R/get_gnps_tables.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Get GNPS Tables
#'
#' @description This function gets GNPS tables from corresponding job ID.
#'
#' @include get_file.R
#'
#' @param gnps_job_id GNPS job ID
#' @param gnps_job_example GNPS job example
#' @param filename Name of the file
#' @param workflow Character string indicating the type of workflow,
#'    either "fbmn" or "classical"
#' @param path_features Path to features
#' @param path_metadata Path to metadata
#' @param path_spectra Path to spectra
#' @param path_source Path to store the source files
#' @param path_interim_a Path to store the interim annotations file
#' @param path_interim_f Path to store the interim features files
#'
#' @return The downloaded GNPS tables
#'
#' @export
#'
#' @examples NULL
get_gnps_tables <-
  function(gnps_job_id,
           gnps_job_example = parse_yaml_paths()$gnps$example,
           filename,
           workflow = "fbmn",
           path_features,
           path_metadata,
           path_spectra,
           path_source = parse_yaml_paths()$data$source$path,
           path_interim_a = parse_yaml_paths()$data$interim$annotations$path,
           path_interim_f = parse_yaml_paths()$data$interim$features$path) {
    if (!is.null(gnps_job_id)) {
      if (gnps_job_id == "") {
        gnps_job_id <- NULL
      }
    }
    if (!is.null(gnps_job_id)) {
      stopifnot(
        "Your GNPS job ID is invalid" =
          stringi::stri_length(str = gnps_job_id) == 32
      )
      stopifnot(
        "Your workflow is not supported,
        supported workflows are 'fbmn' and 'classical'" =
          workflow %in% c("fbmn", "classical")
      )

      gnps_url <-
        "https://gnps.ucsd.edu/ProteoSAFe/DownloadResultFile?task="
      gnps_block <- "&block=main&file="

      ## Little hack for the example
      if (gnps_job_id == gnps_job_example) {
        names(gnps_job_id) <- "example"
      } else {
        names(gnps_job_id) <- gnps_job_id
      }

      log_debug("... Inputs")
      log_debug("... Features")
      file_features <-
        file.path(path_source, paste0(names(gnps_job_id), "_features.csv"))
      if (!file.exists(file_features)) {
        get_file(
          url = paste0(
            gnps_url,
            gnps_job_id,
            gnps_block,
            "quantification_table_reformatted/"
          ),
          export = file_features
        )
      }
      log_debug("... Metadata")
      file_metadata <-
        file.path(
          path_source,
          paste0(names(gnps_job_id), "_metadata.tsv")
        )
      if (!file.exists(file_metadata)) {
        url <- paste0(
          gnps_url,
          gnps_job_id,
          gnps_block,
          "metadata_table/"
        )

        log_debug("Checking response...")
        if (url |>
          httr2::request() |>
          httr2::req_method("GET") |>
          httr2::req_error(
            is_error = function(resp) {
              return(FALSE)
            }
          ) |>
          httr2::req_perform() |>
          httr2::resp_status_desc() == "OK") {
          log_debug("Status OK!")
          get_file(
            url = url,
            export = file_metadata
          )
        } else {
          log_debug("The given GNPS job ID has no metadata")
          log_debug("Returning empty dataframes instead")
          fake_metadata <- data.frame(
            filename = NULL,
            ATTRIBUTE_species = NULL
          )
          export_output(
            x = fake_metadata,
            file = file_metadata
          )
        }
      }

      log_debug("... Spectra")
      file_spectra <-
        file.path(path_source, paste0(names(gnps_job_id), "_spectra.mgf"))
      if (!file.exists(file_spectra)) {
        get_file(
          url = paste0(
            gnps_url,
            gnps_job_id,
            gnps_block,
            "spectra/"
          ),
          export = file_spectra
        )
      }

      log_debug("... Results")
      log_debug("... Annotations")
      file_annotations <- file.path(
        path_interim_a,
        paste0(names(gnps_job_id), "_gnps.tsv")
      )
      if (!file.exists(file_annotations)) {
        get_file(
          url = paste0(
            gnps_url,
            gnps_job_id,
            gnps_block,
            switch(workflow,
              "fbmn" = "DB_result/",
              "classical" = "result_specnets_DB/"
            )
          ),
          export = file_annotations
        )
      }
      log_debug("... Components")
      file_components <- file.path(
        path_interim_f,
        paste0(
          names(gnps_job_id),
          "_components.tsv"
        )
      )
      if (!file.exists(file_components)) {
        get_file(
          url = paste0(
            gnps_url,
            gnps_job_id,
            gnps_block,
            switch(workflow,
              "fbmn" = "clusterinfo_summary/",
              "classical" =
                "clusterinfosummarygroup_attributes_withIDs_withcomponentID/"
            )
          ),
          export = file_components
        )
      }
      log_debug("... Edges")
      file_edges <- file.path(
        path_interim_f,
        paste0(names(gnps_job_id), "_edges_spectra.tsv")
      )
      if (!file.exists(file_edges)) {
        get_file(
          url = paste0(
            gnps_url,
            gnps_job_id,
            gnps_block,
            "networkedges_selfloop/"
          ),
          export = file_edges
        )
      }

      return(
        c(
          "features" = file_features,
          "metadata" = file_metadata,
          "spectra" = file_spectra,
          "annotations" = file_annotations,
          "components" = file_components,
          "edges" = file_edges
        )
      )
    } else {
      log_debug("No GNPS job ID provided")
      log_debug("Returning empty dataframes instead")
      fake_annotations <- data.frame(
        `#Scan#` = NA,
        MassDiff = NA,
        MZErrorPPM = NA,
        Precursor_MZ = NA,
        LibraryName = NA,
        Compound_Name = NA,
        INCHI = NA,
        InChIKey = NA,
        `InChIKey-Planar` = NA,
        ExactMass = NA,
        MQScore = NA,
        SharedPeaks = NA,
        npclassifier_pathway = NA,
        npclassifier_superclass = NA,
        npclassifier_class = NA,
        superclass = NA,
        class = NA,
        subclass = NA,
        check.names = FALSE
      )
      export_output(
        x = fake_annotations,
        file = file.path(
          path_interim_a,
          paste0(filename, "_gnps.tsv")
        )
      )
      fake_components <- data.frame(
        `cluster index` = 0,
        componentindex = 0,
        check.names = FALSE
      )
      export_output(
        x = fake_components,
        file = file.path(
          path_interim_f,
          paste0(filename, "_components.tsv")
        )
      )

      fake_edges <- data.frame(
        CLUSTERID1 = 0,
        CLUSTERID2 = 0
      )
      export_output(
        x = fake_edges,
        file = file.path(
          path_interim_f,
          paste0(filename, "_edges_spectra.tsv")
        )
      )
      if (is.list(path_metadata)) {
        path_metadata <- unlist(path_metadata)
      }
      if (is.null(path_metadata)) {
        path_metadata <- ""
      }
      if (length(path_metadata) == 0 || !file.exists(path_metadata)) {
        path_metadata <- "data/source/metadata.tsv"
        fake_metadata <- data.frame(
          filename = NA,
          ATTRIBUTE_species = NA
        )
        export_output(
          x = fake_metadata,
          file = path_metadata
        )
      }

      return(
        c(
          "features" = path_features,
          "metadata" = path_metadata,
          "spectra" = path_spectra,
          "annotations" = file.path(
            path_interim_a,
            paste0(
              filename,
              "_gnps.tsv"
            )
          ),
          "components" = file.path(
            path_interim_f,
            paste0(
              filename,
              "_components.tsv"
            )
          ),
          "edges" = file.path(
            path_interim_f,
            paste0(
              filename,
              "_edges_spectra.tsv"
            )
          )
        )
      )
    }
  }