From d710bf31333de45e4de5be03c97d1c6b360c4eb7 Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Mon, 24 Jun 2024 17:34:52 -0400 Subject: [PATCH] fix plant pathogenity to plant pathogenicity in the curation file --- R/bugphyzz.R | 15 --------------- inst/extdata/attributes.tsv | 2 +- 2 files changed, 1 insertion(+), 16 deletions(-) diff --git a/R/bugphyzz.R b/R/bugphyzz.R index 92e9fe9..11bb003 100644 --- a/R/bugphyzz.R +++ b/R/bugphyzz.R @@ -73,21 +73,6 @@ importBugphyzz <- function( output <- lapply(output, function(x) split(x, x$Attribute)) output <- purrr::list_flatten(output) - ## TODO correct plant pathogenicity name earlier in the workflow or - ## better yet, directly in the curation - pos <- which(names(output) == "plant pathogenity") - names(output)[pos] <- "plant pathogenicity" - output <- purrr::map(output, ~ { - .x |> - dplyr::mutate( - Attribute = ifelse( - Attribute == "plant pathogenity", - "plant pathogenicity", - Attribute - ) - ) - }) - names(output) <- purrr::map_chr(output, ~ unique(.x$Attribute)) val <- .validationData() |> dplyr::filter(rank == "all") |> diff --git a/inst/extdata/attributes.tsv b/inst/extdata/attributes.tsv index a674c77..757e3bd 100644 --- a/inst/extdata/attributes.tsv +++ b/inst/extdata/attributes.tsv @@ -193,7 +193,7 @@ "growth temperature" "growth temperature" "numeric" NA NA "oral" "habitat" "logical" NA NA "optimal ph" "optimal ph" "numeric" NA NA -"plant pathogenity" "plant pathogenicity" "numeric" NA NA +"plant pathogenicity" "plant pathogenicity" "numeric" NA NA "blade of grass from raritan river nj, usa" "isolation site" "logical" NA NA "hot swamp from kunashir island, russia" "isolation site" "logical" NA NA "30-m-tall sulfide mound in the iheya north field, japan" "isolation site" "logical" NA NA