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(v0.7.1.9058) as.mo() improvement
This commit is contained in:
172
R/mo.R
172
R/mo.R
@ -314,6 +314,7 @@ exec_as.mo <- function(x,
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options(mo_uncertainties = NULL)
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options(mo_renamed = NULL)
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}
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options(mo_renamed_last_run = NULL)
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if (NCOL(x) == 2) {
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# support tidyverse selection like: df %>% select(colA, colB)
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@ -336,9 +337,12 @@ exec_as.mo <- function(x,
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}
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notes <- character(0)
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uncertainties <- data.frame(input = character(0),
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uncertainties <- data.frame(uncertainty = integer(0),
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input = character(0),
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fullname = character(0),
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mo = character(0))
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renamed_to = character(0),
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mo = character(0),
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stringsAsFactors = FALSE)
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failures <- character(0)
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uncertainty_level <- translate_allow_uncertain(allow_uncertain)
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@ -488,11 +492,13 @@ exec_as.mo <- function(x,
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# replace minus by a space
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x <- gsub("-+", " ", x)
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# replace hemolytic by haemolytic
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x <- gsub("ha?emoly", "haemoly", x)
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x <- gsub("ha?emoly", "haemoly", x, ignore.case = TRUE)
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# place minus back in streptococci
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x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x)
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x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x, ignore.case = TRUE)
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# remove genus as first word
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x <- gsub("^Genus ", "", x)
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x <- gsub("^genus ", "", x, ignore.case = TRUE)
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# remove 'uncertain' like texts
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x <- trimws(gsub("(uncertain|susp[ie]c[a-z]+|verdacht)", "", x, ignore.case = TRUE))
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# allow characters that resemble others = dyslexia_mode ----
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if (dyslexia_mode == TRUE) {
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x <- tolower(x)
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@ -514,10 +520,11 @@ exec_as.mo <- function(x,
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x <- gsub("(.)\\1+", "\\1+", x)
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# allow ending in -en or -us
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x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, ignore.case = TRUE, perl = TRUE)
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# if the input is longer than 10 characters, add a [.] between all characters, as some might have forgotten a character
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# if the input is longer than 10 characters, allow any constant between all characters, as some might have forgotten a character
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# this will allow "Pasteurella damatis" to be correctly read as "Pasteurella dagmatis".
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x[nchar(x_backup_without_spp) > 10] <- gsub("([a-z])([a-z])", "\\1.*\\2", x[nchar(x_backup_without_spp) > 10], ignore.case = TRUE)
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x[nchar(x_backup_without_spp) > 10] <- gsub("[+]", "+.*", x[nchar(x_backup_without_spp) > 10])
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constants <- paste(letters[!letters %in% c("a", "e", "i", "o", "u")], collapse = "")
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#x[nchar(x_backup_without_spp) > 10] <- gsub("([a-z])([a-z])", paste0("\\1[", constants, "]?\\2"), x[nchar(x_backup_without_spp) > 10], ignore.case = TRUE)
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x[nchar(x_backup_without_spp) > 10] <- gsub("[+]", paste0("+[", constants, "]?"), x[nchar(x_backup_without_spp) > 10])
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}
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x <- strip_whitespace(x)
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@ -825,10 +832,9 @@ exec_as.mo <- function(x,
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set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
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}
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uncertainties <- rbind(uncertainties,
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data.frame(uncertainty = 1,
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data.frame(uncertainty_level = 1,
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input = x_backup_without_spp[i],
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fullname = microorganismsDT[mo == "B_SLMNL_ENT", fullname][[1]],
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mo = "B_SLMNL_ENT"))
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result_mo = "B_SLMNL_ENT"))
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}
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next
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}
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@ -1051,6 +1057,7 @@ exec_as.mo <- function(x,
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} else {
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x[i] <- microorganismsDT[col_id == found[1, col_id_new], ..property][[1]]
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}
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options(mo_renamed_last_run = found[1, fullname])
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was_renamed(name_old = found[1, fullname],
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name_new = microorganismsDT[col_id == found[1, col_id_new], fullname],
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ref_old = found[1, ref],
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@ -1081,7 +1088,7 @@ exec_as.mo <- function(x,
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# (1) look again for old taxonomic names, now for G. species ----
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 1] (1) look again for old taxonomic names, now for G. species\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (1) look again for old taxonomic names, now for G. species\n")
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}
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if (isTRUE(debug)) {
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message("Running '", c.x_withspaces_start_end, "' and '", d.x_withspaces_start_only, "'")
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@ -1102,11 +1109,11 @@ exec_as.mo <- function(x,
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ref_old = found[1, ref],
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ref_new = microorganismsDT[col_id == found[1, col_id_new], ref],
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mo = microorganismsDT[col_id == found[1, col_id_new], mo])
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options(mo_renamed_last_run = found[1, fullname])
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = found[1, fullname],
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mo = paste("CoL", found[1, col_id])))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = microorganismsDT[col_id == found[1, col_id_new], mo]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(x, property), 1, force = force_mo_history)
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}
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@ -1116,7 +1123,7 @@ exec_as.mo <- function(x,
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# (2) Try with misspelled input ----
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# just rerun with dyslexia_mode = TRUE will used the extensive regex part above
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 1] (2) Try with misspelled input\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (2) Try with misspelled input\n")
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}
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if (isTRUE(debug)) {
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message("Running '", a.x_backup, "'")
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@ -1131,10 +1138,9 @@ exec_as.mo <- function(x,
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
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mo = found_result[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(found[1L], property), 1, force = force_mo_history)
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}
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@ -1148,7 +1154,7 @@ exec_as.mo <- function(x,
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# (3) look for genus only, part of name ----
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 2] (3) look for genus only, part of name\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (3) look for genus only, part of name\n")
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}
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if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like% " ") {
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if (!grepl("^[A-Z][a-z]+", b.x_trimmed, ignore.case = FALSE)) {
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@ -1160,10 +1166,9 @@ exec_as.mo <- function(x,
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if (length(found) > 0) {
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x[i] <- found[1L]
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found[1L], fullname][[1]],
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mo = found[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(x, property), 2, force = force_mo_history)
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}
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@ -1174,7 +1179,7 @@ exec_as.mo <- function(x,
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# (4) strip values between brackets ----
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 2] (4) strip values between brackets\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (4) strip values between brackets\n")
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}
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a.x_backup_stripped <- gsub("( *[(].*[)] *)", " ", a.x_backup)
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a.x_backup_stripped <- trimws(gsub(" +", " ", a.x_backup_stripped))
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@ -1191,10 +1196,9 @@ exec_as.mo <- function(x,
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
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mo = found_result[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
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}
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@ -1203,7 +1207,7 @@ exec_as.mo <- function(x,
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# (5) inverse input ----
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 2] (5) inverse input\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (5) inverse input\n")
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}
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a.x_backup_inversed <- paste(rev(unlist(strsplit(a.x_backup, split = " "))), collapse = " ")
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if (isTRUE(debug)) {
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@ -1219,10 +1223,9 @@ exec_as.mo <- function(x,
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
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mo = found_result[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
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}
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@ -1231,7 +1234,7 @@ exec_as.mo <- function(x,
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# (6) try to strip off half an element from end and check the remains ----
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 2] (6) try to strip off half an element from end and check the remains\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (6) try to strip off half an element from end and check the remains\n")
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}
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x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
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if (length(x_strip) > 1) {
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@ -1254,10 +1257,9 @@ exec_as.mo <- function(x,
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
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mo = found_result[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
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}
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@ -1268,7 +1270,7 @@ exec_as.mo <- function(x,
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}
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# (7) try to strip off one element from end and check the remains ----
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 2] (7) try to strip off one element from end and check the remains\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (7) try to strip off one element from end and check the remains\n")
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}
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if (length(x_strip) > 1) {
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for (i in 1:(length(x_strip) - 1)) {
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@ -1287,10 +1289,9 @@ exec_as.mo <- function(x,
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
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mo = found_result[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
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}
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@ -1301,17 +1302,16 @@ exec_as.mo <- function(x,
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}
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# (8) check for unknown yeasts/fungi ----
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 2] (8) check for unknown yeasts/fungi\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (8) check for unknown yeasts/fungi\n")
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}
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if (b.x_trimmed %like% "yeast") {
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found <- "F_YEAST"
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
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mo = found_result[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
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}
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@ -1322,10 +1322,9 @@ exec_as.mo <- function(x,
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
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mo = found_result[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
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}
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@ -1333,7 +1332,7 @@ exec_as.mo <- function(x,
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}
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# (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 2] (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n")
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}
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x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
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if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
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@ -1354,10 +1353,9 @@ exec_as.mo <- function(x,
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# uncertainty level 2 only if searched part contains a space (otherwise it will be found with lvl 3)
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if (x_strip_collapsed %like% " ") {
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
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mo = found_result[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
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}
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@ -1374,7 +1372,7 @@ exec_as.mo <- function(x,
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# (10) try to strip off one element from start and check the remains (any text size) ----
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if (isTRUE(debug)) {
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cat("\n[UNCERTAINLY LEVEL 3] (10) try to strip off one element from start and check the remains (any text size)\n")
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cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (10) try to strip off one element from start and check the remains (any text size)\n")
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}
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x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
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if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
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@ -1393,10 +1391,9 @@ exec_as.mo <- function(x,
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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uncertainties <<- rbind(uncertainties,
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data.frame(uncertainty = now_checks_for_uncertainty_level,
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input = a.x_backup,
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fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
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mo = found_result[1L]))
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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result_mo = found_result[1L]))
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(found[1L], property), 3, force = force_mo_history)
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}
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@ -1407,7 +1404,7 @@ exec_as.mo <- function(x,
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# (11) try to strip off one element from end and check the remains (any text size) ----
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# (this is in fact 7 but without nchar limit of >=6)
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if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 3] (11) try to strip off one element from end and check the remains (any text size)\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (11) try to strip off one element from end and check the remains (any text size)\n")
|
||||
}
|
||||
if (length(x_strip) > 1) {
|
||||
for (i in 1:(length(x_strip) - 1)) {
|
||||
@ -1425,10 +1422,9 @@ exec_as.mo <- function(x,
|
||||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_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)
|
||||
}
|
||||
@ -1439,7 +1435,7 @@ exec_as.mo <- function(x,
|
||||
|
||||
# (12) part of a name (very unlikely match) ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 3] (12) part of a name (very unlikely match)\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (12) part of a name (very unlikely match)\n")
|
||||
}
|
||||
if (isTRUE(debug)) {
|
||||
message("Running '", f.x_withspaces_end_only, "'")
|
||||
@ -1450,10 +1446,9 @@ exec_as.mo <- function(x,
|
||||
if (!empty_result(found_result) & nchar(g.x_backup_without_spp) >= 6) {
|
||||
found <- microorganismsDT[mo == found_result[1L], ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 3, force = force_mo_history)
|
||||
}
|
||||
@ -1654,6 +1649,29 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
|
||||
options(mo_renamed = total[order(names(total))])
|
||||
}
|
||||
|
||||
format_uncertainty_as_df <- function(uncertainty_level,
|
||||
input,
|
||||
result_mo) {
|
||||
if (!is.null(getOption("mo_renamed_last_run", default = NULL))) {
|
||||
# was found as a renamed mo
|
||||
df <- data.frame(uncertainty = uncertainty_level,
|
||||
input = input,
|
||||
fullname = getOption("mo_renamed_last_run"),
|
||||
renamed_to = microorganismsDT[mo == result_mo, fullname][[1]],
|
||||
mo = result_mo,
|
||||
stringsAsFactors = FALSE)
|
||||
options(mo_renamed_last_run = NULL)
|
||||
} else {
|
||||
df <- data.frame(uncertainty = uncertainty_level,
|
||||
input = input,
|
||||
fullname = microorganismsDT[mo == result_mo, fullname][[1]],
|
||||
renamed_to = NA_character_,
|
||||
mo = result_mo,
|
||||
stringsAsFactors = FALSE)
|
||||
}
|
||||
df
|
||||
}
|
||||
|
||||
#' @exportMethod print.mo
|
||||
#' @export
|
||||
#' @noRd
|
||||
@ -1805,7 +1823,9 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
}
|
||||
msg <- paste(msg,
|
||||
paste0(colour2(paste0(" [", x[i, "uncertainty"], "] ")), ' "', x[i, "input"], '" -> ',
|
||||
colour1(paste0(italic(x[i, "fullname"]), " (", x[i, "mo"], ")"))),
|
||||
colour1(paste0(italic(x[i, "fullname"]),
|
||||
ifelse(!is.na(x[i, "renamed_to"]), paste(", renamed to", italic(x[i, "renamed_to"])), ""),
|
||||
" (", x[i, "mo"], ")"))),
|
||||
sep = "\n")
|
||||
}
|
||||
cat(msg)
|
||||
|
||||
Reference in New Issue
Block a user