R/CreateCohorts.R

In ohdsi-studies/VaccineEffectivenessEvaluation: Evaluating Use of Methods for Vaccine Effectiveness

# Copyright 2021 Observational Health Data Sciences and Informatics
#
# This file is part of Eumaeus
#
# 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 = "Eumaeus",
                                           dbms = connection@dbms,
                                           cohort_database_schema = cohortDatabaseSchema,
                                           cohort_table = cohortTable)
  DatabaseConnector::executeSql(connection, sql, progressBar = FALSE, reportOverallTime = FALSE)
  
  
  
  # Instantiate cohorts:
  cohortsToCreate <- loadCohortsToCreate()
  for (i in 1:nrow(cohortsToCreate)) {
    ParallelLogger::logInfo(paste("Creating cohort:", cohortsToCreate$name[i]))
    sql <- SqlRender::loadRenderTranslateSql(sqlFilename = paste0(cohortsToCreate$name[i], ".sql"),
                                             packageName = "Eumaeus",
                                             dbms = connection@dbms,
                                             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)
  }

}