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(v1.7.1.9055) added EUCAST 3.3 and all LPSN records numbers

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dr. M.S. (Matthijs) Berends
2021-11-29 10:38:38 +01:00
parent 694cf5ba77
commit c8698347cb
26 changed files with 70986 additions and 70827 deletions
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60
R/mo_property.R
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@ -216,9 +216,9 @@ mo_shortname <- function(x, language = get_locale(), ...) {
shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
# exceptions for streptococci: Group A Streptococcus -> GAS
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"], perl = TRUE), "S")
# unknown species etc.
shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")")
shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")
shortnames[is.na(x.mo)] <- NA_character_
load_mo_failures_uncertainties_renamed(metadata)
@ -518,7 +518,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
x <- mo_validate(x = x, property = "ref", language = language, ...)
# remove last 4 digits and presumably the comma and space that preceed them
x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)], perl = TRUE)
suppressWarnings(x)
}
@ -534,7 +534,7 @@ mo_year <- function(x, language = get_locale(), ...) {
x <- mo_validate(x = x, property = "ref", language = language, ...)
# get last 4 digits
x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)])
x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)], perl = TRUE)
suppressWarnings(as.integer(x))
}
@ -564,17 +564,17 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
x <- as.mo(x, language = language, ...)
metadata <- get_mo_failures_uncertainties_renamed()
result <- list(kingdom = mo_kingdom(x, language = language),
phylum = mo_phylum(x, language = language),
class = mo_class(x, language = language),
order = mo_order(x, language = language),
family = mo_family(x, language = language),
genus = mo_genus(x, language = language),
species = mo_species(x, language = language),
subspecies = mo_subspecies(x, language = language))
out <- list(kingdom = mo_kingdom(x, language = language),
phylum = mo_phylum(x, language = language),
class = mo_class(x, language = language),
order = mo_order(x, language = language),
family = mo_family(x, language = language),
genus = mo_genus(x, language = language),
species = mo_species(x, language = language),
subspecies = mo_subspecies(x, language = language))
load_mo_failures_uncertainties_renamed(metadata)
result
out
}
#' @rdname mo_property
@ -652,31 +652,23 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
meet_criteria(open, allow_class = "logical", has_length = 1)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
mo <- as.mo(x = x, language = language, ... = ...)
mo_names <- mo_name(mo)
x.mo <- as.mo(x = x, language = language, ... = ...)
metadata <- get_mo_failures_uncertainties_renamed()
df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
df$url <- ifelse(df$source == "CoL",
paste0(CATALOGUE_OF_LIFE$url_CoL, "details/species/id/", df$species_id, "/"),
NA_character_)
df <- microorganisms[match(x.mo, microorganisms$mo), c("mo", "fullname", "source", "kingdom", "rank")]
df$url <- ifelse(df$source == "LPSN",
paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(df$fullname), fixed = TRUE)),
paste0(CATALOGUE_OF_LIFE$url_CoL, "/data/search?type=EXACT&q=", gsub(" ", "%20", df$fullname, fixed = TRUE)))
genera <- which(df$kingdom == "Bacteria" & df$rank == "genus")
df$url[genera] <- gsub("/species/", "/genus/", df$url[genera], fixed = TRUE)
subsp <- which(df$kingdom == "Bacteria" & df$rank %in% c("subsp.", "infraspecies"))
df$url[subsp] <- gsub("/species/", "/subspecies/", df$url[subsp], fixed = TRUE)
u <- df$url
u[mo_kingdom(mo) == "Bacteria"] <- paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(mo_names), fixed = TRUE))
u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"] <- gsub("/species/",
"/genus/",
u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"],
fixed = TRUE)
u[mo_kingdom(mo) == "Bacteria" &
mo_rank(mo) %in% c("subsp.", "infraspecies")] <- gsub("/species/",
"/subspecies/",
u[mo_kingdom(mo) == "Bacteria" &
mo_rank(mo) %in% c("subsp.", "infraspecies")],
fixed = TRUE)
names(u) <- df$fullname
names(u) <- mo_names
if (open == TRUE) {
if (isTRUE(open)) {
if (length(u) > 1) {
warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
}