Changeset: ab762b4058c7 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=ab762b4058c7
Modified Files:
clients/R/MonetDB.R/DESCRIPTION
clients/R/MonetDB.R/NEWS
clients/R/MonetDB.R/R/dbi.R
clients/R/MonetDB.R/R/dplyr.R
clients/R/Tests/dbapply.R
clients/R/Tests/dbi.R
clients/R/Tests/dbi.stable.err
clients/R/Tests/dplyr.R
Branch: embedded
Log Message:
no longer importing dbi
diffs (264 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
@@ -6,8 +6,7 @@ Authors@R: c(person("Hannes Muehleisen",
person("Thomas Lumley", role = "ctb"))
Author: Hannes Muehleisen [aut, cre], Anthony Damico [aut], Thomas Lumley [ctb]
Maintainer: Hannes Muehleisen <[email protected]>
-Depends: DBI (>= 0.3.1)
-Imports: digest (>= 0.6.4), methods, codetools
+Imports: DBI (>= 0.3.1), digest (>= 0.6.4), methods, codetools
Enhances: dplyr (>= 0.3.0), MonetDBLite
Description: Allows to pull data from MonetDB into R. Includes a DBI
implementation and a dplyr backend.
License: MPL (== 2.0)
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
@@ -1,7 +1,7 @@
1.0.1
- added isIdCurrent for improved compatibility with RSQLite
- new option monetdb.log.query allows export of dbSendQuery statements to file
-
+- no longer depends on DBI but imports it
1.0.0
- Added support for esoteric data types such as MONTH_INTERVAL (Thanks, Roman)
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
@@ -21,7 +21,7 @@ setMethod("dbGetInfo", "MonetDBDriver",
list(name="MonetDBDriver",
driver.version=utils::packageVersion("MonetDB.R"),
DBI.version=utils::packageVersion("DBI"),
- client.version="NA",
+ client.version=NA,
max.connections=125) # R can only handle 128 connections, three of
which are pre-allocated
)
diff --git a/clients/R/MonetDB.R/R/dplyr.R b/clients/R/MonetDB.R/R/dplyr.R
--- a/clients/R/MonetDB.R/R/dplyr.R
+++ b/clients/R/MonetDB.R/R/dplyr.R
@@ -1,11 +1,10 @@
src_monetdb <- function(dbname="demo", host = "localhost", port = 50000L, user
= "monetdb",
password = "monetdb", con = FALSE, ...) {
- if (!inherits(con, "MonetDBConnection") || !dbIsValid(con)) {
- con <- dbConnect(MonetDB.R(), dbname = dbname , host = host, port = port,
+ if (!inherits(con, "MonetDBConnection") || !DBI::dbIsValid(con)) {
+ con <- DBI::dbConnect(MonetDB.R(), dbname = dbname , host = host, port =
port,
user = user, password = password, ...)
}
- requireNamespace("dplyr")
- dplyr::src_sql("monetdb", con, info = dbGetInfo(con))
+ dplyr::src_sql("monetdb", con, info = DBI::dbGetInfo(con))
}
src_translate_env.src_monetdb <- function(x) {
@@ -38,7 +37,7 @@ sample_n.tbl_monetdb <- function(x, size
stop("Sorry, replace and weight are not supported for MonetDB tables. \
Consider collect()'ing first.")
}
- dbGetQuery(x$src$con, dplyr::build_sql(x$query$sql, " SAMPLE ",
as.integer(size)))
+ DBI::dbGetQuery(x$src$con, dplyr::build_sql(x$query$sql, " SAMPLE ",
as.integer(size)))
}
sample_frac.tbl_monetdb <- function(tbl, frac=1, replace = FALSE, weight =
NULL) {
@@ -54,11 +53,11 @@ sample_frac.tbl_monetdb <- function(tbl,
db_query_fields.MonetDBConnection <- function(con, sql, ...) {
# prepare gives us column info without actually running a query. Nice.
- dbGetQuery(con, dplyr::build_sql("PREPARE SELECT * FROM ", sql))$column
+ DBI::dbGetQuery(con, dplyr::build_sql("PREPARE SELECT * FROM ", sql))$column
}
db_query_fields.MonetDBEmbeddedConnection <- function(con, sql, ...) {
- names(dbGetQuery(con, dplyr::build_sql("SELECT * FROM ", sql), notreally=T))
+ names(DBI::dbGetQuery(con, dplyr::build_sql("SELECT * FROM ", sql),
notreally=T))
}
db_query_rows.MonetDBConnection <- function(con, sql, ...) {
@@ -70,15 +69,15 @@ db_query_rows.MonetDBEmbeddedConnection
}
db_insert_into.MonetDBConnection <- function(con, table, values, ...) {
- dbWriteTable(con,dbQuoteIdentifier(con,table),values,
- append=T,transaction=F,csvdump=T)
+ DBI::dbWriteTable(con, DBI::dbQuoteIdentifier(con, table), values,
+ append=T, transaction=F, csvdump=T)
}
db_save_query.MonetDBConnection <- function(con, sql, name, temporary = TRUE,
...) {
tt_sql <- dplyr::build_sql("CREATE TEMPORARY TABLE ", dplyr::ident(name), "
AS ",
sql, " WITH DATA ON COMMIT PRESERVE ROWS", con = con)
- dbGetQuery(con, tt_sql)
+ DBI::dbGetQuery(con, tt_sql)
name
}
diff --git a/clients/R/Tests/dbapply.R b/clients/R/Tests/dbapply.R
--- a/clients/R/Tests/dbapply.R
+++ b/clients/R/Tests/dbapply.R
@@ -2,7 +2,7 @@ ll <- NULL
if (Sys.getenv("TSTTRGDIR") != "") {
ll <- paste0(Sys.getenv("TSTTRGDIR"),"/rlibdir")
}
-library(MonetDB.R,quietly=T,lib.loc=ll)
+library(DBI, quietly = T)
args <- commandArgs(trailingOnly = TRUE)
dbport <- 50000
@@ -17,7 +17,7 @@ options(monetdb.profile=F)
tname <- "monetdbtest"
-con <- dbConnect(MonetDB(), port=dbport, dbname=dbname, wait=T)
+con <- dbConnect(MonetDB.R::MonetDB(), port=dbport, dbname=dbname, wait=T)
stopifnot(dbIsValid(con))
#options(monetdb.debug.query=T)
@@ -55,7 +55,7 @@ print(length(predictions))
# make sure we bubble up the error
haderror <- FALSE
tryCatch({
- res <- mdbapply(con,tname,function(d) {
+ res <- MonetDB.R::mdbapply(con,tname,function(d) {
stop("i am an error")
})
}, error=function(e) {
diff --git a/clients/R/Tests/dbi.R b/clients/R/Tests/dbi.R
--- a/clients/R/Tests/dbi.R
+++ b/clients/R/Tests/dbi.R
@@ -2,7 +2,7 @@ ll <- NULL
if (Sys.getenv("TSTTRGDIR") != "") {
ll <- paste0(Sys.getenv("TSTTRGDIR"),"/rlibdir")
}
-library(MonetDB.R,quietly=T,lib.loc=ll)
+library(DBI)
args <- commandArgs(trailingOnly = TRUE)
dbport <- 50000
@@ -18,8 +18,8 @@ options(monetdb.profile=F)
tname <- "monetdbtest"
-drv <- dbDriver("MonetDB")
-stopifnot(identical(dbGetInfo(drv)$name,"MonetDBDriver"))
+drv <- MonetDB.R::MonetDB()
+stopifnot(identical(dbGetInfo(drv)$name, "MonetDBDriver"))
con <- conn <- dbConnect(drv, port=dbport, dbname=dbname, wait=T)
stopifnot(identical(class(con)[[1]],"MonetDBConnection"))
@@ -37,10 +37,10 @@ stopifnot(identical(dbExistsTable(con,tn
# test raw handling
-dbSendUpdate(con,"CREATE TABLE monetdbtest (a varchar(10),b integer,c blob)")
+MonetDB.R::dbSendUpdate(con,"CREATE TABLE monetdbtest (a varchar(10),b
integer,c blob)")
stopifnot(identical(dbExistsTable(con,tname),TRUE))
-dbSendUpdate(con,"INSERT INTO monetdbtest VALUES ('one',1,'1111')")
-dbSendUpdate(con,"INSERT INTO monetdbtest VALUES ('two',2,'22222222')")
+MonetDB.R::dbSendUpdate(con,"INSERT INTO monetdbtest VALUES ('one',1,'1111')")
+MonetDB.R::dbSendUpdate(con,"INSERT INTO monetdbtest VALUES
('two',2,'22222222')")
stopifnot(identical(dbGetQuery(con,"SELECT count(*) FROM
monetdbtest")[[1]],2L))
stopifnot(identical(dbReadTable(con,tname)[[3]],list(charToRaw("1111"),charToRaw("22222222"))))
dbRemoveTable(con,tname)
@@ -62,7 +62,7 @@ stopifnot(identical(dim(iris),dim(iris2)
# then manually
res <- dbSendQuery(con,"SELECT \"Species\", \"Sepal.Width\" FROM monetdbtest")
stopifnot(dbIsValid(res))
-stopifnot(isIdCurrent(res))
+stopifnot(MonetDB.R::isIdCurrent(res))
stopifnot(identical(class(res)[[1]],"MonetDBResult"))
stopifnot(identical(res@env$success,TRUE))
@@ -95,8 +95,8 @@ tf <- tempfile()
write.table(iris,tf,sep=",",row.names=FALSE)
tname2 <- "Need to quote this table name"
tname3 <- "othermethod"
-monetdb.read.csv(con,tf,tname)
-monetdb.read.csv(con,tf,tname2)
+MonetDB.R::monetdb.read.csv(con,tf,tname)
+MonetDB.R::monetdb.read.csv(con,tf,tname2)
dbWriteTable(con, tname3, tf)
###
@@ -161,7 +161,7 @@ dbWriteTable(conn,tname,mtcars,append=F,
dbRemoveTable(conn,tname)
# info
-stopifnot(identical("MonetDBDriver", dbGetInfo(MonetDB.R())$name))
+stopifnot(identical("MonetDBDriver", dbGetInfo(MonetDB.R::MonetDB.R())$name))
stopifnot(identical("MonetDBConnection", dbGetInfo(conn)$name))
# transactions...
@@ -186,7 +186,7 @@ sq <- dbSendQuery(conn,"CREATE TABLE mon
sq <- dbSendQuery(conn,"INSERT INTO monetdbtest VALUES ('Роман
Mühleisen')")
stopifnot(identical("Роман Mühleisen", dbGetQuery(conn,"SELECT a FROM
monetdbtest")$a[[1]]))
sq <- dbSendQuery(conn,"DELETE FROM monetdbtest")
-dbSendUpdate(conn, "INSERT INTO monetdbtest (a) VALUES (?)", "Роман
Mühleisen")
+MonetDB.R::dbSendUpdate(conn, "INSERT INTO monetdbtest (a) VALUES (?)", "Ð
оман Mühleisen")
stopifnot(identical("Роман Mühleisen", dbGetQuery(conn,"SELECT a FROM
monetdbtest")$a[[1]]))
dbRollback(conn)
diff --git a/clients/R/Tests/dbi.stable.err b/clients/R/Tests/dbi.stable.err
--- a/clients/R/Tests/dbi.stable.err
+++ b/clients/R/Tests/dbi.stable.err
@@ -32,7 +32,7 @@ stderr of test 'dbi` in directory 'clien
Identifier(s) "Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width",
"Species" contain uppercase or reserved SQL characters and need(s) to be quoted
in queries.
Warning message:
-'isIdCurrent' is deprecated.
+'MonetDB.R::isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Identifier(s) "Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width",
"Species" contain uppercase or reserved SQL characters and need(s) to be quoted
in queries.
diff --git a/clients/R/Tests/dplyr.R b/clients/R/Tests/dplyr.R
--- a/clients/R/Tests/dplyr.R
+++ b/clients/R/Tests/dplyr.R
@@ -8,11 +8,8 @@ ff <- textConnection("asdf", open="w")
# so if things go south it might be a good idea to uncomment the cat(dd) below
dd <- capture.output( suppressMessages ( {
-library(MonetDB.R,quietly=T,lib.loc=ll)
-library(dplyr,quietly=T)
-library(Lahman,quietly=T)
-
-options(monetdb.profile=F)
+library(dplyr, quietly = T)
+library(Lahman, quietly = T)
args <- commandArgs(trailingOnly = TRUE)
dbport <- 50000
@@ -23,20 +20,11 @@ if (length(args) > 1)
dbname <- args[[2]]
-# old way
-if (exists("lahman_monetdb")) {
- # overwrite all args because lahman_monetdb sets a default arg in the
first pos.
- dps <- lahman_monetdb(host="localhost", dbname=dbname, port=dbport ,
-
user="monetdb",password="monetdb",timeout=100,wait=T,language="sql")
-# new way
-} else {
- dps <- src_monetdb(dbname=dbname, port=dbport)
- copy_lahman(dps)
-}
+dps <- MonetDB.R::src_monetdb(dbname=dbname, port=dbport)
+copy_lahman(dps)
+
}))
-#cat(dd)
-
# the remainder is pretty much the example from the manpage.
# Methods -------------------------------------------------------------------
@@ -140,7 +128,7 @@ print(nrow(aa))
-dbRemoveTable(dps$con, "mtcars")
+DBI::dbRemoveTable(dps$con, "mtcars")
print("SUCCESS")
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