ocr-provenance-mcp 1.0.0

package/dist/tools/clm.js.map

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

@@ -0,0 +1,13 @@
+/**
+ * Document Clustering & Auto-Classification MCP Tools
+ *
+ * Tools: ocr_cluster_documents, ocr_cluster_list, ocr_cluster_get,
+ *        ocr_cluster_assign, ocr_cluster_delete, ocr_cluster_reassign, ocr_cluster_merge
+ *
+ * CRITICAL: NEVER use console.log() - stdout is reserved for JSON-RPC protocol.
+ *
+ * @module tools/clustering
+ */
+import { type ToolDefinition } from './shared.js';
+export declare const clusteringTools: Record<string, ToolDefinition>;
+//# sourceMappingURL=clustering.d.ts.map

package/dist/tools/clustering.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"clustering.d.ts","sourceRoot":"","sources":["../../src/tools/clustering.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAIH,OAAO,EAIL,KAAK,cAAc,EAEpB,MAAM,aAAa,CAAC;AAsiBrB,eAAO,MAAM,eAAe,EAAE,MAAM,CAAC,MAAM,EAAE,cAAc,CA2C1D,CAAC"}

package/dist/tools/clustering.js

@@ -0,0 +1,498 @@
+/**
+ * Document Clustering & Auto-Classification MCP Tools
+ *
+ * Tools: ocr_cluster_documents, ocr_cluster_list, ocr_cluster_get,
+ *        ocr_cluster_assign, ocr_cluster_delete, ocr_cluster_reassign, ocr_cluster_merge
+ *
+ * CRITICAL: NEVER use console.log() - stdout is reserved for JSON-RPC protocol.
+ *
+ * @module tools/clustering
+ */
+import { z } from 'zod';
+import { v4 as uuidv4 } from 'uuid';
+import { formatResponse, handleError, fetchProvenanceChain, } from './shared.js';
+import { validateInput } from '../utils/validation.js';
+import { requireDatabase } from '../server/state.js';
+import { MCPError } from '../server/errors.js';
+import { successResult } from '../server/types.js';
+import { ProvenanceType } from '../models/provenance.js';
+import { computeHash } from '../utils/hash.js';
+import { runClustering, computeDocumentEmbeddings, cosineSimilarity, } from '../services/clustering/clustering-service.js';
+import { getCluster, listClusters, getClusterDocuments, deleteClustersByRunId, insertDocumentCluster, getClusterSummariesByRunId, reassignDocument, mergeClusters, } from '../services/storage/database/cluster-operations.js';
+// ═══════════════════════════════════════════════════════════════════════════════
+// INPUT SCHEMAS
+// ═══════════════════════════════════════════════════════════════════════════════
+const ClusterDocumentsInput = z.object({
+    algorithm: z
+        .enum(['hdbscan', 'agglomerative', 'kmeans'])
+        .default('hdbscan')
+        .describe('Clustering algorithm. HDBSCAN auto-detects cluster count.'),
+    n_clusters: z
+        .number()
+        .int()
+        .min(2)
+        .max(100)
+        .optional()
+        .describe('Number of clusters. Required for kmeans/agglomerative. Ignored for hdbscan.'),
+    min_cluster_size: z
+        .number()
+        .int()
+        .min(2)
+        .max(100)
+        .default(3)
+        .describe('HDBSCAN: minimum documents per cluster'),
+    distance_threshold: z
+        .number()
+        .min(0.1)
+        .max(2.0)
+        .optional()
+        .describe('Agglomerative: distance threshold for auto-detection. Used when n_clusters not set.'),
+    linkage: z
+        .enum(['average', 'complete', 'single'])
+        .default('average')
+        .describe('Agglomerative linkage. Ward excluded (incompatible with cosine).'),
+    document_filter: z
+        .array(z.string())
+        .optional()
+        .describe('Cluster only these document IDs. Default: all documents with embeddings.'),
+});
+const ClusterListInput = z.object({
+    run_id: z.string().optional().describe('Filter by clustering run ID'),
+    classification_tag: z.string().optional().describe('Filter by classification tag'),
+    limit: z.number().int().min(1).max(100).default(50),
+    offset: z.number().int().min(0).default(0),
+});
+const ClusterGetInput = z.object({
+    cluster_id: z.string().min(1).describe('Cluster ID'),
+    include_documents: z.boolean().default(true).describe('Include member document list'),
+    include_provenance: z.boolean().default(false).describe('Include provenance chain'),
+});
+const ClusterAssignInput = z.object({
+    document_id: z.string().min(1).describe('Document ID to classify'),
+    run_id: z.string().min(1).describe('Run ID to classify against'),
+});
+const ClusterDeleteInput = z.object({
+    run_id: z.string().min(1).describe('Clustering run ID to delete'),
+    confirm: z.literal(true).describe('Must be true to confirm deletion'),
+});
+const ClusterReassignInput = z.object({
+    document_id: z.string().min(1).describe('Document ID to reassign'),
+    target_cluster_id: z.string().min(1).describe('Target cluster ID to move the document to'),
+});
+const ClusterMergeInput = z.object({
+    cluster_id_1: z.string().min(1).describe('First cluster ID (surviving cluster)'),
+    cluster_id_2: z.string().min(1).describe('Second cluster ID (will be merged into first and deleted)'),
+});
+// ═══════════════════════════════════════════════════════════════════════════════
+// HANDLERS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Handle ocr_cluster_documents - Run clustering on documents
+ */
+async function handleClusterDocuments(params) {
+    try {
+        const input = validateInput(ClusterDocumentsInput, params);
+        const { db, vector } = requireDatabase();
+        // Validate: kmeans and agglomerative without distance_threshold require n_clusters
+        if (input.algorithm === 'kmeans' && !input.n_clusters) {
+            throw new MCPError('VALIDATION_ERROR', 'n_clusters is required for kmeans algorithm');
+        }
+        const config = {
+            algorithm: input.algorithm ?? 'hdbscan',
+            n_clusters: input.n_clusters ?? null,
+            min_cluster_size: input.min_cluster_size ?? 3,
+            distance_threshold: input.distance_threshold ?? null,
+            linkage: input.linkage ?? 'average',
+        };
+        const result = await runClustering(db, vector, config, input.document_filter);
+        return formatResponse(successResult({
+            run_id: result.run_id,
+            algorithm: result.algorithm,
+            n_clusters: result.n_clusters,
+            total_documents: result.total_documents,
+            noise_count: result.noise_document_ids.length,
+            noise_document_ids: result.noise_document_ids,
+            silhouette_score: result.silhouette_score,
+            processing_duration_ms: result.processing_duration_ms,
+            clusters: result.clusters.map((c) => ({
+                cluster_index: c.cluster_index,
+                document_count: c.document_count,
+                coherence_score: c.coherence_score,
+                document_ids: c.document_ids,
+            })),
+            next_steps: [
+                { tool: 'ocr_cluster_list', description: 'Browse all clusters and their documents' },
+            ],
+        }));
+    }
+    catch (error) {
+        return handleError(error);
+    }
+}
+/**
+ * Handle ocr_cluster_list - List clusters with filtering
+ */
+async function handleClusterList(params) {
+    try {
+        const input = validateInput(ClusterListInput, params);
+        const { db } = requireDatabase();
+        const conn = db.getConnection();
+        const clusters = listClusters(conn, {
+            run_id: input.run_id,
+            classification_tag: input.classification_tag,
+            limit: input.limit,
+            offset: input.offset,
+        });
+        const items = clusters.map((c) => ({
+            id: c.id,
+            run_id: c.run_id,
+            cluster_index: c.cluster_index,
+            label: c.label,
+            description: c.description,
+            classification_tag: c.classification_tag,
+            document_count: c.document_count,
+            coherence_score: c.coherence_score,
+            algorithm: c.algorithm,
+            silhouette_score: c.silhouette_score,
+            created_at: c.created_at,
+        }));
+        return formatResponse(successResult({
+            clusters: items,
+            total: items.length,
+            offset: input.offset,
+            next_steps: items.length === 0
+                ? [
+                    { tool: 'ocr_cluster_documents', description: 'Run clustering to group documents by similarity' },
+                    { tool: 'ocr_document_list', description: 'Browse documents available for clustering' },
+                ]
+                : [
+                    { tool: 'ocr_cluster_get', description: 'Inspect a specific cluster' },
+                    { tool: 'ocr_cluster_documents', description: 'Run a new clustering' },
+                    { tool: 'ocr_comparison_matrix', description: 'View NxN document similarity matrix' },
+                ],
+        }));
+    }
+    catch (error) {
+        return handleError(error);
+    }
+}
+/**
+ * Handle ocr_cluster_get - Get detailed cluster info
+ */
+async function handleClusterGet(params) {
+    try {
+        const input = validateInput(ClusterGetInput, params);
+        const { db } = requireDatabase();
+        const conn = db.getConnection();
+        const cluster = getCluster(conn, input.cluster_id);
+        if (!cluster) {
+            throw new MCPError('DOCUMENT_NOT_FOUND', `Cluster "${input.cluster_id}" not found`);
+        }
+        const result = {
+            id: cluster.id,
+            run_id: cluster.run_id,
+            cluster_index: cluster.cluster_index,
+            label: cluster.label,
+            description: cluster.description,
+            classification_tag: cluster.classification_tag,
+            document_count: cluster.document_count,
+            coherence_score: cluster.coherence_score,
+            algorithm: cluster.algorithm,
+            algorithm_params: cluster.algorithm_params_json
+                ? JSON.parse(cluster.algorithm_params_json)
+                : null,
+            silhouette_score: cluster.silhouette_score,
+            content_hash: cluster.content_hash,
+            provenance_id: cluster.provenance_id,
+            created_at: cluster.created_at,
+            processing_duration_ms: cluster.processing_duration_ms,
+        };
+        if (input.include_documents) {
+            result.documents = getClusterDocuments(conn, input.cluster_id);
+        }
+        if (input.include_provenance) {
+            result.provenance_chain =
+                fetchProvenanceChain(db, cluster.provenance_id, 'clustering') ?? null;
+        }
+        result.next_steps = [
+            { tool: 'ocr_document_compare', description: 'Compare two documents from this cluster' },
+        ];
+        return formatResponse(successResult(result));
+    }
+    catch (error) {
+        return handleError(error);
+    }
+}
+/**
+ * Handle ocr_cluster_assign - Assign a document to nearest cluster
+ */
+async function handleClusterAssign(params) {
+    try {
+        const input = validateInput(ClusterAssignInput, params);
+        const { db } = requireDatabase();
+        const conn = db.getConnection();
+        // Verify document exists and has embeddings
+        const doc = db.getDocument(input.document_id);
+        if (!doc) {
+            throw new MCPError('DOCUMENT_NOT_FOUND', `Document "${input.document_id}" not found`);
+        }
+        // Compute document embedding
+        const docEmbeddings = computeDocumentEmbeddings(conn, [input.document_id]);
+        if (docEmbeddings.length === 0) {
+            throw new MCPError('VALIDATION_ERROR', `Document "${input.document_id}" has no chunk embeddings`);
+        }
+        const docEmb = docEmbeddings[0].embedding;
+        // Get all clusters for the specified run
+        const clusters = getClusterSummariesByRunId(conn, input.run_id);
+        if (clusters.length === 0) {
+            throw new MCPError('DOCUMENT_NOT_FOUND', `No clusters found for run "${input.run_id}"`);
+        }
+        // Load centroids and find nearest cluster
+        let bestClusterId = null;
+        let bestSimilarity = -1;
+        let bestClusterIndex = -1;
+        for (const cluster of clusters) {
+            const fullCluster = getCluster(conn, cluster.id);
+            if (!fullCluster?.centroid_json)
+                continue;
+            const centroid = JSON.parse(fullCluster.centroid_json);
+            const similarity = cosineSimilarity(docEmb, centroid);
+            if (similarity > bestSimilarity) {
+                bestSimilarity = similarity;
+                bestClusterId = cluster.id;
+                bestClusterIndex = cluster.cluster_index;
+            }
+        }
+        if (!bestClusterId) {
+            throw new MCPError('INTERNAL_ERROR', 'No valid cluster centroids found');
+        }
+        // Insert document_cluster assignment
+        const now = new Date().toISOString();
+        const dc = {
+            id: uuidv4(),
+            document_id: input.document_id,
+            cluster_id: bestClusterId,
+            run_id: input.run_id,
+            similarity_to_centroid: Math.round(bestSimilarity * 1000000) / 1000000,
+            membership_probability: 1.0,
+            is_noise: false,
+            assigned_at: now,
+        };
+        insertDocumentCluster(conn, dc);
+        // Update cluster document_count
+        conn
+            .prepare('UPDATE clusters SET document_count = document_count + 1 WHERE id = ?')
+            .run(bestClusterId);
+        // Create provenance record for cluster assignment
+        const assignProvId = uuidv4();
+        db.insertProvenance({
+            id: assignProvId,
+            type: ProvenanceType.CLUSTERING,
+            created_at: now,
+            processed_at: now,
+            source_file_created_at: null,
+            source_file_modified_at: null,
+            source_type: 'CLUSTERING',
+            source_path: null,
+            source_id: doc.provenance_id,
+            root_document_id: doc.provenance_id,
+            location: null,
+            content_hash: computeHash(JSON.stringify({
+                document_id: input.document_id,
+                cluster_id: bestClusterId,
+                run_id: input.run_id,
+                similarity_to_centroid: dc.similarity_to_centroid,
+            })),
+            input_hash: null,
+            file_hash: null,
+            processor: 'cluster-reassign',
+            processor_version: '1.0.0',
+            processing_params: {
+                document_id: input.document_id,
+                cluster_id: bestClusterId,
+                run_id: input.run_id,
+                similarity_to_centroid: dc.similarity_to_centroid,
+            },
+            processing_duration_ms: null,
+            processing_quality_score: null,
+            parent_id: doc.provenance_id,
+            parent_ids: JSON.stringify([doc.provenance_id]),
+            chain_depth: 2,
+            chain_path: '["DOCUMENT","CLUSTERING"]',
+        });
+        return formatResponse(successResult({
+            document_id: input.document_id,
+            cluster_id: bestClusterId,
+            cluster_index: bestClusterIndex,
+            similarity_to_centroid: dc.similarity_to_centroid,
+            run_id: input.run_id,
+            assigned: true,
+            provenance_id: assignProvId,
+            next_steps: [{ tool: 'ocr_cluster_get', description: 'Inspect the assigned cluster' }, { tool: 'ocr_document_get', description: 'View the classified document' }],
+        }));
+    }
+    catch (error) {
+        return handleError(error);
+    }
+}
+/**
+ * Handle ocr_cluster_delete - Delete a clustering run
+ */
+async function handleClusterDelete(params) {
+    try {
+        const input = validateInput(ClusterDeleteInput, params);
+        const { db } = requireDatabase();
+        const conn = db.getConnection();
+        // Collect provenance IDs before deletion (lightweight: no centroid blobs)
+        const provenanceIds = conn
+            .prepare('SELECT provenance_id FROM clusters WHERE run_id = ?')
+            .all(input.run_id);
+        if (provenanceIds.length === 0) {
+            throw new MCPError('DOCUMENT_NOT_FOUND', `No clusters found for run "${input.run_id}"`);
+        }
+        const deletedCount = deleteClustersByRunId(conn, input.run_id);
+        // Clean up provenance records for deleted clusters
+        const deleteProvStmt = conn.prepare('DELETE FROM provenance WHERE id = ?');
+        for (const { provenance_id } of provenanceIds) {
+            try {
+                deleteProvStmt.run(provenance_id);
+            }
+            catch (err) {
+                console.error(`[clustering] Failed to delete provenance ${provenance_id}: ${err instanceof Error ? err.message : String(err)}`);
+            }
+        }
+        return formatResponse(successResult({
+            run_id: input.run_id,
+            clusters_deleted: deletedCount,
+            deleted: true,
+            next_steps: [{ tool: 'ocr_cluster_documents', description: 'Run a new clustering' }, { tool: 'ocr_cluster_list', description: 'List remaining clusters' }],
+        }));
+    }
+    catch (error) {
+        return handleError(error);
+    }
+}
+// ═══════════════════════════════════════════════════════════════════════════════
+// CLUSTER REASSIGN & MERGE HANDLERS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Handle ocr_cluster_reassign - Move a document between clusters
+ */
+async function handleClusterReassign(params) {
+    try {
+        const input = validateInput(ClusterReassignInput, params);
+        const { db } = requireDatabase();
+        const conn = db.getConnection();
+        // Verify document exists
+        const doc = db.getDocument(input.document_id);
+        if (!doc) {
+            throw new MCPError('DOCUMENT_NOT_FOUND', `Document "${input.document_id}" not found`);
+        }
+        // Verify target cluster exists
+        const targetCluster = getCluster(conn, input.target_cluster_id);
+        if (!targetCluster) {
+            throw new MCPError('DOCUMENT_NOT_FOUND', `Cluster "${input.target_cluster_id}" not found`);
+        }
+        // Perform reassignment
+        const result = reassignDocument(conn, input.document_id, input.target_cluster_id);
+        return formatResponse(successResult({
+            document_id: input.document_id,
+            target_cluster_id: input.target_cluster_id,
+            old_cluster_id: result.old_cluster_id,
+            run_id: result.run_id,
+            reassigned: result.old_cluster_id !== input.target_cluster_id,
+            message: result.old_cluster_id === input.target_cluster_id
+                ? 'Document is already in the target cluster'
+                : result.old_cluster_id
+                    ? `Document moved from cluster "${result.old_cluster_id}" to "${input.target_cluster_id}"`
+                    : `Document assigned to cluster "${input.target_cluster_id}"`,
+            next_steps: [{ tool: 'ocr_cluster_get', description: 'Inspect the target cluster' }, { tool: 'ocr_cluster_list', description: 'Browse all clusters' }],
+        }));
+    }
+    catch (error) {
+        return handleError(error);
+    }
+}
+/**
+ * Handle ocr_cluster_merge - Merge two clusters into one
+ */
+async function handleClusterMerge(params) {
+    try {
+        const input = validateInput(ClusterMergeInput, params);
+        const { db } = requireDatabase();
+        const conn = db.getConnection();
+        if (input.cluster_id_1 === input.cluster_id_2) {
+            throw new MCPError('VALIDATION_ERROR', 'Cannot merge a cluster with itself. Provide two different cluster IDs.');
+        }
+        // Verify both clusters exist
+        const cluster1 = getCluster(conn, input.cluster_id_1);
+        if (!cluster1) {
+            throw new MCPError('DOCUMENT_NOT_FOUND', `Cluster "${input.cluster_id_1}" not found`);
+        }
+        const cluster2 = getCluster(conn, input.cluster_id_2);
+        if (!cluster2) {
+            throw new MCPError('DOCUMENT_NOT_FOUND', `Cluster "${input.cluster_id_2}" not found`);
+        }
+        // Verify same run
+        if (cluster1.run_id !== cluster2.run_id) {
+            throw new MCPError('VALIDATION_ERROR', `Cannot merge clusters from different runs: "${cluster1.run_id}" vs "${cluster2.run_id}"`);
+        }
+        // Perform merge
+        const result = mergeClusters(conn, input.cluster_id_1, input.cluster_id_2);
+        // Get updated cluster info
+        const updatedCluster = getCluster(conn, result.merged_cluster_id);
+        return formatResponse(successResult({
+            merged_cluster_id: result.merged_cluster_id,
+            deleted_cluster_id: input.cluster_id_2,
+            documents_moved: result.documents_moved,
+            new_document_count: updatedCluster?.document_count ?? 0,
+            run_id: cluster1.run_id,
+            message: `Merged cluster "${input.cluster_id_2}" into "${input.cluster_id_1}". ${result.documents_moved} document(s) moved.`,
+            next_steps: [{ tool: 'ocr_cluster_get', description: 'Inspect the merged cluster' }, { tool: 'ocr_cluster_list', description: 'Browse all clusters' }],
+        }));
+    }
+    catch (error) {
+        return handleError(error);
+    }
+}
+// ═══════════════════════════════════════════════════════════════════════════════
+// TOOL DEFINITIONS FOR MCP REGISTRATION
+// ═══════════════════════════════════════════════════════════════════════════════
+export const clusteringTools = {
+    ocr_cluster_documents: {
+        description: '[PROCESSING] Group documents by similarity using HDBSCAN, agglomerative, or k-means. Returns assignments with coherence scores. Requires embeddings.',
+        inputSchema: ClusterDocumentsInput.shape,
+        handler: handleClusterDocuments,
+    },
+    ocr_cluster_list: {
+        description: '[ANALYSIS] Browse existing clusters with optional run_id or tag filter. Returns summaries with labels and doc counts.',
+        inputSchema: ClusterListInput.shape,
+        handler: handleClusterList,
+    },
+    ocr_cluster_get: {
+        description: '[ANALYSIS] Use to inspect a cluster: member documents, label, and statistics. Returns cluster details with document list. Use after ocr_cluster_list.',
+        inputSchema: ClusterGetInput.shape,
+        handler: handleClusterGet,
+    },
+    ocr_cluster_assign: {
+        description: '[ANALYSIS] Use to auto-classify a new document into an existing cluster by embedding similarity. Returns nearest cluster and similarity score. Requires a completed clustering run_id.',
+        inputSchema: ClusterAssignInput.shape,
+        handler: handleClusterAssign,
+    },
+    ocr_cluster_delete: {
+        description: '[DESTRUCTIVE] Use to delete all clusters and assignments for a clustering run. Returns deletion count. Requires confirm=true.',
+        inputSchema: ClusterDeleteInput.shape,
+        handler: handleClusterDelete,
+    },
+    ocr_cluster_reassign: {
+        description: '[MANAGE] Use to move a document from one cluster to another within the same run. Returns old and new cluster IDs.',
+        inputSchema: ClusterReassignInput.shape,
+        handler: handleClusterReassign,
+    },
+    ocr_cluster_merge: {
+        description: '[MANAGE] Use to merge two clusters into one within the same run. All documents from the second cluster move to the first. Returns merged cluster details.',
+        inputSchema: ClusterMergeInput.shape,
+        handler: handleClusterMerge,
+    },
+};
+//# sourceMappingURL=clustering.js.map

package/dist/tools/clustering.js.map

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package/dist/tools/collaboration.d.ts

@@ -0,0 +1,15 @@
+/**
+ * Document Collaboration Tools
+ *
+ * Provides 11 MCP tools for annotations, document locking, and search alerts:
+ * - ocr_annotation_create/list/get/update/delete/summary (6 annotation tools)
+ * - ocr_document_lock/unlock/lock_status (3 lock tools)
+ * - ocr_search_alert_enable/check (2 search alert tools)
+ *
+ * CRITICAL: NEVER use console.log() - stdout is reserved for JSON-RPC protocol.
+ *
+ * @module tools/collaboration
+ */
+import { type ToolDefinition } from './shared.js';
+export declare const collaborationTools: Record<string, ToolDefinition>;
+//# sourceMappingURL=collaboration.d.ts.map

package/dist/tools/collaboration.d.ts.map

@@ -0,0 +1 @@
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