From cbef6da6fc8448b8ab86fa9ee467369ecdaff227 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 12 May 2026 12:33:43 +0100 Subject: [PATCH 1/2] Switch to Roxygen 8.0.0 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index e5e72e97..31914c46 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -81,6 +81,6 @@ Suggests: DSOpal, DSMolgenisArmadillo, DSLite -RoxygenNote: 7.3.3 Encoding: UTF-8 Language: en-GB +Config/roxygen2/version: 8.0.0 From 1dff16127d61063d83b68190c4cd7b41460704e2 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Thu, 28 May 2026 12:31:01 +0100 Subject: [PATCH 2/2] Integration of STANDARDISE datasets --- .../init_studies_datasets.R | 82 ++++++++++++++ .../testthat/data_files/STANDARDISE/std_1.csv | 101 ++++++++++++++++++ .../testthat/data_files/STANDARDISE/std_1.rda | Bin 0 -> 1474 bytes .../data_files/STANDARDISE/std_1_d.csv | 101 ++++++++++++++++++ .../data_files/STANDARDISE/std_1_d.rda | Bin 0 -> 2228 bytes .../testthat/data_files/STANDARDISE/std_2.csv | 101 ++++++++++++++++++ .../testthat/data_files/STANDARDISE/std_2.rda | Bin 0 -> 1706 bytes .../data_files/STANDARDISE/std_2_d.csv | 101 ++++++++++++++++++ .../data_files/STANDARDISE/std_2_d.rda | Bin 0 -> 2461 bytes .../testthat/data_files/STANDARDISE/std_3.csv | 101 ++++++++++++++++++ .../testthat/data_files/STANDARDISE/std_3.rda | Bin 0 -> 1597 bytes .../data_files/STANDARDISE/std_3_d.csv | 101 ++++++++++++++++++ .../data_files/STANDARDISE/std_3_d.rda | Bin 0 -> 2343 bytes ...lgenis_armadillo-upload_testing_datasets.R | 8 ++ .../obiba_opal-upload_testing_datasets.R | 8 ++ 15 files changed, 704 insertions(+) create mode 100644 tests/testthat/data_files/STANDARDISE/std_1.csv create mode 100644 tests/testthat/data_files/STANDARDISE/std_1.rda create mode 100644 tests/testthat/data_files/STANDARDISE/std_1_d.csv create mode 100644 tests/testthat/data_files/STANDARDISE/std_1_d.rda create mode 100644 tests/testthat/data_files/STANDARDISE/std_2.csv create mode 100644 tests/testthat/data_files/STANDARDISE/std_2.rda create mode 100644 tests/testthat/data_files/STANDARDISE/std_2_d.csv create mode 100644 tests/testthat/data_files/STANDARDISE/std_2_d.rda create mode 100644 tests/testthat/data_files/STANDARDISE/std_3.csv create mode 100644 tests/testthat/data_files/STANDARDISE/std_3.rda create mode 100644 tests/testthat/data_files/STANDARDISE/std_3_d.csv create mode 100644 tests/testthat/data_files/STANDARDISE/std_3_d.rda diff --git a/tests/testthat/connection_to_datasets/init_studies_datasets.R b/tests/testthat/connection_to_datasets/init_studies_datasets.R index 0639aac6..f86d040f 100644 --- a/tests/testthat/connection_to_datasets/init_studies_datasets.R +++ b/tests/testthat/connection_to_datasets/init_studies_datasets.R @@ -221,6 +221,62 @@ init.studies.dataset.gamlss <- function(variables) } } +init.studies.dataset.stand <- function(variables) +{ + if (ds.test_env$secure_login_details) + { + if (ds.test_env$driver == "OpalDriver") + { + builder <- DSI::newDSLoginBuilder(.silent = TRUE) + builder$append(server = "sim1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "STANDARDISE.std_1", options=ds.test_env$options_1) + builder$append(server = "sim2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "STANDARDISE.std_1", options=ds.test_env$options_2) + builder$append(server = "sim3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "STANDARDISE.std_1", options=ds.test_env$options_3) + ds.test_env$login.data <- builder$build() + } + else if (ds.test_env$driver == "ArmadilloDriver") + { + builder <- DSI::newDSLoginBuilder(.silent = TRUE) + builder$append(server = "sim1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/standardise/std_1", driver = ds.test_env$driver) + builder$append(server = "sim2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/standardise/std_2", driver = ds.test_env$driver) + builder$append(server = "sim3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/standardise/std_3", driver = ds.test_env$driver) + ds.test_env$login.data <- builder$build() + } + else + { + ds.test_env$login.data <- DSLite::setupCNSIMTest("dsBase", env = ds.test_env) + } + ds.test_env$stats.var <- variables + } +} + +init.studies.dataset.stand_disclosure <- function(variables) +{ + if (ds.test_env$secure_login_details) + { + if (ds.test_env$driver == "OpalDriver") + { + builder <- DSI::newDSLoginBuilder(.silent = TRUE) + builder$append(server = "sim1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "STANDARDISE.std_1_d", options=ds.test_env$options_1) + builder$append(server = "sim2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "STANDARDISE.std_2_d", options=ds.test_env$options_2) + builder$append(server = "sim3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "STANDARDISE.std_3_d", options=ds.test_env$options_3) + ds.test_env$login.data <- builder$build() + } + else if (ds.test_env$driver == "ArmadilloDriver") + { + builder <- DSI::newDSLoginBuilder(.silent = TRUE) + builder$append(server = "sim1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/standardise/std_1_d", driver = ds.test_env$driver) + builder$append(server = "sim2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/standardise/std_2_d", driver = ds.test_env$driver) + builder$append(server = "sim3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/standardise/std_3_d", driver = ds.test_env$driver) + ds.test_env$login.data <- builder$build() + } + else + { + ds.test_env$login.data <- DSLite::setupCNSIMTest("dsBase", env = ds.test_env) + } + ds.test_env$stats.var <- variables + } +} + connect.studies.dataset.cnsim <- function(variables) { @@ -278,6 +334,22 @@ connect.studies.dataset.gamlss <- function(variables) log.in.data.server() } +connect.studies.dataset.stand <- function(variables) +{ + log.out.data.server() + source("connection_to_datasets/login_details.R") + init.studies.dataset.stand(variables) + log.in.data.server() +} + +connect.studies.dataset.stand_disclosure <- function(variables) +{ + log.out.data.server() + source("connection_to_datasets/login_details.R") + init.studies.dataset.stand_disclosure(variables) + log.in.data.server() +} + disconnect.studies.dataset.cnsim <- function() { log.out.data.server() @@ -312,3 +384,13 @@ disconnect.studies.dataset.gamlss <- function() { log.out.data.server() } + +disconnect.studies.dataset.stand <- function() +{ + log.out.data.server() +} + +disconnect.studies.dataset.stand_disclosure <- function() +{ + log.out.data.server() +} diff --git a/tests/testthat/data_files/STANDARDISE/std_1.csv b/tests/testthat/data_files/STANDARDISE/std_1.csv new file mode 100644 index 00000000..32890959 --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_1.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,fac_col6,fac_col9,col12,col15,col18 +High,Blue,Yes,3,NA,Bird,True,28.757752012461424,31,TRUE +High,Blue,Yes,3,NA,Bird,True,78.83051354438066,79,TRUE +High,Blue,Yes,3,NA,Bird,True,40.89769218116999,51,TRUE +Medium,Green,No,2,NA,Dog,False,88.301740400493145,14,FALSE +High,Blue,Yes,3,NA,Bird,True,94.04672842938453,67,TRUE +Medium,Green,No,2,NA,Dog,False,4.555649938993156,42,FALSE 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a/tests/testthat/data_files/molgenis_armadillo-upload_testing_datasets.R b/tests/testthat/data_files/molgenis_armadillo-upload_testing_datasets.R index 9e129971..545467bc 100644 --- a/tests/testthat/data_files/molgenis_armadillo-upload_testing_datasets.R +++ b/tests/testthat/data_files/molgenis_armadillo-upload_testing_datasets.R @@ -69,4 +69,12 @@ upload_testing_dataset_table('datashield', 'testing', 'DATASET1', 'TESTING/DATAS upload_testing_dataset_table('datashield', 'testing', 'DATASET2', 'TESTING/DATASET2.rda') upload_testing_dataset_table('datashield', 'testing', 'DATASET3', 'TESTING/DATASET3.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_1', 'STANDARDISE/std_1.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_2', 'STANDARDISE/std_2.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_3', 'STANDARDISE/std_3.rda') + +upload_testing_dataset_table('datashield', 'standardise', 'std_1_d', 'STANDARDISE/std_1_d.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_2_d', 'STANDARDISE/std_2_d.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_3_d', 'STANDARDISE/std_3_d.rda') + print(MolgenisArmadillo::armadillo.list_tables('datashield')) diff --git a/tests/testthat/data_files/obiba_opal-upload_testing_datasets.R b/tests/testthat/data_files/obiba_opal-upload_testing_datasets.R index 52b66e31..b14f2aa6 100644 --- a/tests/testthat/data_files/obiba_opal-upload_testing_datasets.R +++ b/tests/testthat/data_files/obiba_opal-upload_testing_datasets.R @@ -72,4 +72,12 @@ upload_testing_dataset_table(opal, 'TESTING', 'DATASET1', 'TESTING/DATASET1.rda' upload_testing_dataset_table(opal, 'TESTING', 'DATASET2', 'TESTING/DATASET2.rda') upload_testing_dataset_table(opal, 'TESTING', 'DATASET3', 'TESTING/DATASET3.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_1', 'STANDARDISE/std_1.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_2', 'STANDARDISE/std_2.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_3', 'STANDARDISE/std_3.rda') + +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_1_d', 'STANDARDISE/std_1_d.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_2_d', 'STANDARDISE/std_2_d.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_3_d', 'STANDARDISE/std_3_d.rda') + opal.logout(opal)