added skip_on_cran

.Rbuildignore

@@ -11,7 +11,7 @@ codemeta.json
 revdep/
 vignettes/
 LICENSE.md
-data-raw/
-/R/new_feature/
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^tests/fixtures
+^tests/bold_trace_files

DESCRIPTION

@@ -1,11 +1,15 @@
 Package: bold
-Version: 1.3.0
+Version: 1.4.1
 Title: Interface to Bold Systems API
 Authors@R: c(person("Salix", "Dubois", role = c("aut", "cre"), 
-                    email = "[email protected]"),
+                    email = "[email protected]",
+                    comment = c(ORCID="0009-0003-0183-8825")),
              person("Scott", "Chamberlain", role = c("aut"),
                     email = "[email protected]",
                     comment = c(ORCID="0000-0003-1444-9135")))
+Author: Salix Dubois [aut, cre],
+  Scott Chamberlain [aut]
+Maintainer: Salix Dubois <[email protected]>
 Depends: 
     R (>= 2.10)
 Suggests:
@@ -21,17 +25,17 @@ Imports:
     data.table,
     methods
 Description: A programmatic interface to the Web Service methods provided by
-    Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data.
+    Bold Systems (<https://www.boldsystems.org/>) for genetic 'barcode' data.
     Functions include methods for searching by sequences by taxonomic names,
     ids, collectors, and institutions; as well as a function for searching
     for specimens, and downloading trace files.
 License: MIT + file LICENSE
-URL: https://docs.ropensci.org/bold/ (documentation), https://github.com/ropensci/bold (source)
+URL: https://docs.ropensci.org/bold/, https://github.com/ropensci/bold
 BugReports: https://github.com/ropensci/bold/issues
 LazyData: yes
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 X-schema.org-applicationCategory: Data Access
 X-schema.org-keywords: biodiversity, barcode, DNA, sequences, fasta
 X-schema.org-isPartOf: https://ropensci.org

R/bold-package.R

@@ -3,8 +3,8 @@
 #' @section About:
 #'
 #' This package gives you access to data from BOLD System
-#' http://www.boldsystems.org/ via their API
-#' (http://v4.boldsystems.org/index.php/api_home)
+#' https://www.boldsystems.org/ via their API
+#' (https://v4.boldsystems.org/index.php/api_home)
 #'
 #' @section Functions:
 #'
@@ -32,10 +32,9 @@
 #' @importFrom methods setGeneric setMethod
 #' @import data.table
 #' @import stringi
-#' @docType package
 #' @name bold-package
 #' @aliases bold
-NULL
+"_PACKAGE"
 
 #' List of 3 nucleotide sequences to use in examples for the
 #' \code{\link{bold_identify}} function

tests/bold_trace_files/ids/TRACE_FILE_INFO.txt

@@ -1,5 +1,5 @@
 PROCESSID	TAXON	MARKER	GENBANK_ACCESSION	TRACEFILE
-ACRJP618-11	Lepidoptera	COI-5P		ACRJP/ACRJP618-11[LepF1,LepR1]_F+1329172726.ab1
-ACRJP619-11	Lepidoptera	COI-5P		ACRJP/ACRJP619-11[LepF1,LepR1]_R+1329177943.ab1
-ACRJP619-11	Lepidoptera	COI-5P		ACRJP/ACRJP619-11[LepF1,LepR1]_F+1329172726.ab1
+ACRJP618-11	Prepona amydon zenodorus	COI-5P		ACRJP/ACRJP618-11[LepF1,LepR1]_F+1329172726.ab1
+ACRJP619-11	Prepona amydon amydonius	COI-5P		ACRJP/ACRJP619-11[LepF1,LepR1]_R+1329177943.ab1
+ACRJP619-11	Prepona amydon amydonius	COI-5P		ACRJP/ACRJP619-11[LepF1,LepR1]_F+1329172726.ab1
 

tests/bold_trace_files/taxon/TRACE_FILE_INFO.txt

@@ -3,6 +3,8 @@ BBBO256-10	Bombus ignitus	COI-5P		BBBO/BBBO256-10[LepF1,LepR1]_R+1288149881.ab1
 BBBO256-10	Bombus ignitus	COI-5P		BBBO/BBBO256-10[LepF1,LepR1]_F+1288144746.ab1
 BBBO257-10	Bombus ignitus	COI-5P		BBBO/BBBO257-10[LepF1,LepR1]_R+1288149881.ab1
 BBBO257-10	Bombus ignitus	COI-5P		BBBO/BBBO257-10[LepF1,LepR1]_F+1288144746.ab1
-BBBO400-11	Bombus ignitus	COI-5P		BBBO/BBBO400-11[RonMWASPdeg_t1,LepR1]_R+1313556977.ab1
 BBBO400-11	Bombus ignitus	COI-5P		BBBO/BBBO400-11[RonMWASPdeg_t1,LepR1]_F+1313551803.ab1
+BBBO400-11	Bombus ignitus	COI-5P		BBBO/BBBO400-11[RonMWASPdeg_t1,LepR1]_R+1313556977.ab1
+BOFTH106-08	Bombus ignitus	COI-5P		BOFJ/BOFTH106-08_F+1221866614.ab1
+BOFTH106-08	Bombus ignitus	COI-5P		BOFJ/BOFTH106-08_R+1221872058.ab1
 

tests/fixtures/bold_trace.yml

@@ -6,7 +6,7 @@ http_interactions:
       encoding: ''
       string: ''
     headers:
-      User-Agent: libcurl/7.64.1 r-curl/4.3.3 crul/1.3
+      User-Agent: libcurl/8.3.0 r-curl/5.2.3 crul/1.5.0
       Accept-Encoding: gzip, deflate
       Accept: application/json, text/xml, application/xml, */*
   response:
@@ -17,27 +17,27 @@ http_interactions:
     headers:
       status: HTTP/1.1 200 OK
       server: nginx
-      date: Tue, 28 Feb 2023 00:15:06 GMT
+      date: Fri, 13 Dec 2024 21:46:44 GMT
       content-type: application/x-tar
       transfer-encoding: chunked
       connection: keep-alive
       x-powered-by: PHP/5.3.15
       content-disposition: attachment; filename="trace_files.tar
       set-cookie: https=on;Path=/;Max-Age=3600;httponly;SameSite=Lax
     body:
-      encoding: UTF-8
+      encoding: ''
       file: yes
-      string: D:\02_rOpenSci\bold\tests\testthat\bold_trace_files/bold_trace_files.tar
-  recorded_at: 2023-02-28 00:15:09 GMT
-  recorded_with: vcr/1.0.2, webmockr/0.8.0
+      string: D:\02_rOpenSci\bold\tests\bold_trace_files/bold_trace_files.tar
+  recorded_at: 2024-12-13 21:46:47 GMT
+  recorded_with: vcr/1.6.0, webmockr/1.0.0
 - request:
     method: get
     uri: https://v4.boldsystems.org/index.php/API_Public/trace?ids=ACRJP618-11%7CACRJP619-11
     body:
       encoding: ''
       string: ''
     headers:
-      User-Agent: libcurl/7.64.1 r-curl/4.3.3 crul/1.3
+      User-Agent: libcurl/8.3.0 r-curl/5.2.3 crul/1.5.0
       Accept-Encoding: gzip, deflate
       Accept: application/json, text/xml, application/xml, */*
   response:
@@ -48,16 +48,16 @@ http_interactions:
     headers:
       status: HTTP/1.1 200 OK
       server: nginx
-      date: Tue, 28 Feb 2023 00:15:08 GMT
+      date: Fri, 13 Dec 2024 21:46:46 GMT
       content-type: application/x-tar
       transfer-encoding: chunked
       connection: keep-alive
       x-powered-by: PHP/5.3.15
       content-disposition: attachment; filename="trace_files.tar
       set-cookie: https=on;Path=/;Max-Age=3600;httponly;SameSite=Lax
     body:
-      encoding: UTF-8
+      encoding: ''
       file: yes
-      string: D:\02_rOpenSci\bold\tests\testthat\bold_trace_files/bold_trace_files.tar
-  recorded_at: 2023-02-28 00:15:09 GMT
-  recorded_with: vcr/1.0.2, webmockr/0.8.0
+      string: D:\02_rOpenSci\bold\tests\bold_trace_files/bold_trace_files.tar
+  recorded_at: 2024-12-13 21:46:47 GMT
+  recorded_with: vcr/1.6.0, webmockr/1.0.0

tests/setup_cassettes.R

@@ -0,0 +1,140 @@
+tests_set_cassette_bold_specimens <- function() {
+  message("Recording the 'bold_specimens' cassette.")
+  vcr::use_cassette("bold_specimens", {
+    bold_specimens(taxon = 'Coelioxys')
+    bold_specimens(taxon = 'Coelioxys', format = 'xml')
+  })
+}
+tests_set_cassette_bold_seqspec <- function() {
+  message("Recording the 'bold_seqspec' cassette.")
+  vcr::use_cassette("bold_seqspec", {
+    bold_seqspec(taxon = 'Coelioxys')
+  })
+}
+tests_set_cassette_bold_seq <- function() {
+  message("Recording the 'bold_seq' cassette.")
+  vcr::use_cassette("bold_seq", {
+    bold_seq(taxon = 'Coelioxys')
+    bold_seq(bin = 'BOLD:AAA5125')
+  })
+}
+tests_set_cassette_bold_stats <- function() {
+  message("Recording  the 'bold_stats' cassette.")
+  vcr::use_cassette("bold_stats", {
+    bold_stats(taxon = "Coelioxys")
+    bold_stats(taxon = "Coelioxys", simplify = TRUE)
+    bold_stats(taxon = "Coelioxys",
+               simplify = TRUE,
+               dataType = "overview")
+    bold_stats(taxon = c("Coelioxys", "Osmia"))
+  })
+}
+tests_set_cassette_bold_trace <- function() {
+  message("Recording  the 'bold_trace' cassette.")
+  vcr::use_cassette("bold_trace", {
+    dest.dir <- vcr::vcr_configuration()$write_disk_path
+    bold_trace(
+      taxon = "Bombus ignitus",
+      geo = "Japan",
+      dest = file.path(dest.dir, "taxon")
+    )
+    bold_trace(
+      ids = c('ACRJP618-11', 'ACRJP619-11'),
+      dest = file.path(dest.dir, "ids")
+    )
+  })
+}
+tests_set_cassette_bold_tax_id2 <- function() {
+  message("Recording the 'bold_tax_id2' cassette.")
+  vcr::use_cassette("bold_tax_id2", {
+    bold_tax_id2(id = 88899)
+    bold_tax_id2(id = c(88899, 125295))
+    bold_tax_id2(id = 88899, includeTree = TRUE)
+    bold_tax_id2(id = 88899, dataTypes = "all")
+    bold_tax_id2(id = 88899, dataTypes = "stats")
+    bold_tax_id2(id = 88899, dataTypes = "geo")
+    bold_tax_id2(id = 88899, dataTypes = "sequencinglabs")
+    bold_tax_id2(
+      id = 88899,
+      dataTypes = c("basic", "geo"),
+      includeTree = TRUE
+    )
+    bold_tax_id2(id = 660837, dataTypes = "stats") # no public marker sequences
+    bold_tax_id2(id = 660837, dataTypes = c("basic", "stats")) # no public marker sequences
+  })
+}
+tests_set_cassette_bold_tax_name <- function() {
+  message("Recording the 'bold_tax_name' cassette.")
+  vcr::use_cassette("bold_tax_name", {
+    bold_tax_name(name = "Diplura")
+    bold_tax_name(name = c("Apis", "Puma concolor", "Pinus concolor"))
+    bold_tax_name(name = "Diplur", fuzzy = TRUE)
+    bold_tax_name(name = "Diplur", fuzzy = FALSE)
+    bold_tax_name(name = c(
+      "Diplurodes sp.",
+      "Chlamydomonas sp. 18 (FA)",
+      "Chlamydomonas sp. 'Chile J'"
+    ))
+  })
+}
+tests_set_cassette_bold_identify_parents <- function() {
+  message("Recording the 'bold_identify_parents' cassette.")
+  vcr::use_cassette("bold_identify_parents", {
+    load("tests/testthat/bold_identify_list.rda")
+    bold_identify_parents(bold_identify_list)
+  })
+}
+tests_set_cassette_bold_identify_taxonomy <- function() {
+  message("Recording the 'bold_identify_taxonomy' cassette.")
+  vcr::use_cassette("bold_identify_taxonomy", {
+    load("tests/testthat/bold_identify_list.rda")
+    bold_identify_taxonomy(x = bold_identify_list)
+  })
+}
+tests_set_cassette_bold_identify <- function() {
+  message("Recording the '", bold_identify, "' cassette.")
+  vcr::use_cassette("bold_identify", {
+    bold_identify(sequences$seq1)
+    bold_identify(sequences$seq1, db = 'COX1_SPECIES')
+    bold_identify(
+      "AACCCTATACTTTTTATTTGGAATTTGAGCGGGTATAGTAGGTACTAGCTTAAGTATATTAATTCGTCTAGAGCTAGGACAACCCGGTGTATTTTTAGAAGATGACCAAACCTATAACGTTATTGTAACAGCCCACGCTTTTATTATAATTTTCTTCATAATTATACCAATCATAATTGGA"
+    )
+  })
+}
+tests_setup_cassettes <- function(cassette = "all") {
+  invisible(vcr::vcr_configure(
+    dir = normalizePath(file.path(getwd(), "tests/fixtures")),
+    write_disk_path = normalizePath(file.path(getwd(), "tests/bold_trace_files"))
+  ))
+  if (length(cassette) == 1 && cassette == "all") {
+    cassette <- c(
+      "bold_specimens",
+      "bold_seqspec",
+      "bold_seq",
+      "bold_stats",
+      "bold_trace",
+      "bold_tax_id2",
+      "bold_tax_name",
+      "bold_identify_parents",
+      "bold_identify_taxonomy",
+      "bold_identify"
+    )
+  }
+  for (x in cassette) {
+    switch (
+      x,
+      bold_specimens = tests_set_cassette_bold_specimens(),
+      bold_seqspec = tests_set_cassette_bold_seqspec(),
+      bold_seq = tests_set_cassette_bold_seq(),
+      bold_stats = tests_set_cassette_bold_stats(),
+      bold_trace = tests_set_cassette_bold_trace(),
+      bold_tax_id2 = tests_set_cassette_bold_tax_id2(),
+      bold_tax_name = tests_set_cassette_bold_tax_name(),
+      bold_identify_parents = tests_set_cassette_bold_identify_parents(),
+      bold_identify_taxonomy = tests_set_cassette_bold_identify_taxonomy(),
+      bold_identify = tests_set_cassette_bold_identify(),
+      stop("No cassette named ", cassette)
+    )
+  }
+}
+# tests_setup_cassettes()

tests/testthat/helper-bold.R

@@ -1,3 +1,8 @@
 # set up vcr
-library("vcr")
-invisible(vcr::vcr_configure(dir = "../fixtures", write_disk_path = "../bold_trace_files"))
+library(vcr)
+invisible(vcr::vcr_configure(
+  # dir = normalizePath(file.path(getwd(), "tests/fixtures")),
+  # write_disk_path = normalizePath(file.path(getwd(), "tests/bold_trace_files"))
+  dir = normalizePath("../fixtures"),
+  write_disk_path = normalizePath("../bold_trace_files")
+))