Merge pull request datashield#534 from datashield/v6.4.0-dev

Update with changes to v6.4.0-dev

Author: StuartWheater

tests/docker/armadillo/standard/config/application.yml

@@ -68,6 +68,6 @@ logging:
   level:
     root: INFO
     ## change to DEBUG to have more details, typically when developing
-    org.molgenis: DEBUG
+    org.molgenis: INFO
     ## Don't log upload data
     org.apache.coyote.http11.Http11InputBuffer: INFO

tests/testthat/test-perf-ds.abs.R

@@ -0,0 +1,46 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+context("ds.abs::perf::setup")
+connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG"))
+
+#
+# Tests
+#
+
+context("ds.abs::perf:0")
+test_that("combine - performance", {
+    .durationSec  <- 30 # seconds
+    .count        <- 0
+    .start.time   <- Sys.time()
+    .current.time <- .start.time
+
+    while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
+        ds.abs("D$LAB_TSC", newobj = "abs.newobj")
+
+        .count <- .count + 1
+        .current.time <- Sys.time()
+    }
+    expect_true(TRUE)
+
+    print(paste("ds.abs::perf::0:", format(.count / (difftime(.current.time, .start.time, units = "secs")[[1]]), digits = 8)))
+})
+
+#
+# Done
+#
+
+context("ds.abs::perf::shutdown")
+disconnect.studies.dataset.cnsim()
+context("ds.abs::perf::done")

tests/testthat/test-perf-ds.asList.R

@@ -0,0 +1,46 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+context("ds.asList::perf::setup")
+connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG"))
+
+#
+# Tests
+#
+
+context("ds.asList::perf:0")
+test_that("combine - performance", {
+    .durationSec  <- 30 # seconds
+    .count        <- 0
+    .start.time   <- Sys.time()
+    .current.time <- .start.time
+
+    while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
+        ds.asList("D$LAB_TSC", newobj = "asList.newobj")
+
+        .count <- .count + 1
+        .current.time <- Sys.time()
+    }
+    expect_true(TRUE)
+
+    print(paste("ds.asList::perf::0:", format(.count / (difftime(.current.time, .start.time, units = "secs")[[1]]), digits = 8)))
+})
+
+#
+# Done
+#
+
+context("ds.asList::perf::shutdown")
+disconnect.studies.dataset.cnsim()
+context("ds.asList::perf::done")

tests/testthat/test-perf-ds.asNumeric.R

@@ -0,0 +1,46 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+context("ds.asNumeric::perf::setup")
+connect.studies.dataset.cnsim(list("GENDER"))
+
+#
+# Tests
+#
+
+context("ds.asNumeric::perf:0")
+test_that("combine - performance", {
+    .durationSec  <- 30 # seconds
+    .count        <- 0
+    .start.time   <- Sys.time()
+    .current.time <- .start.time
+
+    while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
+        ds.asNumeric("D$GENDER", newobj = "asNumeric.newobj")
+
+        .count <- .count + 1
+        .current.time <- Sys.time()
+    }
+    expect_true(TRUE)
+
+    print(paste("ds.asNumeric::perf::0:", format(.count / (difftime(.current.time, .start.time, units = "secs")[[1]]), digits = 8)))
+})
+
+#
+# Done
+#
+
+context("ds.asNumeric::perf::shutdown")
+disconnect.studies.dataset.cnsim()
+context("ds.asNumeric::perf::done")

tests/testthat/test-perf-ds.assign.R

@@ -0,0 +1,46 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+context("ds.assign::perf::setup")
+connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG"))
+
+#
+# Tests
+#
+
+context("ds.assign::perf::0")
+test_that("performance", {
+    .durationSec  <- 30 # seconds
+    .count        <- 0
+    .start.time   <- Sys.time()
+    .current.time <- .start.time
+
+    while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
+        ds.assign("D$LAB_TSC", newobj = "assign.newobj")
+
+        .count <- .count + 1
+        .current.time <- Sys.time()
+    }
+    expect_true(TRUE)
+
+    print(paste("ds.assign::perf::0:", format(.count / (difftime(.current.time, .start.time, units = "secs")[[1]]), digits = 8)))
+})
+
+#
+# Done
+#
+
+context("ds.assign::perf::shutdown")
+disconnect.studies.dataset.cnsim()
+context("ds.assign::perf::done")