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Merged
mtran-code merged 7 commits into from
Oct 21, 2025
Merged

feat: enable parallel queries for unichem #68

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276cf3f
feat: enable parallel querying
mtran-code Oct 21, 2025
45063a0
test: add unichem tests for multi-input
mtran-code Oct 21, 2025
3c028ed
docs: roxygenize
mtran-code Oct 21, 2025
cd0818f
refactor: retain names for parallel unichem queries
mtran-code Oct 21, 2025
1345c03
fix: validate unichem source ids against catalog
mtran-code Oct 21, 2025
0869a84
test: assert exact unichem source columns
mtran-code Oct 21, 2025
aaa1c43
fix: preserve UniChem results when a query fails
mtran-code Oct 21, 2025
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335 changes: 249 additions & 86 deletions R/unichem.R
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Original file line number Diff line number Diff line change
@@ -1,12 +1,11 @@

# Unichem API documentation: https://www.ebi.ac.uk/unichem/info/webservices

#' Get the list of sources in UniChem.
#'
#'
#' @param all_columns `boolean` Whether to return all columns. Defaults to FALSE.
#'
#'

#'
#'
#' Returns a `data.table` with the following columns:
#' - `CompoundCount` (integer): Total of compounds provided by that source
#' - `BaseURL` (string): Source Base URL for compounds
Expand All @@ -21,120 +20,284 @@
#' - `ReleaseNumber` (integer): Release number of the source database data stored in UniChEM
#' - `URL` (string): Main URL for the source
#' - `UpdateComments` (string): Notes about the update process of that source to UniChEM
#'
#'
#'
#'
#' @return A data.table with the list of sources in UniChem.
#'
#'
#' @export
getUnichemSources <- function(all_columns = FALSE) {
funContext <- .funContext("AnnotationGx::getUnichemSources")

response <- .build_unichem_query("sources") |>
.build_request() |>
.perform_request() |>
.parse_resp_json()

if(response$response != "Success"){
.err(funContext, "Unichem API request failed.")
}
funContext <- .funContext("AnnotationGx::getUnichemSources")

.debug(funContext, sprintf("Unichem sourceCount: %s", response$totalSources))
response <- .build_unichem_query("sources") |>
.build_request() |>
.perform_request() |>
.parse_resp_json()

sources_dt <- .asDT(response$sources)
if (response$response != "Success") {
.err(funContext, "Unichem API request failed.")
}

old_names <- c(
"UCICount", "baseIdUrl", "description", "lastUpdated", "name",
"nameLabel", "nameLong", "sourceID", "srcDetails", "srcReleaseDate",
"srcReleaseNumber", "srcUrl", "updateComments")
.debug(
funContext,
sprintf("Unichem sourceCount: %s", response$totalSources)
)

new_names <- c(
"CompoundCount", "BaseURL", "Description", "LastUpdated", "Name",
"NameLabel", "NameLong", "SourceID", "Details", "ReleaseDate",
"ReleaseNumber", "URL", "UpdateComments")

data.table::setnames(sources_dt, old_names, new_names)

new_order <- c(
"Name", "NameLabel", "NameLong", "SourceID", "CompoundCount",
"BaseURL", "URL", "Details",
"Description", "ReleaseNumber", "ReleaseDate", "LastUpdated",
"UpdateComments"
)
sources_dt <- .asDT(response$sources)

old_names <- c(
"UCICount",
"baseIdUrl",
"description",
"lastUpdated",
"name",
"nameLabel",
"nameLong",
"sourceID",
"srcDetails",
"srcReleaseDate",
"srcReleaseNumber",
"srcUrl",
"updateComments"
)

new_names <- c(
"CompoundCount",
"BaseURL",
"Description",
"LastUpdated",
"Name",
"NameLabel",
"NameLong",
"SourceID",
"Details",
"ReleaseDate",
"ReleaseNumber",
"URL",
"UpdateComments"
)

data.table::setnames(sources_dt, old_names, new_names)

sources_dt <- sources_dt[, new_order, with = FALSE]
new_order <- c(
"Name",
"NameLabel",
"NameLong",
"SourceID",
"CompoundCount",
"BaseURL",
"URL",
"Details",
"Description",
"ReleaseNumber",
"ReleaseDate",
"LastUpdated",
"UpdateComments"
)

if(all_columns) return(sources_dt)
sources_dt <- sources_dt[, new_order, with = FALSE]

sources_dt[, c("Name", "SourceID")]
if (all_columns) {
return(sources_dt)
}

sources_dt[, c("Name", "SourceID")]
}

#' Query UniChem for a compound.
#'
#'
#' This function queries the UniChem API for a compound based on the provided parameters.
#'
#' @param compound `character` or `integer` The compound identifier to search for.
#'
#' @param compound `character`, `integer`, or a list of such values. When a vector
#' or list is supplied, each element is queried and the results are returned as
#' a named list.
#' @param type `character` The type of compound identifier to search for. Valid types are "uci", "inchi", "inchikey", and "sourceID".
#' @param sourceID `integer` The source ID to search for if the type is "sourceID". Defaults to NULL.
#' @param sourceID `integer` The source ID to search for if the type is "sourceID".
#' When querying multiple compounds, this can be a vector the same length as
#' `compound` or a single value recycled to all queries. Defaults to `NA`.
#' @param request_only `boolean` Whether to return the request only. Defaults to FALSE.
#' @param raw `boolean` Whether to return the raw response. Defaults to FALSE.
#' @param progress `logical` or `character`. Passed through to
#' `.perform_request_parallel()` when multiple compounds are supplied. Use a
#' character string to customise the progress label. Defaults to
#' `"Querying UniChem..."`.
#' @param ... Additional arguments.
#'
#' @return A list with the external mappings and the UniChem mappings.
#'
#'
#' @return For a single query, a list with the external mappings and the UniChem
#' mappings. For multiple queries, a named list of such results (one per
#' compound). If `raw = TRUE`, raw responses are returned instead.
#'
#' @examples
#' queryUnichemCompound(type = "sourceID", compound = "444795", sourceID = 22)
#'
#'
#' @export
queryUnichemCompound <- function(
compound, type, sourceID = NA_integer_, request_only = FALSE, raw = FALSE, ...
){
checkmate::assert_string(type)
checkmate::assert_atomic(compound)
checkmate::assert_integerish(sourceID)
checkmate::assertLogical(request_only)
checkmate::assertLogical(raw)

request <- .build_unichem_compound_req(type, compound, sourceID,...)
if(request_only) return(request)

response <- request |>
.perform_request() |>
.parse_resp_json()

if(raw) return(response)

if(response$response != "Success"){
msg <- paste(
"Unichem API request failed for compound", compound, "
with type", type,
" . Error:", response$error
)
.err(.funContext("AnnotationGx::queryUnichemCompound"), msg)
compound,
type,
sourceID = NA_integer_,
request_only = FALSE,
raw = FALSE,
progress = "Querying UniChem...",
...
) {
checkmate::assert_string(type)
checkmate::assert_flag(request_only)
checkmate::assert_flag(raw)
checkmate::assert(
checkmate::check_flag(progress),
checkmate::check_string(progress, min.chars = 1)
)

Comment on lines +142 to +149
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@coderabbitai coderabbitai bot Oct 21, 2025

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⚠️ Potential issue | 🟠 Major

Validate type against allowed choices early.

Prevents ambiguous errors downstream.

   checkmate::assert_string(type)
+  checkmate::assert_choice(type, c("uci", "inchi", "inchikey", "sourceID"))
🤖 Prompt for AI Agents 
In R/unichem.R around lines 142 to 149, the parameter `type` is asserted as a
string but not checked against the allowed set; add an explicit choice
validation early (e.g. define an `allowed_types` vector and call
checkmate::assert_choice(type, choices = allowed_types)) so invalid values fail
fast with a clear message; place this check immediately after the existing
checkmate assertions for `type` and before any downstream logic that depends on
specific `type` values.

compounds <- if (is.list(compound)) {
unlist(compound, recursive = TRUE, use.names = TRUE)
} else {
compound
}
checkmate::assert_atomic_vector(compounds, min.len = 1)

many_queries <- length(compounds) > 1

validate_source_ids <- function(src_ids) {
if (type != "sourceID") {
return(rep(NA_integer_, length(compounds)))
}

# Mapping names to be consistent with other API calls
mapped_sources_dt <- .asDT(response$compounds$sources)
old_names <- c("compoundId", "shortName", "longName", "id", "url")
checkmate::assert_integerish(src_ids, any.missing = FALSE)

new_names <- c("compoundID", "Name", "NameLong", "sourceID", "sourceURL")
data.table::setnames(mapped_sources_dt, old = old_names, new = new_names)
if (length(src_ids) == 1L) {
src_ids <- rep(src_ids, length(compounds))
} else if (length(src_ids) != length(compounds)) {
stop(
"`sourceID` must be length 1 or match the number of compounds ",
"when type = 'sourceID'"
)
}
checkmate::assert_integerish(src_ids, any.missing = FALSE)

valid_ids <- getUnichemSources()$SourceID
invalid_ids <- setdiff(unique(src_ids), valid_ids)
if (length(invalid_ids) > 0L) {
stop(
"`sourceID` contains value(s) not available in UniChem: ",
paste(invalid_ids, collapse = ", "),
"\nValid source IDs: ",
paste(valid_ids, collapse = ", ")
)
}
src_ids
}

source_ids <- validate_source_ids(sourceID)

build_request <- function(cmp, src) {
.build_unichem_compound_req(
type = type,
compound = cmp,
sourceID = if (is.na(src)) NULL else src,
...
)
}

parse_response <- function(parsed, cmp_label) {
if (parsed$response != "Success") {
msg <- paste(
"Unichem API request failed for compound",
cmp_label,
"with type",
type,
". Error:",
parsed$error
)
.err(.funContext("AnnotationGx::queryUnichemCompound"), msg)
}

mapped_sources_dt <- .asDT(parsed$compounds$sources)
old_names <- c("compoundId", "shortName", "longName", "id", "url")
new_names <- c(
"compoundID",
"Name",
"NameLong",
"sourceID",
"sourceURL"
)
data.table::setnames(
mapped_sources_dt,
old = old_names,
new = new_names
)

External_Mappings <- mapped_sources_dt[, new_names, with = FALSE]

UniChem_Mappings <- list(
UniChem.UCI = response$compounds$uci,
UniChem.InchiKey = response$compounds$standardInchiKey,
UniChem.Inchi = response$compounds$inchi$inchi,
UniChem.formula = response$compounds$inchi$formula,
UniChem.connections = response$compounds$inchi$connections,
UniChem.hAtoms = response$compounds$inchi$hAtoms
UniChem.UCI = parsed$compounds$uci,
UniChem.InchiKey = parsed$compounds$standardInchiKey,
UniChem.Inchi = parsed$compounds$inchi$inchi,
UniChem.formula = parsed$compounds$inchi$formula,
UniChem.connections = parsed$compounds$inchi$connections,
UniChem.hAtoms = parsed$compounds$inchi$hAtoms
)

list(
External_Mappings = External_Mappings,
UniChem_Mappings = UniChem_Mappings
External_Mappings = External_Mappings,
UniChem_Mappings = UniChem_Mappings
)
}

if (many_queries) {
requests <- Map(build_request, compounds, source_ids)
name_candidates <- names(compounds)
if (
!is.null(name_candidates) && length(name_candidates) == length(compounds)
) {
names(requests) <- name_candidates
} else {
names(requests) <- as.character(compounds)
}

if (request_only) {
return(requests)
}

responses <- .perform_request_parallel(requests, progress = progress)
names(responses) <- names(requests)

parsed_responses <- Map(.parse_resp_json, responses)

if (raw) {
names(parsed_responses) <- names(responses)
return(parsed_responses)
}

results <- Map(
function(parsed, cmp_label) {
tryCatch(
parse_response(parsed, cmp_label),
error = function(e) {
structure(
list(error = conditionMessage(e)),
class = c("unichem_error", "list")
)
}
)
},
parsed_responses,
names(responses)
)

}
names(results) <- names(responses)
return(results)
}

request <- build_request(compounds[[1L]], source_ids[[1L]])
if (request_only) {
return(request)
}

response <- request |> .perform_request()
parsed <- .parse_resp_json(response)

if (raw) {
return(parsed)
}

parse_response(parsed, compounds[[1L]])
}
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