Changeset: 35651576c4c5 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=35651576c4c5
Added Files:
clients/R/monet.frame/DESCRIPTION
clients/R/monet.frame/NAMESPACE
clients/R/monet.frame/NEWS
clients/R/monet.frame/R/monetframe.R
clients/R/monet.frame/db.tests/monetframe.test.R
clients/R/monet.frame/man/aggregatef.Rd
clients/R/monet.frame/man/as.data.frame.Rd
clients/R/monet.frame/man/as.list.Rd
clients/R/monet.frame/man/mf.Rd
clients/R/monet.frame/man/monet.frame.Rd
clients/R/monet.frame/man/sample.Rd
clients/R/monet.frame/man/sd.Rd
clients/R/monet.frame/man/set.debug.Rd
clients/R/monet.frame/man/tabulate.Rd
clients/R/monet.frame/man/tabulate.monet.frame.Rd
clients/R/monet.frame/man/var.Rd
Removed Files:
clients/R/MonetDB.R/R/monetframe.R
clients/R/MonetDB.R/man/aggregatef.Rd
clients/R/MonetDB.R/man/as.data.frame.Rd
clients/R/MonetDB.R/man/as.list.Rd
clients/R/MonetDB.R/man/mf.Rd
clients/R/MonetDB.R/man/monet.frame.Rd
clients/R/MonetDB.R/man/sample.Rd
clients/R/MonetDB.R/man/sd.Rd
clients/R/MonetDB.R/man/set.debug.Rd
clients/R/MonetDB.R/man/tabulate.Rd
clients/R/MonetDB.R/man/tabulate.monet.frame.Rd
clients/R/MonetDB.R/man/var.Rd
Modified Files:
clients/R/MonetDB.R/DESCRIPTION
clients/R/MonetDB.R/NAMESPACE
clients/R/MonetDB.R/NEWS
clients/R/MonetDB.R/R/monetdb.R
clients/R/MonetDB.R/man/MonetDB.R.Rd
Branch: default
Log Message:
R Connector: Moved monet.frame virtual data object into its own R package
diffs (truncated from 3694 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: 0.8.0
-Date: 2013-10-13
+Version: 0.8.2
+Date: 2013-10-16
Title: Connect MonetDB to R
Authors@R: c(person("Hannes Muehleisen", role = c("aut", "cre"),email =
"han...@cwi.nl"),
person("Thomas Lumley", role = "ctb"),
person("Anthony Damico", role = "ctb"))
-Depends: DBI (>= 0.2-5), digest (>= 0.6.0), methods, utils, stats
+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/NAMESPACE b/clients/R/MonetDB.R/NAMESPACE
--- a/clients/R/MonetDB.R/NAMESPACE
+++ b/clients/R/MonetDB.R/NAMESPACE
@@ -1,4 +1,4 @@
-import(DBI,utils,stats,digest,methods)
+import(DBI,digest,methods)
# export only driver constructor, everything else is DBI stuff..
export(MonetDB,MonetR,MonetDBR,MonetDB.R)
@@ -8,78 +8,14 @@ exportMethods(dbSendUpdate,dbSendUpdateA
export(monetdbGetTransferredBytes)
export(monetdbRtype)
-# monet.frame things, this is an S3 class
-# constructors
-export(monet.frame)
-export(mf)
-export(set.debug)
-
# shorthand for db connections
export(mc)
-# conversion to native R
-S3method(as.list,monet.frame)
-S3method(as.data.frame,monet.frame)
-S3method(as.vector,monet.frame)
-export(av)
-export(adf)
-
-# inspection
-S3method(str,monet.frame)
-S3method(print,monet.frame)
-S3method(Summary,monet.frame)
-S3method(summary,monet.frame)
-S3method(names,monet.frame)
-S3method(dim,monet.frame)
-S3method(length,monet.frame)
-S3method(na.fail,monet.frame)
-
-# subsetting
-S3method(head,monet.frame)
-S3method(tail,monet.frame)
-S3method("[",monet.frame)
-S3method("$",monet.frame)
-S3method(subset,monet.frame)
-S3method(na.omit,monet.frame)
-S3method(sample, monet.frame)
-S3method(sample, default)
-export(sample)
-
-
-
-# math/stats
-S3method(Ops,monet.frame)
-S3method(Math,monet.frame)
-S3method(mean,monet.frame)
-S3method(sd, monet.frame)
-S3method(sd, default)
-export(sd)
-S3method(var, monet.frame)
-S3method(var, default)
-export(var)
-S3method(quantile,monet.frame)
-S3method(median,monet.frame)
-S3method(aggregate,monet.frame)
-export(aggregatef) # temp!
-
-export(tabulate)
-S3method(tabulate, monet.frame)
-S3method(tabulate, default)
-
-S3method(unique, monet.frame)
-S3method(range, monet.frame)
-
-# reorganization
-S3method(rbind,monet.frame)
-S3method(merge,monet.frame)
-S3method(sort,monet.frame)
-
# control.R
export(monetdb.server.setup)
export(monetdb.server.start)
export(monetdb.server.stop)
-
useDynLib(MonetDB.R)
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
@@ -1,3 +1,7 @@
+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)
- new dbConnect() parameter organization (!)
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
@@ -239,13 +239,13 @@ 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"
else if (is.raw(obj)) "BLOB"
- else "VARCHAR(255)"
+ else "STRING"
}, valueClass = "character")
diff --git a/clients/R/MonetDB.R/R/monetframe.R
b/clients/R/MonetDB.R/R/monetframe.R
deleted file mode 100644
--- a/clients/R/MonetDB.R/R/monetframe.R
+++ /dev/null
@@ -1,1218 +0,0 @@
-# this wraps a sql database (in particular MonetDB) with a DBI connector
-# to have it appear like a data.frame
-
-# shorthand constructor, also creates connection to db
-mf <-
function(database,table,host="localhost",port=50000,user="monetdb",pass="monetdb",debug=FALSE,timeout=100)
{
- dburl <- paste0("monetdb://",host,":",port,"/",database)
- con <- dbConnect(MonetDB.R(), dburl,user,pass,timeout=timeout)
- monet.frame(con,table,debug)
-}
-
-# can either be given a query or simply a table name
-# now supports hints on table structure to speed up initialization
-monet.frame <- monetframe <- function(conn,tableOrQuery,debug=FALSE)
monet.frame.internal(conn,tableOrQuery,debug)
-
-monet.frame.internal <-
function(conn,tableOrQuery,debug=FALSE,rtypes.hint=NA,cnames.hint=NA,ncol.hint=NA,nrow.hint=NA)
{
- if(missing(conn)) stop("'conn' must be specified")
- if(missing(tableOrQuery)) stop("a sql query or a table name must be
specified")
-
- obj = new.env()
- class(obj) = "monet.frame"
- attr(obj,"conn") <- conn
- query <- tableOrQuery
-
- if (length(grep("^SELECT.*",tableOrQuery,ignore.case=TRUE)) == 0) {
- query <- paste0("SELECT * FROM
",make.db.names(conn,tableOrQuery,allow.keywords=FALSE))
- }
-
- attr(obj,"query") <- query
- attr(obj,"debug") <- debug
-
- if (debug) cat(paste0("QQ: '",query,"'\n",sep=""))
- # do this here, in case the nrow thing needs it
- coltestquery <- gsub("SELECT (.*?) FROM (.*?)
(ORDER|LIMIT|OFFSET).*","SELECT \\1 FROM \\2",query,ignore.case=TRUE)
-
- if (!is.na(cnames.hint) && !is.na(ncol.hint) && !is.na(rtypes.hint)) {
- attr(obj,"cnames") <- cnames.hint
- attr(obj,"ncol") <- ncol.hint
- attr(obj,"rtypes") <- rtypes.hint
-
- } else {
- # strip away things the prepare does not like
- coltestquery <- gsub("SELECT (.*?) FROM (.*?)
(ORDER|LIMIT|OFFSET).*","SELECT \\1 FROM \\2",query,ignore.case=TRUE)
-
- # get column names and types from prepare response
- res <- dbGetQuery(conn, paste0("PREPARE ",coltestquery))
- attr(obj,"cnames") <- res$column
- attr(obj,"ncol") <- length(res$column)
- attr(obj,"rtypes") <- lapply(res$type,monetdbRtype)
-
- if (debug) cat(paste0("II: 'Re-Initializing column
info.'\n",sep=""))
-
- }
-
- if (!is.na(nrow.hint)) {
- attr(obj,"nrow") <- nrow.hint
- }
- else {
- # get result set length by rewriting to count(*), should be
much faster
- # temporarily remove offset/limit, as this screws up counting
- counttestquery <- sub("(SELECT )(.*?)(
FROM.*)","\\1COUNT(*)\\3",coltestquery,ignore.case=TRUE)
- nrow <- dbGetQuery(conn,counttestquery)[[1,1]] -
.getOffset(query)
-
- limit <- .getLimit(query)
- if (limit > 0) nrow <- min(nrow,limit)
- if (nrow < 1)
- warning(query, " has zero-row result set.")
-
- attr(obj,"nrow") <- nrow
- if (debug) cat(paste0("II: 'Re-Initializing row
count.'\n",sep=""))
-
- }
- return(obj)
-}
-
-set.debug <- function(x,debug){
- attr(x,"debug") <- debug
-}
-
-.is.debug <- function(x) {
- attr(x,"debug")
-}
-
-.element.limit <- 10000000
-
-as.data.frame.monet.frame <- adf <- function(x, row.names, optional,
warnSize=TRUE,...) {
- # check if amount of tuples/fields is larger than some limit
- # raise error if over limit and warnSize==TRUE
- if (ncol(x)*nrow(x) > .element.limit && warnSize)
- stop(paste0("The total number of elements to be loaded is
larger than ",.element.limit,". This is probably very slow. Consider dropping
columns and/or rows, e.g. using the [] function. If you really want to do this,
call as.data.frame() with the warnSize parameter set to FALSE."))
- # get result set object from frame
- if (.is.debug(x)) cat(paste0("EX: '",attr(x,"query"),"'\n",sep=""))
-
- return(dbGetQuery(attr(x,"conn"),attr(x,"query")))
-}
-
-as.vector.monet.frame <- av <- function(x,...) {
- if (ncol(x) != 1)
- stop("as.vector can only be used on one-column monet.frame
objects. Consider using $.")
- as.data.frame(x)[[1]]
-}
-
-# this is the fun part. this method has infinity ways of being invoked :(
-#
http://stat.ethz.ch/R-manual/R-patched/library/base/html/Extract.data.frame.html
-
-# TODO: handle negative indices and which() calls. which() like subset!
-# TODO: subset calls destroy nrows hint
-
-"[.monet.frame" <- function(x, k, j,drop=TRUE) {
- nquery <- query <- getQuery(x)
-
- cols <- NA
- rows <- NA
-
- nrow.hint <- nrow(x)
- ncol.hint <- ncol(x)
- cnames.hint <- NA
- rtypes.hint <- NA
-
- # biiig fun with nargs to differentiate d[1,] and d[1]
- # all in the presence of the optional drop argument, yuck!
- args <- nargs()
- if (!missing(drop)) {
- args <- args-1
- }
- if (args == 2 && missing(j)) cols <- k
- if (args == 3 && !missing(j)) cols <- j
- if (args == 3 && !missing(k)) rows <- k
-
- if (length(cols) > 1 || !is.na(cols)) { # get around an error if cols
is a vector...
- # if we have a numeric column spec, find the appropriate names
- if (is.numeric(cols)) {
- if (min(cols) < 1 || max(cols) > ncol(x))
- stop(paste0("Invalid column specification
'",cols,"'. Column indices have to be in range [1,",ncol(x),"].",sep=""))
- cols <- names(x)[cols]
- }
- if (!all(cols %in% names(x)))
- stop(paste0("Invalid column specification '",cols,"'.
Column names have to be in set {",paste(names(x),collapse=", "),"}.",sep=""))
-
- rtypes.hint <- rTypes(x)[match(cols,names(x)),drop=TRUE]
- ncol.hint <- length(cols)
- cnames.hint <- cols
-
- nquery <- sub("SELECT.+FROM",paste0("SELECT
",paste0(make.db.names(attr(x,"conn"),cols),collapse=", ")," FROM"),query)
- }
-
- if (length(rows) > 1 || !is.na(rows)) { # get around an error if cols
is a vector...
- if (min(rows) < 1 || max(rows) > nrow(x))
- stop("Invalid row specification. Row indices have to be
in range [1,",nrow(x),"].",sep="")
-
- if (.is.sequential(rows)) {
- # find out whether we already have limit and/or offset
set
- # our values are relative to them
-
- offset <- .getOffset(nquery) + min(rows)-1 # offset
means skip n rows, but r lower limit includes them
- limit <- max(rows)-min(rows)+1
-
- # remove old limit/offset from query
- # TODO: is this safe? UNION queries are particularly
dangerous, again...
- nquery <- gsub("limit[ ]+\\d+|offset[
]+\\d+","",nquery,ignore.case=TRUE)
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