R/CreateCohorts.R

In OHDSI/Legend: Large-Scale Evidence Generation and Evaluation in a Network of Databases

# Copyright 2018 Observational Health Data Sciences and Informatics
#
# This file is part of Legend
#
# 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,
                           indicationId) {

    # Create study cohort table structure:
    sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "CreateCohortTable.sql",
                                             packageName = "Legend",
                                             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", "OutcomesOfInterest.csv", package = "Legend")
    cohortsToCreate <- read.csv(pathToCsv)
    cohortsToCreate <- cohortsToCreate[cohortsToCreate$indicationId == indicationId, ]
    for (i in 1:nrow(cohortsToCreate)) {
        writeLines(paste("Creating cohort:", cohortsToCreate$name[i]))
        sql <- SqlRender::loadRenderTranslateSql(sqlFilename = paste0(cohortsToCreate$name[i], ".sql"),
                                                 packageName = "Legend",
                                                 dbms = attr(connection, "dbms"),
                                                 oracleTempSchema = oracleTempSchema,
                                                 cdm_database_schema = cdmDatabaseSchema,
                                                 vocabulary_database_schema = vocabularyDatabaseSchema,
                                                 target_database_schema = cohortDatabaseSchema,
                                                 target_cohort_table = cohortTable,
                                                 target_cohort_id = cohortsToCreate$cohortId[i])
        DatabaseConnector::executeSql(connection, sql)
    }
}