tests/testthat/test_template_table_attributes.R

In EDIorg/EMLassemblyline: A tool kit for building EML metadata workflows

context('Create table attributes template')
library(EMLassemblyline)

# File inputs = two data tables -----------------------------------------------

testthat::test_that('Test usage with file inputs', {
  
  # Missing path results in error
  
  expect_error(
    suppressMessages(
      template_table_attributes(
        data.path = system.file(
          '/examples/data',
          package = 'EMLassemblyline'
        ),
        data.table = c(
          'decomp.csv',
          'nitrogen.csv'
        ),
        write.file = FALSE
      )
    )
  )
  
  # Invalid data path results in error
  
  expect_error(
    suppressMessages(
      template_table_attributes(
        path = system.file(
          '/examples',
          package = 'EMLassemblyline'
        ),
        data.table = c(
          'decomp.csv',
          'nitrogen.csv'
        ),
        write.file = FALSE
      )
    )
  )
  
  # Invalid data tables result in error
  
  expect_error(
    suppressMessages(
      template_table_attributes(
        path = system.file(
          '/examples',
          package = 'EMLassemblyline'
        ),
        data.path = system.file(
          '/examples/data',
          package = 'EMLassemblyline'
        ),
        data.table = c(
          'decompppp.csv',
          'nitrogennnnn.csv'
        ),
        write.file = FALSE
      )
    )
  )
  
  
  # New imports result in messages
  
  expect_message(
    template_table_attributes(
      path = tempdir(),
      data.path = system.file(
        '/examples/data',
        package = 'EMLassemblyline'
      ),
      data.table = c(
        'decomp.csv',
        'nitrogen.csv'
      ),
      write.file = TRUE
    )
  )
  
  # Attempt to import templates when they already exist results in messages
  
  expect_message(
    template_table_attributes(
      path = tempdir(),
      data.path = system.file(
        '/examples/data',
        package = 'EMLassemblyline'
      ),
      data.table = c(
        'decomp.csv',
        'nitrogen.csv'
      ),
      write.file = TRUE
    )
  )
  
  # write.file = TRUE writes files to path
  
  file.remove(
    paste0(
      tempdir(),
      '/attributes_decomp.txt'
    )
  )
  
  file.remove(
    paste0(
      tempdir(),
      '/attributes_nitrogen.txt'
    )
  )
  
  file.remove(
    paste0(
      tempdir(),
      '/custom_units.txt'
    )
  )
  
  expect_message(
    template_table_attributes(
      path = tempdir(),
      data.path = system.file(
        '/examples/data',
        package = 'EMLassemblyline'
      ),
      data.table = c(
        'decomp.csv',
        'nitrogen.csv'
      ),
      write.file = TRUE
    )
  )
  
  expect_true(
    'custom_units.txt' %in% list.files(tempdir())
  )
  
})

# x inputs = data tables ------------------------------------------------------

testthat::test_that('x inputs = data tables', {
  
  # Make function call
  
  x <- template_arguments(
    data.path = system.file(
      '/examples/data',
      package = 'EMLassemblyline'
    ),
    data.table = c(
      'decomp.csv',
      'nitrogen.csv'
    )
  )
  
  x <- x$x
  
  # Missing path results in messages
  
  expect_message(
    template_table_attributes(
      x = x,
      write.file = FALSE
    )
  )
  
  # Missing path results in messages
  
  expect_message(
    template_table_attributes(
      data.path = system.file(
        '/examples/data',
        package = 'EMLassemblyline'
      ),
      x = x,
      write.file = FALSE
    )
  )
  
  # Missing data path results in messages
  
  expect_message(
    template_table_attributes(
      path = system.file(
        '/examples',
        package = 'EMLassemblyline'
      ),
      x = x,
      write.file = FALSE
    )
  )
  
  # Valid data path and data tables results in messages
  
  # expect_message(
  #   template_table_attributes(
  #     data.path = system.file(
  #       '/examples/data',
  #       package = 'EMLassemblyline'
  #     ),
  #     data.table = c(
  #       'decomp.csv',
  #       'nitrogen.csv'
  #     ),
  #     x = x,
  #     write.file = FALSE
  #   )
  # )
  
  # Valid data path and data tables result in addition of attributes templates
  # with expected names, class, column names, and nrows > 1. Custom units
  # template is also added.
  
  output <- suppressMessages(
    template_table_attributes(
      data.path = system.file(
        '/examples/data',
        package = 'EMLassemblyline'
      ),
      data.table = c(
        'decomp.csv',
        'nitrogen.csv'
      ),
      x = x,
      write.file = FALSE
    )
  )
  
  attr_names <- paste0(
    'attributes_',
    stringr::str_remove(
      string = names(output$data.table),
      pattern = '.csv'
    ),
    '.txt'
  )
  
  for (i in 1:length(attr_names)){
    
    expect_equal(
      attr_names[i] %in% names(output$template),
      TRUE
    )
    
    expect_equal(
      class(output$template[[attr_names[i]]]$content),
      'data.frame'
    )
    
    expect_equal(
      all(
        colnames(output$template[[attr_names[i]]]$content) %in%
          c('id', 'attributeName', 'attributeDefinition', 'class', 'unit', 
            'dateTimeFormatString', 'missingValueCode', 
            'missingValueCodeExplanation')
      ),
      TRUE
    )
    
    expect_equal(
      nrow(output$template[[attr_names[i]]]$content) > 1,
      TRUE
    )
    
  }
  
  expect_true(
    'custom_units.txt' %in% names(output$template)
  )
  
  # Attempt to import templates when they already exist results in messages
  
  expect_message(
    template_table_attributes(
      data.path = system.file(
        '/examples/data',
        package = 'EMLassemblyline'
      ),
      data.table = c(
        'decomp.csv',
        'nitrogen.csv'
      ),
      x = output,
      write.file = FALSE
    )
  )
  
  # write.file = TRUE writes files to path
  
  expect_message(
    template_table_attributes(
      path = tempdir(),
      data.path = system.file(
        '/examples/data',
        package = 'EMLassemblyline'
      ),
      data.table = c(
        'decomp.csv',
        'nitrogen.csv'
      ),
      x = x,
      write.file = TRUE
    )
  )
  
})

# UTF-8 encoding --------------------------------------------------------------

testthat::test_that("UTF-8 encoding", {
  
  # # Header has UTF-8 encoded characters
  # 
  # file.copy(
  #   from = system.file(
  #     '/examples/pkg_260/data_objects/nitrogen.csv', 
  #     package = 'EMLassemblyline'),
  #   to = tempdir())
  # f <- paste0(tempdir(), "/nitrogen.csv")
  # d <- data.table::fread(f)
  # 
  # x <- c("Ekstr\xf8m", "J\xf6reskog", "bi\xdfchen Z\xfcrcher")
  # Encoding(x) <- "latin1"
  # test <- iconv(xx, "UTF-16LE", "UTF-8")
  # Encoding(test)
  # test <- iconv(xx, "UTF-8", "UTF-16LE")
  # Encoding(test)
  # colnames(d)
  
})