R/test_module.R

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

#' @import roxygen2
test_module <- function(modulePath){

  context(paste('Testing module', basename(gsub('.R$', '', modulePath))))
  
  time <- system.time({
    
    moduleName <- basename(gsub('.R$', '', modulePath))
    
    roxy_parse <- ZoonModuleParse(modulePath)
    
    ## GENERIC TESTS
    test_that(paste('Check roxy_parse', moduleName),{
      
      # Check roxy_parse is good
      expect_is(roxy_parse, 'list', info = 'Your function appears to the empty, or not a function')
      
    })
    
    test_that(paste('Check for generic tags', moduleName),{
      
      # Check for the required generic tags
      expect_true('title' %in% names(roxy_parse))
      expect_true('description' %in% names(roxy_parse))
      expect_true('name' %in% names(roxy_parse))
      expect_true('family' %in% names(roxy_parse))
      expect_true('author' %in% names(roxy_parse))
      expect_true('section' %in% names(roxy_parse))
      expect_true(any(grepl('^Version: ', roxy_parse[grepl('section', names(roxy_parse))])))
      expect_true(any(grepl('^Date submitted: ', roxy_parse[grepl('section', names(roxy_parse))])))
      
    })
    
    # If the family tag is present continue (this error will be reported above)
    if('family' %in% names(roxy_parse)){
      
      ## Test for module specific tags
      test_that('Check for module specific tags', {
        
        if(roxy_parse$family == 'process' | roxy_parse$family == 'model' | roxy_parse$family == 'occurrence'){
          expect_true('section' %in% names(roxy_parse), info = 'Section tag missing')
          expect_true(any(grepl('^Data type: ', roxy_parse[grepl('section', names(roxy_parse))])),
                      info = 'Data types have not been specified using the @section tag')
          if(any(grepl('^Data type: ', roxy_parse[grepl('section', names(roxy_parse))]))){
            
            sections <- roxy_parse[grepl('section', names(roxy_parse))]
            data_types <- trimws(strsplit(gsub('Data type: ', '', sections[grepl('Data type: ', sections)]),
                                          split = ',')[[1]])
            data_types_tf <- data_types %in% c('presence-only', 'presence/background',
                                               'presence/absence', 'abundance', 'proportion')
            expect_true(all(data_types_tf),
                        info = paste('Data types', paste(data_types[!data_types_tf], collapse = ', '),
                                     "not supported. Data types must be one of: 'presence-only', 'presence/background', 'presence/absence', 'abundance', 'proportion'"
                                    )
                        )
          }
        }
      })
      
      ## PARAMETER TESTS
      if(roxy_parse$family == 'occurrence'){
        
        test_parameters(roxy_parse, modulePath = modulePath)
          
      }
      
      if(roxy_parse$family == 'covariate'){
        
        test_parameters(roxy_parse, modulePath = modulePath)
        
      }  
      
      if(roxy_parse$family == 'process'){
        
        test_parameters(roxy_parse, defaultParams = '.data',
                        modulePath = modulePath)
        
      }  
      
      if(roxy_parse$family == 'model'){
        
        test_parameters(roxy_parse, defaultParams = '.df',
                        modulePath = modulePath)
        
      }
      
      if(roxy_parse$family == 'output'){
        
        test_parameters(roxy_parse, defaultParams = c('.model', '.ras'),
                        modulePath = modulePath)
        
      }
      
      ## FUNCTION OUTPUT TESTS
      test_outputs(roxy_parse, modulePath)
      
    }
  }) #time
  
  expect_true(time['elapsed'] < 120,
              info = paste('Module tests should not take a long time, yours took', time['elapsed'], 'seconds, please change your defualt values so that test workflow runs do not take too long'))
  
}