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Fix chembl_query() for the compound structural alerts resource #446

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Merged
stitam merged 4 commits into from
Nov 3, 2025
Merged

Fix chembl_query() for the compound structural alerts resource #446

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5296f3b
Make formatting ChEMBL output optional
stitam Oct 31, 2025
2ecd3ac
Fix ChEMBL compound structural alerts
stitam Oct 31, 2025
8c57778
Suppress test warning
stitam Oct 31, 2025
e1d6695
Update NEWS
stitam Oct 31, 2025
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5 changes: 5 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,11 @@
## MINOR IMPROVEMENTS

* `chembl_query()` now returns a named list and uses better formatting for nested output.
* Added new argument `tidy = TRUE` to `chembl_query()` so we can now control whether we want to try to convert the output to a flat format.

## BUG FIXES

* `chembl_query()` did not work with the "compound_structural_alerts" resource. This has been fixed.

# webchem 1.3.1

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32 changes: 18 additions & 14 deletions R/chembl.R
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Expand Up @@ -191,6 +191,7 @@ chembl_files <- function(version = "latest") {
#' @param query character; a vector of ChEMBL IDs.
#' @param resource character; the ChEMBL resource to query. Use
#' [chembl_resources()] to see all available resources.
#' @param tidy logical; attempt to convert output to a simpler structure.
#' @param cache_file character; the name of the cache file without the file
#' extension. If \code{NULL}, results are not cached.
#' @param verbose logical; should a verbose output be printed on the console?
Expand Down Expand Up @@ -245,8 +246,8 @@ chembl_files <- function(version = "latest") {
#' chembl_query("CHEMBL1", resource = "chembl_id_lookup")
#' # Resource: compound_record - requires record ID
#' chembl_query("1", resource = "compound_record")
#' # Resource: compound_structural_alert - requires compound structural alert ID
#' chembl_query("79048021", resource = "compound_structural_alert")
#' # Resource: compound_structural_alert - requires compound ChEMBL ID
#' chembl_query("CHEMBL266429", resource = "compound_structural_alert")
#' # Resource: document - requires document ChEMBL ID
#' chembl_query("CHEMBL1158643", resource = "document")
#' # Resource: document_similarity - requires document 1 ChEMBL ID
Expand Down Expand Up @@ -294,6 +295,7 @@ chembl_files <- function(version = "latest") {
#' @export
chembl_query <- function(query,
resource = "molecule",
tidy = TRUE,
cache_file = NULL,
similarity = 70,
verbose = getOption("verbose"),
Expand All @@ -317,17 +319,16 @@ chembl_query <- function(query,
query <- chembl_validate_query(query, resource, verbose)
if (is.na(query)) return(NA)
if (verbose) webchem_message("query", query, appendLF = FALSE)
if (resource == "similarity") {
url <- ifelse(
test_service_down, "",
paste0(stem, "/", resource, "/", query, "/", similarity, ".json")
)
if (test_service_down) {
url <- ""
} else if (resource == "similarity") {
url <- paste0(stem, "/", resource, "/", query, "/", similarity, ".json")
} else if (resource == "compound_structural_alert") {
url <- paste0(stem, "/", resource, ".json?molecule_chembl_id=", query)
} else {
url <- ifelse(
test_service_down, "",
paste0(stem, "/", resource, "/", query, ".json")
)
url <- paste0(stem, "/", resource, "/", query, ".json")
}

webchem_sleep(type = "API")
res <- try(httr::RETRY("GET",
url,
Expand All @@ -344,7 +345,9 @@ chembl_query <- function(query,
}
if (verbose) message(httr::message_for_status(res))
cont <- httr::content(res, type = "application/json")
cont <- format_chembl(cont)
if (tidy) {
cont <- format_chembl(cont)
}
return(cont)
}
if (is.null(cache_file)) {
Expand Down Expand Up @@ -488,7 +491,6 @@ chembl_validate_query <- function(query, resource, verbose) {
"activity",
"binding_site",
"compund_record",
"compound_structural_alert",
"drug_indication",
"drug_warning",
"mechanism",
Expand All @@ -506,6 +508,7 @@ chembl_validate_query <- function(query, resource, verbose) {
"assay",
"biotherapeutic",
"chembl_id_lookup",
"compound_structural_alert",
"document",
"document_similarity",
"drug",
Expand Down Expand Up @@ -621,6 +624,7 @@ format_chembl <- function(cont) {
"biotherapeutic",
"biocomponents",
"chembl_release",
"compound_structural_alerts",
"cross_references",
"go_slims",
"indication_refs",
Expand Down Expand Up @@ -844,7 +848,7 @@ chembl_example_query <- function(resource) {
cell_line = c("CHEMBL3307241", "CHEMBL3307242"),
chembl_id_lookup = "CHEMBL1",
compound_record = "1",
compound_structural_alert = "79048021",
compound_structural_alert = "CHEMBL266429",
document = c("CHEMBL1158643", "CHEMBL1132398", "CHEMBL5303573", "CHEMBL3639173"),
document_similarity = "CHEMBL1148466",
drug = "CHEMBL2",
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7 changes: 5 additions & 2 deletions man/chembl_query.Rd
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9 changes: 5 additions & 4 deletions tests/testthat/test-chembl.R
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Original file line number Diff line number Diff line change
Expand Up @@ -63,8 +63,8 @@ test_that("chembl_query() examples", {
o7 <- chembl_query("CHEMBL1", resource = "chembl_id_lookup")
# Resource: compound_record - requires record ID
o8 <- chembl_query("1", resource = "compound_record")
# Resource: compound_structural_alert - requires compound structural alert ID
o9 <- chembl_query("79048021", resource = "compound_structural_alert")
# Resource: compound_structural_alert - requires compound ChEMBL ID
o9 <- chembl_query("CHEMBL266429", resource = "compound_structural_alert", tidy = FALSE)
# Resource: document - requires document ChEMBL ID
o10 <- chembl_query("CHEMBL1158643", resource = "document")
# Resource: document_similarity - requires document 1 ChEMBL ID
Expand All @@ -91,7 +91,8 @@ test_that("chembl_query() examples", {
# Resource: protein_classification - requires protein class ID
o22 <- chembl_query("1", resource = "protein_classification")
# Resource: similarity - requires SMILES
o23 <- chembl_query("CC(=O)Oc1ccccc1C(=O)O", resource = "similarity")
o23 <- suppressWarnings(
chembl_query("CC(=O)Oc1ccccc1C(=O)O", resource = "similarity"))
# Resource: source - requires source ID
o24 <- chembl_query("1", resource = "source")
# Resource: substructure - requires SMILES
Expand Down Expand Up @@ -119,7 +120,7 @@ test_that("chembl_query() examples", {
expect_true(inherits(o6, "list") & length(o6[[1]]) == 11)
expect_true(inherits(o7, "list") & length(o7[[1]]) == 5)
expect_true(inherits(o8, "list") & length(o8[[1]]) == 6)
#expect_true(inherits(o9, "list") & length(o9[[1]]) == 3)
expect_true(inherits(o9, "list") & length(o9[[1]][[1]]) == 7)
expect_true(inherits(o10, "list") & length(o10[[1]]) == 19)
expect_true(inherits(o11, "list") & length(o11[[1]]) == 4)
expect_true(inherits(o12, "list") & length(o12[[1]]) == 30)
Expand Down