Protokoll #912

{
    "event": "PreToolUse",
    "tool_name": "Edit",
    "tool_input": {
        "file_path": "\/var\/www\/dev.campus.systemische-tools.de\/src\/Infrastructure\/SemanticExplorerRepository.php",
        "old_string": "    public function getSemanticStats(): array\n    {\n        return $this->db->query(\n            'SELECT\n                COUNT(*) as total,\n                SUM(CASE WHEN sentiment = \"positive\" THEN 1 ELSE 0 END) as positive,\n                SUM(CASE WHEN sentiment = \"negative\" THEN 1 ELSE 0 END) as negative,\n                SUM(CASE WHEN sentiment = \"neutral\" THEN 1 ELSE 0 END) as neutral,\n                SUM(CASE WHEN sentiment = \"mixed\" THEN 1 ELSE 0 END) as mixed\n             FROM chunk_semantics'\n        )->fetch();\n    }\n}",
        "new_string": "    public function getSemanticStats(): array\n    {\n        return $this->db->query(\n            'SELECT\n                COUNT(*) as total,\n                SUM(CASE WHEN sentiment = \"positive\" THEN 1 ELSE 0 END) as positive,\n                SUM(CASE WHEN sentiment = \"negative\" THEN 1 ELSE 0 END) as negative,\n                SUM(CASE WHEN sentiment = \"neutral\" THEN 1 ELSE 0 END) as neutral,\n                SUM(CASE WHEN sentiment = \"mixed\" THEN 1 ELSE 0 END) as mixed\n             FROM chunk_semantics'\n        )->fetch();\n    }\n\n    \/\/ =========================================================================\n    \/\/ ENTITIES - CRUD\n    \/\/ =========================================================================\n\n    public function createEntity(string $name, string $type, ?string $description = null): int\n    {\n        $stmt = $this->db->prepare(\n            'INSERT INTO entities (name, canonical_name, type, description, created_at, updated_at)\n             VALUES (:name, :canonical, :type, :description, NOW(), NOW())'\n        );\n        $stmt->execute([\n            'name' => $name,\n            'canonical' => strtolower(trim($name)),\n            'type' => $type,\n            'description' => $description,\n        ]);\n\n        return (int) $this->db->lastInsertId();\n    }\n\n    public function updateEntity(int $id, string $name, string $type, ?string $description = null): bool\n    {\n        $stmt = $this->db->prepare(\n            'UPDATE entities SET name = :name, canonical_name = :canonical, type = :type,\n             description = :description, updated_at = NOW() WHERE id = :id'\n        );\n\n        return $stmt->execute([\n            'id' => $id,\n            'name' => $name,\n            'canonical' => strtolower(trim($name)),\n            'type' => $type,\n            'description' => $description,\n        ]);\n    }\n\n    public function deleteEntity(int $id): bool\n    {\n        \/\/ Check for relations\n        $stmt = $this->db->prepare(\n            'SELECT COUNT(*) FROM entity_relations\n             WHERE source_entity_id = :id OR target_entity_id = :id2'\n        );\n        $stmt->execute(['id' => $id, 'id2' => $id]);\n\n        if ((int) $stmt->fetchColumn() > 0) {\n            return false; \/\/ Has relations, cannot delete\n        }\n\n        \/\/ Delete synonyms first\n        $stmt = $this->db->prepare('DELETE FROM entity_synonyms WHERE entity_id = :id');\n        $stmt->execute(['id' => $id]);\n\n        \/\/ Delete chunk associations\n        $stmt = $this->db->prepare('DELETE FROM chunk_entities WHERE entity_id = :id');\n        $stmt->execute(['id' => $id]);\n\n        \/\/ Delete entity\n        $stmt = $this->db->prepare('DELETE FROM entities WHERE id = :id');\n\n        return $stmt->execute(['id' => $id]);\n    }\n\n    public function getEntityTypes(): array\n    {\n        return ['person', 'organization', 'location', 'concept', 'method', 'tool', 'event', 'other'];\n    }\n\n    public function getAllEntitiesSimple(): array\n    {\n        return $this->db->query('SELECT id, name, type FROM entities ORDER BY name')->fetchAll();\n    }\n\n    \/\/ =========================================================================\n    \/\/ RELATIONS - CRUD\n    \/\/ =========================================================================\n\n    public function getRelation(int $id): ?array\n    {\n        $stmt = $this->db->prepare(\n            'SELECT er.*,\n                    es.name as source_name, es.type as source_type,\n                    et.name as target_name, et.type as target_type\n             FROM entity_relations er\n             JOIN entities es ON er.source_entity_id = es.id\n             JOIN entities et ON er.target_entity_id = et.id\n             WHERE er.id = :id'\n        );\n        $stmt->execute(['id' => $id]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    public function createRelation(int $sourceId, int $targetId, string $type, float $strength = 1.0): int\n    {\n        $stmt = $this->db->prepare(\n            'INSERT INTO entity_relations (source_entity_id, target_entity_id, relation_type, strength, created_at)\n             VALUES (:source, :target, :type, :strength, NOW())'\n        );\n        $stmt->execute([\n            'source' => $sourceId,\n            'target' => $targetId,\n            'type' => $type,\n            'strength' => $strength,\n        ]);\n\n        return (int) $this->db->lastInsertId();\n    }\n\n    public function updateRelation(int $id, string $type, float $strength): bool\n    {\n        $stmt = $this->db->prepare(\n            'UPDATE entity_relations SET relation_type = :type, strength = :strength WHERE id = :id'\n        );\n\n        return $stmt->execute(['id' => $id, 'type' => $type, 'strength' => $strength]);\n    }\n\n    public function deleteRelation(int $id): bool\n    {\n        $stmt = $this->db->prepare('DELETE FROM entity_relations WHERE id = :id');\n\n        return $stmt->execute(['id' => $id]);\n    }\n\n    public function getRelationTypesList(): array\n    {\n        return ['RELATED_TO', 'PART_OF', 'DEVELOPED_BY', 'INFLUENCED_BY', 'USED_IN', 'WORKS_WITH', 'TEACHES', 'CREATED'];\n    }\n\n    \/\/ =========================================================================\n    \/\/ TAXONOMY - CRUD\n    \/\/ =========================================================================\n\n    public function getTaxonomyTerm(int $id): ?array\n    {\n        $stmt = $this->db->prepare('SELECT * FROM taxonomy_terms WHERE id = :id');\n        $stmt->execute(['id' => $id]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    public function createTaxonomyTerm(string $name, ?int $parentId = null): int\n    {\n        \/\/ Calculate depth and path\n        $depth = 0;\n        $path = $name;\n\n        if ($parentId !== null) {\n            $parent = $this->getTaxonomyTerm($parentId);\n            if ($parent !== null) {\n                $depth = (int) $parent['depth'] + 1;\n                $path = $parent['path'] . '\/' . $name;\n            }\n        }\n\n        $stmt = $this->db->prepare(\n            'INSERT INTO taxonomy_terms (name, parent_id, depth, path, created_at)\n             VALUES (:name, :parent, :depth, :path, NOW())'\n        );\n        $stmt->execute([\n            'name' => $name,\n            'parent' => $parentId,\n            'depth' => $depth,\n            'path' => $path,\n        ]);\n\n        return (int) $this->db->lastInsertId();\n    }\n\n    public function updateTaxonomyTerm(int $id, string $name, ?int $parentId = null): bool\n    {\n        \/\/ Calculate new depth and path\n        $depth = 0;\n        $path = $name;\n\n        if ($parentId !== null) {\n            $parent = $this->getTaxonomyTerm($parentId);\n            if ($parent !== null) {\n                $depth = (int) $parent['depth'] + 1;\n                $path = $parent['path'] . '\/' . $name;\n            }\n        }\n\n        $stmt = $this->db->prepare(\n            'UPDATE taxonomy_terms SET name = :name, parent_id = :parent, depth = :depth, path = :path WHERE id = :id'\n        );\n\n        return $stmt->execute([\n            'id' => $id,\n            'name' => $name,\n            'parent' => $parentId,\n            'depth' => $depth,\n            'path' => $path,\n        ]);\n    }\n\n    public function deleteTaxonomyTerm(int $id): bool\n    {\n        \/\/ Check for children\n        $stmt = $this->db->prepare('SELECT COUNT(*) FROM taxonomy_terms WHERE parent_id = :id');\n        $stmt->execute(['id' => $id]);\n\n        if ((int) $stmt->fetchColumn() > 0) {\n            return false; \/\/ Has children, cannot delete\n        }\n\n        \/\/ Delete chunk associations\n        $stmt = $this->db->prepare('DELETE FROM chunk_taxonomy WHERE taxonomy_term_id = :id');\n        $stmt->execute(['id' => $id]);\n\n        \/\/ Delete term\n        $stmt = $this->db->prepare('DELETE FROM taxonomy_terms WHERE id = :id');\n\n        return $stmt->execute(['id' => $id]);\n    }\n\n    public function getTaxonomyTermsForSelect(): array\n    {\n        return $this->db->query(\n            'SELECT id, name, depth, path FROM taxonomy_terms ORDER BY path, name'\n        )->fetchAll();\n    }\n\n    \/\/ =========================================================================\n    \/\/ ONTOLOGY - CRUD\n    \/\/ =========================================================================\n\n    public function getOntologyClass(int $id): ?array\n    {\n        $stmt = $this->db->prepare('SELECT * FROM ontology_classes WHERE id = :id');\n        $stmt->execute(['id' => $id]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    public function createOntologyClass(string $name, ?int $parentId = null, ?string $description = null, array $properties = []): int\n    {\n        $stmt = $this->db->prepare(\n            'INSERT INTO ontology_classes (name, parent_class_id, description, properties, created_at)\n             VALUES (:name, :parent, :description, :properties, NOW())'\n        );\n        $stmt->execute([\n            'name' => $name,\n            'parent' => $parentId,\n            'description' => $description,\n            'properties' => json_encode($properties),\n        ]);\n\n        return (int) $this->db->lastInsertId();\n    }\n\n    public function updateOntologyClass(int $id, string $name, ?int $parentId = null, ?string $description = null, array $properties = []): bool\n    {\n        $stmt = $this->db->prepare(\n            'UPDATE ontology_classes SET name = :name, parent_class_id = :parent,\n             description = :description, properties = :properties WHERE id = :id'\n        );\n\n        return $stmt->execute([\n            'id' => $id,\n            'name' => $name,\n            'parent' => $parentId,\n            'description' => $description,\n            'properties' => json_encode($properties),\n        ]);\n    }\n\n    public function deleteOntologyClass(int $id): bool\n    {\n        \/\/ Check for subclasses\n        $stmt = $this->db->prepare('SELECT COUNT(*) FROM ontology_classes WHERE parent_class_id = :id');\n        $stmt->execute(... [TRUNCATED-44ccab54ff7dc543]"
    }
}

{
    "tool_response": {
        "filePath": "\/var\/www\/dev.campus.systemische-tools.de\/src\/Infrastructure\/SemanticExplorerRepository.php",
        "oldString": "    public function getSemanticStats(): array\n    {\n        return $this->db->query(\n            'SELECT\n                COUNT(*) as total,\n                SUM(CASE WHEN sentiment = \"positive\" THEN 1 ELSE 0 END) as positive,\n                SUM(CASE WHEN sentiment = \"negative\" THEN 1 ELSE 0 END) as negative,\n                SUM(CASE WHEN sentiment = \"neutral\" THEN 1 ELSE 0 END) as neutral,\n                SUM(CASE WHEN sentiment = \"mixed\" THEN 1 ELSE 0 END) as mixed\n             FROM chunk_semantics'\n        )->fetch();\n    }\n}",
        "newString": "    public function getSemanticStats(): array\n    {\n        return $this->db->query(\n            'SELECT\n                COUNT(*) as total,\n                SUM(CASE WHEN sentiment = \"positive\" THEN 1 ELSE 0 END) as positive,\n                SUM(CASE WHEN sentiment = \"negative\" THEN 1 ELSE 0 END) as negative,\n                SUM(CASE WHEN sentiment = \"neutral\" THEN 1 ELSE 0 END) as neutral,\n                SUM(CASE WHEN sentiment = \"mixed\" THEN 1 ELSE 0 END) as mixed\n             FROM chunk_semantics'\n        )->fetch();\n    }\n\n    \/\/ =========================================================================\n    \/\/ ENTITIES - CRUD\n    \/\/ =========================================================================\n\n    public function createEntity(string $name, string $type, ?string $description = null): int\n    {\n        $stmt = $this->db->prepare(\n            'INSERT INTO entities (name, canonical_name, type, description, created_at, updated_at)\n             VALUES (:name, :canonical, :type, :description, NOW(), NOW())'\n        );\n        $stmt->execute([\n            'name' => $name,\n            'canonical' => strtolower(trim($name)),\n            'type' => $type,\n            'description' => $description,\n        ]);\n\n        return (int) $this->db->lastInsertId();\n    }\n\n    public function updateEntity(int $id, string $name, string $type, ?string $description = null): bool\n    {\n        $stmt = $this->db->prepare(\n            'UPDATE entities SET name = :name, canonical_name = :canonical, type = :type,\n             description = :description, updated_at = NOW() WHERE id = :id'\n        );\n\n        return $stmt->execute([\n            'id' => $id,\n            'name' => $name,\n            'canonical' => strtolower(trim($name)),\n            'type' => $type,\n            'description' => $description,\n        ]);\n    }\n\n    public function deleteEntity(int $id): bool\n    {\n        \/\/ Check for relations\n        $stmt = $this->db->prepare(\n            'SELECT COUNT(*) FROM entity_relations\n             WHERE source_entity_id = :id OR target_entity_id = :id2'\n        );\n        $stmt->execute(['id' => $id, 'id2' => $id]);\n\n        if ((int) $stmt->fetchColumn() > 0) {\n            return false; \/\/ Has relations, cannot delete\n        }\n\n        \/\/ Delete synonyms first\n        $stmt = $this->db->prepare('DELETE FROM entity_synonyms WHERE entity_id = :id');\n        $stmt->execute(['id' => $id]);\n\n        \/\/ Delete chunk associations\n        $stmt = $this->db->prepare('DELETE FROM chunk_entities WHERE entity_id = :id');\n        $stmt->execute(['id' => $id]);\n\n        \/\/ Delete entity\n        $stmt = $this->db->prepare('DELETE FROM entities WHERE id = :id');\n\n        return $stmt->execute(['id' => $id]);\n    }\n\n    public function getEntityTypes(): array\n    {\n        return ['person', 'organization', 'location', 'concept', 'method', 'tool', 'event', 'other'];\n    }\n\n    public function getAllEntitiesSimple(): array\n    {\n        return $this->db->query('SELECT id, name, type FROM entities ORDER BY name')->fetchAll();\n    }\n\n    \/\/ =========================================================================\n    \/\/ RELATIONS - CRUD\n    \/\/ =========================================================================\n\n    public function getRelation(int $id): ?array\n    {\n        $stmt = $this->db->prepare(\n            'SELECT er.*,\n                    es.name as source_name, es.type as source_type,\n                    et.name as target_name, et.type as target_type\n             FROM entity_relations er\n             JOIN entities es ON er.source_entity_id = es.id\n             JOIN entities et ON er.target_entity_id = et.id\n             WHERE er.id = :id'\n        );\n        $stmt->execute(['id' => $id]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    public function createRelation(int $sourceId, int $targetId, string $type, float $strength = 1.0): int\n    {\n        $stmt = $this->db->prepare(\n            'INSERT INTO entity_relations (source_entity_id, target_entity_id, relation_type, strength, created_at)\n             VALUES (:source, :target, :type, :strength, NOW())'\n        );\n        $stmt->execute([\n            'source' => $sourceId,\n            'target' => $targetId,\n            'type' => $type,\n            'strength' => $strength,\n        ]);\n\n        return (int) $this->db->lastInsertId();\n    }\n\n    public function updateRelation(int $id, string $type, float $strength): bool\n    {\n        $stmt = $this->db->prepare(\n            'UPDATE entity_relations SET relation_type = :type, strength = :strength WHERE id = :id'\n        );\n\n        return $stmt->execute(['id' => $id, 'type' => $type, 'strength' => $strength]);\n    }\n\n    public function deleteRelation(int $id): bool\n    {\n        $stmt = $this->db->prepare('DELETE FROM entity_relations WHERE id = :id');\n\n        return $stmt->execute(['id' => $id]);\n    }\n\n    public function getRelationTypesList(): array\n    {\n        return ['RELATED_TO', 'PART_OF', 'DEVELOPED_BY', 'INFLUENCED_BY', 'USED_IN', 'WORKS_WITH', 'TEACHES', 'CREATED'];\n    }\n\n    \/\/ =========================================================================\n    \/\/ TAXONOMY - CRUD\n    \/\/ =========================================================================\n\n    public function getTaxonomyTerm(int $id): ?array\n    {\n        $stmt = $this->db->prepare('SELECT * FROM taxonomy_terms WHERE id = :id');\n        $stmt->execute(['id' => $id]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    public function createTaxonomyTerm(string $name, ?int $parentId = null): int\n    {\n        \/\/ Calculate depth and path\n        $depth = 0;\n        $path = $name;\n\n        if ($parentId !== null) {\n            $parent = $this->getTaxonomyTerm($parentId);\n            if ($parent !== null) {\n                $depth = (int) $parent['depth'] + 1;\n                $path = $parent['path'] . '\/' . $name;\n            }\n        }\n\n        $stmt = $this->db->prepare(\n            'INSERT INTO taxonomy_terms (name, parent_id, depth, path, created_at)\n             VALUES (:name, :parent, :depth, :path, NOW())'\n        );\n        $stmt->execute([\n            'name' => $name,\n            'parent' => $parentId,\n            'depth' => $depth,\n            'path' => $path,\n        ]);\n\n        return (int) $this->db->lastInsertId();\n    }\n\n    public function updateTaxonomyTerm(int $id, string $name, ?int $parentId = null): bool\n    {\n        \/\/ Calculate new depth and path\n        $depth = 0;\n        $path = $name;\n\n        if ($parentId !== null) {\n            $parent = $this->getTaxonomyTerm($parentId);\n            if ($parent !== null) {\n                $depth = (int) $parent['depth'] + 1;\n                $path = $parent['path'] . '\/' . $name;\n            }\n        }\n\n        $stmt = $this->db->prepare(\n            'UPDATE taxonomy_terms SET name = :name, parent_id = :parent, depth = :depth, path = :path WHERE id = :id'\n        );\n\n        return $stmt->execute([\n            'id' => $id,\n            'name' => $name,\n            'parent' => $parentId,\n            'depth' => $depth,\n            'path' => $path,\n        ]);\n    }\n\n    public function deleteTaxonomyTerm(int $id): bool\n    {\n        \/\/ Check for children\n        $stmt = $this->db->prepare('SELECT COUNT(*) FROM taxonomy_terms WHERE parent_id = :id');\n        $stmt->execute(['id' => $id]);\n\n        if ((int) $stmt->fetchColumn() > 0) {\n            return false; \/\/ Has children, cannot delete\n        }\n\n        \/\/ Delete chunk associations\n        $stmt = $this->db->prepare('DELETE FROM chunk_taxonomy WHERE taxonomy_term_id = :id');\n        $stmt->execute(['id' => $id]);\n\n        \/\/ Delete term\n        $stmt = $this->db->prepare('DELETE FROM taxonomy_terms WHERE id = :id');\n\n        return $stmt->execute(['id' => $id]);\n    }\n\n    public function getTaxonomyTermsForSelect(): array\n    {\n        return $this->db->query(\n            'SELECT id, name, depth, path FROM taxonomy_terms ORDER BY path, name'\n        )->fetchAll();\n    }\n\n    \/\/ =========================================================================\n    \/\/ ONTOLOGY - CRUD\n    \/\/ =========================================================================\n\n    public function getOntologyClass(int $id): ?array\n    {\n        $stmt = $this->db->prepare('SELECT * FROM ontology_classes WHERE id = :id');\n        $stmt->execute(['id' => $id]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    public function createOntologyClass(string $name, ?int $parentId = null, ?string $description = null, array $properties = []): int\n    {\n        $stmt = $this->db->prepare(\n            'INSERT INTO ontology_classes (name, parent_class_id, description, properties, created_at)\n             VALUES (:name, :parent, :description, :properties, NOW())'\n        );\n        $stmt->execute([\n            'name' => $name,\n            'parent' => $parentId,\n            'description' => $description,\n            'properties' => json_encode($properties),\n        ]);\n\n        return (int) $this->db->lastInsertId();\n    }\n\n    public function updateOntologyClass(int $id, string $name, ?int $parentId = null, ?string $description = null, array $properties = []): bool\n    {\n        $stmt = $this->db->prepare(\n            'UPDATE ontology_classes SET name = :name, parent_class_id = :parent,\n             description = :description, properties = :properties WHERE id = :id'\n        );\n\n        return $stmt->execute([\n            'id' => $id,\n            'name' => $name,\n            'parent' => $parentId,\n            'description' => $description,\n            'properties' => json_encode($properties),\n        ]);\n    }\n\n    public function deleteOntologyClass(int $id): bool\n    {\n        \/\/ Check for subclasses\n        $stmt = $this->db->prepare('SELECT COUNT(*) FROM ontology_classes WHERE parent_class_id = :id');\n        $stmt->execute(... [TRUNCATED-44ccab54ff7dc543]",
        "originalFile": "<?php\n\nnamespace Infrastructure;\n\nuse Infrastructure\\Config\\DatabaseFactory;\n\n\/**\n * SemanticExplorerRepository - Database Access for Semantic Explorer\n *\n * Handles all database operations for documents, chunks, entities,\n * relations, taxonomy, ontology, and semantics.\n *\/\nclass SemanticExplorerRepository\n{\n    private \\PDO $db;\n\n    public function __construct()\n    {\n        $this->db = DatabaseFactory::content();\n    }\n\n    \/\/ =========================================================================\n    \/\/ DOCUMENTS\n    \/\/ =========================================================================\n\n    public function getDocumentStats(): array\n    {\n        return $this->db->query(\n            'SELECT\n                COUNT(*) as total,\n                SUM(CASE WHEN status = \"done\" THEN 1 ELSE 0 END) as processed,\n                SUM(CASE WHEN status = \"error\" THEN 1 ELSE 0 END) as errors\n             FROM documents'\n        )->fetch();\n    }\n\n    public function getDocuments(): array\n    {\n        return $this->db->query(\n            'SELECT d.id, d.filename, d.folder_path, d.mime_type, d.file_size,\n                    d.status, d.imported_at, d.processed_at,\n                    (SELECT COUNT(*) FROM chunks WHERE document_id = d.id) as chunk_count\n             FROM documents d\n             ORDER BY d.imported_at DESC'\n        )->fetchAll();\n    }\n\n    public function getDocumentsFiltered(string $status = '', string $search = ''): array\n    {\n        $sql = 'SELECT d.id, d.filename, d.folder_path, d.source_path, d.mime_type,\n                       d.file_size, d.status, d.imported_at, d.processed_at, d.error_message,\n                       (SELECT COUNT(*) FROM chunks WHERE document_id = d.id) as chunk_count,\n                       (SELECT COALESCE(SUM(token_count), 0) FROM chunks WHERE document_id = d.id) as token_count\n                FROM documents d WHERE 1=1';\n\n        $params = [];\n\n        if ($status !== '') {\n            $sql .= ' AND d.status = :status';\n            $params['status'] = $status;\n        }\n\n        if ($search !== '') {\n            $sql .= ' AND (d.filename LIKE :search OR d.source_path LIKE :search2)';\n            $params['search'] = '%' . $search . '%';\n            $params['search2'] = '%' . $search . '%';\n        }\n\n        $sql .= ' ORDER BY d.imported_at DESC';\n\n        $stmt = $this->db->prepare($sql);\n        $stmt->execute($params);\n\n        return $stmt->fetchAll();\n    }\n\n    public function getDocument(int $id): ?array\n    {\n        $stmt = $this->db->prepare('SELECT * FROM documents WHERE id = :id');\n        $stmt->execute(['id' => $id]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    \/\/ =========================================================================\n    \/\/ CHUNKS\n    \/\/ =========================================================================\n\n    public function getChunkStats(): array\n    {\n        return $this->db->query(\n            'SELECT\n                COUNT(*) as total,\n                COALESCE(SUM(token_count), 0) as tokens,\n                SUM(CASE WHEN qdrant_id IS NOT NULL THEN 1 ELSE 0 END) as embedded\n             FROM chunks'\n        )->fetch();\n    }\n\n    public function getRecentChunks(int $limit = 5): array\n    {\n        $stmt = $this->db->prepare(\n            'SELECT c.id, c.content, c.token_count, c.created_at, c.qdrant_id, d.filename\n             FROM chunks c\n             JOIN documents d ON c.document_id = d.id\n             ORDER BY c.created_at DESC\n             LIMIT :limit'\n        );\n        $stmt->bindValue(':limit', $limit, \\PDO::PARAM_INT);\n        $stmt->execute();\n\n        return $stmt->fetchAll();\n    }\n\n    public function getChunksForDocument(int $documentId): array\n    {\n        $stmt = $this->db->prepare(\n            'SELECT c.id, c.chunk_index, c.content, c.token_count, c.heading_path,\n                    c.metadata, c.qdrant_id, c.created_at\n             FROM chunks c\n             WHERE c.document_id = :id\n             ORDER BY c.chunk_index'\n        );\n        $stmt->execute(['id' => $documentId]);\n\n        return $stmt->fetchAll();\n    }\n\n    public function getChunksFiltered(string $search = '', string $embedded = '', int $limit = 50, int $offset = 0): array\n    {\n        $sql = 'SELECT c.id, c.chunk_index, c.content, c.token_count, c.qdrant_id, c.created_at,\n                       d.filename, d.id as document_id\n                FROM chunks c\n                JOIN documents d ON c.document_id = d.id\n                WHERE 1=1';\n\n        $params = [];\n\n        if ($search !== '') {\n            $sql .= ' AND c.content LIKE :search';\n            $params['search'] = '%' . $search . '%';\n        }\n\n        if ($embedded === 'yes') {\n            $sql .= ' AND c.qdrant_id IS NOT NULL';\n        } elseif ($embedded === 'no') {\n            $sql .= ' AND c.qdrant_id IS NULL';\n        }\n\n        $sql .= ' ORDER BY c.created_at DESC LIMIT ' . $limit . ' OFFSET ' . $offset;\n\n        $stmt = $this->db->prepare($sql);\n        $stmt->execute($params);\n\n        return $stmt->fetchAll();\n    }\n\n    public function getChunksCount(string $search = '', string $embedded = ''): int\n    {\n        $sql = 'SELECT COUNT(*) FROM chunks c\n                JOIN documents d ON c.document_id = d.id\n                WHERE 1=1';\n\n        $params = [];\n\n        if ($search !== '') {\n            $sql .= ' AND c.content LIKE :search';\n            $params['search'] = '%' . $search . '%';\n        }\n\n        if ($embedded === 'yes') {\n            $sql .= ' AND c.qdrant_id IS NOT NULL';\n        } elseif ($embedded === 'no') {\n            $sql .= ' AND c.qdrant_id IS NULL';\n        }\n\n        $stmt = $this->db->prepare($sql);\n        $stmt->execute($params);\n\n        return (int) $stmt->fetchColumn();\n    }\n\n    public function getChunk(int $id): ?array\n    {\n        $stmt = $this->db->prepare(\n            'SELECT c.*, d.filename, d.source_path, d.id as document_id\n             FROM chunks c\n             JOIN documents d ON c.document_id = d.id\n             WHERE c.id = :id'\n        );\n        $stmt->execute(['id' => $id]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    public function getChunkByDocumentAndIndex(int $documentId, int $chunkIndex): ?array\n    {\n        $stmt = $this->db->prepare(\n            'SELECT id, chunk_index FROM chunks\n             WHERE document_id = :doc_id AND chunk_index = :idx'\n        );\n        $stmt->execute(['doc_id' => $documentId, 'idx' => $chunkIndex]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    public function getChunkById(int $chunkId): ?array\n    {\n        $stmt = $this->db->prepare(\n            'SELECT c.*, d.filename, d.source_path\n             FROM chunks c\n             JOIN documents d ON c.document_id = d.id\n             WHERE c.id = :id'\n        );\n        $stmt->execute(['id' => $chunkId]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    \/\/ =========================================================================\n    \/\/ ENTITIES\n    \/\/ =========================================================================\n\n    public function getEntitiesFiltered(string $type = '', string $search = '', int $limit = 100): array\n    {\n        $sql = 'SELECT e.*,\n                       COUNT(DISTINCT ce.chunk_id) as chunk_count,\n                       COUNT(DISTINCT er.id) as relation_count\n                FROM entities e\n                LEFT JOIN chunk_entities ce ON e.id = ce.entity_id\n                LEFT JOIN entity_relations er ON e.id = er.source_entity_id OR e.id = er.target_entity_id\n                WHERE 1=1';\n\n        $params = [];\n\n        if ($type !== '') {\n            $sql .= ' AND e.type = :type';\n            $params['type'] = $type;\n        }\n\n        if ($search !== '') {\n            $sql .= ' AND (e.name LIKE :search OR e.description LIKE :search2)';\n            $params['search'] = '%' . $search . '%';\n            $params['search2'] = '%' . $search . '%';\n        }\n\n        $sql .= ' GROUP BY e.id ORDER BY chunk_count DESC, e.name LIMIT ' . $limit;\n\n        $stmt = $this->db->prepare($sql);\n        $stmt->execute($params);\n\n        return $stmt->fetchAll();\n    }\n\n    public function getEntityStats(): array\n    {\n        return $this->db->query(\n            'SELECT type, COUNT(*) as count FROM entities GROUP BY type'\n        )->fetchAll();\n    }\n\n    public function getEntity(int $id): ?array\n    {\n        $stmt = $this->db->prepare('SELECT * FROM entities WHERE id = :id');\n        $stmt->execute(['id' => $id]);\n        $result = $stmt->fetch();\n\n        return $result === false ? null : $result;\n    }\n\n    public function getEntitySynonyms(int $entityId): array\n    {\n        $stmt = $this->db->prepare('SELECT * FROM entity_synonyms WHERE entity_id = :id');\n        $stmt->execute(['id' => $entityId]);\n\n        return $stmt->fetchAll();\n    }\n\n    public function getOutgoingRelations(int $entityId): array\n    {\n        $stmt = $this->db->prepare(\n            'SELECT er.*, e.name as target_name, e.type as target_type\n             FROM entity_relations er\n             JOIN entities e ON er.target_entity_id = e.id\n             WHERE er.source_entity_id = :id\n             ORDER BY er.strength DESC'\n        );\n        $stmt->execute(['id' => $entityId]);\n\n        return $stmt->fetchAll();\n    }\n\n    public function getIncomingRelations(int $entityId): array\n    {\n        $stmt = $this->db->prepare(\n            'SELECT er.*, e.name as source_name, e.type as source_type\n             FROM entity_relations er\n             JOIN entities e ON er.source_entity_id = e.id\n             WHERE er.target_entity_id = :id\n             ORDER BY er.strength DESC'\n        );\n        $stmt->execute(['id' => $entityId]);\n\n        return $stmt->fetchAll();\n    }\n\n    public function getChunksForEntity(int $entityId, int $limit = 20): array\n    {\n  ... [TRUNCATED-ac261bdede1b7799]",
        "structuredPatch": [
            {
                "oldStart": 498,
                "oldLines": 4,
                "newStart": 498,
                "newLines": 300,
                "lines": [
                    "              FROM chunk_semantics'",
                    "         )->fetch();",
                    "     }",
                    "+",
                    "+    \/\/ =========================================================================",
                    "+    \/\/ ENTITIES - CRUD",
                    "+    \/\/ =========================================================================",
                    "+",
                    "+    public function createEntity(string $name, string $type, ?string $description = null): int",
                    "+    {",
                    "+        $stmt = $this->db->prepare(",
                    "+            'INSERT INTO entities (name, canonical_name, type, description, created_at, updated_at)",
                    "+             VALUES (:name, :canonical, :type, :description, NOW(), NOW())'",
                    "+        );",
                    "+        $stmt->execute([",
                    "+            'name' => $name,",
                    "+            'canonical' => strtolower(trim($name)),",
                    "+            'type' => $type,",
                    "+            'description' => $description,",
                    "+        ]);",
                    "+",
                    "+        return (int) $this->db->lastInsertId();",
                    "+    }",
                    "+",
                    "+    public function updateEntity(int $id, string $name, string $type, ?string $description = null): bool",
                    "+    {",
                    "+        $stmt = $this->db->prepare(",
                    "+            'UPDATE entities SET name = :name, canonical_name = :canonical, type = :type,",
                    "+             description = :description, updated_at = NOW() WHERE id = :id'",
                    "+        );",
                    "+",
                    "+        return $stmt->execute([",
                    "+            'id' => $id,",
                    "+            'name' => $name,",
                    "+            'canonical' => strtolower(trim($name)),",
                    "+            'type' => $type,",
                    "+            'description' => $description,",
                    "+        ]);",
                    "+    }",
                    "+",
                    "+    public function deleteEntity(int $id): bool",
                    "+    {",
                    "+        \/\/ Check for relations",
                    "+        $stmt = $this->db->prepare(",
                    "+            'SELECT COUNT(*) FROM entity_relations",
                    "+             WHERE source_entity_id = :id OR target_entity_id = :id2'",
                    "+        );",
                    "+        $stmt->execute(['id' => $id, 'id2' => $id]);",
                    "+",
                    "+        if ((int) $stmt->fetchColumn() > 0) {",
                    "+            return false; \/\/ Has relations, cannot delete",
                    "+        }",
                    "+",
                    "+        \/\/ Delete synonyms first",
                    "+        $stmt = $this->db->prepare('DELETE FROM entity_synonyms WHERE entity_id = :id');",
                    "+        $stmt->execute(['id' => $id]);",
                    "+",
                    "+        \/\/ Delete chunk associations",
                    "+        $stmt = $this->db->prepare('DELETE FROM chunk_entities WHERE entity_id = :id');",
                    "+        $stmt->execute(['id' => $id]);",
                    "+",
                    "+        \/\/ Delete entity",
                    "+        $stmt = $this->db->prepare('DELETE FROM entities WHERE id = :id');",
                    "+",
                    "+        return $stmt->execute(['id' => $id]);",
                    "+    }",
                    "+",
                    "+    public function getEntityTypes(): array",
                    "+    {",
                    "+        return ['person', 'organization', 'location', 'concept', 'method', 'tool', 'event', 'other'];",
                    "+    }",
                    "+",
                    "+    public function getAllEntitiesSimple(): array",
                    "+    {",
                    "+        return $this->db->query('SELECT id, name, type FROM entities ORDER BY name')->fetchAll();",
                    "+    }",
                    "+",
                    "+    \/\/ =========================================================================",
                    "+    \/\/ RELATIONS - CRUD",
                    "+    \/\/ =========================================================================",
                    "+",
                    "+    public function getRelation(int $id): ?array",
                    "+    {",
                    "+        $stmt = $this->db->prepare(",
                    "+            'SELECT er.*,",
                    "+                    es.name as source_name, es.type as source_type,",
                    "+                    et.name as target_name, et.type as target_type",
                    "+             FROM entity_relations er",
                    "+             JOIN entities es ON er.source_entity_id = es.id",
                    "+             JOIN entities et ON er.target_entity_id = et.id",
                    "+             WHERE er.id = :id'",
                    "+        );",
                    "+        $stmt->execute(['id' => $id]);",
                    "+        $result = $stmt->fetch();",
                    "+",
                    "+        return $result === false ? null : $result;",
                    "+    }",
                    "+",
                    "+    public function createRelation(int $sourceId, int $targetId, string $type, float $strength = 1.0): int",
                    "+    {",
                    "+        $stmt = $this->db->prepare(",
                    "+            'INSERT INTO entity_relations (source_entity_id, target_entity_id, relation_type, strength, created_at)",
                    "+             VALUES (:source, :target, :type, :strength, NOW())'",
                    "+        );",
                    "+        $stmt->execute([",
                    "+            'source' => $sourceId,",
                    "+            'target' => $targetId,",
                    "+            'type' => $type,",
                    "+            'strength' => $strength,",
                    "+        ]);",
                    "+",
                    "+        return (int) $this->db->lastInsertId();",
                    "+    }",
                    "+",
                    "+    public function updateRelation(int $id, string $type, float $strength): bool",
                    "+    {",
                    "+        $stmt = $this->db->prepare(",
                    "+            'UPDATE entity_relations SET relation_type = :type, strength = :strength WHERE id = :id'",
                    "+        );",
                    "+",
                    "+        return $stmt->execute(['id' => $id, 'type' => $type, 'strength' => $strength]);",
                    "+    }",
                    "+",
                    "+    public function deleteRelation(int $id): bool",
                    "+    {",
                    "+        $stmt = $this->db->prepare('DELETE FROM entity_relations WHERE id = :id');",
                    "+",
                    "+        return $stmt->execute(['id' => $id]);",
                    "+    }",
                    "+",
                    "+    public function getRelationTypesList(): array",
                    "+    {",
                    "+        return ['RELATED_TO', 'PART_OF', 'DEVELOPED_BY', 'INFLUENCED_BY', 'USED_IN', 'WORKS_WITH', 'TEACHES', 'CREATED'];",
                    "+    }",
                    "+",
                    "+    \/\/ =========================================================================",
                    "+    \/\/ TAXONOMY - CRUD",
                    "+    \/\/ =========================================================================",
                    "+",
                    "+    public function getTaxonomyTerm(int $id): ?array",
                    "+    {",
                    "+        $stmt = $this->db->prepare('SELECT * FROM taxonomy_terms WHERE id = :id');",
                    "+        $stmt->execute(['id' => $id]);",
                    "+        $result = $stmt->fetch();",
                    "+",
                    "+        return $result === false ? null : $result;",
                    "+    }",
                    "+",
                    "+    public function createTaxonomyTerm(string $name, ?int $parentId = null): int",
                    "+    {",
                    "+        \/\/ Calculate depth and path",
                    "+        $depth = 0;",
                    "+        $path = $name;",
                    "+",
                    "+        if ($parentId !== null) {",
                    "+            $parent = $this->getTaxonomyTerm($parentId);",
                    "+            if ($parent !== null) {",
                    "+                $depth = (int) $parent['depth'] + 1;",
                    "+                $path = $parent['path'] . '\/' . $name;",
                    "+            }",
                    "+        }",
                    "+",
                    "+        $stmt = $this->db->prepare(",
                    "+            'INSERT INTO taxonomy_terms (name, parent_id, depth, path, created_at)",
                    "+             VALUES (:name, :parent, :depth, :path, NOW())'",
                    "+        );",
                    "+        $stmt->execute([",
                    "+            'name' => $name,",
                    "+            'parent' => $parentId,",
                    "+            'depth' => $depth,",
                    "+            'path' => $path,",
                    "+        ]);",
                    "+",
                    "+        return (int) $this->db->lastInsertId();",
                    "+    }",
                    "+",
                    "+    public function updateTaxonomyTerm(int $id, string $name, ?int $parentId = null): bool",
                    "+    {",
                    "+        \/\/ Calculate new depth and path",
                    "+        $depth = 0;",
                    "+        $path = $name;",
                    "+",
                    "+        if ($parentId !== null) {",
                    "+            $parent = $this->getTaxonomyTerm($parentId);",
                    "+            if ($parent !== null) {",
                    "+                $depth = (int) $parent['depth'] + 1;",
                    "+                $path = $parent['path'] . '\/' . $name;",
                    "+            }",
                    "+        }",
                    "+",
                    "+        $stmt = $this->db->prepare(",
                    "+            'UPDATE taxonomy_terms SET name = :name, parent_id = :parent, depth = :depth, path = :path WHERE id = :id'",
                    "+        );",
                    "+",
                    "+        return $stmt->execute([",
                    "+            'id' => $id,",
                    "+            'name' => $name,",
                    "+            'parent' => $parentId,",
                    "+            'depth' => $depth,",
                    "+            'path' => $path,",
                    "+        ]);",
                    "+    }",
                    "+",
                    "+    public function deleteTaxonomyTerm(int $id): bool",
                    "+    {",
                    "+        \/\/ Check for children",
                    "+        $stmt = $this->db->prepare('SELECT COUNT(*) FROM taxonomy_terms WHERE parent_id = :id');",
                    "+        $stmt->execute(['id' => $id]);",
                    "+",
                    "+        if ((int) $stmt->fetchColumn() > 0) {",
                    "+            return false; \/\/ Has children, cannot delete",
                    "+        }",
                    "+",
                    "+        \/\/ Delete chunk associations",
                    "+        $stmt = $this->db->prepare('DELETE FROM chunk_taxonomy WHERE taxonomy_term_id = :id');",
                    "+        $stmt->execute(['id' => $id]);",
                    "+",
                    "+        \/\/ Delete term",
                    "+        $stmt = $this->db->prepare('DELETE FROM taxonomy_terms WHERE id = :id');",
                    "+",
                    "+        return $stmt->execute(['id' => $id]);",
                    "+    }",
                    "+",
                    "+    public function getTaxonomyTermsForSelect(): array",
                    "+    {",
                    "+        return $this->db->query(",
                    "+            'SELECT id, name, depth, path FROM taxonomy_terms ORDER BY path, name'",
                    "+        )->fetchAll();",
                    "+    }",
                    "+",
                    "+    \/\/ =========================================================================",
                    "+    \/\/ ONTOLOGY - CRUD",
                    "+    \/\/ =========================================================================",
                    "+",
                    "+    public function getOntologyClass(int $id): ?array",
                    "+    {",
                    "+        $stmt = $this->db->prepare('SELECT * FROM ontology_classes WHERE id = :id');",
                    "+        $stmt->execute(['id' => $id]);",
                    "+        $result = $stmt->fetch();",
                    "+",
                    "+        return $result === false ? null : $result;",
                    "+    }",
                    "+",
                    "+    public function createOntologyClass(string $name, ?int $parentId = null, ?string $description = null, array $properties = []): int",
                    "+    {",
                    "+        $stmt = $this->db->prepare(",
                    "+            'INSERT INTO ontology_classes (name, parent_class_id, description, properties, created_at)",
                    "+             VALUES (:name, :parent, :description, :properties, NOW())'",
                    "+        );",
                    "+        $stmt->execute([",
                    "+            'name' => $name,",
                    "+            'parent' => $parentId,",
                    "+            'description' => $description,",
                    "+            'properties' => json_encode($properties),",
                    "+        ]);",
                    "+",
                    "+        return (int) $this->db->lastInsertId();",
                    "+    }",
                    "+",
                    "+    public function updateOntologyClass(int $id, string $name, ?int $parentId = null, ?string $description = null, array $properties = []): bool",
                    "+    {",
                    "+        $stmt = $this->db->prepare(",
                    "+            'UPDATE ontology_classes SET name = :name, parent_class_id = :parent,",
                    "+             description = :description, properties = :properties WHERE id = :id'",
                    "+        );",
                    "+",
                    "+        return $stmt->execute([",
                    "+            'id' => $id,",
                    "+            'name' => $name,",
                    "+            'parent' => $parentId,",
                    "+            'description' => $description,",
                    "+            'properties' => json_encode($properties),",
                    "+        ]);",
                    "+    }",
                    "+",
                    "+    public function deleteOntologyClass(int $id): bool",
                    "+    {",
                    "+        \/\/ Check for subclasses",
                    "+        $stmt = $this->db->prepare('SELECT COUNT(*) FROM ontology_classes WHERE parent_class_id = :id');",
                    "+        $stmt->execute(['id' => $id]);",
                    "+",
                    "+        if ((int) $stmt->fetchColumn() > 0) {",
                    "+            return false; \/\/ Has subclasses, cannot delete",
                    "+        }",
                    "+",
                    "+        \/\/ Delete entity classifications",
                    "+        $stmt = $this->db->prepare('DELETE FROM entity_classifications WHERE ontology_class_id = :id');",
                    "+        $stmt->execute(['id' => $id]);",
                    "+",
                    "+        \/\/ Delete class",
                    "+        $stmt = $this->db->prepare('DELETE FROM ontology_classes WHERE id = :id');",
                    "+",
                    "+        return $stmt->execute(['id' => $id]);",
                    "+    }",
                    "+",
                    "+    public function getOntologyClassesForSelect(): array",
                    "+    {",
                    "+        return $this->db->query('SELECT id, name FROM ontology_classes ORDER BY name')->fetchAll();",
                    "+    }",
                    " }"
                ]
            }
        ],
        "userModified": false,
        "replaceAll": false
    }
}