@alisio/plugin-thesis 0.1.0

package/dist/research/flow.js.map

@@ -0,0 +1 @@
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package/dist/research/library.d.ts

@@ -0,0 +1,79 @@
+import { type EvidenceRecord, type EvidenceStatus, type SectionId } from "../types.js";
+import { type RecordDraft } from "./verify.js";
+/** Paths relative to the thesis root. */
+export declare const evidencePaths: {
+    readonly library: "evidence/library.jsonl";
+    readonly rejected: "evidence/rejected.jsonl";
+    readonly searchLog: "evidence/search-log.jsonl";
+    readonly bibliography: "bibliography/references.bib";
+    readonly dossiers: "evidence/dossiers";
+};
+/** Schema validation of one library line (check EVD-001). Returns human-readable problems. */
+export declare function validateEvidenceRecord(value: unknown): string[];
+export interface LibraryParse {
+    records: EvidenceRecord[];
+    errors: {
+        line: number;
+        message: string;
+    }[];
+}
+export declare function parseLibraryText(text: string | undefined): LibraryParse;
+export declare function readLibrary(base: string): Promise<EvidenceRecord[]>;
+export declare function serializeLibrary(records: readonly EvidenceRecord[]): string;
+export declare function writeLibrary(base: string, records: readonly EvidenceRecord[]): Promise<void>;
+export declare const evidenceId: (counter: number) => string;
+/** Next id counter: never below the state counter or the highest id already in the library. */
+export declare function nextEvidenceCounter(stateCounter: number, records: readonly EvidenceRecord[]): number;
+/** `[a-z][a-z0-9]{1,30}\d{4}[a-z]?`: author family (or a title word), year, then a disambiguator. */
+export declare function allocateCiteKey(draft: Pick<RecordDraft, "authors" | "title" | "year">, taken: ReadonlySet<string>): string;
+export interface AppraisalInput {
+    relevance: "high" | "medium" | "low";
+    evidenceType: string;
+    limitations: string[];
+    supports: string[];
+    location?: string | undefined;
+    permittedUse: EvidenceRecord["permittedUse"];
+}
+export interface AddResult {
+    record: EvidenceRecord;
+    merged: boolean;
+}
+/**
+ * Add a verified draft to the in-memory library, or merge it into the oldest duplicate. The
+ * `counter` object is advanced when a new id is allocated.
+ */
+export declare function addOrMerge(records: EvidenceRecord[], draft: RecordDraft, appraisal: AppraisalInput, sectionId: SectionId, counter: {
+    value: number;
+}, status?: EvidenceStatus): AddResult;
+export declare const isCitable: (record: Pick<EvidenceRecord, "status">) => boolean;
+/** Citable for a section: a citable status, or CONTEXTUAL_ONLY with the user's explicit approval. */
+export declare function citableForSection(record: EvidenceRecord, contextualApprovals: readonly string[] | undefined): boolean;
+export interface RejectedEntry {
+    at: string;
+    sectionId: SectionId;
+    identifier: string;
+    title?: string;
+    status: "UNVERIFIED" | "REJECTED";
+    reason: string;
+    detail?: string;
+}
+export interface SearchLogEntry {
+    at: string;
+    sectionId: SectionId;
+    source: string;
+    query: string;
+    filters: {
+        fromYear?: number;
+        toYear?: number;
+        language?: string;
+        limit: number;
+    };
+    hits: number;
+    selected: string[];
+    error?: string;
+}
+export declare function readJsonl<T>(path: string): Promise<T[]>;
+export declare function appendSearchLog(base: string, entries: readonly SearchLogEntry[]): Promise<void>;
+export declare function readSearchLog(base: string): Promise<SearchLogEntry[]>;
+export declare function appendRejected(base: string, entries: readonly RejectedEntry[]): Promise<void>;
+//# sourceMappingURL=library.d.ts.map

package/dist/research/library.d.ts.map

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package/dist/research/library.js

@@ -0,0 +1,319 @@
+import { readFile } from "node:fs/promises";
+import { join } from "node:path";
+import { atomicWrite, canonicalLine } from "../storage.js";
+import { citableStatuses, evidenceStatuses, evidenceTypes, idPatterns, permittedUses, } from "../types.js";
+import { fold, foldFamily, titleKey } from "./verify.js";
+/** Paths relative to the thesis root. */
+export const evidencePaths = {
+    library: "evidence/library.jsonl",
+    rejected: "evidence/rejected.jsonl",
+    searchLog: "evidence/search-log.jsonl",
+    bibliography: "bibliography/references.bib",
+    dossiers: "evidence/dossiers",
+};
+const isRecord = (value) => Boolean(value) && typeof value === "object" && !Array.isArray(value);
+const isIso = (value) => typeof value === "string" && !Number.isNaN(Date.parse(value));
+const knownKeys = new Set([
+    "id",
+    "citeKey",
+    "type",
+    "title",
+    "authors",
+    "year",
+    "containerTitle",
+    "volume",
+    "issue",
+    "pages",
+    "publisher",
+    "placeOfPublication",
+    "doi",
+    "isbn",
+    "issn",
+    "url",
+    "language",
+    "retrievedAt",
+    "verification",
+    "status",
+    "appraisal",
+    "permittedUse",
+    "sections",
+]);
+const optionalStrings = [
+    "containerTitle",
+    "volume",
+    "issue",
+    "pages",
+    "publisher",
+    "placeOfPublication",
+    "doi",
+    "isbn",
+    "issn",
+    "url",
+    "language",
+];
+/** Schema validation of one library line (check EVD-001). Returns human-readable problems. */
+export function validateEvidenceRecord(value) {
+    if (!isRecord(value))
+        return ["record must be a JSON object"];
+    const errors = [];
+    for (const key of Object.keys(value))
+        if (!knownKeys.has(key))
+            errors.push(`unknown field ${key}`);
+    if (typeof value.id !== "string" || !idPatterns.evidence.test(value.id))
+        errors.push("id must look like EVD-00231");
+    if (typeof value.citeKey !== "string" || !idPatterns.citationKey.test(value.citeKey))
+        errors.push("citeKey is not a valid citation key");
+    if (!evidenceTypes.includes(value.type))
+        errors.push("type is not a known evidence type");
+    if (typeof value.title !== "string" || !value.title.trim() || value.title.length > 600)
+        errors.push("title must be 1 to 600 characters");
+    if (!Array.isArray(value.authors) ||
+        !value.authors.every((author) => isRecord(author) && typeof author.family === "string" && author.family.trim())) {
+        errors.push("authors must be a list of { family }");
+    }
+    if (!Number.isInteger(value.year) ||
+        value.year < 1000 ||
+        value.year > 2200)
+        errors.push("year must be an integer");
+    for (const key of optionalStrings) {
+        if (value[key] !== undefined && typeof value[key] !== "string")
+            errors.push(`${key} must be a string`);
+    }
+    if (!isIso(value.retrievedAt))
+        errors.push("retrievedAt must be an ISO date");
+    const verification = value.verification;
+    if (!isRecord(verification) ||
+        !["crossref", "openalex", "arxiv", "official_domain", "user_supplied"].includes(verification.method) ||
+        typeof verification.metadataMatch !== "number" ||
+        verification.metadataMatch < 0 ||
+        verification.metadataMatch > 1 ||
+        typeof verification.retracted !== "boolean" ||
+        !isIso(verification.checkedAt)) {
+        errors.push("verification is malformed");
+    }
+    if (!evidenceStatuses.includes(value.status))
+        errors.push("status is not a known status");
+    const appraisal = value.appraisal;
+    if (!isRecord(appraisal) ||
+        !["high", "medium", "low"].includes(appraisal.relevance) ||
+        typeof appraisal.evidenceType !== "string" ||
+        !Array.isArray(appraisal.limitations) ||
+        !Array.isArray(appraisal.supports)) {
+        errors.push("appraisal is malformed");
+    }
+    if (!Array.isArray(value.permittedUse) ||
+        !value.permittedUse.every((use) => permittedUses.includes(use))) {
+        errors.push("permittedUse is malformed");
+    }
+    if (!Array.isArray(value.sections) ||
+        !value.sections.every((section) => typeof section === "string" && idPatterns.section.test(section))) {
+        errors.push("sections must be a list of SEC ids");
+    }
+    return errors;
+}
+export function parseLibraryText(text) {
+    const result = { records: [], errors: [] };
+    if (!text)
+        return result;
+    text.split("\n").forEach((raw, index) => {
+        if (!raw.trim())
+            return;
+        let value;
+        try {
+            value = JSON.parse(raw);
+        }
+        catch {
+            result.errors.push({ line: index + 1, message: "line is not valid JSON" });
+            return;
+        }
+        const problems = validateEvidenceRecord(value);
+        if (problems.length > 0) {
+            for (const message of problems)
+                result.errors.push({ line: index + 1, message });
+            return;
+        }
+        result.records.push(value);
+    });
+    return result;
+}
+async function readText(path) {
+    try {
+        return await readFile(path, "utf8");
+    }
+    catch (error) {
+        if (error.code === "ENOENT")
+            return undefined;
+        throw error;
+    }
+}
+export async function readLibrary(base) {
+    const parsed = parseLibraryText(await readText(join(base, evidencePaths.library)));
+    if (parsed.errors.length > 0) {
+        const first = parsed.errors[0];
+        throw new Error(`evidence/library.jsonl is invalid (line ${first?.line}: ${first?.message}); run /thesis:check`);
+    }
+    return parsed.records;
+}
+const byId = (a, b) => (a.id < b.id ? -1 : a.id > b.id ? 1 : 0);
+export function serializeLibrary(records) {
+    const lines = [...records].sort(byId).map((record) => canonicalLine(record));
+    return lines.length ? `${lines.join("\n")}\n` : "";
+}
+export async function writeLibrary(base, records) {
+    await atomicWrite(join(base, evidencePaths.library), serializeLibrary(records));
+}
+// ---------------------------------------------------------------------------------------------
+// Ids and citation keys
+// ---------------------------------------------------------------------------------------------
+export const evidenceId = (counter) => `EVD-${String(counter).padStart(5, "0")}`;
+/** Next id counter: never below the state counter or the highest id already in the library. */
+export function nextEvidenceCounter(stateCounter, records) {
+    const highest = records.reduce((max, record) => Math.max(max, Number(record.id.slice(4))), 0);
+    return Math.max(stateCounter, highest) + 1;
+}
+const stopForKey = new Set([
+    "the",
+    "a",
+    "an",
+    "el",
+    "la",
+    "los",
+    "las",
+    "de",
+    "del",
+    "un",
+    "una",
+    "of",
+    "on",
+    "for",
+]);
+/** `[a-z][a-z0-9]{1,30}\d{4}[a-z]?`: author family (or a title word), year, then a disambiguator. */
+export function allocateCiteKey(draft, taken) {
+    const first = draft.authors[0]?.family;
+    let stem = first ? foldFamily(first) : "";
+    if (!stem) {
+        stem =
+            fold(draft.title)
+                .split(/[^a-z0-9]+/)
+                .filter((word) => word && !stopForKey.has(word))[0] ?? "";
+    }
+    stem = stem.replace(/^[^a-z]+/, "").slice(0, 24);
+    if (stem.length < 2)
+        stem = "anon";
+    const base = `${stem}${draft.year}`;
+    if (!taken.has(base))
+        return base;
+    for (const letter of "bcdefghijklmnopqrstuvwxyz") {
+        const candidate = `${base}${letter}`;
+        if (!taken.has(candidate))
+            return candidate;
+    }
+    throw new Error(`Too many records share the citation key base ${base}`);
+}
+const relevanceRank = { high: 0, medium: 1, low: 2 };
+function findDuplicate(records, draft) {
+    const doi = draft.doi?.toLowerCase();
+    const key = titleKey(draft.title);
+    return [...records]
+        .sort(byId)
+        .find((record) => (doi !== undefined && record.doi?.toLowerCase() === doi) ||
+        (record.year === draft.year && titleKey(record.title) === key));
+}
+/**
+ * Add a verified draft to the in-memory library, or merge it into the oldest duplicate. The
+ * `counter` object is advanced when a new id is allocated.
+ */
+export function addOrMerge(records, draft, appraisal, sectionId, counter, status = draft.status) {
+    const existing = findDuplicate(records, draft);
+    if (existing) {
+        const sections = new Set([...existing.sections, sectionId]);
+        existing.sections = [...sections].sort();
+        existing.appraisal = {
+            ...existing.appraisal,
+            relevance: relevanceRank[appraisal.relevance] < relevanceRank[existing.appraisal.relevance]
+                ? appraisal.relevance
+                : existing.appraisal.relevance,
+            limitations: [...new Set([...existing.appraisal.limitations, ...appraisal.limitations])],
+            supports: [...new Set([...existing.appraisal.supports, ...appraisal.supports])],
+        };
+        existing.permittedUse = permittedUses.filter((use) => existing.permittedUse.includes(use) || appraisal.permittedUse.includes(use));
+        return { record: existing, merged: true };
+    }
+    const taken = new Set(records.map((record) => record.citeKey));
+    const record = {
+        id: evidenceId(counter.value),
+        citeKey: allocateCiteKey(draft, taken),
+        type: draft.type,
+        title: draft.title,
+        authors: draft.authors,
+        year: draft.year,
+        ...(draft.containerTitle ? { containerTitle: draft.containerTitle } : {}),
+        ...(draft.volume ? { volume: draft.volume } : {}),
+        ...(draft.issue ? { issue: draft.issue } : {}),
+        ...(draft.pages ? { pages: draft.pages } : {}),
+        ...(draft.publisher ? { publisher: draft.publisher } : {}),
+        ...(draft.placeOfPublication ? { placeOfPublication: draft.placeOfPublication } : {}),
+        ...(draft.doi ? { doi: draft.doi } : {}),
+        ...(draft.isbn ? { isbn: draft.isbn } : {}),
+        ...(draft.issn ? { issn: draft.issn } : {}),
+        ...(draft.url ? { url: draft.url } : {}),
+        ...(draft.language ? { language: draft.language } : {}),
+        retrievedAt: draft.verification.checkedAt.slice(0, 10),
+        verification: draft.verification,
+        status,
+        appraisal: {
+            relevance: appraisal.relevance,
+            evidenceType: appraisal.evidenceType,
+            limitations: appraisal.limitations,
+            supports: appraisal.supports,
+            ...(appraisal.location ? { location: appraisal.location } : {}),
+        },
+        permittedUse: appraisal.permittedUse,
+        sections: [sectionId],
+    };
+    counter.value += 1;
+    records.push(record);
+    return { record, merged: false };
+}
+export const isCitable = (record) => citableStatuses.includes(record.status);
+/** Citable for a section: a citable status, or CONTEXTUAL_ONLY with the user's explicit approval. */
+export function citableForSection(record, contextualApprovals) {
+    return (isCitable(record) ||
+        (record.status === "CONTEXTUAL_ONLY" && (contextualApprovals ?? []).includes(record.id)));
+}
+async function appendLines(path, entries) {
+    if (entries.length === 0)
+        return;
+    const current = (await readText(path)) ?? "";
+    const prefix = current && !current.endsWith("\n") ? `${current}\n` : current;
+    await atomicWrite(path, `${prefix}${entries.map((entry) => canonicalLine(entry)).join("\n")}\n`);
+}
+export async function readJsonl(path) {
+    const text = await readText(path);
+    if (!text)
+        return [];
+    const values = [];
+    for (const line of text.split("\n")) {
+        if (!line.trim())
+            continue;
+        try {
+            values.push(JSON.parse(line));
+        }
+        catch {
+            // A damaged log line never blocks a research run.
+        }
+    }
+    return values;
+}
+export async function appendSearchLog(base, entries) {
+    await appendLines(join(base, evidencePaths.searchLog), entries);
+}
+export async function readSearchLog(base) {
+    return readJsonl(join(base, evidencePaths.searchLog));
+}
+export async function appendRejected(base, entries) {
+    const known = new Set((await readJsonl(join(base, evidencePaths.rejected))).map((entry) => `${entry.sectionId}|${entry.identifier}|${entry.reason}`));
+    const fresh = entries.filter((entry) => !known.has(`${entry.sectionId}|${entry.identifier}|${entry.reason}`));
+    await appendLines(join(base, evidencePaths.rejected), fresh);
+}
+//# sourceMappingURL=library.js.map

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package/dist/research/verify.d.ts

@@ -0,0 +1,80 @@
+import type { ComplianceProfile } from "../policy/resolver.js";
+import { type EvidenceRecord, type EvidenceStatus, type EvidenceType } from "../types.js";
+import { type Identifier, type ScholarClient, type ScholarRecord } from "./client.js";
+/** Lowercase, remove diacritics. */
+export declare function fold(text: string): string;
+export declare function titleTokens(title: string, language?: string | null): Set<string>;
+export declare function jaccard(a: ReadonlySet<string>, b: ReadonlySet<string>): number;
+export declare function titleSimilarity(a: string, b: string, language?: string | null): number;
+/** Stable key for duplicate detection: folded title tokens in order, plus the year. */
+export declare function titleKey(title: string): string;
+export declare function foldFamily(name: string): string;
+export interface OfficialDomains {
+    primary: {
+        hosts: string[];
+        allowedTypes: EvidenceType[];
+    }[];
+    indexing: string[];
+}
+export declare const officialDomainsFromProfile: (profile: ComplianceProfile | undefined) => OfficialDomains;
+/** The lowercase hostname of an http(s) URL without credentials; undefined otherwise. */
+export declare function hostOf(url: string | undefined | null): string | undefined;
+export declare const primaryTypes: readonly EvidenceType[];
+export type DomainDecision = {
+    tier: "primary";
+} | {
+    tier: "indexing";
+} | {
+    tier: "type_not_allowed";
+} | {
+    tier: "none";
+};
+export declare function classifyHost(url: string | undefined | null, type: EvidenceType | undefined, domains: OfficialDomains): DomainDecision;
+/** What a child claims about a candidate; code compares it with what the source returns. */
+export interface Candidate {
+    identifier: string;
+    title: string;
+    firstAuthor?: string | null;
+    year: number;
+    type?: EvidenceType;
+    url?: string;
+    language?: string;
+    /** The user supplied this source; there is no claimed metadata to compare with. */
+    userSupplied?: boolean;
+}
+export type RecordDraft = Pick<EvidenceRecord, "type" | "title" | "authors" | "year" | "containerTitle" | "volume" | "issue" | "pages" | "publisher" | "placeOfPublication" | "doi" | "isbn" | "issn" | "url" | "language" | "verification" | "status">;
+export interface VerificationResult {
+    status: EvidenceStatus;
+    /** Machine reason when the status is UNVERIFIED or REJECTED. */
+    reason?: string;
+    detail?: string;
+    /** Present whenever a source answered, even for UNVERIFIED/REJECTED outcomes. */
+    record?: RecordDraft;
+    /** Abstract of the resolved record (not persisted); helps the auditor appraise relevance. */
+    abstract?: string;
+}
+export interface VerifyContext {
+    client: Pick<ScholarClient, "resolve">;
+    domains: OfficialDomains;
+    now: () => Date;
+    signal?: AbortSignal;
+    /** Ask OpenAlex too after a Crossref hit, so `is_retracted` is honored (default true). */
+    crossCheckRetraction?: boolean;
+}
+export declare const similarityThreshold = 0.85;
+/** The status code would give a resolved record whose metadata matches (spec 8.4). */
+export declare function suggestStatus(record: ScholarRecord, domains: OfficialDomains, extraUrl?: string): EvidenceStatus;
+/**
+ * Resolve an identifier; after a Crossref hit also ask OpenAlex so `is_retracted` is honored.
+ * Throws the client's fixed error messages when a source is unavailable.
+ */
+export declare function resolveChecked(client: Pick<ScholarClient, "resolve">, identifier: Identifier, signal?: AbortSignal, crossCheck?: boolean): Promise<{
+    record: ScholarRecord;
+    retracted: boolean;
+} | undefined>;
+export declare function verifyCandidate(candidate: Candidate, context: VerifyContext): Promise<VerificationResult>;
+/** Lower is stronger. */
+export declare const statusRank: (status: EvidenceStatus) => number;
+export declare function isUpgrade(from: EvidenceStatus, to: EvidenceStatus): boolean;
+export declare function applyAuditorStatus(assigned: EvidenceStatus, requested: EvidenceStatus | undefined): EvidenceStatus;
+//# sourceMappingURL=verify.d.ts.map

package/dist/research/verify.d.ts.map

@@ -0,0 +1 @@
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