R: Database I/O for 'opm'

opm_dbput {opmextra}

R Documentation

Database I/O for opm

Description

Methods for inserting, querying and deleting OPMX objects into or from (SQL-based) relational databases using RODBC.

Usage

  ## S4 method for signature 'integer,RODBC'
opm_dbclear(object, conn, map.tables = NULL, klass = "OPM_DB")

  ## S4 method for signature 'character,RODBC'
opm_dbfind(object, conn, map.tables = NULL, klass = "OPM_DB")

  ## S4 method for signature 'integer,RODBC'
opm_dbget(object, conn,
    map.tables = NULL, include = 2L, klass = c(opm_dbclass(include), "MOPMX")) 

  ## S4 method for signature 'DBTABLES,RODBC'
opm_dbnext(object, conn, map.tables = NULL)

  ## S4 method for signature 'DBTABLES,RODBC'
opm_dbput(object, conn,
    map.tables = NULL, start = opm_dbnext(object, conn, map.tables))

Arguments

`object`	`OPMX`, `MOPMX` or `OPM_DB` object, integer vector containing real or potential primary keys of a database table, or character scalar containing a partial SQL query (the part after the ‘WHERE’ keyword).
`conn`	Database connection object. `RODBC` objects as created by the RODBC package are supported.
`map.tables`	Passed as `do_map` argument to `by` from the pkgutils package. Necessary if table names that deviate from the defaults are to be used.
`klass`	Character vector indicating one or several class names. For PM data this argument should not be changed.
`include`	Integer scalar indicating whether aggregated data (1) or aggregated and discretised data (2) or neither (0) should be added to the result. The numeric method of `opm_dbnext` needs the same kind of `object` argument.
`start`	Integer vector determining the minimum primary keys to which those in `object` should be coerced. Necessary for appending to a database table without overwriting previously inserted data.
`...`	Optional arguments passed between the methods.

Details

The RODBC methods use a simple quoting scheme for table and column names.

Note that the deletion mechanism is based on ON DELETE CASCADE. To enable this in SQLite, PRAGMA foreign_keys = ON; has to be called each time a database is opened. See the according demo entry.

Value

The main functions are those for create, search, read and delete operations:

opm_dbput returns an integer vector containing the primary keys of the inserted plates.
opm_dbfind returns an integer vector containing the primary keys of the found plates.
opm_dbget returns a MOPMX object with one element per plate type.
opm_dbclear invisibly returns the result of dbGetQuery (which is usually NULL).

Regarding the helper functions, opm_dbnext returns an integer scalar that is suitable as start argument of opm_dbput, whereas opm_dbclass returns a character scalar with the name of the intermediary class (derived from OPM_DB) to be created for database I/O. These need not normally be called by an opm user.

For checking whether a database (connection) is correctly set up, opm_dbcheck is available in the opm package, which returns a character vector whose elements are either ok or a description of the error that has occurred at that step of the checking process.

Examples

# The SQL files for generating the expected database tables. Tables can
# be renamed, but then an according 'map.tables' argument must be used.
library(opm)
opm_files("sql")

## [1] "/usr/local/lib/R/library/opm/auxiliary/001_rdbms_drop.sql"  
## [2] "/usr/local/lib/R/library/opm/auxiliary/002_rdbms_create.sql"
## [3] "/usr/local/lib/R/library/opm/auxiliary/003_rdbms_delete.sql"

# Usage examples are given in these demos. An according database must be
# made accessible beforehand.
if (interactive())
  demo(package = "opmextra")

[Package opmextra version 0.0.10 Index]