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more unit tests

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dr. M.S. (Matthijs) Berends
2018-11-02 10:27:57 +01:00
parent e601fd259a
commit 40a159e78d
5 changed files with 87 additions and 89 deletions
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105
R/mo.R
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@ -320,6 +320,18 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x[i] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
next
}
if (tolower(x[i]) %like% '^gram[ -]+nega.*'
| tolower(x_trimmed[i]) %like% '^gram[ -]+nega.*') {
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == 'B_GRAMN', ..property][[1]][1L]
next
}
if (tolower(x[i]) %like% '^gram[ -]+posi.*'
| tolower(x_trimmed[i]) %like% '^gram[ -]+posi.*') {
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == 'B_GRAMP', ..property][[1]][1L]
next
}
}
# FIRST TRY FULLNAMES AND CODES
@ -404,6 +416,22 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
next
}
# try splitting of characters in the middle and then find ID ----
# only when text length is 6 or lower
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
if (nchar(x_trimmed[i]) <= 6) {
x_length <- nchar(x_trimmed[i])
x[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2),
'.* ',
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length))
found <- microorganisms.prevDT[fullname %like% paste0('^', x[i]), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
}
# try fullname without start and stop regex, to also find subspecies ----
# like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
found <- microorganisms.prevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
@ -412,37 +440,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
next
}
# try splitting of characters in the middle and then find ID ----
# only when text length is 6 or lower
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
if (nchar(x_trimmed[i]) <= 6) {
x_split <- x
x_length <- nchar(x_trimmed[i])
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
'.* ',
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
found <- microorganisms.prevDT[fullname %like% paste0('^', x_split[i]), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
}
# try any match with text before and after original search string ----
# so "negative rods" will be "GNR"
# if (x_trimmed[i] %like% "^Gram") {
# x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
# # remove leading and trailing spaces again
# x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
# }
# if (!is.na(x_trimmed[i])) {
# found <- microorganisms.prevDT[fullname %like% x_trimmed[i], ..property][[1]]
# if (length(found) > 0) {
# x[i] <- found[1L]
# next
# }
# }
# THEN TRY ALL OTHERS ----
found <- microorganisms.unprevDT[tolower(fullname) == tolower(x_backup[i]), ..property][[1]]
# most probable: is exact match in fullname
@ -490,6 +487,21 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
next
}
# try splitting of characters in the middle and then find ID ----
# only when text length is 6 or lower
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
if (nchar(x_trimmed[i]) <= 6) {
x_length <- nchar(x_trimmed[i])
x[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2),
'.* ',
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length))
found <- microorganisms.unprevDT[fullname %like% paste0('^', x[i]), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
}
# try fullname without start and stop regex, to also find subspecies ----
# like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
found <- microorganisms.unprevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
@ -498,37 +510,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
next
}
# try splitting of characters in the middle and then find ID ----
# only when text length is 6 or lower
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
if (nchar(x_trimmed[i]) <= 6) {
x_split <- x
x_length <- nchar(x_trimmed[i])
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
'.* ',
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
found <- microorganisms.unprevDT[fullname %like% paste0('^', x_split[i]), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
}
# # try any match with text before and after original search string ----
# # so "negative rods" will be "GNR"
# if (x_trimmed[i] %like% "^Gram") {
# x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
# # remove leading and trailing spaces again
# x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
# }
# if (!is.na(x_trimmed[i])) {
# found <- microorganisms.unprevDT[fullname %like% x_trimmed[i], ..property][[1]]
# if (length(found) > 0) {
# x[i] <- found[1L]
# next
# }
# }
# MISCELLANEOUS ----
# look for old taxonomic names ----