knowledge-mcp-server 1.0.0

package/dist/writer.js

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+import { writeFileSync, mkdirSync, unlinkSync } from "node:fs";
+import { join, relative } from "node:path";
+import { stringify as stringifyYaml } from "yaml";
+import { deriveParentId, VALID_TYPES } from "./loader.js";
+import { updateBm25Index, embedSingleDocument, removeEmbedding, } from "./embeddings.js";
+const ID_PATTERN = /^[a-z][a-z0-9-]*(\/[a-z][a-z0-9-]*)*$/;
+function validateWriteParams(params, validDomains, validPhaseIds) {
+    if (!ID_PATTERN.test(params.id)) {
+        throw new Error(`Invalid document ID "${params.id}". Must match pattern: lowercase letters, digits, hyphens, separated by slashes.`);
+    }
+    if (validDomains && !validDomains.includes(params.domain)) {
+        throw new Error(`Invalid domain "${params.domain}". Must be one of: ${validDomains.join(", ")}`);
+    }
+    if (!VALID_TYPES.includes(params.type)) {
+        throw new Error(`Invalid type "${params.type}". Must be one of: ${VALID_TYPES.join(", ")}`);
+    }
+    for (const p of params.phase) {
+        if (validPhaseIds) {
+            if (!validPhaseIds.includes(p)) {
+                throw new Error(`Invalid phase value ${p}. Must be one of: ${validPhaseIds.join(", ")}`);
+            }
+        }
+        else if (p < 1 || !Number.isInteger(p)) {
+            throw new Error(`Invalid phase value ${p}. Must be a positive integer.`);
+        }
+    }
+    if (!params.title.trim()) {
+        throw new Error("Title must not be empty.");
+    }
+    if (!params.content.trim()) {
+        throw new Error("Content must not be empty.");
+    }
+}
+function findClosestTag(tag, knownTags) {
+    const lower = tag.toLowerCase();
+    let bestMatch = null;
+    let bestScore = 0;
+    for (const known of knownTags) {
+        const knownLower = known.toLowerCase();
+        // Exact case-insensitive match
+        if (knownLower === lower)
+            return known;
+        // Substring containment: tag is part of known or known is part of tag
+        if (knownLower.includes(lower) || lower.includes(knownLower)) {
+            const score = Math.min(lower.length, knownLower.length) / Math.max(lower.length, knownLower.length);
+            if (score > bestScore) {
+                bestScore = score;
+                bestMatch = known;
+            }
+        }
+    }
+    // Only suggest if the match is reasonably close (>40% overlap ratio)
+    return bestScore > 0.4 ? bestMatch : null;
+}
+function validateTags(tags, taxonomy, warnings) {
+    const correctedTags = [];
+    for (const tag of tags) {
+        const lower = tag.toLowerCase();
+        // Check alias map first
+        const aliasTarget = taxonomy.aliases.get(lower);
+        if (aliasTarget) {
+            correctedTags.push(aliasTarget);
+            warnings.push(`Tag "${tag}" auto-corrected to "${aliasTarget}" (known alias).`);
+            continue;
+        }
+        // Check if it's a known tag
+        if (taxonomy.knownTags.has(tag)) {
+            correctedTags.push(tag);
+            continue;
+        }
+        // Unknown tag — find closest match and warn
+        const closest = findClosestTag(tag, taxonomy.knownTags);
+        if (closest) {
+            warnings.push(`Tag "${tag}" is not in the taxonomy. Did you mean "${closest}"?`);
+        }
+        else {
+            warnings.push(`Tag "${tag}" is not in the taxonomy. Consider adding it to .tags.json.`);
+        }
+        correctedTags.push(tag);
+    }
+    return correctedTags;
+}
+export function writeDocument(graph, tfidfIndex, knowledgeDir, params, validDomains, validPhaseIds) {
+    validateWriteParams(params, validDomains ?? null, validPhaseIds ?? null);
+    // Validate and auto-correct tags against taxonomy (warnings only)
+    const tagWarnings = [];
+    if (graph.tagTaxonomy) {
+        params.tags = validateTags(params.tags, graph.tagTaxonomy, tagWarnings);
+    }
+    const parentId = deriveParentId(params.id);
+    const warnings = [...tagWarnings];
+    // Parent must exist (unless this is a top-level domain doc whose parent is "root")
+    if (parentId && !graph.documents.has(parentId)) {
+        throw new Error(`Parent document "${parentId}" does not exist. Create parent summary documents first.`);
+    }
+    // Validate related references (warn, not error)
+    if (params.related) {
+        for (const relId of params.related) {
+            if (!graph.documents.has(relId)) {
+                warnings.push(`Related reference "${relId}" does not exist in the knowledge graph.`);
+            }
+        }
+    }
+    // Derive file path: summary type uses _summary.md, others use {last-segment}.md
+    const segments = params.id.split("/");
+    const isSummary = params.type === "summary";
+    const fileName = isSummary ? "_summary.md" : `${segments[segments.length - 1]}.md`;
+    const dirPath = isSummary
+        ? join(knowledgeDir, ...segments)
+        : join(knowledgeDir, ...segments.slice(0, -1));
+    const filePath = join(dirPath, fileName);
+    const isUpdate = graph.documents.has(params.id);
+    // If updating, remove old entries from tag, domain, phase, and backlink indices
+    if (isUpdate) {
+        const oldDoc = graph.documents.get(params.id);
+        for (const tag of oldDoc.tags) {
+            const tagSet = graph.tagIndex.get(tag.toLowerCase());
+            if (tagSet) {
+                tagSet.delete(params.id);
+                if (tagSet.size === 0)
+                    graph.tagIndex.delete(tag.toLowerCase());
+            }
+        }
+        const domainSet = graph.domainIndex.get(oldDoc.domain.toLowerCase());
+        if (domainSet) {
+            domainSet.delete(params.id);
+            if (domainSet.size === 0)
+                graph.domainIndex.delete(oldDoc.domain.toLowerCase());
+        }
+        for (const phase of oldDoc.phase) {
+            const phaseSet = graph.phaseIndex.get(phase);
+            if (phaseSet) {
+                phaseSet.delete(params.id);
+                if (phaseSet.size === 0)
+                    graph.phaseIndex.delete(phase);
+            }
+        }
+        // Remove from type index
+        const typeSet = graph.typeIndex.get(oldDoc.type);
+        if (typeSet) {
+            typeSet.delete(params.id);
+            if (typeSet.size === 0)
+                graph.typeIndex.delete(oldDoc.type);
+        }
+        // Remove old backlink entries
+        for (const targetId of oldDoc.related) {
+            const backlinks = graph.backlinkIndex.get(targetId);
+            if (backlinks) {
+                backlinks.delete(params.id);
+                if (backlinks.size === 0)
+                    graph.backlinkIndex.delete(targetId);
+            }
+        }
+    }
+    // For summary updates, merge provided children with existing auto-discovered children
+    let childrenIds = [];
+    if (isUpdate && isSummary) {
+        const existingDoc = graph.documents.get(params.id);
+        const existingChildren = new Set(existingDoc.childrenIds);
+        if (params.children) {
+            for (const c of params.children)
+                existingChildren.add(c);
+        }
+        childrenIds = [...existingChildren];
+    }
+    else if (params.children) {
+        childrenIds = params.children;
+    }
+    const wordCount = params.content.split(/\s+/).filter(Boolean).length;
+    // Build frontmatter
+    const frontmatter = {
+        id: params.id,
+        title: params.title,
+        type: params.type,
+        domain: params.domain,
+    };
+    if (params.subdomain)
+        frontmatter.subdomain = params.subdomain;
+    frontmatter.tags = params.tags;
+    frontmatter.phase = params.phase;
+    if (params.related && params.related.length > 0)
+        frontmatter.related = params.related;
+    if (childrenIds.length > 0 && isSummary)
+        frontmatter.children = childrenIds;
+    const docStatus = params.status || "active";
+    if (docStatus !== "active")
+        frontmatter.status = docStatus;
+    if (params.superseded_by)
+        frontmatter.superseded_by = params.superseded_by;
+    if (params.type === "decision") {
+        if (params.decision_status)
+            frontmatter.decision_status = params.decision_status;
+        if (params.alternatives_considered && params.alternatives_considered.length > 0)
+            frontmatter.alternatives_considered = params.alternatives_considered;
+        if (params.decision_date)
+            frontmatter.decision_date = params.decision_date;
+    }
+    frontmatter.word_count = wordCount;
+    frontmatter.last_updated = new Date().toISOString().split("T")[0];
+    const fileContent = `---\n${stringifyYaml(frontmatter).trim()}\n---\n\n${params.content}`;
+    // Write file (create directories as needed)
+    mkdirSync(dirPath, { recursive: true });
+    writeFileSync(filePath, fileContent, "utf-8");
+    const lastUpdated = frontmatter.last_updated;
+    // Build the in-memory document
+    const doc = {
+        id: params.id,
+        title: params.title,
+        type: params.type,
+        domain: params.domain,
+        subdomain: params.subdomain,
+        tags: params.tags,
+        phase: params.phase,
+        related: params.related || [],
+        parentId,
+        childrenIds,
+        contentBody: params.content,
+        filePath: relative(join(knowledgeDir, ".."), filePath),
+        wordCount,
+        status: docStatus,
+        supersededBy: params.superseded_by,
+        lastUpdated,
+        decisionStatus: params.decision_status,
+        alternativesConsidered: params.alternatives_considered,
+        decisionDate: params.decision_date,
+    };
+    // Update in-memory graph
+    graph.documents.set(params.id, doc);
+    // Update tag index
+    for (const tag of doc.tags) {
+        const lower = tag.toLowerCase();
+        if (!graph.tagIndex.has(lower))
+            graph.tagIndex.set(lower, new Set());
+        graph.tagIndex.get(lower).add(doc.id);
+    }
+    // Update domain index
+    const domainLower = doc.domain.toLowerCase();
+    if (!graph.domainIndex.has(domainLower))
+        graph.domainIndex.set(domainLower, new Set());
+    graph.domainIndex.get(domainLower).add(doc.id);
+    // Update type index
+    if (!graph.typeIndex.has(doc.type))
+        graph.typeIndex.set(doc.type, new Set());
+    graph.typeIndex.get(doc.type).add(doc.id);
+    // Update phase index
+    for (const phase of doc.phase) {
+        if (!graph.phaseIndex.has(phase))
+            graph.phaseIndex.set(phase, new Set());
+        graph.phaseIndex.get(phase).add(doc.id);
+    }
+    // Update backlink index
+    for (const targetId of doc.related) {
+        if (!graph.backlinkIndex.has(targetId))
+            graph.backlinkIndex.set(targetId, new Set());
+        graph.backlinkIndex.get(targetId).add(doc.id);
+    }
+    // Update parent's childrenIds
+    if (parentId) {
+        const parent = graph.documents.get(parentId);
+        if (parent && !parent.childrenIds.includes(doc.id)) {
+            parent.childrenIds.push(doc.id);
+        }
+    }
+    // Incremental BM25 index update (no full rebuild)
+    updateBm25Index(tfidfIndex, doc.id, doc);
+    // Fire-and-forget inline embedding
+    embedSingleDocument(graph.embeddings, knowledgeDir, doc).catch(() => { });
+    return {
+        id: params.id,
+        filePath: relative(join(knowledgeDir, ".."), filePath),
+        parentId,
+        status: isUpdate ? "updated" : "created",
+        tfidfIndex,
+        warnings,
+    };
+}
+export function deleteDocument(graph, tfidfIndex, knowledgeDir, id) {
+    const doc = graph.documents.get(id);
+    if (!doc) {
+        throw new Error(`Document not found: "${id}".`);
+    }
+    const warnings = [];
+    // Warn about children
+    if (doc.childrenIds.length > 0) {
+        warnings.push(`Document has ${doc.childrenIds.length} children that will be orphaned: ${doc.childrenIds.join(", ")}`);
+    }
+    // Warn about documents that reference this one (via backlink index)
+    const backlinks = graph.backlinkIndex.get(id);
+    if (backlinks) {
+        for (const sourceId of backlinks) {
+            warnings.push(`Document "${sourceId}" has a related reference to this document.`);
+        }
+    }
+    // Remove from tag index
+    for (const tag of doc.tags) {
+        const tagSet = graph.tagIndex.get(tag.toLowerCase());
+        if (tagSet) {
+            tagSet.delete(id);
+            if (tagSet.size === 0)
+                graph.tagIndex.delete(tag.toLowerCase());
+        }
+    }
+    // Remove from domain index
+    const domainSet = graph.domainIndex.get(doc.domain.toLowerCase());
+    if (domainSet) {
+        domainSet.delete(id);
+        if (domainSet.size === 0)
+            graph.domainIndex.delete(doc.domain.toLowerCase());
+    }
+    // Remove from type index
+    const delTypeSet = graph.typeIndex.get(doc.type);
+    if (delTypeSet) {
+        delTypeSet.delete(id);
+        if (delTypeSet.size === 0)
+            graph.typeIndex.delete(doc.type);
+    }
+    // Remove from phase index
+    for (const phase of doc.phase) {
+        const phaseSet = graph.phaseIndex.get(phase);
+        if (phaseSet) {
+            phaseSet.delete(id);
+            if (phaseSet.size === 0)
+                graph.phaseIndex.delete(phase);
+        }
+    }
+    // Remove from parent's childrenIds
+    if (doc.parentId) {
+        const parent = graph.documents.get(doc.parentId);
+        if (parent) {
+            parent.childrenIds = parent.childrenIds.filter((c) => c !== id);
+        }
+    }
+    // Remove from backlink index (forward links this doc had)
+    for (const targetId of doc.related) {
+        const bl = graph.backlinkIndex.get(targetId);
+        if (bl) {
+            bl.delete(id);
+            if (bl.size === 0)
+                graph.backlinkIndex.delete(targetId);
+        }
+    }
+    // Remove backlink entry for this doc
+    graph.backlinkIndex.delete(id);
+    // Remove from documents map
+    graph.documents.delete(id);
+    // Delete file from disk
+    const fullPath = join(knowledgeDir, "..", doc.filePath);
+    try {
+        unlinkSync(fullPath);
+    }
+    catch {
+        warnings.push(`Could not delete file: ${doc.filePath}`);
+    }
+    // Incremental BM25 index update (remove doc, no full rebuild)
+    updateBm25Index(tfidfIndex, id, null);
+    // Remove stale embedding
+    removeEmbedding(graph.embeddings, knowledgeDir, id);
+    return { id, warnings, tfidfIndex };
+}
+//# sourceMappingURL=writer.js.map

package/dist/writer.js.map

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package/package.json

@@ -0,0 +1,58 @@
+{
+  "name": "knowledge-mcp-server",
+  "version": "1.0.0",
+  "description": "MCP server for semantic search, CRUD, and graph operations over hierarchical knowledge bases stored as Markdown with YAML frontmatter",
+  "type": "module",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "bin": {
+    "knowledge-mcp-server": "dist/cli.js"
+  },
+  "files": [
+    "dist/**/*.js",
+    "dist/**/*.d.ts",
+    "dist/**/*.js.map",
+    "README.md",
+    "LICENSE",
+    "CHANGELOG.md"
+  ],
+  "scripts": {
+    "build": "tsc",
+    "start": "node dist/cli.js",
+    "dev": "tsc --watch",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "lint": "eslint src/",
+    "lint:fix": "eslint src/ --fix",
+    "format": "prettier --write \"src/**/*.ts\"",
+    "format:check": "prettier --check \"src/**/*.ts\"",
+    "prepublishOnly": "npm run build && npm run test"
+  },
+  "keywords": [
+    "mcp",
+    "knowledge-graph",
+    "markdown",
+    "semantic-search",
+    "model-context-protocol",
+    "rag",
+    "bm25"
+  ],
+  "license": "MIT",
+  "engines": {
+    "node": ">=20"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.12.1",
+    "yaml": "^2.7.1"
+  },
+  "devDependencies": {
+    "@eslint/js": "^10.0.1",
+    "@types/node": "^22.15.3",
+    "eslint": "^10.1.0",
+    "eslint-config-prettier": "^10.1.8",
+    "prettier": "^3.8.1",
+    "typescript": "^5.8.3",
+    "typescript-eslint": "^8.57.1",
+    "vitest": "^4.1.0"
+  }
+}