MySQL

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Installation issues

Fail to start

On Ubuntu 12.04, we can use 

sudo dpkg-reconfigure mysql-server-5.5

InnoDB vs MyISAM

The default is InnoDB.

Under Shell

Manual/Documentation

https://dev.mysql.com/doc/refman

Installation and setup root password

Debian 9 (Stretch) package now ships with the UNIX_SOCKET authentication plugin enabled and you are no longer asked to set a root password when installing the package. Even when setting a root password via the mysql_secure_installation script you are still denied. So we need to run 'update'; see the command below.

See a solution at Debian 9 “Stretch” and MySQL/MariaDB root password. 

$ sudo apt-get install mysql-server
$ sudo mysql_secure_installation
$ sudo mysql -u root mysql -e "update user set plugin='' where user='root'; flush privileges;"
$ mysql -u root -p
...
Welcome to the MariaDB monitor.  Commands end with ; or \g.
Your MariaDB connection id is 12
Server version: 10.1.23-MariaDB-9+deb9u1 Raspbian 9.0
...
MariaDB [(none)]> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mysql              |
| performance_schema |
+--------------------+
3 rows in set (0.02 sec)

MariaDB [(none)]> exit
Bye

How do I turn off the mysql password validation?

Normally a password as short as 3 characters is enough for the root user.

Create a new user account to grant access to a database

http://www.cyberciti.biz/faq/mysql-user-creation/

NOTE: please be mindful when creating a user name. There is no protection against creating an old user's name. If you accidentally create a same user name as say mediawiki DB user, then mediawiki will not be working. 

$ mysql -u root -p
OR
$ mysql -u root -h myserver-sever.com -p

Create a new mysql database called demo; 

mysql> CREATE DATABASE testdb;

Create a new user called user1 for database demo 

mysql> GRANT ALL ON testdb.* TO user1@localhost IDENTIFIED BY 'mypassword';

If we quit mysql and log in again using the new account, the 'SHOW DATABASES' will only show databases that the new account can access 

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| testdb             |
+--------------------+
2 rows in set (0.00 sec)

User user1 can connect to mysql server demo database using following command: 

$ mysql -u user1 -p testdb
OR
$ mysql -u user1 -h mysql.server.com -p testdb

Show all users

SELECT User, Host, Password FROM mysql.user; 

SELECT DISTINCT User FROM mysql.user;

Show the privileges of a user

mysql> SHOW GRANTS FOR 'user1'@'localhost';
+--------------------------------------------------------------------------------------------------------------+
| Grants for user1@localhost                                                                                   |
+--------------------------------------------------------------------------------------------------------------+
| GRANT USAGE ON *.* TO 'user1'@'localhost' IDENTIFIED BY PASSWORD '*FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF' |
| GRANT ALL PRIVILEGES ON `testdb`.* TO 'user1'@'localhost'                                                    |
+--------------------------------------------------------------------------------------------------------------+
2 rows in set (0.00 sec)

Another way is through phpMyAdmin. Click on 'Databases' and in the Action column click 'Check Privileges' in the corresponding row of the desired database.

Remove an account

DROP USER 'jeffrey'@'localhost';

Remove a database

mysql> DROP DATABASE db_name;
mysql> SHOW DATABASES;

Show the current user

mysql> SELECT USER();

Show the current database

mysql> SELECT DATABASE();

Version vs Distrib number of MySQL

https://stackoverflow.com/questions/8645184/version-vs-distrib-number-of-mysql

  • Ver refers to the version of the mysql command line client - what you are envoking by typing 'mysql'
  • Distrib refers to the mysql server version your client was built with. This is not to be confused with the mysql server you are connected to, which can be obtained with SELECT VERSION();

On Ubuntu 14.04 

$ mysql --version
mysql  Ver 14.14 Distrib 5.5.58, for debian-linux-gnu (x86_64) using readline 6.3

$ mysql -u root -p -e 'select version()'
Enter password: 
+-------------------------+
| version()               |
+-------------------------+
| 5.5.58-0ubuntu0.14.04.1 |
+-------------------------+

On Docker's MySQL 

# mysql --version
mysql  Ver 14.14 Distrib 5.7.20, for Linux (x86_64) using  EditLine wrapper

# mysql --user=root --password=$MYSQL_ROOT_PASSWORD -e 'select version()'
mysql: [Warning] Using a password on the command line interface can be insecure.
+-----------+
| version() |
+-----------+
| 5.7.20    |
+-----------+

MYSQL commands

Find out about your MySQL version and all installed plugins: 

mysql> select version();
mysql> show plugins;

Executing SQL Statements from a Text File

https://dev.mysql.com/doc/refman/5.7/en/mysql-batch-commands.html 

$ mysql db_name

$ mysql -h host -u user -p db_name # db_name is not a password !

$ mysql -h host -u user -pPASSWORD db_name # no space after "-p"

$ mysql db_name < text_file # text_file that contains the statements you wish to execute/Batch mode
$ mysql db_name < text_file > output.txt
mysql> source file_name

Create a table

Note that a database have multiple tables. 

mysql> CREATE DATABASE testdb;
mysql> USE testdb
mysql> CREATE TABLE pet (name VARCHAR(20), owner VARCHAR(20),
    -> species VARCHAR(20), sex CHAR(1), birth DATE, death DATE);

OR put it in a text file 

mysql> CREATE TABLE pet
{
    name VARCHAR(20),
    owner VARCHAR(20),
    species VARCHAR(20), 
    sex CHAR(1), 
    birth DATE, 
    death DATE
}

Show all tables. 

mysql> SHOW TABLES;

Verify your table 

mysql> DESCRIBE pet;

Loading data into a table

https://dev.mysql.com/doc/refman/5.7/en/loading-tables.html 

mysql> LOAD DATA LOCAL INFILE '/path/pet.txt' INTO TABLE pet;

OR using the mysqlimport utility from the shell 

$ mysqlimport --local pet /path/pet.txt

You could add a new record using an INSERT statement like this: 

mysql> INSERT INTO pet
    -> VALUES ('Puffball','Diane','hamster','f','1999-03-30',NULL);

Retrieve data

https://dev.mysql.com/doc/refman/5.7/en/retrieving-data.html General form 

SELECT what_to_select
FROM which_table
WHERE conditions_to_satisfy;

Some examples 

mysql> SELECT * FROM pet;

mysql> UPDATE pet SET birth = '1989-08-31' WHERE name = 'Bowser';

mysql> SELECT * FROM pet WHERE name = 'Bowser';

mysql> SELECT * FROM pet WHERE birth >= '1998-1-1';

mysql> SELECT * FROM pet WHERE species = 'dog' AND sex = 'f';

mysql> SELECT * FROM pet WHERE (species = 'cat' AND sex = 'm')
    -> OR (species = 'dog' AND sex = 'f');

mysql> SELECT name, birth FROM pet;

mysql> SELECT DISTINCT owner FROM pet;

mysql> SELECT name, birth FROM pet ORDER BY birth;

mysql> SELECT name, birth FROM pet ORDER BY birth DESC;  # To sort in reverse (descending) order

mysql> SELECT name, birth FROM pet WHERE MONTH(birth) = 5;

Pattern match 

mysql> SELECT * FROM pet WHERE name LIKE 'b%'; # find names beginning with b, case-insensitive

mysql> SELECT * FROM pet WHERE name LIKE '%fy'; # find names ending with fy:

mysql> SELECT * FROM pet WHERE name LIKE '%w%'; # find names containing a w:

Count rows 

mysql> SELECT COUNT(*) FROM pet;

mysql> SELECT COUNT(DISTINCT owner) FROM pet;

mysql> SELECT owner, COUNT(*) FROM pet GROUP BY owner;

Retrieve information from multiple tables https://dev.mysql.com/doc/refman/5.7/en/multiple-tables.html 

# suppose we have two tables event & score; each has a column called event_id
# score table has columns: name, event_id, score
# event table has columns: event_id, date, type
mysql> SELECT student_id, date, score, type 
    -> FROM event, score
    -> WHERE date = "1999-09-20"
    -> AND event.event_id = score.event_id;

Mysql list tables and sizes - order by size

https://stackoverflow.com/questions/14569940/mysql-list-tables-and-sizes-order-by-size 

SELECT TABLE_NAME, table_rows, data_length, index_length, 
    round(((data_length + index_length) / 1024 / 1024),2) "Size in MB"
    FROM information_schema.TABLES WHERE table_schema = "schema_name"
    ORDER BY (data_length + index_length) DESC;

Note: replace "schema_name" with your database name.

Find first and last record from mysql table

https://stackoverflow.com/questions/2735395/how-to-find-first-and-last-record-from-mysql-table 

# To get the first record:
select col1 from tab1 order by col1 asc limit 1;   

# To get the last record:
select col1 from tab1 order by col1 desc  limit 1;

Write/save a table/query to a text file

# Method 1. mysql. Get a permission denied error 
$ mysql -u root -p
> SELECT * FROM tbl_name INTO OUTFILE '/tmp/orders.txt';

# Method 2. shell. Simple solution; does not need to change FILE privileges.
# https://stackoverflow.com/questions/9462416/shell-one-line-query
mysql -u root -pmy_password -h ip_add --port=13306 -D DATABASENAME -e "SELECT * FROM tbl_name;" > output.txt

Create a database 'demo' and a table 'employee'

http://www.thegeekstuff.com/2011/10/mysql-tutorial-basics/ 

mysql -u guest -p demo
show databases;
use demo;
show tables;
create table employee .............;
desc employee;
insert into employee .............;
select * from employee;


Access mysql using perl

http://www.cyberciti.biz/faq/how-to-access-mysql-database-using-perl

How to See Which MySQL Tables are Taking the Most Space

https://www.howtogeekpro.com/166/how-to-see-which-mysql-tables-are-taking-the-most-space/

Administration

Default port

3306

phpMyAdmin

http://localhost/phpmyadmin with default username: root and the admin password you have chosen during the installation of phpMyAdmin.

phpMyAdmin is installed under /usr/share/phpmyadmin.

Note that index.php file does not appear in /var/www/html directory. Why? A standard Apache Alias pointing every request starting with /phpmyadmin to the phpMyAdmin installation directory. See Setting up and securing a phpMyAdmin install on Ubuntu 10.04 

udooer@udoo:~$ ls -l /var/www/html
total 12
-rw-r--r-- 1 root root 11510 Dec 24 13:44 index.html
lrwxrwxrwx 1 root root    18 Dec 24 14:00 mediawiki -> /var/lib/mediawiki

udooer@udoo:~$ ls -lah /etc/apache2/
total 88K
drwxr-xr-x   8 root root 4.0K Dec 24 13:44 .
drwxr-xr-x 121 root root 4.0K Dec 25 08:15 ..
-rw-r--r--   1 root root 7.0K Jan  7  2014 apache2.conf
drwxr-xr-x   2 root root 4.0K Dec 25 08:15 conf-available
drwxr-xr-x   2 root root 4.0K Dec 25 08:15 conf-enabled
-rw-r--r--   1 root root 1.8K Jan  3  2014 envvars
-rw-r--r--   1 root root  31K Jan  3  2014 magic
drwxr-xr-x   2 root root  12K Dec 24 13:45 mods-available
drwxr-xr-x   2 root root 4.0K Dec 24 13:45 mods-enabled
-rw-r--r--   1 root root  320 Jan  7  2014 ports.conf
drwxr-xr-x   2 root root 4.0K Dec 24 13:44 sites-available
drwxr-xr-x   2 root root 4.0K Dec 24 13:44 sites-enabled

udooer@udoo:~$ ls -laH /etc/apache2/sites-available/
total 20
drwxr-xr-x 2 root root 4096 Dec 24 13:44 .
drwxr-xr-x 8 root root 4096 Dec 24 13:44 ..
-rw-r--r-- 1 root root 1332 Jan  7  2014 000-default.conf
-rw-r--r-- 1 root root 6437 Jan  7  2014 default-ssl.conf

udooer@udoo:~$ ls -lah /etc/apache2/conf-enabled/
total 8.0K
drwxr-xr-x 2 root root 4.0K Dec 25 08:15 .
drwxr-xr-x 8 root root 4.0K Dec 24 13:44 ..
lrwxrwxrwx 1 root root   30 Dec 24 13:44 charset.conf -> ../conf-available/charset.conf
lrwxrwxrwx 1 root root   40 Dec 25 08:13 javascript-common.conf -> ../conf-available/javascript-common.conf
lrwxrwxrwx 1 root root   44 Dec 24 13:44 localized-error-pages.conf -> ../conf-available/localized-error-pages.conf
lrwxrwxrwx 1 root root   46 Dec 24 13:44 other-vhosts-access-log.conf -> ../conf-available/other-vhosts-access-log.conf
lrwxrwxrwx 1 root root   33 Dec 25 08:15 phpmyadmin.conf -> ../conf-available/phpmyadmin.conf
lrwxrwxrwx 1 root root   31 Dec 24 13:44 security.conf -> ../conf-available/security.conf
lrwxrwxrwx 1 root root   36 Dec 24 13:44 serve-cgi-bin.conf -> ../conf-available/serve-cgi-bin.conf

udooer@udoo:~$ cat /etc/apache2/conf-available/phpmyadmin.conf 
# phpMyAdmin default Apache configuration

Alias /phpmyadmin /usr/share/phpmyadmin

<Directory /usr/share/phpmyadmin>
	Options FollowSymLinks
	DirectoryIndex index.php

	<IfModule mod_php5.c>
		AddType application/x-httpd-php .php

		php_flag magic_quotes_gpc Off
		php_flag track_vars On
		php_flag register_globals Off
		php_admin_flag allow_url_fopen Off
		php_value include_path .
		php_admin_value upload_tmp_dir /var/lib/phpmyadmin/tmp
		php_admin_value open_basedir /usr/share/phpmyadmin/:/etc/phpmyadmin/:/var/lib/phpmyadmin/:/usr/share/php/php-gettext/:/usr/share/javascript/
	</IfModule>

</Directory>

If we want to change the URL or the port number of phpMyAdmin, follow this.

Configuration file

MySQL Docker Containers: Understanding the basics

This can be found by using mysql --help or mysqld --help --verbose. On Ubuntu 16.04, it shows 

$ mysql --help
...
Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf ~/.my.cnf
...
$ tree /etc/mysql/
/etc/mysql/
├── conf.d
│   ├── mysql.cnf
│   └── mysqldump.cnf
├── debian.cnf
├── debian-start
├── my.cnf -> /etc/alternatives/my.cnf
├── my.cnf.fallback
├── mysql.cnf
└── mysql.conf.d
    ├── mysqld.cnf
    └── mysqld_safe_syslog.cnf

2 directories, 9 files

Default database location

On Debian/Ubuntu, it is /var/lib/mysql. 

$ mysql -uroot -p -e 'SHOW VARIABLES WHERE Variable_Name = "datadir"'

OR 

mysql> select @@datadir;

Change data location

https://stackoverflow.com/questions/1795176/how-to-change-mysql-data-directory

  1. sudo /etc/init.d/mysql stop
  2. sudo cp -R -p /var/lib/mysql /newpath
  3. sudo gedit /etc/mysql/my.cnf
  4. Look for the entry for datadir, and change the path (which should be /var/lib/mysql) to the new data directory.
  5. sudo gedit /etc/apparmor.d/usr.sbin.mysqld
  6. Look for lines beginning with /var/lib/mysql. Change /var/lib/mysql in the lines with the new path.
  7. sudo /etc/init.d/apparmor reload
  8. sudo /etc/init.d/mysql restart

How to backup/export and load/import a single database and/or table from a MySQL database

# Export
$ mysqldump -u USERNAME --password="PW" DB_NAME > sql_backup_file # Or use 'backup.sql' to be clear

# Import
# Method 1
$ mysql -u UserName -p Password -h Hostname DB_NAME < sql_backup_file
# Method 2
$ mysqlimport -u UserName -p Password sql_backup_file

Note that

  1. the back up file is a text file.
  2. the user information will not be retained in the backup file.
  3. the original database name is saved in the backup file
  4. the database name DB_NAME in importing is required. The database name does not to be the same as the original. However the database DB_NAME has to be created beforehand (mysql> CREATE DATABASE DB_NAME2). If the database has not existed or we omit the DB_NAME in importing, we will get an error
ERROR 1046 (3D000) at line 22: No database selected

# or
ERROR 1049 (42000): Unknown database 'testdb'

Move the MySQL data directory

Use through R

Examples from r-bloggers

Installation

Ubuntu/Debian

First, log in using root. 

install.packages("DBI")

Go to shell and 

# sudo apt-get install libdbd-mysql (this line seems not necessary)
# sudo apt-get install libmysqlclient-dev (Ubuntu 14)      
sudo apt-get install -y libmariadb-dev (Debian Stretch)
# R
# install.packages("RMySQL")

Windows

Check my note with complete screenshots at File:Install MySQL on Windows.pdf.

Open and close connection: dbConnect/dbDisconnect

con <- dbConnect(MySQL(), user="me", password="nuts2u", dbname="my_db", host="localhost")
on.exit(dbDisconnect(con))

dbListTables(con)
head(dbReadTable(con, "recentchanges"))

List tables and fields: dbListTables and dbListFields

dbListTables(mydb)
dbListFields(mydb, 'some_table')

Read and write entire tables: dbReadTable and dbWriteTable

We can create tables in the database using R dataframes. 

df = dbReadTable(con, 'motortrend')
dbWriteTable(mydb, name='table_name', value=data.frame.name)

Query: dbGetQuery and dbSendQuery

You can process query results row by row, in blocks or all at once. The highly useful function dbGetQuery(con, sql) returns all query results as a data frame. With dbSendQuery, you can get all or partial results with fetch. 

con <- dbConnect(MySQL(), user="network_portal", password="monkey2us", dbname=db.name, host="localhost")
rs <- dbSendQuery(con, "select name from genes limit 10;") # results in in mysql
data <- fetch(rs, n=10) # return result to R as a data frame; use n=-1 to retrieve all pending records.
huh <- dbHasCompleted(rs)
dbClearResult(rs)
dbDisconnect(con)

Aggregate and Sort

df = dbGetQuery(con, "SELECT mfg, avg(hp) AS meanHP FROM motortrend GROUP BY mfg ORDER BY meanHP DESC")
df = dbGetQuery(con, "SELECT cyl as cylinders, avg(hp) as meanHP FROM motortrend GROUP by cyl ORDER BY cyl")

dbApply()

sql = "SELECT cyl, hp FROM motortrend ORDER BY cyl"
rs = dbSendQuery(con, sql)
dbApply(rs, INDEX='cyl', FUN=function(x, grp) quantile(x$hp))

Retrieving AUTO_INCREMENT IDs

create.network <- function(species.id, network.name, data.source, description) {
  
  con <- dbConnect(MySQL(),
           user="super_schmuck", password="nuts2u",
           dbname="my_db", host="localhost")
  on.exit(dbDisconnect(con))

  sql <- sprintf("insert into networks
                  (species_id, name, data_source, description, created_at)
                  values (%d, '%s', '%s', '%s', NOW());",
                 species.id, network.name, data.source, description)
  rs <- dbSendQuery(con, sql)
  dbClearResult(rs)

  id <- dbGetQuery(con, "select last_insert_id();")[1,1]

  return(id)
}

Full example from Jeffrey Breen

http://www.r-bloggers.com/slides-%E2%80%9Caccessing-databases-from-r%E2%80%9D-rstats/

First, create new database & user in MySQL: 

mysql> create database testrdb;
mysql> grant all privileges on testrdb.* to 'testuser'@'localhost' identified by 'testpass';
mysql> flush privileges;

In R, load the “mtcars” data.frame, clean it up, and write it to a new “motortrend” table: 

library(stringr)
library(RMySQL)
 
data(mtcars)
 
# car name is data.frame's rownames. Let's split into manufacturer and model columns:
mtcars$mfg = str_split_fixed(rownames(mtcars), ' ', 2)[,1]
mtcars$mfg[mtcars$mfg=='Merc'] = 'Mercedes'
mtcars$model = str_split_fixed(rownames(mtcars), ' ', 2)[,2]

> dim(mtcars)
[1] 32 13
> mtcars[1:3,]
               mpg cyl disp  hp drat    wt  qsec vs am gear carb    mfg   model
Mazda RX4     21.0   6  160 110 3.90 2.620 16.46  0  1    4    4  Mazda     RX4
Mazda RX4 Wag 21.0   6  160 110 3.90 2.875 17.02  0  1    4    4  Mazda RX4 Wag
Datsun 710    22.8   4  108  93 3.85 2.320 18.61  1  1    4    1 Datsun     710
 
# connect to local MySQL database (host='localhost' by default)
con = dbConnect("MySQL", "testrdb", username="testuser", password="testpass")
 
dbWriteTable(con, 'motortrend', mtcars)
 
dbDisconnect(con)

And check the database from mysql 

mli@PhenomIIx6:~$ mysql -u testuser -p
Enter password:
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 153
Server version: 5.1.63-0ubuntu0.11.10.1 (Ubuntu)

Copyright (c) 2000, 2011, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| testrdb            |
+--------------------+
2 rows in set (0.00 sec)

mysql> use testrdb;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-------------------+
| Tables_in_testrdb |
+-------------------+
| motortrend        |
+-------------------+
1 row in set (0.00 sec)

mysql> describe motortrend;
+-----------+--------+------+-----+---------+-------+
| Field     | Type   | Null | Key | Default | Extra |
+-----------+--------+------+-----+---------+-------+
| row_names | text   | YES  |     | NULL    |       |
| mpg       | double | YES  |     | NULL    |       |
| cyl       | double | YES  |     | NULL    |       |
| disp      | double | YES  |     | NULL    |       |
| hp        | double | YES  |     | NULL    |       |
| drat      | double | YES  |     | NULL    |       |
| wt        | double | YES  |     | NULL    |       |
| qsec      | double | YES  |     | NULL    |       |
| vs        | double | YES  |     | NULL    |       |
| am        | double | YES  |     | NULL    |       |
| gear      | double | YES  |     | NULL    |       |
| carb      | double | YES  |     | NULL    |       |
| mfg       | text   | YES  |     | NULL    |       |
| model     | text   | YES  |     | NULL    |       |
+-----------+--------+------+-----+---------+-------+
14 rows in set (0.01 sec)

mysql> SELECT * FROM motortrend WHERE row_names like "Mazda%" order by mpg;
+---------------+------+------+------+------+------+-------+-------+------+------+------+------+-------+---------+
| row_names     | mpg  | cyl  | disp | hp   | drat | wt    | qsec  | vs   | am   | gear | carb | mfg   | model   |
+---------------+------+------+------+------+------+-------+-------+------+------+------+------+-------+---------+
| Mazda RX4     |   21 |    6 |  160 |  110 |  3.9 |  2.62 | 16.46 |    0 |    1 |    4 |    4 | Mazda | RX4     |
| Mazda RX4 Wag |   21 |    6 |  160 |  110 |  3.9 | 2.875 | 17.02 |    0 |    1 |    4 |    4 | Mazda | RX4 Wag |
+---------------+------+------+------+------+------+-------+-------+------+------+------+------+-------+---------+
2 rows in set (0.00 sec)
mysql> SELECT row_names, wt, model  FROM motortrend WHERE row_names like "Mazda%" order by wt;
+---------------+-------+---------+
| row_names     | wt    | model   |
+---------------+-------+---------+
| Mazda RX4     |  2.62 | RX4     |
| Mazda RX4 Wag | 2.875 | RX4 Wag |
+---------------+-------+---------+
2 rows in set (0.00 sec)

mysql>

dbplyr

RODBC

SQLite

PostgreSQL

CouchDB

How to Install Apache CouchDB on Ubuntu 18.04 LTS

InFluxDB

MongoDB

Find database online

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