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 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 +Medium,Green,No,2,NA,Dog,False,52.810548804700375,50,FALSE +Medium,Green,No,2,NA,Dog,False,89.2419044394046,43,FALSE +High,Blue,Yes,3,NA,Bird,True,55.14350144658238,14,TRUE +Low,NA,Yes,1,NA,Cat,True,45.661473530344665,25,TRUE +Medium,Green,No,2,NA,Dog,False,95.68333453498781,90,FALSE 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+High,Blue,Yes,3,NA,Bird,True,51.15054599009454,23,TRUE diff --git a/tests/testthat/data_files/STANDARDISE/std_1.rda b/tests/testthat/data_files/STANDARDISE/std_1.rda new file mode 100644 index 00000000..df5a8854 Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_1.rda differ diff --git a/tests/testthat/data_files/STANDARDISE/std_1_d.csv b/tests/testthat/data_files/STANDARDISE/std_1_d.csv new file mode 100644 index 00000000..9fe7462f --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_1_d.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,28.7577520124614,31,TRUE +High,Blue,Yes,3,NA,Bird,True,78.8305135443807,79,TRUE +High,Blue,Yes,3,NA,Bird,True,40.89769218117,51,TRUE +Medium,Green,No,2,NA,Dog,False,88.3017404004931,14,FALSE +High,Blue,Yes,3,NA,Bird,True,94.0467284293845,67,TRUE +Medium,Green,No,2,NA,Dog,False,4.55564993899316,42,FALSE 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+Medium,Green,Yes,2,NA,Dog,True,78.2294301316142,96,TRUE +Low,NA,No,1,NA,Cat,False,9.35949867125601,71,FALSE +High,Blue,Yes,3,NA,Bird,True,46.677904156968,67,TRUE +High,Blue,Yes,3,NA,Bird,True,51.1505459900945,23,TRUE diff --git a/tests/testthat/data_files/STANDARDISE/std_1_d.rda b/tests/testthat/data_files/STANDARDISE/std_1_d.rda new file mode 100644 index 00000000..4387f72b Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_1_d.rda differ diff --git a/tests/testthat/data_files/STANDARDISE/std_2.csv b/tests/testthat/data_files/STANDARDISE/std_2.csv new file mode 100644 index 00000000..9c20866c --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_2.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,fac_col7,fac_col10,col13,col16,col19 +High,NA,NA,C,2,Large,Left,o,28.757752012461424,31 +High,NA,NA,C,2,Large,Left,s,78.83051354438066,79 +High,NA,NA,C,2,Large,Left,n,40.89769218116999,51 +Medium,Green,No,B,3,Medium,Right,c,88.301740400493145,14 +High,NA,NA,C,2,Large,Left,j,94.04672842938453,67 +Medium,Green,No,B,3,Medium,Right,r,4.555649938993156,42 +Medium,Green,No,B,3,Medium,Right,v,52.810548804700375,50 +Medium,Green,No,B,3,Medium,Right,k,89.2419044394046,43 +High,NA,NA,C,2,Large,Left,e,55.14350144658238,14 +Low,Red,NA,A,1,Small,Left,t,45.661473530344665,25 +Medium,Green,No,B,3,Medium,Right,n,95.68333453498781,90 +Medium,Green,No,B,3,Medium,Right,v,45.33341561909765,91 +Low,Red,No,A,1,Small,Right,y,67.75706354528666,69 +Medium,Green,NA,B,3,Medium,Left,z,57.26334019564092,91 +High,NA,No,C,2,Large,Right,e,10.292468266561627,57 +Low,Red,NA,A,1,Small,Left,s,89.98249704018235,92 +High,NA,No,C,2,Large,Right,y,24.60877343546599,9 +High,NA,NA,C,2,Large,Left,y,4.205953353084624,93 +Low,Red,NA,A,1,Small,Left,i,32.79207192827016,99 +Low,Red,NA,A,1,Small,Left,c,95.45036491472274,72 +Low,Red,NA,A,1,Small,Left,h,88.95393160637468,26 +Low,Red,No,A,1,Small,Right,z,69.28034061565995,7 +High,NA,NA,C,2,Large,Left,g,64.05068137682974,42 +Medium,Green,NA,B,3,Medium,Left,j,99.42697766236961,9 +High,NA,NA,C,2,Large,Left,i,65.57057991158217,83 +Medium,Green,NA,B,3,Medium,Left,s,70.85304681677371,36 +Low,Red,No,A,1,Small,Right,d,54.40660247113556,78 +Medium,Green,No,B,3,Medium,Right,n,59.41420204471797,81 +High,NA,NA,C,2,Large,Left,q,28.91597372945398,43 +Medium,Green,No,B,3,Medium,Right,k,14.711364731192589,76 +Low,Red,NA,A,1,Small,Left,g,96.30242325365543,15 +High,NA,No,C,2,Large,Right,u,90.22990451194346,32 +High,NA,NA,C,2,Large,Left,l,69.07052784226835,7 +Low,Red,No,A,1,Small,Right,o,79.54674176871777,9 +High,NA,No,C,2,Large,Right,j,2.461368450894952,41 +Medium,Green,NA,B,3,Medium,Left,m,47.77959710918367,74 +Low,Red,NA,A,1,Small,Left,g,75.84595375228673,23 +High,NA,NA,C,2,Large,Left,i,21.640793583355844,27 +Low,Red,NA,A,1,Small,Left,i,31.818100763484836,60 +Low,Red,No,A,1,Small,Right,j,23.16257853526622,53 +Medium,Green,NA,B,3,Medium,Left,w,14.280002238228917,7 +High,NA,No,C,2,Large,Right,u,41.45463358145207,53 +High,NA,No,C,2,Large,Right,g,41.372432629577816,27 +Low,Red,NA,A,1,Small,Left,u,36.884545092470944,96 +High,NA,NA,C,2,Large,Left,f,15.244474774226546,38 +Low,Red,NA,A,1,Small,Left,y,13.880606344901025,89 +High,NA,NA,C,2,Large,Left,b,23.303409945219755,34 +Medium,Green,No,B,3,Medium,Right,e,46.59624502528459,93 +Low,Red,NA,A,1,Small,Left,h,26.597264036536217,69 +Medium,Green,NA,B,3,Medium,Left,l,85.78277153428644,72 +Low,Red,No,A,1,Small,Right,m,4.583116667345166,76 +Low,Red,NA,A,1,Small,Left,r,44.220007420517504,63 +High,NA,NA,C,2,Large,Left,a,79.89248456433415,13 +Low,Red,NA,A,1,Small,Left,y,12.189925997518003,82 +Medium,Green,NA,B,3,Medium,Left,y,56.094798375852406,97 +Low,Red,No,A,1,Small,Right,f,20.65313896164298,91 +Low,Red,No,A,1,Small,Right,u,12.753165024332702,25 +High,NA,NA,C,2,Large,Left,o,75.33078643027693,38 +Low,Red,No,A,1,Small,Right,i,89.50453591533005,21 +Medium,Green,NA,B,3,Medium,Left,o,37.44627758860588,79 +Low,Red,NA,A,1,Small,Left,z,66.51151946280152,41 +High,NA,No,C,2,Large,Right,p,9.484066092409194,47 +Low,Red,No,A,1,Small,Right,t,38.39696377981454,90 +High,NA,NA,C,2,Large,Left,f,27.43836445733905,60 +Medium,Green,NA,B,3,Medium,Left,k,81.46400388795882,95 +High,NA,No,C,2,Large,Right,h,44.851634139195085,16 +Medium,Green,NA,B,3,Medium,Left,v,81.00643530488014,94 +Medium,Green,NA,B,3,Medium,Left,v,81.23895095195621,6 +High,NA,NA,C,2,Large,Left,g,79.43423211108893,72 +Medium,Green,NA,B,3,Medium,Left,p,43.983168760314584,86 +Medium,Green,No,B,3,Medium,Right,q,75.44751586392522,86 +High,NA,NA,C,2,Large,Left,v,62.922113155946136,39 +High,NA,NA,C,2,Large,Left,r,71.01824013516307,31 +Low,Red,NA,A,1,Small,Left,q,0.062477332539856434,81 +Medium,Green,NA,B,3,Medium,Left,b,47.53165740985423,50 +Medium,Green,No,B,3,Medium,Right,d,22.011888516135514,34 +Low,Red,No,A,1,Small,Right,m,37.98165377229452,4 +Medium,Green,NA,B,3,Medium,Left,e,61.277100327424705,13 +Low,Red,No,A,1,Small,Right,v,35.179790924303234,69 +Low,Red,No,A,1,Small,Right,s,11.113542434759438,25 +Medium,Green,No,B,3,Medium,Right,y,24.361947271972895,52 +High,NA,No,C,2,Large,Right,t,66.80555874481797,22 +High,NA,NA,C,2,Large,Left,v,41.764677967876196,89 +Low,Red,No,A,1,Small,Right,y,78.81958340294659,32 +Medium,Green,No,B,3,Medium,Right,n,10.286464425735176,25 +Low,Red,No,A,1,Small,Right,y,43.489274149760604,87 +Medium,Green,NA,B,3,Medium,Left,w,98.49569799844176,35 +Low,Red,NA,A,1,Small,Left,c,89.30511143989861,40 +High,NA,No,C,2,Large,Right,h,88.64690607879311,30 +High,NA,NA,C,2,Large,Left,p,17.505265027284622,12 +Medium,Green,No,B,3,Medium,Right,l,13.069569156505167,31 +High,NA,No,C,2,Large,Right,y,65.31019250396639,30 +Low,Red,NA,A,1,Small,Left,n,34.3516472261399,64 +Medium,Green,No,B,3,Medium,Right,c,65.67581279668957,99 +Medium,Green,No,B,3,Medium,Right,n,32.03732424881309,14 +High,NA,NA,C,2,Large,Left,g,18.769111926667392,93 +Medium,Green,NA,B,3,Medium,Left,c,78.22943013161421,96 +Low,Red,No,A,1,Small,Right,w,9.359498671256006,71 +High,NA,NA,C,2,Large,Left,v,46.677904156968,67 +High,NA,NA,C,2,Large,Left,z,51.15054599009454,23 diff --git a/tests/testthat/data_files/STANDARDISE/std_2.rda b/tests/testthat/data_files/STANDARDISE/std_2.rda new file mode 100644 index 00000000..cbe3d279 Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_2.rda differ diff --git a/tests/testthat/data_files/STANDARDISE/std_2_d.csv b/tests/testthat/data_files/STANDARDISE/std_2_d.csv new file mode 100644 index 00000000..0a5a46eb --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_2_d.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,fac_col7,fac_col10,col13,col16,col19 +High,NA,NA,C,2,Large,Left,o,28.7577520124614,31 +High,NA,NA,C,2,Large,Left,s,78.8305135443807,79 +High,NA,NA,C,2,Large,Left,n,40.89769218117,51 +Medium,Green,No,B,3,Medium,Right,c,88.3017404004931,14 +High,NA,NA,C,2,Large,Left,j,94.0467284293845,67 +Medium,Green,No,B,3,Medium,Right,r,4.55564993899316,42 +Medium,Green,No,B,3,Medium,Right,v,52.8105488047004,50 +Medium,Green,No,B,3,Medium,Right,k,89.2419044394046,43 +High,NA,NA,C,2,Large,Left,e,55.1435014465824,14 +Low,Red,NA,A,1,Small,Left,t,45.6614735303447,25 +Medium,Green,No,B,3,Medium,Right,n,95.6833345349878,90 +Medium,Green,No,B,3,Medium,Right,v,45.3334156190977,91 +Low,Red,No,A,1,Small,Right,y,67.7570635452867,69 +Medium,Green,NA,B,3,Medium,Left,z,57.2633401956409,91 +High,NA,No,C,2,Large,Right,e,10.2924682665616,57 +Low,Red,NA,A,1,Small,Left,s,89.9824970401824,92 +High,NA,No,C,2,Large,Right,y,24.608773435466,9 +High,NA,NA,C,2,Large,Left,y,4.20595335308462,93 +Low,Red,NA,A,1,Small,Left,i,32.7920719282702,99 +Low,Red,NA,A,1,Small,Left,c,95.4503649147227,72 +Low,Red,NA,A,1,Small,Left,h,88.9539316063747,26 +Low,Red,No,A,1,Small,Right,z,69.28034061566,7 +High,NA,NA,C,2,Large,Left,g,64.0506813768297,42 +Medium,Green,NA,B,3,Medium,Left,j,99.4269776623696,9 +High,NA,NA,C,2,Large,Left,i,65.5705799115822,83 +Medium,Green,NA,B,3,Medium,Left,s,70.8530468167737,36 +Low,Red,No,A,1,Small,Right,d,54.4066024711356,78 +Medium,Green,No,B,3,Medium,Right,n,59.414202044718,81 +High,NA,NA,C,2,Large,Left,q,28.915973729454,43 +Medium,Green,No,B,3,Medium,Right,k,14.7113647311926,76 +Low,Red,NA,A,1,Small,Left,g,96.3024232536554,15 +High,NA,No,C,2,Large,Right,u,90.2299045119435,32 +High,NA,NA,C,2,Large,Left,l,69.0705278422683,7 +Low,Red,No,A,1,Small,Right,o,79.5467417687178,9 +High,NA,No,C,2,Large,Right,j,2.46136845089495,41 +Medium,Green,NA,B,3,Medium,Left,m,47.7795971091837,74 +Low,Red,NA,A,1,Small,Left,g,75.8459537522867,23 +High,NA,NA,C,2,Large,Left,i,21.6407935833558,27 +Low,Red,NA,A,1,Small,Left,i,31.8181007634848,60 +Low,Red,No,A,1,Small,Right,j,23.1625785352662,53 +Medium,Green,NA,B,3,Medium,Left,w,14.2800022382289,7 +High,NA,No,C,2,Large,Right,u,41.4546335814521,53 +High,NA,No,C,2,Large,Right,g,41.3724326295778,27 +Low,Red,NA,A,1,Small,Left,u,36.8845450924709,96 +High,NA,NA,C,2,Large,Left,f,15.2444747742265,38 +Low,Red,NA,A,1,Small,Left,y,13.880606344901,89 +High,NA,NA,C,2,Large,Left,b,23.3034099452198,34 +Medium,Green,No,B,3,Medium,Right,e,46.5962450252846,93 +Low,Red,NA,A,1,Small,Left,h,26.5972640365362,69 +Medium,Green,NA,B,3,Medium,Left,l,85.7827715342864,72 +Low,Red,No,A,1,Small,Right,m,4.58311666734517,76 +Low,Red,NA,A,1,Small,Left,r,44.2200074205175,63 +High,NA,NA,C,2,Large,Left,a,79.8924845643342,13 +Low,Red,NA,A,1,Small,Left,y,12.189925997518,82 +Medium,Green,NA,B,3,Medium,Left,y,56.0947983758524,97 +Low,Red,No,A,1,Small,Right,f,20.653138961643,91 +Low,Red,No,A,1,Small,Right,u,12.7531650243327,25 +High,NA,NA,C,2,Large,Left,o,75.3307864302769,38 +Low,Red,No,A,1,Small,Right,i,89.50453591533,21 +Medium,Green,NA,B,3,Medium,Left,o,37.4462775886059,79 +Low,Red,NA,A,1,Small,Left,z,66.5115194628015,41 +High,NA,No,C,2,Large,Right,p,9.48406609240919,47 +Low,Red,No,A,1,Small,Right,t,38.3969637798145,90 +High,NA,NA,C,2,Large,Left,f,27.438364457339,60 +Medium,Green,NA,B,3,Medium,Left,k,81.4640038879588,95 +High,NA,No,C,2,Large,Right,h,44.8516341391951,16 +Medium,Green,NA,B,3,Medium,Left,v,81.0064353048801,94 +Medium,Green,NA,B,3,Medium,Left,v,81.2389509519562,6 +High,NA,NA,C,2,Large,Left,g,79.4342321110889,72 +Medium,Green,NA,B,3,Medium,Left,p,43.9831687603146,86 +Medium,Green,No,B,3,Medium,Right,q,75.4475158639252,86 +High,NA,NA,C,2,Large,Left,v,62.9221131559461,39 +High,NA,NA,C,2,Large,Left,r,71.0182401351631,31 +Low,Red,NA,A,1,Small,Left,q,0.0624773325398564,81 +Medium,Green,NA,B,3,Medium,Left,b,47.5316574098542,50 +Medium,Green,No,B,3,Medium,Right,d,22.0118885161355,34 +Low,Red,No,A,1,Small,Right,m,37.9816537722945,4 +Medium,Green,NA,B,3,Medium,Left,e,61.2771003274247,13 +Low,Red,No,A,1,Small,Right,v,35.1797909243032,69 +Low,Red,No,A,1,Small,Right,s,11.1135424347594,25 +Medium,Green,No,B,3,Medium,Right,y,24.3619472719729,52 +High,NA,No,C,2,Large,Right,t,66.805558744818,22 +High,NA,NA,C,2,Large,Left,v,41.7646779678762,89 +Low,Red,No,A,1,Small,Right,y,78.8195834029466,32 +Medium,Green,No,B,3,Medium,Right,n,10.2864644257352,25 +Low,Red,No,A,1,Small,Right,y,43.4892741497606,87 +Medium,Green,NA,B,3,Medium,Left,w,98.4956979984418,35 +Low,Red,NA,A,1,Small,Left,c,89.3051114398986,40 +High,NA,No,C,2,Large,Right,h,88.6469060787931,30 +High,NA,NA,C,2,Large,Left,p,17.5052650272846,12 +Medium,Green,No,B,3,Medium,Right,l,13.0695691565052,31 +High,NA,No,C,2,Large,Right,y,65.3101925039664,30 +Low,Red,NA,A,1,Small,Left,n,34.3516472261399,64 +Medium,Green,No,B,3,Medium,Right,c,65.6758127966896,99 +Medium,Green,No,B,3,Medium,Right,n,32.0373242488131,14 +High,NA,NA,C,2,Large,Left,g,18.7691119266674,93 +Medium,Green,NA,B,3,Medium,Left,c,78.2294301316142,96 +Low,Red,No,A,1,Small,Right,w,9.35949867125601,71 +High,NA,NA,C,2,Large,Left,v,46.677904156968,67 +High,NA,NA,C,2,Large,Left,z,51.1505459900945,23 diff --git a/tests/testthat/data_files/STANDARDISE/std_2_d.rda b/tests/testthat/data_files/STANDARDISE/std_2_d.rda new file mode 100644 index 00000000..cad2198a Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_2_d.rda differ diff --git a/tests/testthat/data_files/STANDARDISE/std_3.csv b/tests/testthat/data_files/STANDARDISE/std_3.csv new file mode 100644 index 00000000..583c9a22 --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_3.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,col11,col14,col17,col20 +High,Blue,Yes,C,Three,31,TRUE,o,28.757752012461424 +High,Blue,Yes,C,Three,79,TRUE,s,78.83051354438066 +High,Blue,Yes,C,Three,51,TRUE,n,40.89769218116999 +Medium,NA,NA,B,Two,14,FALSE,c,88.301740400493145 +High,Blue,Yes,C,Three,67,TRUE,j,94.04672842938453 +Medium,NA,NA,B,Two,42,FALSE,r,4.555649938993156 +Medium,NA,NA,B,Two,50,FALSE,v,52.810548804700375 +Medium,NA,NA,B,Two,43,FALSE,k,89.2419044394046 +High,Blue,Yes,C,Three,14,TRUE,e,55.14350144658238 +Low,NA,Yes,A,One,25,TRUE,t,45.661473530344665 +Medium,NA,NA,B,Two,90,FALSE,n,95.68333453498781 +Medium,NA,NA,B,Two,91,FALSE,v,45.33341561909765 +Low,NA,NA,A,One,69,FALSE,y,67.75706354528666 +Medium,NA,Yes,B,Two,91,TRUE,z,57.26334019564092 +High,Blue,NA,C,Three,57,FALSE,e,10.292468266561627 +Low,NA,Yes,A,One,92,TRUE,s,89.98249704018235 +High,Blue,NA,C,Three,9,FALSE,y,24.60877343546599 +High,Blue,Yes,C,Three,93,TRUE,y,4.205953353084624 +Low,NA,Yes,A,One,99,TRUE,i,32.79207192827016 +Low,NA,Yes,A,One,72,TRUE,c,95.45036491472274 +Low,NA,Yes,A,One,26,TRUE,h,88.95393160637468 +Low,NA,NA,A,One,7,FALSE,z,69.28034061565995 +High,Blue,Yes,C,Three,42,TRUE,g,64.05068137682974 +Medium,NA,Yes,B,Two,9,TRUE,j,99.42697766236961 +High,Blue,Yes,C,Three,83,TRUE,i,65.57057991158217 +Medium,NA,Yes,B,Two,36,TRUE,s,70.85304681677371 +Low,NA,NA,A,One,78,FALSE,d,54.40660247113556 +Medium,NA,NA,B,Two,81,FALSE,n,59.41420204471797 +High,Blue,Yes,C,Three,43,TRUE,q,28.91597372945398 +Medium,NA,NA,B,Two,76,FALSE,k,14.711364731192589 +Low,NA,Yes,A,One,15,TRUE,g,96.30242325365543 +High,Blue,NA,C,Three,32,FALSE,u,90.22990451194346 +High,Blue,Yes,C,Three,7,TRUE,l,69.07052784226835 +Low,NA,NA,A,One,9,FALSE,o,79.54674176871777 +High,Blue,NA,C,Three,41,FALSE,j,2.461368450894952 +Medium,NA,Yes,B,Two,74,TRUE,m,47.77959710918367 +Low,NA,Yes,A,One,23,TRUE,g,75.84595375228673 +High,Blue,Yes,C,Three,27,TRUE,i,21.640793583355844 +Low,NA,Yes,A,One,60,TRUE,i,31.818100763484836 +Low,NA,NA,A,One,53,FALSE,j,23.16257853526622 +Medium,NA,Yes,B,Two,7,TRUE,w,14.280002238228917 +High,Blue,NA,C,Three,53,FALSE,u,41.45463358145207 +High,Blue,NA,C,Three,27,FALSE,g,41.372432629577816 +Low,NA,Yes,A,One,96,TRUE,u,36.884545092470944 +High,Blue,Yes,C,Three,38,TRUE,f,15.244474774226546 +Low,NA,Yes,A,One,89,TRUE,y,13.880606344901025 +High,Blue,Yes,C,Three,34,TRUE,b,23.303409945219755 +Medium,NA,NA,B,Two,93,FALSE,e,46.59624502528459 +Low,NA,Yes,A,One,69,TRUE,h,26.597264036536217 +Medium,NA,Yes,B,Two,72,TRUE,l,85.78277153428644 +Low,NA,NA,A,One,76,FALSE,m,4.583116667345166 +Low,NA,Yes,A,One,63,TRUE,r,44.220007420517504 +High,Blue,Yes,C,Three,13,TRUE,a,79.89248456433415 +Low,NA,Yes,A,One,82,TRUE,y,12.189925997518003 +Medium,NA,Yes,B,Two,97,TRUE,y,56.094798375852406 +Low,NA,NA,A,One,91,FALSE,f,20.65313896164298 +Low,NA,NA,A,One,25,FALSE,u,12.753165024332702 +High,Blue,Yes,C,Three,38,TRUE,o,75.33078643027693 +Low,NA,NA,A,One,21,FALSE,i,89.50453591533005 +Medium,NA,Yes,B,Two,79,TRUE,o,37.44627758860588 +Low,NA,Yes,A,One,41,TRUE,z,66.51151946280152 +High,Blue,NA,C,Three,47,FALSE,p,9.484066092409194 +Low,NA,NA,A,One,90,FALSE,t,38.39696377981454 +High,Blue,Yes,C,Three,60,TRUE,f,27.43836445733905 +Medium,NA,Yes,B,Two,95,TRUE,k,81.46400388795882 +High,Blue,NA,C,Three,16,FALSE,h,44.851634139195085 +Medium,NA,Yes,B,Two,94,TRUE,v,81.00643530488014 +Medium,NA,Yes,B,Two,6,TRUE,v,81.23895095195621 +High,Blue,Yes,C,Three,72,TRUE,g,79.43423211108893 +Medium,NA,Yes,B,Two,86,TRUE,p,43.983168760314584 +Medium,NA,NA,B,Two,86,FALSE,q,75.44751586392522 +High,Blue,Yes,C,Three,39,TRUE,v,62.922113155946136 +High,Blue,Yes,C,Three,31,TRUE,r,71.01824013516307 +Low,NA,Yes,A,One,81,TRUE,q,0.062477332539856434 +Medium,NA,Yes,B,Two,50,TRUE,b,47.53165740985423 +Medium,NA,NA,B,Two,34,FALSE,d,22.011888516135514 +Low,NA,NA,A,One,4,FALSE,m,37.98165377229452 +Medium,NA,Yes,B,Two,13,TRUE,e,61.277100327424705 +Low,NA,NA,A,One,69,FALSE,v,35.179790924303234 +Low,NA,NA,A,One,25,FALSE,s,11.113542434759438 +Medium,NA,NA,B,Two,52,FALSE,y,24.361947271972895 +High,Blue,NA,C,Three,22,FALSE,t,66.80555874481797 +High,Blue,Yes,C,Three,89,TRUE,v,41.764677967876196 +Low,NA,NA,A,One,32,FALSE,y,78.81958340294659 +Medium,NA,NA,B,Two,25,FALSE,n,10.286464425735176 +Low,NA,NA,A,One,87,FALSE,y,43.489274149760604 +Medium,NA,Yes,B,Two,35,TRUE,w,98.49569799844176 +Low,NA,Yes,A,One,40,TRUE,c,89.30511143989861 +High,Blue,NA,C,Three,30,FALSE,h,88.64690607879311 +High,Blue,Yes,C,Three,12,TRUE,p,17.505265027284622 +Medium,NA,NA,B,Two,31,FALSE,l,13.069569156505167 +High,Blue,NA,C,Three,30,FALSE,y,65.31019250396639 +Low,NA,Yes,A,One,64,TRUE,n,34.3516472261399 +Medium,NA,NA,B,Two,99,FALSE,c,65.67581279668957 +Medium,NA,NA,B,Two,14,FALSE,n,32.03732424881309 +High,Blue,Yes,C,Three,93,TRUE,g,18.769111926667392 +Medium,NA,Yes,B,Two,96,TRUE,c,78.22943013161421 +Low,NA,NA,A,One,71,FALSE,w,9.359498671256006 +High,Blue,Yes,C,Three,67,TRUE,v,46.677904156968 +High,Blue,Yes,C,Three,23,TRUE,z,51.15054599009454 diff --git a/tests/testthat/data_files/STANDARDISE/std_3.rda b/tests/testthat/data_files/STANDARDISE/std_3.rda new file mode 100644 index 00000000..80362674 Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_3.rda differ diff --git a/tests/testthat/data_files/STANDARDISE/std_3_d.csv b/tests/testthat/data_files/STANDARDISE/std_3_d.csv new file mode 100644 index 00000000..5dfce08f --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_3_d.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,col11,col14,col17,col20 +High,Blue,Yes,C,Three,31,TRUE,o,28.7577520124614 +High,Blue,Yes,C,Three,79,TRUE,s,78.8305135443807 +High,Blue,Yes,C,Three,51,TRUE,n,40.89769218117 +Medium,NA,NA,B,Two,14,FALSE,c,88.3017404004931 +High,Blue,Yes,C,Three,67,TRUE,j,94.0467284293845 +Medium,NA,NA,B,Two,42,FALSE,r,4.55564993899316 +Medium,NA,NA,B,Two,50,FALSE,v,52.8105488047004 +Medium,NA,NA,B,Two,43,FALSE,k,89.2419044394046 +High,Blue,Yes,C,Three,14,TRUE,e,55.1435014465824 +Low,NA,Yes,A,One,25,TRUE,t,45.6614735303447 +Medium,NA,NA,B,Two,90,FALSE,n,95.6833345349878 +Medium,NA,NA,B,Two,91,FALSE,v,45.3334156190977 +Low,NA,NA,A,One,69,FALSE,y,67.7570635452867 +Medium,NA,Yes,B,Two,91,TRUE,z,57.2633401956409 +High,Blue,NA,C,Three,57,FALSE,e,10.2924682665616 +Low,NA,Yes,A,One,92,TRUE,s,89.9824970401824 +High,Blue,NA,C,Three,9,FALSE,y,24.608773435466 +High,Blue,Yes,C,Three,93,TRUE,y,4.20595335308462 +Low,NA,Yes,A,One,99,TRUE,i,32.7920719282702 +Low,NA,Yes,A,One,72,TRUE,c,95.4503649147227 +Low,NA,Yes,A,One,26,TRUE,h,88.9539316063747 +Low,NA,NA,A,One,7,FALSE,z,69.28034061566 +High,Blue,Yes,C,Three,42,TRUE,g,64.0506813768297 +Medium,NA,Yes,B,Two,9,TRUE,j,99.4269776623696 +High,Blue,Yes,C,Three,83,TRUE,i,65.5705799115822 +Medium,NA,Yes,B,Two,36,TRUE,s,70.8530468167737 +Low,NA,NA,A,One,78,FALSE,d,54.4066024711356 +Medium,NA,NA,B,Two,81,FALSE,n,59.414202044718 +High,Blue,Yes,C,Three,43,TRUE,q,28.915973729454 +Medium,NA,NA,B,Two,76,FALSE,k,14.7113647311926 +Low,NA,Yes,A,One,15,TRUE,g,96.3024232536554 +High,Blue,NA,C,Three,32,FALSE,u,90.2299045119435 +High,Blue,Yes,C,Three,7,TRUE,l,69.0705278422683 +Low,NA,NA,A,One,9,FALSE,o,79.5467417687178 +High,Blue,NA,C,Three,41,FALSE,j,2.46136845089495 +Medium,NA,Yes,B,Two,74,TRUE,m,47.7795971091837 +Low,NA,Yes,A,One,23,TRUE,g,75.8459537522867 +High,Blue,Yes,C,Three,27,TRUE,i,21.6407935833558 +Low,NA,Yes,A,One,60,TRUE,i,31.8181007634848 +Low,NA,NA,A,One,53,FALSE,j,23.1625785352662 +Medium,NA,Yes,B,Two,7,TRUE,w,14.2800022382289 +High,Blue,NA,C,Three,53,FALSE,u,41.4546335814521 +High,Blue,NA,C,Three,27,FALSE,g,41.3724326295778 +Low,NA,Yes,A,One,96,TRUE,u,36.8845450924709 +High,Blue,Yes,C,Three,38,TRUE,f,15.2444747742265 +Low,NA,Yes,A,One,89,TRUE,y,13.880606344901 +High,Blue,Yes,C,Three,34,TRUE,b,23.3034099452198 +Medium,NA,NA,B,Two,93,FALSE,e,46.5962450252846 +Low,NA,Yes,A,One,69,TRUE,h,26.5972640365362 +Medium,NA,Yes,B,Two,72,TRUE,l,85.7827715342864 +Low,NA,NA,A,One,76,FALSE,m,4.58311666734517 +Low,NA,Yes,A,One,63,TRUE,r,44.2200074205175 +High,Blue,Yes,C,Three,13,TRUE,a,79.8924845643342 +Low,NA,Yes,A,One,82,TRUE,y,12.189925997518 +Medium,NA,Yes,B,Two,97,TRUE,y,56.0947983758524 +Low,NA,NA,A,One,91,FALSE,f,20.653138961643 +Low,NA,NA,A,One,25,FALSE,u,12.7531650243327 +High,Blue,Yes,C,Three,38,TRUE,o,75.3307864302769 +Low,NA,NA,A,One,21,FALSE,i,89.50453591533 +Medium,NA,Yes,B,Two,79,TRUE,o,37.4462775886059 +Low,NA,Yes,A,One,41,TRUE,z,66.5115194628015 +High,Blue,NA,C,Three,47,FALSE,p,9.48406609240919 +Low,NA,NA,A,One,90,FALSE,t,38.3969637798145 +High,Blue,Yes,C,Three,60,TRUE,f,27.438364457339 +Medium,NA,Yes,B,Two,95,TRUE,k,81.4640038879588 +High,Blue,NA,C,Three,16,FALSE,h,44.8516341391951 +Medium,NA,Yes,B,Two,94,TRUE,v,81.0064353048801 +Medium,NA,Yes,B,Two,6,TRUE,v,81.2389509519562 +High,Blue,Yes,C,Three,72,TRUE,g,79.4342321110889 +Medium,NA,Yes,B,Two,86,TRUE,p,43.9831687603146 +Medium,NA,NA,B,Two,86,FALSE,q,75.4475158639252 +High,Blue,Yes,C,Three,39,TRUE,v,62.9221131559461 +High,Blue,Yes,C,Three,31,TRUE,r,71.0182401351631 +Low,NA,Yes,A,One,81,TRUE,q,0.0624773325398564 +Medium,NA,Yes,B,Two,50,TRUE,b,47.5316574098542 +Medium,NA,NA,B,Two,34,FALSE,d,22.0118885161355 +Low,NA,NA,A,One,4,FALSE,m,37.9816537722945 +Medium,NA,Yes,B,Two,13,TRUE,e,61.2771003274247 +Low,NA,NA,A,One,69,FALSE,v,35.1797909243032 +Low,NA,NA,A,One,25,FALSE,s,11.1135424347594 +Medium,NA,NA,B,Two,52,FALSE,y,24.3619472719729 +High,Blue,NA,C,Three,22,FALSE,t,66.805558744818 +High,Blue,Yes,C,Three,89,TRUE,v,41.7646779678762 +Low,NA,NA,A,One,32,FALSE,y,78.8195834029466 +Medium,NA,NA,B,Two,25,FALSE,n,10.2864644257352 +Low,NA,NA,A,One,87,FALSE,y,43.4892741497606 +Medium,NA,Yes,B,Two,35,TRUE,w,98.4956979984418 +Low,NA,Yes,A,One,40,TRUE,c,89.3051114398986 +High,Blue,NA,C,Three,30,FALSE,h,88.6469060787931 +High,Blue,Yes,C,Three,12,TRUE,p,17.5052650272846 +Medium,NA,NA,B,Two,31,FALSE,l,13.0695691565052 +High,Blue,NA,C,Three,30,FALSE,y,65.3101925039664 +Low,NA,Yes,A,One,64,TRUE,n,34.3516472261399 +Medium,NA,NA,B,Two,99,FALSE,c,65.6758127966896 +Medium,NA,NA,B,Two,14,FALSE,n,32.0373242488131 +High,Blue,Yes,C,Three,93,TRUE,g,18.7691119266674 +Medium,NA,Yes,B,Two,96,TRUE,c,78.2294301316142 +Low,NA,NA,A,One,71,FALSE,w,9.35949867125601 +High,Blue,Yes,C,Three,67,TRUE,v,46.677904156968 +High,Blue,Yes,C,Three,23,TRUE,z,51.1505459900945 diff --git a/tests/testthat/data_files/STANDARDISE/std_3_d.rda b/tests/testthat/data_files/STANDARDISE/std_3_d.rda new file mode 100644 index 00000000..4165f098 Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_3_d.rda differ diff --git 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)