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AMR
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C stack error fix

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dr. M.S. (Matthijs) Berends 2018-12-14 11:44:15 +01:00
parent 857f565db0
commit ecebc60bfd
1 changed files with 31 additions and 31 deletions
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62
R/mo.R
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@ -622,12 +622,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# check for uncertain results ---- # check for uncertain results ----
if (allow_uncertain == TRUE) { if (allow_uncertain == TRUE) {
uncertain_fn <- function(x_backup, x_trimmed, x_withspaces, x_withspaces_start) { uncertain_fn <- function(a.x_backup, b.x_trimmed, c.x_withspaces, d.x_withspaces_start, e.x) {
# (1) look again for old taxonomic names, now for G. species ---- # (1) look again for old taxonomic names, now for G. species ----
found <- microorganisms.oldDT[name %like% x_withspaces found <- microorganisms.oldDT[name %like% c.x_withspaces
| name %like% x_withspaces_start | name %like% d.x_withspaces_start
| name %like% x,] | name %like% e.x,]
if (NROW(found) > 0 & nchar(x_trimmed) >= 6) { if (NROW(found) > 0 & nchar(b.x_trimmed) >= 6) {
if (property == "ref") { if (property == "ref") {
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so: # 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("Chlamydia psittaci) = "Page, 1968" (with warning)
@ -637,7 +637,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
x <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]] x <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
} }
warning(red(paste0('UNCERTAIN - "', warning(red(paste0('UNCERTAIN - "',
x_backup, '" -> ', italic(found[1, name]))), a.x_backup, '" -> ', italic(found[1, name]))),
call. = FALSE, immediate. = FALSE) call. = FALSE, immediate. = FALSE)
notes <<- c(notes, notes <<- c(notes,
renamed_note(name_old = found[1, name], renamed_note(name_old = found[1, name],
@ -649,39 +649,38 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
} }
# (2) strip values between brackets ---- # (2) strip values between brackets ----
x_backup_stripped <- gsub("( [(].*[)])", "", x_backup) a.x_backup_stripped <- gsub("( [(].*[)])", "", a.x_backup)
x_backup_stripped <- trimws(gsub(" ", " ", x_backup_stripped, fixed = TRUE)) a.x_backup_stripped <- trimws(gsub(" ", " ", a.x_backup_stripped, fixed = TRUE))
found <- suppressMessages(suppressWarnings(exec_as.mo(x_backup_stripped, clear_options = FALSE))) found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup_stripped, clear_options = FALSE, allow_uncertain = FALSE)))
if (!is.na(found) & nchar(x_trimmed) >= 6) { if (!is.na(found) & nchar(b.x_trimmed) >= 6) {
found <- microorganismsDT[mo == found, ..property][[1]] found <- microorganismsDT[mo == found, ..property][[1]]
warning(red(paste0('UNCERTAIN - "', warning(red(paste0('UNCERTAIN - "',
x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")), a.x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
call. = FALSE, immediate. = FALSE) call. = FALSE, immediate. = FALSE)
return(found[1L]) return(found[1L])
} }
# (3) try to strip off one element and check the remains ---- # (3) try to strip off one element and check the remains ----
look_for_part <- function(z) { x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
x_strip <- z %>% strsplit(" ") %>% unlist() if (length(x_strip) > 1 & nchar(b.x_trimmed) >= 6) {
if (length(x_strip) > 1 & nchar(x_trimmed) >= 6) { for (i in 1:(length(x_strip) - 1)) {
for (i in 1:(length(x_strip) - 1)) { x_strip_collapsed <- paste(x_strip[1:(length(x_strip) - i)], collapse = " ")
x_strip_collapsed <- paste(x_strip[1:(length(x_strip) - i)], collapse = " ") found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, clear_options = FALSE, allow_uncertain = FALSE)))
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, clear_options = FALSE))) if (!is.na(found)) {
if (!is.na(found)) { found <- microorganismsDT[mo == found, ..property][[1]]
found <- microorganismsDT[mo == found, ..property][[1]] warning(red(paste0('UNCERTAIN - "',
warning(red(paste0('UNCERTAIN - "', a.x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
z, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")), call. = FALSE, immediate. = FALSE)
call. = FALSE, immediate. = FALSE) return(found[1L])
return(found[1L])
}
} }
} }
return(NA_character_)
} }
return(look_for_part(x_backup))
# didn't found in uncertain results too
return(NA_character_)
} }
x[i] <- uncertain_fn(x_backup[i], x_trimmed[i], x_withspaces[i], x_withspaces_start[i]) x[i] <- uncertain_fn(x_backup[i], x_trimmed[i], x_withspaces[i], x_withspaces_start[i], x[i])
if (!is.na(x[i])) { if (!is.na(x[i])) {
next next
} }
@ -701,10 +700,11 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
warning(n_distinct(failures), " different values could not be coerced to a valid MO code. See mo_failures() to review them.", warning(n_distinct(failures), " different values could not be coerced to a valid MO code. See mo_failures() to review them.",
call. = FALSE) call. = FALSE)
} else { } else {
warning("These ", length(failures) , " values could not be coerced to a valid MO code: ", warning(red(paste0("These ", length(failures) , " values could not be coerced to a valid MO code: ",
paste('"', unique(failures), '"', sep = "", collapse = ', '), paste('"', unique(failures), '"', sep = "", collapse = ', '),
". See mo_failures() to review them.", ". See mo_failures() to review them.")),
call. = FALSE) call. = FALSE,
immediate. = FALSE)
} }
} }