@jokerized/getresearchdone 0.4.1

package/dist/lib/citations.js

@@ -0,0 +1,642 @@
+'use strict';
+Object.defineProperty(exports, "__esModule", { value: true });
+const fs = require('fs');
+const path = require('path');
+const { safeReadFile } = require('./utils');
+// --- Helpers ------------------------------------------------------------------
+/**
+ * Extract the content of a named section from markdown.
+ * Returns the text after `## Section Name` until the next `##` heading or end of file.
+ * The sectionName may be a regex pattern (e.g., 'missing.?components').
+ */
+function extractSection(content, sectionName) {
+    const pattern = new RegExp(`(?:^|\\n)#{2,3}\\s+${sectionName}[^\\n]*\\n([\\s\\S]*?)(?=\\n#{2,3}\\s|$)`, 'i');
+    const match = content.match(pattern);
+    return match ? match[1].trim() : '';
+}
+/**
+ * Parse a yes/no/true/false string into a boolean.
+ */
+function parseBool(value) {
+    const lower = value.trim().toLowerCase();
+    return lower === 'yes' || lower === 'true';
+}
+// --- parseMissingComponents ---------------------------------------------------
+/**
+ * Parse missing_components section from PAPERS.md content.
+ *
+ * Supports two formats:
+ *   Table: | Name | Source Paper | Description | Code Available |
+ *   List:  - **Name**: description (source: paper, code: yes/no)
+ *
+ * Also supports the plan-specified structured list format:
+ *   - **name:** ComponentName
+ *     - source_paper: paper-slug-or-title
+ *     - description: What the component does
+ *     - code_available: true|false
+ *
+ * Returns empty array if no section found or no entries parsed.
+ *
+ * @param content - Raw markdown content of a PAPERS.md entry
+ * @returns Array of MissingComponent objects
+ */
+function parseMissingComponents(content) {
+    const section = extractSection(content, 'missing.?components');
+    if (!section)
+        return [];
+    const results = [];
+    // Table format: | Name | Source Paper | Description | Code Available |
+    // Skip header row and separator row (contains ---)
+    const tableRowPattern = /^\|([^|]+)\|([^|]+)\|([^|]+)\|([^|]+)\|/gm;
+    let tableMatch;
+    let hasTableRows = false;
+    while ((tableMatch = tableRowPattern.exec(section)) !== null) {
+        const name = tableMatch[1].trim();
+        const sourcePaper = tableMatch[2].trim();
+        const description = tableMatch[3].trim();
+        const codeAvailableStr = tableMatch[4].trim();
+        // Skip header/separator rows
+        if (name.toLowerCase() === 'name' || /^[-\s]+$/.test(name))
+            continue;
+        hasTableRows = true;
+        results.push({
+            name,
+            source_paper: sourcePaper,
+            description,
+            code_available: parseBool(codeAvailableStr),
+        });
+    }
+    if (hasTableRows)
+        return results;
+    // Structured list format:
+    //   - **name:** ComponentName
+    //     - source_paper: paper-slug
+    //     - description: text
+    //     - code_available: true/false
+    const structuredBlockPattern = /^-\s+\*\*name:\*\*\s+(.+)\n(?:\s+-\s+source_paper:\s+(.+)\n)?(?:\s+-\s+description:\s+(.+)\n)?(?:\s+-\s+code_available:\s+(.+))?/gim;
+    let structuredMatch;
+    let hasStructured = false;
+    while ((structuredMatch = structuredBlockPattern.exec(section)) !== null) {
+        hasStructured = true;
+        results.push({
+            name: structuredMatch[1].trim(),
+            source_paper: structuredMatch[2] ? structuredMatch[2].trim() : '',
+            description: structuredMatch[3] ? structuredMatch[3].trim() : '',
+            code_available: structuredMatch[4] ? parseBool(structuredMatch[4]) : false,
+        });
+    }
+    if (hasStructured)
+        return results;
+    // Inline list format: - **Name**: description (source: paper, code: yes/no)
+    const listPattern = /^-\s+\*\*([^*]+)\*\*\s*:\s*([^(]+)\(source:\s*([^,]+),\s*code:\s*([^)]+)\)/gm;
+    let listMatch;
+    while ((listMatch = listPattern.exec(section)) !== null) {
+        results.push({
+            name: listMatch[1].trim(),
+            source_paper: listMatch[3].trim(),
+            description: listMatch[2].trim(),
+            code_available: parseBool(listMatch[4]),
+        });
+    }
+    return results;
+}
+// --- parseBorrowedComponents --------------------------------------------------
+/**
+ * Parse borrowed_components section from PAPERS.md content.
+ *
+ * Supports two formats:
+ *   Table: | Name | Source Paper | Description |
+ *   List:  - **Name**: description (source: paper)
+ *
+ * The code_available field is not relevant for borrowed components.
+ * Returns empty array if no section found or no entries parsed.
+ *
+ * @param content - Raw markdown content of a PAPERS.md entry
+ * @returns Array of BorrowedComponent objects
+ */
+function parseBorrowedComponents(content) {
+    const section = extractSection(content, 'borrowed.?components');
+    if (!section)
+        return [];
+    const results = [];
+    // Table format: | Name | Source Paper | Description |
+    const tableRowPattern = /^\|([^|]+)\|([^|]+)\|([^|]+)\|/gm;
+    let tableMatch;
+    let hasTableRows = false;
+    while ((tableMatch = tableRowPattern.exec(section)) !== null) {
+        const name = tableMatch[1].trim();
+        const sourcePaper = tableMatch[2].trim();
+        const description = tableMatch[3].trim();
+        if (name.toLowerCase() === 'name' || /^[-\s]+$/.test(name))
+            continue;
+        hasTableRows = true;
+        results.push({ name, source_paper: sourcePaper, description });
+    }
+    if (hasTableRows)
+        return results;
+    // Structured list format:
+    //   - **name:** ComponentName
+    //     - source_paper: paper-slug
+    //     - description: text
+    const structuredBlockPattern = /^-\s+\*\*name:\*\*\s+(.+)\n(?:\s+-\s+source_paper:\s+(.+)\n)?(?:\s+-\s+description:\s+(.+))?/gim;
+    let structuredMatch;
+    let hasStructured = false;
+    while ((structuredMatch = structuredBlockPattern.exec(section)) !== null) {
+        hasStructured = true;
+        results.push({
+            name: structuredMatch[1].trim(),
+            source_paper: structuredMatch[2] ? structuredMatch[2].trim() : '',
+            description: structuredMatch[3] ? structuredMatch[3].trim() : '',
+        });
+    }
+    if (hasStructured)
+        return results;
+    // Inline list format: - **Name**: description (source: paper)
+    const listPattern = /^-\s+\*\*([^*]+)\*\*\s*:\s*([^(]+)\(source:\s*([^,)]+)[^)]*\)/gm;
+    let listMatch;
+    while ((listMatch = listPattern.exec(section)) !== null) {
+        results.push({
+            name: listMatch[1].trim(),
+            source_paper: listMatch[3].trim(),
+            description: listMatch[2].trim(),
+        });
+    }
+    return results;
+}
+// --- buildCitationGraph -------------------------------------------------------
+/**
+ * Read all .md files in papersDir and build a typed CitationGraph.
+ *
+ * For each file:
+ *   - Extracts the paper slug from the filename (without .md extension)
+ *   - Parses missing_components and borrowed_components sections
+ *   - Creates CitationNode entries for the paper itself and all referenced papers
+ *   - Creates CitationEdge entries for each dependency relationship
+ *   - Writes per-paper JSON to {papersDir}/../citations/{paper-slug}.json
+ *
+ * Priority escalation: MissingComponent with code_available=false => dep node priority='critical'
+ * All nodes start with resolved=false.
+ * Returns a graph with empty arrays when the directory is empty or missing.
+ *
+ * @param papersDir - Absolute or relative path to directory containing .md files
+ * @returns CitationGraph with nodes, edges, and built_at ISO timestamp
+ */
+function buildCitationGraph(papersDir) {
+    const built_at = new Date().toISOString();
+    // Handle missing or non-directory paths gracefully
+    if (!fs.existsSync(papersDir)) {
+        return { nodes: [], edges: [], built_at };
+    }
+    let files;
+    try {
+        const entries = fs.readdirSync(papersDir);
+        files = entries.filter((f) => f.endsWith('.md'));
+    }
+    catch {
+        return { nodes: [], edges: [], built_at };
+    }
+    if (files.length === 0) {
+        return { nodes: [], edges: [], built_at };
+    }
+    // Track nodes by slug to avoid duplicates; edges are collected in order
+    const nodeMap = new Map();
+    const edges = [];
+    /**
+     * Ensure a node exists for slug. Escalates priority to 'critical' if needed.
+     * Merges component arrays for the primary paper node.
+     */
+    function ensureNode(slug, priority = 'normal', missing = [], borrowed = []) {
+        if (!nodeMap.has(slug)) {
+            nodeMap.set(slug, {
+                slug,
+                title: slug,
+                resolved: false,
+                priority,
+                technique_summary: '',
+                missing_components: missing,
+                borrowed_components: borrowed,
+            });
+        }
+        else {
+            const existing = nodeMap.get(slug);
+            if (priority === 'critical') {
+                existing.priority = 'critical';
+            }
+            // Merge component arrays when the primary paper node is registered
+            if (missing.length > 0)
+                existing.missing_components = missing;
+            if (borrowed.length > 0)
+                existing.borrowed_components = borrowed;
+        }
+    }
+    for (const file of files) {
+        const slug = path.basename(file, '.md');
+        const filePath = path.join(papersDir, file);
+        // Use safeReadFile for reading; fall back to empty string on null
+        const raw = safeReadFile(filePath);
+        const content = raw !== null ? raw : '';
+        const missing = parseMissingComponents(content);
+        const borrowed = parseBorrowedComponents(content);
+        ensureNode(slug, 'normal', missing, borrowed);
+        for (const component of missing) {
+            const depSlug = component.source_paper;
+            const depPriority = component.code_available ? 'normal' : 'critical';
+            ensureNode(depSlug, depPriority);
+            edges.push({
+                from_slug: slug,
+                to_slug: depSlug,
+                type: 'missing',
+                component_name: component.name,
+            });
+        }
+        for (const component of borrowed) {
+            const depSlug = component.source_paper;
+            ensureNode(depSlug, 'normal');
+            edges.push({
+                from_slug: slug,
+                to_slug: depSlug,
+                type: 'borrowed',
+                component_name: component.name,
+            });
+        }
+    }
+    const graph = {
+        nodes: Array.from(nodeMap.values()),
+        edges,
+        built_at,
+    };
+    // Write per-paper JSON to {papersDir}/../citations/{paper-slug}.json
+    const citationsDir = path.join(papersDir, '..', 'citations');
+    try {
+        fs.mkdirSync(citationsDir, { recursive: true });
+        for (const node of graph.nodes) {
+            const jsonPath = path.join(citationsDir, `${node.slug}.json`);
+            fs.writeFileSync(jsonPath, JSON.stringify(node, null, 2), 'utf-8');
+        }
+    }
+    catch {
+        // Non-fatal: if we cannot write JSON, still return the complete graph
+    }
+    return graph;
+}
+// --- resolveCitations ---------------------------------------------------------
+/**
+ * Default fetch function using Node's built-in https module.
+ * Returns the response body as a string, or null on any error.
+ */
+function defaultFetchFn(url, _timeoutMs) {
+    return new Promise((resolve) => {
+        const https = require('https');
+        const http = require('http');
+        const parsed = new URL(url);
+        const transport = parsed.protocol === 'https:' ? https : http;
+        try {
+            const req = transport.get(url, (res) => {
+                if (!res.statusCode || res.statusCode < 200 || res.statusCode >= 300) {
+                    resolve(null);
+                    return;
+                }
+                const chunks = [];
+                res.on('data', (chunk) => chunks.push(chunk));
+                res.on('end', () => resolve(Buffer.concat(chunks).toString('utf-8')));
+                res.on('error', () => resolve(null));
+            });
+            req.on('error', () => resolve(null));
+            req.setTimeout(_timeoutMs, () => {
+                req.destroy();
+                resolve(null);
+            });
+        }
+        catch {
+            resolve(null);
+        }
+    });
+}
+/**
+ * Extract a text summary from an arXiv Atom XML response.
+ * Returns the first 200 chars of the summary element, or null.
+ */
+function extractArxivSummary(xml) {
+    const match = xml.match(/<summary[^>]*>([\s\S]*?)<\/summary>/i);
+    if (!match)
+        return null;
+    const text = match[1].replace(/\s+/g, ' ').trim();
+    return text ? text.slice(0, 200) : null;
+}
+/**
+ * Extract a text abstract from a Semantic Scholar JSON response.
+ * Returns the first 200 chars of the abstract field, or null.
+ */
+function extractSemanticAbstract(json) {
+    try {
+        const data = JSON.parse(json);
+        // Response is { data: [ { title, abstract, ... } ] }
+        const dataArr = Array.isArray(data.data) ? data.data : null;
+        if (dataArr && dataArr.length > 0) {
+            const abstract = dataArr[0].abstract;
+            if (typeof abstract === 'string' && abstract.trim()) {
+                return abstract.slice(0, 200);
+            }
+        }
+    }
+    catch {
+        // not valid JSON
+    }
+    return null;
+}
+/**
+ * Iterate over unresolved CitationNodes and attempt to fetch metadata from
+ * arXiv and/or Semantic Scholar APIs.
+ *
+ * Accepts an optional fetchFn for dependency injection (enables mocking in tests).
+ * The default fetchFn uses Node's built-in https.get.
+ *
+ * @param graph - The CitationGraph to update (mutated in place)
+ * @param apiConfig - Controls which APIs are queried and timeout behaviour
+ * @param fetchFn - Optional injectable fetch function for testing
+ * @returns The updated CitationGraph (same reference as input)
+ */
+async function resolveCitations(graph, apiConfig, fetchFn) {
+    const fetch = fetchFn ?? defaultFetchFn;
+    const timeoutMs = apiConfig.timeout_ms ?? 5000;
+    for (const node of graph.nodes) {
+        if (node.resolved)
+            continue;
+        const titleEncoded = encodeURIComponent(node.title);
+        let summary = null;
+        if (apiConfig.arxiv_enabled) {
+            const arxivUrl = `https://export.arxiv.org/api/query?search_query=ti:${titleEncoded}&max_results=1`;
+            try {
+                const body = await fetch(arxivUrl, timeoutMs);
+                if (body) {
+                    summary = extractArxivSummary(body);
+                }
+            }
+            catch {
+                // non-fatal
+            }
+        }
+        if (!summary && apiConfig.semantic_scholar_enabled) {
+            const ssUrl = `https://api.semanticscholar.org/graph/v1/paper/search?query=${titleEncoded}&limit=1`;
+            try {
+                const body = await fetch(ssUrl, timeoutMs);
+                if (body) {
+                    summary = extractSemanticAbstract(body);
+                }
+            }
+            catch {
+                // non-fatal
+            }
+        }
+        if (summary !== null) {
+            node.resolved = true;
+            node.technique_summary = summary;
+        }
+    }
+    return graph;
+}
+// --- findUnresolved -----------------------------------------------------------
+/**
+ * Return all unresolved CitationNodes in the graph.
+ * If priority is provided, only nodes with that priority are returned.
+ *
+ * @param graph - The CitationGraph to search
+ * @param priority - Optional priority filter ('critical' | 'normal' | 'low')
+ * @returns Array of CitationNode objects where resolved is false
+ */
+function findUnresolved(graph, priority) {
+    return graph.nodes.filter((node) => {
+        if (node.resolved)
+            return false;
+        if (priority !== undefined)
+            return node.priority === priority;
+        return true;
+    });
+}
+// --- traverseCitationGraph ---------------------------------------------------
+/**
+ * Perform BFS traversal of the citation graph from all root nodes (nodes with
+ * no incoming edges), respecting depth and node-count limits.
+ *
+ * Cycle detection: tracks visited slugs in a Set; any slug already visited is
+ * skipped, preventing infinite loops on circular citation chains.
+ *
+ * Limits:
+ *   - max_depth: BFS depth from root nodes. Nodes at this depth are visited but
+ *     their children are not enqueued.
+ *   - max_nodes: Total node visit cap. Processing halts once total_visited
+ *     reaches this limit.
+ *
+ * Unresolved leaves: A node with no outgoing edges in the adjacency map and
+ * resolved=false is added to unresolved_leaves.
+ *
+ * @param graph - The CitationGraph to traverse
+ * @param options - Optional partial TraversalOptions (merged with defaults)
+ * @returns TraversalResult with visited nodes, traversed edges, and statistics
+ */
+function traverseCitationGraph(graph, options) {
+    const opts = {
+        max_depth: options?.max_depth ?? 3,
+        max_nodes: options?.max_nodes ?? 50,
+    };
+    const emptyResult = {
+        visited_nodes: [],
+        edges_traversed: [],
+        unresolved_leaves: [],
+        depth_reached: 0,
+        total_visited: 0,
+    };
+    if (graph.nodes.length === 0) {
+        return emptyResult;
+    }
+    // Build adjacency map: slug → outgoing edges
+    const adjacency = new Map();
+    for (const edge of graph.edges) {
+        if (!adjacency.has(edge.from_slug)) {
+            adjacency.set(edge.from_slug, []);
+        }
+        adjacency.get(edge.from_slug).push(edge);
+    }
+    // Build node lookup map: slug → CitationNode
+    const nodeMap = new Map();
+    for (const node of graph.nodes) {
+        nodeMap.set(node.slug, node);
+    }
+    // Find root nodes: nodes that appear as from_slug but never as to_slug
+    // (i.e., have no incoming edges). If all nodes have incoming edges (e.g., cycle),
+    // treat all nodes as roots to avoid empty traversal.
+    const hasIncoming = new Set();
+    for (const edge of graph.edges) {
+        hasIncoming.add(edge.to_slug);
+    }
+    const rootNodes = graph.nodes.filter((n) => !hasIncoming.has(n.slug));
+    const seeds = rootNodes.length > 0 ? rootNodes : graph.nodes;
+    // BFS
+    const visited = new Set();
+    const visitedNodes = [];
+    const edgesTraversed = [];
+    const unresolvedLeaves = [];
+    let depthReached = 0;
+    let totalVisited = 0;
+    const queue = [];
+    for (const seed of seeds) {
+        if (!visited.has(seed.slug)) {
+            visited.add(seed.slug);
+            queue.push({ node: seed, depth: 0 });
+        }
+    }
+    let qi = 0;
+    while (qi < queue.length) {
+        if (totalVisited >= opts.max_nodes)
+            break;
+        const { node, depth } = queue[qi++];
+        visitedNodes.push(node);
+        totalVisited++;
+        if (depth > depthReached)
+            depthReached = depth;
+        if (totalVisited >= opts.max_nodes)
+            break;
+        const outgoing = adjacency.get(node.slug) ?? [];
+        // Check if leaf (no outgoing edges)
+        if (outgoing.length === 0 && !node.resolved) {
+            unresolvedLeaves.push(node);
+        }
+        // If at max depth, do not enqueue children
+        if (depth >= opts.max_depth)
+            continue;
+        for (const edge of outgoing) {
+            const targetNode = nodeMap.get(edge.to_slug);
+            if (!targetNode)
+                continue;
+            if (visited.has(edge.to_slug))
+                continue;
+            if (totalVisited + (queue.length - qi) >= opts.max_nodes) {
+                // Approximate cap: stop enqueuing if we're near the limit
+                // (exact cap enforced at dequeue time above)
+            }
+            visited.add(edge.to_slug);
+            edgesTraversed.push(edge);
+            queue.push({ node: targetNode, depth: depth + 1 });
+        }
+    }
+    return {
+        visited_nodes: visitedNodes,
+        edges_traversed: edgesTraversed,
+        unresolved_leaves: unresolvedLeaves,
+        depth_reached: depthReached,
+        total_visited: totalVisited,
+    };
+}
+// --- resolveTransitiveDeps ---------------------------------------------------
+/**
+ * Expand a CitationGraph by performing BFS traversal and merging all
+ * transitively discovered nodes and edges into the graph.
+ *
+ * Deduplication:
+ *   - Nodes: only added if their slug is not already in graph.nodes
+ *   - Edges: only added if not already present (keyed by from_slug + to_slug + component_name)
+ *
+ * Returns a new CitationGraph (does not mutate the input).
+ *
+ * @param graph - The CitationGraph to expand
+ * @param options - Optional partial TraversalOptions passed to traverseCitationGraph
+ * @returns A new CitationGraph with merged transitive nodes and edges
+ */
+function resolveTransitiveDeps(graph, options) {
+    const result = traverseCitationGraph(graph, options);
+    // Build set of existing node slugs
+    const existingSlugs = new Set(graph.nodes.map((n) => n.slug));
+    // Merge new nodes (not already in graph)
+    const newNodes = result.visited_nodes.filter((n) => !existingSlugs.has(n.slug));
+    const mergedNodes = [...graph.nodes, ...newNodes];
+    // Build set of existing edge keys for deduplication
+    const edgeKey = (e) => `${e.from_slug}::${e.to_slug}::${e.component_name}`;
+    const existingEdgeKeys = new Set(graph.edges.map(edgeKey));
+    // Merge new edges
+    const newEdges = result.edges_traversed.filter((e) => !existingEdgeKeys.has(edgeKey(e)));
+    const mergedEdges = [...graph.edges, ...newEdges];
+    return {
+        nodes: mergedNodes,
+        edges: mergedEdges,
+        built_at: new Date().toISOString(),
+    };
+}
+// --- fetchExternalPaper -------------------------------------------------------
+/**
+ * Attempt to auto-retrieve metadata for a single paper slug from external APIs.
+ *
+ * Uses arXiv-first, Semantic Scholar-fallback strategy (same as resolveCitations),
+ * but operates on a single slug rather than iterating over a graph.
+ *
+ * Accepts an optional fetchFn for dependency injection (enables mocking in tests).
+ * The default fetchFn uses Node's built-in https.get with a 5-second timeout.
+ *
+ * On success: returns a CitationNode with resolved=true and technique_summary populated.
+ * On failure (both APIs return null): writes a warning to stderr and returns null.
+ * Any thrown error is caught and returns null.
+ *
+ * @param slug - Paper slug to look up (used as query title)
+ * @param fetchFn - Optional injectable fetch function for testing
+ * @returns CitationNode with resolved=true on success, null on failure
+ */
+async function fetchExternalPaper(slug, fetchFn) {
+    const fetch = fetchFn ?? defaultFetchFn;
+    const timeoutMs = 5000;
+    try {
+        const slugEncoded = encodeURIComponent(slug);
+        let summary = null;
+        // arXiv-first: search by title
+        const arxivUrl = `https://export.arxiv.org/api/query?search_query=ti:${slugEncoded}&max_results=1`;
+        try {
+            const body = await fetch(arxivUrl, timeoutMs);
+            if (body) {
+                summary = extractArxivSummary(body);
+            }
+        }
+        catch {
+            // non-fatal
+        }
+        // Semantic Scholar fallback: only if arXiv returned no summary
+        if (summary === null) {
+            const ssUrl = `https://api.semanticscholar.org/graph/v1/paper/search?query=${slugEncoded}&limit=1`;
+            try {
+                const body = await fetch(ssUrl, timeoutMs);
+                if (body) {
+                    summary = extractSemanticAbstract(body);
+                }
+            }
+            catch {
+                // non-fatal
+            }
+        }
+        if (summary !== null) {
+            return {
+                slug,
+                title: slug,
+                resolved: true,
+                priority: 'normal',
+                technique_summary: summary,
+                missing_components: [],
+                borrowed_components: [],
+            };
+        }
+        // Both APIs failed — warn and return null
+        process.stderr.write(`[grd] WARNING: fetchExternalPaper: could not resolve "${slug}" from arXiv or Semantic Scholar\n`);
+        return null;
+    }
+    catch {
+        return null;
+    }
+}
+// --- Exports -----------------------------------------------------------------
+module.exports = {
+    parseMissingComponents,
+    parseBorrowedComponents,
+    buildCitationGraph,
+    resolveCitations,
+    findUnresolved,
+    traverseCitationGraph,
+    resolveTransitiveDeps,
+    fetchExternalPaper,
+};
+//# sourceMappingURL=citations.js.map

package/dist/lib/citations.js.map

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package/dist/lib/cleanup.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=cleanup.d.ts.map

package/dist/lib/cleanup.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"cleanup.d.ts","sourceRoot":"","sources":["../../lib/cleanup.ts"],"names":[],"mappings":""}