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fixed etox_basic #229

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merged 5 commits into from
Mar 26, 2020
Merged

fixed etox_basic #229

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7cc3ae3
fixed html_table parsing
andschar Mar 25, 2020
9243256
re-activated some tests
andschar Mar 25, 2020
ba319ea
updated example + supresswarnings + soure_url
andschar Mar 25, 2020
657db51
changed back changes
andschar Mar 26, 2020
762ce2f
Merge branch 'master' into master
stitam Mar 26, 2020
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41 changes: 36 additions & 5 deletions R/etox.R
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Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,7 @@ get_etoxid <- function(query,
#' id <- get_etoxid('Triclosan', match = 'best')
#' etox_basic(id$etoxid)
#'
#' # Retrieve CAS for multiple inputs
#' # Retrieve data for multiple inputs
#' ids <- c("20179", "9051")
#' out <- etox_basic(ids)
#' out
Expand All @@ -179,7 +179,6 @@ etox_basic <- function(id, verbose = TRUE) {
message('ID is NA! Returning NA.\n')
return(NA)
}
# id <- '20179'
baseurl <- 'https://webetox.uba.de/webETOX/public/basics/stoff.do?language=en&id='
qurl <- paste0(baseurl, id)
if (verbose)
Expand All @@ -190,10 +189,14 @@ etox_basic <- function(id, verbose = TRUE) {
message('ID not found! Returning NA.\n')
return(NA)
}
tabs <- html_table(tt, fill = TRUE)
tabs <- try(suppressWarnings(html_table(tt, fill = TRUE)), silent = TRUE)
if (inherits(tabs, 'try-error')) {
message('ID found. No data available. Returning NA.\n')
return(NA)
}
binf <- tabs[[length(tabs)]]
cas <- binf[, 1][binf[, 2] == 'CAS']
ec <- binf[, 1][grepl('EINEC', binf[, 2])]
ec <- binf[, 1][grepl('^EC$|EINEC', binf[, 2])]
gsbl <- binf[, 1][binf[, 2] == 'GSBL']

syns <- tabs[[2]][c(1, 3, 4)]
Expand All @@ -206,8 +209,36 @@ etox_basic <- function(id, verbose = TRUE) {
out <- list(cas = cas, ec = ec, gsbl = gsbl, synonyms = syns,
source_url = qurl)
return(out)

# CODE FOR A POSSIBLE FUTURE RELEASE
# binf <- tabs[[length(tabs)]]
# cas <- binf[, 1][binf[, 2] == 'CAS']
# ec <- binf[, 1][grepl('^EC$|EINEC', binf[, 2])]
# gsbl <- binf[, 1][binf[, 2] == 'GSBL']
#
# syns <- tabs[[2]][c(1, 3, 4)]
# names(syns) <- tolower(gsub('\\s+', '_', names(syns)))
# group <- tolower(syns[ syns$substance_name_typ == 'GROUP_USE' &
# syns$language == 'English', ]$notation)
# syn <- syns[ syns$substance_name_typ == 'SYNONYM', ]
# syn <- syn[ ,-2]
# names(syn) <- c('name', 'language')
# # return list of data.frames
# l <- list(cas = cas,
# ec = ec,
# gsbl = gsbl,
# source_url = qurl)
# data <- as.data.frame(t(do.call(rbind, l)),
# stringsAsFactors = FALSE)
# chem_group <- as.data.frame(t(group), stringsAsFactors = FALSE)
# names(chem_group) <- chem_group[1, ]
# chem_group[1, ] <- TRUE
# out <- list(data = data,
# chemical_group = chem_group,
# synonyms = syn)
### END
}
out <- lapply(id, foo,verbose = verbose)
out <- lapply(id, foo, verbose = verbose)
out <- setNames(out, id)
class(out) <- c('etox_basic','list')
return(out)
Expand Down
23 changes: 9 additions & 14 deletions R/extractors.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ cas <- function(x, ...){
UseMethod("cas")
}

# CAS ---------------------------------------------------------------------
#' @export
cas.default <- function(x, ...) {
sapply(x, function(y) {
Expand All @@ -17,7 +18,6 @@ cas.default <- function(x, ...) {
y$cas
})
}

#' @export
cas.chebi_comp_entity <- function(x, ...) {
sapply(x, function(y) {
Expand All @@ -30,12 +30,19 @@ cas.chebi_comp_entity <- function(x, ...) {
cas.pan_query <- function(x, ...) {
sapply(x, function(y) y$`CAS Number`)
}

#' @export
cas.wd_ident <- function(x, ...) {
x$cas
}

cas.etox_basic <- function(x, ...) {
sapply(x, function(y) {
if (length(y) == 1 && is.na(y))
return(NA)
unique(y[[1]]$cas)
})
}

# InChIKey ----------------------------------------------------------------
#' @rdname extractors
#' @export
Expand Down Expand Up @@ -68,12 +75,10 @@ inchikey.chebi_comp_entity <- function(x, ...) {
inchikey.cs_compinfo <- function(x, ...) {
x$inchikey
}

#' @export
inchikey.cs_extcompinfo <- function(x, ...) {
x$inchikey
}

#' @export
inchikey.etox_basic <- function(x, ...) {
stop("InChIkey is not returned by this datasource!")
Expand All @@ -87,15 +92,13 @@ inchikey.pan_query <- function(x, ...) {
inchikey.opsin_query <- function(x, ...) {
x$stdinchikey
}

#' @export
inchikey.pc_prop <- function(x, ...) {
if (!"InChIKey" %in% names(x)) {
stop("InChIKey not queried!")
}
x$InChIKey
}

#' @export
inchikey.wd_ident <- function(x, ...) {
x$inchikey
Expand All @@ -112,7 +115,6 @@ smiles <- function(x, ...){
smiles.default <- function(x, ...) {
sapply(x, function(y) y$smiles)
}

#' @export
smiles.chebi_comp_entity <- function(x, ...) {
sapply(x, function(y) {
Expand All @@ -125,18 +127,14 @@ smiles.chebi_comp_entity <- function(x, ...) {
smiles.cs_compinfo <- function(x, ...) {
x$smiles
}

#' @export
smiles.cs_extcompinfo <- function(x, ...) {
x$smiles
}


#' @export
smiles.cts_compinfo <- function(x, ...) {
stop("SMILES is not returned by this datasource!")
}

#' @export
smiles.etox_basic <- function(x, ...) {
stop("InChIkey is not returned by this datasource!")
Expand All @@ -145,7 +143,6 @@ smiles.etox_basic <- function(x, ...) {
smiles.pan_query <- function(x, ...) {
stop("SMILES is not returned by this datasource!")
}

#' @export
smiles.opsin_query <- function(x, ...) {
x$smiles
Expand All @@ -154,15 +151,13 @@ smiles.opsin_query <- function(x, ...) {
smiles.aw_query <- function(x, ...) {
stop("SMILES is not returned by this datasource!")
}

#' @export
smiles.pc_prop <- function(x, ...) {
if (!"CanonicalSMILES" %in% names(x)) {
stop("CanonicalSMILES not queried!")
}
x$CanonicalSMILES
}

#' @export
smiles.wd_ident <- function(x, ...) {
x$smiles
Expand Down