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# @file getTemporalData
#
# Copyright 2023 Observational Health Data Sciences and Informatics
#
# This file is part of Achilles
#
# 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 Observational Health Data Sciences and Informatics
# @author Martijn Schuemie
# @author Patrick Ryan
# @author Frank DeFalco
# @author Vojtech Huser
# @author Chris Knoll
# @author Ajit Londhe
# @author Taha Abdul-Basser
# @author Anthony Molinaro
#' @title
#' getTemporalData
#'
#' @description
#' \code{getTemporalData} Retrieve specific monthly analyses data to support temporal
#' characterization.
#'
#' @details
#' \code{getTemporalData} Assumes \code{achilles} has been run. \preformatted{Currently supported
#' Achilles monthly analyses are: 202 - Visit Occurrence 402 - Condition occurrence 602 - Procedure
#' Occurrence 702 - Drug Exposure 802 - Observation 1802 - Measurement 2102 - Device}
#'
#' @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 analysisIds (OPTIONAL) A vector containing the set of Achilles analysisIds for
#' which results will be returned. The following are supported:
#' \code{202,402,602,702,802,1802,2102}. If not specified, data for all
#' analysis will be returned. Ignored if \code{conceptId} is given.
#' @param conceptId (OPTIONAL) A SNOMED concept_id from the \code{CONCEPT} table for
#' which a monthly Achilles analysis exists. If not specified, all
#' concepts for a given analysis will be returned.
#' @return
#' A data frame of query results from \code{DatabaseConnector}
#'
#' @examples
#' \dontrun{
#' pneumonia <- 255848
#' monthlyResults <- getTemporalData(connectionDetails = connectionDetails,
#' cdmDatabaseSchema = "cdm",
#'
#' resultsDatabaseSchema = "results", conceptId = pneumonia)
#' }
#'
#' @export
getTemporalData <- function(connectionDetails,
cdmDatabaseSchema,
resultsDatabaseSchema,
analysisIds = NULL,
conceptId = NULL) {
if (!is.null(conceptId)) {
print(paste0("Retrieving Achilles monthly data for temporal support for concept_id: ",
conceptId))
conceptIdGiven <- TRUE
analysisIdGiven <- FALSE
} else if (!is.null(analysisIds)) {
print(paste0("Retrieving Achilles monthly data for temporal support for analyses: ",
paste(analysisIds,
collapse = ", ")))
conceptIdGiven <- FALSE
analysisIdGiven <- TRUE
} else {
print("Retrieving Achilles monthly data for temporal support for all supported analyses")
conceptIdGiven <- FALSE
analysisIdGiven <- FALSE
}
if (typeof(connectionDetails$server) == "character")
dbName <- toupper(strsplit(connectionDetails$server,
"/")[[1]][2]) else dbName <- toupper(strsplit(connectionDetails$server(), "/")[[1]][2])
translatedSql <- SqlRender::loadRenderTranslateSql(sqlFilename = "temporal/achilles_temporal_data.sql",
packageName = "Achilles", dbms = connectionDetails$dbms, db_name = dbName, cdm_schema = cdmDatabaseSchema,
results_schema = resultsDatabaseSchema, concept_id = conceptId, analysis_ids = analysisIds, concept_id_given = conceptIdGiven,
analysis_id_given = analysisIdGiven)
conn <- DatabaseConnector::connect(connectionDetails)
queryResults <- DatabaseConnector::querySql(conn, translatedSql)
on.exit(DatabaseConnector::disconnect(conn))
return(queryResults)
}
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