Changeset: 0360a448af4f for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=0360a448af4f
Modified Files:
clients/R/MonetDB.R/DESCRIPTION
clients/R/MonetDB.R/NAMESPACE
clients/R/MonetDB.R/NEWS
clients/R/MonetDB.R/R/dbi.R
clients/R/MonetDB.R/R/dplyr.R
clients/R/MonetDB.R/R/mapi.R
clients/R/Tests/dbi.R
clients/R/Tests/dbi.stable.out
clients/R/Tests/dplyr.R
clients/R/Tests/dplyr.stable.err
clients/R/Tests/dplyr.stable.out
Branch: Oct2014
Log Message:
R Connector: Bugfixes
Unterschiede (gekürzt von 1388 auf 300 Zeilen):
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
@@ -5,13 +5,9 @@ Authors@R: c(person("Hannes Muehleisen",
person("Thomas Lumley", role = "ctb"),
person("Anthony Damico", role = "ctb"))
Depends: DBI (>= 0.3), digest (>= 0.6.4), bitops (>= 1.0), methods
-Suggests: dplyr(>= 0.2.0.9000)
-Description: Allows to pull data from MonetDB into R
+Suggests: dplyr(>= 0.3)
+Description: Allows to pull data from MonetDB into R. Includes a DBI
implementation and a dplyr backend.
License: MPL (== 1.1)
URL: http://monetr.r-forge.r-project.org
Maintainer: Hannes Muehleisen <han...@cwi.nl>
-SystemRequirements: MonetDB installation, available at
- http://www.monetdb.org
-Author: Hannes Muehleisen [aut, cre],
- Thomas Lumley [ctb],
- Anthony Damico [ctb]
+SystemRequirements: MonetDB, available from http://www.monetdb.org
\ No newline at end of file
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
@@ -18,8 +18,8 @@ useDynLib(MonetDB.R)
# dplyr.R
export(src_monetdb)
-export(translate_env.src_monetdb)
-export(brief_desc.src_monetdb)
+export(src_translate_env.src_monetdb)
+export(src_desc.src_monetdb)
export(tbl.src_monetdb)
export(db_query_fields.MonetDBConnection)
export(db_query_rows.MonetDBConnection)
@@ -27,5 +27,6 @@ export(db_save_query.MonetDBConnection)
export(db_insert_into.MonetDBConnection)
export(db_create_index.MonetDBConnection)
export(db_analyze.MonetDBConnection)
-export(db_begin.MonetDBConnection)
export(sql_subquery.MonetDBConnection)
+export(sql_join.MonetDBConnection)
+export(monetdb_queryinfo)
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
@@ -1,12 +1,12 @@
0.9.5
-- Fixed package date (Thanks, Dimitar)
+- Removed package date (Thanks, Dimitar)
- Added sys. schema name to internal queries, so SET SCHEMA xx would not break
things (Thanks again, Dimitar)
- Fixed monetdb:// URL handling on newer R versions (Thanks, Alex)
- DBI 0.3 compatibility (isValid etc.)
- deprecated dbTransaction() (DBI has standardized dbBegin())
- Back to R socket code for peace of mind
- Code cleanup
-- dplyr integration moved to MonetDB.R
+- dplyr integration moved to MonetDB.R package
0.9.4
- dbWriteTable overhaul (thanks, Anthony)
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
@@ -24,11 +24,11 @@ setGeneric("dbIsValid",
valueClass = "logical")
setMethod("dbIsValid", "MonetDBDriver", def=function(dbObj, ...) {
- return(TRUE) # driver object cannot be invalid
+ return(invisible(TRUE)) # driver object cannot be invalid
})
setMethod("dbUnloadDriver", "MonetDBDriver", def=function(drv, ...) {
- return(TRUE) # there is nothing to really unload here...
+ return(invisible(TRUE)) # there is nothing to really unload here...
})
setMethod("dbGetInfo", "MonetDBDriver", def=function(dbObj, ...)
@@ -124,7 +124,7 @@ setMethod("dbConnect", "MonetDBDriver",
}
# make new socket with user-specified timeout
- socket <- .mapiConnect(host, port, 5)
+ socket <- .mapiConnect(host, port, timeout)
.mapiAuthenticate(socket, dbname, user, password, language=language)
connenv <- new.env(parent=emptyenv())
connenv$lock <- 0
@@ -156,7 +156,7 @@ setMethod("dbGetInfo", "MonetDBConnectio
})
setMethod("dbIsValid", "MonetDBConnection", def=function(dbObj, ...) {
- return(!is.na(tryCatch(dbGetInfo(dbObj), error=function(e){NA})))
+ return(invisible(!is.na(tryCatch({dbGetInfo(dbObj);TRUE},
error=function(e){NA}))))
})
setMethod("dbDisconnect", "MonetDBConnection", def=function(conn, ...) {
@@ -315,7 +315,7 @@ setMethod("dbWriteTable", "MonetDBConnec
if (overwrite && append) {
stop("Setting both overwrite and append to true makes no sense.")
}
- qname <- dbQuoteIdentifier(conn, name)
+ qname <- make.db.names(conn, name)
if (dbExistsTable(conn, qname)) {
if (overwrite) dbRemoveTable(conn, qname)
if (!overwrite && !append) stop("Table ", qname, " already exists. Set
overwrite=TRUE if you want
@@ -324,7 +324,7 @@ setMethod("dbWriteTable", "MonetDBConnec
}
if (!dbExistsTable(conn, qname)) {
fts <- sapply(value, dbDataType, dbObj=conn)
- fdef <- paste(dbQuoteIdentifier(conn, names(value)), fts, collapse=', ')
+ fdef <- paste(make.db.names(conn, names(value)), fts, collapse=', ')
ct <- paste("CREATE TABLE ", qname, " (", fdef, ")", sep= '')
dbSendUpdate(conn, ct)
}
@@ -580,21 +580,21 @@ setMethod("dbClearResult", "MonetDBResul
res@env$open <- FALSE
}
}
- invisible(TRUE)
+ return(invisible(TRUE))
}, valueClass = "logical")
setMethod("dbHasCompleted", "MonetDBResult", def = function(res, ...) {
if (res@env$info$type == Q_TABLE) {
return(res@env$delivered == res@env$info$rows)
}
- return(TRUE)
+ return(invisible(TRUE))
}, valueClass = "logical")
setMethod("dbIsValid", signature(dbObj="MonetDBResult"), def=function(dbObj,
...) {
if (dbObj@env$info$type == Q_TABLE) {
return(dbObj@env$open)
}
- return(TRUE)
+ return(invisible(TRUE))
})
monetTypes <- rep(c("numeric", "character", "character", "logical", "raw"),
c(9, 3, 4, 1, 1))
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
@@ -5,7 +5,7 @@ src_monetdb <- function(dbname, host = "
src_sql("monetdb", con, info = dbGetInfo(con))
}
-translate_env.src_monetdb <- function(x) {
+src_translate_env.src_monetdb <- function(x) {
sql_variant(
base_scalar,
sql_translator(.parent = base_agg,
@@ -17,19 +17,22 @@ translate_env.src_monetdb <- function(x)
)
}
-brief_desc.src_monetdb <- function(x) {
+sql_join.MonetDBConnection <- function(con, x, y, type = "inner", by = NULL,
...) {
+ NextMethod("sql_join",...)
+}
+
+src_desc.src_monetdb <- function(x) {
paste0("MonetDB ",x$info$monet_version, " (",x$info$monet_release, ") [",
x$info$merovingian_uri,"]")
}
tbl.src_monetdb <- function(src, from, ...) {
monetdb_check_subquery(from)
- tbl_sql("mownetdb", src = src, from = from, ...)
+ tbl_sql("monetdb", src = src, from = from, ...)
}
db_query_fields.MonetDBConnection <- function(con, sql, ...) {
- # prepare gives us column info without actually running a query
- # TODO: how about more complex queries?
- dbGetQuery(con,build_sql("PREPARE SELECT * FROM ", ident(sql)))$column
+ # prepare gives us column info without actually running a query. Nice.
+ dbGetQuery(con, build_sql("PREPARE SELECT * FROM ", sql))$column
}
db_query_rows.MonetDBConnection <- function(con, sql, ...) {
@@ -48,10 +51,6 @@ db_save_query.MonetDBConnection <- funct
name
}
-db_begin.MonetDBConnection <- function(con, ...) {
- dbBegin(con)
-}
-
db_create_index.MonetDBConnection <- function(con, table, columns, name = NULL,
...) {
TRUE
@@ -62,6 +61,7 @@ db_analyze.MonetDBConnection <- function
}
sql_subquery.MonetDBConnection <- function(con, sql, name = unique_name(),
...) {
+ print(str(sql))
if (is.ident(sql)) return(sql)
monetdb_check_subquery(sql)
build_sql("(", sql, ") AS ", ident(name), con = con)
@@ -87,4 +87,14 @@ monetdb_queryinfo <- function(conn, quer
.mapiRequest(conn, paste0("Xreply_size ", REPLY_SIZE))
})
info
-}
\ No newline at end of file
+}
+
+# copied from dplyr's utils.r, sql_subquery needs it
+unique_name <- local({
+ i <- 0
+
+ function() {
+ i <<- i + 1
+ paste0("_W", i)
+ }
+})
\ No newline at end of file
diff --git a/clients/R/MonetDB.R/R/mapi.R b/clients/R/MonetDB.R/R/mapi.R
--- a/clients/R/MonetDB.R/R/mapi.R
+++ b/clients/R/MonetDB.R/R/mapi.R
@@ -192,7 +192,9 @@ REPLY_SIZE <- 100 # Apparently, -1 me
.mapiParseResponse <- function(response) {
#lines <- .Call("mapiSplitLines", response, PACKAGE="MonetDB.R")
lines <- strsplit(response, "\n", fixed=TRUE, useBytes=TRUE)[[1]]
-
+ if (length(lines) < 1) {
+ stop("Invalid response from server. Try re-connecting.")
+ }
typeLine <- lines[[1]]
resKey <- substring(typeLine, 1, 1)
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
@@ -46,20 +46,21 @@ stopifnot(identical(dbExistsTable(con,tn
stopifnot(identical(dbExistsTable(con,"monetdbtest2"),FALSE))
stopifnot(tname %in% dbListTables(con))
-stopifnot(identical(dbListFields(con,tname),c("Sepal.Length","Sepal.Width","Petal.Length","Petal.Width","Species")))
+stopifnot(identical(dbListFields(con,tname),c("sepal_length","sepal_width",
+ "petal_length","petal_width","species")))
# get stuff, first very convenient
iris2 <- dbReadTable(con,tname)
stopifnot(identical(dim(iris),dim(iris2)))
# then manually
-res <- dbSendQuery(con,"SELECT \"Species\", \"Sepal.Width\" FROM monetdbtest")
+res <- dbSendQuery(con,"SELECT species, sepal_width FROM monetdbtest")
stopifnot(dbIsValid(res))
stopifnot(identical(class(res)[[1]],"MonetDBResult"))
stopifnot(identical(res@env$success,TRUE))
-stopifnot(dbColumnInfo(res)[[1,1]] == "Species")
-stopifnot(dbColumnInfo(res)[[2,1]] == "Sepal.Width")
+stopifnot(dbColumnInfo(res)[[1,1]] == "species")
+stopifnot(dbColumnInfo(res)[[2,1]] == "sepal_width")
stopifnot(dbGetInfo(res)$row.count == 150 && res@env$info$rows == 150)
@@ -90,7 +91,8 @@ unlink(file)
stopifnot(identical(dbExistsTable(con,tname),TRUE))
iris3 <- dbReadTable(con,tname)
stopifnot(identical(dim(iris),dim(iris3)))
-stopifnot(identical(dbListFields(con,tname),c("Sepal.Length","Sepal.Width","Petal.Length","Petal.Width","Species")))
+stopifnot(identical(dbListFields(con,tname),c("sepal_length","sepal_width",
+ "petal_length","petal_width","species")))
dbRemoveTable(con,tname)
stopifnot(identical(dbExistsTable(con,tname),FALSE))
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
@@ -64,6 +64,11 @@ 1 150
[1] FALSE
[1] TRUE
[1] TRUE
+[1] TRUE
+[1] TRUE
+[1] TRUE
+[1] TRUE
+[1] TRUE
[1] "SUCCESS"
# 14:24:04 >
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
@@ -9,21 +9,30 @@ dbname <- "mTests_clients_R"
if (length(args) > 0)
dbport <- args[[1]]
+if (exists("lahman_monetdb")) {
+ # overwrite all args because lahman_monetdb sets a default arg in the
first pos.
+ srct <- function() lahman_monetdb(host="localhost", dbname=dbname,
port=dbport ,
+
user="monetdb",password="monetdb",timeout=100,wait=T,language="sql")
+} else {
+ srct <- function() src_monetdb(dbname=dbname, port=dbport)
+ copy_lahman(srct())
+}
+
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