R/CancerTargetDiscovery.R

In bhklab/AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data

# NOTE: This file is deprecated until the Cancer Target Discovery and Development (CTD2) works again
# as of today, the https://ctd2-dashboard.nci.nih.gov/ doesnt work at all


# # CancerTargetDiscoveryDevelopment Functions

# #' Map Compound to CTD
# #'
# #' This function maps a drug compound to the Cancer Target Discovery (CTD) database.
# #' It retrieves information about the compound from the CTD database and returns the results as a data table.
# #'
# #' @param compounds A character vector of drug compounds to map to the CTD database.
# #' @param base_url The base URL of the CTD API. Default is "https://ctd2-dashboard.nci.nih.gov/dashboard/get".
# #' @param endpoint The API endpoint for the compound mapping. Default is "compound".
# #' @param nParallel The number of parallel processes to use. Default is one less than the number of available cores.
# #' @param raw Logical indicating whether to return the raw response from the API. Default is FALSE.
# #' @param query_only Logical indicating whether to only return the API request URL without making the actual request. Default is FALSE.
# #'
# #' @return A data table containing the mapped information for the drug compound.
# #' If the API request fails, a data table with the drug compound name will be returned.
# #' If \code{raw} is set to TRUE, the raw response from the API will be returned.
# #'
# #' @export
# mapCompound2CTD <- function(
#     compounds,
#     base_url = "https://ctd2-dashboard.nci.nih.gov/dashboard/get",
#     endpoint = "compound",
#     nParallel = parallel::detectCores() - 1,
#     raw = FALSE,
#     query_only = FALSE
# ) {
#     # March 06 2025:
#     # this function is deprecated until
#     # the Cancer Target Discovery and Development (CTD2) works again
#     # as of today, the https://ctd2-dashboard.nci.nih.gov/ doesnt work at all
#     # we will raise an error for now
#     errmsg <- "The CTD2 API is currently not working. Please check the status of the API at https://ctd2-dashboard.nci.nih.gov/"
#     stop(errmsg)

#     funContext <- .funContext("mapCompound2CTD")

#     # Check input types
#     checkmate::assert_character(compounds)
#     checkmate::assert_character(base_url)
#     checkmate::assert_character(endpoint)
#     checkmate::assert_logical(raw)
#     checkmate::assert_logical(query_only)

#     .info(funContext,
#         sprintf("Creating requests for %s compounds", length(compounds)))

#     requests <- parallel::mclapply(compounds, function(compound){
#         compound <- gsub(" ", "-", compound)

#         .buildURL(base_url, endpoint, compound) |>
#             .build_request()
#     })
#     if(query_only) return(requests)

#     .info(funContext, "Performing requests w/", nParallel, "parallel processes..")
#     resps <- .perform_request_parallel(requests)
#     names(resps) <- compounds

#     results <- parallel::mclapply(
#         names(resps) ,
#         function(compound){
#             resp <- resps[[compound]]

#             if(all(class(resp) != "httr2_response") || resp$status_code != 200){
#                 dt <- data.table::data.table(
#                     displayName = compound)
#                 return(dt)
#             }

#             resp <- .parse_resp_json(resp)
#             if(raw) return(resp)

#             original_dt <- .asDT(resp$xrefs)[, c("databaseId", "databaseName")]
#             original_dt[, "displayName" := resp$displayName]

#             dt <- data.table::dcast(
#                     original_dt,
#                     formula = displayName ~ databaseName,
#                     value.var = "databaseId"
#                 )
#             return(dt)
#         },
#         mc.cores = nParallel
#     )
#     if(raw) {
#         names(results) <- compounds
#         return(results)
#     }

#     return(data.table::rbindlist(results, fill = TRUE))
# }