Release/0.0.7

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rgeco
 Type: Package
 Title: R package for accessing the Generable API
-Version: 0.0.6
+Version: 0.0.7-9000
 Author: Generable Inc
 Maintainer: Jacqueline Buros <[email protected]>
 Description: The Generable API is a HTTP REST API that provides access to data and inferences. The rgeco package provides convenient access to the information in the API in an R-friendly format.
@@ -34,7 +34,10 @@ Imports:
     table1,
     reticulate,
     boot,
-    cli
+    cli,
+    data.table,
+    httpcache,
+    keyring
 Suggests: 
     testthat,
     knitr,
@@ -43,5 +46,5 @@ Suggests:
     scales,
     tidyverse,
     utils
-RoxygenNote: 7.2.0
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr

NAMESPACE

@@ -1,6 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+export(configure)
+export(drop_configs)
 export(extract_subsample_info)
+export(fetch_aes)
 export(fetch_association_state)
 export(fetch_biomarker_params)
 export(fetch_biomarkers)
@@ -23,6 +26,7 @@ export(find_runs)
 export(flog.logger)
 export(format_quantiles_as_widths)
 export(list_biomarker_names)
+export(list_configs)
 export(list_datasets)
 export(list_models)
 export(list_parameter_names)
@@ -36,10 +40,12 @@ export(prep_pkpd_data)
 export(sample_groups)
 import(checkmate)
 import(cli)
-import(httr)
+import(keyring)
 importFrom(RJSONIO,fromJSON)
 importFrom(boot,inv.logit)
 importFrom(broom,tidy)
+importFrom(data.table,data.table)
+importFrom(data.table,setkeyv)
 importFrom(dplyr,arrange)
 importFrom(dplyr,desc)
 importFrom(dplyr,distinct)
@@ -49,7 +55,15 @@ importFrom(dplyr,select)
 importFrom(dplyr,semi_join)
 importFrom(futile.logger,flog.logger)
 importFrom(glue,glue_safe)
+importFrom(httpcache,GET)
+importFrom(httpcache,POST)
+importFrom(httr,add_headers)
+importFrom(httr,content)
+importFrom(httr,http_error)
 importFrom(httr,modify_url)
+importFrom(httr,status_code)
+importFrom(httr,user_agent)
+importFrom(keyring,backend_file)
 importFrom(lubridate,ymd_hms)
 importFrom(magrittr,"%>%")
 importFrom(rlang,"!!!")

R/geco_aes.R

@@ -0,0 +1,75 @@
+
+#' Fetch AE data from the Generable API
+#'
+#' Fetch AE data from the Generable API for a specific project.
+#'
+#' This function retrieves AE data from the Generable API.
+#' It requires authentication (see \code{\link{login}}) prior to use
+#' and this pulls data from the Generable API.
+#'
+#' @note
+#' A project can be specified by using the project name or a specific project version.
+#' \enumerate{
+#'   \item If a project is specified using the name, data is fetched for the latest version of the project.
+#'   \item If a project is specified using the project version, the project name is not required.
+#'   \item If neither a project nor a project version is provided, the default project or project version is used. These are set by the environment variables GECO_API_PROJECT and GECO_API_PROJECT_VERSION
+#' }
+#'
+#' @param project Project name. If NULL, defaults to value of environment variable GECO_API_PROJECT
+#' @param project_version_id Project version. If NULL, defaults to the most recent version of the project if provided, or the value of environment variable GECO_API_PROJECT_VERSION
+#' @param event_type Limits the event_types to the names provided. NULL is unfiltered. Default is NULL.
+#' @param ... Optional filters applied to events data, provided as name-value pairs to limit returned values.
+#'      Example: trial_id = unique(subjects$trial_id)
+#' @return data.frame with one record per subject and event type
+#' @export
+fetch_aes <- function(project = NULL, project_version_id = NULL, event_type = NULL,
+                      serious_event_flag = NULL, ...) {
+  where <- rlang::list2(...)
+  pv_id <- .process_project_inputs(project = project, project_version_id = project_version_id)
+  if (!is.null(event_type)) {
+    where <- .update_filter(where, event_type = event_type)
+  }
+  if (!is.null(serious_event_flag)) {
+    where <- .update_filter(where, serious_event_flag = serious_event_flag)
+  }
+  events <- .fetch_ae_data(project_version_id = pv_id, where = where)
+  if (nrow(events) == 0 && !is.null(project)) {
+    futile.logger::flog.info(glue::glue('No ae information available for this version of project {project} data.'))
+  } else if (nrow(events) == 0) {
+    futile.logger::flog.debug(glue::glue('No ae information available for this project_version_id: {project_version_id}.'))
+  }
+  events
+}
+
+
+#' @importFrom rlang .data
+pivot_ae_wider <- function(.d) {
+  tidyr::pivot_wider(.d,
+                     id_cols = c(.data$subject_id),
+                     names_from = c(.data$event_type),
+                     values_from = c(.data$event_flag, .data$event_trial_day, .data$event_id, .data$event_created_at),
+                     names_glue = "{event_type}_{.value}")
+}
+
+
+#' @importFrom magrittr %>%
+.fetch_ae_data <- function(project = NULL, project_version_id = NULL, where = list()) {
+  pv_id <- .process_project_inputs(project = project, project_version_id = project_version_id)
+  filter <- .prepare_filter(where, endpoint = 'AES')
+  events <- geco_api(AES, project_version_id = pv_id, url_query_parameters = filter)
+  d <- as_dataframe.geco_api_data(events, flatten_names = c('params'))
+  if ('params' %in% names(d)) {
+    d <- d %>%
+      tidyr::unnest_wider(.data$params, names_repair = 'universal')
+  }
+  d <- .apply_filters(d, where)
+  suppressWarnings({
+    d <- d %>%
+      dplyr::rename_at(.vars = dplyr::vars(-dplyr::one_of(c('subject_id'))),
+                       .funs = ~ stringr::str_c('ae_', .x))
+  })
+  d
+}
+
+
+

R/geco_api.R

@@ -14,6 +14,7 @@ PROJECTVERSIONS <- 'data/project/{project}/projectversions'
 PROJECTS <- 'data/projects'
 LESIONS <- 'data/projectversion/{project_version_id}/lesions'
 LESIONTV <- 'data/projectversion/{project_version_id}/lesiontvs'
+AES <- 'data/projectversion/{project_version_id}/ae'
 
 # ---- inference api endpoints ----
 IDATA <- 'inferences/projectversion/{project_version_id}/dataset/attributes'
@@ -56,6 +57,20 @@ geco_api_url <- function(..., project = NULL, project_version_id = NULL, run_id=
   glue::glue_safe(url)
 }
 
+#' Never cache certain endpoints
+.clean_cache <- function() {
+  nocache_endpoints <- c(
+    LOGIN,
+    PROJECTVERSIONS,
+    PROJECTS,
+    IDATA,
+    IMODELS,
+    IRUNS
+  )
+  nocache_endpoints |>
+    purrr::walk(httpcache::dropOnly)
+}
+
 #' Log in to the Generable API
 #'
 #' This function logs the user into the Generable API.
@@ -72,20 +87,155 @@ geco_api_url <- function(..., project = NULL, project_version_id = NULL, run_id=
 #' @param password User password. If not provided, will read the `GECO_API_PASSWORD` environment variable.
 #' @return The OAuth 2.0 Bearer Token for the Generable API
 #' @export
-login <- function(user, password) {
-  if (missing(user)) {
-    user <- Sys.getenv('GECO_API_USER')
+login <- function(user, password, host) {
+  url <- .get_url(host)
+  if (missing(password) || missing(user)) {
+    use_keyring <- Sys.getenv('GECO_API_NO_KEYRING') == ""
+    if (!use_keyring) {
+      user <- Sys.getenv('GECO_API_USER')
+      password <- Sys.getenv('GECO_API_PASSWORD')
+    } else {
+      # get credentials from keyring
+      creds <- .get_credentials(host = host, user = user)
+      user = creds[1]
+      password = creds[2]
+    }
   }
-  if (missing(password)) {
-    password <- Sys.getenv('GECO_API_PASSWORD')
+  if (is.null(user)) {
+    cli::cli_inform('Note: credential storage has changed; please run `configure()` to migrate to the new storage.')
   }
   body <- list(email = user, password = password)
   resp <- geco_api(LOGIN, body = body, encode = 'json', method = 'POST')
   ENV$.GECO_AUTH <- resp$content
   invisible(resp$content)
 }
 
+#' Configure Geco credentials, saving in keyring
+#' @param user Geco user name (email address). Defaults to GECO_API_USER environment variable
+#' @param password Geco password (will prompt if not provided). Defaults to GECO_API_PASSWORD environment variable
+#' @param host (optional) alternate host for API, only used for testing
+#' @import keyring
+#' @export
+configure <- function(user, password, host) {
+  cli::cli_inform('Configuring credentials for Geco API')
+  url <- .get_url(host)
+  if (missing(user)) {
+    cli::cli_inform('Reading username from environment variable: GECO_API_USER')
+    user <- Sys.getenv('GECO_API_USER', unset = '')
+    if (user == '') {
+      stop('Username not provided.')
+    }
+  }
+  if (missing(password)) {
+    cli::cli_inform('Reading password from environment variable: GECO_API_PASSWORD')
+    password <- Sys.getenv('GECO_API_PASSWORD', unset = '')
+    cli::cli_inform('GECO_API_PASSWORD not found. Prompting you for your geco password.')
+    if (password == '' && interactive()) {
+      password <- rstudioapi::askForPassword(prompt = 'Please enter your geco password.')
+    }
+  }
+  cli::cli_inform('Attempting to log in ...')
+  res <- tryCatch(login(user=user, password = password, host=host))
+  if (inherits(res, 'try-error')) {
+    cli::cli_alert_warning('Failed to authenticate.')
+  } else {
+    cli::cli_alert_success('Success!')
+    if (keyring::has_keyring_support() && interactive() && askYesNo("Do you want to save credentials in your keyring?")) {
+      keyring::key_set_with_value(service = .get_keyring_service(),
+                                  username = user, password = password)
+      cli::cli_alert_success('Credentials saved.')
+    } else {
+      cli::cli_inform('Populating credentials in environment variables.')
+      Sys.setenv('GECO_API_USER'=user)
+      Sys.setenv('GECO_API_PASSWORD'=password)
+      Sys.setenv('GECO_API_URL'=url)
+    }
+  }
+}
+
+#' List saved configurations
+#' @param host Host identifier, defaults to 'geco'
+#' @export
+list_configs <- function(host='geco') {
+  service <- .get_keyring_service(host)
+  key_list(service)
+}
+
+#' Drop saved configurations
+#' Warning! this will remove all saved configurations from the host.
+#' @param host Host identifier, defaults to 'geco'
+#' @param user Optional username, provided as a string.
+#' @seealso [list_configs()]
+#' @export
+drop_configs <- function(user, host='geco') {
+  service <- .get_keyring_service(host)
+  keys <- key_list(service)
+  if (!missing(user)) {
+    keys <- keys %>%
+      filter(username == !!user)
+  }
+  if (nrow(keys) == 0) {
+    cli::cli_alert_info('No keys found.')
+  } else {
+    cli::cli_alert_warning('This will drop _ALL_ saved configs listed.')
+    print(keys)
+    confirm <- askYesNo("Do you want to drop these configs from your keyring?",
+                        default = FALSE)
+    if (!is.na(confirm) && isTRUE(confirm)) {
+      keys %>%
+        dplyr::pull(username) %>%
+        purrr::walk(~ keyring::key_delete(service=service, username = .))
+    }
+  }
+}
+
+
+.get_keyring_service <- function(host) {
+  url <- .get_url(host)
+  stringr::str_c('R-GECO_API', url, sep = '-')
+}
+.get_url <- function(host) {
+  if (missing(host)) {
+    url <- Sys.getenv('GECO_API_URL', unset = 'https://geco.generable.com')
+  } else {
+    url <- glue::glue('https://{host}.generable.com')
+    Sys.setenv('GECO_API_URL' = url)
+  }
+  url
+}
+
+# returns vector as username, password
+.get_credentials <- function(host, user) {
+  if (!keyring::has_keyring_support()) {
+    if (missing(user)) {
+      user <- Sys.getenv('GECO_API_USER')
+    }
+    password <- Sys.getenv('GECO_API_PASSWORD')
+    return(c(user, password))
+  }
+  # get user & reconcile with keychain
+  service <- .get_keyring_service(host)
+  keys <- key_list(service)
+  if (missing(user)) {
+    if (nrow(keys) == 1) {
+      user <- unique(keys$username)
+    } else {
+      user <- Sys.getenv('GECO_API_USER', unset = 'null')
+      if (is.null(user)) {
+        stop("Multiple users configured; please set default user with GECO_API_USER environment variable")
+      }
+    }
+  } else if (user %in% keys$username) {
+    Sys.setenv('GECO_API_USER' = user)
+  } else {
+    stop('User does not exist in keyring; please run `configure()`')
+  }
+  # get password
+  password <- key_get(service, username = user)
+  return(c(user, password))
+}
 
+#' @importFrom httr add_headers
 get_auth <- function() {
   if (!exists(envir = ENV, '.GECO_AUTH')) {
     futile.logger::flog.error('Not logged in. Use `login(user, password)` to login.')
@@ -94,23 +244,26 @@ get_auth <- function() {
   httr::add_headers(.headers = unlist(ENV$.GECO_AUTH))
 }
 
-#' @import httr
+#' @importFrom httr user_agent http_error content status_code
+#' @importFrom httpcache GET POST
 #' @importFrom RJSONIO fromJSON
 geco_api <- function(path, ..., method = c('GET', 'POST'), project = NULL, project_version_id = NULL, run_id=NULL, type=NULL, parameter=NULL, filters=NULL, url_query_parameters=NULL) {
   url <- geco_api_url(path, project = project, project_version_id = project_version_id, run_id=run_id, type=type, parameter=parameter, filters=filters, url_query_parameters=url_query_parameters)
 
   ua <- httr::user_agent("https://github.com/generable/rgeco")
+  .clean_cache()
 
   method <- match.arg(method, several.ok = FALSE)
   if (method == 'GET')
-    resp <- try(httr::GET(url, ..., get_auth(), ua))
+    resp <- try(httpcache::GET(url, ..., get_auth(), ua))
   else if (method == 'POST')
-    resp <- try(httr::POST(url, ..., ua))
+    resp <- try(httpcache::POST(url, ..., ua))
   #if (httr::http_type(resp) != "application/json") {
   #  stop("API did not return json", call. = FALSE)
   #}
   if (inherits(resp, 'try-error')) {
     stop(glue::glue("Error connecting to API: {url} {print(resp)}"))
+    httpcache::dropOnly(url)
   }
 
   parsed <- try(RJSONIO::fromJSON(httr::content(resp, "text", encoding = 'UTF-8'), simplify = FALSE), silent = T)

R/geco_biomarkers.R

@@ -61,7 +61,7 @@ fetch_biomarkers <- function(project = NULL, project_version_id = NULL, measurem
   biomarkers <- geco_api(TIMEVARYING, project_version_id = pv_id, url_query_parameters = filters)
   b <- as_dataframe.geco_api_data(biomarkers, flatten_names = 'params')
   if (nrow(b) > 0 && 'params' %in% names(b) && isTRUE(annotate)) {
-    b <- b %>% tidyr::unnest_wider(.data$params)
+    b <- b %>% tidyr::unnest_wider(.data$params, names_repair = 'universal')
   }
   suppressWarnings({
     b <- b %>%