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(v1.5.0.9023) mo properties speed improvement

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-02-21 23:19:40 +01:00
parent 062c49fca1
commit 0fdabff1ba
18 changed files with 62 additions and 86 deletions
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1
R/globals.R
View File

@ -26,6 +26,7 @@
globalVariables(c(".rowid",
"ab",
"ab_txt",
"affect_mo_name",
"angle",
"antibiotic",
"antibiotics",

15
R/mo.R
View File

@ -766,21 +766,24 @@ exec_as.mo <- function(x,
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB)
x[i] <- lookup(mo == toupper(gsub("g([abcdfghk])s",
"B_STRPT_GRP\\1",
x_backup_without_spp[i])), uncertainty = -1)
x_backup_without_spp[i],
perl = TRUE)), uncertainty = -1)
next
}
if (x_backup_without_spp[i] %like_case% "(streptococ|streptokok).* [abcdfghk]$") {
# Streptococci in different languages, like "estreptococos grupo B"
x[i] <- lookup(mo == toupper(gsub(".*(streptococ|streptokok|estreptococ).* ([abcdfghk])$",
"B_STRPT_GRP\\2",
x_backup_without_spp[i])), uncertainty = -1)
x_backup_without_spp[i],
perl = TRUE)), uncertainty = -1)
next
}
if (x_backup_without_spp[i] %like_case% "group [abcdfghk] (streptococ|streptokok|estreptococ)") {
# Streptococci in different languages, like "Group A Streptococci"
x[i] <- lookup(mo == toupper(gsub(".*group ([abcdfghk]) (streptococ|streptokok|estreptococ).*",
"B_STRPT_GRP\\1",
x_backup_without_spp[i])), uncertainty = -1)
x_backup_without_spp[i],
perl = TRUE)), uncertainty = -1)
next
}
if (x_backup_without_spp[i] %like_case% "haemoly.*strep") {
@ -843,7 +846,7 @@ exec_as.mo <- function(x,
# Salmonella Group A to Z, just return S. species for now
x[i] <- lookup(genus == "Salmonella", uncertainty = -1)
next
} else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup[i], ignore.case = FALSE) &
} else if (x_backup[i] %like_case% "[sS]almonella [A-Z][a-z]+ ?.*" &
!x_backup[i] %like% "t[iy](ph|f)[iy]") {
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
# except for S. typhi, S. paratyphi, S. typhimurium
@ -1108,7 +1111,7 @@ exec_as.mo <- function(x,
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (3) look for genus only, part of name\n"))
}
if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like_case% " ") {
if (!grepl("^[A-Z][a-z]+", b.x_trimmed, ignore.case = FALSE)) {
if (!b.x_trimmed %like_case% "^[A-Z][a-z]+") {
if (isTRUE(debug)) {
message("Running '", paste(b.x_trimmed, "species"), "'")
}
@ -1852,7 +1855,7 @@ print.mo_uncertainties <- function(x, ...) {
width = 0.98 * getOption("width")),
collapse = "")
# after strwrap, make taxonomic names italic
candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates)
candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates, perl = TRUE)
candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "),
"Also matched",
candidates, fixed = TRUE)

6
R/mo_property.R
View File

@ -723,12 +723,6 @@ mo_validate <- function(x, property, language, ...) {
x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...)
} else if (!all(x %in% MO_lookup[, property, drop = TRUE])
| has_Becker_or_Lancefield) {
accepted_args <- names(as.list(args("as.mo")))
accepted_args <- accepted_args[!accepted_args %in% c("", "...", "x", "property")]
stop_if(!all(names(dots) %in% names(as.list(args("as.mo")))),
"invalid argument(s): ", vector_and(names(dots)[!names(dots) %in% names(as.list(args("as.mo")))], quotes = "'"),
".\nAccepted arguments are ", vector_and(accepted_args, quotes = "'"), ".",
call = FALSE)
x <- exec_as.mo(x, property = property, language = language, ...)
}