Changeset: 2ffee97139b5 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=2ffee97139b5
Added Files:
clients/R/db.tests/monetdb.test.R
clients/R/db.tests/monetframe.test.R
clients/R/db.tests/sqlsurvey.test.R
Modified Files:
clients/R/MonetDB.R/DESCRIPTION
clients/R/MonetDB.R/NEWS
clients/R/MonetDB.R/R/monetdb.R
clients/R/MonetDB.R/man/monetdb.read.csv.Rd
clients/R/MonetDB.R/src/mapisplit.c
Branch: default
Log Message:
R Connector updates for CRAN
diffs (truncated from 415 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
@@ -1,11 +1,11 @@
Package: MonetDB.R
-Version: 0.8.2
-Date: 2013-10-16
+Version: 0.9
+Date: 2013-01-21
Title: Connect MonetDB to R
Authors@R: c(person("Hannes Muehleisen", role = c("aut", "cre"),email =
"[email protected]"),
person("Thomas Lumley", role = "ctb"),
person("Anthony Damico", role = "ctb"))
-Depends: DBI (>= 0.2-5), digest (>= 0.6.0),methods
+Depends: DBI (>= 0.2-5), digest (>= 0.6.0), methods
Description: Allows to pull data from MonetDB into R
License: MPL (== 1.1)
URL: http://monetr.r-forge.r-project.org
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
@@ -1,6 +1,18 @@
+0.8.5
+- added parameters newline and quote to monetdb.write.csv
+
+0.8.4
+- fixed bug when reading empty table (Thanks, Anthony)
+- removed assertion in mapisplit.c that triggered sometimes for unclear reasons
+
+0.8.3
+- fixed a problem where integer SEXPs turned to double somehow
+
+0.8.2
+- fixed bug in dbConnect() where port and timeout were not always integer
values
+
0.8.1
- fixed bug in dbWriteTable() where VARCHAR(255) was used for character data
instead of STRING
-- moved monet.frame into separate package
0.8
- New All-C socket code (Thanks, Windows)
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
@@ -27,21 +27,24 @@ MonetR <- MonetDB <- MonetDBR <- MonetDB
setMethod("dbGetInfo", "MonetDBDriver", def=function(dbObj, ...)
list(name="MonetDBDriver",
- driver.version="0.8.0",
+ driver.version="0.9",
DBI.version="0.2-5",
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=50000, timeout=86400, wait=FALSE,...) {
+mc <- function(dbname="demo", user="monetdb", password="monetdb",
host="localhost",port=50000L, timeout=86400L, wait=FALSE,...) {
dbConnect(MonetDB.R(),dbname,user,password,host,port,timeout,wait,...)
}
-setMethod("dbConnect", "MonetDBDriver", def=function(drv,dbname="demo",
user="monetdb", password="monetdb", host="localhost",port=50000, timeout=86400,
wait=FALSE,...,url="") {
+setMethod("dbConnect", "MonetDBDriver", def=function(drv,dbname="demo",
user="monetdb", password="monetdb", host="localhost",port=50000L,
timeout=86400L, wait=FALSE,...,url="") {
if (substring(url,1,10) == "monetdb://") {
dbname <- url
}
+ port <- as.integer(port)
+ timeout <- as.integer(timeout)
+
if (substring(dbname,1,10) == "monetdb://") {
#warning("MonetDB.R: Using 'monetdb://...' URIs
in dbConnect() is deprecated. Please switch to dbname, host, port named
arguments.")
rest <- substring(dbname,11,nchar(dbname))
@@ -239,7 +242,7 @@ setMethod("dbWriteTable", "MonetDBConnec
})
-setMethod("dbDataType", signature(dbObj="MonetDBConnection", obj = "ANY"),
def=function(dbObj, obj, ...) {
+setMethod("dbDataType", signature(dbObj="MonetDBConnection", obj = "ANY"), def
= function(dbObj, obj, ...) {
if (is.logical(obj)) "BOOLEAN"
else if (is.integer(obj)) "INTEGER"
else if (is.numeric(obj)) "DOUBLE PRECISION"
@@ -412,7 +415,7 @@ setMethod("fetch", signature(res="MonetD
#parts[parts=="NULL"] <- NA
# call to a faster C implementation for the hard and
annoying task of splitting everyting into fields
- parts <- .Call("mapiSplit",
res@env$data[1:n],info$cols, PACKAGE=C_LIBRARY)
+ parts <- .Call("mapiSplit",
res@env$data[1:n],as.integer(info$cols), PACKAGE=C_LIBRARY)
# convert values column by column
for (j in seq.int(info$cols)) {
@@ -642,8 +645,8 @@ REPLY_SIZE <- 100 # Apparently, -1 me
env$types <- env$dbtypes <-
toupper(.mapiParseTableHeader(lines[4]))
env$lengths <- .mapiParseTableHeader(lines[5])
- env$tuples <-lines[6:length(lines)]
-
+ if (env$rows > 0) env$tuples <- lines[6:length(lines)]
+
stopifnot(length(env$tuples) == header$index)
return(env)
}
@@ -779,13 +782,21 @@ REPLY_SIZE <- 100 # Apparently, -1 me
}
+.hasColFunc <- function(conn,func) {
+ tryCatch({
+ r <- dbSendQuery(conn,paste0("SELECT
",func,"(1);"))
+ TRUE
+ }, error = function(e) {
+ FALSE
+ })
+}
# copied from RMonetDB, no java-specific things in here...
# TODO: read first few rows with read.table and check types etc.
-monet.read.csv <- monetdb.read.csv <-
function(conn,files,tablename,nrows,header=TRUE,locked=FALSE,na.strings="",...,nrow.check=500,delim=","){
+monet.read.csv <- monetdb.read.csv <-
function(conn,files,tablename,nrows,header=TRUE,locked=FALSE,na.strings="",nrow.check=500,delim=",",newline="\\n",quote="\"",...){
if (length(na.strings)>1) stop("na.strings must be of length 1")
- headers<-lapply(files,read.csv,na.strings="NA",...,nrows=nrow.check)
+
headers<-lapply(files,read.csv,na.strings="NA",quote=quote,nrows=nrow.check,...)
if (length(files)>1){
nn<-sapply(headers,ncol)
@@ -797,17 +808,19 @@ monet.read.csv <- monetdb.read.csv <- fu
}
dbWriteTable(conn, tablename, headers[[1]][FALSE,])
+
+ delimspec <- paste0("USING DELIMITERS
'",delim,"','",newline,"','",quote,"'")
if(header || !missing(nrows)){
if (length(nrows)==1) nrows<-rep(nrows,length(files))
for(i in seq_along(files)) {
cat(files[i],thefile<-normalizePath(files[i]),"\n")
- dbSendUpdate(conn,
paste("copy",format(nrows[i],scientific=FALSE),"offset 2 records into",
tablename,"from",paste("'",thefile,"'",sep=""),"using delimiters ',','\\n','\"'
NULL as",paste("'",na.strings[1],"'",sep=""),if(locked) "LOCKED"))
+ dbSendUpdate(conn,
paste("COPY",format(nrows[i],scientific=FALSE),"OFFSET 2 RECORDS INTO",
tablename,"FROM",paste("'",thefile,"'",sep=""),delimspec,"NULL
as",paste("'",na.strings[1],"'",sep=""),if(locked) "LOCKED"))
}
} else {
for(i in seq_along(files)) {
cat(files[i],thefile<-normalizePath(files[i]),"\n")
- dbSendUpdate(conn, paste0("copy into ", tablename,"
from ",paste("'",thefile,"'",sep="")," using delimiters '",delim,"','\\n','\"'
NULL as ",paste("'",na.strings[1],"'",sep=""),if(locked) " LOCKED "))
+ dbSendUpdate(conn, paste0("COPY INTO ", tablename,"
FROM ",paste("'",thefile,"'",sep=""),delimspec,"NULL as
",paste("'",na.strings[1],"'",sep=""),if(locked) " LOCKED "))
}
}
dbGetQuery(conn,paste("select count(*) from",tablename))
diff --git a/clients/R/MonetDB.R/man/monetdb.read.csv.Rd
b/clients/R/MonetDB.R/man/monetdb.read.csv.Rd
--- a/clients/R/MonetDB.R/man/monetdb.read.csv.Rd
+++ b/clients/R/MonetDB.R/man/monetdb.read.csv.Rd
@@ -10,7 +10,8 @@
}
\usage{
monetdb.read.csv (conn, files, tablename, nrows, header=TRUE,
- locked=FALSE, na.strings="", ..., nrow.check=500, delim=",")
+ locked=FALSE, na.strings="", nrow.check=500, delim=",",
+ newline = "\\\\n", quote = "\"", ...)
}
\arguments{
\item{conn}{A MonetDB.R database connection. Created using
\code{\link[DBI]{dbConnect}} with the
@@ -26,6 +27,8 @@
\item{nrow.check}{Amount of rows that should be read from the CSV when the
table is being created to determine column types.}
\item{delim}{Field separator in CSV file.}
+ \item{newline}{Newline in CSV file, usually \\n for UNIX-like systems and
\\r\\r on Windows.}
+ \item{quote}{Quote character(s) in CSV file.}
}
\value{
diff --git a/clients/R/MonetDB.R/src/mapisplit.c
b/clients/R/MonetDB.R/src/mapisplit.c
--- a/clients/R/MonetDB.R/src/mapisplit.c
+++ b/clients/R/MonetDB.R/src/mapisplit.c
@@ -131,7 +131,6 @@ SEXP mapiSplit(SEXP mapiLinesVector, SEX
break;
}
}
- assert(cCol == cols - 1);
}
free(valPtr);
diff --git a/clients/R/db.tests/monetdb.test.R
b/clients/R/db.tests/monetdb.test.R
new file mode 100644
--- /dev/null
+++ b/clients/R/db.tests/monetdb.test.R
@@ -0,0 +1,93 @@
+library(MonetDB.R)
+
+drv <- dbDriver("MonetDB")
+stopifnot(identical(dbGetInfo(drv)$name,"MonetDBDriver"))
+
+con <- dbConnect(drv, "monetdb://localhost:50000/monetdbrtest", "monetdb",
"monetdb",timeout=100,debug.queries=T)
+stopifnot(identical(class(con)[[1]],"MonetDBConnection"))
+# overwrite variable to force destructor
+con <- dbConnect(drv, "monetdb://localhost:50000/monetdbrtest", "monetdb",
"monetdb",timeout=100,debug.queries=T)
+con <- dbConnect(drv, "monetdb://localhost:50000/monetdbrtest", "monetdb",
"monetdb",timeout=100,debug.queries=T)
+gc()
+
+# basic MAPI/SQL test
+stopifnot(identical(dbGetQuery(con,"SELECT 'DPFKG!'")[[1]],"DPFKG!"))
+
+# remove test table
+if (dbExistsTable(con,"monetdbtest")) dbRemoveTable(con,"monetdbtest")
+stopifnot(identical(dbExistsTable(con,"monetdbtest"),FALSE))
+
+
+# test raw handling
+dbSendUpdate(con,"CREATE TABLE monetdbtest (a varchar(10),b integer,c blob)")
+stopifnot(identical(dbExistsTable(con,"monetdbtest"),TRUE))
+dbSendUpdate(con,"INSERT INTO monetdbtest VALUES ('one',1,'1111')")
+dbSendUpdate(con,"INSERT INTO monetdbtest VALUES ('two',2,'22222222')")
+stopifnot(identical(dbGetQuery(con,"SELECT count(*) FROM monetdbtest")[[1]],2))
+stopifnot(identical(dbReadTable(con,"monetdbtest")[[3]],list(charToRaw("1111"),charToRaw("22222222"))))
+
+dbRemoveTable(con,"monetdbtest")
+stopifnot(identical(dbExistsTable(con,"monetdbtest"),FALSE))
+
+
+# write test table iris
+data(iris)
+dbWriteTable(con,"monetdbtest",iris)
+
+stopifnot(identical(dbExistsTable(con,"monetdbtest"),TRUE))
+stopifnot(identical(dbExistsTable(con,"monetdbtest2"),FALSE))
+stopifnot("monetdbtest" %in% dbListTables(con))
+
+stopifnot(identical(dbListFields(con,"monetdbtest"),c("sepal_length","sepal_width","petal_length","petal_width","species")))
+# get stuff, first very convenient
+iris2 <- dbReadTable(con,"monetdbtest")
+stopifnot(identical(dim(iris),dim(iris2)))
+
+
+# then manually
+res <- dbSendQuery(con,"SELECT species, sepal_width FROM monetdbtest")
+stopifnot(identical(class(res)[[1]],"MonetDBResult"))
+stopifnot(identical(res@env$success,TRUE))
+
+stopifnot(dbColumnInfo(res)[[1,1]] == "species")
+stopifnot(dbColumnInfo(res)[[2,1]] == "sepal_width")
+
+stopifnot(dbGetInfo(res)$row.count == 150 && res@env$info$rows == 150)
+
+data <- fetch(res,10)
+stopifnot(dim(data)[[1]] == 10)
+stopifnot(dim(data)[[2]] == 2)
+stopifnot(res@env$delivered == 10)
+stopifnot(dbHasCompleted(res) == FALSE)
+
+data2 <- fetch(res,-1)
+stopifnot(dim(data2)[[1]] == 140)
+stopifnot(dbHasCompleted(res) == TRUE)
+
+dbClearResult(res)
+
+# remove table again
+dbRemoveTable(con,"monetdbtest")
+stopifnot(identical(dbExistsTable(con,"monetdbtest"),FALSE))
+
+# test csv import
+file <- tempfile()
+write.table(iris,file,sep=",")
+monetdb.read.csv(con,file,"monetdbtest",150)
+unlink(file)
+stopifnot(identical(dbExistsTable(con,"monetdbtest"),TRUE))
+iris3 <- dbReadTable(con,"monetdbtest")
+stopifnot(identical(dim(iris),dim(iris3)))
+stopifnot(identical(dbListFields(con,"monetdbtest"),c("sepal_length","sepal_width","petal_length","petal_width","species")))
+dbRemoveTable(con,"monetdbtest")
+stopifnot(identical(dbExistsTable(con,"monetdbtest"),FALSE))
+
+
+
+stopifnot(identical(dbDisconnect(con),TRUE))
+stopifnot(identical(dbDisconnect(con),TRUE))
+stopifnot(identical(dbDisconnect(con),TRUE))
+
+#thrice to catch pointer errors
+
+print("SUCCESS")
diff --git a/clients/R/db.tests/monetframe.test.R
b/clients/R/db.tests/monetframe.test.R
new file mode 100644
--- /dev/null
+++ b/clients/R/db.tests/monetframe.test.R
@@ -0,0 +1,75 @@
+library(monet.frame)
+
+con <- dbConnect(dbDriver("MonetDB"),
"monetdb://localhost:50000/monetdbrtest", "monetdb", "monetdb",timeout=100)
+
+table <- "monetframetest"
+
+
+fcmp <- function(f1,f2,epsilon) {
+ abs(f1-f2) < epsilon
+}
+
+# basic MAPI/SQL test
+stopifnot(identical(dbGetQuery(con,"SELECT 'DPFKG!'")[[1]],"DPFKG!"))
+
+if (!dbExistsTable(con,table)) {
+ data(iris)
+ dbWriteTable(con,table,iris, overwrite=TRUE)
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