@concordance-wiki/inference 0.1.0

package/dist/duplicates/similarity.js

@@ -0,0 +1,86 @@
+const combiningMarks = /\p{M}+/gu;
+const separators = /[^\p{L}\p{N}]+/gu;
+/** The form base names and titles are compared on: lowercase, accents stripped, punctuation folded to spaces. */
+export function comparisonKey(text) {
+    return text
+        .normalize("NFD")
+        .replace(combiningMarks, "")
+        .toLowerCase()
+        .replace(separators, " ")
+        .trim();
+}
+// Code units rather than code points: base names are compared by the thousands and the keys are already folded.
+function jaro(a, b) {
+    const window = Math.max(0, Math.floor(Math.max(a.length, b.length) / 2) - 1);
+    const matchedA = new Uint8Array(a.length);
+    const matchedB = new Uint8Array(b.length);
+    let matches = 0;
+    for (let index = 0; index < a.length; index++) {
+        const code = a.charCodeAt(index);
+        const end = Math.min(index + window + 1, b.length);
+        for (let other = Math.max(0, index - window); other < end; other++) {
+            if (matchedB[other] === 1 || b.charCodeAt(other) !== code)
+                continue;
+            matchedA[index] = 1;
+            matchedB[other] = 1;
+            matches++;
+            break;
+        }
+    }
+    if (matches === 0)
+        return 0;
+    let transpositions = 0;
+    let other = 0;
+    for (let index = 0; index < a.length; index++) {
+        if (matchedA[index] !== 1)
+            continue;
+        while (matchedB[other] !== 1)
+            other++;
+        if (a.charCodeAt(index) !== b.charCodeAt(other))
+            transpositions++;
+        other++;
+    }
+    return (matches / a.length + matches / b.length + (matches - transpositions / 2) / matches) / 3;
+}
+/** Jaro similarity with the Winkler bonus for a common prefix of up to four characters. */
+export function jaroWinkler(a, b) {
+    const similarity = jaro(a, b);
+    let prefix = 0;
+    // Past the end of either string the code unit is NaN, which never compares equal.
+    while (prefix < 4 && a.charCodeAt(prefix) === b.charCodeAt(prefix))
+        prefix++;
+    return similarity + prefix * 0.1 * (1 - similarity);
+}
+export function nameProfile(key) {
+    const counts = new DataView(new ArrayBuffer(32));
+    let classes = 0;
+    for (let index = 0; index < key.length; index++) {
+        const unitClass = key.charCodeAt(index) & 31;
+        counts.setUint8(unitClass, counts.getUint8(unitClass) + 1);
+        classes |= 1 << unitClass;
+    }
+    return { key, counts, classes };
+}
+/**
+ * An upper bound of the code units two names have in common: their counts merged by class, since
+ * a minimum of sums is at least a sum of minimums. Walks the shared classes only.
+ */
+export function sharedCodeUnits(a, b) {
+    let shared = 0;
+    for (let remaining = a.classes & b.classes; remaining !== 0;) {
+        const unitClass = 31 - Math.clz32(remaining);
+        remaining ^= 1 << unitClass;
+        shared += Math.min(a.counts.getUint8(unitClass), b.counts.getUint8(unitClass));
+    }
+    return shared;
+}
+/** Depth of the common prefix over the deeper folder, 1 for the same folder; the root has depth 0. */
+export function directoryProximity(a, b) {
+    const segmentsA = a.split("/");
+    const segmentsB = b.split("/");
+    let common = 0;
+    while (common < segmentsA.length && segmentsA[common] === segmentsB[common])
+        common++;
+    return common / Math.max(segmentsA.length, segmentsB.length);
+}
+//# sourceMappingURL=similarity.js.map

package/dist/duplicates/similarity.js.map

@@ -0,0 +1 @@
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package/dist/duplicates/types.d.ts

@@ -0,0 +1,97 @@
+import type { Clock, Finding } from "@concordance-wiki/core";
+/** What the reconciliation needs of a resource; `text` is extracted text, never binary content. */
+export interface DuplicateResource {
+    /** Unique per resource; the lock file names resources by it. */
+    id: string;
+    source: string;
+    /** Forward-slash path relative to the source root. */
+    path: string;
+    /** Folder part of `path`, empty at the root. */
+    folder: string;
+    /** File name without its extension. */
+    baseName: string;
+    /** Document property, as a reader plugin reports it. */
+    title?: string;
+    /** First level-one heading of a markdown note. */
+    heading?: string;
+    /** Frontmatter `source`: the twin a note declares, relative to its folder or `<source>:<path>`. */
+    declaredSource?: string;
+    commit?: string;
+    text: string;
+}
+export type DuplicateMode = "estimate" | "exact" | "auto";
+export interface DuplicateOptions {
+    mode: DuplicateMode;
+    /** Estimated Jaccard from which `auto` recomputes the exact one. */
+    exactAbove: number;
+    /** Word-count ratio under which the content signal is capped at the lower weight. */
+    sizeRatioMin: number;
+    shingleSize: number;
+    minhashFunctions: number;
+    /** Strictly above: merged. */
+    mergeAbove: number;
+    /** At least: a `W-DUP-CANDIDATE` finding. */
+    candidateAbove: number;
+}
+/** Ordered pairs of resource identifiers, as `duplicates.merged` and `duplicates.separated` of the lock file. */
+export interface DuplicateLock {
+    merged?: readonly (readonly [string, string])[];
+    separated?: readonly (readonly [string, string])[];
+}
+export interface DuplicateInput {
+    resources: readonly DuplicateResource[];
+    /** The words of a text in comparison form, stopwords removed; the language pack of the source provides it. */
+    normalizeText: (text: string) => string[];
+    lock?: DuplicateLock;
+    /** Measures the time spent; without it the statistics report zero. */
+    clock?: Clock;
+}
+/** One contribution to the score of a pair. */
+export interface DuplicateSignal {
+    name: "declared" | "same_name" | "similar_name" | "same_title" | "similar_content" | "same_commit" | "same_directory";
+    weight: number;
+    /** Named in the finding message next to the weight. */
+    detail: string;
+}
+export interface DuplicatePair {
+    /** The lower identifier. */
+    a: string;
+    b: string;
+    /** Sum of the signal weights, capped at 1 and rounded to four decimals. */
+    score: number;
+    /** By weight then by name, so that the first one names the grouping criterion. */
+    signals: DuplicateSignal[];
+}
+export interface DuplicateRepresentation {
+    id: string;
+    path: string;
+    /** `markdown` for a note, otherwise the lowercase extension, `file` without one. */
+    format: string;
+}
+/** Several resources merged into one entity. */
+export interface DuplicateGroup {
+    /** The identifier of the markdown representation, or the lowest identifier without one. */
+    id: string;
+    representations: DuplicateRepresentation[];
+    /** What grouped the resources, for the page to name it. */
+    criterion: string;
+}
+export interface DuplicateStats {
+    resources: number;
+    /** Pairs enumerated by the LSH banding, the only ones whose content is compared. */
+    candidatePairs: number;
+    /** Pairs whose signals were scored: brought together by their content, a base name, a title or a declaration, and not separated by the lock. */
+    scoredPairs: number;
+    exactVerifications: number;
+    merged: number;
+    candidates: number;
+    timeMs: number;
+}
+export interface DuplicateResult {
+    groups: DuplicateGroup[];
+    findings: Finding[];
+    /** Every scored pair, at or above `candidateAbove`, by identifiers. */
+    pairs: DuplicatePair[];
+    stats: DuplicateStats;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/duplicates/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/duplicates/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/duplicates/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/duplicates/types.ts"],"names":[],"mappings":""}

package/dist/explicit/links.d.ts

@@ -0,0 +1,30 @@
+import type { ExplicitLinksInput, ExplicitLinksResult, LinkableEntity } from "./types.js";
+/** The files of every source, by source name. */
+export type SourceFiles = ReadonlyMap<string, ReadonlySet<string>>;
+/** Where a written link lands: a file of a source, another source when cross-source links are off, nothing, or the web. */
+export type LocatedLink = {
+    kind: "external";
+} | {
+    kind: "denied";
+    source: string;
+} | {
+    kind: "missing";
+} | {
+    kind: "file";
+    source: string;
+    path: string;
+    anchor?: string;
+};
+/**
+ * The file a link target reaches from a note: in its own source, in a source named as a prefix
+ * or reached as a sibling folder when cross-source links are on.
+ */
+export declare function locateLink(target: string, from: Pick<LinkableEntity["source"], "name" | "path">, files: SourceFiles, crossSource: boolean): LocatedLink;
+/**
+ * Markdown links are the strongest relation the tool knows: every link written in a note gives a
+ * link at the confidence of `explicit_link`, with the file, the line and the text as provenance. A
+ * link to another note is `related` until the relation typing step names it from the type pair; a
+ * link to a non-markdown file is `documents`, from the resource to the note.
+ */
+export declare function explicitLinks(input: ExplicitLinksInput): ExplicitLinksResult;
+//# sourceMappingURL=links.d.ts.map

package/dist/explicit/links.d.ts.map

@@ -0,0 +1 @@
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package/dist/explicit/links.js

@@ -0,0 +1,173 @@
+import { compareFindings, compareLinks, compareProvenances, identifierFor, } from "@concordance-wiki/core";
+import { resolveLink } from "@concordance-wiki/ingest";
+const NO_FILES = new Set();
+function fileKey(source, path) {
+    return `${source}/${path}`;
+}
+function anchorOf(anchor) {
+    return anchor === undefined ? {} : { anchor };
+}
+function inSource(source, path, anchor) {
+    return { kind: "file", source, path, ...anchorOf(anchor) };
+}
+/** `<source>:<path>` names another source; any other prefix is a URL scheme left to `resolveLink`. */
+function prefixedSource(target, files) {
+    const colon = target.indexOf(":");
+    if (colon === -1)
+        return undefined;
+    const source = target.slice(0, colon);
+    const sourceFiles = files.get(source);
+    return sourceFiles === undefined
+        ? undefined
+        : { source, rest: target.slice(colon + 1), sourceFiles };
+}
+/**
+ * A relative link that climbs one level above the source root and lands in `<source>/<path>` reaches
+ * a sibling source: the sources of one repository are often sibling folders.
+ */
+function siblingSource(path, files) {
+    const [up, source, ...rest] = path.split("/");
+    if (up !== ".." || source === undefined || rest.length === 0)
+        return undefined;
+    const sourceFiles = files.get(source);
+    return sourceFiles === undefined ? undefined : { source, rest: rest.join("/"), sourceFiles };
+}
+/**
+ * The file a link target reaches from a note: in its own source, in a source named as a prefix
+ * or reached as a sibling folder when cross-source links are on.
+ */
+export function locateLink(target, from, files, crossSource) {
+    const prefixed = prefixedSource(target, files);
+    if (prefixed !== undefined) {
+        if (!crossSource)
+            return { kind: "denied", source: prefixed.source };
+        const resolved = resolveLink(prefixed.rest, { path: "", sourceFiles: prefixed.sourceFiles });
+        // An empty path resolves to the linking file, which is never a file of the other source.
+        return resolved.kind === "internal" && prefixed.sourceFiles.has(resolved.path)
+            ? inSource(prefixed.source, resolved.path, resolved.anchor)
+            : { kind: "missing" };
+    }
+    const resolved = resolveLink(target, {
+        path: from.path,
+        sourceFiles: files.get(from.name) ?? NO_FILES,
+    });
+    if (resolved.kind === "external")
+        return { kind: "external" };
+    if (resolved.kind === "internal")
+        return inSource(from.name, resolved.path, resolved.anchor);
+    const sibling = siblingSource(resolved.path, files);
+    if (sibling === undefined)
+        return { kind: "missing" };
+    if (!crossSource)
+        return { kind: "denied", source: sibling.source };
+    return sibling.sourceFiles.has(sibling.rest)
+        ? inSource(sibling.source, sibling.rest, resolved.anchor)
+        : { kind: "missing" };
+}
+function brokenLink(entity, link) {
+    return {
+        check: "E-LINK-BROKEN",
+        severity: "error",
+        source: entity.source.name,
+        path: entity.source.path,
+        line: link.line,
+        entity: entity.id,
+        message: `link "${link.target}" in ${entity.source.path} points to no file of source ${entity.source.name}`,
+        remediation: "Fix the path; the linter rewrites the link under --fix when exactly one file matches the old name.",
+    };
+}
+function crossSourceLink(entity, link, source) {
+    return {
+        check: "W-LINK-CROSS-SOURCE",
+        severity: "warning",
+        source: entity.source.name,
+        path: entity.source.path,
+        line: link.line,
+        entity: entity.id,
+        message: `link "${link.target}" in ${entity.source.path} leaves source ${entity.source.name} for source ${source}; cross-source links are disabled`,
+        remediation: "Set inference.cross_source_links to true in concordance.yaml to resolve links across sources, or link to a note of the same source.",
+    };
+}
+function outcomeOf(entity, link, context) {
+    const target = locateLink(link.target, entity.source, context.files, context.crossSource);
+    if (target.kind === "denied")
+        return { finding: crossSourceLink(entity, link, target.source) };
+    if (target.kind === "missing")
+        return { finding: brokenLink(entity, link) };
+    if (target.kind === "external")
+        return undefined;
+    const provenance = {
+        method: "explicit_link",
+        confidence: context.confidence,
+        path: entity.source.path,
+        line: link.line,
+        text: link.text,
+        ...anchorOf(target.anchor),
+    };
+    if (!target.path.endsWith(".md")) {
+        // The resource entities are named from their path alone, so the same derivation finds them.
+        const resource = identifierFor({ source: target.source, path: target.path, typeSuffixes: [] });
+        return { from: resource.id, to: entity.id, relation: "documents", provenance };
+    }
+    const to = context.entities.get(fileKey(target.source, target.path));
+    if (to === undefined || to.id === entity.id)
+        return undefined;
+    // A written link says that two notes are related, not how: the relation typing step names it.
+    return { from: entity.id, to: to.id, relation: "related", provenance };
+}
+/** Several links to the same target keep every provenance; combining their confidences is a later step. */
+function record(merged, found, confidence) {
+    const { from, to, relation, provenance } = found;
+    const key = `${from} ${to} ${relation}`;
+    const existing = merged.get(key);
+    if (existing === undefined) {
+        merged.set(key, { from, to, relation, attributes: {}, confidence, provenance: [provenance] });
+    }
+    else {
+        existing.provenance.push(provenance);
+    }
+}
+/**
+ * Markdown links are the strongest relation the tool knows: every link written in a note gives a
+ * link at the confidence of `explicit_link`, with the file, the line and the text as provenance. A
+ * link to another note is `related` until the relation typing step names it from the type pair; a
+ * link to a non-markdown file is `documents`, from the resource to the note.
+ */
+export function explicitLinks(input) {
+    const confidence = input.profile.confidence.explicit_link ?? 1;
+    const files = new Map();
+    for (const resource of input.resources) {
+        const paths = files.get(resource.source) ?? new Set();
+        paths.add(resource.path);
+        files.set(resource.source, paths);
+    }
+    const entities = new Map(input.entities.map((entity) => [fileKey(entity.source.name, entity.source.path), entity]));
+    const context = {
+        entities,
+        files,
+        crossSource: input.inference?.cross_source_links ?? false,
+        confidence,
+    };
+    const merged = new Map();
+    const findings = [];
+    for (const [key, document] of input.documents) {
+        const entity = entities.get(key);
+        if (entity === undefined)
+            continue;
+        for (const link of document.links) {
+            const outcome = outcomeOf(entity, link, context);
+            if (outcome === undefined)
+                continue;
+            if ("finding" in outcome) {
+                findings.push(outcome.finding);
+                continue;
+            }
+            record(merged, outcome, confidence);
+        }
+    }
+    const links = [...merged.values()].sort(compareLinks);
+    for (const link of links)
+        link.provenance.sort(compareProvenances);
+    return { links, findings: findings.toSorted(compareFindings) };
+}
+//# sourceMappingURL=links.js.map

package/dist/explicit/links.js.map

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package/dist/explicit/types.d.ts

@@ -0,0 +1,35 @@
+import type { Finding, InferenceConfig, Link } from "@concordance-wiki/core";
+import type { ParsedMarkdown } from "@concordance-wiki/ingest";
+import type { Profile } from "@concordance-wiki/profile";
+/** What inference needs of a typed entity: its identifier, its type, its title, its frontmatter and the file it comes from. */
+export interface LinkableEntity {
+    id: string;
+    type: string;
+    title: string;
+    /** Frontmatter keys that are not common attributes; references are raw strings or lists of strings. */
+    attributes: Record<string, unknown>;
+    source: {
+        name: string;
+        /** Forward-slash path relative to the source root. */
+        path: string;
+    };
+}
+/** Every ingested file of every source, markdown or not. */
+export interface SourceResource {
+    source: string;
+    /** Forward-slash path relative to the source root. */
+    path: string;
+}
+export interface ExplicitLinksInput {
+    entities: readonly LinkableEntity[];
+    resources: readonly SourceResource[];
+    /** Parsed markdown files keyed by `<source name>/<path>`. */
+    documents: ReadonlyMap<string, ParsedMarkdown>;
+    profile: Profile;
+    inference?: InferenceConfig;
+}
+export interface ExplicitLinksResult {
+    links: Link[];
+    findings: Finding[];
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/explicit/types.d.ts.map

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package/dist/explicit/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/explicit/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/explicit/types.ts"],"names":[],"mappings":""}

package/dist/frontmatter/links.d.ts

@@ -0,0 +1,21 @@
+import { type Finding, type Link } from "@concordance-wiki/core";
+import type { Profile } from "@concordance-wiki/profile";
+import type { LinkableEntity } from "../explicit/types.js";
+export interface FrontmatterLinksInput {
+    entities: readonly LinkableEntity[];
+    profile: Profile;
+    /** Overrides `confidence.frontmatter_ref` of the profile. */
+    confidence?: number;
+}
+export interface FrontmatterLinksResult {
+    links: Link[];
+    findings: Finding[];
+}
+/**
+ * A reference-typed attribute with a relation in the profile turns each of its values into a link of
+ * that relation, carrying the attributes the profile declares, such as `accesses` in `read` mode for
+ * `reads`. A value that resolves to nothing or to several titles is reported and gives no link; a
+ * note of a type the attribute does not accept gives its link, for the relation typing step to judge.
+ */
+export declare function frontmatterLinks(input: FrontmatterLinksInput): FrontmatterLinksResult;
+//# sourceMappingURL=links.d.ts.map

package/dist/frontmatter/links.d.ts.map

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package/dist/frontmatter/links.js

@@ -0,0 +1,131 @@
+import { compareFindings, compareLinks, } from "@concordance-wiki/core";
+import { indexEntities, resolveReference } from "./resolve.js";
+/** The confidence the specification gives the method when the profile is silent. */
+const DEFAULT_CONFIDENCE = 0.9;
+const REMEDIATION = "Write the identifier, the path relative to the source root or the exact title of an existing note, or remove the reference.";
+function isReference(definition) {
+    return ((definition.type === "ref" || definition.type === "ref[]") && definition.relation !== undefined);
+}
+// Code-unit order, not locale order: the output must not depend on the collation data of the runtime.
+function byCodeUnit(a, b) {
+    return Number(a > b) - Number(a < b);
+}
+function canonical(attributes) {
+    return JSON.stringify(Object.keys(attributes)
+        .sort(byCodeUnit)
+        .map((key) => [key, attributes[key]]));
+}
+function unresolved(reference, message) {
+    const { entity, attribute } = reference;
+    return {
+        check: "W-REF-UNRESOLVED",
+        severity: "warning",
+        source: entity.source.name,
+        path: entity.source.path,
+        line: 1,
+        entity: entity.id,
+        message: `${message} in attribute ${attribute} of ${entity.source.path}`,
+        remediation: REMEDIATION,
+    };
+}
+/**
+ * The note a value names, whatever its type: a reference to an existing note of a type the relation
+ * does not admit is a link outside the profile matrix, which the relation typing step drops with
+ * `E-META-REL`, not an unresolved reference.
+ */
+function targetOf(value, reference, index) {
+    const resolution = resolveReference(value, { from: reference.entity, index });
+    if (resolution.kind === "unresolved") {
+        return {
+            finding: unresolved(reference, `reference "${value}" matches no identifier, path or title`),
+        };
+    }
+    if (resolution.kind === "ambiguous") {
+        const candidates = resolution.candidates.map((candidate) => candidate.id).join(", ");
+        return {
+            finding: unresolved(reference, `reference "${value}" is the title of several notes (${candidates})`),
+        };
+    }
+    return { target: resolution.entity };
+}
+function record(collector, reference, target) {
+    const { entity, attribute, definition } = reference;
+    const { relation } = definition;
+    const [from, to] = definition.inverse === true ? [target.id, entity.id] : [entity.id, target.id];
+    const attributes = { ...definition.attributes };
+    const serialised = canonical(attributes);
+    const provenance = {
+        method: "frontmatter_ref",
+        confidence: collector.confidence,
+        path: entity.source.path,
+        line: 1,
+        attribute,
+    };
+    const key = `${from} ${to} ${relation} ${serialised}`;
+    const existing = collector.merged.get(key);
+    if (existing === undefined) {
+        collector.merged.set(key, {
+            link: {
+                from,
+                to,
+                relation,
+                attributes,
+                confidence: collector.confidence,
+                provenance: [provenance],
+            },
+            attributes: serialised,
+        });
+    }
+    else {
+        // Several references to one target keep every provenance; combining their confidences is a later step.
+        existing.link.provenance.push(provenance);
+    }
+}
+/** Every value of one reference attribute: a string names a note, anything else is reported. */
+function collect(collector, reference, raw) {
+    const values = Array.isArray(raw) ? raw : [raw];
+    for (const value of values) {
+        if (typeof value !== "string") {
+            const detail = `value ${JSON.stringify(value)} is neither a string nor a list of strings`;
+            collector.findings.push(unresolved(reference, detail));
+            continue;
+        }
+        const resolved = targetOf(value, reference, collector.index);
+        if ("finding" in resolved) {
+            collector.findings.push(resolved.finding);
+        }
+        else if (resolved.target.id !== reference.entity.id) {
+            record(collector, reference, resolved.target);
+        }
+    }
+}
+/**
+ * A reference-typed attribute with a relation in the profile turns each of its values into a link of
+ * that relation, carrying the attributes the profile declares, such as `accesses` in `read` mode for
+ * `reads`. A value that resolves to nothing or to several titles is reported and gives no link; a
+ * note of a type the attribute does not accept gives its link, for the relation typing step to judge.
+ */
+export function frontmatterLinks(input) {
+    const { entities, profile } = input;
+    const collector = {
+        index: indexEntities(entities),
+        confidence: input.confidence ?? profile.confidence.frontmatter_ref ?? DEFAULT_CONFIDENCE,
+        merged: new Map(),
+        findings: [],
+    };
+    for (const entity of entities) {
+        const declared = profile.types[entity.type]?.attributes ?? {};
+        for (const [attribute, definition] of Object.entries(declared)) {
+            const raw = entity.attributes[attribute];
+            if (!isReference(definition) || raw === undefined)
+                continue;
+            collect(collector, { entity, attribute, definition }, raw);
+        }
+    }
+    // The provenances of one link all come from one note, at line 1: they are already in canonical order.
+    const links = [...collector.merged.values()]
+        .sort((a, b) => compareLinks(a.link, b.link) || byCodeUnit(a.attributes, b.attributes))
+        .map((entry) => entry.link);
+    return { links, findings: collector.findings.toSorted(compareFindings) };
+}
+//# sourceMappingURL=links.js.map

package/dist/frontmatter/links.js.map

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