diff --git a/armadillo_azure-pipelines.yml b/armadillo_azure-pipelines.yml index 4a26a02d..347288fe 100644 --- a/armadillo_azure-pipelines.yml +++ b/armadillo_azure-pipelines.yml @@ -59,10 +59,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.5-dev + displayName: Nightly build - v6.3.6-dev branches: include: - - v6.3.5-dev + - v6.3.6-dev always: true ######################################################################################### @@ -133,7 +133,7 @@ jobs: sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')" diff --git a/azure-pipelines.yml b/azure-pipelines.yml index bfddaa03..4b16d07a 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -45,10 +45,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.5-dev + displayName: Nightly build - v6.3.6-dev branches: include: - - v6.3.5-dev + - v6.3.6-dev always: true ######################################################################################### @@ -114,7 +114,7 @@ jobs: sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" diff --git a/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index bfddaa03..4b16d07a 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -45,10 +45,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.5-dev + displayName: Nightly build - v6.3.6-dev branches: include: - - v6.3.5-dev + - v6.3.6-dev always: true ######################################################################################### @@ -114,7 +114,7 @@ jobs: sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" diff --git a/tests/testthat/connection_to_datasets/init_discordant_datasets.R b/tests/testthat/connection_to_datasets/init_discordant_datasets.R index a117deb7..b701f67d 100644 --- a/tests/testthat/connection_to_datasets/init_discordant_datasets.R +++ b/tests/testthat/connection_to_datasets/init_discordant_datasets.R @@ -5,17 +5,17 @@ init.discordant.dataset.simple <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "discordant1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "DISCORDANT.DISCORDANT_STUDY1", options=ds.test_env$options_1) - builder$append(server = "discordant2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "DISCORDANT.DISCORDANT_STUDY2", options=ds.test_env$options_2) - builder$append(server = "discordant3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "DISCORDANT.DISCORDANT_STUDY3", options=ds.test_env$options_3) + builder$append(server = "discordant1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "DISCORDANT.DISCORDANT_STUDY1", options=ds.test_env$options_1) + builder$append(server = "discordant2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "DISCORDANT.DISCORDANT_STUDY2", options=ds.test_env$options_2) + builder$append(server = "discordant3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "DISCORDANT.DISCORDANT_STUDY3", 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$append(server = "discordant1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/discordant/DISCORDANT_STUDY1", driver = "ArmadilloDriver") - builder$append(server = "discordant2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/discordant/DISCORDANT_STUDY2", driver = "ArmadilloDriver") - builder$append(server = "discordant3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/discordant/DISCORDANT_STUDY3", driver = "ArmadilloDriver") + builder$append(server = "discordant1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/discordant/DISCORDANT_STUDY1", driver = "ArmadilloDriver") + builder$append(server = "discordant2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/discordant/DISCORDANT_STUDY2", driver = "ArmadilloDriver") + builder$append(server = "discordant3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/discordant/DISCORDANT_STUDY3", driver = "ArmadilloDriver") ds.test_env$login.data <- builder$build() } else diff --git a/tests/testthat/connection_to_datasets/init_local_settings.R b/tests/testthat/connection_to_datasets/init_local_settings.R index 11ac245f..c3fc555a 100644 --- a/tests/testthat/connection_to_datasets/init_local_settings.R +++ b/tests/testthat/connection_to_datasets/init_local_settings.R @@ -1,28 +1,33 @@ -#this file stores some settings for the continuous integration and local testing. +# +# The file "connection_to_datasets/local_settings.csv" (within the directory "tests/testthat") contains, if present, +# values which can be used to affect the behavious of the continuous integration. +# +# The server URL is in a CVS file, being the value of the first column, first row. +# -init.ip.address <- function() +init.server.url <- function() { file.name <- init.local.settings() if (file.exists(file.name)) { - content <- read.csv(file.name, header = FALSE) - ip.address <- as.character(content[[1]][1]) + content <- read.csv(file.name, header = FALSE) + server.url <- as.character(content[[1]][1]) } else { - # ip.address <- "127.0.0.1" - ip.address <- "localhost" + # server.url <- "http://127.0.0.1:8080/" + server.url <- "http://localhost:8080/" } - return (ip.address) + return (server.url) } init.local.settings <- function() { - path <- getwd() + path <- getwd() sub.folder.name <- "/connection_to_datasets/" - file.name <- "local_settings.csv" - return(paste(path, sub.folder.name,file.name, sep="")) - + file.name <- "local_settings.csv" + + return(paste(path, sub.folder.name, file.name, sep="")) } diff --git a/tests/testthat/connection_to_datasets/init_mediation_datasets.R b/tests/testthat/connection_to_datasets/init_mediation_datasets.R index 479266ec..89e5f8e6 100644 --- a/tests/testthat/connection_to_datasets/init_mediation_datasets.R +++ b/tests/testthat/connection_to_datasets/init_mediation_datasets.R @@ -5,9 +5,9 @@ init.mediation.dataset.upb <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.UPBdata1", options=ds.test_env$options_1) - builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "MEDIATION.UPBdata2", options=ds.test_env$options_2) - builder$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "MEDIATION.UPBdata3", options=ds.test_env$options_3) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.UPBdata1", options=ds.test_env$options_1) + builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "MEDIATION.UPBdata2", options=ds.test_env$options_2) + builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "MEDIATION.UPBdata3", options=ds.test_env$options_3) ds.test_env$login.data <- builder$build() } else @@ -25,7 +25,7 @@ init.mediation.dataset.student <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.student", options=ds.test_env$options_1) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.student", options=ds.test_env$options_1) ds.test_env$login.data <- builder$build() } else @@ -43,7 +43,7 @@ init.mediation.dataset.framing <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.framing", options=ds.test_env$options_1) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.framing", options=ds.test_env$options_1) ds.test_env$login.data <- builder$build() } else @@ -61,7 +61,7 @@ init.mediation.dataset.vv2015 <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.vv2015", options=ds.test_env$options_1) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.vv2015", options=ds.test_env$options_1) ds.test_env$login.data <- builder$build() } else diff --git a/tests/testthat/connection_to_datasets/init_studies_datasets.R b/tests/testthat/connection_to_datasets/init_studies_datasets.R index 0639aac6..58126a60 100644 --- a/tests/testthat/connection_to_datasets/init_studies_datasets.R +++ b/tests/testthat/connection_to_datasets/init_studies_datasets.R @@ -5,17 +5,17 @@ init.studies.dataset.cnsim <- function(variables) 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$password_1, table = "CNSIM.CNSIM1", options=ds.test_env$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 = "CNSIM.CNSIM2", 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$password_3, table = "CNSIM.CNSIM3", options=ds.test_env$options_3) + builder$append(server = "sim1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "CNSIM.CNSIM1", options=ds.test_env$options_1) + builder$append(server = "sim2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "CNSIM.CNSIM2", options=ds.test_env$options_2) + builder$append(server = "sim3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "CNSIM.CNSIM3", 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/cnsim/CNSIM1", 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$password_2, table = "datashield/cnsim/CNSIM2", driver = ds.test_env$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/cnsim/CNSIM3", driver = ds.test_env$driver) + builder$append(server = "sim1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/cnsim/CNSIM1", driver = ds.test_env$driver) + builder$append(server = "sim2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/cnsim/CNSIM2", driver = ds.test_env$driver) + builder$append(server = "sim3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/cnsim/CNSIM3", driver = ds.test_env$driver) ds.test_env$login.data <- builder$build() } else @@ -33,17 +33,17 @@ init.studies.dataset.dasim <- function(variables) 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$password_1, table = "DASIM.DASIM1", options=ds.test_env$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 = "DASIM.DASIM2", 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$password_3, table = "DASIM.DASIM3", options=ds.test_env$options_3) + builder$append(server = "sim1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "DASIM.DASIM1", options=ds.test_env$options_1) + builder$append(server = "sim2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "DASIM.DASIM2", options=ds.test_env$options_2) + builder$append(server = "sim3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "DASIM.DASIM3", 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/dasim/DASIM1", 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$password_2, table = "datashield/dasim/DASIM2", driver = ds.test_env$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/dasim/DASIM3", driver = ds.test_env$driver) + builder$append(server = "sim1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/dasim/DASIM1", driver = ds.test_env$driver) + builder$append(server = "sim2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/dasim/DASIM2", driver = ds.test_env$driver) + builder$append(server = "sim3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/dasim/DASIM3", driver = ds.test_env$driver) ds.test_env$login.data <- builder$build() } else @@ -61,17 +61,17 @@ init.studies.dataset.survival <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "survival1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "SURVIVAL.EXPAND_WITH_MISSING1", options=ds.test_env$options_1) - builder$append(server = "survival2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "SURVIVAL.EXPAND_WITH_MISSING2", options=ds.test_env$options_2) - builder$append(server = "survival3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "SURVIVAL.EXPAND_WITH_MISSING3", options=ds.test_env$options_3) + builder$append(server = "survival1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "SURVIVAL.EXPAND_WITH_MISSING1", options=ds.test_env$options_1) + builder$append(server = "survival2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "SURVIVAL.EXPAND_WITH_MISSING2", options=ds.test_env$options_2) + builder$append(server = "survival3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "SURVIVAL.EXPAND_WITH_MISSING3", 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$append(server = "survival1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/survival/EXPAND_WITH_MISSING1", driver = ds.test_env$driver) - builder$append(server = "survival2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/survival/EXPAND_WITH_MISSING2", driver = ds.test_env$driver) - builder$append(server = "survival3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/survival/EXPAND_WITH_MISSING3", driver = ds.test_env$driver) + builder$append(server = "survival1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/survival/EXPAND_WITH_MISSING1", driver = ds.test_env$driver) + builder$append(server = "survival2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/survival/EXPAND_WITH_MISSING2", driver = ds.test_env$driver) + builder$append(server = "survival3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/survival/EXPAND_WITH_MISSING3", driver = ds.test_env$driver) ds.test_env$login.data <- builder$build() } else @@ -94,17 +94,17 @@ init.studies.dataset.cluster.int <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "cluster.int1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "CLUSTER.CLUSTER_INT1", options=ds.test_env$options_1) - builder$append(server = "cluster.int2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "CLUSTER.CLUSTER_INT2", options=ds.test_env$options_2) - builder$append(server = "cluster.int3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "CLUSTER.CLUSTER_INT3", options=ds.test_env$options_3) + builder$append(server = "cluster.int1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "CLUSTER.CLUSTER_INT1", options=ds.test_env$options_1) + builder$append(server = "cluster.int2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "CLUSTER.CLUSTER_INT2", options=ds.test_env$options_2) + builder$append(server = "cluster.int3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "CLUSTER.CLUSTER_INT3", 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$append(server = "cluster.int1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/cluster/CLUSTER_INT1", driver = ds.test_env$driver) - builder$append(server = "cluster.int2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/cluster/CLUSTER_INT2", driver = ds.test_env$driver) - builder$append(server = "cluster.int3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/cluster/CLUSTER_INT3", driver = ds.test_env$driver) + builder$append(server = "cluster.int1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/cluster/CLUSTER_INT1", driver = ds.test_env$driver) + builder$append(server = "cluster.int2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/cluster/CLUSTER_INT2", driver = ds.test_env$driver) + builder$append(server = "cluster.int3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/cluster/CLUSTER_INT3", driver = ds.test_env$driver) ds.test_env$login.data <- builder$build() } else @@ -128,17 +128,17 @@ init.studies.dataset.cluster.slo <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "cluster.slo1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "CLUSTER.CLUSTER_SLO1", options=ds.test_env$options_1) - builder$append(server = "cluster.slo2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "CLUSTER.CLUSTER_SLO2", options=ds.test_env$options_2) - builder$append(server = "cluster.slo3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "CLUSTER.CLUSTER_SLO3", options=ds.test_env$options_3) + builder$append(server = "cluster.slo1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "CLUSTER.CLUSTER_SLO1", options=ds.test_env$options_1) + builder$append(server = "cluster.slo2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "CLUSTER.CLUSTER_SLO2", options=ds.test_env$options_2) + builder$append(server = "cluster.slo3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "CLUSTER.CLUSTER_SLO3", 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$append(server = "cluster.slo1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/cluster/CLUSTER_SLO1", driver = ds.test_env$driver) - builder$append(server = "cluster.slo2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/cluster/CLUSTER_SLO2", driver = ds.test_env$driver) - builder$append(server = "cluster.slo3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/cluster/CLUSTER_SLO3", driver = ds.test_env$driver) + builder$append(server = "cluster.slo1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/cluster/CLUSTER_SLO1", driver = ds.test_env$driver) + builder$append(server = "cluster.slo2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/cluster/CLUSTER_SLO2", driver = ds.test_env$driver) + builder$append(server = "cluster.slo3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/cluster/CLUSTER_SLO3", driver = ds.test_env$driver) ds.test_env$login.data <- builder$build() } else @@ -163,17 +163,17 @@ init.studies.dataset.anthro <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "ANTHRO.anthro1", options=ds.test_env$options_1) - builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "ANTHRO.anthro2", options=ds.test_env$options_2) - builder$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "ANTHRO.anthro3", options=ds.test_env$options_3) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "ANTHRO.anthro1", options=ds.test_env$options_1) + builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "ANTHRO.anthro2", options=ds.test_env$options_2) + builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "ANTHRO.anthro3", 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$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/anthro/anthro1", driver = ds.test_env$driver) - builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/anthro/anthro2", driver = ds.test_env$driver) - builder$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/anthro/anthro3", driver = ds.test_env$driver) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/anthro/anthro1", driver = ds.test_env$driver) + builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/anthro/anthro2", driver = ds.test_env$driver) + builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/anthro/anthro3", driver = ds.test_env$driver) ds.test_env$login.data <- builder$build() } else @@ -198,17 +198,17 @@ init.studies.dataset.gamlss <- function(variables) if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "GAMLSS.gamlss1", options=ds.test_env$options_1) - builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "GAMLSS.gamlss2", options=ds.test_env$options_2) - builder$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "GAMLSS.gamlss3", options=ds.test_env$options_3) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "GAMLSS.gamlss1", options=ds.test_env$options_1) + builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "GAMLSS.gamlss2", options=ds.test_env$options_2) + builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "GAMLSS.gamlss3", 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$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/gamlss/gamlss1", driver = ds.test_env$driver) - builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/gamlss/gamlss2", driver = ds.test_env$driver) - builder$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/gamlss/gamlss3", driver = ds.test_env$driver) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/gamlss/gamlss1", driver = ds.test_env$driver) + builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/gamlss/gamlss2", driver = ds.test_env$driver) + builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/gamlss/gamlss3", driver = ds.test_env$driver) ds.test_env$login.data <- builder$build() } else diff --git a/tests/testthat/connection_to_datasets/init_testing_datasets.R b/tests/testthat/connection_to_datasets/init_testing_datasets.R index 52fb7fcf..ff445777 100644 --- a/tests/testthat/connection_to_datasets/init_testing_datasets.R +++ b/tests/testthat/connection_to_datasets/init_testing_datasets.R @@ -21,17 +21,17 @@ init.testing.datasets <- function() if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "TESTING.DATASET1", options=ds.test_env$options_1) - builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "TESTING.DATASET2", options=ds.test_env$options_2) - builder$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "TESTING.DATASET3", options=ds.test_env$options_3) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "TESTING.DATASET1", options=ds.test_env$options_1) + builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "TESTING.DATASET2", options=ds.test_env$options_2) + builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "TESTING.DATASET3", 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$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/testing/DATASET1", driver = "ArmadilloDriver") - builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/testing/DATASET2", driver = "ArmadilloDriver") - builder$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/testing/DATASET3", driver = "ArmadilloDriver") + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/testing/DATASET1", driver = "ArmadilloDriver") + builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/testing/DATASET2", driver = "ArmadilloDriver") + builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/testing/DATASET3", driver = "ArmadilloDriver") ds.test_env$login.data <- builder$build() } else @@ -56,13 +56,13 @@ init.dataset.3 <- function() if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "TESTING.DATASET3", options=ds.test_env$options_3) + builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "TESTING.DATASET3", 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$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/testing/DATASET3", driver = "ArmadilloDriver") + builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/testing/DATASET3", driver = "ArmadilloDriver") ds.test_env$login.data <- builder$build() } else @@ -88,13 +88,13 @@ init.dataset.2 <- function() if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "TESTING.DATASET2", options=ds.test_env$options_2) + builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "TESTING.DATASET2", options=ds.test_env$options_2) ds.test_env$login.data <- builder$build() } else if (ds.test_env$driver == "ArmadilloDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/testing/DATASET2", driver = "ArmadilloDriver") + builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/testing/DATASET2", driver = "ArmadilloDriver") ds.test_env$login.data <- builder$build() } else @@ -120,13 +120,13 @@ init.dataset.1 <- function() if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "TESTING.DATASET1", options=ds.test_env$options_1) + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "TESTING.DATASET1", options=ds.test_env$options_1) ds.test_env$login.data <- builder$build() } else if (ds.test_env$driver == "ArmadilloDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/testing/DATASET1", driver = "ArmadilloDriver") + builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/testing/DATASET1", driver = "ArmadilloDriver") ds.test_env$login.data <- builder$build() } else @@ -159,17 +159,17 @@ init.testing.dataset.factor_levels <- function() if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "GROUP1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "FACTOR_LEVELS.FACTOR_LEVELS1", options=ds.test_env$options_1) - builder$append(server = "GROUP2", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "FACTOR_LEVELS.FACTOR_LEVELS2", options=ds.test_env$options_2) - builder$append(server = "GROUP3", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "FACTOR_LEVELS.FACTOR_LEVELS3", options=ds.test_env$options_3) + builder$append(server = "GROUP1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "FACTOR_LEVELS.FACTOR_LEVELS1", options=ds.test_env$options_1) + builder$append(server = "GROUP2", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "FACTOR_LEVELS.FACTOR_LEVELS2", options=ds.test_env$options_2) + builder$append(server = "GROUP3", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "FACTOR_LEVELS.FACTOR_LEVELS3", 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$append(server = "GROUP1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/factor_levels/FACTOR_LEVELS1", driver = "ArmadilloDriver") - builder$append(server = "GROUP2", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/factor_levels/FACTOR_LEVELS2", driver = "ArmadilloDriver") - builder$append(server = "GROUP3", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/factor_levels/FACTOR_LEVELS3", driver = "ArmadilloDriver") + builder$append(server = "GROUP1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/factor_levels/FACTOR_LEVELS1", driver = "ArmadilloDriver") + builder$append(server = "GROUP2", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/factor_levels/FACTOR_LEVELS2", driver = "ArmadilloDriver") + builder$append(server = "GROUP3", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/factor_levels/FACTOR_LEVELS3", driver = "ArmadilloDriver") ds.test_env$login.data <- builder$build() } else @@ -192,13 +192,13 @@ init.testing.dataset.factor_levels.1 <- function() if (ds.test_env$driver == "OpalDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "GROUP1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "FACTOR_LEVELS.FACTOR_LEVELS1", options=ds.test_env$options_1) + builder$append(server = "GROUP1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "FACTOR_LEVELS.FACTOR_LEVELS1", options=ds.test_env$options_1) ds.test_env$login.data <- builder$build() } else if (ds.test_env$driver == "ArmadilloDriver") { builder <- DSI::newDSLoginBuilder(.silent = TRUE) - builder$append(server = "GROUP1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/factor_levels/FACTOR_LEVELS1", driver = "ArmadilloDriver") + builder$append(server = "GROUP1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/factor_levels/FACTOR_LEVELS1", driver = "ArmadilloDriver") ds.test_env$login.data <- builder$build() } else diff --git a/tests/testthat/connection_to_datasets/login_details.R b/tests/testthat/connection_to_datasets/login_details.R index b725d21f..d0856b7c 100644 --- a/tests/testthat/connection_to_datasets/login_details.R +++ b/tests/testthat/connection_to_datasets/login_details.R @@ -2,7 +2,7 @@ source("connection_to_datasets/init_local_settings.R") -init.ip.address() +init.server.url() # create blank environment of test data ds.test_env <- new.env() @@ -10,7 +10,7 @@ ds.test_env <- new.env() # this option helps DSI to find the connection objects by looking in the right environment options(datashield.env=ds.test_env) -ds.test_env$server_ip_address <- init.ip.address() +ds.test_env$server_url <- init.server.url() if (! is.null(getOption("default_driver"))) { ds.test_env$driver <- getOption("default_driver") @@ -22,18 +22,14 @@ if (! is.null(getOption("default_driver"))) { } if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver")) { - if (ds.test_env$server_ip_address == "localhost") { - opal.url <- "https://localhost:8443" - } else { - opal.url <- ds.test_env$server_ip_address - } + opal.url <- ds.test_env$server_url - ds.test_env$ping_address <- opal.url - ds.test_env$ping_config <- config(timeout=5, ssl_verifyhost=0, ssl_verifypeer=0) + ds.test_env$ping_url <- opal.url + ds.test_env$ping_config <- config(timeout=5) - ds.test_env$ip_address_1 <- opal.url - ds.test_env$ip_address_2 <- opal.url - ds.test_env$ip_address_3 <- opal.url + ds.test_env$server_url_1 <- opal.url + ds.test_env$server_url_2 <- opal.url + ds.test_env$server_url_3 <- opal.url ds.test_env$user_1 <- getOption("opal.user", "administrator") ds.test_env$user_2 <- getOption("opal.user", "administrator") @@ -43,24 +39,20 @@ if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver ds.test_env$password_2 <- getOption("opal.password", "datashield_test&") ds.test_env$password_3 <- getOption("opal.password", "datashield_test&") - ds.test_env$options_1 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)" - ds.test_env$options_2 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)" - ds.test_env$options_3 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)" + ds.test_env$options_1 <- "list()" + ds.test_env$options_2 <- "list()" + ds.test_env$options_3 <- "list()" ds.test_env$secure_login_details <- TRUE } else if (ds.test_env$driver == "ArmadilloDriver") { - if (ds.test_env$server_ip_address == "localhost") { - armadillo.url <- "http://localhost:8080" - } else { - armadillo.url <- ds.test_env$server_ip_address - } + armadillo.url <- ds.test_env$server_url - ds.test_env$ping_address <- armadillo.url + ds.test_env$ping_url <- armadillo.url ds.test_env$ping_config <- config(timeout=5) - ds.test_env$ip_address_1 <- armadillo.url - ds.test_env$ip_address_2 <- armadillo.url - ds.test_env$ip_address_3 <- armadillo.url + ds.test_env$server_url_1 <- armadillo.url + ds.test_env$server_url_2 <- armadillo.url + ds.test_env$server_url_3 <- armadillo.url ds.test_env$user_1 <- getOption("armadillo.user", "admin") ds.test_env$user_2 <- getOption("armadillo.user", "admin") diff --git a/tests/testthat/test-_-vm-test.R b/tests/testthat/test-_-vm-test.R index 7b5af1f4..e27bef89 100644 --- a/tests/testthat/test-_-vm-test.R +++ b/tests/testthat/test-_-vm-test.R @@ -26,7 +26,7 @@ init.testing.datasets() test_that("The virtual machine is loaded. ", { - response <- httr::HEAD(url=ds.test_env$ping_address, config=ds.test_env$ping_config) + response <- httr::HEAD(url=ds.test_env$ping_url, config=ds.test_env$ping_config) expect_true(http_status(response)$reason %in% c("OK", "Unauthorized")) })