inst/doc/datashield-admin.R

In opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils

## ----eval=FALSE---------------------------------------------------------------
#  library(opalr)
#  o <- opal.login("administrator", "password", "https://opal-demo.obiba.org")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.package_descriptions(o, profile = "default")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.install_package(o, pkg = "dsBase", profile = "default")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.install_github_package(o, pkg = "dsSurvival", username = "neelsoumya", ref = "v1.0.0", profile = "default")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.install_local_package(o, devtools::build(), profile = "default")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.remove_package(o, pkg = "dsSurvival", profile = "default")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.profiles(o)

## ----eval=FALSE---------------------------------------------------------------
#  # ensure the profile does not exist
#  if (dsadmin.profile_exists(o, "demo"))
#    dsadmin.profile_delete(o, "demo")
#  # create a profile, disabled
#  dsadmin.profile_create(o, "demo", cluster = "default")
#  # make only dsBase and resourcer packages visible
#  dsadmin.profile_init(o, "demo", packages = c("dsBase", "resourcer"))
#  # ready to be used
#  dsadmin.profile_enable(o, "demo")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.profile_perm_add(o, "demo", subject = "testers", type = "group")
#  # verify permissions
#  dsadmin.profile_perm(o, "demo")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.get_methods(o, type = "aggregate", profile = "demo")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.set_method(o, "hello", func = function(x) { paste0("Hello ", x, "!") }, type = "aggregate", profile = "demo")
#  # verfiy custom method
#  dsadmin.get_method(o, "hello", type = "aggregate", profile = "demo")

## ----eval=FALSE---------------------------------------------------------------
#  library(DSOpal)
#  builder <- DSI::newDSLoginBuilder()
#  builder$append(server = "study1",  url = "https://opal-demo.obiba.org",
#                 user = "administrator", password = "password",
#                 profile = "demo")
#  logindata <- builder$build()
#  conns <- DSI::datashield.login(logins = logindata)
#  # call the hello() function on the R server
#  datashield.aggregate(conns, expr = quote(hello('friends')))
#  datashield.logout(conns)

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.set_option(o, "datashield.privacyLevel", "10", profile = "demo")
#  # verify options
#  dsadmin.get_options(o, profile = "demo")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.profile_rparser(o, "demo", rParser = "v1")

## ----eval=FALSE---------------------------------------------------------------
#  if (oadmin.user_exists(o, "userx"))
#    oadmin.user_delete(o, "userx")
#  # generated password
#  password <- oadmin.user_add(o, "userx", groups = c("demo", "datashield"))
#  # verify user
#  subset(oadmin.users(o), name == "userx")

## ----eval=FALSE---------------------------------------------------------------
#  lapply(opal.tables(o, "CNSIM")$name, function(table) {
#    opal.table_perm_add(o, "CNSIM", table, subject = "demo", type = "group", permission = "view")
#  })
#  # verify table permissions
#  opal.table_perm(o, "CNSIM", "CNSIM1")

## ----eval=FALSE---------------------------------------------------------------
#  opal.resources_perm_add(o, "RSRC", subject = "demo", type = "group", permission = "view")
#  # verify permissions
#  opal.resources_perm(o, "RSRC")

## ----eval=FALSE---------------------------------------------------------------
#  dsadmin.perm_add(o, subject = "datashield", type = "group", permission = "use")
#  # verify permissions
#  dsadmin.perm(o)

## ----eval=FALSE---------------------------------------------------------------
#  opal.logout(o)