R/VisitContext.R

In OHDSI/CohortDiagnostics: Diagnostics for OHDSI Cohorts

# Copyright 2024 Observational Health Data Sciences and Informatics
#
# This file is part of CohortDiagnostics
#
# 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.

getVisitContext <- function(connectionDetails = NULL,
                            connection = NULL,
                            cdmDatabaseSchema,
                            tempEmulationSchema = NULL,
                            cohortDatabaseSchema = cdmDatabaseSchema,
                            cohortTable = "cohort",
                            cohortIds,
                            conceptIdTable = NULL,
                            cdmVersion = 5) {
  if (!cdmVersion == 5) {
    warning("Only OMOP CDM v5.x.x is supported. Continuing execution.")
  }

  start <- Sys.time()

  if (is.null(connection)) {
    connection <- DatabaseConnector::connect(connectionDetails)
    on.exit(DatabaseConnector::disconnect(connection))
  }

  sql <- SqlRender::loadRenderTranslateSql(
    "VisitContext.sql",
    packageName = utils::packageName(),
    dbms = connection@dbms,
    tempEmulationSchema = tempEmulationSchema,
    visit_context_table = "#visit_context",
    cdm_database_schema = cdmDatabaseSchema,
    cohort_database_schema = cohortDatabaseSchema,
    cohort_table = cohortTable,
    cohort_ids = cohortIds
  )
  DatabaseConnector::executeSql(connection, sql)
  sql <- "SELECT * FROM @visit_context_table;"
  visitContext <-
    DatabaseConnector::renderTranslateQuerySql(
      connection = connection,
      sql = sql,
      tempEmulationSchema = tempEmulationSchema,
      visit_context_table = "#visit_context",
      snakeCaseToCamelCase = TRUE
    )

  if (!is.null(conceptIdTable)) {
    sql <- "INSERT INTO @unique_concept_id_table (concept_id)
            SELECT DISTINCT visit_concept_id
            FROM @visit_context_table;"
    DatabaseConnector::renderTranslateExecuteSql(
      connection = connection,
      sql = sql,
      tempEmulationSchema = tempEmulationSchema,
      unique_concept_id_table = conceptIdTable,
      visit_context_table = "#visit_context",
      progressBar = FALSE,
      reportOverallTime = FALSE
    )
  }
  sql <-
    "TRUNCATE TABLE @visit_context_table;\nDROP TABLE @visit_context_table;"
  DatabaseConnector::renderTranslateExecuteSql(
    connection = connection,
    sql = sql,
    tempEmulationSchema = tempEmulationSchema,
    visit_context_table = "#visit_context",
    progressBar = FALSE,
    reportOverallTime = FALSE
  )

  delta <- Sys.time() - start
  ParallelLogger::logInfo(
    "Retrieving visit context took ",
    signif(delta, 3),
    " ",
    attr(delta, "units")
  )
  return(visitContext)
}

executeVisitContextDiagnostics <- function(connection,
                                           tempEmulationSchema,
                                           cdmDatabaseSchema,
                                           cohortDatabaseSchema,
                                           cohortTable,
                                           cdmVersion,
                                           databaseId,
                                           exportFolder,
                                           minCellCount,
                                           cohorts,
                                           instantiatedCohorts,
                                           recordKeepingFile,
                                           incremental) {
  ParallelLogger::logInfo("Retrieving visit context for index dates")
  subset <- subsetToRequiredCohorts(
    cohorts = cohorts %>%
      dplyr::filter(.data$cohortId %in% instantiatedCohorts),
    task = "runVisitContext",
    incremental = incremental,
    recordKeepingFile = recordKeepingFile
  )

  if (incremental &&
    (length(instantiatedCohorts) - nrow(subset)) > 0) {
    ParallelLogger::logInfo(sprintf(
      "Skipping %s cohorts in incremental mode.",
      length(instantiatedCohorts) - nrow(subset)
    ))
  }
  if (nrow(subset) > 0) {
    data <- getVisitContext(
      connection = connection,
      tempEmulationSchema = tempEmulationSchema,
      cdmDatabaseSchema = cdmDatabaseSchema,
      cohortDatabaseSchema = cohortDatabaseSchema,
      cohortTable = cohortTable,
      cdmVersion = cdmVersion,
      cohortIds = subset$cohortId,
      conceptIdTable = "#concept_ids"
    )
    data <- makeDataExportable(
      x = data,
      tableName = "visit_context",
      minCellCount = minCellCount,
      databaseId = databaseId
    )
    writeToCsv(
      data = data,
      fileName = file.path(exportFolder, "visit_context.csv"),
      incremental = incremental,
      cohortId = subset$cohortId
    )
    recordTasksDone(
      cohortId = subset$cohortId,
      task = "runVisitContext",
      checksum = subset$checksum,
      recordKeepingFile = recordKeepingFile,
      incremental = incremental
    )
  }
}