run.R

#' --------------------------------------
#' Project: RACE SURVEY APP
#' Developed by: Zack Oyafuso, Sarah Friedman, Emily Markowitz
#' --------------------------------------

## Import packages, authenticate google drive ----------------------------------

source("sub_tasks/01_import_R_packages.R")
googledrive::drive_deauth()
googledrive::drive_auth()
1

## Import helper functions -----------------------------------------------------
srvys <- c("NBS", "EBS", "BS", "AI")
source("sub_tasks/02_functions.R")

##   Clear the html files in docs/ folder. Since it takes a while to create
##   all of the fish ID pages, remake_species_pages can be set to F to skip
##   remaking those pages. In clear_htmls() the species id pages (those that
##   start with "zz") are not cleared from the docs/ folder.

remake_species_pages <- FALSE
clear_htmls() # removes all existing htmls in docs folder

##   Import and clean up data. If access_to_internet == TRUE, a local copy
##   of the various data input are saved in the data/ folder.

access_to_internet <- TRUE
source("sub_tasks/03_data.R")

# Check that links work: listed below are links that do not work ---------------

# checkLinks(URLs = website_content$url_loc)
# checkLinks(URLs = website_content$url_web)

# Identify what combination of pages will be created ---------------------------

## Find combination of webpages using the generic template. dir_pdfs is a
## vector of subpages that link to pdfs and not htmls so we note that here.

dir_pdfs <- c("Codebook", "Emergency Flow Chart")

comb <- website_content %>%
  dplyr::select(page, sub_page) %>%
  dplyr::distinct() %>%
  dplyr::mutate(template_rmd = "template.rmd") %>%
  dplyr::mutate(web_page = gsub(
    x = paste0(page, "_", sub_page, ".html"),
    pattern = " ",
    replacement = "_"
  ))

comb$template_rmd <- ifelse(comb$sub_page %in% dir_pdfs,
  yes = "",
  no = comb$template_rmd
)

comb$web_page[match(x = dir_pdfs, table = comb$sub_page)] <-
  website_content$url_loc[match(x = dir_pdfs, table = website_content$sub_page)]

## Add comb information for webpages that use a custom template
custom_comb <- tribble(
  ~page, ~sub_page, ~template_rmd,
  "FPC and Deck Lead", "Tasklist 1 - Beginning of Survey or Leg", "tasklist.rmd",
  "FPC and Deck Lead", "Tasklist 2 - End of Leg", "tasklist.rmd",
  "FPC and Deck Lead", "Tasklist 3 - End of Survey", "tasklist.rmd",
  "Personnel", "Flight Itineraries", "personnel_flight_itineraries.Rmd",
  "Species ID", "Minimum ID", "species_id_minimum_id.Rmd",
  "Species ID", "Guides", "species_id_guides.Rmd",
  "Species ID", "Fish ID by Taxa", "species_id_id_by_taxa.Rmd"
)

custom_comb$web_page <-
  gsub(
    x = paste0(custom_comb$page, "_", custom_comb$sub_page, ".html"),
    pattern = " ",
    replacement = "_"
  )

comb <- rbind(comb, custom_comb)
source("sub_tasks/04_render_main_page.R")


# Render ID by Taxa page. ------------------------------------------------------

##   If remake_species_pages == TRUE, remake species pages
source("sub_tasks/05_render_species_pages.R")



##   Loop over comb df and render each page ------------------------------------

for (jj in 1:nrow(comb)) { ## Loop over pages -- start
  if (comb$template_rmd[jj] == "") next # direct pdfs

  ## Page specific information
  page_title <- comb$page[jj]
  page_desc <- ifelse(test = is.na(x = comb$sub_page[jj]),
    yes = "Parent directory",
    no = comb$sub_page[jj]
  )
  page_dat <- website_content %>%
    dplyr::filter(page == page_title &
      sub_page == page_desc &
      (title != "" | Links != ""))

  ## Render document
  rmarkdown::render(
    input = paste0("templates/", comb$template_rmd[jj]),
    output_dir = "docs/",
    output_file = comb$web_page[jj]
  )
} ## Loop over pages -- end