@monoes/monograph 1.1.0 → 1.2.1

package/dist/src/pipeline/phases/llm-extract.js

@@ -0,0 +1,143 @@
+import { makeId, toNormLabel, CONFIDENCE_SCORE } from '../../types.js';
+import { insertNodes } from '../../storage/node-store.js';
+import { insertEdges } from '../../storage/edge-store.js';
+const ALLOWED_RELATIONS = new Set([
+    'DESCRIBES', 'CAUSES', 'CONTRASTS_WITH', 'PART_OF', 'RELATED_TO', 'USES',
+]);
+const SYSTEM_PROMPT = `You extract knowledge graph relationships from technical documentation chunks.
+
+Return ONLY a JSON array of relationships, each with:
+- "node_1": first concept (short, specific, lowercase, max 4 words)
+- "node_2": second concept (short, specific, lowercase, max 4 words)
+- "relation": one of DESCRIBES, CAUSES, CONTRASTS_WITH, PART_OF, RELATED_TO, USES
+- "edge": brief 3-6 word phrase describing the relationship
+
+Rules:
+- Concepts must be specific technical terms (not "thing", "item", "way", "use")
+- Maximum 8 relationships per chunk
+- Skip if text is too short, navigational, or has no meaningful concepts
+- Return [] for non-substantive content
+
+Return only valid JSON array, no explanation.`;
+async function callClaude(content, apiKey) {
+    try {
+        const res = await fetch('https://api.anthropic.com/v1/messages', {
+            method: 'POST',
+            headers: {
+                'x-api-key': apiKey,
+                'anthropic-version': '2023-06-01',
+                'content-type': 'application/json',
+            },
+            body: JSON.stringify({
+                model: 'claude-haiku-4-5-20251001',
+                max_tokens: 512,
+                system: SYSTEM_PROMPT,
+                messages: [{ role: 'user', content: content.slice(0, 1500) }],
+            }),
+        });
+        if (!res.ok)
+            return null;
+        const data = await res.json();
+        const text = data.content[0]?.text ?? '[]';
+        const parsed = JSON.parse(text.match(/\[[\s\S]*\]/)?.[0] ?? '[]');
+        return Array.isArray(parsed) ? parsed : null;
+    }
+    catch {
+        return null;
+    }
+}
+export const llmExtractPhase = {
+    name: 'llm-extract',
+    deps: ['docs-parse', 'pdf-parse'],
+    async execute(ctx) {
+        const apiKey = process.env.ANTHROPIC_API_KEY;
+        const maxSections = ctx.options.llmMaxSections;
+        if (!apiKey || maxSections <= 0 || ctx.options.codeOnly) {
+            return { triplesExtracted: 0, sectionsProcessed: 0 };
+        }
+        // Fetch Section nodes with non-trivial content
+        const sections = ctx.db
+            .prepare(`
+        SELECT id, name, properties FROM nodes
+        WHERE label = 'Section'
+        AND properties IS NOT NULL
+        AND json_extract(properties, '$.content') IS NOT NULL
+        AND length(json_extract(properties, '$.content')) > 200
+        LIMIT ?
+      `)
+            .all(maxSections);
+        if (sections.length === 0)
+            return { triplesExtracted: 0, sectionsProcessed: 0 };
+        const conceptNodes = new Map();
+        const allEdges = [];
+        const seenEdges = new Set();
+        let sectionsProcessed = 0;
+        // Fetch existing concept IDs to avoid duplicate node creation
+        const existingConcepts = new Set(ctx.db.prepare(`SELECT id FROM nodes WHERE label = 'Concept'`).all()
+            .map(r => r.id));
+        for (const section of sections) {
+            const props = JSON.parse(section.properties);
+            const content = props.content;
+            if (!content)
+                continue;
+            const triples = await callClaude(`Section: "${section.name}"\n\n${content}`, apiKey);
+            if (!triples || triples.length === 0)
+                continue;
+            sectionsProcessed++;
+            for (const triple of triples) {
+                const { node_1, node_2, relation, edge } = triple;
+                if (!node_1 || !node_2 || !relation)
+                    continue;
+                const rel = relation.toUpperCase();
+                if (!ALLOWED_RELATIONS.has(rel))
+                    continue;
+                // Normalize concept names (lowercase, collapse spaces)
+                const n1 = node_1.toLowerCase().trim().replace(/\s+/g, '_').replace(/[^a-z0-9_]/g, '');
+                const n2 = node_2.toLowerCase().trim().replace(/\s+/g, '_').replace(/[^a-z0-9_]/g, '');
+                if (!n1 || !n2 || n1 === n2)
+                    continue;
+                const c1Id = makeId('concept', n1);
+                const c2Id = makeId('concept', n2);
+                for (const [cId, cName] of [[c1Id, n1], [c2Id, n2]]) {
+                    if (!conceptNodes.has(cId) && !existingConcepts.has(cId)) {
+                        conceptNodes.set(cId, {
+                            id: cId, label: 'Concept',
+                            name: cName.replace(/_/g, ' '), normLabel: toNormLabel(cName),
+                            isExported: false,
+                            properties: { source: 'llm', edgeLabel: edge },
+                        });
+                    }
+                }
+                // Section → concept_1 (DESCRIBES)
+                const e1Id = makeId(section.id, c1Id, 'describes');
+                if (!seenEdges.has(e1Id)) {
+                    seenEdges.add(e1Id);
+                    allEdges.push({
+                        id: e1Id, sourceId: section.id, targetId: c1Id,
+                        relation: 'DESCRIBES', confidence: 'INFERRED', confidenceScore: CONFIDENCE_SCORE.INFERRED,
+                    });
+                }
+                // concept_1 → concept_2 (semantic relation)
+                const e2Id = makeId(c1Id, c2Id, rel.toLowerCase());
+                if (!seenEdges.has(e2Id)) {
+                    seenEdges.add(e2Id);
+                    allEdges.push({
+                        id: e2Id, sourceId: c1Id, targetId: c2Id,
+                        relation: rel, confidence: 'INFERRED', confidenceScore: CONFIDENCE_SCORE.INFERRED,
+                        weight: 1,
+                    });
+                }
+            }
+        }
+        if (conceptNodes.size > 0)
+            insertNodes(ctx.db, [...conceptNodes.values()]);
+        if (allEdges.length > 0)
+            insertEdges(ctx.db, allEdges);
+        ctx.onProgress?.({
+            phase: 'llm-extract',
+            message: `LLM processed ${sectionsProcessed} sections → ${allEdges.length} semantic edges, ${conceptNodes.size} new concepts`,
+        });
+        return { triplesExtracted: allEdges.length, sectionsProcessed };
+    },
+};
+//# sourceMappingURL=llm-extract.js.map

package/dist/src/pipeline/phases/llm-extract.js.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/phases/markdown.d.ts

@@ -0,0 +1,8 @@
+import type { PipelinePhase } from '../types.js';
+import type { MonographNode, MonographEdge } from '../../types.js';
+export interface MarkdownOutput {
+    documentNodes: MonographNode[];
+    referencesEdges: MonographEdge[];
+}
+export declare const markdownPhase: PipelinePhase<MarkdownOutput>;
+//# sourceMappingURL=markdown.d.ts.map

package/dist/src/pipeline/phases/markdown.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/phases/markdown.js

@@ -0,0 +1,103 @@
+import { readFileSync, statSync } from 'fs';
+import { extname, basename } from 'path';
+import { makeId, toNormLabel } from '../../types.js';
+import { insertNodes } from '../../storage/node-store.js';
+import { insertEdges } from '../../storage/edge-store.js';
+const MARKDOWN_EXTENSIONS = new Set(['.md', '.mdx']);
+// Inline code span: `identifier`
+const INLINE_CODE_RE = /`([^`]+)`/g;
+// Module-level constant: compiled once per process, not per isIdentifier() call.
+const IDENTIFIER_RE = /^[A-Za-z_$][A-Za-z0-9_$.-]*$/;
+export const markdownPhase = {
+    name: 'markdown',
+    // Must run after parse so symbols are already in the DB for name lookup.
+    // Also depends on structure to get the list of file nodes.
+    // Runs before communities so REFERENCES edges are visible to graph analyses.
+    deps: ['parse', 'structure'],
+    async execute(ctx, deps) {
+        if (ctx.options.codeOnly)
+            return { documentNodes: [], referencesEdges: [] };
+        const { fileNodes } = deps.get('structure');
+        const documentNodes = [];
+        const referencesEdges = [];
+        const mdFiles = fileNodes.filter(fn => {
+            const ext = extname(fn.name).toLowerCase();
+            return MARKDOWN_EXTENSIONS.has(ext);
+        });
+        for (const fileNode of mdFiles) {
+            // fileNode.filePath is already relative per codebase convention
+            const relPath = fileNode.filePath ?? '';
+            const absPath = `${ctx.repoPath}/${relPath}`;
+            let source;
+            try {
+                const stat = statSync(absPath);
+                if (stat.size > ctx.options.maxFileSizeBytes)
+                    continue;
+                source = readFileSync(absPath, 'utf-8');
+            }
+            catch {
+                continue;
+            }
+            const nameWithoutExt = basename(relPath).replace(/\.(mdx?)$/, '');
+            // Use 'doc' suffix to avoid collision with the 'file'-suffixed File node
+            const docId = makeId(relPath.replace(/\//g, '_'), 'doc');
+            const docNode = {
+                id: docId,
+                label: 'Document',
+                name: nameWithoutExt,
+                normLabel: toNormLabel(nameWithoutExt),
+                filePath: relPath,
+                isExported: false,
+                language: 'markdown',
+            };
+            documentNodes.push(docNode);
+            // Extract inline code spans and match against symbol names in the DB
+            if (ctx.db) {
+                const spans = extractCodeSpans(source);
+                // Hoist prepared statement outside the span loop — avoids re-compiling the
+                // SQL query for every identifier in every markdown file (N+1 preparation).
+                const symbolLookup = ctx.db.prepare(`SELECT id FROM nodes WHERE name = ?
+           AND label NOT IN ('File', 'Folder', 'Document')`);
+                for (const span of spans) {
+                    // Only match single-word identifiers (not shell commands, paths, etc.)
+                    if (!isIdentifier(span))
+                        continue;
+                    // Exact name match, excluding structural nodes to avoid matching file names
+                    const rows = symbolLookup.all(span);
+                    if (rows.length === 1) {
+                        const edgeId = makeId(docId, rows[0].id, 'references');
+                        referencesEdges.push({
+                            id: edgeId,
+                            sourceId: docId,
+                            targetId: rows[0].id,
+                            relation: 'REFERENCES',
+                            confidence: 'INFERRED',
+                            // Literal 0.8 — intentionally higher than CONFIDENCE_SCORE.INFERRED (0.5)
+                            // because inline code span matches are reasonably strong documentation signals.
+                            confidenceScore: 0.8,
+                        });
+                    }
+                }
+            }
+        }
+        if (ctx.db) {
+            insertNodes(ctx.db, documentNodes);
+            insertEdges(ctx.db, referencesEdges);
+        }
+        return { documentNodes, referencesEdges };
+    },
+};
+function extractCodeSpans(source) {
+    const spans = [];
+    let match;
+    const re = new RegExp(INLINE_CODE_RE.source, 'g');
+    while ((match = re.exec(source)) !== null) {
+        spans.push(match[1].trim());
+    }
+    return spans;
+}
+/** Accept only simple identifiers — letters, digits, underscores, hyphens, dots (for namespaced names). */
+function isIdentifier(span) {
+    return IDENTIFIER_RE.test(span);
+}
+//# sourceMappingURL=markdown.js.map

package/dist/src/pipeline/phases/markdown.js.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/phases/middleware-extractor.d.ts

@@ -0,0 +1,14 @@
+export type WrapperPattern = 'compose' | 'nested' | 'array' | 'none';
+export interface MiddlewareInfo {
+    middlewareNames: string[];
+    wrapperPattern: WrapperPattern;
+}
+/**
+ * Extracts the middleware chain wrapping a named handler in source code.
+ *
+ * @param source     Full source text of the handler file.
+ * @param handlerName  The name of the handler function to look for.
+ * @returns  MiddlewareInfo with names in outermost-first order.
+ */
+export declare function extractMiddlewareChain(source: string, handlerName: string): MiddlewareInfo;
+//# sourceMappingURL=middleware-extractor.d.ts.map

package/dist/src/pipeline/phases/middleware-extractor.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"middleware-extractor.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/middleware-extractor.ts"],"names":[],"mappings":"AAcA,MAAM,MAAM,cAAc,GAAG,SAAS,GAAG,QAAQ,GAAG,OAAO,GAAG,MAAM,CAAC;AAErE,MAAM,WAAW,cAAc;IAC7B,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,cAAc,EAAE,cAAc,CAAC;CAChC;AAID;;;;;;GAMG;AACH,wBAAgB,sBAAsB,CAAC,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,cAAc,CA4C1F"}

package/dist/src/pipeline/phases/middleware-extractor.js

@@ -0,0 +1,104 @@
+// ── Middleware chain extractor ────────────────────────────────────────────────
+//
+// Pure regex-based extraction (no tree-sitter). Only scans the first 3000 chars
+// of source for performance. Handles four patterns:
+//
+//   1. nested:  withAuth(withRateLimit(handler))
+//   2. compose: compose(withAuth, withRateLimit)(handler)
+//   3. array:   app.get('/path', authMiddleware, handler)   (args before handler)
+//   4. none:    plain handler usage
+//
+// Next.js middleware.ts detection: if the source file itself exports a
+// `middleware` function with a `matcher` config, it is treated as a middleware
+// file rather than performing per-route handler scanning.
+const SCAN_LIMIT = 3000;
+/**
+ * Extracts the middleware chain wrapping a named handler in source code.
+ *
+ * @param source     Full source text of the handler file.
+ * @param handlerName  The name of the handler function to look for.
+ * @returns  MiddlewareInfo with names in outermost-first order.
+ */
+export function extractMiddlewareChain(source, handlerName) {
+    const snippet = source.slice(0, SCAN_LIMIT);
+    // ── Pattern 0: Next.js middleware.ts ──────────────────────────────────────
+    // If the file exports a `middleware` function and has a `matcher` config,
+    // treat it as a global middleware file — no per-route wrapping to extract.
+    const isNextMiddleware = /export\s+(?:default\s+)?(?:async\s+)?function\s+middleware\b/.test(snippet) &&
+        /matcher/.test(snippet);
+    if (isNextMiddleware) {
+        return { middlewareNames: ['middleware.ts'], wrapperPattern: 'none' };
+    }
+    // ── Pattern 1: compose / pipe ─────────────────────────────────────────────
+    // Matches: compose(withAuth, withRateLimit)(handler)  or  pipe(...)(handler)
+    const composeRe = /(?:compose|pipe)\s*\(([\s\S]*?)\)\s*\(\s*HANDLER_NAME\s*\)/;
+    const composeSrc = composeRe.source.replace('HANDLER_NAME', escapeRe(handlerName));
+    const composeMatch = new RegExp(composeSrc, 'i').exec(snippet);
+    if (composeMatch) {
+        const names = composeMatch[1]
+            .split(',')
+            .map((s) => s.trim())
+            .filter((s) => /^[A-Za-z_$][\w$]*$/.test(s));
+        if (names.length > 0) {
+            return { middlewareNames: names, wrapperPattern: 'compose' };
+        }
+    }
+    // ── Pattern 2: nested wrappers ────────────────────────────────────────────
+    // Matches: withAuth(withRateLimit(handler)) — walks outward iteratively.
+    const nestedNames = extractNestedWrappers(snippet, handlerName);
+    if (nestedNames.length > 0) {
+        return { middlewareNames: nestedNames, wrapperPattern: 'nested' };
+    }
+    // ── Pattern 3: array / positional args (Express-style) ───────────────────
+    // Matches: app.METHOD('/path', mw1, mw2, handler)
+    // Extract identifiers that appear *before* the handler in the same call.
+    const arrayNames = extractArrayMiddleware(snippet, handlerName);
+    if (arrayNames.length > 0) {
+        return { middlewareNames: arrayNames, wrapperPattern: 'array' };
+    }
+    return { middlewareNames: [], wrapperPattern: 'none' };
+}
+// ── Helpers ───────────────────────────────────────────────────────────────────
+/** Escape a string for use as a regex literal. */
+function escapeRe(s) {
+    return s.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+}
+/**
+ * Walk outward from the innermost `wrapper(handler)` occurrence.
+ * Returns names in outermost-first order, e.g. ['withAuth', 'withRateLimit']
+ * for `withAuth(withRateLimit(handler))`.
+ */
+function extractNestedWrappers(snippet, handlerName) {
+    const wrappers = [];
+    let inner = escapeRe(handlerName);
+    // Each iteration tries to find `someIdent(inner)` in the snippet.
+    // Limit iterations to prevent pathological loops.
+    for (let i = 0; i < 10; i++) {
+        const re = new RegExp(`([A-Za-z_$][\\w$]*)\\s*\\(\\s*${inner}\\s*\\)`, 'i');
+        const m = re.exec(snippet);
+        if (!m)
+            break;
+        wrappers.unshift(m[1]); // outermost first
+        inner = escapeRe(m[1]) + `\\s*\\(\\s*${inner}\\s*\\)`;
+    }
+    return wrappers;
+}
+/**
+ * Detect Express-style middleware arrays:
+ *   app.get('/path', mw1, mw2, handler)
+ * Returns identifier args that appear before `handler` in the same call.
+ */
+function extractArrayMiddleware(snippet, handlerName) {
+    // Match: something.method('path', ...args, handler  — capture everything before handler
+    const re = new RegExp(`\\.(?:get|post|put|delete|patch|use)\\s*\\(\\s*['"][^'"]*['"]\\s*,\\s*([^)]+?)\\s*\\b${escapeRe(handlerName)}\\b`, 'i');
+    const m = re.exec(snippet);
+    if (!m)
+        return [];
+    const before = m[1];
+    const names = before
+        .split(',')
+        .map((s) => s.trim())
+        .filter((s) => /^[A-Za-z_$][\w$]*$/.test(s));
+    return names;
+}
+//# sourceMappingURL=middleware-extractor.js.map

package/dist/src/pipeline/phases/middleware-extractor.js.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/phases/mro.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"mro.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/mro.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAmB,MAAM,aAAa,CAAC;AAClE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AAIpD,MAAM,WAAW,SAAS;IACxB,QAAQ,EAAE,aAAa,EAAE,CAAC;CAC3B;AAED,eAAO,MAAM,QAAQ,EAAE,aAAa,CAAC,SAAS,CA8C7C,CAAC"}

package/dist/src/pipeline/phases/mro.js

@@ -1,12 +1,15 @@
 import { makeId, CONFIDENCE_SCORE } from '../../types.js';
 export const mroPhase = {
     name: 'mro',
-    deps: ['cross-file'],
+    deps: ['parse'],
     async execute(_ctx, deps) {
         const { allEdges, symbolNodes } = deps.get('parse');
+        // Method nodes — used to filter CONTAINS edges (the relation actually emitted by the extractor)
+        const methodIds = new Set(symbolNodes.filter(n => n.label === 'Method').map(n => n.id));
         const classMethodsIndex = new Map();
         for (const edge of allEdges) {
-            if (edge.relation === 'HAS_METHOD') {
+            // Extractor emits CONTAINS for method-in-class; HAS_METHOD is never produced
+            if (edge.relation === 'CONTAINS' && methodIds.has(edge.targetId)) {
                 const methods = classMethodsIndex.get(edge.sourceId) ?? [];
                 methods.push(edge.targetId);
                 classMethodsIndex.set(edge.sourceId, methods);

package/dist/src/pipeline/phases/mro.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/phases/orm.d.ts

@@ -0,0 +1,17 @@
+import type { PipelinePhase } from '../types.js';
+export interface FieldDef {
+    name: string;
+    type: string;
+    fieldNodeId: string;
+}
+export interface EntityDef {
+    name: string;
+    filePath: string;
+    fields: FieldDef[];
+    entityNodeId: string;
+}
+export interface OrmOutput {
+    entities: EntityDef[];
+}
+export declare const ormPhase: PipelinePhase<OrmOutput>;
+//# sourceMappingURL=orm.d.ts.map

package/dist/src/pipeline/phases/orm.d.ts.map

@@ -0,0 +1 @@
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