Title: | Database Interface and MariaDB Driver |
---|---|
Description: | Implements a DBI-compliant interface to MariaDB (<https://mariadb.org/>) and MySQL (<https://www.mysql.com/>) databases. |
Authors: | Kirill Müller [aut, cre] , Jeroen Ooms [aut] , David James [aut], Saikat DebRoy [aut], Hadley Wickham [aut], Jeffrey Horner [aut], R Consortium [fnd], RStudio [cph] |
Maintainer: | Kirill Müller <[email protected]> |
License: | MIT + file LICENSE |
Version: | 1.3.3.9000 |
Built: | 2024-11-24 08:27:52 UTC |
Source: | https://github.com/r-dbi/rmariadb |
Implements a DBI-compliant interface to MariaDB (https://mariadb.org/) and MySQL (https://www.mysql.com/) databases.
Maintainer: Kirill Müller [email protected] (ORCID)
Authors:
Jeroen Ooms (ORCID)
David James
Saikat DebRoy
Hadley Wickham
Jeffrey Horner
Other contributors:
R Consortium [funder]
RStudio [copyright holder]
Useful links:
Report bugs at https://github.com/r-dbi/RMariaDB/issues
Use for the client.flag
argument to DBI::dbConnect()
, multiple flags can be
combined with +
or bitwOr()
.
The flags are provided for completeness.
To enforce SSL for the DB connection, add the flag CLIENT_SSL
.
The flags
argument at https://mariadb.com/kb/en/library/mysql_real_connect.
## Not run: library(DBI) library(RMariaDB) con1 <- dbConnect(MariaDB(), client.flag = CLIENT_COMPRESS) con2 <- dbConnect( MariaDB(), client.flag = bitwOr(CLIENT_COMPRESS, CLIENT_SSL) ) ## End(Not run)
## Not run: library(DBI) library(RMariaDB) con1 <- dbConnect(MariaDB(), client.flag = CLIENT_COMPRESS) con2 <- dbConnect( MariaDB(), client.flag = bitwOr(CLIENT_COMPRESS, CLIENT_SSL) ) ## End(Not run)
This method is a straight-forward implementation of the corresponding generic function.
## S4 method for signature 'MariaDBConnection' dbDataType(dbObj, obj, ...) ## S4 method for signature 'MariaDBDriver' dbDataType(dbObj, obj, ...)
## S4 method for signature 'MariaDBConnection' dbDataType(dbObj, obj, ...) ## S4 method for signature 'MariaDBDriver' dbDataType(dbObj, obj, ...)
dbObj |
A MariaDBDriver or MariaDBConnection object. |
obj |
R/S-Plus object whose SQL type we want to determine. |
... |
any other parameters that individual methods may need. |
dbDataType(RMariaDB::MariaDB(), "a") dbDataType(RMariaDB::MariaDB(), 1:3) dbDataType(RMariaDB::MariaDB(), 2.5)
dbDataType(RMariaDB::MariaDB(), "a") dbDataType(RMariaDB::MariaDB(), 1:3) dbDataType(RMariaDB::MariaDB(), 2.5)
These methods are straight-forward implementations of the corresponding generic functions.
MariaDB() ## S4 method for signature 'MariaDBDriver' dbConnect( drv, dbname = NULL, username = NULL, password = NULL, host = NULL, unix.socket = NULL, port = 0, client.flag = 0, group = "rs-dbi", default.file = NULL, ssl.key = NULL, ssl.cert = NULL, ssl.ca = NULL, ssl.capath = NULL, ssl.cipher = NULL, ..., groups = NULL, load_data_local_infile = FALSE, bigint = c("integer64", "integer", "numeric", "character"), timeout = 10, timezone = "+00:00", timezone_out = NULL, reconnect = FALSE, mysql = NULL )
MariaDB() ## S4 method for signature 'MariaDBDriver' dbConnect( drv, dbname = NULL, username = NULL, password = NULL, host = NULL, unix.socket = NULL, port = 0, client.flag = 0, group = "rs-dbi", default.file = NULL, ssl.key = NULL, ssl.cert = NULL, ssl.ca = NULL, ssl.capath = NULL, ssl.cipher = NULL, ..., groups = NULL, load_data_local_infile = FALSE, bigint = c("integer64", "integer", "numeric", "character"), timeout = 10, timezone = "+00:00", timezone_out = NULL, reconnect = FALSE, mysql = NULL )
drv |
an object of class MariaDBDriver or MariaDBConnection. |
dbname |
string with the database name or NULL. If not NULL, the connection sets the default database to this value. |
username , password
|
Username and password. If username omitted, defaults to the current user. If password is omitted, only users without a password can log in. |
host |
string identifying the host machine running the MariaDB server or
NULL. If NULL or the string |
unix.socket |
(optional) string of the unix socket or named pipe. |
port |
(optional) integer of the TCP/IP default port. |
client.flag |
(optional) integer setting various MariaDB client flags, see Client-flags for details. |
group |
string identifying a section in the |
default.file |
string of the filename with MariaDB client options,
only relevant if |
ssl.key |
(optional) string of the filename of the SSL key file to use.
Expanded with |
ssl.cert |
(optional) string of the filename of the SSL certificate to
use. Expanded with |
ssl.ca |
(optional) string of the filename of an SSL certificate
authority file to use. Expanded with |
ssl.capath |
(optional) string of the path to a directory containing
the trusted SSL CA certificates in PEM format. Expanded with
|
ssl.cipher |
(optional) string list of permitted ciphers to use for SSL encryption. |
... |
Unused, needed for compatibility with generic. |
groups |
deprecated, use |
load_data_local_infile |
Set to |
bigint |
The R type that 64-bit integer types should be mapped to, default is bit64::integer64, which allows the full range of 64 bit integers. |
timeout |
Connection timeout, in seconds. Use |
timezone |
(optional) time zone for the connection,
the default corresponds to UTC.
Set this argument if your server or database is configured with a different
time zone than UTC.
Set to |
timezone_out |
The time zone returned to R.
The default is to use the value of the |
reconnect |
(experimental) Set to |
mysql |
Set to |
MySQL and MariaDB support named time zones, they must be installed on the server. See https://dev.mysql.com/doc/mysql-g11n-excerpt/8.0/en/time-zone-support.html for more details. Without installation, time zone support is restricted to UTC offset, which cannot take into account DST offsets.
Avoid storing passwords hard-coded in the code, use e.g. the keyring package to store and retrieve passwords in a secure way.
The MySQL client library (but not MariaDB) supports a .mylogin.cnf
file
that can be passed in the default.file
argument.
This file can contain an obfuscated password, which is not a secure way
to store passwords but may be acceptable if the user is aware of the
restrictions.
The availability of this feature depends on the client library used
for compiling the RMariaDB package.
Windows and macOS binaries on CRAN are compiled against the MariaDB Connector/C
client library which do not support this feature.
Configuration files: https://mariadb.com/kb/en/library/configuring-mariadb-with-mycnf/
if (mariadbHasDefault()) { # connect to a database and load some data con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") dbWriteTable(con, "USArrests", datasets::USArrests, temporary = TRUE) # query rs <- dbSendQuery(con, "SELECT * FROM USArrests") d1 <- dbFetch(rs, n = 10) # extract data in chunks of 10 rows dbHasCompleted(rs) d2 <- dbFetch(rs, n = -1) # extract all remaining data dbHasCompleted(rs) dbClearResult(rs) dbListTables(con) # clean up dbDisconnect(con) } ## Not run: # Connect to a MariaDB database running locally con <- dbConnect(RMariaDB::MariaDB(), dbname = "mydb") # Connect to a remote database with username and password con <- dbConnect(RMariaDB::MariaDB(), host = "mydb.mycompany.com", user = "abc", password = "def" ) # But instead of supplying the username and password in code, it's usually # better to set up a group in your .my.cnf (usually located in your home # directory). Then it's less likely you'll inadvertently share them. con <- dbConnect(RMariaDB::MariaDB(), group = "test") # To connect to a remote database and require the use of SSL (and an example of using environment variables for your sensitive info) con <- dbConnect(RMariaDB::MariaDB(), dbname = Sys.getenv('DB_NAME'), host = Sys.getenv('DB_HOST'), user = Sys.getenv('DB_USER'), password = Sys.getenv('DB_PASSWORD'), client.flag = CLIENT_SSL ) # Always cleanup by disconnecting the database dbDisconnect(con) ## End(Not run) # All examples use the rs-dbi group by default. if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") con dbDisconnect(con) }
if (mariadbHasDefault()) { # connect to a database and load some data con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") dbWriteTable(con, "USArrests", datasets::USArrests, temporary = TRUE) # query rs <- dbSendQuery(con, "SELECT * FROM USArrests") d1 <- dbFetch(rs, n = 10) # extract data in chunks of 10 rows dbHasCompleted(rs) d2 <- dbFetch(rs, n = -1) # extract all remaining data dbHasCompleted(rs) dbClearResult(rs) dbListTables(con) # clean up dbDisconnect(con) } ## Not run: # Connect to a MariaDB database running locally con <- dbConnect(RMariaDB::MariaDB(), dbname = "mydb") # Connect to a remote database with username and password con <- dbConnect(RMariaDB::MariaDB(), host = "mydb.mycompany.com", user = "abc", password = "def" ) # But instead of supplying the username and password in code, it's usually # better to set up a group in your .my.cnf (usually located in your home # directory). Then it's less likely you'll inadvertently share them. con <- dbConnect(RMariaDB::MariaDB(), group = "test") # To connect to a remote database and require the use of SSL (and an example of using environment variables for your sensitive info) con <- dbConnect(RMariaDB::MariaDB(), dbname = Sys.getenv('DB_NAME'), host = Sys.getenv('DB_HOST'), user = Sys.getenv('DB_USER'), password = Sys.getenv('DB_PASSWORD'), client.flag = CLIENT_SSL ) # Always cleanup by disconnecting the database dbDisconnect(con) ## End(Not run) # All examples use the rs-dbi group by default. if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") con dbDisconnect(con) }
These methods read or write entire tables from a MariaDB database.
## S4 method for signature 'MariaDBConnection' dbAppendTable(conn, name, value, ..., row.names = NULL) ## S4 method for signature 'MariaDBConnection,character' dbExistsTable(conn, name, ...) ## S4 method for signature 'MariaDBConnection' dbListObjects(conn, prefix = NULL, ...) ## S4 method for signature 'MariaDBConnection' dbListTables(conn, ...) ## S4 method for signature 'MariaDBConnection,character' dbReadTable(conn, name, ..., row.names = FALSE, check.names = TRUE) ## S4 method for signature 'MariaDBConnection,character' dbRemoveTable(conn, name, ..., temporary = FALSE, fail_if_missing = TRUE) ## S4 method for signature 'MariaDBConnection,character,character' dbWriteTable( conn, name, value, field.types = NULL, overwrite = FALSE, append = FALSE, header = TRUE, row.names = FALSE, nrows = 50, sep = ",", eol = "\n", skip = 0, quote = "\"", temporary = FALSE, ... ) ## S4 method for signature 'MariaDBConnection,character,data.frame' dbWriteTable( conn, name, value, field.types = NULL, row.names = FALSE, overwrite = FALSE, append = FALSE, ..., temporary = FALSE )
## S4 method for signature 'MariaDBConnection' dbAppendTable(conn, name, value, ..., row.names = NULL) ## S4 method for signature 'MariaDBConnection,character' dbExistsTable(conn, name, ...) ## S4 method for signature 'MariaDBConnection' dbListObjects(conn, prefix = NULL, ...) ## S4 method for signature 'MariaDBConnection' dbListTables(conn, ...) ## S4 method for signature 'MariaDBConnection,character' dbReadTable(conn, name, ..., row.names = FALSE, check.names = TRUE) ## S4 method for signature 'MariaDBConnection,character' dbRemoveTable(conn, name, ..., temporary = FALSE, fail_if_missing = TRUE) ## S4 method for signature 'MariaDBConnection,character,character' dbWriteTable( conn, name, value, field.types = NULL, overwrite = FALSE, append = FALSE, header = TRUE, row.names = FALSE, nrows = 50, sep = ",", eol = "\n", skip = 0, quote = "\"", temporary = FALSE, ... ) ## S4 method for signature 'MariaDBConnection,character,data.frame' dbWriteTable( conn, name, value, field.types = NULL, row.names = FALSE, overwrite = FALSE, append = FALSE, ..., temporary = FALSE )
conn |
a MariaDBConnection object, produced by
|
name |
a character string specifying a table name. |
value |
A data frame. |
... |
Unused, needed for compatibility with generic. |
row.names |
Either If A string is equivalent to For backward compatibility, |
prefix |
A fully qualified path in the database's namespace, or |
check.names |
If |
temporary |
If |
fail_if_missing |
If |
field.types |
Optional, overrides default choices of field types, derived from the classes of the columns in the data frame. |
overwrite |
a logical specifying whether to overwrite an existing table
or not. Its default is |
append |
a logical specifying whether to append to an existing table
in the DBMS. If appending, then the table (or temporary table)
must exist, otherwise an error is reported. Its default is |
header |
logical, does the input file have a header line? Default is the
same heuristic used by |
nrows |
number of lines to rows to import using |
sep |
field separator character |
eol |
End-of-line separator |
skip |
number of lines to skip before reading data in the input file. |
quote |
the quote character used in the input file (defaults to
|
When using load_data_local_infile = TRUE
in DBI::dbConnect()
,
pass safe = FALSE
to dbAppendTable()
to avoid transactions.
Because LOAD DATA INFILE
is used internally, this means that
rows violating primary key constraints are now silently ignored.
A data.frame in the case of dbReadTable()
; otherwise a logical
indicating whether the operation was successful.
The data.frame returned by dbReadTable()
only has
primitive data, e.g., it does not coerce character data to factors.
Temporary tables are ignored for dbExistsTable()
and dbListTables()
due to
limitations of the underlying C API. For this reason, a prior existence check
is performed only before creating a regular persistent table; an attempt to
create a temporary table with an already existing name will fail with a
message from the database driver.
if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") # By default, row names are written in a column to row_names, and # automatically read back into the row.names() dbWriteTable(con, "mtcars", mtcars[1:5, ], temporary = TRUE) dbReadTable(con, "mtcars") dbReadTable(con, "mtcars", row.names = FALSE) }
if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") # By default, row names are written in a column to row_names, and # automatically read back into the row.names() dbWriteTable(con, "mtcars", mtcars[1:5, ], temporary = TRUE) dbReadTable(con, "mtcars") dbReadTable(con, "mtcars", row.names = FALSE) }
This function prints out the compiled and loaded client library versions.
mariadbClientLibraryVersions()
mariadbClientLibraryVersions()
A named integer vector of length two, the first element representing the compiled library version and the second element representing the loaded client library version.
mariadbClientLibraryVersions()
mariadbClientLibraryVersions()
RMariaDB examples and tests connect to a database defined by the
rs-dbi
group in ~/.my.cnf
. This function checks if that
database is available, and if not, displays an informative message.
mariadbDefault()
works similarly but throws a testthat skip condition
on failure, making it suitable for use in tests.
mariadbHasDefault() mariadbDefault()
mariadbHasDefault() mariadbDefault()
if (mariadbHasDefault()) { db <- dbConnect(RMariaDB::MariaDB(), dbname = "test") dbListTables(db) dbDisconnect(db) }
if (mariadbHasDefault()) { db <- dbConnect(RMariaDB::MariaDB(), dbname = "test") dbListTables(db) dbDisconnect(db) }
To retrieve results a chunk at a time, use DBI::dbSendQuery()
,
DBI::dbFetch()
, then DBI::dbClearResult()
. Alternatively, if you want all the
results (and they'll fit in memory) use DBI::dbGetQuery()
which sends,
fetches and clears for you. For data manipulation queries (i.e. queries
that do not return data, such as UPDATE
, DELETE
, etc.),
DBI::dbSendStatement()
serves as a counterpart to DBI::dbSendQuery()
, while
DBI::dbExecute()
corresponds to DBI::dbGetQuery()
.
## S4 method for signature 'MariaDBResult' dbBind(res, params, ...) ## S4 method for signature 'MariaDBResult' dbClearResult(res, ...) ## S4 method for signature 'MariaDBResult' dbFetch(res, n = -1, ..., row.names = FALSE) ## S4 method for signature 'MariaDBResult' dbGetStatement(res, ...) ## S4 method for signature 'MariaDBConnection,character' dbSendQuery(conn, statement, params = NULL, ..., immediate = FALSE) ## S4 method for signature 'MariaDBConnection,character' dbSendStatement(conn, statement, params = NULL, ..., immediate = FALSE)
## S4 method for signature 'MariaDBResult' dbBind(res, params, ...) ## S4 method for signature 'MariaDBResult' dbClearResult(res, ...) ## S4 method for signature 'MariaDBResult' dbFetch(res, n = -1, ..., row.names = FALSE) ## S4 method for signature 'MariaDBResult' dbGetStatement(res, ...) ## S4 method for signature 'MariaDBConnection,character' dbSendQuery(conn, statement, params = NULL, ..., immediate = FALSE) ## S4 method for signature 'MariaDBConnection,character' dbSendStatement(conn, statement, params = NULL, ..., immediate = FALSE)
res |
A MariaDBResult object. |
params |
A list of query parameters to be substituted into a parameterised query. |
... |
Unused. Needed for compatibility with generic. |
n |
Number of rows to retrieve. Use -1 to retrieve all rows. |
row.names |
Either If A string is equivalent to For backward compatibility, |
conn |
A MariaDBConnection object. |
statement |
A character vector of length one specifying the SQL statement that should be executed. Only a single SQL statement should be provided. |
immediate |
If TRUE, uses the |
if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") dbWriteTable(con, "arrests", datasets::USArrests, temporary = TRUE) # Run query to get results as dataframe dbGetQuery(con, "SELECT * FROM arrests limit 3") # Send query to pull requests in batches res <- dbSendQuery(con, "SELECT * FROM arrests") data <- dbFetch(res, n = 2) data dbHasCompleted(res) dbClearResult(res) dbDisconnect(con) }
if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") dbWriteTable(con, "arrests", datasets::USArrests, temporary = TRUE) # Run query to get results as dataframe dbGetQuery(con, "SELECT * FROM arrests limit 3") # Send query to pull requests in batches res <- dbSendQuery(con, "SELECT * FROM arrests") data <- dbFetch(res, n = 2) data dbHasCompleted(res) dbClearResult(res) dbDisconnect(con) }
See documentation of generics for more details.
## S4 method for signature 'MariaDBResult' dbColumnInfo(res, ...) ## S4 method for signature 'MariaDBResult' dbGetRowCount(res, ...) ## S4 method for signature 'MariaDBResult' dbGetRowsAffected(res, ...) ## S4 method for signature 'MariaDBResult' dbHasCompleted(res, ...)
## S4 method for signature 'MariaDBResult' dbColumnInfo(res, ...) ## S4 method for signature 'MariaDBResult' dbGetRowCount(res, ...) ## S4 method for signature 'MariaDBResult' dbGetRowsAffected(res, ...) ## S4 method for signature 'MariaDBResult' dbHasCompleted(res, ...)
res |
An object of class MariaDBResult |
... |
Ignored. Needed for compatibility with generic |
if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") dbWriteTable(con, "t1", datasets::USArrests, temporary = TRUE) rs <- dbSendQuery(con, "SELECT * FROM t1 WHERE UrbanPop >= 80") rs dbGetStatement(rs) dbHasCompleted(rs) dbColumnInfo(rs) dbFetch(rs) rs dbClearResult(rs) dbDisconnect(con) }
if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") dbWriteTable(con, "t1", datasets::USArrests, temporary = TRUE) rs <- dbSendQuery(con, "SELECT * FROM t1 WHERE UrbanPop >= 80") rs dbGetStatement(rs) dbHasCompleted(rs) dbColumnInfo(rs) dbFetch(rs) rs dbClearResult(rs) dbDisconnect(con) }
Commits or roll backs the current transaction in an MariaDB connection.
Note that in MariaDB DDL statements (e.g. CREATE TABLE
) cannot
be rolled back.
## S4 method for signature 'MariaDBConnection' dbBegin(conn, ...) ## S4 method for signature 'MariaDBConnection' dbCommit(conn, ...) ## S4 method for signature 'MariaDBConnection' dbRollback(conn, ...)
## S4 method for signature 'MariaDBConnection' dbBegin(conn, ...) ## S4 method for signature 'MariaDBConnection' dbCommit(conn, ...) ## S4 method for signature 'MariaDBConnection' dbRollback(conn, ...)
conn |
a MariaDBConnection object, as produced by
|
... |
Unused. |
if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") df <- data.frame(id = 1:5) dbWriteTable(con, "df", df, temporary = TRUE) dbBegin(con) dbExecute(con, "UPDATE df SET id = id * 10") dbGetQuery(con, "SELECT id FROM df") dbRollback(con) dbGetQuery(con, "SELECT id FROM df") dbDisconnect(con) }
if (mariadbHasDefault()) { con <- dbConnect(RMariaDB::MariaDB(), dbname = "test") df <- data.frame(id = 1:5) dbWriteTable(con, "df", df, temporary = TRUE) dbBegin(con) dbExecute(con, "UPDATE df SET id = id * 10") dbGetQuery(con, "SELECT id FROM df") dbRollback(con) dbGetQuery(con, "SELECT id FROM df") dbDisconnect(con) }