Changeset: 58b47875e389 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=58b47875e389
Modified Files:
clients/R/MonetDB.R/NEWS
clients/R/MonetDB.R/R/dbi.R
clients/R/MonetDB.R/man/monetdb.read.csv.Rd
clients/R/Tests/dbi.stable.out
Branch: default
Log Message:
R Connector: new col.names parameter to monetdb.read.csv() that allows to
explicitly set the column names in the generated table
diffs (141 lines):
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
@@ -8,7 +8,8 @@ 1.0.0
- Fix for case when query only returns a prompt (CALL ..., Thanks, Roman)
- Fix for empty result set on dbGetQuery(), no longer returning NULL (Thanks,
Fabian)
- Fix for dbConnect(), it ignored the url parameter somehow, which broke some
sqlsurvey (Thanks, Anthony)
-- Added lower.case.names= to monet.read.csv() in case users want to avoid
quoting
+- Added col.names argument to monet.read.csv()
+- Fix for dbConnect() that should be more robust to invalid connections
0.9.7
- Fixed crash on Windows (Sorry, everyone)
diff --git a/clients/R/MonetDB.R/R/dbi.R b/clients/R/MonetDB.R/R/dbi.R
--- a/clients/R/MonetDB.R/R/dbi.R
+++ b/clients/R/MonetDB.R/R/dbi.R
@@ -103,7 +103,7 @@ setMethod("dbConnect", "MonetDBDriver",
break
}, error = function(e) {
if ("connection" %in% class(socket)) {
- close(socket)
+ tryCatch(close(socket), error=function(e){})
}
message("Server not ready(", e$message, "), retrying (ESC or CTRL+C to
abort)")
Sys.sleep(1)
@@ -283,8 +283,6 @@ setMethod("dbSendQuery", signature(conn=
invisible(new("MonetDBResult", env=env))
})
-
-
# quoting
quoteIfNeeded <- function(conn, x, ...) {
chars <- !grepl("^[a-z][a-z0-9_]*$", x, perl=T) & !grepl("^\"[^\"]*\"$", x,
perl=T)
@@ -315,7 +313,7 @@ setMethod("dbWriteTable", "MonetDBConnec
if (!is.data.frame(value)) value <- as.data.frame(value)
}
if (overwrite && append) {
- stop("Setting both overwrite and append to true makes no sense.")
+ stop("Setting both overwrite and append to TRUE makes no sense.")
}
qname <- quoteIfNeeded(conn, name)
@@ -622,7 +620,8 @@ setMethod("dbGetInfo", "MonetDBResult",
# adapted from RMonetDB, no java-specific things in here...
monet.read.csv <- monetdb.read.csv <- function(conn, files, tablename,
nrows=NA, header=TRUE,
locked=FALSE, na.strings="",
nrow.check=500,
- delim=",", newline="\\n",
quote="\"", create=TRUE, lower.case.names=FALSE, ...){
+ delim=",", newline="\\n",
quote="\"", create=TRUE,
+ col.names=NULL,
lower.case.names=FALSE, ...){
if (length(na.strings)>1) stop("na.strings must be of length 1")
headers <- lapply(files, utils::read.csv, sep=delim, na.strings=na.strings,
quote=quote, nrows=nrow.check,
@@ -631,7 +630,7 @@ monet.read.csv <- monetdb.read.csv <- fu
if (!missing(nrows)) {
warning("monetdb.read.csv(): nrows parameter is not neccessary any more
and deprecated.")
}
-
+
if (length(files)>1){
nn <- sapply(headers, ncol)
if (!all(nn==nn[1])) stop("Files have different numbers of columns")
@@ -642,9 +641,19 @@ monet.read.csv <- monetdb.read.csv <- fu
}
if (create){
- if(lower.case.names) names(headers[[1]]) <- tolower(names( headers[[1]]))
+ if(lower.case.names) names(headers[[1]]) <- tolower(names(headers[[1]]))
+ if(!is.null(col.names)) {
+ if (lower.case.names) {
+ warning("Ignoring lower.case.names parameter as overriding col.names
are supplied.")
+ }
+ col.names <- as.character(col.names)
+ if (length(unique(col.names)) != length(names(headers[[1]]))) {
+ stop("You supplied ", length(unique(col.names)), " unique column
names, but file has ",
+ length(names(headers[[1]])), " columns.")
+ }
+ names(headers[[1]]) <- quoteIfNeeded(conn, col.names)
+ }
dbWriteTable(conn, tablename, headers[[1]][FALSE, ])
-
}
delimspec <- paste0("USING DELIMITERS '", delim, "','", newline, "','",
quote, "'")
@@ -663,6 +672,6 @@ monet.read.csv <- monetdb.read.csv <- fu
delimspec, "NULL as ", paste("'", na.strings[1], "'", sep=""),
if(locked) " LOCKED "))
}
}
- dbGetQuery(conn, paste("select count(*) from", tablename))
+ dbGetQuery(conn, paste("SELECT COUNT(*) FROM", tablename))[[1]]
}
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
@@ -11,14 +11,14 @@
\usage{
monetdb.read.csv (conn, files, tablename, nrows=NA, header=TRUE,
locked=FALSE, na.strings="", nrow.check=500, delim=",",
- newline = "\\\\n", quote = "\"", create=TRUE, lower.case.names=FALSE, ...)
+ newline = "\\\\n", quote = "\"", create=TRUE, col.names=NULL,
lower.case.names=FALSE, ...)
}
\arguments{
\item{conn}{A MonetDB.R database connection. Created using
\code{\link[DBI]{dbConnect}} with the
\code{\link[MonetDB.R]{MonetDB.R}} database driver.}
\item{files}{A single string or a vector of strings containing the absolute
file names of the CSV files to be imported.}
\item{tablename}{Name of the database table the CSV files should be
imported in. Created if necessary.}
- \item{nrows}{Total number of rows to import. Can be an upper bound.}
+ \item{nrows}{Total number of rows to import (deprecated).}
\item{header}{Whether or not the CSV files contain a header line.}
\item{locked}{Whether or not to disable transactions for import.
Setting this to TRUE can greatly improve the import performance.}
@@ -31,6 +31,7 @@
\item{quote}{Quote character(s) in CSV file.}
\item{create}{Create table before importing?}
\item{lower.case.names}{Convert all column names to lowercase in the
database?}
+ \item{col.names}{Optional column names in case the ones from CSV file should
not be used}
}
\value{
@@ -48,6 +49,6 @@ data(iris)
file <- tempfile()
write.table(iris, file, sep=",")
# create table and import CSV
-monetdb.read.csv(conn, file, "iris", 150)
+monetdb.read.csv(conn, file, "iris")
}}
\keyword{interface}
diff --git a/clients/R/Tests/dbi.stable.out b/clients/R/Tests/dbi.stable.out
--- a/clients/R/Tests/dbi.stable.out
+++ b/clients/R/Tests/dbi.stable.out
@@ -52,8 +52,7 @@ Ready.
[1] TRUE
[1] TRUE
[1] TRUE
- L1
-1 150
+[1] 150
[1] TRUE
[1] TRUE
[1] TRUE
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