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(v0.7.1.9004) atc class removal

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dr. M.S. (Matthijs) Berends
2019-06-27 11:57:45 +02:00
parent 6013fbefae
commit 65c6702b21
49 changed files with 393 additions and 706 deletions
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39
R/mo.R
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@ -486,7 +486,7 @@ exec_as.mo <- function(x,
# remove genus as first word
x <- gsub("^Genus ", "", x)
# allow characters that resemble others
if (initial_search == FALSE) {
if (uncertainty_level >= 2) {
x <- tolower(x)
x <- gsub("[iy]+", "[iy]+", x)
x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x)
@ -494,9 +494,13 @@ exec_as.mo <- function(x,
x <- gsub("(th|t)+", "(th|t)+", x)
x <- gsub("a+", "a+", x)
x <- gsub("u+", "u+", x)
# allow any ending of -um, -us, -ium, -ius and -a (needs perl for the negative backward lookup):
x <- gsub("(um|u\\[sz\\]\\+|\\[iy\\]\\+um|\\[iy\\]\\+u\\[sz\\]\\+|a\\+)(?![a-z[])",
"(um|us|ium|ius|a)", x, ignore.case = TRUE, perl = TRUE)
# allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica and -a (needs perl for the negative backward lookup):
x <- gsub("(u\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+)(?![a-z[])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, ignore.case = TRUE, perl = TRUE)
x <- gsub("(\\[iy\\]\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+a\\+)(?![a-z[])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, ignore.case = TRUE, perl = TRUE)
x <- gsub("(\\[iy\\]\\+u\\+m)(?![a-z[])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, ignore.case = TRUE, perl = TRUE)
x <- gsub("e+", "e+", x, ignore.case = TRUE)
x <- gsub("o+", "o+", x, ignore.case = TRUE)
x <- gsub("(.)\\1+", "\\1+", x)
@ -1078,8 +1082,33 @@ exec_as.mo <- function(x,
return(found[1L])
}
# (5) try to strip off one element from end and check the remains ----
# (5a) try to strip off half an element from end and check the remains ----
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
if (length(x_strip) > 1) {
for (i in 1:(length(x_strip) - 1)) {
lastword <- x_strip[length(x_strip) - i + 1]
lastword_half <- substr(lastword, 1, as.integer(nchar(lastword) / 2))
# remove last half of the second term
x_strip_collapsed <- paste(c(x_strip[1:(length(x_strip) - i)], lastword_half), collapse = " ")
if (nchar(x_strip_collapsed) >= 4) {
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE)))
if (!empty_result(found)) {
found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]]
uncertainties <<- rbind(uncertainties,
data.frame(uncertainty = 2,
input = a.x_backup,
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
}
return(found[1L])
}
}
}
}
# (5b) try to strip off one element from end and check the remains ----
if (length(x_strip) > 1) {
for (i in 1:(length(x_strip) - 1)) {
x_strip_collapsed <- paste(x_strip[1:(length(x_strip) - i)], collapse = " ")