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"oldString": "<?php\n\nnamespace Infrastructure;\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 = new \\PDO(\n 'mysql:host=localhost;dbname=ki_content;charset=utf8mb4',\n 'root',\n $this->getPassword(),\n [\n \\PDO::ATTR_ERRMODE => \\PDO::ERRMODE_EXCEPTION,\n \\PDO::ATTR_DEFAULT_FETCH_MODE => \\PDO::FETCH_ASSOC,\n ]\n );\n }\n\n private function getPassword(): string\n {\n $file = '\/var\/www\/docs\/credentials\/credentials.md';\n $content = file_get_contents($file);\n foreach (explode(\"\\n\", $content) as $line) {\n if (str_contains($line, 'MariaDB') && str_contains($line, 'root')) {\n $parts = explode('|', $line);\n if (count($parts) >= 4) {\n return trim($parts[3]);\n }\n }\n }\n\n return '';\n }",
"newString": "<?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 }",
"originalFile": "<?php\n\nnamespace Infrastructure;\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 = new \\PDO(\n 'mysql:host=localhost;dbname=ki_content;charset=utf8mb4',\n 'root',\n $this->getPassword(),\n [\n \\PDO::ATTR_ERRMODE => \\PDO::ERRMODE_EXCEPTION,\n \\PDO::ATTR_DEFAULT_FETCH_MODE => \\PDO::FETCH_ASSOC,\n ]\n );\n }\n\n private function getPassword(): string\n {\n $file = '\/var\/www\/docs\/credentials\/credentials.md';\n $content = file_get_contents($file);\n foreach (explode(\"\\n\", $content) as $line) {\n if (str_contains($line, 'MariaDB') && str_contains($line, 'root')) {\n $parts = explode('|', $line);\n if (count($parts) >= 4) {\n return trim($parts[3]);\n }\n }\n }\n\n return '';\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 ... 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"- 'mysql:host=localhost;dbname=ki_content;charset=utf8mb4',",
"- 'root',",
"- $this->getPassword(),",
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"- \\PDO::ATTR_ERRMODE => \\PDO::ERRMODE_EXCEPTION,",
"- \\PDO::ATTR_DEFAULT_FETCH_MODE => \\PDO::FETCH_ASSOC,",
"- ]",
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"+ $this->db = DatabaseFactory::content();",
" }",
" ",
"- private function getPassword(): string",
"- {",
"- $file = '\/var\/www\/docs\/credentials\/credentials.md';",
"- $content = file_get_contents($file);",
"- foreach (explode(\"\\n\", $content) as $line) {",
"- if (str_contains($line, 'MariaDB') && str_contains($line, 'root')) {",
"- $parts = explode('|', $line);",
"- if (count($parts) >= 4) {",
"- return trim($parts[3]);",
"- }",
"- }",
"- }",
"-",
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"- }",
"-",
" \/\/ =========================================================================",
" \/\/ DOCUMENTS",
" \/\/ ========================================================================="
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