What are some common pitfalls or challenges when working with complex database structures that may limit the use of standard SQL queries for data manipulation in PHP applications?

One common challenge when working with complex database structures is the need to perform multiple joins or subqueries in SQL queries, which can make queries difficult to read and maintain. One way to address this is by breaking down complex queries into smaller, more manageable parts, using temporary tables or views to simplify the logic.

// Example of breaking down a complex query into smaller parts using temporary tables

// Create a temporary table to store intermediate results
$pdo->exec("CREATE TEMPORARY TABLE temp_table AS
            SELECT column1, column2
            FROM table1
            WHERE condition1");

// Use the temporary table in subsequent queries
$query = "SELECT column1, column2
          FROM temp_table
          JOIN table2 ON temp_table.column1 = table2.column1
          WHERE condition2";

$stmt = $pdo->prepare($query);
$stmt->execute();
$results = $stmt->fetchAll(PDO::FETCH_ASSOC);

// Drop the temporary table after use
$pdo->exec("DROP TEMPORARY TABLE temp_table");