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StuartWheaterStuartWheater
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Merge branch 'datashield:v6.3.6-dev' into 6.4.0-6.3.6_update
2 parents 3edd081 + bfe21f0 commit 6fde4ad

21 files changed

Lines changed: 966 additions & 53 deletions

‎azure-pipelines.yml‎

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sleep 60
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R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
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R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
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workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files

‎opal_azure-pipelines.yml‎

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sleep 60
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R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
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R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
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workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files

‎tests/testthat/perf_files/armadillo_azure-pipeline_perf-profile.csv‎

Lines changed: 28 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,29 @@
11
"refer_name","rate","lower_tolerance","upper_tolerance"
2-
"conndisconn::perf::simple0","0.1661","0.5","2"
3-
"ds.abs::perf::0","6.247","0.5","2"
4-
"ds.asInteger::perf:0","5.691","0.5","2"
5-
"ds.asList::perf:0","12.50","0.5","2"
6-
"ds.asNumeric::perf:0","5.723","0.5","2"
7-
"ds.assign::perf::0","10.52","0.5","2"
8-
"ds.class::perf::combine:0","13.73","0.5","2"
9-
"ds.colnames::perf:0","25.64","0.5","2"
10-
"ds.exists::perf::combine:0","25.73","0.5","2"
11-
"ds.length::perf::combine:0","25.44","0.5","2"
12-
"ds.mean::perf::combine:0","25.70","0.5","2"
13-
"ds.mean::perf::split:0","25.72","0.5","2"
14-
"void::perf::void::0","53016.0","0.5","2"
2+
"conndisconn::perf::simple0","0.1621","0.5","2"
3+
"ds.abs::perf::0","5.989","0.5","2"
4+
"ds.asCharacter::perf::0","5.413","0.5","2"
5+
"ds.asDataMatrix::perf::0","5.466","0.5","2"
6+
"ds.asInteger::perf:0","5.570","0.5","2"
7+
"ds.asList::perf:0","11.72","0.5","2"
8+
"ds.asLogical::perf::0","5.516","0.5","2"
9+
"ds.asMatrix::perf::0","5.507","0.5","2"
10+
"ds.asNumeric::perf:0","5.552","0.5","2"
11+
"ds.assign::perf::0","10.21","0.5","2"
12+
"ds.class::perf::combine:0","12.30","0.5","2"
13+
"ds.colnames::perf:0","24.39","0.5","2"
14+
"ds.completeCases::perf::combine:0","5.521","0.5","2"
15+
"ds.dim::perf::combine:0","24.63","0.5","2"
16+
"ds.exists::perf::combine:0","24.74","0.5","2"
17+
"ds.exp::perf::0","6.218","0.5","2"
18+
"ds.isNA::perf::combine:0","9.480","0.5","2"
19+
"ds.length::perf::combine:0","24.94","0.5","2"
20+
"ds.levels::perf::combine:0","9.551","0.5","2"
21+
"ds.log::perf::0","6.286","0.5","2"
22+
"ds.ls::perf::combine:0","25.05","0.5","2"
23+
"ds.mean::perf::combine:0","24.63","0.5","2"
24+
"ds.mean::perf::split:0","25.20","0.5","2"
25+
"ds.names::perf::combine:0","12.37","0.5","2"
26+
"ds.numNA::perf::combine:0","9.64","0.5","2"
27+
"ds.sqrt::perf::0","6.218","0.5","2"
28+
"ds.unique::perf::combine:0","10.20","0.5","2"
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"void::perf::void::0","51340.0","0.5","2"

‎tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv‎

Lines changed: 28 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,29 @@
11
"refer_name","rate","lower_tolerance","upper_tolerance"
2-
"conndisconn::perf::simple0","0.06790","0.5","2"
3-
"ds.abs::perf::0","1.998","0.5","2"
4-
"ds.asInteger::perf:0","2.111","0.5","2"
5-
"ds.asList::perf:0","4.550","0.5","2"
6-
"ds.asNumeric::perf:0","1.879","0.5","2"
7-
"ds.assign::perf::0","4.806","0.5","2"
8-
"ds.class::perf::combine:0","3.865","0.5","2"
9-
"ds.colnames::perf:0","9.577","0.5","2"
10-
"ds.exists::perf::combine:0","8.411","0.5","2"
11-
"ds.length::perf::combine:0","7.957","0.5","2"
12-
"ds.mean::perf::combine:0","9.049","0.5","2"
13-
"ds.mean::perf::split:0","9.429","0.5","2"
14-
"void::perf::void::0","21400.0","0.5","2"
2+
"conndisconn::perf::simple0","0.07683","0.5","2"
3+
"ds.abs::perf::0","2.473","0.5","2"
4+
"ds.asCharacter::perf::0","2.295","0.5","2"
5+
"ds.asDataMatrix::perf::0","1.999","0.5","2"
6+
"ds.asInteger::perf:0","1.148","0.5","2"
7+
"ds.asList::perf:0","3.398","0.5","2"
8+
"ds.asLogical::perf::0","1.660","0.5","2"
9+
"ds.asMatrix::perf::0","1.835","0.5","2"
10+
"ds.asNumeric::perf:0","1.632","0.5","2"
11+
"ds.assign::perf::0","3.487","0.5","2"
12+
"ds.class::perf::combine:0","5.037","0.5","2"
13+
"ds.colnames::perf:0","8.219","0.5","2"
14+
"ds.completeCases::perf::combine:0","1.896","0.5","2"
15+
"ds.dim::perf::combine:0","8.337","0.5","2"
16+
"ds.exists::perf::combine:0","9.133","0.5","2"
17+
"ds.exp::perf::0","2.317","0.5","2"
18+
"ds.isNA::perf::combine:0","3.035","0.5","2"
19+
"ds.length::perf::combine:0","9.551","0.5","2"
20+
"ds.levels::perf::combine:0","3.275","0.5","2"
21+
"ds.log::perf::0","2.297","0.5","2"
22+
"ds.ls::perf::combine:0","8.168","0.5","2"
23+
"ds.mean::perf::combine:0","8.168","0.5","2"
24+
"ds.mean::perf::split:0","8.465","0.5","2"
25+
"ds.names::perf::combine:0","4.190","0.5","2"
26+
"ds.numNA::perf::combine:0","3.588","0.5","2"
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"ds.sqrt::perf::0","2.278","0.5","2"
28+
"ds.unique::perf::combine:0","3.909","0.5","2"
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"void::perf::void::0","20280.0","0.5","2"

‎tests/testthat/perf_files/opal_default_perf-profile.csv‎

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This file was deleted.

‎tests/testthat/perf_files/opal_hp-laptop-quay_perf-profile.csv‎

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11
"refer_name","rate","lower_tolerance","upper_tolerance"
2-
"conndisconn::perf::simple0","0.147643461923159","0.5","2"
3-
"ds.abs::perf::0","0.631818039001181","0.5","2"
4-
"ds.asInteger::perf:0","0.675696161933654","0.5","2"
5-
"ds.asList::perf:0","1.59078428438764","0.5","2"
6-
"ds.asNumeric::perf:0","0.692813012683229","0.5","2"
7-
"ds.assign::perf::0","1.89351857736982","0.5","2"
8-
"ds.class::perf::combine:0","1.62870246867488","0.5","2"
9-
"ds.colnames::perf:0","2.7125071","0.5","2"
10-
"ds.exists::perf::combine:0","3.45004426293124","0.5","2"
11-
"ds.length::perf::combine:0","2.78832377100152","0.5","2"
12-
"ds.mean::perf::combine:0","2.7801284055162","0.5","2"
13-
"ds.mean::perf::split:0","3.67443474363821","0.5","2"
14-
"void::perf::void::0","18974.1385397392","0.5","2"
2+
"conndisconn::perf::simple0","0.1267","0.5","2"
3+
"ds.abs::perf::0","0.7542","0.5","2"
4+
"ds.asCharacter::perf::0","0.8126","0.5","2"
5+
"ds.asDataMatrix::perf::0","0.8100","0.5","2"
6+
"ds.asInteger::perf:0","0.8600","0.5","2"
7+
"ds.asList::perf:0","","0.5","2"
8+
"ds.asLogical::perf::0","1.660","0.5","2"
9+
"ds.asMatrix::perf::0","0.8557","0.5","2"
10+
"ds.asNumeric::perf:0","0.7912","0.5","2"
11+
"ds.assign::perf::0","2.003","0.5","2"
12+
"ds.class::perf::combine:0","1.645","0.5","2"
13+
"ds.colnames::perf:0","3.392","0.5","2"
14+
"ds.completeCases::perf::combine:0","0.8218","0.5","2"
15+
"ds.dim::perf::combine:0","3.265","0.5","2"
16+
"ds.exists::perf::combine:0","4.042","0.5","2"
17+
"ds.exp::perf::0","0.8963","0.5","2"
18+
"ds.isNA::perf::combine:0","1.297","0.5","2"
19+
"ds.length::perf::combine:0","3.212","0.5","2"
20+
"ds.levels::perf::combine:0","1.326","0.5","2"
21+
"ds.log::perf::0","0.9260","0.5","2"
22+
"ds.ls::perf::combine:0","3.282","0.5","2"
23+
"ds.mean::perf::combine:0","3.281","0.5","2"
24+
"ds.mean::perf::split:0","4.029","0.5","2"
25+
"ds.names::perf::combine:0","1.713","0.5","2"
26+
"ds.numNA::perf::combine:0","1.274","0.5","2"
27+
"ds.sqrt::perf::0","0.9233","0.5","2"
28+
"ds.unique::perf::combine:0","1.628","0.5","2"
29+
"void::perf::void::0","23600","0.5","2"

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

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#-------------------------------------------------------------------------------
2+
#
3+
# This program and the accompanying materials
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# are made available under the terms of the GNU Public License v3.0.
5+
#
6+
# You should have received a copy of the GNU General Public License
7+
# along with this program. If not, see <http://www.gnu.org/licenses/>.
8+
#-------------------------------------------------------------------------------
9+
10+
#
11+
# Set up
12+
#
13+
14+
# context("ds.asCharacter::perf::setup")
15+
connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG"))
16+
17+
#
18+
# Tests
19+
#
20+
21+
# context("ds.asCharacter::perf:0")
22+
test_that("combine - performance", {
23+
.durationSec <- perf.testduration(30)
24+
.count <- 0
25+
.start.time <- Sys.time()
26+
.current.time <- .start.time
27+
28+
while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
29+
ds.asCharacter("D$LAB_TSC", newobj = "perf.newobj")
30+
31+
.count <- .count + 1
32+
.current.time <- Sys.time()
33+
}
34+
35+
.current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]])
36+
.reference.rate <- perf.reference.rate("ds.asCharacter::perf::0")
37+
if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) {
38+
print(paste("ds.asCharacter::perf::0 ", .current.rate, 0.5, 2.0))
39+
perf.reference.save("ds.asCharacter::perf::0", .current.rate, 0.5, 2.0)
40+
} else {
41+
print(paste("ds.asCharacter::perf::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''))
42+
}
43+
44+
.reference.rate <- perf.reference.rate("ds.asCharacter::perf::0")
45+
.reference.tolerance.lower <- perf.reference.tolerance.lower("ds.asCharacter::perf::0")
46+
.reference.tolerance.upper <- perf.reference.tolerance.upper("ds.asCharacter::perf::0")
47+
48+
expect_gt(.current.rate, .reference.rate * .reference.tolerance.lower, label = "Observed rate", expected.label = "lower threshold on rate")
49+
expect_lt(.current.rate, .reference.rate * .reference.tolerance.upper, label = "Observed rate", expected.label = "upper threshold on rate")
50+
})
51+
52+
#
53+
# Done
54+
#
55+
56+
# context("ds.asCharacter::perf::shutdown")
57+
disconnect.studies.dataset.cnsim()
58+
# context("ds.asCharacter::perf::done")

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

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#-------------------------------------------------------------------------------
2+
#
3+
# This program and the accompanying materials
4+
# are made available under the terms of the GNU Public License v3.0.
5+
#
6+
# You should have received a copy of the GNU General Public License
7+
# along with this program. If not, see <http://www.gnu.org/licenses/>.
8+
#-------------------------------------------------------------------------------
9+
10+
#
11+
# Set up
12+
#
13+
14+
# context("ds.asDataMatrix::perf::setup")
15+
connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG"))
16+
17+
#
18+
# Tests
19+
#
20+
21+
# context("ds.asDataMatrix::perf:0")
22+
test_that("combine - performance", {
23+
.durationSec <- perf.testduration(30)
24+
.count <- 0
25+
.start.time <- Sys.time()
26+
.current.time <- .start.time
27+
28+
while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
29+
ds.asDataMatrix(x.name = "D", newobj = "perf.newobj")
30+
31+
.count <- .count + 1
32+
.current.time <- Sys.time()
33+
}
34+
35+
.current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]])
36+
.reference.rate <- perf.reference.rate("ds.asDataMatrix::perf::0")
37+
if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) {
38+
print(paste("ds.asDataMatrix::perf::0 ", .current.rate, 0.5, 2.0))
39+
perf.reference.save("ds.asDataMatrix::perf::0", .current.rate, 0.5, 2.0)
40+
} else {
41+
print(paste("ds.asDataMatrix::perf::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''))
42+
}
43+
44+
.reference.rate <- perf.reference.rate("ds.asDataMatrix::perf::0")
45+
.reference.tolerance.lower <- perf.reference.tolerance.lower("ds.asDataMatrix::perf::0")
46+
.reference.tolerance.upper <- perf.reference.tolerance.upper("ds.asDataMatrix::perf::0")
47+
48+
expect_gt(.current.rate, .reference.rate * .reference.tolerance.lower, label = "Observed rate", expected.label = "lower threshold on rate")
49+
expect_lt(.current.rate, .reference.rate * .reference.tolerance.upper, label = "Observed rate", expected.label = "upper threshold on rate")
50+
})
51+
52+
#
53+
# Done
54+
#
55+
56+
# context("ds.asDataMatrix::perf::shutdown")
57+
disconnect.studies.dataset.cnsim()
58+
# context("ds.asDataMatrix::perf::done")

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

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1+
#-------------------------------------------------------------------------------
2+
#
3+
# This program and the accompanying materials
4+
# are made available under the terms of the GNU Public License v3.0.
5+
#
6+
# You should have received a copy of the GNU General Public License
7+
# along with this program. If not, see <http://www.gnu.org/licenses/>.
8+
#-------------------------------------------------------------------------------
9+
10+
#
11+
# Set up
12+
#
13+
14+
# context("ds.asLogical::perf::setup")
15+
connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG"))
16+
17+
#
18+
# Tests
19+
#
20+
21+
# context("ds.asLogical::perf:0")
22+
test_that("combine - performance", {
23+
.durationSec <- perf.testduration(30)
24+
.count <- 0
25+
.start.time <- Sys.time()
26+
.current.time <- .start.time
27+
28+
while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
29+
ds.asLogical("D$LAB_TSC", newobj = "perf.newobj")
30+
31+
.count <- .count + 1
32+
.current.time <- Sys.time()
33+
}
34+
35+
.current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]])
36+
.reference.rate <- perf.reference.rate("ds.asLogical::perf::0")
37+
if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) {
38+
print(paste("ds.asLogical::perf::0 ", .current.rate, 0.5, 2.0))
39+
perf.reference.save("ds.asLogical::perf::0", .current.rate, 0.5, 2.0)
40+
} else {
41+
print(paste("ds.asLogical::perf::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''))
42+
}
43+
44+
.reference.rate <- perf.reference.rate("ds.asLogical::perf::0")
45+
.reference.tolerance.lower <- perf.reference.tolerance.lower("ds.asLogical::perf::0")
46+
.reference.tolerance.upper <- perf.reference.tolerance.upper("ds.asLogical::perf::0")
47+
48+
expect_gt(.current.rate, .reference.rate * .reference.tolerance.lower, label = "Observed rate", expected.label = "lower threshold on rate")
49+
expect_lt(.current.rate, .reference.rate * .reference.tolerance.upper, label = "Observed rate", expected.label = "upper threshold on rate")
50+
})
51+
52+
#
53+
# Done
54+
#
55+
56+
# context("ds.asLogical::perf::shutdown")
57+
disconnect.studies.dataset.cnsim()
58+
# context("ds.asLogical::perf::done")

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

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1+
#-------------------------------------------------------------------------------
2+
#
3+
# This program and the accompanying materials
4+
# are made available under the terms of the GNU Public License v3.0.
5+
#
6+
# You should have received a copy of the GNU General Public License
7+
# along with this program. If not, see <http://www.gnu.org/licenses/>.
8+
#-------------------------------------------------------------------------------
9+
10+
#
11+
# Set up
12+
#
13+
14+
# context("ds.asMatrix::perf::setup")
15+
connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG"))
16+
17+
#
18+
# Tests
19+
#
20+
21+
# context("ds.asMatrix::perf:0")
22+
test_that("combine - performance", {
23+
.durationSec <- perf.testduration(30)
24+
.count <- 0
25+
.start.time <- Sys.time()
26+
.current.time <- .start.time
27+
28+
while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
29+
ds.asMatrix(x.name = "D$LAB_TSC", newobj = "perf.newobj")
30+
31+
.count <- .count + 1
32+
.current.time <- Sys.time()
33+
}
34+
35+
.current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]])
36+
.reference.rate <- perf.reference.rate("ds.asMatrix::perf::0")
37+
if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) {
38+
print(paste("ds.asMatrix::perf::0 ", .current.rate, 0.5, 2.0))
39+
perf.reference.save("ds.asMatrix::perf::0", .current.rate, 0.5, 2.0)
40+
} else {
41+
print(paste("ds.asMatrix::perf::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''))
42+
}
43+
44+
.reference.rate <- perf.reference.rate("ds.asMatrix::perf::0")
45+
.reference.tolerance.lower <- perf.reference.tolerance.lower("ds.asMatrix::perf::0")
46+
.reference.tolerance.upper <- perf.reference.tolerance.upper("ds.asMatrix::perf::0")
47+
48+
expect_gt(.current.rate, .reference.rate * .reference.tolerance.lower, label = "Observed rate", expected.label = "lower threshold on rate")
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expect_lt(.current.rate, .reference.rate * .reference.tolerance.upper, label = "Observed rate", expected.label = "upper threshold on rate")
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})
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#
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# Done
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#
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# context("ds.asMatrix::perf::shutdown")
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disconnect.studies.dataset.cnsim()
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# context("ds.asMatrix::perf::done")

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