Changeset: 1e7af0c1cb4c for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=1e7af0c1cb4c
Added Files:
monetdb5/modules/mal/Tests/pqueue3.mal
sql/benchmarks/tpch/drop.sql
sql/test/BugTracker-2014/Tests/integer-cast.Bug-3424.sql
sql/test/BugTracker-2014/Tests/integer-cast.Bug-3424.stable.err
sql/test/BugTracker-2014/Tests/integer-cast.Bug-3424.stable.out
sql/test/BugTracker-2014/Tests/python-microseconds.Bug-3439.SQL.py
sql/test/BugTracker-2014/Tests/python-microseconds.Bug-3439.stable.err
sql/test/BugTracker-2014/Tests/python-microseconds.Bug-3439.stable.out
sql/test/BugTracker-2014/Tests/temporary.Bug-3430.stable.err
sql/test/BugTracker-2014/Tests/temporary.Bug-3430.stable.out
sql/test/Tests/alastair_udf_mergetable_bug.py
sql/test/Tests/alastair_udf_mergetable_bug.stable.err
sql/test/Tests/alastair_udf_mergetable_bug.stable.out
Modified Files:
clients/R/MonetDB.R/DESCRIPTION
clients/R/MonetDB.R/NAMESPACE
clients/R/MonetDB.R/NEWS
clients/R/MonetDB.R/R/control.R
clients/R/MonetDB.R/R/monetdb.R
clients/R/MonetDB.R/man/mc.Rd
clients/R/MonetDB.R/src/mapi.c
clients/R/db.tests/monetdb.test.R
clients/R/db.tests/monetframe.test.R
clients/R/db.tests/sqlsurvey.test.R
clients/Tests/MAL-signatures.stable.out
clients/Tests/MAL-signatures_gsl.stable.out
clients/Tests/MAL-signatures_nocfitsio.stable.out
clients/Tests/MAL-signatures_sphinxclient.stable.out
clients/Tests/SQL-dump.stable.out
clients/Tests/SQL-dump.stable.out.64bit.oid32
clients/Tests/SQL-dump_gsl.stable.out
clients/Tests/SQL-dump_gsl.stable.out.oid32
clients/Tests/SQL-dump_nogeom.stable.out
clients/Tests/exports.stable.out
clients/mapiclient/dump.c
clients/mapiclient/mclient.c
clients/python2/monetdb/sql/pythonize.py
clients/python3/monetdb/sql/pythonize.py
common/stream/stream.c
common/utils/msabaoth.c
common/utils/mutils.c
configure.ag
gdk/gdk_atoms.c
gdk/gdk_bbp.c
gdk/gdk_calc.c
gdk/gdk_heap.c
gdk/gdk_posix.c
gdk/gdk_storage.c
gdk/gdk_utils.c
java/src/nl/cwi/monetdb/jdbc/MonetPreparedStatement.java
monetdb5/extras/sphinx/sphinx.c
monetdb5/mal/Tests/tst013.stable.out
monetdb5/mal/Tests/tst036.stable.out
monetdb5/mal/Tests/tst050.stable.out
monetdb5/mal/Tests/tst070.stable.out
monetdb5/mal/Tests/tst105.stable.out
monetdb5/mal/Tests/tst106.stable.out
monetdb5/mal/Tests/tst150.stable.out
monetdb5/mal/Tests/tst2504.mal
monetdb5/mal/Tests/tst2504.stable.out
monetdb5/mal/Tests/tst611.stable.out
monetdb5/mal/mal_atom.c
monetdb5/mal/mal_builder.c
monetdb5/mal/mal_factory.c
monetdb5/mal/mal_import.c
monetdb5/mal/mal_instruction.c
monetdb5/mal/mal_interpreter.c
monetdb5/mal/mal_linker.c
monetdb5/mal/mal_module.c
monetdb5/mal/mal_namespace.c
monetdb5/mal/mal_parser.c
monetdb5/mal/mal_profiler.c
monetdb5/mal/mal_readline.c
monetdb5/mal/mal_resolve.c
monetdb5/mal/mal_session.c
monetdb5/modules/atoms/inet.c
monetdb5/modules/atoms/json.c
monetdb5/modules/atoms/json.h
monetdb5/modules/atoms/json.mal
monetdb5/modules/atoms/str.c
monetdb5/modules/mal/Tests/All
monetdb5/modules/mal/Tests/pqueue.stable.out
monetdb5/modules/mal/Tests/pqueue2.mal
monetdb5/modules/mal/bbp.c
monetdb5/modules/mal/manifold.c
monetdb5/modules/mal/pqueue.c
monetdb5/modules/mal/pqueue.h
monetdb5/modules/mal/pqueue.mal
monetdb5/modules/mal/sample.mal
monetdb5/optimizer/Tests/inline08.stable.out
monetdb5/optimizer/opt_accumulators.c
monetdb5/optimizer/opt_aliases.c
monetdb5/optimizer/opt_centipede.c
monetdb5/optimizer/opt_dataflow.c
monetdb5/optimizer/opt_macro.c
monetdb5/optimizer/opt_mapreduce.c
monetdb5/optimizer/opt_mergetable.c
monetdb5/optimizer/opt_octopus.c
monetdb5/optimizer/opt_pushselect.c
monetdb5/optimizer/opt_support.c
monetdb5/scheduler/run_octopus.c
monetdb5/scheduler/srvpool.c
monetdb5/tests/BugDay_2005-10-06_4.9.3/Tests/ADT_not_available.SF-850137.stable.out
monetdb5/tests/BugReports/Tests/lngssaretruncated.stable.out
monetdb5/tests/BugTracker/Tests/parser.SF-2051309.stable.out
sql/backends/monet5/rel_bin.c
sql/backends/monet5/sql.c
sql/backends/monet5/sql.h
sql/backends/monet5/sql.mal
sql/backends/monet5/sql_gencode.c
sql/backends/monet5/sql_scenario.c
sql/backends/monet5/sql_statement.c
sql/backends/monet5/sql_statement.h
sql/benchmarks/ssbm/Tests/02-explain.stable.out
sql/benchmarks/ssbm/Tests/02-plan.stable.out
sql/benchmarks/ssbm/Tests/03-explain.stable.out
sql/benchmarks/ssbm/Tests/03-plan.stable.out
sql/benchmarks/ssbm/Tests/07-explain.stable.out
sql/benchmarks/ssbm/Tests/07-plan.stable.out
sql/benchmarks/ssbm/Tests/08-explain.stable.out
sql/benchmarks/ssbm/Tests/08-plan.stable.out
sql/benchmarks/tpch/Tests/01-explain.stable.out
sql/benchmarks/tpch/Tests/01-plan.stable.out
sql/benchmarks/tpch/Tests/02-explain.stable.out
sql/benchmarks/tpch/Tests/03-explain.stable.out
sql/benchmarks/tpch/Tests/03-plan.stable.out
sql/benchmarks/tpch/Tests/08-explain.stable.out
sql/benchmarks/tpch/Tests/08-plan.stable.out
sql/benchmarks/tpch/Tests/10-explain.stable.out
sql/benchmarks/tpch/Tests/18-explain.stable.out
sql/benchmarks/tpch/Tests/21-explain.stable.out
sql/common/sql_string.c
sql/common/sql_types.c
sql/scripts/40_json.sql
sql/server/rel_distribute.c
sql/server/rel_dump.c
sql/server/rel_optimizer.c
sql/server/rel_psm.c
sql/server/sql_mvc.c
sql/storage/bat/bat_storage.c
sql/storage/restrict/restrict_storage.c
sql/storage/sql_storage.h
sql/test/ADT2006/bram.sql
sql/test/BugTracker-2009/Tests/old_views_incorrectly_reused.SF-2863804.stable.out
sql/test/BugTracker-2010/Tests/LIMIT_OFFSET_big-endian.Bug-2622.stable.out
sql/test/BugTracker-2010/Tests/group-by_ordered_column.Bug-2564.stable.out
sql/test/BugTracker-2012/Tests/table_function_with_column_subselects.Bug-3172.stable.err
sql/test/BugTracker-2013/Tests/qualified_aggrname.Bug-3332.stable.out
sql/test/BugTracker-2014/Tests/All
sql/test/BugTracker-2014/Tests/crash_on_or_with_in.Bug-3461.stable.out
sql/test/BugTracker-2014/Tests/in_incorrect_multi.Bug-3462.stable.out
sql/test/Tests/orderby_non_selection_column.stable.out
sql/test/Tests/systemfunctions.stable.out
sql/test/json/Tests/parsing.stable.err
sql/test/leaks/Tests/check1.stable.out
sql/test/leaks/Tests/check1_gsl.stable.out
sql/test/leaks/Tests/check1_nogeom.stable.out
sql/test/leaks/Tests/check2.stable.out
sql/test/leaks/Tests/check2_gsl.stable.out
sql/test/leaks/Tests/check2_nogeom.stable.out
sql/test/leaks/Tests/check3.stable.out
sql/test/leaks/Tests/check3_gsl.stable.out
sql/test/leaks/Tests/check3_nogeom.stable.out
sql/test/leaks/Tests/check4.stable.out
sql/test/leaks/Tests/check4_gsl.stable.out
sql/test/leaks/Tests/check4_nogeom.stable.out
sql/test/leaks/Tests/check5.stable.out
sql/test/leaks/Tests/check5_gsl.stable.out
sql/test/leaks/Tests/check5_nogeom.stable.out
testing/process.py
tools/merovingian/daemon/argvcmds.c
tools/merovingian/daemon/merovingian.c
tools/mserver/mserver5.c
Branch: multifarm
Log Message:
Merge with default branch.
diffs (truncated from 36811 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
@@ -1,6 +1,6 @@
Package: MonetDB.R
Version: 0.9.2
-Date: 2013-03-18
+Date: 2013-04-22
Title: Connect MonetDB to R
Authors@R: c(person("Hannes Muehleisen", role = c("aut", "cre"),email =
"[email protected]"),
person("Thomas Lumley", role = "ctb"),
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
@@ -12,6 +12,9 @@ export(monetdb_queryinfo)
# shorthand for db connections
export(mc)
+# shorthand for db queries
+export(mq)
+
# control.R
export(monetdb.server.setup)
export(monetdb.server.start)
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
@@ -1,6 +1,13 @@
0.9.2
- monetdb_queryinfo method to find out things about an arbitrary query cheaply
-- new option monetdb.sequential
+- new options monetdb.sequential, monetdb.debug.query and monetdb.debug.mapi
+- debug output now uses the message() function
+- source code cleanup
+- dbListTables() now hides system tables per default, also got options to
include the
+ 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
@@ -4,343 +4,393 @@ require(digest)
C_LIBRARY <- "MonetDB.R"
.onLoad <- function(lib, pkg) {
- library.dynam( C_LIBRARY, pkg, lib )
- .Call("mapiInit",PACKAGE=C_LIBRARY)
+ library.dynam( C_LIBRARY, pkg, lib )
+ .Call("mapiInit", PACKAGE=C_LIBRARY)
}
-# TODO: make these values configurable in the call to dbConnect
-DEBUG_IO <- FALSE
-DEBUG_QUERY <- FALSE
-
# Make S4 aware of S3 classes
-setOldClass(c("sockconn","connection","monetdb_mapi_conn"))
+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")
+ new("MonetDBDriver")
}
setMethod("dbGetInfo", "MonetDBDriver", def=function(dbObj, ...)
- list(name="MonetDBDriver",
- driver.version="0.9.1",
- DBI.version="0.2-7",
- client.version=NA,
- max.connections=NA)
+ list(name="MonetDBDriver",
+ driver.version="0.9.2",
+ DBI.version="0.2-7",
+ client.version=NA,
+ max.connections=NA)
)
# 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,...)
+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, ...)
}
-# TODO: document, export etc
-mq <- function(db,query,...) {
- conn <- mc(db,...)
- res <- dbGetQuery(conn,query)
+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
- }
- port <- as.integer(port)
- timeout <- as.integer(timeout)
-
- if (substring(dbname,1,10) == "monetdb://") {
- #warning("MonetDB.R: Using 'monetdb://...' URIs
in dbConnect() is deprecated. Please switch to 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)
{
- hostportsplit <-
strsplit(hostport,":",fixed=TRUE)
- host <- hostportsplit[[1]][1]
- port <- hostportsplit[[1]][2]
- } else {
- host <- hostport
- }
- }
-
- if (DEBUG_QUERY) cat(paste0("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.\n"))
- socket <- FALSE
- if (wait) {
- repeat {
- continue <- FALSE
- tryCatch ({
- # open socket
with 5-sec timeout so we can check whether everything works
- socket <-
socket <<- .Call("mapiConnect",host,port,5,PACKAGE=C_LIBRARY)
- # authenticate
-
.monetAuthenticate(socket,dbname,user,password,language=language)
- # test the
connection to make sure it works before
-
.Call("mapiDisconnect",socket,PACKAGE=C_LIBRARY)
- break
- }, error = function(e) {
- if
("connection" %in% class(socket)) {
-
.Call("mapiDisconnect",socket,PACKAGE=C_LIBRARY)
- }
-
cat(paste0("Server not ready(",e$message,"), retrying (ESC or CTRL+C to
abort)\n"))
- Sys.sleep(1)
- continue <<-
TRUE
- })
- }
- }
-
- # make new socket with user-specified timeout
- #socket <- socket <<- socketConnection(host = host,
port = port,
- # blocking = TRUE, open="r+b",timeout = timeout)
- socket <-
.Call("mapiConnect",host,port,timeout,PACKAGE=C_LIBRARY)
-
.monetAuthenticate(socket,dbname,user,password,language=language)
- connenv <- new.env(parent=emptyenv())
- connenv$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'")
+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
+ }
+ port <- as.integer(port)
+ 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
+ }
+ }
+ }
+
+ # 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 <<- .Call("mapiConnect", host, port, 5,
PACKAGE=C_LIBRARY)
+ # authenticate
+ .monetAuthenticate(socket, dbname, user, password, language=language)
+ # test the connection to make sure it works before
+ .Call("mapiDisconnect", socket, PACKAGE=C_LIBRARY)
+ break
+ }, error = function(e) {
+ if ("connection" %in% class(socket)) {
+ .Call("mapiDisconnect", socket, PACKAGE=C_LIBRARY)
+ }
+ message("Server not ready(", e$message, "), retrying (ESC or CTRL+C to
abort)")
+ Sys.sleep(1)
+ continue <<- TRUE
+ })
+ }
+ }
+
+ # make new socket with user-specified timeout
+ socket <- .Call("mapiConnect", host, port, timeout, PACKAGE=C_LIBRARY)
+ .monetAuthenticate(socket, dbname, user, password, language=language)
+ connenv <- new.env(parent=emptyenv())
+ connenv$lock <- 0
+ connenv$deferred <- list()
+ connenv$exception <- list()
+
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