R/CreateCohorts.R

In lhjohn/EmcWaltersDementiaModel: A Package Skeleton for Replicating Published Prediction Models

# Copyright 2020 Observational Health Data Sciences and Informatics
#
# This file is part of EmcWaltersDementiaModel
#
# 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.

.createCohorts <- function(connection,
                           cdmDatabaseSchema,
                           vocabularyDatabaseSchema = cdmDatabaseSchema,
                           cohortDatabaseSchema,
                           cohortTable,
                           oracleTempSchema,
                           outputFolder) {
  
  # Create study cohort table structure:
  sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "CreateCohortTable.sql",
                                           packageName = "EmcWaltersDementiaModel",
                                           dbms = attr(connection, "dbms"),
                                           oracleTempSchema = oracleTempSchema,
                                           cohort_database_schema = cohortDatabaseSchema,
                                           cohort_table = cohortTable)
  DatabaseConnector::executeSql(connection, sql, progressBar = FALSE, reportOverallTime = FALSE)
  
  
  
  # Instantiate cohorts:
  pathToCsv <- system.file("settings", "CohortsToCreate.csv", package = "EmcWaltersDementiaModel")
  cohortsToCreate <- utils::read.csv(pathToCsv)
  for (i in 1:nrow(cohortsToCreate)) {
    writeLines(paste("Creating cohort:", cohortsToCreate$name[i]))
    sql <- SqlRender::loadRenderTranslateSql(sqlFilename = paste0(cohortsToCreate$name[i], ".sql"),
                                             packageName = "EmcWaltersDementiaModel",
                                             dbms = attr(connection, "dbms"),
                                             oracleTempSchema = oracleTempSchema,
                                             cdm_database_schema = cdmDatabaseSchema,
                                             vocabulary_database_schema = vocabularyDatabaseSchema,
                                             
                                             target_database_schema = cohortDatabaseSchema,
                                             target_cohort_table = cohortTable,
                                             target_cohort_id = cohortsToCreate$cohortId[i])
    DatabaseConnector::executeSql(connection, sql)
  }
  
}

createCovariateCohorts  <- function(connectionDetails,
                                    cdmDatabaseSchema,
                                    vocabularyDatabaseSchema = cdmDatabaseSchema,
                                    cohortDatabaseSchema,
                                    cohortTable,
                                    oracleTempSchema,
                                    cohortVarsToCreate){

  if(sum(colnames(cohortVarsToCreate)%in%c('atlasId', 'cohortName'))!=2){
    stop('Issue with cohortVariableSetting - make sure it is NULL or a setting')  
  }
  
  connection <- DatabaseConnector::connect(connectionDetails)
  
  cohortTableExists <-   tolower(cohortTable)%in%tolower(DatabaseConnector::getTableNames(connection = connection, 
                                                                         databaseSchema = cohortDatabaseSchema))
  if(!cohortTableExists){
  sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "CreateCohortTable.sql",
                                           packageName = "EmcWaltersDementiaModel",
                                           dbms = attr(connection, "dbms"),
                                           oracleTempSchema = oracleTempSchema,
                                           cohort_database_schema = cohortDatabaseSchema,
                                           cohort_table = cohortTable)
  DatabaseConnector::executeSql(connection, sql, progressBar = FALSE, reportOverallTime = FALSE)
  }
  
  cohortVarsToCreate <- unique(cohortVarsToCreate[,c('atlasId', 'cohortName')])
  for (i in 1:nrow(cohortVarsToCreate)) {
    writeLines(paste("Creating cohort:", cohortVarsToCreate$cohortName[i]))
    sql <- SqlRender::loadRenderTranslateSql(sqlFilename = paste0(cohortVarsToCreate$cohortName[i], ".sql"),
                                             packageName = "EmcWaltersDementiaModel",
                                             dbms = attr(connection, "dbms"),
                                             oracleTempSchema = oracleTempSchema,
                                             cdm_database_schema = cdmDatabaseSchema,
                                             vocabulary_database_schema = vocabularyDatabaseSchema,
                                             
                                             target_database_schema = cohortDatabaseSchema,
                                             target_cohort_table = cohortTable,
                                             target_cohort_id = cohortVarsToCreate$atlasId[i])
    DatabaseConnector::executeSql(connection, sql)
  }
  
  DatabaseConnector::disconnect(connection)
}