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small CI fix

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dr. M.S. (Matthijs) Berends
2018-12-06 16:07:06 +01:00
parent 60fe98bbbd
commit 74a7f4453b
4 changed files with 21 additions and 10 deletions
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23
R/mo.R
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@ -380,7 +380,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_trimmed[i])) {
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
x[i] <- microorganismsDT[mo == 'B_SLMNL_ENT', ..property][[1]][1L]
base::message(magenta(paste0("Note: ", italic(x_trimmed[i]), " is a subspecies of ", italic("Salmonella enterica"), " (B_SLMNL_ENT)")))
base::message(magenta(paste0("Note: ", italic(x_trimmed[i]), " will be considered a subspecies of ", italic("Salmonella enterica"), " (B_SLMNL_ENT)")))
next
}
}
@ -595,7 +595,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
renamed_note(name_old = found[1, name],
name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
ref_old = found[1, ref],
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref])
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref],
mo = microorganismsDT[tsn == found[1, tsn_new], mo])
next
}
@ -607,6 +608,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
| name %like% x[i],]
if (NROW(found) > 0 & nchar(x_trimmed[i]) >= 6) {
if (property == "ref") {
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
# mo_ref("Chlamydia psittaci) = "Page, 1968" (with warning)
# mo_ref("Chlamydophila psittaci) = "Everett et al., 1999"
x[i] <- found[1, ref]
} else {
x[i] <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
@ -617,7 +621,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
renamed_note(name_old = found[1, name],
name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
ref_old = found[1, ref],
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref])
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref],
mo = microorganismsDT[tsn == found[1, tsn_new], mo])
next
}
@ -754,8 +759,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
x
}
#' @importFrom crayon blue
renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
#' @importFrom crayon blue italic
renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "") {
if (!is.na(ref_old)) {
ref_old <- paste0(" (", ref_old, ")")
} else {
@ -766,7 +771,13 @@ renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
} else {
ref_new <- ""
}
msg <- paste0("'", name_old, "'", ref_old, " was renamed '", name_new, "'", ref_new)
if (!is.na(mo)) {
mo <- paste0(" (", mo, ")")
} else {
mo <- ""
}
msg <- paste0(italic(name_old), ref_old, " was renamed ", italic(name_new), ref_new, mo)
msg <- gsub("et al.", italic("et al."), msg)
msg_plain <- paste0(name_old, ref_old, " -> ", name_new, ref_new)
msg_plain <- c(getOption("mo_renamed", character(0)), msg_plain)
options(mo_renamed = sort(msg_plain))