## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", cache = FALSE, out.width = "100%", cache = FALSE, screenshot.opts = list(vwidth = 2000, vheight = 600, zoom = 3, selector = "div.html-widget") ) # save the built-in output hook hook_output <- knitr::knit_hooks$get("output") hook_message <- knitr::knit_hooks$get("message") # define a truncation helper truncate_lines_tail <- function(x, lines) { x <- unlist(strsplit(x, "\n")) more <- "..." if (length(lines) == 1) { if (length(x) > lines) { # truncate the output, but add `more` # x <- c(head(x, n = lines), more) x <- c(more, tail(x, n = lines)) } } else { x <- c(more, x[lines], more) } paste(c(x, ""), collapse = "\n") } # set the new hooks knitr::knit_hooks$set( output = function(x, options) { lines <- options$out.lines if (is.null(lines)) return(hook_output(x, options)) x <- truncate_lines_tail(x, lines) return(hook_output(x, options)) }, message = function(x, options) { lines <- options$out.lines if (is.null(lines)) return(hook_message(x, options)) x <- truncate_lines_tail(x, lines) return(hook_message(x, options)) } ) # helper function to get the number of rows of an RO-Crate rocrate_lines <- function(rocrate) { rocrate_txt(rocrate) |> length() } # helper function to read RO-Crate as text file rocrate_txt <- function(rocrate) { # create tmp file to write a JSON file with the output tmp_file <- tempfile(fileext = ".json") on.exit(unlink(tmp_file, force = TRUE)) # write RO-Crate in tmp file rocrateR::write_rocrate(rocrate, tmp_file) # read RO-Crate as text file readLines(tmp_file) } ## ----setup-------------------------------------------------------------------- library(dsROCrate) # show all the lines in the RO-Crate oopt <- options(max_lines = Inf) on.exit(options(oopt), add = TRUE) ## ----eval = FALSE------------------------------------------------------------- # vignette("deploy-local-datashield-server-with-opal", package = "dsROCrate") ## ----------------------------------------------------------------------------- # define global variables ## Opal server access USERNAME <- "administrator" USERPASS <- "password" SERVER <- "https://opal-demo.obiba.org" ## Credentials for `dsuser` ### NOTE: this is only used to simulate an analysis and generate logs DSUSERPASS <- "P@ssw0rd" ## ----------------------------------------------------------------------------- ## Five safes variables PEOPLE <- "dsuser" PROJECT <- "CNSIM" TABLES <- c("CNSIM1") ## ----------------------------------------------------------------------------- # login to local server with `USERNAME` and `USERPASS`. o <- opalr::opal.login( username = USERNAME, password = USERPASS, url = SERVER ) print(o) ## ----eval = FALSE, echo = TRUE------------------------------------------------ # # install.packages("pak") # pak::pak("rocrateR") # # # for development version use # pak::pak("ResearchObject/ro-crate-r@dev") ## ----------------------------------------------------------------------------- basic_rocrate <- rocrateR::rocrate_5s() ## ----------------------------------------------------------------------------- print(basic_rocrate) ## ----out.lines=-(rocrate_lines(basic_rocrate) - 2)---------------------------- basic_rocrate <- o |> dsROCrate::safe_data(rocrate = basic_rocrate, project = PROJECT, tables = TABLES) print(basic_rocrate) # note that the output will be truncated ## ----out.lines=-(rocrate_lines(basic_rocrate) - 2)---------------------------- basic_rocrate <- o |> dsROCrate::safe_project(rocrate = basic_rocrate, project = PROJECT) print(basic_rocrate) # note that the output will be truncated ## ----safe_people, out.lines=-(rocrate_lines(basic_rocrate) + 1)--------------- basic_rocrate <- o |> dsROCrate::safe_people(rocrate = basic_rocrate, user = PEOPLE) print(basic_rocrate) # note that the output will be truncated ## ----eval = FALSE------------------------------------------------------------- # # close previous connection # opalr::opal.logout(o) # # # open new connection as administrator # o <- opalr::opal.login( # username = "administrator", # password = "password", # url = SERVER # ) ## ----out.lines=-(rocrate_lines(basic_rocrate) - 2)---------------------------- basic_rocrate <- o |> dsROCrate::safe_setting(rocrate = basic_rocrate) print(basic_rocrate) # note that the output will be truncated ## ----eval = FALSE------------------------------------------------------------- # # close previous connection # opalr::opal.logout(o) # # # open new connection as administrator # o <- opalr::opal.login( # username = "administrator", # password = "password", # url = SERVER # ) ## ----eval = FALSE------------------------------------------------------------- # pak::pak("DSI") # pak::pak("DSOpal") # pak::pak("dsBaseClient") ## ----eval = TRUE-------------------------------------------------------------- # run some test commands with dsBaseClient ## needed to defined the OpalDriver class in the current environment DSOpal::Opal() ## create new login object, note that here we use the `dsuser` builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", url = SERVER, user = "dsuser", password = DSUSERPASS, driver = "OpalDriver") logindata <- builder$build() conns <- DSI::datashield.login(logins = logindata) ## ----eval = TRUE-------------------------------------------------------------- ## assign data DSI::datashield.assign.table(conns["study1"], symbol = "dsROCrate_test", table = paste0(PROJECT, ".", TABLES[1]), errors.print = TRUE) dsBaseClient::ds.ls(datasources = conns["study1"]) dsBaseClient::ds.summary("dsROCrate_test") ## ----echo = FALSE, warning = FALSE, message = FALSE--------------------------- # check if there are any logs available, if not simulate some operations ## ----safe_outputs_internal, echo=FALSE---------------------------------------- lines_before_safe_outputs <- rocrate_lines(basic_rocrate) ## ----safe_outputs------------------------------------------------------------- basic_rocrate <- o |> dsROCrate::safe_output(rocrate = basic_rocrate, logs_from = Sys.time() - 60, # capture the last minute logs_to = Sys.time()) ## ----out.lines=-(lines_before_safe_outputs + 1)------------------------------- print(basic_rocrate) # note that the output will be truncated ## ----------------------------------------------------------------------------- opalr::opal.logout(o) ## ----------------------------------------------------------------------------- # create temp directory tmp_path_bag <- file.path(tempdir(), "dsROCrate-getting-started") dir.create(tmp_path_bag, showWarnings = FALSE) # create RO-Crate bag path_to_rocrate_bag <- basic_rocrate |> rocrateR::bag_rocrate(path = tmp_path_bag, overwrite = TRUE) ## ----------------------------------------------------------------------------- # extract files in temporary directory path_to_rocrate_bag |> # extract contents inside /tmp_path_bag/ROC rocrateR::unbag_rocrate(output = file.path(tmp_path_bag, "ROC"), quiet = TRUE) |> # create tree with the files fs::dir_tree() ## ----------------------------------------------------------------------------- unlink(tmp_path_bag, recursive = TRUE, force = TRUE) ## ----warning=FALSE------------------------------------------------------------ safe_people_crate_v1 <- opalr::opal.login( username = USERNAME, password = USERPASS, url = SERVER ) |> dsROCrate::audit(user = "dsuser", project = "CNSIM") print(safe_people_crate_v1) ## ----safe_people_crate_audit_v1----------------------------------------------- safe_people_crate_v1_rmd <- tempfile(fileext = ".Rmd") # temporary file safe_people_crate_contents <- safe_people_crate_v1 |> dsROCrate::report(filepath = safe_people_crate_v1_rmd, render = FALSE) # display Overview diagram safe_people_crate_contents$overview_diagram # display Overview data (Safe People, Safe Projects and Safe Data) safe_people_crate_contents$overview_data |> knitr::kable() ## ----eval = FALSE------------------------------------------------------------- # safe_people_crate_v1 |> # dsROCrate::report(filepath = safe_people_crate_v1_rmd, # title = "DataSHIELD Safe People - Audit Report", # render = TRUE, # overwrite = TRUE) ## ----warning=FALSE------------------------------------------------------------ safe_project_crate_v1 <- opalr::opal.login( username = USERNAME, password = USERPASS, url = SERVER ) |> dsROCrate::audit(project = "CNSIM") print(safe_project_crate_v1) ## ----safe_project_crate_audit_v1---------------------------------------------- safe_project_crate_v1_rmd <- tempfile(fileext = ".Rmd") # temporary file safe_project_crate_contents <- safe_project_crate_v1 |> dsROCrate::report(filepath = safe_project_crate_v1_rmd, render = FALSE) # display Overview diagram safe_project_crate_contents$overview_diagram # display Overview data (Safe People, Safe Projects and Safe Data) safe_project_crate_contents$overview_data |> knitr::kable() ## ----eval = FALSE------------------------------------------------------------- # safe_project_crate_v1 |> # dsROCrate::report(filepath = safe_project_crate_v1_rmd, # title = "DataSHIELD Safe Project - Audit Report", # render = TRUE, # overwrite = TRUE) ## ----warning=FALSE------------------------------------------------------------ study_crate_v1 <- list( "opal_test" = opalr::opal.login( username = USERNAME, password = USERPASS, url = "https://opal-test.obiba.org" ), "opal_demo" = opalr::opal.login( username = USERNAME, password = USERPASS, url = "https://opal-demo.obiba.org" ) ) |> dsROCrate::audit(project = "CNSIM") print(study_crate_v1) ## ----study_crate_audit_v1----------------------------------------------------- study_crate_v1_rmd <- tempfile(fileext = ".Rmd") # temporary file safe_project_crate_contents <- study_crate_v1 |> dsROCrate::report(filepath = study_crate_v1_rmd, render = FALSE) # display Overview diagram safe_project_crate_contents$overview_diagram # display Overview data (Safe People, Safe Projects and Safe Data) safe_project_crate_contents$overview_data |> knitr::kable() ## ----eval = FALSE------------------------------------------------------------- # study_crate_v1 |> # dsROCrate::report(filepath = study_crate_v1_rmd, # title = "DataSHIELD Study audit", # render = TRUE, # overwrite = TRUE) ## ----echo = FALSE, message = FALSE, error = FALSE----------------------------- unlink(safe_people_crate_v1_rmd, TRUE, TRUE) unlink(safe_project_crate_v1_rmd, TRUE, TRUE) unlink(study_crate_v1_rmd, TRUE, TRUE) # reverse options options(oopt)