Merge pull request #111 from TIBHannover/development

Release v0.9.1

.travis.yml

@@ -1,6 +1,7 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
 language: R
+r: devel
 sudo: false
 cache: packages
 

BacDiveR.Rproj

@@ -17,3 +17,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: BacDiveR
-Title: Programmatic Interface For The DSMZ' Bacterial Diversity Metadatabase
-Version: 0.9.0
-Date: 2019-04-30
+Title: Programmatic Interface For The Bacterial Diversity
+    Metadatabase by DSMZ
+Version: 0.9.1
 Authors@R: 
     person(given = "Katrin",
            family = "Leinweber",
@@ -12,23 +12,24 @@ Description: 'BacDive' focuses on providing organism-linked
     information covering the multifarious aspects of bacterial
     biodiversity: taxonomic classification, morphology, physiology,
     cultivation, origin natural habitat and more, both for bacterial and
-    archaeal strains (see Söhngen et al. (2014) <doi:10.1093/nar/gkt1058>).
-    BacDiveR helps you investigate this data offline, and semi-automatically in R.
+    archaeal strains (see Söhngen et al. (2014)
+    <doi:10.1093/nar/gkt1058>).  BacDiveR helps you investigate this data
+    offline, and semi-automatically in R.
 License: MIT + file LICENSE
 URL: https://github.com/TIBHannover/BacDiveR
 BugReports: https://github.com/TIBHannover/BacDiveR/issues
 Imports: 
-    httr (>= 1.3.0),
-    jsonlite (>= 1.5),
+    httr (>= 1.4.0),
+    jsonlite (>= 1.6),
     utils (>= 3.5.0)
 Suggests:
-    ggplot2 (>= 3.0.0),
-    knitr (>= 1.20),
+    ggplot2 (>= 3.2.0),
+    knitr (>= 1.23),
     magrittr (>= 1.5),
-    purrr (>= 0.2.5),
-    rmarkdown (>= 1.10),
-    spelling (>= 1.2),
-    testthat (>= 2.0.0)
+    purrr (>= 0.3.2),
+    rmarkdown (>= 1.13),
+    spelling (>= 2.1),
+    testthat (>= 2.1.1)
 VignetteBuilder: 
     knitr
 ByteCompile: true

NAMESPACE

@@ -6,3 +6,5 @@ export(bd_retrieve_by_search)
 export(bd_retrieve_by_sequence)
 export(bd_retrieve_taxon)
 export(prepare_Renviron)
+import(httr)
+importFrom(jsonlite,fromJSON)

NEWS.md

@@ -7,6 +7,19 @@
 ### Fixed
 ### Security
 
+
+## BacDiveR 0.9.1
+
+### Fixed
+
+- Expose a previously silent download error (#110; Thanks to @jfy133!)
+
+### Changed
+
+- Repair outdated links in documentation
+- Improve some code sections in minor ways
+
+
 ## BacDiveR 0.9.0
 
 All notable changes to this project will be documented in this file.

R/bd_retrieve.R

@@ -10,8 +10,8 @@
 #'
 #' @export
 #' @examples
-#'   dataset_717 <- bd_retrieve(id = 717)
-#'   dataset_717 <- bd_retrieve(id = "717")
+#' dataset_717 <- bd_retrieve(id = 717)
+#' dataset_717 <- bd_retrieve(id = "717")
 #' @rdname bd_retrieve
 bd_retrieve <- function(id) {
   bd_retrieve_data(searchTerm = as.character(id), searchType = "bacdive_id")

R/bd_retrieve_by_culture.R

@@ -3,7 +3,7 @@
 #'   number by which the associated dataset(s) will be retrieved.
 #' @export
 #' @examples
-#'   dataset_DSM_319 <- bd_retrieve_by_culture(collection_no = "DSM 319")
+#' dataset_DSM_319 <- bd_retrieve_by_culture(collection_no = "DSM 319")
 bd_retrieve_by_culture <- function(collection_no) {
   bd_retrieve_data(searchTerm = collection_no, searchType = "culturecollectionno")
 }

R/bd_retrieve_by_search.R

@@ -12,23 +12,27 @@
 #' @export
 #'
 #' @examples
-#'   plant_animal_pathogens <-
-#'     bd_retrieve_by_search(
-#'       queryURL = paste(
-#'         "https://bacdive.dsmz.de/advsearch?site=advsearchsearch",
-#'         "params%5B5%5D%5Bsearchterm%5D=1",
-#'         "searchparams%5B157%5D%5Bsearchterm%5D=1",
-#'         "searchparams%5B158%5D%5Bsearchterm%5D=1",
-#'         "advsearch=search", sep = "&")
-#'         )
+#' plant_animal_pathogens <-
+#'   bd_retrieve_by_search(
+#'     queryURL = paste(
+#'       "https://bacdive.dsmz.de/advsearch?site=advsearchsearch",
+#'       "params%5B5%5D%5Bsearchterm%5D=1",
+#'       "searchparams%5B157%5D%5Bsearchterm%5D=1",
+#'       "searchparams%5B158%5D%5Bsearchterm%5D=1",
+#'       "advsearch=search",
+#'       sep = "&"
+#'     )
+#'   )
 bd_retrieve_by_search <- function(queryURL) {
   # guard against other URLs
   if (!grepl(pattern = "^https:\\/\\/bacdive\\.dsmz\\.de\\/advsearch", queryURL) |
-      !grepl("[?&]site=advsearch", queryURL) |
-      !grepl("[?&]advsearch=search", queryURL) |
-      !grepl("\\&searchparams", queryURL)) {
+    !grepl("[?&]site=advsearch", queryURL) |
+    !grepl("[?&]advsearch=search", queryURL) |
+    !grepl("\\&searchparams", queryURL)) {
     stop(
-      "I'm sorry, but this doesn't seem like an advanced search URL from https://BacDive.DSMZ.de/advsearch! Aborting...\nPlease read https://TIBHannover.GitHub.io/BacDiveR/#how-to-use"
+      "I'm sorry, but this doesn't seem like an advanced search URL from
+ https://BacDive.DSMZ.de/advsearch! Aborting...\nPlease read
+ https://TIBHannover.GitHub.io/BacDiveR/#how-to-use"
     )
   }
 
@@ -46,8 +50,10 @@ bd_retrieve_by_search <- function(queryURL) {
     httr::content(response, as = "text", encoding = "UTF-8")
 
   if (grepl("^[[:digit:]]", payload)) {
-    aggregate_datasets(payload = strsplit(x = payload, split = "\\n")[[1]],
-                       from_IDs = TRUE)
+    aggregate_datasets(
+      payload = strsplit(x = payload, split = "\\n")[[1]],
+      from_IDs = TRUE
+    )
   } else if (grepl("^<!DOCTYPE", payload)) {
     warning("No datasets found. Please check your advanced search and copy-paste the URL again.")
     list()

R/bd_retrieve_by_sequence.R

@@ -3,7 +3,7 @@
 #'   which the associated dataset(s) will be retrieved.
 #' @export
 #' @examples
-#'   dataset_AJ000733 <- bd_retrieve_by_sequence(accession = "AJ000733")
+#' dataset_AJ000733 <- bd_retrieve_by_sequence(accession = "AJ000733")
 bd_retrieve_by_sequence <- function(accession) {
   bd_retrieve_data(searchTerm = accession, searchType = "sequence")
 }

R/bd_retrieve_data.R

@@ -93,13 +93,12 @@ sanitise_type <- function(searchType) {
 construct_url <- function(searchTerm,
                           searchType = "bacdive_id") {
   utils::URLencode(
-    paste0(
-      "https://bacdive.dsmz.de/api/bacdive/",
+    paste(
+      "https://bacdive.dsmz.de/api/bacdive",
       searchType,
-      "/",
       searchTerm,
-      "/",
-      "?format=json"
+      "?format=json",
+      sep = "/"
     )
   )
 }

R/util-download.R

@@ -1,16 +1,24 @@
 #' Download Something from BacDive
 #'
+#' Both `user` and `password` are read from the .Renviron file by default.
+#'
 #' @param URL A correctly encoded character string, either from construct_url()
 #'   or a JSON list
 #'
 #' @return The R object deserialised from the downloaded JSON
 #' @keywords internal
-download <- function(URL) {
+#' @import httr
+#' @importFrom jsonlite fromJSON
+download <- function(URL, user = get_credentials()[1], password = get_credentials()[2]) {
   message(URLs_to_IDs(URL), " ", appendLF = FALSE)
 
-  cred <- get_credentials()
+  response <- GET(URL, authenticate(user, password))
+  payload <- content(response, as = "text", encoding = "UTF-8")
+  data <- fromJSON(payload)
 
-  response <- httr::GET(URL, httr::authenticate(cred[1], cred[2]))
-  payload <- httr::content(response, as = "text", encoding = "UTF-8")
-  jsonlite::fromJSON(payload)
+  if (response$status_code == 403) {
+    stop(paste(data, "\nCheck your .Renviron file, and try copy-pasting your login credentials into https://bacdive.dsmz.de/api/bacdive/ to test them. Correct as necessary and try your data download again."))
+  } else {
+    return(data)
+  }
 }

R/util-get_credentials.R

@@ -1,6 +1,7 @@
 #' Read BacDive Login Credentials from .Renviron
 #'
-#' @return A vector or the two character strings `BacDive_email` and `BacDive_password` representing those two environment variables.
+#' @return A vector or the two character strings `BacDive_email`
+#'   and `BacDive_password` representing those two environment variables.
 #' @keywords internal
 get_credentials <- function() {
   readRenviron(construct_Renviron_path())

tests/testthat/test-bd_retrieve_by_search.R

@@ -25,7 +25,12 @@ test_that("Inconsistent datasets get corrected", {
 })
 
 test_that("Fuzzing of queryURL parameter produces error", {
-  fuzzy_URL <-
-    paste0(sample(strsplit(queryURL, "")[[1]], size = nchar(queryURL)), collapse = "")
+  fuzzy_URL <- paste0(
+    sample(strsplit(queryURL, "")[[1]],
+      size = nchar(queryURL)
+    ),
+    collapse = ""
+  )
+
   expect_error(bd_retrieve_by_search(fuzzy_URL))
 })

tests/testthat/test-download.R

@@ -0,0 +1,4 @@
+test_that("Downloading without preper credentials raises an error", {
+  random <- sample(letters, 8)
+  expect_error(download(construct_url(717), user = random, password = random))
+})

tests/testthat/test-utils.R

@@ -4,6 +4,7 @@ test_that("preparing .Renviron file works", {
   prepare_Renviron()
   r_env_lines <- readLines(construct_Renviron_path())
 
-  for (type in c("email", "password"))
+  for (type in c("email", "password")) {
     expect_true(any(grepl(paste0("^BacDive_", type, "="), r_env_lines)))
+  }
 })