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mo_url fix

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dr. M.S. (Matthijs) Berends
2022-09-17 12:58:43 +02:00
parent ae9059ab99
commit 98cf1ba0b3
13 changed files with 15 additions and 20 deletions
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1
R/aa_globals.R
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@ -138,7 +138,6 @@ globalVariables(c(
"se_max",
"se_min",
"species",
"species_id",
"total",
"txt",
"type",

26
R/mo_property.R
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@ -678,24 +678,20 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), ...) {
meet_criteria(open, allow_class = "logical", has_length = 1)
language <- validate_language(language)
stop("FIX mo_url")
x.mo <- as.mo(x = x, language = language, ... = ...)
metadata <- get_mo_failures_uncertainties_renamed()
#
# df <- AMR::microorganisms[match(x.mo, AMR::microorganisms$mo), c("mo", "fullname", "source", "kingdom", "rank"), drop = FALSE]
# df$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
names(u) <- df$fullname
x.rank <- microorganisms$rank[match(x.mo, microorganisms$mo)]
x.name <- microorganisms$fullname[match(x.mo, microorganisms$mo)]
x.lpsn <- microorganisms$lpsn[match(x.mo, microorganisms$mo)]
x.gbif <- microorganisms$gbif[match(x.mo, microorganisms$mo)]
u <- character(length(x))
u[!is.na(x.gbif)] <- paste0(TAXONOMY_VERSION$GBIF$url, "/species/", x.gbif[!is.na(x.gbif)])
# overwrite with LPSN:
u[!is.na(x.lpsn)] <- paste0(TAXONOMY_VERSION$LPSN$url, "/", x.rank[!is.na(x.lpsn)], "/", gsub(" ", "-", tolower(x.name[!is.na(x.lpsn)]), fixed = TRUE))
names(u) <- x.name
if (isTRUE(open)) {
if (length(u) > 1) {