🔀 Merge pull request #29 from cnr-ibba/issue-26

🛂 remove auth part from code

.gitignore

@@ -6,3 +6,4 @@
 docs
 inst/doc
 vignettes/*.txt
+*.zip

DESCRIPTION

@@ -1,24 +1,26 @@
 Package: smarterapi
 Title: Fetch SMARTER Data Through REST API
 Version: 0.2.0.9000
-Authors@R: 
-    person("Paolo", "Cozzi", , "[email protected]", 
-           role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-0388-6874"))
-Description: smarterapi is an interface which interacts with SMARTER REST API
-    by querying data using token authentication and providing results into 
-    dataframes.
+Authors@R:
+    person(
+        "Paolo", "Cozzi",
+        email = "[email protected]",
+        role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0003-0388-6874")
+    )
+Description:
+    Provides functions to fetch data from the SMARTER API, a RESTful
+    web service that provides access to data from the SMARTER database.
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-Suggests: 
+Suggests:
     lintr,
     styler,
     testthat (>= 3.0.0),
     rcmdcheck,
     roxygen2,
-    utils,
     usethis,
     leaflet,
     knitr,
@@ -34,22 +36,26 @@ Suggests:
     rnaturalearth,
     rnaturalearthdata
 Config/testthat/edition: 3
-Config/renv/profiles/dev/dependencies: 
+Config/renv/profiles/dev/dependencies:
     lintr,
     rcmdcheck,
     roxygen2,
     styler,
     testthat,
-    usethis
-Imports: 
+    usethis,
+    devtools
+Imports:
     jsonlite,
     httr,
     urltools,
-    lubridate,
+    RCurl,
+    fs,
+    utils,
     logger,
     dplyr,
     tidyr,
-    sf
+    sf,
+    geojsonsf
 URL: https://cnr-ibba.github.io/r-smarter-api/
 BugReports: https://github.com/cnr-ibba/r-smarter-api/issues
 VignetteBuilder: knitr

NAMESPACE

@@ -3,9 +3,9 @@
 export(get_smarter_breeds)
 export(get_smarter_countries)
 export(get_smarter_datasets)
+export(get_smarter_genotypes)
 export(get_smarter_geojson)
 export(get_smarter_info)
 export(get_smarter_samples)
 export(get_smarter_supportedchips)
-export(get_smarter_token)
 export(get_smarter_variants)

R/breeds.R

@@ -2,11 +2,8 @@
 #' Get SMARTER Breeds
 #'
 #' Fetch SMARTER REST API breeds endpoint and returns results in a dataframe.
-#' Cached token is used or a new token is generated if not provided when calling
-#' this function (see \code{\link{get_smarter_token}} for more information)
 #'
 #' @param query a \code{list} of query arguments
-#' @param token a string with a valid token
 #'
 #' @return Returns a dataframe with selected breeds
 #' @export
@@ -26,16 +23,10 @@
 #'
 #' selected_breeds <- get_smarter_breeds(query = list(search = "mer"))
 #' \dontrun{
-#'
 #' all_breeds <- get_smarter_breeds()
-#'
 #' sheep_breeds <- get_smarter_breeds(query = list(species = "Sheep"))
 #' }
-get_smarter_breeds <- function(query = list(), token = NULL) {
-  if (is.null(token)) {
-    token <- smarterapi::get_smarter_token()
-  }
-
+get_smarter_breeds <- function(query = list()) {
   logger::log_info("Get data from breeds endpoint")
 
   # setting the URL endpoint
@@ -45,7 +36,7 @@ get_smarter_breeds <- function(query = list(), token = NULL) {
   )
 
   # reading our data
-  data <- get_smarter_data(url, token, query)
+  data <- get_smarter_data(url, query)
 
   logger::log_info("Done!")
 

R/countries.R

@@ -2,8 +2,6 @@
 #' Get SMARTER Countries
 #'
 #' Fetch SMARTER REST API countries endpoint and returns results in a dataframe.
-#' Cached token is used or a new token is generated if not provided when calling
-#' this function (see \code{\link{get_smarter_token}} for more information)
 #'
 #' @inheritParams get_smarter_breeds
 #'
@@ -30,11 +28,7 @@
 #' sheep_countries <- get_smarter_countries(query = list(species = "Sheep"))
 #' }
 #'
-get_smarter_countries <- function(query = list(), token = NULL) {
-  if (is.null(token)) {
-    token <- smarterapi::get_smarter_token()
-  }
-
+get_smarter_countries <- function(query = list()) {
   logger::log_info("Get data from countries endpoint")
 
   # setting the URL endpoint
@@ -44,7 +38,7 @@ get_smarter_countries <- function(query = list(), token = NULL) {
   )
 
   # reading our data
-  data <- get_smarter_data(url, token, query)
+  data <- get_smarter_data(url, query)
 
   logger::log_info("Done!")
 

R/datasets.R

@@ -2,8 +2,6 @@
 #' Get SMARTER Datasets
 #'
 #' Fetch SMARTER REST API datasets endpoint and returns results in a dataframe.
-#' Cached token is used or a new token is generated if not provided when calling
-#' this function (see \code{\link{get_smarter_token}} for more information)
 #'
 #' @inheritParams get_smarter_breeds
 #'
@@ -32,19 +30,15 @@
 #'
 #' all_datasets <- get_smarter_datasets()
 #' }
-get_smarter_datasets <- function(query = list(), token = NULL) {
-  if (is.null(token)) {
-    token <- smarterapi::get_smarter_token()
-  }
-
+get_smarter_datasets <- function(query = list()) {
   logger::log_info("Get data from datasets endpoint")
 
   url <- httr::modify_url(
     smarterapi_globals$base_url,
     path = sprintf("%s/datasets", smarterapi_globals$base_endpoint)
   )
 
-  data <- get_smarter_data(url, token, query)
+  data <- get_smarter_data(url, query)
 
   logger::log_info("Done!")
 

R/genotypes.R

@@ -0,0 +1,82 @@
+
+#' Get SMARTER Genotypes
+#'
+#' Retrieve genotypes data from SMARTER database. Only information about the
+#' supported assemblies are returned (see \code{\link{get_smarter_info}} for
+#' more information).
+#'
+#' @inheritParams get_smarter_variants
+#' @param dest_path the path where the file will be downloaded. If NULL, the
+#' file will be downloaded in the current working directory
+#'
+#' @return a character string with the path to the downloaded file is returned
+#' @export
+#'
+#' @section About SMARTER supported assemblies:
+#' Currently SMARTER supports *OAR3* and *OAR4* assemblies for Sheep and *CHI1*
+#' and *ARS1* assemblies for goat. Genotypes are provided in PLINK binary
+#' format, and compressed in a zip file.
+#'
+#' @examples
+#' \dontrun{
+#' # get genotypes for sheep OAR3 in current directory
+#' get_smarter_genotypes(species = "Sheep", assembly = "OAR3")
+#' }
+get_smarter_genotypes <- function(species, assembly, dest_path = NULL) {
+  # mind that species is lowercase in endpoint url
+  species <- toupper(species)
+  assembly <- toupper(assembly)
+
+  url <- httr::modify_url(
+    smarterapi_globals$ftp_url,
+    path = sprintf("%s/%s/%s/", smarterapi_globals$ftp_path, species, assembly)
+  )
+
+  tmp <- RCurl::getURL(url, ftp.use.epsv = FALSE, dirlistonly = TRUE)
+  file_list <- strsplit(tmp, "\n")[[1]]
+
+  info <- get_smarter_info()
+
+  # Use grep to find the file name that version and have zip extension
+  pattern <- sprintf("%s.*\\.zip$", info$version)
+  matching_file <- grep(pattern, file_list, value = TRUE)
+
+  # check that matching_file is one length
+  # if not, return an error
+  if (length(matching_file) != 1) {
+    stop("No matching file found")
+    return(NULL)
+  }
+
+  # now get the full path of the genotype file
+  url <- httr::modify_url(
+    smarterapi_globals$ftp_url,
+    path = sprintf(
+      "%s/%s/%s/%s",
+      smarterapi_globals$ftp_path,
+      species,
+      assembly,
+      matching_file
+    )
+  )
+
+  if (is.null(dest_path)) {
+    dest_file <- fs::path(getwd(), matching_file)
+  } else {
+    dest_file <- fs::path(dest_path, matching_file)
+  }
+
+  # Use tryCatch to handle potential errors
+  tryCatch({
+    utils::download.file(url, destfile = dest_file, mode = "wb")
+    if (file.exists(dest_file)) {
+      print(sprintf("File downloaded successfully in %s.", dest_file))
+    } else {
+      print("File download failed.")
+    }
+  }, error = function(e) {
+    print(paste("An error occurred:", e$message))
+  })
+
+  return(dest_file)
+}