R/reEvaluateThresholds.R

In DataQualityDashboard: Execute and View Data Quality Checks on OMOP CDM Database

# Copyright 2026 Observational Health Data Sciences and Informatics
#
# This file is part of DataQualityDashboard
#
# 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.

#' @title Re-evaluate Thresholds
#'
#' @description Re-evaluate an existing DQD result against an updated thresholds file.
#'
#' @param jsonFilePath              Path to the JSON results file generated using the execute function
#' @param outputFolder              The folder to output new JSON result file to
#' @param outputFile                File to write results JSON object to
#' @param tableCheckThresholdLoc    The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied.
#' @param fieldCheckThresholdLoc    The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
#' @param conceptCheckThresholdLoc  The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.
#' @param cdmVersion                The CDM version to target for the data source. By default, 5.3 is used.
#'
#' @return A list containing the re-evaluated DQD results
#'
#' @export

reEvaluateThresholds <- function(jsonFilePath,
                                 outputFolder,
                                 outputFile,
                                 tableCheckThresholdLoc = "default",
                                 fieldCheckThresholdLoc = "default",
                                 conceptCheckThresholdLoc = "default",
                                 cdmVersion = "5.3") {
  # Read in results to data frame --------------------------------------
  dqdResults <- jsonlite::read_json(path = jsonFilePath)

  df <- lapply(dqdResults$CheckResults, function(cr) {
    cr[sapply(cr, is.null)] <- NA
    as.data.frame(cr)
  })
  df <- do.call(plyr::rbind.fill, df)

  # Add required fields that might be missing due to writing to json
  if (!("cdmFieldName" %in% colnames(df))) {
    df$cdmFieldName <- NA
  }
  if (!("error" %in% colnames(df))) {
    df$error <- NA
  }
  if (!("conceptId" %in% colnames(df))) {
    df$conceptId <- NA
  }
  if (!("unitConceptId" %in% colnames(df))) {
    df$unitConceptId <- NA
  }

  # Read in  new thresholds ----------------------------------------------
  tableChecks <- .readThresholdFile(tableCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion))
  fieldChecks <- .readThresholdFile(fieldCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion))
  fieldChecks$cdmFieldName <- toupper(fieldChecks$cdmFieldName) # Uppercase in results, lowercase in threshold files
  conceptChecks <- .readThresholdFile(conceptCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion))
  conceptChecks$cdmFieldName <- toupper(conceptChecks$cdmFieldName)

  newCheckResults <- .evaluateThresholds(
    checkResults = df,
    tableChecks = tableChecks,
    fieldChecks = fieldChecks,
    conceptChecks = conceptChecks
  )

  newOverview <- .summarizeResults(checkResults = newCheckResults)

  newDqdResults <- dqdResults
  newDqdResults$CheckResults <- newCheckResults
  newDqdResults$Overview <- newOverview

  .writeResultsToJson(
    result = newDqdResults,
    outputFolder = outputFolder,
    outputFile = outputFile
  )

  return(newDqdResults)
}