fix plant pathogenity to plant pathogenicity in the curation file

waldronlab · Jun 24, 2024 · d710bf3 · d710bf3
1 parent b5d6a15
commit d710bf3
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Showing 2 changed files with 1 addition and 16 deletions.
diff --git 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
@@ -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