Changeset: 290e78554f01 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=290e78554f01
Added Files:
clients/R/MonetDB.R/R/dbi.R
clients/R/MonetDB.R/R/dplyr.R
clients/R/MonetDB.R/R/mapi.R
Removed Files:
clients/R/MonetDB.R/R/monetdb.R
Modified Files:
clients/R/MonetDB.R/DESCRIPTION
clients/R/MonetDB.R/NAMESPACE
clients/R/MonetDB.R/NEWS
clients/R/Tests/dplyr.R
configure.ag
gdk/gdk_calc_compare.h
gdk/gdk_join.c
sql/backends/monet5/sql_round_impl.h
sql/server/rel_dump.c
sql/server/rel_optimizer.c
sql/server/rel_schema.c
sql/server/rel_select.c
sql/server/sql_decimal.c
sql/server/sql_decimal.h
sql/server/sql_parser.y
sql/server/sql_scan.c
sql/storage/bat/bat_storage.c
sql/test/BugTracker-2010/Tests/ORDER_BY_over_UNION_EXCEPT_INTERSECT.Bug-2606.stable.out
sql/test/Tests/identifiers.stable.err
sql/test/Tests/identifiers.stable.out
sql/test/bugs/Tests/alter_add_column-bug.stable.err
Branch: transaction-replication
Log Message:
Merge with default branch
diffs (truncated from 2936 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
@@ -5,6 +5,7 @@ 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
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
@@ -4,16 +4,9 @@ import(DBI,digest,methods,bitops)
export(MonetDB,MonetR,MonetDBR,MonetDB.R)
export(monet.read.csv,monetdb.read.csv)
# this one is not in the DBI
-exportMethods(dbSendUpdate,dbSendUpdateAsync,dbTransaction)
-export(monetdbGetTransferredBytes)
-export(monetdbRtype)
-export(monetdb_queryinfo)
-
-# shorthand for db connections
-export(mc)
-
-# shorthand for db queries
-export(mq)
+exportMethods(dbSendUpdate,dbSendUpdateAsync,dbTransaction,dbIsValid)
+# shorthands
+export(mc,mq)
# control.R
export(monetdb.server.setup)
@@ -22,3 +15,17 @@ export(monetdb.server.stop)
export(monetdbd.liststatus)
export(monetdb.liststatus)
useDynLib(MonetDB.R)
+
+# dplyr.R
+export(src_monetdb)
+export(translate_env.src_monetdb)
+export(brief_desc.src_monetdb)
+export(tbl.src_monetdb)
+export(db_query_fields.MonetDBConnection)
+export(db_query_rows.MonetDBConnection)
+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)
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
@@ -5,6 +5,8 @@ 0.9.5
- 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
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
new file mode 100644
--- /dev/null
+++ b/clients/R/MonetDB.R/R/dbi.R
@@ -0,0 +1,657 @@
+C_LIBRARY <- "MonetDB.R"
+
+.onLoad <- function(lib, pkg) {
+ if (getOption("monetdb.clib", FALSE)) {
+ library.dynam( C_LIBRARY, pkg, lib )
+ .Call("mapiInit", PACKAGE=C_LIBRARY)
+ }
+}
+
+# Make S4 aware of S3 classes
+setOldClass(c("sockconn", "connection", "monetdb_mapi_conn"))
+
+### MonetDBDriver
+setClass("MonetDBDriver", representation("DBIDriver"))
+
+# allow instantiation of this driver with MonetDB to allow existing programs
to work
+MonetR <- MonetDB <- MonetDBR <- MonetDB.R <- function() {
+ 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
+})
+
+setMethod("dbUnloadDriver", "MonetDBDriver", def=function(drv, ...) {
+ return(TRUE) # there is nothing to really unload here...
+})
+
+setMethod("dbGetInfo", "MonetDBDriver", def=function(dbObj, ...)
+ list(name="MonetDBDriver",
+ driver.version=packageVersion("MonetDB.R"),
+ DBI.version=packageVersion("DBI"),
+ client.version="NA",
+ max.connections=125) # R can only handle 128 connections, three of
which are pre-allocated
+)
+
+# shorthand for connecting to the DB, very handy, e.g. dbListTables(mc("acs"))
+mc <- function(dbname="demo", user="monetdb", password="monetdb",
host="localhost", port=50000L,
+ timeout=86400L, wait=FALSE, language="sql", ...) {
+
+ dbConnect(MonetDB.R(), dbname, user, password, host, port, timeout, wait,
language, ...)
+}
+
+mq <- function(dbname, query, ...) {
+ conn <- mc(dbname, ...)
+ res <- dbGetQuery(conn, query)
+ dbDisconnect(conn)
+ return(res)
+}
+
+setMethod("dbConnect", "MonetDBDriver", def=function(drv, dbname="demo",
user="monetdb",
+ password="monetdb",
host="localhost", port=50000L, timeout=86400L, wait=FALSE, language="sql",
+ ..., url="") {
+
+ if (substring(url, 1, 10) == "monetdb://") {
+ dbname <- url
+ }
+ timeout <- as.integer(timeout)
+
+ if (substring(dbname, 1, 10) == "monetdb://") {
+ rest <- substring(dbname, 11, nchar(dbname))
+ # split at /, so we get the dbname
+ slashsplit <- strsplit(rest, "/", fixed=TRUE)
+ hostport <- slashsplit[[1]][1]
+ dbname <- slashsplit[[1]][2]
+
+ # count the number of : in the string
+ ndc <- nchar(hostport) - nchar(gsub(":","",hostport,fixed=T))
+ if (ndc == 0) {
+ host <- hostport
+ }
+ if (ndc == 1) { # ipv4 case, any ipv6 address has more than one :
+ hostportsplit <- strsplit(hostport, ":", fixed=TRUE)
+ host <- hostportsplit[[1]][1]
+ port <- hostportsplit[[1]][2]
+ }
+ if (ndc > 1) { # ipv6 case, now we only need to check for ]:
+ if (length(grep("]:", hostport, fixed=TRUE)) == 1) { # ipv6 with port
number
+ hostportsplit <- strsplit(hostport, "]:", fixed=TRUE)
+ host <- substring(hostportsplit[[1]][1],2)
+ port <- hostportsplit[[1]][2]
+ }
+ else {
+ host <- hostport
+ }
+ }
+ }
+ # this is important, otherwise we'll trip an assertion
+ port <- as.integer(port)
+
+ # validate port number
+ if (length(port) != 1 || port < 1 || port > 65535) {
+ stop("Illegal port number ",port)
+ }
+
+ if (getOption("monetdb.debug.mapi", F)) message("II: Connecting to MonetDB
on host ", host, " at "
+ ,"port ", port, " to DB ",
dbname, " with user ", user, " and a non-printed password, timeout is "
+ , timeout, " seconds.")
+ socket <- FALSE
+ if (wait) {
+ repeat {
+ continue <- FALSE
+ tryCatch ({
+ # open socket with 5-sec timeout so we can check whether everything
works
+ socket <- socket <<- .mapiConnect(host, port, 5)
+ # authenticate
+ .mapiAuthenticate(socket, dbname, user, password, language=language)
+ .mapiDisconnect(socket)
+ break
+ }, error = function(e) {
+ if ("connection" %in% class(socket)) {
+ close(socket)
+ }
+ message("Server not ready(", e$message, "), retrying (ESC or CTRL+C to
abort)")
+ Sys.sleep(1)
+ continue <<- TRUE
+ })
+ }
+ }
+
+ # make new socket with user-specified timeout
+ socket <- .mapiConnect(host, port, 5)
+ .mapiAuthenticate(socket, dbname, user, password, language=language)
+ connenv <- new.env(parent=emptyenv())
+ connenv$lock <- 0
+ connenv$deferred <- list()
+ connenv$exception <- list()
+
+ conn <- new("MonetDBConnection", socket=socket, connenv=connenv, Id=-1L)
+ if (getOption("monetdb.sequential", F)) {
+ message("MonetDB: Switching to single-threaded query execution.")
+ dbSendQuery(conn, "set optimizer='sequential_pipe'")
+ }
+
+ return(conn)
+
+},
+valueClass="MonetDBConnection")
+
+
+### MonetDBConnection
+setClass("MonetDBConnection", representation("DBIConnection", socket="ANY",
+ connenv="environment",
fetchSize="integer", Id="integer"))
+
+setMethod("dbGetInfo", "MonetDBConnection", def=function(dbObj, ...) {
+ envdata <- dbGetQuery(dbObj, "SELECT name, value from sys.env()")
+ ll <- as.list(envdata$value)
+ names(ll) <- envdata$name
+ ll$name <- "MonetDBConnection"
+ return(ll)
+})
+
+setMethod("dbIsValid", "MonetDBConnection", def=function(dbObj, ...) {
+ return(!is.na(tryCatch(dbGetInfo(dbObj), error=function(e){NA})))
+})
+
+setMethod("dbDisconnect", "MonetDBConnection", def=function(conn, ...) {
+ .mapiDisconnect(conn@socket)
+ return(invisible(TRUE))
+})
+
+setMethod("dbListTables", "MonetDBConnection", def=function(conn, ...,
sys_tables=F, schema_names=F, quote=F) {
+ q <- "select schemas.name as sn, tables.name as tn from sys.tables join
sys.schemas on tables.schema_id=schemas.id"
+ if (!sys_tables) q <- paste0(q, " where tables.system=false")
+ df <- dbGetQuery(conn, q)
+ if (quote) {
+ df$tn <- paste0("\"", df$tn, "\"")
+ }
+ res <- df$tn
+ if (schema_names) {
+ if (quote) {
+ df$sn <- paste0("\"", df$sn, "\"")
+ }
+ res <- paste0(df$sn, ".", df$tn)
+ }
+ return(as.character(res))
+})
+
+if (is.null(getGeneric("dbTransaction"))) setGeneric("dbTransaction",
function(conn, ...)
+ standardGeneric("dbTransaction"))
+
+setMethod("dbTransaction", signature(conn="MonetDBConnection"),
def=function(conn, ...) {
+ dbBegin(conn)
+ warning("dbTransaction() is deprecated, use dbBegin() from now.")
+ invisible(TRUE)
+})
+
+setMethod("dbBegin", "MonetDBConnection", def=function(conn, ...) {
+ dbSendQuery(conn, "START TRANSACTION")
+ invisible(TRUE)
+})
+
+setMethod("dbCommit", "MonetDBConnection", def=function(conn, ...) {
+ dbSendQuery(conn, "COMMIT")
+ invisible(TRUE)
+})
+
+setMethod("dbRollback", "MonetDBConnection", def=function(conn, ...) {
+ dbSendQuery(conn, "ROLLBACK")
+ invisible(TRUE)
+})
+
+setMethod("dbListFields", "MonetDBConnection", def=function(conn, name, ...) {
+ if (!dbExistsTable(conn, name))
+ stop(paste0("Unknown table: ", name));
+ df <- dbGetQuery(conn, paste0("select columns.name as name from sys.columns
join sys.tables on \
+ columns.table_id=tables.id where tables.name='", name, "';"))
+ df$name
+})
+
+setMethod("dbExistsTable", "MonetDBConnection", def=function(conn, name, ...) {
+ #TODO: make this work with more cases
+ tolower(name) %in% tolower(dbListTables(conn,sys_tables=T))
+})
+
+setMethod("dbGetException", "MonetDBConnection", def=function(conn, ...) {
+ conn@connenv$exception
+})
+
+setMethod("dbReadTable", "MonetDBConnection", def=function(conn, name, ...) {
+ if (!dbExistsTable(conn, name))
+ stop(paste0("Unknown table: ", name));
+ dbGetQuery(conn, paste0("SELECT * FROM ", name))
+})
+
+# This one does all the work in this class
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