opencode-skills-collection 4.0.67 → 4.0.69

package/bundled-skills/mysql/SKILL.md

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+---
+name: mysql
+description: Administer MySQL/MariaDB databases. Configure replication and optimize
+  performance. Use when managing MySQL deployments.
+category: devops
+risk: critical
+source: https://github.com/BagelHole/DevOps-Security-Agent-Skills
+source_repo: BagelHole/DevOps-Security-Agent-Skills
+source_type: community
+date_added: '2026-09-20'
+license: MIT
+license_source: https://github.com/BagelHole/DevOps-Security-Agent-Skills/blob/main/LICENSE
+compatibility: Requires the relevant OS/platform tooling and privileged access where
+  noted. Docs-only; helper scripts and templates not bundled.
+metadata:
+  author: devops-skills
+  version: '1.0'
+---
+
+# MySQL / MariaDB
+
+Administer, optimize, and secure MySQL and MariaDB databases in development and production environments.
+
+## When to Use
+
+- You need a mature, widely supported relational database.
+- Your stack depends on MySQL-specific features or compatibility (WordPress, Magento, many PHP frameworks).
+- You are setting up source-replica replication for read scaling.
+- You want to tune InnoDB for high-throughput transactional workloads.
+
+## Prerequisites
+
+- Linux server (Debian/Ubuntu or RHEL-based) or Docker.
+- Root or sudo access for package installation.
+- Familiarity with SQL fundamentals.
+
+## Installation and Setup
+
+```bash
+# Debian / Ubuntu — MySQL 8
+sudo apt update
+sudo apt install -y mysql-server
+
+# RHEL / Amazon Linux
+sudo dnf install -y mysql-server
+sudo systemctl enable --now mysqld
+
+# Run the secure installation wizard
+sudo mysql_secure_installation
+# Prompts: set root password, remove anonymous users, disable remote root, remove test db
+
+# Verify
+mysql --version
+sudo systemctl status mysql
+```
+
+## Initial User and Database Setup
+
+```bash
+sudo mysql -u root -p
+```
+
+```sql
+-- Create a database
+CREATE DATABASE mydb CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci;
+
+-- Create an application user with strong auth
+CREATE USER 'myapp'@'%' IDENTIFIED BY 'strong_password_here';
+GRANT SELECT, INSERT, UPDATE, DELETE ON mydb.* TO 'myapp'@'%';
+FLUSH PRIVILEGES;
+
+-- Verify
+SHOW GRANTS FOR 'myapp'@'%';
+```
+
+## mysql CLI Reference
+
+```bash
+# Connect
+mysql -u myapp -p -h 127.0.0.1 mydb
+
+# Execute a single statement
+mysql -u myapp -p -e "SELECT COUNT(*) FROM orders;" mydb
+
+# Import a SQL file
+mysql -u myapp -p mydb < schema.sql
+
+# Export query results to CSV
+mysql -u myapp -p -e "SELECT * FROM users" mydb \
+  | tr '\t' ',' > users.csv
+```
+
+```
+-- Inside the mysql shell
+SHOW DATABASES;
+USE mydb;
+SHOW TABLES;
+DESCRIBE users;
+SHOW CREATE TABLE users\G
+SHOW PROCESSLIST;
+SHOW ENGINE INNODB STATUS\G
+```
+
+## Configuration Tuning
+
+Edit `/etc/mysql/mysql.conf.d/mysqld.cnf` (or `/etc/my.cnf` on RHEL).
+
+```ini
+[mysqld]
+# -- Networking --
+bind-address           = 0.0.0.0
+max_connections        = 300
+wait_timeout           = 600
+interactive_timeout    = 600
+
+# -- InnoDB (most impactful settings) --
+innodb_buffer_pool_size   = 4G          # ~70% of RAM on a dedicated server
+innodb_buffer_pool_instances = 4        # 1 per GB of pool (up to 64)
+innodb_log_file_size      = 1G
+innodb_flush_log_at_trx_commit = 1      # 1 = ACID; 2 = faster, slight risk
+innodb_flush_method       = O_DIRECT    # avoids double buffering on Linux
+innodb_io_capacity        = 2000        # raise for SSD
+innodb_io_capacity_max    = 4000
+
+# -- Query cache (disabled in MySQL 8, use ProxySQL or app cache) --
+# query_cache_type = 0
+
+# -- Logging --
+slow_query_log         = 1
+slow_query_log_file    = /var/log/mysql/slow.log
+long_query_time        = 1
+log_error              = /var/log/mysql/error.log
+
+# -- Binary log (required for replication) --
+server-id              = 1
+log_bin                = /var/log/mysql/mysql-bin
+binlog_expire_logs_seconds = 604800     # 7 days
+sync_binlog            = 1
+
+# -- Character set --
+character-set-server   = utf8mb4
+collation-server       = utf8mb4_unicode_ci
+```
+
+```bash
+# Apply changes
+sudo systemctl restart mysql
+
+# Verify a setting at runtime
+mysql -u root -p -e "SHOW VARIABLES LIKE 'innodb_buffer_pool_size';"
+```
+
+## Backup and Restore
+
+### Logical Backups with mysqldump
+
+```bash
+# Single database
+mysqldump -u root -p --single-transaction --routines --triggers \
+  mydb > /backups/mydb_$(date +%F).sql
+
+# All databases
+mysqldump -u root -p --all-databases --single-transaction \
+  > /backups/all_$(date +%F).sql
+
+# Compressed backup
+mysqldump -u root -p --single-transaction mydb \
+  | gzip > /backups/mydb_$(date +%F).sql.gz
+
+# Restore
+mysql -u root -p mydb < /backups/mydb_2025-01-15.sql
+
+# Restore compressed
+gunzip < /backups/mydb_2025-01-15.sql.gz | mysql -u root -p mydb
+```
+
+### Physical Backups with Percona XtraBackup
+
+```bash
+# Install
+sudo apt install -y percona-xtrabackup-80
+
+# Full backup
+xtrabackup --backup --user=root --password=secret \
+  --target-dir=/backups/full_$(date +%F)
+
+# Prepare the backup (apply redo logs)
+xtrabackup --prepare --target-dir=/backups/full_2025-01-15
+
+# Restore (stop MySQL first)
+sudo systemctl stop mysql
+ls /var/lib/mysql/*  # verify this is the correct data dir first
+sudo find /var/lib/mysql -mindepth 1 -delete  # empty the data dir; snapshots must exist (see Limitations)
+xtrabackup --move-back --target-dir=/backups/full_2025-01-15
+sudo chown -R mysql:mysql /var/lib/mysql
+sudo systemctl start mysql
+```
+
+### Incremental Backup with XtraBackup
+
+```bash
+# Incremental based on the full backup
+xtrabackup --backup --user=root --password=secret \
+  --target-dir=/backups/inc_$(date +%F) \
+  --incremental-basedir=/backups/full_2025-01-15
+
+# Prepare: apply full, then incremental
+xtrabackup --prepare --apply-log-only --target-dir=/backups/full_2025-01-15
+xtrabackup --prepare --target-dir=/backups/full_2025-01-15 \
+  --incremental-dir=/backups/inc_2025-01-16
+```
+
+## Source-Replica Replication
+
+### Source (Primary)
+
+```ini
+# /etc/mysql/mysql.conf.d/mysqld.cnf
+[mysqld]
+server-id       = 1
+log_bin         = /var/log/mysql/mysql-bin
+binlog_format   = ROW
+```
+
+```sql
+-- Create replication user
+CREATE USER 'replicator'@'10.0.0.%' IDENTIFIED BY 'repl_secret';
+GRANT REPLICATION SLAVE ON *.* TO 'replicator'@'10.0.0.%';
+FLUSH PRIVILEGES;
+
+-- Get current binary log position
+SHOW MASTER STATUS\G
+```
+
+### Replica
+
+```ini
+# /etc/mysql/mysql.conf.d/mysqld.cnf
+[mysqld]
+server-id  = 2
+relay_log  = /var/log/mysql/relay-bin
+read_only  = ON
+```
+
+```sql
+-- Point replica to source (use SHOW MASTER STATUS values)
+CHANGE REPLICATION SOURCE TO
+  SOURCE_HOST     = '10.0.0.1',
+  SOURCE_USER     = 'replicator',
+  SOURCE_PASSWORD = '...' # replication secret from your vault,
+  SOURCE_LOG_FILE = 'mysql-bin.000003',
+  SOURCE_LOG_POS  = 154;
+
+START REPLICA;
+
+-- Verify
+SHOW REPLICA STATUS\G
+-- Check: Replica_IO_Running = Yes, Replica_SQL_Running = Yes, Seconds_Behind_Source = 0
+```
+
+## Monitoring Queries
+
+```sql
+-- Connection statistics
+SHOW STATUS LIKE 'Threads_connected';
+SHOW STATUS LIKE 'Max_used_connections';
+
+-- InnoDB buffer pool hit ratio (should be > 99%)
+SELECT
+  ROUND(100 - (
+    (SELECT VARIABLE_VALUE FROM performance_schema.global_status WHERE VARIABLE_NAME = 'Innodb_buffer_pool_reads') /
+    (SELECT VARIABLE_VALUE FROM performance_schema.global_status WHERE VARIABLE_NAME = 'Innodb_buffer_pool_read_requests')
+  ) * 100, 2) AS buffer_pool_hit_pct;
+
+-- Top 10 slow queries (requires performance_schema)
+SELECT DIGEST_TEXT, COUNT_STAR, AVG_TIMER_WAIT / 1e12 AS avg_sec
+FROM performance_schema.events_statements_summary_by_digest
+ORDER BY AVG_TIMER_WAIT DESC
+LIMIT 10;
+
+-- Table sizes
+SELECT table_name,
+       ROUND(data_length / 1024 / 1024, 2) AS data_mb,
+       ROUND(index_length / 1024 / 1024, 2) AS index_mb,
+       table_rows
+FROM information_schema.tables
+WHERE table_schema = 'mydb'
+ORDER BY data_length DESC;
+
+-- Check replication lag
+SHOW REPLICA STATUS\G
+-- Look at Seconds_Behind_Source
+```
+
+## Docker Compose Setup
+
+```yaml
+# docker-compose.yml
+version: "3.9"
+
+services:
+  mysql:
+    image: mysql:8.0
+    restart: unless-stopped
+    ports:
+      - "3306:3306"
+    environment:
+      MYSQL_ROOT_PASSWORD: rootpass
+      MYSQL_DATABASE: mydb
+      MYSQL_USER: myapp
+      MYSQL_PASSWORD: secret
+    volumes:
+      - mysql_data:/var/lib/mysql
+      - ./init.sql:/docker-entrypoint-initdb.d/init.sql
+    command: >
+      --innodb-buffer-pool-size=512M
+      --max-connections=200
+      --slow-query-log=ON
+      --long-query-time=1
+      --character-set-server=utf8mb4
+      --collation-server=utf8mb4_unicode_ci
+    healthcheck:
+      test: ["CMD", "mysqladmin", "ping", "-h", "localhost", "-u", "root", "-prootpass"]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+
+  phpmyadmin:
+    image: phpmyadmin:latest
+    restart: unless-stopped
+    ports:
+      - "8080:80"
+    environment:
+      PMA_HOST: mysql
+      PMA_USER: root
+      PMA_PASSWORD: rootpass
+    depends_on:
+      mysql:
+        condition: service_healthy
+
+volumes:
+  mysql_data:
+```
+
+```bash
+docker compose up -d
+mysql -h 127.0.0.1 -u myapp -psecret mydb
+```
+
+## Maintenance Tasks
+
+```bash
+# Optimize a fragmented table (locks the table briefly)
+mysql -u root -p -e "OPTIMIZE TABLE mydb.orders;"
+
+# Analyze tables to update statistics
+mysql -u root -p -e "ANALYZE TABLE mydb.orders;"
+
+# Check and repair a table
+mysql -u root -p -e "CHECK TABLE mydb.orders;"
+mysql -u root -p -e "REPAIR TABLE mydb.orders;"
+
+# Rotate slow query log
+sudo mv /var/log/mysql/slow.log /var/log/mysql/slow.log.old
+mysqladmin -u root -p flush-logs
+```
+
+## Troubleshooting
+
+| Symptom | Likely Cause | Fix |
+|---|---|---|
+| `Too many connections` | Connection limit exceeded | Increase `max_connections`; use connection pooling (ProxySQL) |
+| Slow queries across the board | `innodb_buffer_pool_size` too small | Set to ~70% of available RAM and restart |
+| Replication stopped (`SQL_Running: No`) | Duplicate key or schema mismatch on replica | Check `SHOW REPLICA STATUS\G` error; skip or fix the row |
+| `Table is full` | Disk space exhausted or table limit hit | Free disk space; check `innodb_data_file_path` autoextend |
+| `Lock wait timeout exceeded` | Long-running transaction holding row locks | Identify with `SHOW ENGINE INNODB STATUS`; kill the blocking query |
+| High IOPS / disk usage | Redo log too small causing frequent flushes | Increase `innodb_log_file_size` (requires restart) |
+
+## Related Skills
+
+- postgresql (`postgresql-devsec`) - Alternative relational database
+- database-backups (`database-backups`) - Automated backup strategies
+- redis (`redis`) - Caching layer to reduce database load
+- planetscale (`planetscale`) - Managed MySQL-compatible with branching
+
+## Limitations
+
+- Infrastructure commands can disrupt services: confirm target host/scope and have backups/snapshots before mutating state.
+- Docs-only import: upstream scripts and templates not bundled.
+