Changeset: 19529fe14374 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=19529fe14374
Modified Files:
clients/R/MonetDB.R/DESCRIPTION
clients/R/MonetDB.R/NEWS
clients/R/MonetDB.R/R/monetdb.R
clients/R/MonetDB.R/man/mc.Rd
clients/R/db.tests/monetdb.test.R
Branch: default
Log Message:
R Connector: Preparation for 0.9.2 and code cleanup
diffs (truncated from 1681 to 300 lines):
diff --git a/clients/R/MonetDB.R/DESCRIPTION b/clients/R/MonetDB.R/DESCRIPTION
--- a/clients/R/MonetDB.R/DESCRIPTION
+++ b/clients/R/MonetDB.R/DESCRIPTION
@@ -1,6 +1,6 @@
Package: MonetDB.R
Version: 0.9.2
-Date: 2013-03-18
+Date: 2013-04-16
Title: Connect MonetDB to R
Authors@R: c(person("Hannes Muehleisen", role = c("aut", "cre"),email =
"[email protected]"),
person("Thomas Lumley", role = "ctb"),
diff --git a/clients/R/MonetDB.R/NEWS b/clients/R/MonetDB.R/NEWS
--- a/clients/R/MonetDB.R/NEWS
+++ b/clients/R/MonetDB.R/NEWS
@@ -3,6 +3,11 @@ 0.9.2
- new options monetdb.sequential, monetdb.debug.query and monetdb.debug.mapi
- debug output now uses the message() function
- reinstated warning about monetdb:// db urls, we do not like them
+- source code cleanup
+- dbListTables() now hides system tables per default, also got options to
include the
+ schema name and quoting in the result (sys_tables, schema_names and quote)
+- fixed various TODO's in the code to get closer to 1.0 (exciting)
+- fixed a bug when the error identifier sent by MonetDB was non-numeric
0.9.1
- dbGetInfo() now supported on MonetDBConnection (dplyr compatibility)
diff --git a/clients/R/MonetDB.R/R/monetdb.R b/clients/R/MonetDB.R/R/monetdb.R
--- a/clients/R/MonetDB.R/R/monetdb.R
+++ b/clients/R/MonetDB.R/R/monetdb.R
@@ -4,337 +4,377 @@ require(digest)
C_LIBRARY <- "MonetDB.R"
.onLoad <- function(lib, pkg) {
- library.dynam( C_LIBRARY, pkg, lib )
- .Call("mapiInit",PACKAGE=C_LIBRARY)
+ library.dynam( C_LIBRARY, pkg, lib )
+ .Call("mapiInit", PACKAGE=C_LIBRARY)
}
# Make S4 aware of S3 classes
-setOldClass(c("sockconn","connection","monetdb_mapi_conn"))
+setOldClass(c("sockconn", "connection", "monetdb_mapi_conn"))
### MonetDBDriver
setClass("MonetDBDriver", representation("DBIDriver"))
# allow instantiation of this driver with MonetDB to allow existing programs
to work
MonetR <- MonetDB <- MonetDBR <- MonetDB.R <- function() {
- new("MonetDBDriver")
+ new("MonetDBDriver")
}
setMethod("dbGetInfo", "MonetDBDriver", def=function(dbObj, ...)
- list(name="MonetDBDriver",
- driver.version="0.9.2",
- DBI.version="0.2-7",
- client.version=NA,
- max.connections=NA)
+ list(name="MonetDBDriver",
+ driver.version="0.9.2",
+ DBI.version="0.2-7",
+ client.version=NA,
+ max.connections=NA)
)
# shorthand for connecting to the DB, very handy, e.g. dbListTables(mc("acs"))
-mc <- function(dbname="demo", user="monetdb", password="monetdb",
host="localhost",port=50000L, timeout=86400L, wait=FALSE,language="sql",...) {
-
dbConnect(MonetDB.R(),dbname,user,password,host,port,timeout,wait,language,...)
+mc <- function(dbname="demo", user="monetdb", password="monetdb",
host="localhost", port=50000L,
+ timeout=86400L, wait=FALSE, language="sql", ...) {
+
+ dbConnect(MonetDB.R(), dbname, user, password, host, port, timeout, wait,
language, ...)
}
-# TODO: document
-mq <- function(db,query,...) {
- conn <- mc(db,...)
- res <- dbGetQuery(conn,query)
+mq <- function(dbname, query, ...) {
+ conn <- mc(dbname, ...)
+ res <- dbGetQuery(conn, query)
dbDisconnect(conn)
return(res)
}
-setMethod("dbConnect", "MonetDBDriver", def=function(drv,dbname="demo",
user="monetdb", password="monetdb", host="localhost",port=50000L,
timeout=86400L, wait=FALSE,language="sql",...,url="") {
- if (substring(url,1,10) == "monetdb://") {
- dbname <- url
- }
- port <- as.integer(port)
- timeout <- as.integer(timeout)
-
- if (substring(dbname,1,10) == "monetdb://") {
- message("MonetDB.R: Using 'monetdb://...' URIs
in dbConnect() is deprecated. Please switch to dbname, host, port named
arguments.")
- rest <- substring(dbname,11,nchar(dbname))
- # split at /, so we get the dbname
- slashsplit <- strsplit(rest,"/",fixed=TRUE)
- hostport <- slashsplit[[1]][1]
- dbname <- slashsplit[[1]][2]
-
- # TODO: handle IPv6 IPs, they contain : chars,
later
- if (length(grep(":",hostport,fixed=TRUE)) == 1)
{
- hostportsplit <-
strsplit(hostport,":",fixed=TRUE)
- host <- hostportsplit[[1]][1]
- port <- hostportsplit[[1]][2]
- } else {
- host <- hostport
- }
- }
-
- if (getOption("monetdb.debug.mapi",F)) message("II:
Connecting to MonetDB on host ",host," at port ",port, " to DB ", dbname, "
with user ", user," and a non-printed password, timeout is ",timeout,"
seconds.")
- socket <- FALSE
- if (wait) {
- repeat {
- continue <- FALSE
- tryCatch ({
- # open socket
with 5-sec timeout so we can check whether everything works
- socket <-
socket <<- .Call("mapiConnect",host,port,5,PACKAGE=C_LIBRARY)
- # authenticate
-
.monetAuthenticate(socket,dbname,user,password,language=language)
- # test the
connection to make sure it works before
-
.Call("mapiDisconnect",socket,PACKAGE=C_LIBRARY)
- break
- }, error = function(e) {
- if
("connection" %in% class(socket)) {
-
.Call("mapiDisconnect",socket,PACKAGE=C_LIBRARY)
- }
- message("Server
not ready(",e$message,"), retrying (ESC or CTRL+C to abort)")
- Sys.sleep(1)
- continue <<-
TRUE
- })
- }
- }
-
- # make new socket with user-specified timeout
- socket <-
.Call("mapiConnect",host,port,timeout,PACKAGE=C_LIBRARY)
-
.monetAuthenticate(socket,dbname,user,password,language=language)
- connenv <- new.env(parent=emptyenv())
- connenv$lock <- 0
- connenv$deferred <- list()
- connenv$exception <- list()
-
- conn <- new("MonetDBConnection",socket=socket,connenv=connenv,Id=-1L)
- if (getOption("monetdb.sequential",F)) {
- message("MonetDB: Switching to single-threaded query execution.")
- dbSendQuery(conn,"set optimizer='sequential_pipe'")
- }
+setMethod("dbConnect", "MonetDBDriver", def=function(drv, dbname="demo",
user="monetdb",
+ password="monetdb", host="localhost", port=50000L, timeout=86400L,
wait=FALSE, language="sql",
+ ..., url="") {
+
+ if (substring(url, 1, 10) == "monetdb://") {
+ dbname <- url
+ }
+ port <- as.integer(port)
+ timeout <- as.integer(timeout)
+
+ if (substring(dbname, 1, 10) == "monetdb://") {
+ message("MonetDB.R: Using 'monetdb://...' URIs in dbConnect() is
deprecated. Please switch to ",
+ "dbname, host, port named arguments.")
+ rest <- substring(dbname, 11, nchar(dbname))
+ # split at /, so we get the dbname
+ slashsplit <- strsplit(rest, "/", fixed=TRUE)
+ hostport <- slashsplit[[1]][1]
+ dbname <- slashsplit[[1]][2]
+
+ # TODO: handle IPv6 IPs, they contain : chars, later
+ if (length(grep(":", hostport, fixed=TRUE)) == 1) {
+ hostportsplit <- strsplit(hostport, ":", fixed=TRUE)
+ host <- hostportsplit[[1]][1]
+ port <- hostportsplit[[1]][2]
+ } else {
+ host <- hostport
+ }
+ }
+
+ if (getOption("monetdb.debug.mapi", F)) message("II: Connecting to MonetDB
on host ", host, " at "
+ ,"port ", port, " to DB ", dbname, " with user ", user, " and a
non-printed password, timeout is "
+ , timeout, " seconds.")
+ socket <- FALSE
+ if (wait) {
+ repeat {
+ continue <- FALSE
+ tryCatch ({
+ # open socket with 5-sec timeout so we can check whether everything
works
+ socket <- socket <<- .Call("mapiConnect", host, port, 5,
PACKAGE=C_LIBRARY)
+ # authenticate
+ .monetAuthenticate(socket, dbname, user, password, language=language)
+ # test the connection to make sure it works before
+ .Call("mapiDisconnect", socket, PACKAGE=C_LIBRARY)
+ break
+ }, error = function(e) {
+ if ("connection" %in% class(socket)) {
+ .Call("mapiDisconnect", socket, PACKAGE=C_LIBRARY)
+ }
+ message("Server not ready(", e$message, "), retrying (ESC or CTRL+C to
abort)")
+ Sys.sleep(1)
+ continue <<- TRUE
+ })
+ }
+ }
+
+ # make new socket with user-specified timeout
+ socket <- .Call("mapiConnect", host, port, timeout, PACKAGE=C_LIBRARY)
+ .monetAuthenticate(socket, dbname, user, password, language=language)
+ connenv <- new.env(parent=emptyenv())
+ connenv$lock <- 0
+ connenv$deferred <- list()
+ connenv$exception <- list()
+
+ conn <- new("MonetDBConnection", socket=socket, connenv=connenv, Id=-1L)
+ if (getOption("monetdb.sequential", F)) {
+ message("MonetDB: Switching to single-threaded query execution.")
+ dbSendQuery(conn, "set optimizer='sequential_pipe'")
+ }
+
+ return(conn)
+},
+valueClass="MonetDBConnection")
- return(conn)
- },
- valueClass="MonetDBConnection")
-
-### MonetDBConnection, #monetdb_mapi_conn
-setClass("MonetDBConnection",
representation("DBIConnection",socket="externalptr",connenv="environment",fetchSize="integer",Id="integer"))
+### MonetDBConnection
+setClass("MonetDBConnection", representation("DBIConnection",
socket="externalptr",
+ connenv="environment", fetchSize="integer", Id="integer"))
setMethod("dbGetInfo", "MonetDBConnection", def=function(dbObj, ...) {
- envdata <- dbGetQuery(dbObj,"SELECT name, value from
env()")
- ll <- as.list(envdata$value)
- names(ll) <- envdata$name
- ll$name <- "MonetDBConnection"
- return(ll)
- })
+ envdata <- dbGetQuery(dbObj, "SELECT name, value from env()")
+ ll <- as.list(envdata$value)
+ names(ll) <- envdata$name
+ ll$name <- "MonetDBConnection"
+ return(ll)
+})
setMethod("dbDisconnect", "MonetDBConnection", def=function(conn, ...) {
- .Call("mapiDisconnect",conn@socket,PACKAGE=C_LIBRARY)
- return(invisible(TRUE))
- })
+ .Call("mapiDisconnect", conn@socket, PACKAGE=C_LIBRARY)
+ return(invisible(TRUE))
+})
-setMethod("dbListTables", "MonetDBConnection", def=function(conn, ...) {
- df <- dbGetQuery(conn,"select name from sys.tables")
- df$name
- })
+setMethod("dbListTables", "MonetDBConnection", def=function(conn, ...,
sys_tables=F, schema_names=F, quote=F) {
+ q <- "select schemas.name as sn, tables.name as tn from tables join schemas
on tables.schema_id=schemas.id"
+ if (!sys_tables) q <- paste0(q, " where system=false")
+ df <- dbGetQuery(conn, q)
+ if (quote) {
+ df$tn <- paste0("\"", df$tn, "\"")
+ }
+ res <- df$tn
+ if (schema_names) {
+ if (quote) {
+ df$sn <- paste0("\"", df$sn, "\"")
+ }
+ res <- paste0(df$sn, ".", df$tn)
+ }
+ return(as.character(res))
+})
-if (is.null(getGeneric("dbTransaction"))) setGeneric("dbTransaction",
function(conn,...) standardGeneric("dbTransaction"))
+if (is.null(getGeneric("dbTransaction"))) setGeneric("dbTransaction",
function(conn, ...)
+ standardGeneric("dbTransaction"))
+
setMethod("dbTransaction", signature(conn="MonetDBConnection"),
def=function(conn, ...) {
- dbSendQuery(conn,"start transaction")
- invisible(TRUE)
- })
+ dbSendQuery(conn, "start transaction")
+ invisible(TRUE)
+})
setMethod("dbCommit", "MonetDBConnection", def=function(conn, ...) {
- dbSendQuery(conn,"commit")
- invisible(TRUE)
- })
+ dbSendQuery(conn, "commit")
+ invisible(TRUE)
+})
setMethod("dbRollback", "MonetDBConnection", def=function(conn, ...) {
- dbSendQuery(conn,"rollback")
- invisible(TRUE)
- })
+ dbSendQuery(conn, "rollback")
+ invisible(TRUE)
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