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A Common Database Interface (DBI)

R-Databases Special Interest Group
mailto:r-sig-db@stat.math.ethz.chr-sig-db@stat.math.ethz.ch

26 August 2002 (Updated 16 June 2003)


Contents

Abstract:

This document describes a common interface between the S language (in its R and S-Plus implementations) and database management systems (DBMS). The interface defines a small set of classes and methods similar in spirit to Perl's DBI, Java's JDBC, Python's DB-API, and Microsoft's ODBC.


Version

This document describes version 0.1-6 of the database interface API (application programming interface).


Introduction

The database interface (DBI) separates the connectivity to the DBMS into a ``front-end'' and a ``back-end''. Applications use only the exposed ``front-end'' API. The facilities that communicate with specific DBMS (Oracle, PostgreSQL, etc.) are provided by ``device drivers'' that get invoked automatically by the S language evaluator. The following example illustrates some of the DBI capabilities:

## Choose the proper DBMS driver and connect to the server

drv <- dbDriver("ODBC")
con <- dbConnect(drv, "dsn", "usr", "pwd")

## The interface can work at a higher level importing tables 
## as data.frames and exporting data.frames as DBMS tables.

dbListTables(con)
dbListFields(con, "quakes")
if(dbExistsTable(con, "new_results"))
   dbRemoveTable(con, "new_results")
dbWriteTable(con, "new_results", new.output)

## The interface allows lower-level interface to the DBMS
res <- dbSendQuery(con, paste(
            "SELECT g.id, g.mirror, g.diam, e.voltage",
            "FROM geom_table as g, elec_measures as e",
            "WHERE g.id = e.id and g.mirrortype = 'inside'",
            "ORDER BY g.diam"))
out <- NULL
while(!dbHasCompleted(res)){
   chunk <- fetch(res, n = 10000)
   out <- c(out, doit(chunk))
}

## Free up resources
dbClearResult(res)
dbDisconnect(con)
dbUnloadDriver(drv)
(only the first 2 expressions are DBMS-specific - all others are independent of the database engine itself).

Individual DBI drivers need not implement all the features we list below (we indicate those that are optional). Furthermore, drivers may extend the core DBI facilities, but we suggest to have these extensions clearly indicated and documented.

The following are the elements of the DBI:

  1. A set of classes and methods (Section [*]) that defines what operations are possible and how they are defined, e.g.:

    Some things are left explicitly unspecified, e.g., authentication and even the query language, although it is hard to avoid references to SQL and relational database management systems (RDBMS).

  2. Drivers

    Drivers are collection of functions that implement the functionality defined above in the context of specific DBMS, e.g., mSQL, Informix.

  3. Data type mappings (Section [*].)

    Mappings and conversions between DBMS data types and R/S objects. All drivers should implement the ``basic'' primitives (see below), but may chose to add user-defined conversion function to handle more generic objects (e.g., factors, ordered factors, time series, arrays, images).

  4. Utilities (Section [*].)

    These facilities help with details such as mapping of identifiers between S and DBMS (e.g., "_" is illegal in R/S names, and "." is used for constructing compound SQL identifiers), etc.


DBI Classes and Methods

The following are the main DBI classes. They need to be extended by individual database back-ends (Sybase, Oracle, etc.) Individual drivers need to provide methods for the generic functions listed here (those methods that are optional are so indicated).

Note: Although R releases prior to 1.4 do not have a formal concept of classes, we will use the syntax of the S Version 4 classes and methods (available in R releases 1.4 and later as library methods) to convey precisely the DBI class hierarchy, its methods, and intended behavior.

The DBI classes are DBIObject, DBIDriver, DBIConnection and DBIResult. All these are virtual classes. Drivers define new classes that extend these, e.g., PgSQLDriver, PgSQLConnection, and so on.

Figure 1

Figure: Class hierarchy for the DBI. The top two layers are comprised of virtual classes and each lower layer represents a set of driver-specific implementation classes that provide the functionality defined by the virtual classes above.

DBIObject:
Virtual class1 that groups all other DBI classes.

DBIDriver:
Virtual class that groups all DBMS drivers. Each DBMS driver extends this class. Typically generator functions instantiate the actual driver objects, e.g., PgSQL(), HDF5(), BerkeleyDB().

DBIConnection:
Virtual class that encapsulates connections to DBMS.

DBIResult:
Virtual class that describes the result of a DBMS query or statement.

[Q: Should we distinguish between a simple result of DBMS statements e.g., as delete from DBMS queries (i.e., those that generate data).]

The methods format, print, show, dbGetInfo, and summary are defined (and implemented in the DBI package) for the DBIObject base class, thus available to all implementations; individual drivers, however, are free to override them as they see fit.

format(x, ...):
produces a concise character representation (label) for the DBIObject x.

print(x, ...)/show(x):
prints a one-line identification of the object x.

summary(object, ...):
produces a concise description of the object. The default method for DBIObject simply invokes dbGetInfo(dbObj) and prints the name-value pairs one per line. Individual implementations may tailor this appropriately.

dbGetInfo(dbObj, ...):
extracts information (meta-data) relevant for the DBIObject dbObj. It may return a list of key/value pairs, individual meta-data if supplied in the call, or NULL if the requested meta-data is not available.

Hint: Driver implementations may choose to allow an argument what to specify individual meta-data, e.g., dbGetInfo(drv, what = "max.connections").

In the next few sub-sections we describe in detail each of these classes and their methods.


Class DBIObject

This class simply groups all DBI classes, and thus all extend it.


Class DBIDriver

This class identifies the database management system. It needs to be extended by individual back-ends (Oracle, PostgreSQL, etc.)

The DBI provides the generator dbDriver("driverName") which simply invokes the function driverName(), which in turn instantiates the corresponding driver object.

The DBIDriver class defines the following methods:

driverName():
initializes the driver code. The name driverName refers to the actual generator function for the DBMS, e.g., RPgSQL(), RODBC(), HDF5(). The driver instance object is used with dbConnect (see page [*]) for opening one or possibly more connections to one or more DBMS.

dbListConnections(drv, ...):
list of current connections being handled by the drv driver. May be NULL if there are no open connections. Drivers that do not support multiple connections may return the one open connection.

dbGetInfo(dbObj, ...):
returns a list of name-value pairs of information about the driver.

Hint: Useful entries could include

name:
the driver name (e.g., "RODBC", "RPgSQL");
driver.version:
version of the driver;
DBI.version:
the version of the DBI that the driver implements, e.g., "0.1-2";
client.version:
of the client DBMS libraries (e.g., version of the libpq library in the case of RPgSQL);
max.connections:
maximum number of simultaneous connections;
plus any other relevant information about the implementation, for instance, how the driver handles upper/lower case in identifiers.

dbUnloadDriver("driverName") (optional):
frees all resources (local and remote) used by the driver. Returns a logical to indicate if it succeeded or not.


Class DBIConnection

This virtual class encapsulates the connection to a DBMS, and it provides access to dynamic queries, result sets, DBMS session management (transactions), etc.

Note: Individual drivers are free to implement single or multiple simultaneous connections.

The methods defined by the DBIConnection class include:

dbConnect(drv, ...):
creates and opens a connection to the database implemented by the driver drv (see Section [*]). Each driver will define what other arguments are required, e.g., "dbname" or "dsn" for the database name, "user", and "password". It returns an object that extends DBIConnection in a driver-specific manner (e.g., the MySQL implementation could create an object of class MySQLConnection that extends DBIConnection).

dbDisconnect(conn, ...):
closes the connection, discards all pending work, and frees resources (e.g., memory, sockets). Returns a logical indicating whether it succeeded or not.

dbSendQuery(conn, statement, ...):
submits one statement to the DBMS. It returns a DBIResult object. This object is needed for fetching data in case the statement generates output (see fetch on page [*]), and it may be used for querying the state of the operation; see dbGetInfo and other meta-data methods on page [*].

dbGetQuery(conn, statement, ...):
submit, execute, and extract output in one operation. The resulting object may be a data.frame if the statement generates output. Otherwise the return value should be a logical indicating whether the query succeeded or not.

dbGetException(conn, ...):
returns a list with elements errNum and errMsg with the status of the last DBMS statement sent on a given connection (this information may also be provided by the dbGetInfo() meta-data function on the conn object.

Hint: The ANSI SQL-92 defines both a status code and an status message that could be return as members of the list.

dbGetInfo(dbObj, ...):
returns a list of name-value pairs describing the state of the connection; it may return one or more meta-data, the actual driver method allows to specify individual pieces of meta-data (e.g., maximum number of open results/cursors).

Hint: Useful entries could include

dbname:
the name of the database in use;
db.version:
the DBMS server version (e.g., "Oracle 8.1.7 on Solaris";
host:
host where the database server resides;
user:
user name;
password:
password (is this safe?);
plus any other arguments related to the connection (e.g., thread id, socket or TCP connection type).

dbListResults(conn, ...):
list of DBIResult objects currently active on the connection conn. May be NULL if no result set is active on conn. Drivers that implement only one result set per connection could return that one object (no need to wrap it in a list).

Note: The following are convenience methods that simplify the import/export of (mainly) data.frames. The first five methods implement the core methods needed to attach() remote DBMS to the S search path. (For details, see [2,3].)

Hint: For relational DBMS these methods may be easily implemented using the core DBI methods dbConnect, dbSendQuery, and fetch, due to SQL reflectance (i.e., one easily gets this meta-data by querying the appropriate tables on the RDBMS).

dbListTables(conn, ...):
returns a character vector (possibly of zero-length) of object (table) names available on the conn connection.

dbReadTable(conn, name, ...):
imports the data stored remotely in the table name on connection conn. Use the field row.names as the row.names attribute of the output data.frame. Returns a data.frame.

[Q: should we spell out how row.names should be created? E.g., use a field (with unique values) as row.names? Also, should dbReadTable reproduce a data.frame exported with dbWriteTable?]

dbWriteTable(conn, name, value, ...):
write the object value (perhaps after coercing it to data.frame) into the remote object name in connection conn. Returns a logical indicating whether the operation succeeded or not.

dbExistsTable(conn, name, ...):
does remote object name exist on conn? Returns a logical.

dbRemoveTable(conn, name, ...):
removes remote object name on connection conn. Returns a logical indicating whether the operation succeeded or not.

dbListFields(conn, name, ...):
returns a character vector listing the field names of the remote table name on connection conn (see dbColumnInfo() for extracting data type on a table).

Note: The following methods deal with transactions and stored procedures. All these functions are optional.

dbCommit(conn, ...)(optional):
commits pending transaction on the connection and returns TRUE or FALSE depending on whether the operation succeeded or not.

dbRollback(conn, ...)(optional):
undoes current transaction on the connection and returns TRUE or FALSE depending on whether the operation succeeded or not.

dbCallProc(conn, storedProc, ...)(optional):
invokes a stored procedure in the DBMS and returns a DBIResult object.

[Stored procedures are not part of the ANSI SQL-92 standard and vary substantially from one RDBMS to another.]


Class DBIResult

This virtual class describes the result and state of execution of a DBMS statement (any statement, query or non-query). The result set res keeps track of whether the statement produces output for R/S, how many rows were affected by the operation, how many rows have been fetched (if statement is a query), whether there are more rows to fetch, etc.

Note: Individual drivers are free to allow single or multiple active results per connection.

[Q: Should we distinguish between results that return no data from those that return data?]

The class DBIResult defines the following methods:

fetch(res, n, ...):
fetches the next n elements (rows) from the result set res and return them as a data.frame. A value of n=-1 is interpreted as ``return all elements/rows''.

dbClearResult(res, ...):
flushes any pending data and frees all resources (local and remote) used by the object res on both sides of the connection. Returns a logical indicating success or not.

dbGetInfo(dbObj, ...):
returns a name-value list with the state of the result set.

Hint: Useful entries could include

statement:
a character string representation of the statement being executed;
rows.affected:
number of affected records (changed, deleted, inserted, or extracted);
row.count:
number of rows fetched so far;
has.completed:
has the statement (query) finished?
is.select:
a logical describing whether or not the statement generates output;
plus any other relevant driver-specific meta-data.

dbColumnInfo(res, ...):
produces a data.frame that describes the output of a query. The data.frame should have as many rows as there are output fields in the result set, and each column in the data.frame should describe an aspect of the result set field (field name, type, etc.)

Hint: The data.frame columns could include

field.name:
DBMS field label;
field.type:
DBMS field type (implementation-specific);
data.type:
corresponding R/S data type, e.g., "integer";
precision/scale:
(as in ODBC terminology), display width and number of decimal digits, respectively;
nullable:
whether the corresponding field may contain (DBMS) NULL values;
plus other driver-specific information.

dbSetDataMappings(flds, ...)(optional):
defines a conversion between internal DBMS data types and R/S classes. We expect the default mappings (see Section [*]) to be by far the most common ones, but users that need more control may specify a class generator for individual fields in the result set. [This topic needs further discussion.]

Note: The following are convenience methods that extract information from the result object (they may be implemented by invoking dbGetInfo() with appropriate arguments).

dbGetStatement(res, ...)(optional):
returns the DBMS statement (as a character string) associated with the result res.

dbGetRowsAffected(res, ...)(optional):
returns the number of rows affected by the executed statement (number of records deleted, modified, extracted, etc.)

dbHasCompleted(res, ...)(optional):
returns a logical that indicates whether the operation has been completed (e.g., are there more records to be fetched?).

dbGetRowCount(res, ...)(optional):
returns the number of rows fetched so far.


Data Type Mappings

The data types supported by databases are different than the data types in R and S, but the mapping between the ``primitive'' types is straightforward: Any of the many fixed and varying length character types are mapped to R/S "character". Fixed-precision (non-IEEE) numbers are mapped into either doubles ("numeric") or long ("integer"). Notice that many DBMS do not follow the so-called IEEE arithmetic, so there are potential problems with under/overflows and loss of precision, but given the R/S primitive types we cannot do too much but identify these situations and warn the application (how?).

By default dates and date-time objects are mapped to character using the appropriate TO_CHAR function in the DBMS (which should take care of any locale information). Some RDBMS support the type CURRENCY or MONEY which should be mapped to "numeric" (again with potential round off errors). Large objects (character, binary, file, etc.) also need to be mapped. User-defined functions may be specified to do the actual conversion (as has been done in other inter-systems packages 2).

Specifying user-defined conversion functions still needs to be defined.


Utilities

The core DBI implementation should make available to all drivers some common basic utilities. For instance:
dbGetDBIVersion:
returns the version of the currently attached DBI as a string.

dbDataType(dbObj, obj, ...):
returns a string with the (approximately) appropriate data type for the R/S object obj. The DBI can implement this following the ANSI-92 standard, but individual drivers may want/need to extend it to make use of DBMS-specific types.

make.db.names(dbObj, snames, ...):
maps R/S names (identifiers) to SQL identifiers replacing illegal characters (as ".") by the legal SQL "_".

SQLKeywords(dbObj, ...):
returns a character vector of SQL keywords (reserved words). The default method returns the list of .SQL92Keywords, but drivers should update this vector with the DBMS-specific additional reserved words.

isSQLKeyword(dbObj, name, ...):
for each element in the character vector name determine whether or not it is an SQL keyword, as reported by the generic function SQLKeywords. Returns a logical vector parallel to the input object name.


Open Issues and Limitations

There are a number of issues and limitations that the current DBI conscientiously does not address on the interest of simplicity. We do list here the most important ones.
Non-SQL:
Is it realistic to attempt to encompass non-relational databases, like HDF5, Berkeley DB, etc.?

Security:
allowing users to specify their passwords on R/S scripts may be unacceptable for some applications. We need to consider alternatives where users could store authentication on files (perhaps similar to ODBC's odbc.ini) with more stringent permissions.

Exceptions:
the exception mechanism is a bit too simple, and it does not provide for information when problems stem from the DBMS interface itself. For instance, under/overflow or loss of precision as we move numeric data from DBMS to the more limited primitives in R/S.

Asynchronous communication:
most DBMS support both synchronous and asynchronous communications, allowing applications to submit a query and proceed while the database server process the query. The application is then notified (or it may need to poll the server) when the query has completed. For large computations, this could be very useful, but the DBI would need to specify how to interrupt the server (if necessary) plus other details. Also, some DBMS require applications to use threads to implement asynchronous communication, something that neither R nor S-Plus currently addresses.

SQL scripts:
the DBI only defines how to execute one SQL statement at a time, forcing users to split SQL scripts into individual statements. We need a mechanism by which users can submit SQL scripts that could possibly generate multiple result sets; in this case we may need to introduce new methods to loop over multiple results (similar to Python's nextResultSet).

BLOBS/CLOBS:
large objects (both character and binary) present some challenges both to R and S-Plus. It is becoming more common to store images, sounds, and other data types as binary objects in DBMS, some of which can be in principle quite large. The SQL-92 ANSI standard allows up to 2 gigabytes for some of these objects. We need to carefully plan how to deal with binary objects.

Transactions:
transaction management is not fully described.

Additional methods:
Do we need any additional methods? (e.g., dbListDatabases(conn), dbListTableIndices(conn, name), how do we list all available drivers?)

Bind variables:
the interface is heavily biased towards queries, as opposed to general purpose database development. In particular we made no attempt to define ``bind variables''; this is a mechanism by which the contents of R/S objects are implicitly moved to the database during SQL execution. For instance, the following embedded SQL statement

  /* SQL */
  SELECT * from emp_table where emp_id = :sampleEmployee
would take the vector sampleEmployee and iterate over each of its elements to get the result. Perhaps the DBI could at some point in the future implement this feature.


Resources

The idea of a common interface to databases has been successfully implemented in various environments, for instance:

Java's Database Connectivity (JDBC) (http://www.javasoft.com/products/jdbc/index.htmlwww.javasoft.com).

In C through the Open Database Connectivity (ODBC) (http://www.genix.net/unixODBCwww.genix.net/unixODBC).

Python's Database Application Programming Interface (http://www.python.org/topics/databasewww.python.org).

Perl's Database Interface (http://dbi.perl.orgdbi.perl.org).

Bibliography

1
David Axmark, Michael Widenius, Jeremy Cole, and Paul DuBois.
MySQL Reference Manual.
http://www.mysql.com/documentation/mysql, 2001.

2
John M. Chambers.
Data management in S.
Technical report, Bell Labs, Lucent Technologies, http://stat.bell-labs.com/stat/doc, 1991.

3
John M. Chambers.
Database classes.
Technical report, Bell Labs, Lucent Technologies, http://stat.bell-labs.com/stat/Sbook, 1998.

4
Peter Dalgaard.
The R-Tcl/Tk interface.
In Proceedings of the Distributed Statistical Computing 2001 Workshop, http://www.ci.tuwien.ac.at/Conferences/DSC-2001, 2001. Vienna University of Technology.

5
Alligator Descartes and Tim Bunce.
Programming the Perl DBI.
O'Reilly, 2000.

6
Paul DuBois.
MySQL.
New Riders, 2000.

7
Jon Ellis, Linda Ho, and Maydene Fisher.
JDBC 3.0 Specification.
Sun Microsystems, Inc, http://java.sun.com/Download4, 2000.

8
Torsten Hothorn, David A. James, and Brian D. Ripley.
R/S interfaces to databases.
In Proceedings of the Distributed Statistical Computing 2001 Workshop, http://www.ci.tuwien.ac.at/Conferences/DSC-2001, 2001. Vienna University of Technology.

9
X/Open Company Ltd.
X/Open SQL and RDA Specification.
X/Open Company Ltd., 1994.

10
Microsoft Inc, http://www.microsoft.com/data/odbc/.
Microsoft ODBC, 2001.

11
Erich Neuwirth and Thomas Baier.
Embedding R in standard software, and the other way around.
In Proceedings of the Distributed Statistical Computing 2001 Workshop, http://www.ci.tuwien.ac.at/Conferences/DSC-2001, 2001. Vienna University of Technology.

12
George Reese.
Database Programming with JDBC and Java.
O'Reilly, second edition, 2000.

13
B. D. Ripley and R. M. Ripley.
Applications of R clients and servers.
In Proceedings of the Distributed Statistical Computing 2001 Workshop, http://www.ci.tuwien.ac.at/Conferences/DSC-2001, 2001. Vienna University of Technology.

14
Brian D. Ripley.
Using databases with R.
R News, 1(1):18-20, January 2001.

15
R Development Core Team.
R Data Import/Export.
http://www.r-project.org, 2001.

16
Duncan Temple Lang.
Embedding S in other languages and environments.
In Proceedings of the Distributed Statistical Computing 2001 Workshop, http://www.ci.tuwien.ac.at/Conferences/DSC-2001, 2001. Vienna University of Technology.

About this document ...

A Common Database Interface (DBI)

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The translation was initiated by David A. James on 2003-10-24


Footnotes

... class1
A virtual class allows us to group classes that share some common characteristics, even if their implementations are radically different.
... packages2
Duncan Temple Lang has volunteered to port the data conversion code found in R-Jave, R-Perl, and R-Python packages to the DBI

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David A. James 2003-10-24