R/VocabularyChecks.R

In EHDEN/CdmInspection: R Package to support quality control inspection of an OMOP-CDM instance

# @file VocabularyChecks
#
# Copyright 2020 European Health Data and Evidence Network (EHDEN)
#
# This file is part of CdmInspection
#
# 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
#
#     https://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.
#
# @author European Health Data and Evidence Network
# @author Peter Rijnbeek


#' The vocabulary checks (for v5.x)
#'
#' @description
#' \code{CdmInspection} runs a list of checks on the vocabulary as part of the CDM inspection procedure
#'
#' @details
#' \code{CdmInspection} runs a list of checks on the vocabulary as part of the CDM inspection procedure
#'
#' @param connectionDetails                An R object of type \code{connectionDetails} created using the function \code{createConnectionDetails} in the \code{DatabaseConnector} package.
#' @param cdmDatabaseSchema    	           Fully qualified name of database schema that contains OMOP CDM schema.
#'                                         On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_instance.dbo'.
#' @param resultsDatabaseSchema		         Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema.
#'                                         On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.
#' @param vocabDatabaseSchema		           String name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
#' @param oracleTempSchema                 For Oracle only: the name of the database schema where you want all temporary tables to be managed. Requires create/insert permissions to this database.
#' @param smallCellCount                   To avoid patient identifiability, cells with small counts (<= smallCellCount) are deleted. Set to NULL if you don't want any deletions.
#' @param sourceName		                   String name of the data source name. If blank, CDM_SOURCE table will be queried to try to obtain this.
#' @param sqlOnly                          Boolean to determine if Achilles should be fully executed. TRUE = just generate SQL files, don't actually run, FALSE = run Achilles
#' @param outputFolder                     Path to store logs and SQL files
#' @param verboseMode                      Boolean to determine if the console will show all execution steps. Default = TRUE
#' @return                                 An object of type \code{achillesResults} containing details for connecting to the database containing the results
#' @export
vocabularyChecks <- function(connectionDetails,
                             cdmDatabaseSchema,
                             resultsDatabaseSchema = cdmDatabaseSchema,
                             vocabDatabaseSchema = cdmDatabaseSchema,
                             oracleTempSchema = resultsDatabaseSchema,
                             smallCellCount = 5,
                             sourceName = "",
                             sqlOnly = FALSE,
                             outputFolder = "output",
                             verboseMode = TRUE) {
  ## run all queries
  mappingCompleteness <- executeQuery(outputFolder, "mapping_completeness.sql", "Mapping Completeness query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema)

  drugMapping <- executeQuery(outputFolder, "mapping_levels_drugs.sql", "Drug Level Mapping query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema)
  unmappedDrugs <- executeQuery(outputFolder, "unmapped_drugs.sql", "Unmapped drugs query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  unmappedConditions <- executeQuery(outputFolder, "unmapped_conditions.sql", "Unmapped conditions query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  unmappedMeasurements <- executeQuery(outputFolder, "unmapped_measurements.sql", "Unmapped measurements query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  unmappedObservations <- executeQuery(outputFolder, "unmapped_observations.sql", "Unmapped observations query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  unmappedProcedures <- executeQuery(outputFolder, "unmapped_procedures.sql", "Unmapped procedures query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  unmappedDevices <- executeQuery(outputFolder, "unmapped_devices.sql", "Unmapped devices query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  unmappedVisits <- executeQuery(outputFolder, "unmapped_visits.sql", "Unmapped visits query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  mappedDrugs <- executeQuery(outputFolder, "mapped_drugs.sql", "Mapped drugs query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  mappedConditions <- executeQuery(outputFolder, "mapped_conditions.sql", "Mapped conditions query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  mappedMeasurements <- executeQuery(outputFolder, "mapped_measurements.sql", "Mapped measurements query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  mappedObservations <- executeQuery(outputFolder, "mapped_observations.sql", "Mapped observations query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  mappedProcedures <- executeQuery(outputFolder, "mapped_procedures.sql", "Mapped procedures query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  mappedDevices <- executeQuery(outputFolder, "mapped_devices.sql", "Mapped devices query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  mappedVisits <- executeQuery(outputFolder, "mapped_visits.sql", "Mapped visits query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  conceptCounts <- executeQuery(outputFolder, "concept_counts_by_vocabulary.sql", "Concept counts by vocabulary query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema, smallCellCount)
  vocabularyCounts <- executeQuery(outputFolder, "vocabulary_tables_count.sql", "Count on vocabulary tables query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema)
  sourceConceptFrequency <- executeQuery(outputFolder, "source_to_concept_map_frequency.sql", "Source to concept map breakdown query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema)
  sourceConceptMap <- executeQuery(outputFolder, "get_source_to_concept_map.sql", "Source to concept map query executed successfully", connectionDetails, sqlOnly, cdmDatabaseSchema, vocabDatabaseSchema)

  version <- conceptCounts$result[conceptCounts$result$ID == "None", ]$VERSION

  results <- list(
    version = version,
    mappingCompleteness = mappingCompleteness,
    drugMapping = drugMapping,
    unmappedDrugs = unmappedDrugs,
    unmappedConditions = unmappedConditions,
    unmappedMeasurements = unmappedMeasurements,
    unmappedObservations = unmappedObservations,
    unmappedProcedures = unmappedProcedures,
    unmappedDevices = unmappedDevices,
    unmappedVisits = unmappedVisits,
    mappedDrugs = mappedDrugs,
    mappedConditions = mappedConditions,
    mappedMeasurements = mappedMeasurements,
    mappedObservations = mappedObservations,
    mappedProcedures = mappedProcedures,
    mappedDevices = mappedDevices,
    mappedVisits = mappedVisits,
    conceptCounts = conceptCounts,
    vocabularyCounts = vocabularyCounts,
    sourceConceptFrequency = sourceConceptFrequency,
    sourceConceptMap = sourceConceptMap
  )
  return(results)
}