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Merged
stitam merged 2 commits into from
Oct 31, 2025
Merged

Let bcpc_query also find derivatives #440

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b080b67
Let bcpc_query also find derivatives
jranke Oct 29, 2025
2aa6a04
Merge branch 'master' into bcpc_query_derivatives
jranke Oct 30, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -54,7 +54,7 @@ Suggests:
plot.matrix,
usethis,
vcr (>= 0.6.0)
RoxygenNote: 7.3.2
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/testthat/parallel: true
1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -2,6 +2,7 @@

## NEW FEATURES

* `bcpc_query()` now also looks for derivatives (esters and salts) of active compounds
* Added a new function `chembl_img()` for downloading SVG images from ChEMBL.
* Added a new function `db_download_chembl()` for downloading ChEMBL for fully offline access.

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31 changes: 24 additions & 7 deletions R/bcpc.R
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Expand Up @@ -5,12 +5,12 @@
#' formerly known as Alan Woods Compendium of Pesticide Common Names
#' @import xml2
#'
#' @param query character; search string
#' @param query character; search string
#' @param from character; type of input ('cas' or 'name')
#' @param verbose logical; print message during processing to console?
#' @param ... additional arguments to internal utility functions
#' @param type deprecated
#' @return A list of eight entries: common-name, status, preferred IUPAC Name,
#' @return A list of eleven entries: common-name, status, preferred IUPAC Name,
#' IUPAC Name, cas, formula, activity, subactivity, inchikey, inchi and source
#' url.
#' @note for from = 'cas' only the first matched link is returned.
Expand Down Expand Up @@ -196,6 +196,7 @@ build_bcpc_idx <- function(verbose = getOption("verbose"), force_build = FALSE)
if (verbose) message("Building index. ", appendLF = FALSE)
idx1_url <- "https://pesticidecompendium.bcpc.org/index_rn.html"
idx4_url <- "https://pesticidecompendium.bcpc.org/index_cn.html"
idxd_url <- "https://pesticidecompendium.bcpc.org/derivatives/index-derivatives.html"
res1 <- try(httr::RETRY("GET",
idx1_url,
httr::user_agent(webchem_url()),
Expand Down Expand Up @@ -225,10 +226,10 @@ build_bcpc_idx <- function(verbose = getOption("verbose"), force_build = FALSE)
config = httr::config(accept_encoding = "identity"),
terminate_on = 404,
quiet = TRUE), silent= TRUE)
if (inherits(res4, "try-error")) {
if (verbose) webchem_message("service_down")
return(NA)
}
if (inherits(res4, "try-error")) {
if (verbose) webchem_message("service_down")
return(NA)
}
idx4 <- read_html(res4)
n <- xml_find_all(idx4, "//a")
names <- xml_text(n)
Expand All @@ -238,7 +239,23 @@ build_bcpc_idx <- function(verbose = getOption("verbose"), force_build = FALSE)
links <- links[!rm]
idx4 <- data.frame(names = NA, links = links, linknames = names,
source = "cn", stringsAsFactors = FALSE)
bcpc_idx <- rbind(bcpc_idx, idx4)
resd <- try(httr::RETRY("GET",
idxd_url,
httr::user_agent(webchem_url()),
config = httr::config(accept_encoding = "identity"),
terminate_on = 404,
quiet = TRUE), silent= TRUE)
idxd <- read_html(resd)
n <- xml_find_all(idxd, "//a")
names <- xml_text(n)
rm <- names == "" | names == "Index of Ester and Salt Derivatives"
names <- names[!rm]
links <- xml_attr(n, "href")
links <- links[!rm]
idxd <- data.frame(names = NA, links = paste0("derivatives/", links), linknames = names,
source = "cn", stringsAsFactors = FALSE)

bcpc_idx <- rbind(bcpc_idx, idx4, idxd)

# fix encoding
ln <- bcpc_idx$linknames
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2 changes: 1 addition & 1 deletion man/bcpc_query.Rd
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5 changes: 3 additions & 2 deletions tests/testthat/test-bcpc.R
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Expand Up @@ -25,11 +25,11 @@ test_that("BCPC pesticide compendium, name", {
skip_on_cran()
skip_if_not(up, "BCPC pesticide compendium is down")

comps <- c("Fluazinam", "S-Metolachlor", "balloon", NA)
comps <- c("Fluazinam", "S-Metolachlor", "balloon", NA, "Triclopyr-butotyl")
o1 <- bcpc_query(comps, from = "name")

expect_type(o1, "list")
expect_equal(length(o1), 4)
expect_equal(length(o1), 5)
expect_type(o1[[1]], "list")
expect_type(o1[[2]], "list")
expect_equal(o1[[3]], NA)
Expand All @@ -38,6 +38,7 @@ test_that("BCPC pesticide compendium, name", {
expect_equal(length(o1[["S-Metolachlor"]]$inchikey), 2)
expect_equal(length(o1[["S-Metolachlor"]]$inchi), 2)
expect_equal(length(o1[["Fluazinam"]]), 11)
expect_equal(length(o1[["Triclopyr-butotyl"]]), 11)
})


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