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synced 2025-07-09 19:41:49 +02:00
small CI fix
This commit is contained in:
23
R/mo.R
23
R/mo.R
@ -380,7 +380,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_trimmed[i])) {
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# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
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x[i] <- microorganismsDT[mo == 'B_SLMNL_ENT', ..property][[1]][1L]
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base::message(magenta(paste0("Note: ", italic(x_trimmed[i]), " is a subspecies of ", italic("Salmonella enterica"), " (B_SLMNL_ENT)")))
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base::message(magenta(paste0("Note: ", italic(x_trimmed[i]), " will be considered a subspecies of ", italic("Salmonella enterica"), " (B_SLMNL_ENT)")))
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next
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}
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}
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@ -595,7 +595,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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renamed_note(name_old = found[1, name],
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name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
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ref_old = found[1, ref],
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ref_new = microorganismsDT[tsn == found[1, tsn_new], ref])
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ref_new = microorganismsDT[tsn == found[1, tsn_new], ref],
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mo = microorganismsDT[tsn == found[1, tsn_new], mo])
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next
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}
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@ -607,6 +608,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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| name %like% x[i],]
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if (NROW(found) > 0 & nchar(x_trimmed[i]) >= 6) {
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if (property == "ref") {
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# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
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# mo_ref("Chlamydia psittaci) = "Page, 1968" (with warning)
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# mo_ref("Chlamydophila psittaci) = "Everett et al., 1999"
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x[i] <- found[1, ref]
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} else {
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x[i] <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
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@ -617,7 +621,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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renamed_note(name_old = found[1, name],
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name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
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ref_old = found[1, ref],
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ref_new = microorganismsDT[tsn == found[1, tsn_new], ref])
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ref_new = microorganismsDT[tsn == found[1, tsn_new], ref],
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mo = microorganismsDT[tsn == found[1, tsn_new], mo])
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next
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}
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@ -754,8 +759,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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x
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}
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#' @importFrom crayon blue
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renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
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#' @importFrom crayon blue italic
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renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "") {
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if (!is.na(ref_old)) {
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ref_old <- paste0(" (", ref_old, ")")
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} else {
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@ -766,7 +771,13 @@ renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
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} else {
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ref_new <- ""
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}
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msg <- paste0("'", name_old, "'", ref_old, " was renamed '", name_new, "'", ref_new)
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if (!is.na(mo)) {
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mo <- paste0(" (", mo, ")")
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} else {
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mo <- ""
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}
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msg <- paste0(italic(name_old), ref_old, " was renamed ", italic(name_new), ref_new, mo)
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msg <- gsub("et al.", italic("et al."), msg)
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msg_plain <- paste0(name_old, ref_old, " -> ", name_new, ref_new)
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msg_plain <- c(getOption("mo_renamed", character(0)), msg_plain)
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options(mo_renamed = sort(msg_plain))
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