Skip to content

Commit

Permalink
fix plant pathogenity to plant pathogenicity in the curation file
Browse files Browse the repository at this point in the history
  • Loading branch information
sdgamboa committed Jun 24, 2024
1 parent b5d6a15 commit d710bf3
Show file tree
Hide file tree
Showing 2 changed files with 1 addition and 16 deletions.
15 changes: 0 additions & 15 deletions R/bugphyzz.R
Original file line number Diff line number Diff line change
Expand Up @@ -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") |>
Expand Down
2 changes: 1 addition & 1 deletion inst/extdata/attributes.tsv
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down

0 comments on commit d710bf3

Please sign in to comment.