#' Extract reserach protocols
#'
#' Extracts reserach protocols from the Caisis database and returns a data frame.
#'
#' @param connection ODBC connection object returned by dbConnect.
#' @param patients A character vector of patient medical record numbers. If no
#' limit is desired then set as NULL.
#' @param n Number of records to retrieve. Use n = -1 to retrieve all records.
#' @return Returns a data frame with reserach protocols from the Caisis database.
#' @export
#' @import DBI
extractProtocols <- function(connection, patients = NULL, n = -1) {
if(is.null(patients)){
patients <- "LIKE '%'"
} else {
patients <- paste("IN ('", paste(patients, collapse = "', '"), "')", sep = "")
}
data <- DBI::dbGetQuery(connection, paste("SELECT
PtMRN as 'PatientMRN',
CaisisProd.dbo.vDatasetProtocols.ProtocolNum,
CaisisProd.dbo.vDatasetPatientProtocolStatus.PtProtocolStatusDate,
CaisisProd.dbo.vDatasetPatientProtocolStatus.PtProtocolStatus,
CaisisProd.dbo.vDatasetProtocols.ProtocolInstitution,
CaisisProd.dbo.vDatasetProtocols.ProtocolTitle,
CaisisProd.dbo.vDatasetProtocols.ProtocolNotes,
CaisisProd.dbo.vDatasetProtocols.DiseaseSite,
CaisisProd.dbo.vDatasetProtocols.ProtocolPhase,
CaisisProd.dbo.vDatasetProtocols.ProtocolStatus,
CaisisProd.dbo.vDatasetProtocols.ProtocolPI,
CaisisProd.dbo.vDatasetProtocols.ProtocolOpenDate,
CaisisProd.dbo.vDatasetProtocols.ProtocolClosedDate,
CaisisProd.dbo.vDatasetProtocols.ProtocolNCTID
FROM CaisisProd.dbo.vDatasetPatients
INNER JOIN CaisisProd.dbo.vDatasetPatientProtocols ON CaisisProd.dbo.vDatasetPatients.PatientId = CaisisProd.dbo.vDatasetPatientProtocols.PatientId
INNER JOIN CaisisProd.dbo.vDatasetPatientProtocolStatus ON CaisisProd.dbo.vDatasetPatientProtocols.PatientProtocolId = CaisisProd.dbo.vDatasetPatientProtocolStatus.PatientProtocolId
INNER JOIN CaisisProd.dbo.vDatasetProtocols ON CaisisProd.dbo.vDatasetPatientProtocols.protocolId = CaisisProd.dbo.vDatasetProtocols.protocolId
WHERE CaisisProd.dbo.vDatasetPatients.PtMRN ", patients, sep = ""), n=-1)
data$PatientMRN = as.factor(data$PatientMRN)
data$PtProtocolStatusDate = as.Date(data$PtProtocolStatusDate, format = "%Y-%m-%d")
data$ProtocolOpenDate = as.Date(data$ProtocolOpenDate, format = "%Y-%m-%d")
data$ProtocolClosedDate = as.Date(data$ProtocolClosedDate, format = "%Y-%m-%d")
return(data)
}
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