paperlint 10.1.1 → 10.3.0

package/README.md

@@ -160,6 +160,8 @@ Each stage's skills, what it writes and what checks it, drawn as one flow, with
 | `npx paperlint doctor`                                      | checks the setup and exits non-zero if something is miswired                   |
 | `npx paperlint submission show <paper>`                     | the paper's submission on the venue's portal, and whether it holds your build  |
 | `npx paperlint submission update <paper>`                   | checks a new PDF/abstract against the portal; `--save` sends it for real       |
+| `npx paperlint studies new <paper> "<title>"`               | registers a study: the next id in `repro/studies.json`, its folder, the index  |
+| `npx paperlint studies index <paper>`                       | regenerates the index of the studies in `repro/README.md`                      |
 | `npx paperlint --help`                                      | every command and flag                                                         |
 
 ## 🧠 Skills

package/dist/adapters/study-registry/index.d.ts

@@ -0,0 +1,357 @@
+/**
+ * The schema of `repro/studies.json` — the one place its shape is checked (docs/design/study-registry.md).
+ * The text is parsed once, here, into the domain's `StudyRegistry`; whatever reads a registry after it
+ * never re-validates.
+ *
+ * A row is a loose object: a paper merges its own measurement metadata into its rows (`role`, `frame`,
+ * `rules_under_test`, `outcome` …), and those fields are kept as they are. The top level is strict, so
+ * a misspelt key is an error rather than a key nobody reads. A measurement keeps its extra fields as a
+ * row does; a requirement and an approval are exactly their fields.
+ *
+ * A study's plan (`plan.json`) is parsed here too, strictly: a key of the paper's own goes in `extra`.
+ * Its texts may be empty — the template's are — and the parser says which: a plan comes out ready or
+ * a draft naming its empty texts, so nothing downstream looks at a text again. A plan still named
+ * `prereg.json` has a loose schema of its own.
+ */
+import { z } from "zod";
+import { type Approval, type AuthorCheck, type Measurement, type ParsedPlan, type ParsedRegistry, type Requirement, type Study, type StudyPlan, type StudyRegistry } from "../../domain/study-registry.ts";
+import type { StudyRegistryCodec } from "../../ports/study-registry-codec.ts";
+declare const study: z.ZodObject<{
+    id: z.ZodString;
+    folder: z.ZodString;
+    title: z.ZodString;
+    question: z.ZodString;
+    kind: z.ZodEnum<{
+        data: "data";
+        artifact: "artifact";
+        measurement: "measurement";
+        spike: "spike";
+        tooling: "tooling";
+        salvage: "salvage";
+    }>;
+    status: z.ZodEnum<{
+        done: "done";
+        designing: "designing";
+        running: "running";
+        stopped: "stopped";
+        superseded: "superseded";
+        dropped: "dropped";
+    }>;
+    date: z.ZodISODate;
+    result: z.ZodOptional<z.ZodString>;
+    result_file: z.ZodOptional<z.ZodString>;
+    superseded_by: z.ZodOptional<z.ZodString>;
+    in_paper: z.ZodEnum<{
+        yes: "yes";
+        no: "no";
+        registry: "registry";
+    }>;
+    measurement: z.ZodOptional<z.ZodString>;
+    plan: z.ZodOptional<z.ZodString>;
+}, z.core.$loose>;
+declare const requirement: z.ZodObject<{
+    id: z.ZodString;
+    text: z.ZodString;
+    date: z.ZodISODate;
+    source: z.ZodString;
+}, z.core.$strict>;
+declare const approval: z.ZodObject<{
+    by: z.ZodString;
+    date: z.ZodISODate;
+    quote: z.ZodString;
+    source: z.ZodOptional<z.ZodString>;
+}, z.core.$strict>;
+declare const measurement: z.ZodObject<{
+    id: z.ZodString;
+    title: z.ZodString;
+    rq: z.ZodOptional<z.ZodString>;
+    role: z.ZodEnum<{
+        baseline: "baseline";
+        headline: "headline";
+    }>;
+    approval: z.ZodOptional<z.ZodObject<{
+        by: z.ZodString;
+        date: z.ZodISODate;
+        quote: z.ZodString;
+        source: z.ZodOptional<z.ZodString>;
+    }, z.core.$strict>>;
+    requirements: z.ZodOptional<z.ZodArray<z.ZodString>>;
+}, z.core.$loose>;
+declare const registry: z.ZodObject<{
+    prefix: z.ZodString;
+    author: z.ZodOptional<z.ZodString>;
+    requirements: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        id: z.ZodString;
+        text: z.ZodString;
+        date: z.ZodISODate;
+        source: z.ZodString;
+    }, z.core.$strict>>>;
+    measurements: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        id: z.ZodString;
+        title: z.ZodString;
+        rq: z.ZodOptional<z.ZodString>;
+        role: z.ZodEnum<{
+            baseline: "baseline";
+            headline: "headline";
+        }>;
+        approval: z.ZodOptional<z.ZodObject<{
+            by: z.ZodString;
+            date: z.ZodISODate;
+            quote: z.ZodString;
+            source: z.ZodOptional<z.ZodString>;
+        }, z.core.$strict>>;
+        requirements: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    }, z.core.$loose>>>;
+    studies: z.ZodArray<z.ZodObject<{
+        id: z.ZodString;
+        folder: z.ZodString;
+        title: z.ZodString;
+        question: z.ZodString;
+        kind: z.ZodEnum<{
+            data: "data";
+            artifact: "artifact";
+            measurement: "measurement";
+            spike: "spike";
+            tooling: "tooling";
+            salvage: "salvage";
+        }>;
+        status: z.ZodEnum<{
+            done: "done";
+            designing: "designing";
+            running: "running";
+            stopped: "stopped";
+            superseded: "superseded";
+            dropped: "dropped";
+        }>;
+        date: z.ZodISODate;
+        result: z.ZodOptional<z.ZodString>;
+        result_file: z.ZodOptional<z.ZodString>;
+        superseded_by: z.ZodOptional<z.ZodString>;
+        in_paper: z.ZodEnum<{
+            yes: "yes";
+            no: "no";
+            registry: "registry";
+        }>;
+        measurement: z.ZodOptional<z.ZodString>;
+        plan: z.ZodOptional<z.ZodString>;
+    }, z.core.$loose>>;
+}, z.core.$strict>;
+declare const authorCheck: z.ZodObject<{
+    by: z.ZodString;
+    date: z.ZodISODate;
+    quote: z.ZodString;
+}, z.core.$strict>;
+/** A plan's shape: closed at every level; the paper's own keys go in `extra`. Null is the one "none". */
+declare const planShape: z.ZodObject<{
+    question: z.ZodString;
+    population: z.ZodObject<{
+        source: z.ZodString;
+        draw: z.ZodDiscriminatedUnion<[z.ZodObject<{
+            kind: z.ZodLiteral<"seeded">;
+            method: z.ZodString;
+            seed: z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>;
+        }, z.core.$strict>, z.ZodObject<{
+            kind: z.ZodLiteral<"all">;
+            method: z.ZodString;
+        }, z.core.$strict>], "kind">;
+    }, z.core.$strict>;
+    arms: z.ZodArray<z.ZodObject<{
+        name: z.ZodString;
+    }, z.core.$strict>>;
+    primary_outcome: z.ZodString;
+    author_check: z.ZodNullable<z.ZodObject<{
+        by: z.ZodString;
+        date: z.ZodISODate;
+        quote: z.ZodString;
+    }, z.core.$strict>>;
+    extra: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+}, z.core.$strict>;
+/**
+ * A plan under its old name, `prereg.json`, written by hand before the plan had a schema: open at
+ * every level, its own top-level keys kept in `extra`. A seed makes the draw seeded, none (or null) a
+ * draw of all; a size, and keys of its own deeper down, are not read; the file is never rewritten.
+ */
+declare const legacyAsPlan: z.ZodPipe<z.ZodObject<{
+    question: z.ZodString;
+    population: z.ZodObject<{
+        source: z.ZodString;
+        draw: z.ZodObject<{
+            method: z.ZodString;
+            seed: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>>>;
+        }, z.core.$loose>;
+    }, z.core.$loose>;
+    arms: z.ZodArray<z.ZodObject<{
+        name: z.ZodString;
+    }, z.core.$loose>>;
+    primary_outcome: z.ZodString;
+    author_check: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        by: z.ZodString;
+        date: z.ZodISODate;
+        quote: z.ZodString;
+    }, z.core.$strict>>>;
+}, z.core.$loose>, z.ZodTransform<StudyPlan, {
+    [x: string]: unknown;
+    question: string;
+    population: {
+        [x: string]: unknown;
+        source: string;
+        draw: {
+            [x: string]: unknown;
+            method: string;
+            seed?: string | number | null | undefined;
+        };
+    };
+    arms: {
+        [x: string]: unknown;
+        name: string;
+    }[];
+    primary_outcome: string;
+    author_check?: {
+        by: string;
+        date: string;
+        quote: string;
+    } | null | undefined;
+}>>;
+/** A plan that parsed: ready, or a draft. */
+type ReadyOrDraft = Exclude<ParsedPlan, {
+    readonly kind: "unreadable";
+}>;
+/** A `plan.json`: strict, then ready or draft. */
+declare const plan: z.ZodPipe<z.ZodObject<{
+    question: z.ZodString;
+    population: z.ZodObject<{
+        source: z.ZodString;
+        draw: z.ZodDiscriminatedUnion<[z.ZodObject<{
+            kind: z.ZodLiteral<"seeded">;
+            method: z.ZodString;
+            seed: z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>;
+        }, z.core.$strict>, z.ZodObject<{
+            kind: z.ZodLiteral<"all">;
+            method: z.ZodString;
+        }, z.core.$strict>], "kind">;
+    }, z.core.$strict>;
+    arms: z.ZodArray<z.ZodObject<{
+        name: z.ZodString;
+    }, z.core.$strict>>;
+    primary_outcome: z.ZodString;
+    author_check: z.ZodNullable<z.ZodObject<{
+        by: z.ZodString;
+        date: z.ZodISODate;
+        quote: z.ZodString;
+    }, z.core.$strict>>;
+    extra: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+}, z.core.$strict>, z.ZodTransform<{
+    readonly kind: "ready";
+    readonly plan: StudyPlan;
+} | {
+    readonly kind: "draft";
+    readonly plan: import("../../domain/study-registry.ts").DraftPlan;
+    readonly empty: readonly import("../../domain/study-registry.ts").PlanTextField[];
+}, {
+    question: string;
+    population: {
+        source: string;
+        draw: {
+            kind: "seeded";
+            method: string;
+            seed: string | number;
+        } | {
+            kind: "all";
+            method: string;
+        };
+    };
+    arms: {
+        name: string;
+    }[];
+    primary_outcome: string;
+    author_check: {
+        by: string;
+        date: string;
+        quote: string;
+    } | null;
+    extra?: Record<string, unknown> | undefined;
+}>>;
+/** A `prereg.json`: loose, mapped onto the plan, then ready or draft. */
+declare const legacyPlan: z.ZodPipe<z.ZodPipe<z.ZodObject<{
+    question: z.ZodString;
+    population: z.ZodObject<{
+        source: z.ZodString;
+        draw: z.ZodObject<{
+            method: z.ZodString;
+            seed: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>>>;
+        }, z.core.$loose>;
+    }, z.core.$loose>;
+    arms: z.ZodArray<z.ZodObject<{
+        name: z.ZodString;
+    }, z.core.$loose>>;
+    primary_outcome: z.ZodString;
+    author_check: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        by: z.ZodString;
+        date: z.ZodISODate;
+        quote: z.ZodString;
+    }, z.core.$strict>>>;
+}, z.core.$loose>, z.ZodTransform<StudyPlan, {
+    [x: string]: unknown;
+    question: string;
+    population: {
+        [x: string]: unknown;
+        source: string;
+        draw: {
+            [x: string]: unknown;
+            method: string;
+            seed?: string | number | null | undefined;
+        };
+    };
+    arms: {
+        [x: string]: unknown;
+        name: string;
+    }[];
+    primary_outcome: string;
+    author_check?: {
+        by: string;
+        date: string;
+        quote: string;
+    } | null | undefined;
+}>>, z.ZodTransform<{
+    readonly kind: "ready";
+    readonly plan: StudyPlan;
+} | {
+    readonly kind: "draft";
+    readonly plan: import("../../domain/study-registry.ts").DraftPlan;
+    readonly empty: readonly import("../../domain/study-registry.ts").PlanTextField[];
+}, StudyPlan>>;
+/** `T`, readonly all the way down: zod's outputs are mutable, the domain's are not. */
+type Frozen<T> = T extends readonly (infer U)[] ? readonly Frozen<U>[] : T extends object ? {
+    readonly [K in keyof T]: Frozen<T[K]>;
+} : T;
+/**
+ * True when `A` and `B`, both made readonly all the way down, are one type, optional modifiers
+ * included: two generic signatures whose returns are deferred conditionals are related only when
+ * the conditionals are identical. Written out, not through an alias: an alias is compared by the
+ * variance of its parameter, which misses a dropped optional field.
+ */
+type Same<A, B> = (<T>() => T extends Frozen<A> ? readonly [T] : 2) extends <T>() => T extends Frozen<B> ? readonly [T] : 2 ? true : false;
+/** Compiles only when every schema's output is its domain type. */
+export type SchemasAreTheDomain = [
+    Same<z.output<typeof registry>, StudyRegistry>,
+    Same<z.output<typeof study>, Study>,
+    Same<z.output<typeof measurement>, Measurement>,
+    Same<z.output<typeof requirement>, Requirement>,
+    Same<z.output<typeof approval>, Approval>,
+    Same<z.output<typeof authorCheck>, AuthorCheck>,
+    Same<z.output<typeof planShape>, StudyPlan>,
+    Same<z.output<typeof legacyAsPlan>, StudyPlan>,
+    Same<z.output<typeof plan>, ReadyOrDraft>,
+    Same<z.output<typeof legacyPlan>, ReadyOrDraft>
+] extends true[] ? true : never;
+/** The proof is used, so the build checks it. */
+export declare const SCHEMAS_ARE_THE_DOMAIN: SchemasAreTheDomain;
+/** A `studies.json`'s text, parsed once at the boundary: the registry, or every reason it is not one. */
+export declare function parseStudyRegistry(text: string): ParsedRegistry;
+/** A `plan.json`: strict. */
+export declare const parseStudyPlan: (text: string) => ParsedPlan;
+/** A plan still named `prereg.json`: loose, read only when a row names it. */
+export declare const parseLegacyPlan: (text: string) => ParsedPlan;
+export declare const studyRegistryCodec: StudyRegistryCodec;
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/adapters/study-registry/index.d.ts.map

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package/dist/adapters/study-registry/index.js

@@ -0,0 +1,221 @@
+/**
+ * The schema of `repro/studies.json` — the one place its shape is checked (docs/design/study-registry.md).
+ * The text is parsed once, here, into the domain's `StudyRegistry`; whatever reads a registry after it
+ * never re-validates.
+ *
+ * A row is a loose object: a paper merges its own measurement metadata into its rows (`role`, `frame`,
+ * `rules_under_test`, `outcome` …), and those fields are kept as they are. The top level is strict, so
+ * a misspelt key is an error rather than a key nobody reads. A measurement keeps its extra fields as a
+ * row does; a requirement and an approval are exactly their fields.
+ *
+ * A study's plan (`plan.json`) is parsed here too, strictly: a key of the paper's own goes in `extra`.
+ * Its texts may be empty — the template's are — and the parser says which: a plan comes out ready or
+ * a draft naming its empty texts, so nothing downstream looks at a text again. A plan still named
+ * `prereg.json` has a loose schema of its own.
+ */
+import { z } from "zod";
+import { IN_PAPER, MEASUREMENT_ROLES, PLAN_FIELDS, PLAN_TEXT_FIELDS, PREFIX_PATTERN, STUDY_KINDS, STUDY_STATUSES, } from "../../domain/study-registry.js";
+const study = z.looseObject({
+    id: z.string(),
+    folder: z.string(),
+    title: z.string().min(1),
+    question: z.string(),
+    kind: z.enum(STUDY_KINDS),
+    status: z.enum(STUDY_STATUSES),
+    date: z.iso.date(),
+    result: z.string().optional(),
+    result_file: z.string().optional(),
+    superseded_by: z.string().optional(),
+    in_paper: z.enum(IN_PAPER),
+    measurement: z.string().optional(),
+    plan: z.string().optional(),
+});
+const words = z.string().min(1);
+const requirement = z.strictObject({
+    id: words,
+    text: words,
+    date: z.iso.date(),
+    source: words,
+});
+const approval = z.strictObject({
+    by: words,
+    date: z.iso.date(),
+    quote: words,
+    source: words.optional(),
+});
+const measurement = z.looseObject({
+    id: words,
+    title: words,
+    rq: z.string().optional(),
+    role: z.enum(MEASUREMENT_ROLES),
+    approval: approval.optional(),
+    requirements: z.array(z.string()).optional(),
+});
+const registry = z.strictObject({
+    prefix: z
+        .string()
+        .regex(PREFIX_PATTERN, "a capital letter, then capitals or digits (P1)"),
+    author: words.optional(),
+    requirements: z.array(requirement).optional(),
+    measurements: z.array(measurement).optional(),
+    studies: z.array(study),
+});
+const authorCheck = approval.omit({ source: true });
+/** A draw: seeded, its seed part of it, or of all the population, with none. */
+const draw = z.discriminatedUnion("kind", [
+    z.strictObject({
+        kind: z.literal("seeded"),
+        method: z.string(),
+        seed: z.union([z.string(), z.number()]),
+    }),
+    z.strictObject({ kind: z.literal("all"), method: z.string() }),
+]);
+/** The values that occur more than once in `values`, each once. */
+const repeated = (values) => [
+    ...new Set(values.filter((v, i) => values.indexOf(v) !== i)),
+];
+/** Arms whose names are unique: a repeated name is an error naming it. */
+const uniquelyNamed = (arms, ctx) => {
+    repeated(arms.map((a) => a.name)).forEach((name) => {
+        ctx.addIssue({
+            code: "custom",
+            message: `more than one arm is named «${name}» — an arm's name is unique`,
+        });
+    });
+};
+/** The paper's own keys: none of them a field of the plan, which would say a thing twice. */
+const extra = z.record(z.string(), z.unknown()).superRefine((e, ctx) => {
+    Object.keys(e)
+        .filter((k) => PLAN_FIELDS.some((f) => f === k))
+        .forEach((k) => {
+        ctx.addIssue({
+            code: "custom",
+            path: [k],
+            message: "is a field of the plan itself — set it there, not in extra",
+        });
+    });
+});
+/** A plan's shape: closed at every level; the paper's own keys go in `extra`. Null is the one "none". */
+const planShape = z.strictObject({
+    question: z.string(),
+    population: z.strictObject({ source: z.string(), draw }),
+    arms: z.array(z.strictObject({ name: words })).superRefine(uniquelyNamed),
+    primary_outcome: z.string(),
+    author_check: authorCheck.nullable(),
+    extra: extra.optional(),
+});
+/**
+ * A plan under its old name, `prereg.json`, written by hand before the plan had a schema: open at
+ * every level, its own top-level keys kept in `extra`. A seed makes the draw seeded, none (or null) a
+ * draw of all; a size, and keys of its own deeper down, are not read; the file is never rewritten.
+ */
+const legacyAsPlan = z
+    .looseObject({
+    question: z.string(),
+    population: z.looseObject({
+        source: z.string(),
+        draw: z.looseObject({
+            method: z.string(),
+            seed: z.union([z.string(), z.number()]).nullable().optional(),
+        }),
+    }),
+    arms: z.array(z.looseObject({ name: words })).superRefine(uniquelyNamed),
+    primary_outcome: z.string(),
+    author_check: authorCheck.nullable().optional(),
+})
+    .transform((p) => {
+    const { question, population, arms, primary_outcome, author_check, ...rest } = p;
+    const { method, seed } = population.draw;
+    return {
+        question,
+        population: {
+            source: population.source,
+            draw: seed === undefined || seed === null
+                ? { kind: "all", method }
+                : { kind: "seeded", method, seed },
+        },
+        arms: arms.map((a) => ({ name: a.name })),
+        primary_outcome,
+        author_check: author_check ?? null,
+        extra: rest,
+    };
+});
+/** A text that says something: more than white space. */
+const filled = z.string().regex(/\S/u);
+/** The texts a plan fills before its study runs; what fails here is what is still empty. */
+const readyTexts = z.object({
+    question: filled,
+    population: z.object({
+        source: filled,
+        draw: z.object({ method: filled }),
+    }),
+    primary_outcome: filled,
+});
+/**
+ * A parsed plan, ready when every required text is filled, else a draft naming the empty ones. A
+ * draft that carries the author's check is no plan: the author approved one with empty texts.
+ */
+const readyOrDraft = (p, ctx) => {
+    const checked = readyTexts.safeParse(p);
+    if (checked.success)
+        return { kind: "ready", plan: p };
+    const paths = checked.error.issues.map((i) => i.path.join("."));
+    const empty = PLAN_TEXT_FIELDS.filter((f) => paths.includes(f));
+    if (p.author_check === null)
+        return { kind: "draft", plan: { ...p, author_check: null }, empty };
+    ctx.addIssue({
+        code: "custom",
+        path: ["author_check"],
+        message: `is set, and the plan leaves ${empty.map((f) => `\`${f}\``).join(", ")} empty — the author approves a complete plan: fill them, or set author_check to null`,
+    });
+    return z.NEVER;
+};
+/** A `plan.json`: strict, then ready or draft. */
+const plan = planShape.transform(readyOrDraft);
+/** A `prereg.json`: loose, mapped onto the plan, then ready or draft. */
+const legacyPlan = legacyAsPlan.transform(readyOrDraft);
+/** The proof is used, so the build checks it. */
+export const SCHEMAS_ARE_THE_DOMAIN = true;
+/** The JSON `text` holds, or undefined when it is not JSON. */
+function jsonOf(text) {
+    try {
+        return JSON.parse(text);
+    }
+    catch {
+        return undefined;
+    }
+}
+/** Every reason zod gave, each with the path it is about. */
+const reasons = (issues) => issues
+    .map((i) => `${i.path.length === 0 ? "(top)" : i.path.join(".")}: ${i.message}`)
+    .join("; ");
+/** A `studies.json`'s text, parsed once at the boundary: the registry, or every reason it is not one. */
+export function parseStudyRegistry(text) {
+    const json = jsonOf(text);
+    if (json === undefined)
+        return { ok: false, why: "not JSON" };
+    const parsed = registry.safeParse(json);
+    return parsed.success
+        ? { ok: true, registry: parsed.data }
+        : { ok: false, why: reasons(parsed.error.issues) };
+}
+/** A plan's text, parsed once at the boundary by `schema`: ready, a draft, or every reason it is neither. */
+const planParser = (schema) => (text) => {
+    const json = jsonOf(text);
+    if (json === undefined)
+        return { kind: "unreadable", why: "not JSON" };
+    const parsed = schema.safeParse(json);
+    return parsed.success
+        ? parsed.data
+        : { kind: "unreadable", why: reasons(parsed.error.issues) };
+};
+/** A `plan.json`: strict. */
+export const parseStudyPlan = planParser(plan);
+/** A plan still named `prereg.json`: loose, read only when a row names it. */
+export const parseLegacyPlan = planParser(legacyPlan);
+export const studyRegistryCodec = {
+    parse: parseStudyRegistry,
+    parsePlan: parseStudyPlan,
+    parseLegacyPlan,
+};
+//# sourceMappingURL=index.js.map

package/dist/adapters/study-registry/index.js.map

@@ -0,0 +1 @@
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package/dist/cli.d.ts.map

@@ -1 +1 @@
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