scientify 2.1.0 → 3.0.0

package/dist/src/tools/openreview-lookup.js

@@ -1,414 +0,0 @@
-import { Type } from "@sinclair/typebox";
-import { Result } from "./result.js";
-const OPENREVIEW_API_BASE = "https://api2.openreview.net";
-const OPENREVIEW_WEB_BASE = "https://openreview.net";
-const DEFAULT_MAX_RESULTS = 3;
-const MAX_RESULTS_LIMIT = 10;
-const DEFAULT_REVIEW_LIMIT = 3;
-const MAX_REVIEW_LIMIT = 10;
-const DEFAULT_FORUM_NOTES_LIMIT = 500;
-const SEARCH_FANOUT = 4;
-const SUMMARY_MAX_CHARS = 420;
-const OPENREVIEW_TOKEN_ENV = "OPENREVIEW_API_TOKEN";
-export const OpenReviewLookupSchema = Type.Object({
-    query: Type.Optional(Type.String({
-        description: "Paper title keywords for OpenReview search.",
-    })),
-    paper_id: Type.Optional(Type.String({
-        description: "OpenReview note id (submission or note id).",
-    })),
-    forum_id: Type.Optional(Type.String({
-        description: "OpenReview forum id.",
-    })),
-    external_id: Type.Optional(Type.String({
-        description: "External paper id hint (for example arXiv id like 2603.05344 or a DOI). Used as search term when exact mapping is unavailable.",
-    })),
-    max_results: Type.Optional(Type.Number({
-        description: "Maximum number of papers to return (1-10). Default: 3.",
-        minimum: 1,
-        maximum: MAX_RESULTS_LIMIT,
-    })),
-    include_reviews: Type.Optional(Type.Boolean({
-        description: "Include review snippets and rating/confidence aggregates. Default: true.",
-    })),
-    review_limit: Type.Optional(Type.Number({
-        description: "Maximum review snippets per paper (1-10). Default: 3.",
-        minimum: 1,
-        maximum: MAX_REVIEW_LIMIT,
-    })),
-});
-function readStringParam(params, key) {
-    const value = params[key];
-    if (value === undefined || value === null)
-        return undefined;
-    const text = String(value).trim();
-    return text.length > 0 ? text : undefined;
-}
-function readNumberParam(params, key, fallback, max) {
-    const raw = params[key];
-    if (raw === undefined || raw === null)
-        return fallback;
-    const parsed = Number(raw);
-    if (!Number.isFinite(parsed))
-        return fallback;
-    return Math.max(1, Math.min(max, Math.floor(parsed)));
-}
-function readBooleanParam(params, key, fallback) {
-    const raw = params[key];
-    if (raw === undefined || raw === null)
-        return fallback;
-    return raw === true;
-}
-function normalizeWhitespace(raw) {
-    return raw.replace(/\s+/g, " ").trim();
-}
-function unwrapValue(value) {
-    if (value && typeof value === "object" && !Array.isArray(value) && "value" in value) {
-        return value.value;
-    }
-    return value;
-}
-function contentString(content, key) {
-    if (!content)
-        return null;
-    const raw = unwrapValue(content[key]);
-    if (typeof raw !== "string")
-        return null;
-    const text = normalizeWhitespace(raw);
-    return text.length > 0 ? text : null;
-}
-function contentScalar(content, key) {
-    if (!content)
-        return null;
-    const raw = unwrapValue(content[key]);
-    if (typeof raw === "string") {
-        const text = normalizeWhitespace(raw);
-        return text.length > 0 ? text : null;
-    }
-    if (typeof raw === "number" && Number.isFinite(raw))
-        return raw;
-    return null;
-}
-function contentStringList(content, key) {
-    if (!content)
-        return [];
-    const raw = unwrapValue(content[key]);
-    if (!Array.isArray(raw))
-        return [];
-    return raw
-        .filter((item) => typeof item === "string")
-        .map((item) => normalizeWhitespace(item))
-        .filter((item) => item.length > 0);
-}
-function truncateText(raw, maxChars) {
-    if (!raw)
-        return null;
-    if (raw.length <= maxChars)
-        return raw;
-    return `${raw.slice(0, maxChars - 1)}…`;
-}
-function parseNumericSignal(raw) {
-    if (raw === null)
-        return null;
-    if (typeof raw === "number" && Number.isFinite(raw))
-        return raw;
-    if (typeof raw !== "string")
-        return null;
-    const m = raw.match(/-?\d+(?:\.\d+)?/);
-    if (!m)
-        return null;
-    const parsed = Number(m[0]);
-    return Number.isFinite(parsed) ? parsed : null;
-}
-function avg(values) {
-    if (values.length === 0)
-        return null;
-    const sum = values.reduce((acc, v) => acc + v, 0);
-    return Number((sum / values.length).toFixed(3));
-}
-function selectSubmissionNote(notes, forumId) {
-    const exact = notes.find((note) => note.id === forumId);
-    if (exact)
-        return exact;
-    const withTitle = notes.find((note) => Boolean(contentString(note.content, "title")));
-    if (withTitle)
-        return withTitle;
-    const submissionByInvitation = notes.find((note) => (note.invitations ?? []).some((inv) => /\/-\//.test(inv) && /submission/i.test(inv)));
-    return submissionByInvitation ?? null;
-}
-function selectDecisionNote(notes) {
-    const candidates = notes.filter((note) => {
-        const decision = contentString(note.content, "decision");
-        if (decision)
-            return true;
-        return (note.invitations ?? []).some((inv) => /decision/i.test(inv));
-    });
-    if (candidates.length === 0)
-        return null;
-    candidates.sort((a, b) => (b.mdate ?? b.tcdate ?? b.cdate ?? 0) - (a.mdate ?? a.tcdate ?? a.cdate ?? 0));
-    return candidates[0] ?? null;
-}
-function collectReviewSummaries(notes, limit) {
-    const reviews = notes
-        .filter((note) => {
-        const invitation = (note.invitations ?? [])[0] ?? "";
-        if (/review/i.test(invitation))
-            return true;
-        return Boolean(contentString(note.content, "rating")) || Boolean(contentString(note.content, "confidence"));
-    })
-        .map((note) => {
-        const invitation = (note.invitations ?? [])[0] ?? "";
-        const rating = parseNumericSignal(contentScalar(note.content, "rating"));
-        const confidence = parseNumericSignal(contentScalar(note.content, "confidence"));
-        const summary = contentString(note.content, "summary") ??
-            contentString(note.content, "main_review") ??
-            contentString(note.content, "review") ??
-            contentString(note.content, "comment") ??
-            contentString(note.content, "strengths") ??
-            contentString(note.content, "weaknesses") ??
-            contentString(note.content, "limitations") ??
-            "";
-        return {
-            note_id: note.id,
-            invitation,
-            rating,
-            confidence,
-            summary: truncateText(summary, SUMMARY_MAX_CHARS) ?? "",
-            mdate: note.mdate ?? note.tcdate ?? note.cdate ?? 0,
-        };
-    });
-    const informative = reviews
-        .filter((item) => item.rating !== null || item.confidence !== null || item.summary.length > 0)
-        .sort((a, b) => {
-        const scoreA = (a.rating !== null ? 2 : 0) + (a.confidence !== null ? 1 : 0) + (a.summary.length > 0 ? 1 : 0);
-        const scoreB = (b.rating !== null ? 2 : 0) + (b.confidence !== null ? 1 : 0) + (b.summary.length > 0 ? 1 : 0);
-        if (scoreA !== scoreB)
-            return scoreB - scoreA;
-        return b.mdate - a.mdate;
-    })
-        .slice(0, Math.max(1, Math.min(MAX_REVIEW_LIMIT, limit)));
-    return informative.map(({ mdate: _mdate, ...rest }) => rest);
-}
-async function fetchNotes(params) {
-    const urlParams = new URLSearchParams(params);
-    const url = `${OPENREVIEW_API_BASE}/notes?${urlParams.toString()}`;
-    let response;
-    try {
-        response = await fetch(url, {
-            headers: buildHeaders(),
-        });
-    }
-    catch (error) {
-        throw new Error(`Failed to reach OpenReview notes endpoint: ${error instanceof Error ? error.message : String(error)}`);
-    }
-    if (!response.ok) {
-        const text = await response.text();
-        throw new Error(`OpenReview notes API returned ${response.status}: ${text || response.statusText}`);
-    }
-    const data = (await response.json());
-    return data.notes ?? [];
-}
-async function searchNotes(term, limit) {
-    const urlParams = new URLSearchParams({
-        term,
-        limit: String(limit),
-    });
-    const url = `${OPENREVIEW_API_BASE}/notes/search?${urlParams.toString()}`;
-    let response;
-    try {
-        response = await fetch(url, {
-            headers: buildHeaders(),
-        });
-    }
-    catch (error) {
-        throw new Error(`Failed to reach OpenReview search endpoint: ${error instanceof Error ? error.message : String(error)}`);
-    }
-    if (!response.ok) {
-        const text = await response.text();
-        throw new Error(`OpenReview search API returned ${response.status}: ${text || response.statusText}`);
-    }
-    const data = (await response.json());
-    return data.notes ?? [];
-}
-function buildHeaders() {
-    const token = process.env[OPENREVIEW_TOKEN_ENV]?.trim();
-    if (!token) {
-        return {
-            "User-Agent": "scientify-openreview-lookup/1.0",
-        };
-    }
-    return {
-        "User-Agent": "scientify-openreview-lookup/1.0",
-        Authorization: `Bearer ${token}`,
-    };
-}
-function normalizeExternalSearchTerm(raw) {
-    const value = raw.trim();
-    if (!value)
-        return value;
-    const lower = value.toLowerCase();
-    if (lower.startsWith("arxiv:")) {
-        return value.slice(6).trim();
-    }
-    if (lower.startsWith("doi:")) {
-        return value.slice(4).trim();
-    }
-    return value;
-}
-async function lookupForum(forumId, includeReviews, reviewLimit) {
-    const notes = await fetchNotes({
-        forum: forumId,
-        limit: String(DEFAULT_FORUM_NOTES_LIMIT),
-    });
-    if (notes.length === 0)
-        return null;
-    const submission = selectSubmissionNote(notes, forumId);
-    if (!submission)
-        return null;
-    const content = submission.content ?? {};
-    const title = contentString(content, "title");
-    const authors = contentStringList(content, "authors");
-    const abstractPreview = truncateText(contentString(content, "abstract"), SUMMARY_MAX_CHARS);
-    const venue = contentString(content, "venue");
-    const venueId = contentString(content, "venueid");
-    const pdfUrl = contentString(content, "pdf");
-    const decisionNote = selectDecisionNote(notes);
-    const decisionValue = decisionNote ? contentString(decisionNote.content, "decision") : null;
-    const decisionInvitation = decisionNote ? (decisionNote.invitations ?? [])[0] ?? "unknown" : null;
-    const reviewSummaries = includeReviews ? collectReviewSummaries(notes, reviewLimit) : [];
-    const ratingValues = reviewSummaries
-        .map((review) => review.rating)
-        .filter((value) => typeof value === "number" && Number.isFinite(value));
-    const confidenceValues = reviewSummaries
-        .map((review) => review.confidence)
-        .filter((value) => typeof value === "number" && Number.isFinite(value));
-    return {
-        forum_id: forumId,
-        paper_id: submission.id,
-        title,
-        authors,
-        abstract_preview: abstractPreview,
-        pdf_url: pdfUrl,
-        venue,
-        venue_id: venueId,
-        decision: decisionNote && decisionValue
-            ? {
-                value: decisionValue,
-                note_id: decisionNote.id,
-                invitation: decisionInvitation ?? "unknown",
-            }
-            : null,
-        review_stats: {
-            total_reviews: reviewSummaries.length,
-            rated_reviews: ratingValues.length,
-            confidence_reviews: confidenceValues.length,
-            avg_rating: avg(ratingValues),
-            avg_confidence: avg(confidenceValues),
-        },
-        review_summaries: reviewSummaries,
-        links: {
-            forum: `${OPENREVIEW_WEB_BASE}/forum?id=${forumId}`,
-            note: `${OPENREVIEW_WEB_BASE}/forum?id=${submission.id}`,
-        },
-    };
-}
-function dedupeForums(notes, maxResults) {
-    const seen = new Set();
-    for (const note of notes) {
-        const forumId = (note.forum ?? note.id ?? "").trim();
-        if (!forumId)
-            continue;
-        if (seen.has(forumId))
-            continue;
-        // Keep likely paper/submission entries from mixed search results.
-        const hasTitle = Boolean(contentString(note.content, "title"));
-        const hasVenue = Boolean(contentString(note.content, "venue"));
-        const invitation = (note.invitations ?? [])[0] ?? "";
-        const likelySubmission = note.id === forumId || /submission/i.test(invitation) || (hasTitle && hasVenue);
-        if (!likelySubmission)
-            continue;
-        seen.add(forumId);
-        if (seen.size >= maxResults)
-            break;
-    }
-    return [...seen];
-}
-export function createOpenReviewLookupTool() {
-    return {
-        label: "OpenReview Lookup",
-        name: "openreview_lookup",
-        description: "Lookup OpenReview evidence by title or id. Returns forum-level decision, review rating/confidence aggregates, and review summaries for traceable research assessment.",
-        parameters: OpenReviewLookupSchema,
-        execute: async (_toolCallId, rawArgs) => {
-            const params = (rawArgs ?? {});
-            const query = readStringParam(params, "query");
-            const paperId = readStringParam(params, "paper_id");
-            const forumId = readStringParam(params, "forum_id");
-            const externalId = readStringParam(params, "external_id");
-            const maxResults = readNumberParam(params, "max_results", DEFAULT_MAX_RESULTS, MAX_RESULTS_LIMIT);
-            const includeReviews = readBooleanParam(params, "include_reviews", true);
-            const reviewLimit = readNumberParam(params, "review_limit", DEFAULT_REVIEW_LIMIT, MAX_REVIEW_LIMIT);
-            if (!query && !paperId && !forumId && !externalId) {
-                return Result.err("invalid_params", "Provide at least one of: `query`, `paper_id`, `forum_id`, `external_id`.");
-            }
-            try {
-                const targets = [];
-                let mode = "query";
-                if (forumId) {
-                    mode = "forum_id";
-                    targets.push(forumId);
-                }
-                else if (paperId) {
-                    mode = "paper_id";
-                    const notes = await fetchNotes({ id: paperId, limit: "1" });
-                    const note = notes[0];
-                    if (!note) {
-                        return Result.ok({
-                            mode,
-                            input: paperId,
-                            returned: 0,
-                            results: [],
-                            warning: "No note found for provided paper_id.",
-                        });
-                    }
-                    targets.push((note.forum ?? note.id).trim());
-                }
-                else if (externalId) {
-                    mode = "external_id";
-                    const term = normalizeExternalSearchTerm(externalId);
-                    const notes = await searchNotes(term, maxResults * SEARCH_FANOUT);
-                    targets.push(...dedupeForums(notes, maxResults));
-                }
-                else if (query) {
-                    mode = "query";
-                    const notes = await searchNotes(query, maxResults * SEARCH_FANOUT);
-                    targets.push(...dedupeForums(notes, maxResults));
-                }
-                const uniqueTargets = [...new Set(targets.map((item) => item.trim()).filter((item) => item.length > 0))].slice(0, maxResults);
-                const results = [];
-                for (const targetForum of uniqueTargets) {
-                    const forum = await lookupForum(targetForum, includeReviews, reviewLimit);
-                    if (!forum)
-                        continue;
-                    results.push(forum);
-                }
-                return Result.ok({
-                    mode,
-                    input: forumId ?? paperId ?? externalId ?? query,
-                    returned: results.length,
-                    results,
-                    hints: results.length === 0
-                        ? [
-                            "Try a more specific paper title or pass `forum_id` / `paper_id` directly.",
-                            "For broad queries, OpenReview may return mixed notes; use exact title keywords to improve precision.",
-                        ]
-                        : undefined,
-                });
-            }
-            catch (error) {
-                return Result.err("runtime_error", `openreview_lookup failed: ${error instanceof Error ? error.message : String(error)}`);
-            }
-        },
-    };
-}
-//# sourceMappingURL=openreview-lookup.js.map

package/dist/src/tools/openreview-lookup.js.map

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package/dist/src/tools/paper-browser.d.ts

@@ -1,23 +0,0 @@
-export declare const PaperBrowserToolSchema: import("@sinclair/typebox").TObject<{
-    file_path: import("@sinclair/typebox").TString;
-    start_line: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-    num_lines: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-}>;
-export declare function createPaperBrowserTool(): {
-    label: string;
-    name: string;
-    description: string;
-    parameters: import("@sinclair/typebox").TObject<{
-        file_path: import("@sinclair/typebox").TString;
-        start_line: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-        num_lines: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-    }>;
-    execute: (_toolCallId: string, rawArgs: unknown) => Promise<{
-        content: {
-            type: "text";
-            text: string;
-        }[];
-        details: unknown;
-    }>;
-};
-//# sourceMappingURL=paper-browser.d.ts.map

package/dist/src/tools/paper-browser.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"paper-browser.d.ts","sourceRoot":"","sources":["../../../src/tools/paper-browser.ts"],"names":[],"mappings":"AAOA,eAAO,MAAM,sBAAsB;;;;EAiBjC,CAAC;AAqBH,wBAAgB,sBAAsB;;;;;;;;;2BAOL,MAAM,WAAW,OAAO;;;;;;;EAuFxD"}

package/dist/src/tools/paper-browser.js

@@ -1,121 +0,0 @@
-import { Type } from "@sinclair/typebox";
-import { readFileSync, existsSync, statSync } from "node:fs";
-import { Result } from "./result.js";
-const DEFAULT_VIEWPORT_SIZE = 100;
-const MAX_VIEWPORT_SIZE = 500;
-export const PaperBrowserToolSchema = Type.Object({
-    file_path: Type.String({
-        description: "Path to the paper file (.tex, .md, or any text file).",
-    }),
-    start_line: Type.Optional(Type.Number({
-        description: "Starting line number (1-indexed). Default: 1.",
-        minimum: 1,
-    })),
-    num_lines: Type.Optional(Type.Number({
-        description: `Number of lines to display (default: ${DEFAULT_VIEWPORT_SIZE}, max: ${MAX_VIEWPORT_SIZE}).`,
-        minimum: 1,
-        maximum: MAX_VIEWPORT_SIZE,
-    })),
-});
-function readStringParam(params, key, opts) {
-    const value = params[key];
-    if (value === undefined || value === null) {
-        if (opts?.required) {
-            throw new Error(`Missing required parameter: ${key}`);
-        }
-        return undefined;
-    }
-    return String(value);
-}
-function readNumberParam(params, key, opts) {
-    const value = params[key];
-    if (value === undefined || value === null)
-        return undefined;
-    const num = Number(value);
-    if (isNaN(num))
-        return undefined;
-    return opts?.integer ? Math.floor(num) : num;
-}
-export function createPaperBrowserTool() {
-    return {
-        label: "Paper Browser",
-        name: "paper_browser",
-        description: "Read large paper files (.tex, .md) in paginated chunks. Use this to avoid loading entire multi-thousand-line files into context at once. Returns a viewport of lines with navigation information.",
-        parameters: PaperBrowserToolSchema,
-        execute: async (_toolCallId, rawArgs) => {
-            const params = rawArgs;
-            const filePath = readStringParam(params, "file_path", { required: true });
-            const startLine = Math.max(1, readNumberParam(params, "start_line", { integer: true }) ?? 1);
-            const numLines = Math.min(readNumberParam(params, "num_lines", { integer: true }) ?? DEFAULT_VIEWPORT_SIZE, MAX_VIEWPORT_SIZE);
-            // Validate file exists
-            if (!existsSync(filePath)) {
-                return Result.err("file_not_found", `File does not exist: ${filePath}`);
-            }
-            // Check if it's a file (not directory)
-            let stats;
-            try {
-                stats = statSync(filePath);
-            }
-            catch (error) {
-                return Result.err("file_error", `Cannot access file: ${error instanceof Error ? error.message : String(error)}`);
-            }
-            if (!stats.isFile()) {
-                return Result.err("not_a_file", `Path is not a file: ${filePath}`);
-            }
-            // Read file content
-            let content;
-            try {
-                content = readFileSync(filePath, "utf-8");
-            }
-            catch (error) {
-                return Result.err("read_error", `Failed to read file: ${error instanceof Error ? error.message : String(error)}`);
-            }
-            // Split into lines
-            const lines = content.split("\n");
-            const totalLines = lines.length;
-            // Validate start line
-            if (startLine > totalLines) {
-                return Result.err("invalid_range", `Start line ${startLine} exceeds total lines ${totalLines}`);
-            }
-            // Extract viewport
-            const endLine = Math.min(startLine + numLines - 1, totalLines);
-            const viewportLines = lines.slice(startLine - 1, endLine);
-            // Add line numbers (matching cat -n format for consistency with Read tool)
-            const numberedLines = viewportLines
-                .map((line, idx) => {
-                const lineNum = startLine + idx;
-                return `${lineNum.toString().padStart(6, " ")}\t${line}`;
-            })
-                .join("\n");
-            // Navigation hints
-            const hasMore = endLine < totalLines;
-            const hasPrev = startLine > 1;
-            let navigationHint = "";
-            if (hasMore && hasPrev) {
-                navigationHint = `\n\nNavigate: paper_browser({ file_path: "${filePath}", start_line: ${endLine + 1} }) for next page, or start_line: ${Math.max(1, startLine - numLines)} for previous page.`;
-            }
-            else if (hasMore) {
-                navigationHint = `\n\nMore content below. Use: paper_browser({ file_path: "${filePath}", start_line: ${endLine + 1} })`;
-            }
-            else if (hasPrev) {
-                navigationHint = `\n\nEnd of file. Use: paper_browser({ file_path: "${filePath}", start_line: ${Math.max(1, startLine - numLines)} }) for previous page.`;
-            }
-            else {
-                navigationHint = "\n\n[End of file]";
-            }
-            return Result.ok({
-                file_path: filePath,
-                total_lines: totalLines,
-                viewport: {
-                    start_line: startLine,
-                    end_line: endLine,
-                    num_lines: viewportLines.length,
-                },
-                content: numberedLines + navigationHint,
-                has_more: hasMore,
-                has_prev: hasPrev,
-            });
-        },
-    };
-}
-//# sourceMappingURL=paper-browser.js.map

package/dist/src/tools/paper-browser.js.map

@@ -1 +0,0 @@
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