Changeset: 7e77fb3c3551 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=7e77fb3c3551
Modified Files:
clients/R/MonetDB.R/NEWS
clients/R/MonetDB.R/R/control.R
clients/R/MonetDB.R/R/monetdb.R
Branch: default
Log Message:
R Connector: Some reorganization and IPv6 addressing support
diffs (truncated from 551 to 300 lines):
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
@@ -8,6 +8,7 @@ 0.9.2
schema name and quoting in the result (sys_tables, schema_names and quote)
- fixed various TODO's in the code to get closer to 1.0 (exciting)
- fixed a bug when the error identifier sent by MonetDB was non-numeric
+- IPv6 addresses in dbConnect() should now work (another long-standing TODO)
0.9.1
- dbGetInfo() now supported on MonetDBConnection (dplyr compatibility)
diff --git a/clients/R/MonetDB.R/R/control.R b/clients/R/MonetDB.R/R/control.R
--- a/clients/R/MonetDB.R/R/control.R
+++ b/clients/R/MonetDB.R/R/control.R
@@ -223,4 +223,47 @@ monetdb.server.setup <-
}
# return the filepath to the batch file
bfl
- }
\ No newline at end of file
+ }
+
+
+monetdbd.liststatus <- monetdb.liststatus <- function(passphrase,
host="localhost", port=50000L,
+ timeout=86400L) {
+
+ rawstr <- .monetdbd.command(passphrase, host, port, timeout)
+ lines <- strsplit(rawstr, "\n", fixed=T)[[1]] # split by newline, first line
is "=OK", so skip
+ lines <- lines[grepl("^=sabdb:2:", lines)] # make sure we get a db list
here, protocol v.2
+ lines <- sub("=sabdb:2:", "", lines, fixed=T)
+ # convert value into propert types etc
+ dbdf <- as.data.frame(do.call("rbind", strsplit(lines, ", ", fixed=T)),
stringsAsFactors=F)
+ names(dbdf) <- c("dbname", "uri", "locked", "state", "scenarios",
"startCounter", "stopCounter",
+ "crashCounter", "avgUptime", "maxUptime", "minUptime",
"lastCrash", "lastStart", "lastStop",
+ "crashAvg1", "crashAvg10", "crashAvg30")
+
+ dbdf$locked <- dbdf$locked=="1"
+
+ states <- c("illegal", "running", "crashed", "inactive", "starting")
+ dbdf$state <- factor(states[as.integer(dbdf$state)+1])
+
+ dbdf$startCounter <- as.numeric(dbdf$startCounter)
+ dbdf$stopCounter <- as.numeric(dbdf$stopCounter)
+ dbdf$crashCounter <- as.numeric(dbdf$crashCounter)
+
+ dbdf$avgUptime <- as.numeric(dbdf$avgUptime)
+ dbdf$maxUptime <- as.numeric(dbdf$maxUptime)
+ dbdf$minUptime <- as.numeric(dbdf$minUptime)
+
+ convertts <- function(col) {
+ col[col=="-1"] <- NA
+ return(as.POSIXct(as.numeric(col), origin="1970-01-01"))
+ }
+ dbdf$lastCrash <- convertts(dbdf$lastCrash)
+ dbdf$lastStart <- convertts(dbdf$lastStart)
+ dbdf$lastStop <- convertts(dbdf$lastStop)
+
+ dbdf$crashAvg1 <- dbdf$crashAvg1=="1"
+ dbdfcrashAvg10 <- as.numeric(dbdf$crashAvg10)
+ dbdf$crashAvg30 <- as.numeric(dbdf$crashAvg30)
+ dbdf$scenarios <- gsub("'", ", ", dbdf$scenarios, fixed=T)
+
+ return(dbdf[order(dbdf$dbname), ])
+}
\ No newline at end of file
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
@@ -29,7 +29,7 @@ setMethod("dbGetInfo", "MonetDBDriver",
# 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", ...) {
+ timeout=86400L, wait=FALSE, language="sql", ...) {
dbConnect(MonetDB.R(), dbname, user, password, host, port, timeout, wait,
language, ...)
}
@@ -42,8 +42,8 @@ mq <- function(dbname, query, ...) {
}
setMethod("dbConnect", "MonetDBDriver", def=function(drv, dbname="demo",
user="monetdb",
- password="monetdb", host="localhost", port=50000L, timeout=86400L,
wait=FALSE, language="sql",
- ..., url="") {
+ password="monetdb",
host="localhost", port=50000L, timeout=86400L, wait=FALSE, language="sql",
+ ..., url="") {
if (substring(url, 1, 10) == "monetdb://") {
dbname <- url
@@ -53,26 +53,43 @@ setMethod("dbConnect", "MonetDBDriver",
if (substring(dbname, 1, 10) == "monetdb://") {
message("MonetDB.R: Using 'monetdb://...' URIs in dbConnect() is
deprecated. Please switch to ",
- "dbname, host, port named arguments.")
+ "dbname, host, port named arguments.")
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]
- # TODO: handle IPv6 IPs, they contain : chars, later
- if (length(grep(":", hostport, fixed=TRUE)) == 1) {
+ # 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]
- } else {
- host <- hostport
+ }
+ 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
+ }
}
}
+ # 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.")
+ ,"port ", port, " to DB ",
dbname, " with user ", user, " and a non-printed password, timeout is "
+ , timeout, " seconds.")
socket <- FALSE
if (wait) {
repeat {
@@ -117,7 +134,7 @@ valueClass="MonetDBConnection")
### MonetDBConnection
setClass("MonetDBConnection", representation("DBIConnection",
socket="externalptr",
- connenv="environment", fetchSize="integer", Id="integer"))
+ connenv="environment",
fetchSize="integer", Id="integer"))
setMethod("dbGetInfo", "MonetDBConnection", def=function(dbObj, ...) {
envdata <- dbGetQuery(dbObj, "SELECT name, value from env()")
@@ -190,78 +207,78 @@ setMethod("dbReadTable", "MonetDBConnect
})
setMethod("dbGetQuery", signature(conn="MonetDBConnection",
statement="character"),
- def=function(conn, statement, ...) {
-
- res <- dbSendQuery(conn, statement, ...)
- data <- fetch(res, -1)
- dbClearResult(res)
- return(data)
-})
+ def=function(conn, statement, ...) {
+
+ res <- dbSendQuery(conn, statement, ...)
+ data <- fetch(res, -1)
+ dbClearResult(res)
+ return(data)
+ })
# This one does all the work in this class
setMethod("dbSendQuery", signature(conn="MonetDBConnection",
statement="character"),
- def=function(conn, statement, ..., list=NULL, async=FALSE) {
-
- if(!is.null(list) || length(list(...))){
- if (length(list(...))) statement <- .bindParameters(statement, list(...))
- if (!is.null(list)) statement <- .bindParameters(statement, list)
- }
- conn@connenv$exception <- list()
- env <- NULL
- if (getOption("monetdb.debug.query", F)) message("QQ: '", statement, "'")
- resp <- .mapiParseResponse(.mapiRequest(conn, paste0("s", statement, ";"),
async=async))
-
- env <- new.env(parent=emptyenv())
-
- if (resp$type == Q_TABLE) {
- # we have to pass this as an environment to make conn object available to
result for fetching
- env$success = TRUE
- env$conn <- conn
- env$data <- resp$tuples
- resp$tuples <- NULL # clean up
- env$info <- resp
- env$delivered <- 0
- env$query <- statement
- }
- if (resp$type == Q_UPDATE || resp$type == Q_CREATE || resp$type ==
MSG_ASYNC_REPLY) {
- env$success = TRUE
- env$conn <- conn
- env$query <- statement
- env$info <- resp
- }
- if (resp$type == MSG_MESSAGE) {
- env$success = FALSE
- env$conn <- conn
- env$query <- statement
- env$info <- resp
- env$message <- resp$message
- }
-
- if (!env$success) {
- sp <- strsplit(env$message, "!", fixed=T)[[1]]
- # truncate statement to not hide actual error message
- if (nchar(statement) > 100) { statement <- paste0(substring(statement, 1,
100), "...") }
- if (length(sp) == 3) {
- errno <- sp[[2]]
- errmsg <- sp[[3]]
- conn@connenv$exception <- list(errNum=errno, errMsg=errmsg)
- stop("Unable to execute statement '", statement, "'.\nServer says '",
errmsg, "' [#",
- errno, "].")
- }
- else {
- conn@connenv$exception <- list(errNum=NA, errMsg=env$message)
- stop("Unable to execute statement '", statement, "'.\nServer says '",
env$message, "'.")
- }
- }
-
- return(new("MonetDBResult", env=env))
-})
+ def=function(conn, statement, ..., list=NULL, async=FALSE) {
+
+ if(!is.null(list) || length(list(...))){
+ if (length(list(...))) statement <- .bindParameters(statement,
list(...))
+ if (!is.null(list)) statement <- .bindParameters(statement, list)
+ }
+ conn@connenv$exception <- list()
+ env <- NULL
+ if (getOption("monetdb.debug.query", F)) message("QQ: '",
statement, "'")
+ resp <- .mapiParseResponse(.mapiRequest(conn, paste0("s",
statement, ";"), async=async))
+
+ env <- new.env(parent=emptyenv())
+
+ if (resp$type == Q_TABLE) {
+ # we have to pass this as an environment to make conn object
available to result for fetching
+ env$success = TRUE
+ env$conn <- conn
+ env$data <- resp$tuples
+ resp$tuples <- NULL # clean up
+ env$info <- resp
+ env$delivered <- 0
+ env$query <- statement
+ }
+ if (resp$type == Q_UPDATE || resp$type == Q_CREATE || resp$type ==
MSG_ASYNC_REPLY) {
+ env$success = TRUE
+ env$conn <- conn
+ env$query <- statement
+ env$info <- resp
+ }
+ if (resp$type == MSG_MESSAGE) {
+ env$success = FALSE
+ env$conn <- conn
+ env$query <- statement
+ env$info <- resp
+ env$message <- resp$message
+ }
+
+ if (!env$success) {
+ sp <- strsplit(env$message, "!", fixed=T)[[1]]
+ # truncate statement to not hide actual error message
+ if (nchar(statement) > 100) { statement <-
paste0(substring(statement, 1, 100), "...") }
+ if (length(sp) == 3) {
+ errno <- sp[[2]]
+ errmsg <- sp[[3]]
+ conn@connenv$exception <- list(errNum=errno, errMsg=errmsg)
+ stop("Unable to execute statement '", statement, "'.\nServer
says '", errmsg, "' [#",
+ errno, "].")
+ }
+ else {
+ conn@connenv$exception <- list(errNum=NA, errMsg=env$message)
+ stop("Unable to execute statement '", statement, "'.\nServer
says '", env$message, "'.")
+ }
+ }
+
+ return(new("MonetDBResult", env=env))
+ })
# adapted from RMonetDB, very useful...
setMethod("dbWriteTable", "MonetDBConnection", def=function(conn, name, value,
overwrite=TRUE,
- ...) {
-
+ ...) {
+
if (is.vector(value) && !is.list(value)) value <- data.frame(x=value)
if (length(value)<1) stop("value must have at least one column")
if (is.null(names(value))) names(value) <- paste("V", 1:length(value),
sep='')
@@ -284,7 +301,7 @@ setMethod("dbWriteTable", "MonetDBConnec
if (length(value[[1]])) {
inss <- paste("INSERT INTO ", qname, " VALUES(", paste(rep("?",
length(value)), collapse=', '),
- ")", sep='')
+ ")", sep='')
.mapiRequest(conn, "Xauto_commit 0")
for (j in 1:length(value[[1]])) dbSendUpdate(conn, inss,
list=as.list(value[j, ]))
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