R/mousePhenotypesQuery.R

In otargen: Access Open Target Genetics

#' Retrieve Mouse Phenotypes data for a specified gene.
#'
#' This function queries the Open Targets Genetics GraphQL API to retrieve mouse phenotypes data
#' for a specified gene.
#'
#' @param ensemblId Character: ENSEMBL ID of the target gene (e.g., ENSG00000169174).
#'
#' @return Returns a data frame containing mouse phenotypes data for the specified gene.
#' @examples
#' \dontrun{
#' result <- mousePhenotypesQuery(ensemblId = "ENSG00000169174")
#' }
#' @importFrom magrittr %>%
#' @export
#'
mousePhenotypesQuery <- function(ensemblId) {
  if (missing(ensemblId) || is.null(ensemblId)) {
    stop("Please provide a value for the 'ensemblId' argument.")
  }

  # Set up to query Open Targets Genetics API
  tryCatch({
    cli::cli_progress_step("Connecting to the Open Targets Genetics GraphQL API...", spinner = TRUE)
    con <- ghql::GraphqlClient$new("https://api.platform.opentargets.org/api/v4/graphql")
    qry <- ghql::Query$new()

    query <- "query MousePhenotypes($ensemblId: String!) {
      target(ensemblId: $ensemblId) {
        id
        mousePhenotypes {
          targetInModel
          targetInModelMgiId
          modelPhenotypeId
          modelPhenotypeLabel
          modelPhenotypeClasses {
            id
            label
          }
          biologicalModels {
            id
            allelicComposition
            geneticBackground
            literature
          }
        }
      }
    }"

    variables <- list(
      ensemblId = ensemblId
    )

    qry$query(name = "getMousePhenotypesData", x = query)

    cli::cli_progress_step(paste0("Downloading data for ENSEMBL ID: ", ensemblId, " ..."), spinner = TRUE)

    # Execute the query
    output0 <- con$exec(qry$queries$getMousePhenotypesData, variables)
    output1 <- jsonlite::fromJSON(output0, flatten = TRUE)

    if (!is.null(output1$data$target$mousePhenotypes)) {
      final_output <- output1$data$target$mousePhenotypes
      return(final_output)
    } else {
      message("No data found for the given parameters.")
      return(NULL)
    }

  }, error = function(e) {
    # Handling connection timeout
    if (grepl("Timeout was reached", e$message)) {
      stop("Connection timeout reached while connecting to the Open Targets Genetics GraphQL API.")
    } else {
      stop(e) # Handle other types of errors
    }
  })
}