update importBugphyzz and tests with Zenodo DOI

waldronlab · Apr 16, 2024 · 6c63337 · 6c63337
1 parent 8e189a9
commit 6c63337
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Showing 4 changed files with 15 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: bugphyzz
 Title: A harmonized data resource and software for enrichment analysis of microbial physiologies
-Version: 0.99.0
+Version: 0.99.1
 Authors@R: 
     c(
         person(

diff --git a/R/bugphyzz.R b/R/bugphyzz.R
@@ -54,7 +54,7 @@ utils::globalVariables(c(
 #' names(bp)
 #'
 importBugphyzz <- function(
-        version = "d3fd894", force_download = FALSE, v = 0.5,
+        version = "10.5281/zenodo.10980813", force_download = FALSE, v = 0.5,
         exclude_rarely = TRUE
 
 ) {
@@ -367,7 +367,7 @@ getTaxonSignatures <- function(tax, bp, ...) {
 
     output <- vector("list", length(files))
     for (i in seq_along(output)) {
-        output[[i]] <- utils::read.csv(files, header = TRUE, skip = 1) |>
+        output[[i]] <- utils::read.csv(files[i], header = TRUE, skip = 1) |>
             dplyr::mutate(Attribute = tolower(Attribute))
     }
     return(output)

diff --git a/man/importBugphyzz.Rd b/man/importBugphyzz.Rd
diff --git a/tests/testthat/test-importBugphyzz.R b/tests/testthat/test-importBugphyzz.R
@@ -189,6 +189,17 @@ test_that("importBugphyzz works with hash", {
     expect_true(all(map_lgl(bp, checkUniqueAnnotations)))
 })
 
+test_that("importBugphyzz works with Zenodo DOI", {
+    bp <- importBugphyzz(version = "10.5281/zenodo.10980813", force_download = TRUE)
+    expect_true(all("data.frame" == map_chr(bp, class)))
+    expect_true(all(map_lgl(bp, ~ nrow(.x) > 0)))
+    expect_true(all(map_lgl(bp, checkColumnNames)))
+    expect_true(all(map_lgl(bp, checkColumnTypes)))
+    expect_true(all(map_lgl(bp, checkNAs)))
+    expect_true(all(map_lgl(bp, checkCuration)))
+    expect_true(all(map_lgl(bp, checkUniqueAnnotations)))
+})
+
 ## TODO create test for using Zenodo
 test_that("importBugphyzz doesn't work with other words", {
     expect_error(importBugphyzz(version = "abcd-1234", force_download = TRUE))