R/MainAnalysis.R

In OHDSI/OhdsiStudy2: OHDSI Treatment Pathways Study Protocol 12 months

#' @title Email results
#' 
#' @details
#' This function emails the result CSV files to the study coordinator.
#' 
#' @return 
#' A list of files that were emailed.
#' 
#' @param from     Return email address
#' @param to			Delivery email address (must be a gmail.com acccount)
#' @param subject  Subject line of email
#' @param dataDescription A short description of the database
#' @param sourceName Short name that was be appeneded to results table name
#' @param folder   The name of the local folder to place results;  make sure to use forward slashes (/)
#' @param compress Use GZip compression on transmitted files
#'
#' @export
email <- function(from,
									to = "rijduke@gmail.com",
									subject = "OHDSI Study 2 Results",
									dataDescription,
									sourceName = "source_name",
									folder = getwd(),
									compress = TRUE) {
	
	if (missing(from)) stop("Must provide return address")
	if (missing(dataDescription)) stop("Must provide a data description")
	
	suffix <- c("_person_cnt.csv", "_seq_cnt.csv", "_summary.csv")
	prefix <- c("Dep12mo_", "HTN12mo_", "DM12mo_")
	
	files <- unlist(lapply(prefix, paste, 
												 paste(sourceName, suffix, sep =""), 
												 sep =""))
	absolutePaths <- paste(folder, files, sep="/")
	
	if (compress) {
		
		sapply(absolutePaths, function(name) {
			newName = paste(name, ".gz", sep="")
			tmp <- read.csv(file = name)			
			newFile <- gzfile(newName, "w")
			write.csv(tmp, newFile)
			writeLines(paste("Compressed to file '",newName,"'",sep=""))	
			close(newFile)
		})
		absolutePaths <- paste(absolutePaths, ".gz", sep="")		
	}
	
	result <- mailR::send.mail(from = from,
														 to = to,
														 subject = subject,
														 body = paste("\n", dataDescription, "\n",
														 						 sep = ""),
														 smtp = list(host.name = "aspmx.l.google.com",
														 						port = 25),
														 attach.files = absolutePaths,						
														 authenticate = FALSE,
														 send = TRUE)
	if (result$isSendPartial()) {
		stop("Error in sending email")
	} else {
		writeLines("Emailed the following files:\n")
		writeLines(paste(absolutePaths, collapse="\n"))
		writeLines(paste("\nto:", to))
	}
}

#' @title Execute OHDSI Study 2
#'
#' @details
#' This function executes OHDSI Study 2 -- Treatment Pathways Study 
#' Protocol 12 months.  This is a study of treatment pathways in hypertension,
#' diabetes and depression during the first 12 months after diagnosis.
#' Detailed information and protocol are available on the OHDSI Wiki.
#' 
#' @return
#' Study results are placed in CSV format files in specified local folder.

#' @param dbms              The type of DBMS running on the server. Valid values are
#' \itemize{
#'   \item{"mysql" for MySQL}
#'   \item{"oracle" for Oracle}
#'   \item{"postgresql" for PostgreSQL}
#'   \item{"redshift" for Amazon Redshift}   
#'   \item{"sql server" for Microsoft SQL Server}
#' } 
#' @param user				The user name used to access the server.
#' @param password		The password for that user
#' @param server			The name of the server
#' @param port				(optional) The port on the server to connect to
#' @param cdmSchema  Schema name where your patient-level data in OMOP CDM format resides
#' @param resultsSchema  Schema where you'd like the results tables to be created (requires user to have create/write access)
#' @param minCellCount  The smallest allowable cell count, 1 means all counts are allowed
#' @param sourceName Short name that will be appeneded to results table name
#' @param folder   The name of the local folder to place results;  make sure to use forward slashes (/)
#' 
#' @importFrom DBI dbDisconnect
#' @export
execute <- function(dbms, user, password, server, 
										port = NULL,
										cdmSchema, resultsSchema, 
										minCellCount = 1,
										sourceName = "source_name",
										folder = getwd()) {

	connectionDetails <- DatabaseConnector::createConnectionDetails(dbms=dbms, 
																																	server=server, 
																																	user=user, 
																																	password=password, 
																																	schema=cdmSchema,
																																	port=port)
	
	
	###########################################################
	# End of parameters. Make no changes after this           #
	###########################################################
	
	setwd(folder)
		
	# Create the parameterized SQL files:
	htnSqlFile <- renderStudySpecificSql("HTN12mo",minCellCount,cdmSchema,resultsSchema,sourceName,dbms)
	t2dmSqlFile <- renderStudySpecificSql("DM12mo",minCellCount,cdmSchema,resultsSchema,sourceName,dbms)
	depSqlFile <- renderStudySpecificSql("Dep12mo",minCellCount,cdmSchema,resultsSchema,sourceName,dbms)
	
	# Execute the SQL:
	conn <- DatabaseConnector::connect(connectionDetails)
	DatabaseConnector::executeSql(conn,SqlRender::readSql(htnSqlFile))
	DatabaseConnector::executeSql(conn,SqlRender::readSql(t2dmSqlFile))
	DatabaseConnector::executeSql(conn,SqlRender::readSql(depSqlFile))
	
	# Extract tables to CSV files:
	extractAndWriteToFile(conn, "summary", cdmSchema, resultsSchema, sourceName, "HTN12mo", dbms)
	extractAndWriteToFile(conn, "person_cnt", cdmSchema, resultsSchema, sourceName, "HTN12mo", dbms)
	extractAndWriteToFile(conn, "seq_cnt", cdmSchema, resultsSchema, sourceName, "HTN12mo", dbms)
	
	extractAndWriteToFile(conn, "summary", cdmSchema, resultsSchema, sourceName, "DM12mo", dbms)
	extractAndWriteToFile(conn, "person_cnt", cdmSchema, resultsSchema, sourceName, "DM12mo", dbms)
	extractAndWriteToFile(conn, "seq_cnt", cdmSchema, resultsSchema, sourceName, "DM12mo", dbms)
	
	extractAndWriteToFile(conn, "summary", cdmSchema, resultsSchema, sourceName, "Dep12mo", dbms)
	extractAndWriteToFile(conn, "person_cnt", cdmSchema, resultsSchema, sourceName, "Dep12mo", dbms)
	extractAndWriteToFile(conn, "seq_cnt", cdmSchema, resultsSchema, sourceName, "Dep12mo", dbms)
	
	DBI::dbDisconnect(conn)
	
}