R/cellosaurus_annotations.R

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

#' Annotate Cell Accession
#'
#' This function takes a Cellosaurus accession and returns annotations for the cell line.
#'
#' @param accessions The Cellosaurus accession to annotate.
#' @param to A character vector specifying the types of annotations to retrieve. Possible values include "id", "ac", "hi", "sy", "ca", "sx", "ag", "di", "derived-from-site", "misspelling", and "dt".
#' @param query_only A logical value indicating whether to only return the query string.
#' @param raw A logical value indicating whether to return the raw response.
#' 
#' @return A data frame containing the annotations for the cell line.
#'
#' @examples
#' annotateCellAccession("CVCL_0031")
#' annotateCellAccession("CVCL_0031", to = c("id", "ac", "hi", "sy"))
#'
#' @export
annotateCellAccession <- function(
    accessions,
    to = c("id", "ac", "hi", "sy", "ca", "sx", "ag", "di", "derived-from-site", "misspelling", "dt"),
    query_only = FALSE, raw = FALSE
    )
{
    funContext <- .funContext("annotateCellAccession")

    .info(funContext, "Building Cellosaurus requests...")
    requests <- parallel::mclapply(accessions, function(accession) {
        .build_cellosaurus_request(
            query = accession,
            to = to,
            numResults = 1,
            apiResource = "search/cell-line",
            output = "TXT",
            sort = NULL,
            query_only = FALSE
        )
    })
    
    .info(funContext, "Performing Requests...")
    responses <- .perform_request_parallel(requests, progress = "Querying Cellosaurus...")
    names(responses) <- accessions
    if(raw) return(responses)

    .info(funContext, "Parsing Responses...")
    responses_dt <- parallel::mclapply(accessions, function(name) {
        resp <- responses[[name]]
        .parse_cellosaurus_lines(resp) |> 
            unlist(recursive = FALSE) |> 
            .processEntry() |>
            .formatSynonyms()
        }
    )
    names(responses_dt) <- accessions

    
    responses_dt <- data.table::rbindlist(responses_dt, fill = TRUE)
    
    return(responses_dt)
}