Draft needs reviewing….
These are instructions as to how to run the dsBaseClient tests on your own machine (this version of the instructions will assume Linux based machine)
install.package(. . .) method):DSIDSOpalDSMolgenisArmadilloDSLitelme4e1071DescToolsupdate.package(. . .) method) To specify which server type to use, edit the file tests/testthat/connection_to_datasets/login_details.R
Find the section in which the Driver is specified, and uncomment one Driver.
# switch between "DSLiteDriver" and "OpalDriver", "ArmadilloDriver" to test
# ds.test_env$driver <- "DSLiteDriver"
ds.test_env$driver <- "OpalDriver"
# ds.test_env$driver <- "ArmadilloDriver"Edit the file tests/testthat/connection_to_datasets/local_settings.csv. On a blank line specify the IP address of the server being used, for example, 127.0.0.1.
Within the dsBaseClient directory:
docker compose -f docker-compose_opal.yml updocker compose -f docker-compose_armadillo.yml uptests/testthat/data_files issue the follow command:R -q -f obiba_opal-upload_testing_datasets.RR -q -f molgenis_armadillo-upload_testing_datasets.RR -q:library(testthat)
devtools::test(reporter = ProgressReporter$new(max_failures = 999999))
library(testthat)
devtools::test(filter = “smk-”, reporter = ProgressReporter$new(max_failures = 999999))
library(testthat)
devtools::test(filter = “arg-”, reporter = ProgressReporter$new(max_failures = 999999))The devtools::test argument filter can cause individual test files to be initiated, for example:filter = “smk-ds.asFactor”
Sets of related tests arg, datachk, discctrl, disc, expt_bug, expt_dgr, expt, mathbug, mathdgr math, perf, smk, smkbug, smk_expt and smk_dgr. For example:
filter = “perf-”
orfilter = “perf-|smk-”