#########################################################################################
# ODK hardcopy in PDF v 1.0
#########################################################################################
#
# Step one of this script is a call to ODK briefcase via the command line, which pulls all
# records and media.
#
# Step two is to output individual records to a temp file, then bind their data with
# any images to make a pdf document.
#
# This work is licensed under Creative Commons Attribution-ShareAlike 3.0 Unported License
# http://creativecommons.org/licenses/by-sa/3.0/"
#########################################################################################
# Requirements
#
#needs latex and pandoc (external installations, use homebrew)
library(knitr)
library(readr)
library(dplyr)
library(anytime)
#
#########################################################################################
# call to ODK briefcase
# use full path including first subdirectory
# ie. https://projectx.odk.lshtm.ac.uk/projectx/
# any passwords with special characters will need escape characters
# i.e. password doggy!prunes12 needs to be specified as doggy\\!prunes12
# obviously shouldn't hardcode passwords. Better to call from the console using a readline() command but I am lazy
# Also need to specify the targets for input and output. Here TMIH_example
# I also renamed the jar file for ODK briefcase because I hate whitespace

command<- paste('java -jar ODK_Briefcase.jar -url YOUR_URL_HERE -p YOUR_PASSWORD_HERE -u admin -id YOUR_FORM_NAME_HERE -ed ./FOLDER_TO_EXPORT_IT_IN_ON_YOUR_PC -sd ./STORAGE_DIRECTORY -f FILE_NAME_OF_DOWNLOADED_CSV.csv')
system(command)

# pull in the csv data
df<-read.csv("TMIH_Example/TMIH_Example.csv",header = T)

# enter loop for each row of the csv file
for(i in 1:dim(df)[1])
{
  #send a file for the current record to tmp
  write.table(df[i,],file = "tmp.txt",quote = F,sep = "\t",col.names = T,row.names = F)
  #convert datetimes so that reports sort appropriately by date of submission

  df$SubmissionDate<-anytime(df$SubmissionDate)

  #run RMD script to create report in pdf, pulling in any jpgs
  rmarkdown::render(input = "pdfmaker.Rmd",
                    output_format = "pdf_document",
                    output_file = gsub(pattern = " |:",replacement = "_",x = paste(df$SubmissionDate[i], "_YOUR_FORM_NAME_HERE.pdf", sep='')),
                    output_dir = "reports")

}

#This work is licensed under Creative Commons Attribution-ShareAlike 3.0 Unported License
#http://creativecommons.org/licenses/by-sa/3.0/"

#Nuff respect to VP Nagraj [twitter @vpnagraj] from whose scripts I reused some of the control structure for calling RMD from another R script
#See http://nagraj.net/notes/multiple-rmarkdown-reports/