+        return null;
+    // "subworkflow_external_ref" is TS-specific; map to Python's "subworkflow"
+    if (cls === "subworkflow_external_ref")
+        return "subworkflow";
+    // All other TS failure classes happen to match Python FailureClass literals
+    return cls;
+}
+//# sourceMappingURL=workflows.js.map

package/dist/workflows.js.map

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