fix: Refactor UniChem API functions and add debug statements

R/unichem.R

@@ -24,16 +24,18 @@
 #' 
 #' @export
 getUnichemSources <- function() {
+    funContext <- .funContext("AnnotationGx::getUnichemSources")
+
     response <- .build_unichem_query("sources") |>
         .build_request() |>
         .perform_request() |>
         .parse_resp_json() 
 
     if(response$response != "Success"){
-        .err("Unichem API request failed.")
+        .err(funContext, "Unichem API request failed.")
     }
 
-    .debug(sprintf("Unichem sourceCount: %s", response$totalSources))
+    .debug(funContext, sprintf("Unichem sourceCount: %s", response$totalSources))
 
     sources_dt <- .asDT(response$sources)
 
@@ -65,7 +67,7 @@ getUnichemSources <- function() {
 #' This function queries the UniChem API for a compound based on the provided parameters.
 #' 
 #' @param type `character` The type of compound identifier to search for. Valid types are "uci", "inchi", "inchikey", and "sourceID".
-#' @param compound `character` The compound identifier to search for.
+#' @param compound `character` or `integer` The compound identifier to search for.
 #' @param sourceID `integer` The source ID to search for if the type is "sourceID". Defaults to NULL.
 #' @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.
@@ -81,7 +83,7 @@ queryUnichem <- function(
     type, compound, sourceID = NA_integer_, request_only = FALSE, raw = FALSE, ...
 ){
     checkmate::assert_string(type)
-    checkmate::assert_string(compound)
+    checkmate::assert_atomic(compound)
     checkmate::assert_integerish(sourceID)
     checkmate::assertLogical(request_only)
     checkmate::assertLogical(raw)

R/unichem_helpers.R

@@ -16,6 +16,7 @@
 .build_unichem_query <- function(
     endpoint, query_only = FALSE
 ) {
+    funContext <- .funContext("AnnotationGx:::.build_unichem_query")
 
     valid_endpoints <- c("compounds", "connectivity", "images", "sources")
     checkmate::assert_subset(endpoint, valid_endpoints)
@@ -24,6 +25,8 @@
     url <- httr2::url_parse(unichem_api)
     url$path <- .buildURL(url$path, endpoint)
 
+    .debug(funContext, "URL: ", capture.output(show(url)))
+
     if (query_only) return(url)
 
     return(httr2::url_build(url))
@@ -50,11 +53,15 @@
 .build_unichem_compound_req <- function(
     type, compound, sourceID = NULL, ...
 ){
+    funContext <- .funContext("AnnotationGx:::.build_unichem_compound_req")
+
     valid_types <- c("uci", "inchi", "inchikey", "sourceID")
     checkmate::assert_subset(type, valid_types)
 
     base_url <- .build_unichem_query("compounds")
 
+    .debug(funContext, "Base URL: ", capture.output(show(base_url)))
+
     body <- list(
         type = type,
         compound = compound
@@ -75,6 +82,6 @@
         .build_request() |>
         httr2::req_body_json(body) 
 
+    .debug(funContext, "Request: ", capture.output(show(request)))
     return(request)
-
 }

vignettes/treatment_pipeline.Rmd

@@ -34,13 +34,12 @@ names_to_cids <- AnnotationGx::mapCompound2CID(treatmentMetadata$CTRP.treatmenti
 ```{r use CID in unichem}
 
 sources <- getUnichemSources()
-response <- .build_compound_query(
+response <- queryUnichem(
   type = "sourceID", 
-  names_to_cids[1, cids], 
+  compound = names_to_cids[1, cids], 
   sourceID = sources[Name == "pubchem", SourceID]
 ) 
 
-response |> asdt()
-
+response
 ```