R/SearchFunctions.R

In Boodogs/zoon-clone: Reproducible, Accessible & Shareable Species Distribution Modelling

#'GetModuleList
#'
#'Get a list of all the modules available on the github repo.
#'
#'@return A list with all module names.
#'@name GetModuleList
#'@param renew Download from github even if we already have a module list.
#' @details This function will only work on a platform that supports the 
#' method 'libcurl' in the function url. This can be tested using the function
#' \code{capabilities} (see example).
#'
#'@export
#'@examples 
#'# GetModuleList requires libcurl to be supported
#'if(capabilities('libcurl')) GetModuleList()

GetModuleList <- function(renew = FALSE){

  # Check if we've made an environment called zoonHidden yet
  # If not make one.
  if(!exists('zoonHidden', mode = 'environment')){
    .zoonHidden <- new.env(parent = .GlobalEnv)
  }
  
  # If we've already downloaded a module list, print that.
  # Otherwise download a list from github
  # If renew is TRUE download from github even if we have a list already.
  if(exists('moduleList', envir = .zoonHidden) & !renew){
    moduleNames <- .zoonHidden$moduleList
    return(moduleNames)
  } else {

    # modules we know belong to each type (doesn't matter which they are,
    # but these should be fairly stable)
    canaries <- c(occurrence = 'SpOcc',
                  covariate = 'Bioclim',
                  process = 'NoProcess',
                  model = 'LogisticRegression',
                  output = 'InteractiveMap')
    
    # get URLs for these modules
    canary_urls <- helpURL <- paste0('https://raw.githubusercontent.com/zoonproject/modules/master/man/',
                                     canaries,
                                     '.Rd')
    
    # empty list for results
    moduleNames <- list()
    
    for (i in 1:5) {
      
      # grab the rd file
      rd_i <- readLines(url(canary_urls[i], method = 'libcurl'))
      
      # get the expected module type
      type <- names(canaries)[i]
      
      # find the starting line
      start_line <- grep(sprintf('^Other %s: ', type), rd_i)
      
      # find all section -closing parentheses
      end_lines <- grep('^}$', rd_i)
      
      # find the end of this section
      end_line <- min(end_lines[end_lines > start_line])
      
      # grab the required lines and combine
      text <- paste(rd_i[start_line:end_line],
                    collapse = '')
      
      # remove formatting we don't want
      start_text <- sprintf('^Other %s: ', type)
      text <- gsub(start_text, '', text)
      text <- gsub('\\\\code\\{\\\\link\\{', '', text)
      text <- gsub('\\}', '', text)
      
      # split into vector
      text <- strsplit(text, c(','))[[1]]
      
      # add the target module in
      text <- sort(c(canaries[i], text))
      
      # remove any names
      names(text) <- NULL
      
      # remove spaces
      text <- gsub(' ', '', text)
      
      # add to results
      moduleNames[[i]] <- text
      
    }
    
    names(moduleNames) <- names(canaries)

    .zoonHidden$moduleList <- moduleNames
    return(moduleNames)
  }
}