@publisle/research 0.0.0-stage → 0.1.0

package/dist/profiles.js

@@ -0,0 +1,166 @@
+import {} from "@publisle/schema";
+import { accessibilityProfile } from "@publisle/profiles";
+function contentBlocks(document, context) {
+    return context
+        ? context.traversal
+            .filter((visit) => visit.kind === "node" &&
+            [
+                "heading",
+                "paragraph",
+                "figure",
+                "table",
+                "list",
+                "quote",
+                "code",
+                "math",
+                "diagram",
+                "callout",
+                "embed",
+                "divider",
+                "footnote",
+                "raw-html",
+            ].includes(visit.type ?? ""))
+            .map((visit) => ({
+            id: visit.blockId,
+            type: `publisle:${visit.type ?? ""}`,
+            data: visit.value,
+        }))
+        : document.blocks;
+}
+function record(value) {
+    return value !== null && typeof value === "object" && !Array.isArray(value)
+        ? value
+        : {};
+}
+function plainText(value) {
+    if (!Array.isArray(value))
+        return "";
+    return value
+        .map((entry) => {
+        const node = record(entry);
+        return node["type"] === "text" && typeof node["value"] === "string"
+            ? node["value"]
+            : plainText(node["children"]);
+    })
+        .join("");
+}
+export function researchPaperProfile(options = {}) {
+    return {
+        name: "research-paper",
+        version: JSON.stringify(["2", options.abstractLabel ?? null]),
+        inspect(document, context) {
+            const diagnostics = [];
+            if (!document.metadata?.title?.trim())
+                diagnostics.push({
+                    level: "warning",
+                    code: "missing-title",
+                    message: "A research paper should provide a title.",
+                });
+            if (!document.metadata?.authors?.length)
+                diagnostics.push({
+                    level: "warning",
+                    code: "missing-authors",
+                    message: "A research paper should provide at least one author.",
+                });
+            for (const author of document.metadata?.authors ?? []) {
+                if (!author.affiliation?.trim())
+                    diagnostics.push({
+                        level: "warning",
+                        code: "missing-affiliation",
+                        message: `Author ${author.name} should provide an affiliation.`,
+                    });
+            }
+            let hasAbstract = false;
+            const blocks = contentBlocks(document, context);
+            for (const [index, block] of blocks.entries()) {
+                const data = record(block.data);
+                if (block.type === "publisle:heading") {
+                    const abstractHeading = data["role"] === "abstract" ||
+                        (options.abstractLabel === undefined
+                            ? data["label"] === "abstract" ||
+                                plainText(data["content"]).trim().toLowerCase() === "abstract"
+                            : data["label"] === options.abstractLabel ||
+                                data["role"] === "abstract");
+                    const next = blocks[index + 1];
+                    if (abstractHeading &&
+                        next?.type === "publisle:paragraph" &&
+                        plainText(record(next.data)["content"]).trim())
+                        hasAbstract = true;
+                }
+            }
+            diagnostics.push(...accessibilityProfile().inspect(document, context));
+            if (!hasAbstract)
+                diagnostics.push({
+                    level: "warning",
+                    code: "missing-abstract",
+                    message: "A research paper should provide an abstract heading followed by a nonempty paragraph.",
+                });
+            return diagnostics;
+        },
+    };
+}
+function walkCitations(value, found) {
+    if (Array.isArray(value)) {
+        for (const entry of value)
+            walkCitations(entry, found);
+        return;
+    }
+    if (value === null || typeof value !== "object")
+        return;
+    const node = value;
+    if (node["type"] === "citationReference" && Array.isArray(node["items"])) {
+        for (const item of node["items"]) {
+            const id = record(item)["id"];
+            if (typeof id === "string")
+                found.push({ id });
+        }
+    }
+    for (const entry of Object.values(node))
+        walkCitations(entry, found);
+}
+/** Optional citation targets and section roles. Metadata stays informational. */
+export function scholarlyProfile() {
+    return {
+        name: "scholarly",
+        version: "1",
+        inspect(document) {
+            const diagnostics = [];
+            const entries = new Set();
+            for (const block of document.blocks) {
+                if (block.type !== "publisle:bibliography")
+                    continue;
+                const listed = record(block.data)["entries"];
+                if (!Array.isArray(listed))
+                    continue;
+                for (const entry of listed) {
+                    const id = record(entry)["id"];
+                    if (typeof id !== "string")
+                        continue;
+                    if (entries.has(id))
+                        diagnostics.push({
+                            level: "warning",
+                            code: "duplicate-bibliography-entry",
+                            message: `Bibliography id ${id} is repeated.`,
+                            blockId: block.id,
+                        });
+                    entries.add(id);
+                }
+            }
+            for (const block of document.blocks) {
+                const citations = [];
+                walkCitations(block.data, citations);
+                for (const citation of citations) {
+                    if (!entries.has(citation.id))
+                        diagnostics.push({
+                            level: "warning",
+                            code: "unresolved-citation",
+                            message: `Citation ${citation.id} has no bibliography entry. The reference stays in the source.`,
+                            blockId: block.id,
+                        });
+                }
+            }
+            return diagnostics;
+        },
+    };
+}
+//# sourceMappingURL=profiles.js.map

package/dist/profiles.js.map

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

@@ -0,0 +1,24 @@
+import type { CitationEntry } from "./article.js";
+export interface BibliographyFetchOptions {
+    readonly cacheDirectory: string;
+    readonly refresh?: boolean;
+    readonly fetch?: typeof globalThis.fetch;
+}
+export interface BibliographyImport {
+    readonly entries: readonly CitationEntry[];
+    readonly items: readonly Readonly<Record<string, unknown>>[];
+    readonly provenance: {
+        readonly url: string;
+        readonly fetchedAt: string;
+        readonly sha256: string;
+    };
+}
+/** Preserve complete CSL records for citeproc, alongside the portable bibliography projection. */
+export declare function importCslJson(source: string): {
+    entries: CitationEntry[];
+    items: Record<string, unknown>[];
+};
+/** Opt-in metadata acquisition. Exporters never call this API. Cached results work offline. */
+export declare function fetchBibliography(url: string, options: BibliographyFetchOptions): Promise<BibliographyImport>;
+export declare function lookupDoi(doi: string, options: BibliographyFetchOptions): Promise<BibliographyImport>;
+//# sourceMappingURL=remote.d.ts.map

package/dist/remote.d.ts.map

@@ -0,0 +1 @@
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package/dist/remote.js

@@ -0,0 +1,139 @@
+import { createHash } from "node:crypto";
+import { mkdir, readFile, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+import { parseBibtex } from "./bibtex.js";
+/** Preserve complete CSL records for citeproc, alongside the portable bibliography projection. */
+export function importCslJson(source) {
+    const parsed = JSON.parse(source);
+    const listed = Array.isArray(parsed) ? parsed : [parsed];
+    const items = listed.map((item) => {
+        if (!item || typeof item !== "object" || Array.isArray(item))
+            throw new Error("CSL bibliography items must be objects.");
+        return item;
+    });
+    const entries = items.map((item) => {
+        const id = item["id"] ?? item["DOI"];
+        if (typeof id !== "string" && typeof id !== "number")
+            throw new Error("CSL item requires an id or DOI.");
+        item["id"] = String(id);
+        const authors = Array.isArray(item["author"])
+            ? item["author"].map((name) => {
+                const person = name;
+                return typeof person["literal"] === "string"
+                    ? person["literal"]
+                    : [person["family"], person["given"]]
+                        .filter((value) => typeof value === "string")
+                        .join(", ");
+            })
+            : [];
+        const fields = {};
+        for (const [target, key] of Object.entries({
+            type: "type",
+            title: "title",
+            containerTitle: "container-title",
+            volume: "volume",
+            issue: "issue",
+            page: "page",
+            publisher: "publisher",
+            doi: "DOI",
+            url: "URL",
+        }))
+            if (typeof item[key] === "string")
+                fields[target] = item[key];
+        const issued = item["issued"];
+        const year = issued?.["date-parts"]?.[0]?.[0];
+        return {
+            id: String(id),
+            authors,
+            ...fields,
+            ...(year === undefined ? {} : { issued: String(year) }),
+        };
+    });
+    return { entries, items };
+}
+/** Opt-in metadata acquisition. Exporters never call this API. Cached results work offline. */
+export async function fetchBibliography(url, options) {
+    if (new URL(url).protocol !== "https:")
+        throw new Error("Remote bibliographies require HTTPS.");
+    const key = createHash("sha256").update(url).digest("hex");
+    const path = join(options.cacheDirectory, `${key}.json`);
+    if (!options.refresh) {
+        try {
+            return JSON.parse(await readFile(path, "utf8"));
+        }
+        catch (error) {
+            if (!(typeof error === "object" &&
+                error !== null &&
+                "code" in error &&
+                error.code === "ENOENT"))
+                throw error;
+        }
+    }
+    const request = options.fetch ?? globalThis.fetch;
+    let destination = url;
+    let response;
+    for (let hop = 0; hop < 6; hop++) {
+        response = await request(destination, {
+            redirect: "manual",
+            headers: {
+                Accept: "application/vnd.citationstyles.csl+json, application/x-bibtex;q=0.9",
+            },
+            signal: AbortSignal.timeout(15_000),
+        });
+        if (response.status < 300 || response.status >= 400)
+            break;
+        const location = response.headers.get("location");
+        if (!location)
+            throw new Error("Bibliography redirect lacks a destination.");
+        destination = new URL(location, destination).href;
+        if (new URL(destination).protocol !== "https:")
+            throw new Error("Bibliography redirect requires HTTPS.");
+    }
+    if (!response?.ok)
+        throw new Error(`Bibliography fetch failed: ${String(response?.status)}`);
+    const reader = response.body?.getReader();
+    if (!reader)
+        throw new Error("Bibliography response has no body.");
+    const chunks = [];
+    let size = 0;
+    for (;;) {
+        const { done, value } = await reader.read();
+        if (done)
+            break;
+        size += value.length;
+        if (size > 2 * 1024 * 1024) {
+            await reader.cancel();
+            throw new Error("Bibliography exceeds 2 MiB.");
+        }
+        chunks.push(value);
+    }
+    const bytes = Buffer.concat(chunks);
+    const source = new TextDecoder("utf-8", { fatal: true }).decode(bytes);
+    const data = source.trimStart().startsWith("@")
+        ? { entries: parseBibtex(source), items: [] }
+        : importCslJson(source);
+    const result = {
+        ...data,
+        provenance: {
+            url,
+            fetchedAt: new Date().toISOString(),
+            sha256: createHash("sha256").update(bytes).digest("hex"),
+        },
+    };
+    await mkdir(options.cacheDirectory, { recursive: true });
+    await writeFile(path, JSON.stringify(result) + "\n");
+    return result;
+}
+export async function lookupDoi(doi, options) {
+    const normalized = doi
+        .replace(/^https:\/\/doi\.org\//iu, "")
+        .replace(/^doi:\s*/iu, "")
+        .trim();
+    if (!/^10\.\d{4,9}\/\S+$/u.test(normalized))
+        throw new Error("Invalid DOI.");
+    return fetchBibliography(`https://doi.org/${normalized
+        .split("/")
+        .map((part) => encodeURIComponent(part))
+        .join("/")}`, options);
+}
+//# sourceMappingURL=remote.js.map

package/dist/remote.js.map

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

@@ -0,0 +1,10 @@
+import type { Block, BlockType, Document } from "@publisle/schema";
+import { type Article, type ResearchLoss } from "./article.js";
+import { type CitationForm, type FormattedResearch, type CslOptions } from "./csl.js";
+export interface ResolvedDocument extends FormattedResearch {
+    readonly article: Article;
+    readonly losses: readonly ResearchLoss[];
+}
+export declare function resolveDocument(document: Document<Block<BlockType, unknown>>, style?: string, options?: CslOptions): ResolvedDocument;
+export type { CitationForm };
+//# sourceMappingURL=resolve.d.ts.map

package/dist/resolve.d.ts.map

@@ -0,0 +1 @@
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package/dist/resolve.js

@@ -0,0 +1,62 @@
+import { citationClusters, projectArticle, } from "./article.js";
+import { builtinCsl, formatCitations, citationForm, parseCslStyle, } from "./csl.js";
+export function resolveDocument(document, style = "numeric", options = {}) {
+    const article = projectArticle(document);
+    const parsed = style === "numeric" || style === "author-date"
+        ? builtinCsl(style)
+        : parseCslStyle(style);
+    const formatted = formatCitations(article.entries, citationClusters(article), parsed, {
+        ...options,
+        ...(options.noteIndices === undefined && citationForm(parsed) === "note"
+            ? { noteIndices: citationNoteIndices(article) }
+            : {}),
+    });
+    return {
+        ...formatted,
+        article,
+        losses: [...article.losses, ...formatted.losses],
+    };
+}
+function citationNoteIndices(article) {
+    const result = [];
+    let number = 0;
+    const notes = new Map(article.blocks
+        .filter((block) => block.kind === "footnote")
+        .map((block) => [block.id, block.paragraphs]));
+    const visited = new Set();
+    const visit = (inlines, note) => {
+        for (const inline of inlines) {
+            if (inline.type === "citation")
+                result.push(note ?? ++number);
+            else if (inline.type === "text" &&
+                inline.reference?.kind === "footnote" &&
+                !visited.has(inline.reference.target)) {
+                visited.add(inline.reference.target);
+                const next = ++number;
+                for (const paragraph of notes.get(inline.reference.target) ?? [])
+                    visit(paragraph, next);
+            }
+        }
+    };
+    for (const block of article.blocks) {
+        if (block.kind === "heading" || block.kind === "paragraph")
+            visit(block.inlines);
+        else if (block.kind === "quote")
+            for (const paragraph of block.paragraphs)
+                visit(paragraph);
+        else if (block.kind === "list")
+            for (const item of block.items)
+                visit(item);
+        else if (block.kind === "figure")
+            visit(block.caption);
+        else if (block.kind === "table") {
+            if (block.caption)
+                visit(block.caption);
+            for (const row of block.rows)
+                for (const cell of row)
+                    visit(cell);
+        }
+    }
+    return result;
+}
+//# sourceMappingURL=resolve.js.map

package/dist/resolve.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,56 @@
 {
   "name": "@publisle/research",
-  "version": "0.0.0-stage",
-  "stub": true,
-  "description": "Temporary package placeholder for staged publishing"
+  "version": "0.1.0",
+  "description": "Citation resolution and BibTeX, CSL, LaTeX, JATS, and PDF export. Tooling only; readers must not import it.",
+  "license": "MIT",
+  "type": "module",
+  "sideEffects": false,
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js",
+      "default": "./dist/index.js"
+    },
+    "./node": {
+      "types": "./dist/node.d.ts",
+      "import": "./dist/node.js",
+      "default": "./dist/node.js"
+    },
+    "./legacy-pdf": {
+      "types": "./dist/pdf.d.ts",
+      "import": "./dist/pdf.js",
+      "default": "./dist/pdf.js"
+    }
+  },
+  "dependencies": {
+    "citeproc": "2.4.63",
+    "fflate": "0.8.3",
+    "@publisle/contracts": "0.1.0",
+    "@publisle/profiles": "0.1.0",
+    "@publisle/schema": "0.1.0",
+    "@publisle/template-sdk": "0.1.0",
+    "@publisle/template-article": "0.1.0"
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "files": [
+    "dist",
+    "src",
+    "README.md",
+    "NOTICE.md",
+    "LICENSE",
+    "compiler",
+    "vendor"
+  ],
+  "engines": {
+    "node": ">=24"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/VoidReg/publisle.git",
+    "directory": "packages/research"
+  },
+  "homepage": "https://github.com/VoidReg/publisle#readme",
+  "types": "./dist/index.d.ts"
 }