R/get-num-files-ids.R

In Sage-Bionetworks/dccmonitor: Monitor Data Validation

#' @title Get the number of metadata files
#'
#' @description Get the number of metadata files in a study.
#'
#' @param study_view The file view for the study files.
#'   At minimum, the study_view is a dataframe or tibble
#'   with `metadataType` as a column name. Any `NA` in
#'   this column is assumed to be documentation files,
#'   all others are assumed to be metadata files.
#' @param num_docs Number of document files that are in
#'   the `study_view`. If `NULL`, will call
#'   `num_doc_files()` to get the value. This is here in case
#'   that the number of document files is known already.
#' @return The number of metadata files present in the `study_view`.
num_meta_files <- function(study_view, num_docs = NULL) {
  if (is.null(num_docs)) {
    num_docs <- num_doc_files(study_view)
  }
  num_files <- nrow(study_view) - num_docs
  num_files
}

#' @title Get number of files in manifest
#'
#' @description Get the number of unique files in manifest.
#'
#' @inheritParams num_individuals
#' @return The number of unique files in manifest or
#'   0 if the  manifest is not in the `study_view`.
num_manifest_files <- function(study_view) {
  file_index <- get_file_indices(study_view, "manifest")[[1]]
  if (length(file_index) > 0) {
    # Manifest file should exist in set
    num_files <- length(unique(study_view$file_data[[file_index]]$path))
  } else {
    num_files <- 0
  }
  num_files
}

#' Get the number of documentation files
#'
#' @description Get the number of documentation files
#' in a study.
#'
#' @inheritParams num_meta_files
#' @return The number of documentation files present in
#'   the `study_view`.
num_doc_files <- function(study_view) {
  num_docs <- sum(is.na(study_view$metadataType))
  num_docs
}

#' @title Get number of individuals
#'
#' @description Get the number of unique individuals for a study
#' from the metadata files. Checks for ids in the manifest,
#' individual metadata, and biospecimen metadata.
#'
#' @param study_view The file view for a study, with the
#'   columns 'file_data', where each element is a tibble
#'   with the data, and metadataType, where each element
#'   is the metadataType for the file.
#' @param meta_types List of metadata types to gather ids from.
#'   Default is 'manifest', 'individual', and 'biospecimen'.
#' @return Number of unique individual ids or 0 if no metadataTypes
#'   individual, biospecimen, manifest exist in `study_view`.
num_individuals <- function(study_view,
                            meta_types = c("manifest", "individual", "biospecimen")) { # nolint
  file_indices <- get_file_indices_vector(study_view, meta_types)

  if (!is.null(file_indices)) {
    individuals <- list()
    for (index in file_indices) {
      if ("individualID" %in% names(study_view$file_data[[index]])) {
        individuals <- c(
          individuals,
          study_view$file_data[[index]]$individualID
        )
      }
    }
    num_individuals <- length(unique(individuals))
  } else {
    num_individuals <- 0
  }
  num_individuals
}

#' @title Get number of specimens
#'
#' @description Get the number of unique specimens for a study
#' from the metadata files. Checks for ids in the manifest,
#' biospecimen metadata, and assay metadata.
#'
#' @inheritParams num_individuals
#' @param meta_types List of metadata types to gather ids from.
#'   Default is 'manifest', 'assay', and 'biospecimen'.
#' @return Number of unique specimen ids or 0 if no metadataTypes
#'   manifest, biospecimen, assay exist in `study_view`.
num_specimens <- function(study_view,
                          meta_types = c("manifest", "biospecimen", "assay")) { # nolint
  file_indices <- get_file_indices_vector(study_view, meta_types)

  if (!is.null(file_indices)) {
    specimens <- list()
    for (index in file_indices) {
      if ("specimenID" %in% names(study_view$file_data[[index]])) {
        specimens <- c(specimens, study_view$file_data[[index]]$specimenID)
      }
    }
    num_specimens <- length(unique(specimens))
  } else {
    num_specimens <- 0
  }
  num_specimens
}