R/ResourcesPage_pubmedData.R

In RGLab/ImmuneSpaceAPI: ImmuneSpace Internal API for use in visualizations and reports

#' Prepare pubmed data for serving
#'
#' @import data.table
#' @export
.pubmed_data <- function() {
  allIds <- loadLocalFile("pubmedInfo")

  # Get counts and order by count
  countByPubId <- getCountByPubId(allIds)

  # Setup for easy use in render named list with original_id
  # as key and value {citations, study, datePublished, studyNum, title}
  res <- preparePubMedDataForService(countByPubId)
}

###############################################
###               HELPERS                   ###
###############################################
getCountByPubId <- function(allIds) {
  countByPubId <- allIds[, .(
    Citations = .N,
    datePublished = unique(datePublished),
    title = unique(original_title),
    studyNum = unique(studyNum)
  ),
  by = .(original_id, study)
  ]

  # For papers connected to multiple studies, take first listed
  for (id in unique(countByPubId$original_id)) {
    loc <- which(countByPubId$original_id == id)
    if (length(loc) > 1) {
      locToRemove <- loc[2:length(loc)]
      countByPubId <- countByPubId[-locToRemove, ]
    }
  }

  setorder(countByPubId, -Citations)
  return(countByPubId)
}

preparePubMedDataForService <- function(countByPubId) {
  res <- list()
  for (i in seq(1:nrow(countByPubId))) {
    tmp <- as.vector(countByPubId[i, ])
    res[[i]] <- list(
      citations = tmp$Citations,
      study = tmp$study,
      datePublished = tmp$datePublished,
      studyNum = tmp$studyNum,
      title = tmp$title
    )
  }
  names(res) <- countByPubId$original_id
  return(res)
}