---
params:
  genus: NA
  species: NA
title: "Alert report"
date: "`r format(Sys.time(), '%d %B %Y')`"
output: 
  orgcharts::html_org:
    includes:
      in_header: org_logo.html
---

###############################
# Set directories:
library(shiny)
library(here)
library(lubridate)
library(ezknitr)

# Define the path to the .Rmd file:
rmdwd <- here::here()

# Define the path to the root directory to save the report to (dummy example):
repwd <- "//MyNetworkDrive/Myfolder"

# Auto-calculate the reporting week and year:
repdate <- Sys.Date() - weeks(1)
ryear <- year(repdate)
rweek <- isoweek(repdate)
ryw <- paste0(ryear, rweek)

# Create the year/week sub-directory to save the report in:
outwd <- paste(repwd, "/", ryear, "/", ryw, sep = "")

###############################
# Create user interface:
ui = fluidPage(
    textInput(inputId = "genus", label = "Pathogen genus", value = "NA", placeholder = "To generate an alert report at the genus level, enter the pathogen genus in this box"),
    textInput(inputId = "species", label = "Pathogen species", value = "NA", placeholder = "To generate an alert report at the species level, enter the pathogen genus and species in this box"),
    downloadButton("report", "Generate report")
  )

###############################
# Create server logic:
server <- function(input, output) {
    
    # Create the output: 
    output$report = downloadHandler(
      

      # Set up parameters to pass to Rmd document
      params = list(genus = input$genus, species = input$species),
      
      # Create the temp file name:
      filename = function() {
        
        ifelse(params$genus == "NA", 
                        paste0("AlertReport_", params$species, "_", Sys.Date(), ".html"),
                        paste0("AlertReport_", params$genus, "_", Sys.Date(), ".html"))
      },
      
      # Define the content of the temp file:
      content = function(file) {
        
        # Knit the document, defining the destination path and file name:
        ezknitr::ezknit(file = "ExceedanceReports.Rmd", 
                        wd = rmdwd,
                        out_dir = outwd, 
                        fig_dir = "figs",
                        params = list(genus = "NA", species = "NA"), 
                        keep_md = FALSE, 
                        keep_html = TRUE)
        }
    )
  }

###############################
# Run app:
shinyApp(ui, server)