R/FeatureExtraction.R

In OHDSI/FeatureExtraction: Generating Features for a Cohort

# @file FeatureExtraction.R
#
# Copyright 2024 Observational Health Data Sciences and Informatics
#
# This file is part of FeatureExtraction
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

#' @keywords internal
"_PACKAGE"

#' @importFrom SqlRender loadRenderTranslateSql translate render
#' @importFrom methods is
#' @importFrom utils read.csv
#' @importFrom stats aggregate quantile sd
#' @importFrom rlang .data
#' @import DatabaseConnector
#' @import dplyr
NULL

.onLoad <- function(libname, pkgname) {
  rJava::.jpackage(pkgname, lib.loc = libname)

  # Verify checksum of JAR:
  storedChecksum <- scan(file = system.file("csv", "jarChecksum.txt", package = "FeatureExtraction"), what = character(), quiet = TRUE)
  computedChecksum <- tryCatch(rJava::J("org.ohdsi.featureExtraction.JarChecksum", "computeJarChecksum"),
    error = function(e) {
      warning("Problem connecting to Java. This is normal when runing roxygen.")
      return("")
    }
  )
  if (computedChecksum != "" && (storedChecksum != computedChecksum)) {
    warning("Java library version does not match R package version! Please try reinstalling the FeatureExtraction package.
            Make sure to close all instances of R, and open only one instance before reinstalling. Also make sure your
            R workspace is not reloaded on startup. Delete your .Rdata file if necessary")
  }
}

.toJson <- function(object) {
  return(as.character(jsonlite::toJSON(object, force = TRUE, auto_unbox = TRUE)))
}

.fromJson <- function(json) {
  return(jsonlite::fromJSON(json, simplifyVector = TRUE, simplifyDataFrame = FALSE))
}