increase code coverage

neurogenomics · Dec 22, 2023 · bc242c5 · bc242c5
1 parent 021d37f
commit bc242c5
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Showing 7 changed files with 31 additions and 10 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,7 @@
 
 * Bump version for Bioc 3.19.
 * Use GHCR instead of Dockerhub, update vignette accordingly.
+* Increase code coverage.
 
 ## Bug fixes
 

diff --git a/R/all_species.R b/R/all_species.R
@@ -17,7 +17,7 @@
 #' @examples
 #' species_dt <- all_species()
 all_species <- function(method = NULL,
-                         verbose = TRUE) {
+                        verbose = TRUE) {
     if(is.null(method)){
         method <- eval(formals(map_species)$method)
     }

diff --git a/R/earthworm2human_map.R b/R/earthworm2human_map.R
@@ -30,12 +30,15 @@ earthworm2human_map <- function(evalue_threshold = NULL,
     requireNamespace("piggyback")
 
     file <- "ea_to_hu.csv.gz"
-    dir.create(save_dir,showWarnings = FALSE, recursive = TRUE)
     tmp <- file.path(save_dir,file) 
-    piggyback::pb_download(file = file,
-                           repo = "neurogenomics/orthogene",
-                           dest = save_dir)
-    get_data_check(tmp = tmp) 
+    if(!file.exists(tmp)){
+        dir.create(save_dir,showWarnings = FALSE, recursive = TRUE)
+        piggyback::pb_download(file = file,
+                               repo = "neurogenomics/orthogene",
+                               dest = save_dir, 
+                               tag = "v1.1.1")
+        get_data_check(tmp = tmp) 
+    }
     gene_map <- data.table::fread(tmp)
     #### Filter evalue #### 
     if(!is.null(evalue_threshold)){

diff --git a/R/get_all_orgs.R b/R/get_all_orgs.R
@@ -43,7 +43,7 @@ get_all_orgs <- function(method = c(
     #### method: genomeinfodb ####
     } else if (tolower(method) == "genomeinfodb") {
         #### Load a really big organism reference ####
-        orgs <- rbind(orgs, get_orgdb_genomeinfodbdata(verbose = verbose))
+        orgs <- get_orgdb_genomeinfodbdata(verbose = verbose)
         orgs$source <- "genomeinfodb"
     #### Error ####
     } else {

diff --git a/R/get_orgdb_genomeinfodbdata.R b/R/get_orgdb_genomeinfodbdata.R
@@ -15,11 +15,12 @@
 get_orgdb_genomeinfodbdata <- function(verbose = TRUE) {
     # Avoid confusing biocheck
     scientific_name <- display_name <- genus <- NULL
-    species <- id <- version <- ..keep_cols <- NULL
+    species <- id <- version <- NULL
 
     messager("Preparing organisms reference from: GenomeInfoDb", v = verbose)
     requireNamespace("GenomeInfoDbData")
-    utils::data("specData")
+    utils::data("specData",package = "GenomeInfoDbData")
+    specData <- data.table::as.data.table(get("specData"))
     #### Remove NAs ####
     no_no_list <- c("environmental", "unclassified", NA)
     specData <- specData[(!genus %in% no_no_list) &
@@ -38,6 +39,6 @@ get_orgdb_genomeinfodbdata <- function(verbose = TRUE) {
         "display_name", "id",
         "scientific_name", "taxonomy_id", "version"
     )
-    specData <- unique(specData[, ..keep_cols])
+    specData <- unique(specData[, keep_cols, with=FALSE])
     return(specData)
 }
diff --git a/tests/testthat/test-all_species.R b/tests/testthat/test-all_species.R
@@ -0,0 +1,10 @@
+test_that("all_species works", {
+
+    species_dt <- all_species()
+    testthat::expect_gte(nrow(species_dt), 700)
+
+    if(rworkflows::is_gha()){
+        species_dt <- all_species(method="genomeinfodb")
+        testthat::expect_gte(nrow(species_dt), 2e6) # over 2.5 million species!
+    }
+})
diff --git a/tests/testthat/test-earthworm2human_map.R b/tests/testthat/test-earthworm2human_map.R
@@ -0,0 +1,6 @@
+test_that("earthworm2human_map works", {
+
+    map <- orthogene:::earthworm2human_map()
+    testthat::expect_gte(nrow(map), 4.6e5)
+    testthat::expect_true(all(grepl("^evm",map$qseqid)))
+})