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Merge pull request #686 from molgenis/refactor/tests
refactor: restructure release test script
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| .env | ||
| Rplots.pdf | ||
| molgenis-service-armadillo.Rproj |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,204 @@ | ||
| add_slash_if_not_added <- function(path) { | ||
| if (!endsWith(path, "/")) { | ||
| return(paste0(path, "/")) | ||
| } else { | ||
| return(path) | ||
| } | ||
| } | ||
|
|
||
| remove_slash_if_added <- function(path) { | ||
| if (endsWith(path, "/")) { | ||
| return(gsub("/$", "", path)) | ||
| } else { | ||
| return(path) | ||
| } | ||
| } | ||
|
|
||
| exit_test <- function(msg) { | ||
| cli_alert_danger(msg) | ||
| cond <- structure(list(message = msg), class = c("exit", "condition")) | ||
| signalCondition(cond) | ||
| stop(cond) | ||
| } | ||
|
|
||
| check_cohort_exists <- function(cohort) { | ||
| if (cohort %in% armadillo.list_projects()) { | ||
| cli_alert_success(paste0(cohort, " exists")) | ||
| } else { | ||
| exit_test(paste0(cohort, " doesn't exist!")) | ||
| } | ||
| } | ||
|
|
||
| wait_for_input <- function(interactive) { | ||
| if (interactive) { | ||
| cat("\nPress any key to continue") | ||
| continue <- readLines("stdin", n = 1) | ||
| } else { | ||
| cat("\n\n") | ||
| } | ||
| } | ||
|
|
||
| create_basic_header <- function(pwd) { | ||
| encoded <- base64enc::base64encode( | ||
| charToRaw( | ||
| paste0("admin:", pwd) | ||
| ) | ||
| ) | ||
| return(paste0("Basic ", encoded)) | ||
| } | ||
|
|
||
| # # add/edit user using armadillo api | ||
| set_user <- function(user, admin_pwd, isAdmin, required_projects, url) { | ||
| args <- list(email = user, admin = isAdmin, projects = required_projects) | ||
| response <- put_to_api("access/users", admin_pwd, "basic", args, url) | ||
| if (response$status_code != 204) { | ||
| cli_alert_warning("Altering OIDC user failed, please do this manually") | ||
| update_auto <- "" | ||
| } | ||
| } | ||
|
|
||
| # # armadillo api put request | ||
| put_to_api <- function(endpoint, key, auth_type, body_args, url) { | ||
| auth_header <- get_auth_header(auth_type, key) | ||
| body <- jsonlite::toJSON(body_args, auto_unbox = TRUE) | ||
| response <- PUT(paste0(url, endpoint), | ||
| body = body, encode = "json", | ||
| config = c(httr::content_type_json(), httr::add_headers(auth_header)) | ||
| ) | ||
| return(response) | ||
| } | ||
|
|
||
| do_skip_test <- function(test_name, skip_tests) { | ||
| if (any(skip_tests %in% test_name)) { | ||
| cli_alert_info(sprintf("Test '%s' skipped", test_name)) | ||
| return(TRUE) | ||
| } | ||
| return(FALSE) | ||
| } | ||
|
|
||
| read_parquet_with_message <- function(file_path, dest) { | ||
| cli_alert_info(file_path) | ||
| out <- arrow::read_parquet(paste0(dest, paste0(file_path, ".parquet"))) | ||
| cli_alert_success(paste0(file_path, " read")) | ||
| return(out) | ||
| } | ||
|
|
||
| run_spinner <- function(spinner) { | ||
| lapply(1:1000, function(x) { | ||
| spinner$spin() | ||
| spin_till_done(spinner) | ||
| }) | ||
| } | ||
|
|
||
| # # compare values in two lists | ||
| compare_list_values <- function(list1, list2) { | ||
| vals_to_print <- cli_ul() | ||
| equal <- TRUE | ||
| for (i in 1:length(list1)) { | ||
| val1 <- list1[i] | ||
| val2 <- list2[i] | ||
| if (almost_equal(val1, val2) == TRUE) { | ||
| cli_li(sprintf("%s ~= %s", val1, val2)) | ||
| } else { | ||
| equal <- FALSE | ||
| cli_li(sprintf("%s != %s", val1, val2)) | ||
| } | ||
| } | ||
| cli_end(vals_to_print) | ||
| if (equal) { | ||
| cli_alert_success("Values equal") | ||
| } else { | ||
| cli_alert_danger("Values not equal") | ||
| } | ||
| } | ||
|
|
||
| # theres a bit of noise added in DataSHIELD answers, causing calculations to not always be exactly the same, but close | ||
| # here we check if they're equal enough | ||
| almost_equal <- function(val1, val2) { | ||
| return(all.equal(val1, val2, tolerance = .Machine$double.eps^0.03)) | ||
| } | ||
|
|
||
| generate_random_project_name <- function(skip_tests) { | ||
| test_name <- "generate-project" | ||
| if (do_skip_test(test_name, skip_tests)) { | ||
| return() | ||
| } | ||
|
|
||
| current_projects <- armadillo.list_projects() | ||
| random_project <- stri_rand_strings(1, 10, "[a-z0-9]") | ||
| if (!random_project %in% current_projects) { | ||
| cli_alert_success(sprintf("Project %s created", random_project)) | ||
| cli_alert_success(sprintf("%s passed!", test_name)) | ||
| return(random_project) | ||
| } else { | ||
| generate_random_project_name(current_projects) | ||
| } | ||
| } | ||
|
|
||
| # # armadillo api put request | ||
| put_to_api <- function(endpoint, key, auth_type, body_args, url) { | ||
| auth_header <- get_auth_header(auth_type, key) | ||
| body <- jsonlite::toJSON(body_args, auto_unbox = TRUE) | ||
| response <- PUT(paste0(url, endpoint), | ||
| body = body, encode = "json", | ||
| config = c(httr::content_type_json(), httr::add_headers(auth_header)) | ||
| ) | ||
| return(response) | ||
| } | ||
|
|
||
| get_from_api <- function(endpoint, armadillo_url) { | ||
| cli_alert_info(sprintf("Retrieving [%s%s]", armadillo_url, endpoint)) | ||
| response <- GET(paste0(armadillo_url, endpoint)) | ||
| cat(paste0("get_from_api", " for ", endpoint, " results ", response$status_code, "\n")) | ||
| return(content(response)) | ||
| } | ||
|
|
||
| get_auth_type <- function(ADMIN_MODE) { | ||
| if (ADMIN_MODE) { | ||
| auth_type <- "basic" | ||
| } else { | ||
| auth_type <- "bearer" | ||
| } | ||
| } | ||
|
|
||
| # get request to armadillo api with an authheader | ||
| get_from_api_with_header <- function(endpoint, key, auth_type, url, user) { | ||
| auth_header <- get_auth_header(auth_type, key) | ||
| response <- GET(paste0(url, endpoint), config = c(httr::add_headers(auth_header))) | ||
| if (response$status_code == 403) { | ||
| msg <- sprintf("Permission denied. Is user [%s] admin?", user) | ||
| exit_test(msg) | ||
| } else if (response$status_code != 200) { | ||
| cli_alert_danger(sprintf("Cannot retrieve data from endpoint [%s]", endpoint)) | ||
| exit_test(content(response)$message) | ||
| } | ||
| return(content(response)) | ||
| } | ||
|
|
||
|
|
||
| # make authentication header for api calls, basic or bearer based on type | ||
| get_auth_header <- function(type, key) { | ||
| header_content <- "" | ||
| if (tolower(type) == "bearer") { | ||
| header_content <- create_bearer_header(key) | ||
| } else if (tolower(type) == "basic") { | ||
| header_content <- create_basic_header(key) | ||
| } else { | ||
| exit_test(sprintf("Type [%s] invalid, choose from 'basic' and 'bearer'")) | ||
| } | ||
| return(c("Authorization" = header_content)) | ||
| } | ||
|
|
||
| create_bearer_header <- function(token) { | ||
| return(paste0("Bearer ", token)) | ||
| } | ||
|
|
||
|
|
||
| print_list <- function(list) { | ||
| vals_to_print <- cli_ul() | ||
| for (i in 1:length(list)) { | ||
| val <- list[i] | ||
| cli_li(val) | ||
| } | ||
| cli_end(vals_to_print) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| show_test_info <- function(version, url, user, admin_pwd, dest, profile, ADMIN_MODE, skip_tests) { | ||
| test_name <- "show_test_info" | ||
| if (do_skip_test(test_name, skip_tests)) { | ||
| return() | ||
| } | ||
|
|
||
| if (admin_pwd != "") { | ||
| admin_pwd_msg <- TRUE | ||
| } | ||
|
|
||
| test_message <- cat(sprintf(" | ||
| ,.-----__ Testing version: %s | ||
| ,:::://///,:::-. Test server: %s | ||
| /:''/////// ``:::`;/|/ OIDC User: %s | ||
| /' |||||| :://'`\\ Admin password set: %s | ||
| .' , |||||| `/( e \\ Directory for test files: %s | ||
| -===~__-'\\__X_`````\\_____/~`-._ `. Profile: %s | ||
| ~~ ~~ `~-' Admin-only mode: %s | ||
| ", version, url, user, admin_pwd_msg, dest, profile, ADMIN_MODE)) | ||
|
|
||
| return(test_message) | ||
| } |
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