Changeset: 36e98faec377 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=36e98faec377
Added Files:
clients/Tests/malcheck.sh
clients/Tests/malcheck.stable.err
clients/Tests/malcheck.stable.out
clients/Tests/malcheck.timeout
sql/test/BugTracker-2014/Tests/sign-sorted.Bug-3594.sql
sql/test/BugTracker-2014/Tests/sign-sorted.Bug-3594.stable.err
sql/test/BugTracker-2014/Tests/sign-sorted.Bug-3594.stable.out
testing/malcheck.py
Removed Files:
clients/R/MonetDB.R/man/monetdbGetTransferredBytes.Rd
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
clients/R/Tests/install-dependencies.sh
clients/R/Tests/install.sh
clients/R/Tests/survey.R
clients/Tests/All
clients/Tests/MAL-signatures_all.stable.out
clients/Tests/MAL-signatures_fits_geom.stable.out
clients/Tests/MAL-signatures_geom.stable.out
clients/Tests/MAL-signatures_none.stable.out
clients/Tests/exports.stable.out
gdk/gdk_calc.c
geom/monetdb5/geom.c
java/src/nl/cwi/monetdb/jdbc/MonetDatabaseMetaData.java
monetdb5/NT/M5server.bat
monetdb5/extras/rdf/rdf.h
monetdb5/extras/rdf/rdfalgebra.c
monetdb5/extras/sphinx/sphinx.c
monetdb5/extras/sphinx/sphinx.h
monetdb5/modules/atoms/batxml.c
monetdb5/modules/atoms/mtime.mal
monetdb5/modules/kernel/bat5.mal
monetdb5/modules/kernel/mmath.c
monetdb5/modules/kernel/mmath.h
monetdb5/modules/kernel/mmath.mal
monetdb5/modules/mal/Tests/inspect05.stable.out
monetdb5/modules/mal/mal_mapi.c
monetdb5/modules/mal/mal_mapi.h
sql/backends/monet5/datacell/opt_datacell.c
sql/backends/monet5/datacell/opt_datacell.h
sql/backends/monet5/sql_cast.h
sql/backends/monet5/sql_cast_impl_down_from_flt.h
sql/backends/monet5/sql_cast_impl_down_from_int.h
sql/backends/monet5/sql_cast_impl_up_to_flt.h
sql/backends/monet5/sql_cast_impl_up_to_int.h
sql/test/BugTracker-2014/Tests/All
testing/Makefile.ag
testing/Mtest.py.in
testing/exportutils.py
testing/listexports.py.in
tools/merovingian/daemon/forkmserver.c
tools/merovingian/utils/properties.c
tools/merovingian/utils/properties.h
tools/merovingian/utils/utils.c
tools/merovingian/utils/utils.h
Branch: default
Log Message:
Merge with Oct2014 branch.
diffs (truncated from 3598 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
@@ -4,14 +4,11 @@ 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 (>= 0.3), digest (>= 0.6.4), bitops (>= 1.0), methods
-Suggests: dplyr(>= 0.2.0.9000)
-Description: Allows to pull data from MonetDB into R
+Author: Hannes Muehleisen [aut, cre], Thomas Lumley [ctb], Anthony Damico [ctb]
+Maintainer: Hannes Muehleisen <han...@cwi.nl>
+Depends: DBI (>= 0.3.1), digest (>= 0.6.4), methods, R (>= 3.1.1)
+Suggests: dplyr
+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
@@ -1,10 +1,10 @@
-import(DBI,digest,methods,bitops)
+import(DBI,digest,methods)
# export only driver constructor, everything else is DBI stuff..
export(MonetDB,MonetR,MonetDBR,MonetDB.R)
export(monet.read.csv,monetdb.read.csv)
# this one is not in the DBI
-exportMethods(dbSendUpdate,dbSendUpdateAsync,dbTransaction,dbIsValid)
+exportMethods(dbSendUpdate,dbSendUpdateAsync,dbTransaction)
# shorthands
export(mc,mq)
@@ -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
@@ -18,17 +18,12 @@ MonetR <- MonetDB <- MonetDBR <- MonetDB
new("MonetDBDriver")
}
-# dbIsValid is missing from the DBI 0.3, so redefine
-setGeneric("dbIsValid",
- def = function(dbObj, ...) standardGeneric("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 +119,7 @@ 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$lock <- 0
@@ -156,7 +151,7 @@ setMethod("dbGetInfo", "MonetDBConnectio
})
setMethod("dbIsValid", "MonetDBConnection", def=function(dbObj, ...) {
- return(!is.na(tryCatch(dbGetInfo(dbObj), error=function(e){NA})))
+ return(invisible(!is.na(tryCatch({dbGetInfo(dbObj);TRUE},
error=function(e){NA}))))
})
setMethod("dbDisconnect", "MonetDBConnection", def=function(conn, ...) {
@@ -214,8 +209,9 @@ setMethod("dbListFields", "MonetDBConnec
})
setMethod("dbExistsTable", "MonetDBConnection", def=function(conn, name, ...) {
- #TODO: make this work with more cases
- tolower(name) %in% tolower(dbListTables(conn,sys_tables=T))
+ # TODO: this is evil...
+ return(tolower(gsub("(^\"|\"$)","",as.character(name))) %in%
+ tolower(dbListTables(conn,sys_tables=T)))
})
setMethod("dbGetException", "MonetDBConnection", def=function(conn, ...) {
@@ -225,7 +221,7 @@ setMethod("dbGetException", "MonetDBConn
setMethod("dbReadTable", "MonetDBConnection", def=function(conn, name, ...) {
if (!dbExistsTable(conn, name))
stop(paste0("Unknown table: ", name));
- dbGetQuery(conn, paste0("SELECT * FROM ", name))
+ dbGetQuery(conn,paste0("SELECT * FROM ", name))
})
# This one does all the work in this class
@@ -315,7 +311,7 @@ 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 +320,7 @@ 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 +576,21 @@ 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$open)
}
- return(TRUE)
+ return(invisible(TRUE))
})
monetTypes <- rep(c("numeric", "character", "character", "logical", "raw"),
c(9, 3, 4, 1, 1))
diff --git a/clients/R/MonetDB.R/R/dplyr.R b/clients/R/MonetDB.R/R/dplyr.R
--- a/clients/R/MonetDB.R/R/dplyr.R
+++ b/clients/R/MonetDB.R/R/dplyr.R
@@ -5,7 +5,7 @@ src_monetdb <- function(dbname, host = "
src_sql("monetdb", con, info = dbGetInfo(con))
}
-translate_env.src_monetdb <- function(x) {
+src_translate_env.src_monetdb <- function(x) {
sql_variant(
base_scalar,
sql_translator(.parent = base_agg,
@@ -17,20 +17,22 @@ translate_env.src_monetdb <- function(x)
)
}
-brief_desc.src_monetdb <- function(x) {
+sql_join.MonetDBConnection <- function(con, x, y, type = "inner", by = NULL,
...) {
+ NextMethod("sql_join",...)
+}
+
+src_desc.src_monetdb <- function(x) {
paste0("MonetDB ",x$info$monet_version, " (",x$info$monet_release, ") [",
x$info$merovingian_uri,"]")
}
tbl.src_monetdb <- function(src, from, ...) {
monetdb_check_subquery(from)
- tbl_sql("mownetdb", src = src, from = from, ...)
+ tbl_sql("monetdb", src = src, from = from, ...)
}
-# sql_create_index.src_monetdb
-
db_query_fields.MonetDBConnection <- function(con, sql, ...) {
- # prepare gives us column info without actually running a query
- dbGetQuery(con,build_sql("PREPARE SELECT * FROM ", ident(sql)))$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, ...) {
@@ -38,7 +40,8 @@ db_query_rows.MonetDBConnection <- funct
}
db_insert_into.MonetDBConnection <- function(con, table, values, ...) {
- dbWriteTable(con,table,values,append=T,transaction=F,csvdump=T)
+ dbWriteTable(con,dbQuoteIdentifier(con,table),values,
+ append=T,transaction=F,csvdump=T)
}
db_save_query.MonetDBConnection <- function(con, sql, name, temporary = TRUE,
@@ -49,10 +52,6 @@ db_save_query.MonetDBConnection <- funct
name
}
-db_begin.MonetDBConnection <- function(con, ...) {
- dbBegin(con)
-}
-
db_create_index.MonetDBConnection <- function(con, table, columns, name = NULL,
...) {
TRUE
@@ -62,9 +61,6 @@ db_analyze.MonetDBConnection <- function
TRUE
}
-# this should be the default in dplyr anyways...
-db_begin.MonetDBConnection <- function(con, ...) dbBegin(con)
-
sql_subquery.MonetDBConnection <- function(con, sql, name = unique_name(),
...) {
if (is.ident(sql)) return(sql)
monetdb_check_subquery(sql)
@@ -91,4 +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
@@ -134,8 +134,8 @@ REPLY_SIZE <- 100 # Apparently, -1 me
stop("Empty response from MonetDB server, probably a timeout. You can
increase the time to wait for responses with the 'timeout' parameter to
'dbConnect()'.")
}
- length <- bitShiftR(unpacked,1)
- final <- bitAnd(unpacked,1)
+ length <- bitwShiftR(unpacked,1)
+ final <- bitwAnd(unpacked,1)
if (length == 0) break
resp <- c(resp,readChar(con, length, useBytes = TRUE))
@@ -167,7 +167,7 @@ REPLY_SIZE <- 100 # Apparently, -1 me
bytes <- nchar(req)
pos <- pos + bytes
final <- max(nchar(msg) - pos,0) == 0
- header <- as.integer(bitOr(bitShiftL(bytes,1),as.numeric(final)))
+ header <- as.integer(bitwOr(bitwShiftL(bytes,1),as.numeric(final)))
writeBin(header, con, 2,endian="little")
writeChar(req,con,bytes,useBytes=TRUE,eos=NULL)
}
@@ -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]]
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