R/batch_report_admin.R

In KSSyndromic/KSSPReport: A Data Quality Report Generator for NSSP BioSense Platform. It automatically sends data quality report emails to all the facilities.

#' Batch Job To Create NSSP BioSense Platform Data Quality Summary Reports for All Kansas Facilities in Production for the Hospital Admins
#'
#' @description
#' This function iteratively performs `write_facilty_report`  function for all Kansas Facilities in production targeted toward admins. It will generate summary report for all specified facility.
#' The summary workbook shows percents and counts of nulls and invalids, Additionally it generates a timeliness
#' report and creates a table. 
#' @param facility_spreadsheet location of the facility spreadsheet xlsx
#' @param username Your BioSense username, as a string. This is the same username you may use to log into RStudio or Adminer.
#' @param password Your BioSense password, as a string. This is the same password you may use to log into RStudio or Adminer.
#' @param table The table that you want to retrieve the data from, as a string.
#' @param mft The MFT (master facilities table) from where the facility name will be retrieved, as a string.
#' @param start The start date time that you wish to begin pulling data from, as a string.
#' @param end The end data time that you wish to stop pulling data from, as a string.
#' @param directory The directory where you would like to write the reports to (i.e., "~/Documents/MyReports"), as a string.
#' @param email Default False. If True, then the function will atempt to send out a form
#' @param sender Email address of sender. Make sure it's kdhe.KS.gov
#' @param email_password Your Email Password
#' @param personname Your Name to be used in your email text
#' @param title Your job title to be used in your email text
#' @param phone Your phone number to be used in your email text
#'  @param message The email message to be sent. Allows for composition of costume messages.
#' @return First the program will ask if the facility spread sheet is up to date. If answer is yes, generate report table stored at directory location. If email=TRUE, then a email will be sent. A table with facility, receiver and conformation of email being sent. In addition, there will be a AdminReport.csv file listing whether the email got sent.
#'
#' @examples 
#' library(biosensequality)
#' library(keyring)
#' 
#' ## store passwords for essence
#' key_set(service = "essence")
#' ## store passwords for email
#' key_set(service = "email")
#'batch_all_production_admin(facility_spreadsheet="Facilities Spreadsheet_New.xlsx", username="bzhang02", password=key_get("essence"),
#'  table="KS_PR_Processed", mft="KS_MFT",  start="2020-05-01 00:00:00", 
#'  end="2020-05-30 23:59:59", directory="~",
#'  email =TRUE,sender="bo.zhang@@kdhe.ks.gov",
#' email_password=key_get("email"),personname='Bo Zhang',title='intern',phone='630-457-8915')
#' @import yesno
#' @import dplyr
#' @import tidyr
#' @import readxl
#' @export
batch_all_production_admin<-function(facility_spreadsheet,table, mft, username,password,start, end,directory,email=F, sender,email_password,personname=NA,title=NA, phone=NA,message=NA){
  ready=yesno2("Make sure your facility spread sheet is up to date. Is your facility spread sheet up to date?")
if (ready==T){
  contact=read_excel(facility_spreadsheet, sheet = "ED_POC_New")
  contact <- contact[rowSums(is.na(contact))<ncol(contact),]
  niter= nrow(contact)
  success=NA
  field="Administrative_Sex;Age_Reported;Age_Units_Reported;C_Chief_Complaint;Chief_Complaint_Text_Short;Diagnosis_Code;Diagnosis_Type;Discharge_Date_Time;Discharge_Disposition;Ethnicity_Code;Height;Height_Units;Medical_Record_Number;Patient_City;Patient_State;Patient_Zip;Race_Code;Smoking_Status_Code;Weight;Weight_Units"
  for (i in 1:niter){
    if (is.na(contact$Status[i])==F & contact$Status[i]=="Production"){
      if (is.na(contact$`Facility Administrator Email`[i])==F){
    success[i]=write_facility_report(username=username, password=password, 
                                     table=table, mft=mft,
                                     start=start, 
                                     end=end,
                                     facility=contact$C_Biosense_Facility_ID [i],
                                     directory=directory,field=field,
                                     email =email, sender=sender,receiver=as.character(contact$`Facility Administrator Email`[i]),
                                     email_password=email_password,personname=personname,title=title, phone=phone,message=message)
    
      }else {
      success[i]='No admin email provided'
      }
      }else {
        success[i]='The facility is not in production'
      }
  }
    report=cbind(contact,success)
    report=report %>%
      select(c(`Facility Name`,C_Biosense_Facility_ID,`Facility Administrator Name`,`Facility Administrator Email`,success))
    
    write.csv(report,paste0(directory, "/AdminReport",format(Sys.Date(),'%b_%d_%Y'),".csv"), row.names = TRUE)
    return(report)
  }
  else{
    stop("Please Update The Facility Spreadsheet Before Running The Batch Job")
  }
}