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fixes for microorganisms.codes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-05-28 16:50:40 +02:00
parent 7e0e171512
commit 27380fa021
73 changed files with 679 additions and 412 deletions
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21
R/mo.R
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@ -456,10 +456,19 @@ exec_as.mo <- function(x,
} else if (!all(x %in% AMR::microorganisms[, property])) {
strip_whitespace <- function(x) {
# all whitespaces (tab, new lines, etc.) should be one space
# and spaces before and after should be omitted
trimws(gsub("[\\s]+", " ", x, perl = TRUE), which = "both")
}
x <- strip_whitespace(x)
x_backup <- x
# remove spp and species
x <- trimws(gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x_backup, ignore.case = TRUE), which = "both")
x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x_backup, ignore.case = TRUE)
x <- strip_whitespace(x)
x_backup_without_spp <- x
x_species <- paste(x, "species")
# translate to English for supported languages of mo_property
@ -487,8 +496,8 @@ exec_as.mo <- function(x,
x <- gsub("e+", "e+", x, ignore.case = TRUE)
x <- gsub("o+", "o+", x, ignore.case = TRUE)
# but spaces before and after should be omitted
x <- trimws(x, which = "both")
x <- strip_whitespace(x)
x_trimmed <- x
x_trimmed_species <- paste(x_trimmed, "species")
x_trimmed_without_group <- gsub(" gro.u.p$", "", x_trimmed, ignore.case = TRUE)
@ -1063,7 +1072,7 @@ exec_as.mo <- function(x,
}
}
}
# (6) try to strip off one element from start and check the remains (only allow 2-part name outcome) ----
# (6) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
for (i in 2:(length(x_strip))) {
@ -1072,8 +1081,8 @@ exec_as.mo <- function(x,
if (!empty_result(found)) {
found_result <- found
found <- microorganismsDT[mo == found_result[1L], ..property][[1]]
# uncertainty level 2 only if the fullname contains a space (otherwise it will be found with lvl 3)
if (microorganismsDT[mo == found_result[1L], fullname][[1]] %like% " ") {
# uncertainty level 2 only if searched part contains a space (otherwise it will be found with lvl 3)
if (x_strip_collapsed %like% " ") {
uncertainties <<- rbind(uncertainties,
data.frame(uncertainty = 2,
input = a.x_backup,