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Import XY-Data into R

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tests/testthat/test_read_xyData.R

tests/testthat/test_read_xyData.R
In rxylib: Import XY-Data into R 

test_that("General tests", {
  testthat::skip_on_cran()
  local_edition(3)

  ##force break (file does not exists)
  expect_null(read_xyData(file = "hi"))

  ##check get_version (internal function)
  expect_type(rxylib:::get_version(), type = "character")

  ##force connection error
  expect_null(suppressWarnings(read_xyData(file = "https://github.com/R-Lum/rxylib/raw/master/tests/testdata/BkenExampleSpectrum.CNF")))

  ##force wrong file format read
  expect_null(read_xyData(file = "https://raw.githubusercontent.com/R-Lum/rxylib/master/appveyor.yml", verbose = FALSE))

  ##check broken testdata
  expect_null(read_xyData(file = "https://github.com/R-Lum/rxylib/raw/master/tests/testdata/BrokenExampleSpectrum.CNF"))

  ##check C++ function
  expect_type(
    rxylib:::get_meta_DataSet(path = system.file("extdata/ExampleSpectrum.CNF", package = "rxylib"),
                              format_name = "canberra_cnf", options = ""),
    type = "list")

  ##check metadata argument
  expect_type(read_xyData(file = system.file("extdata/ExampleSpectrum.CNF", package = "rxylib"), metaData = FALSE), type = "list")

  ##check verbose
  expect_silent(read_xyData(file = system.file("extdata/ExampleSpectrum.CNF", package = "rxylib"), verbose =  FALSE))

  ##check list
  l <- c(system.file("extdata/ExampleSpectrum.CNF", package = "rxylib"), system.file("extdata/ExampleSpectrum.CNF", package = "rxylib"))
  expect_type(read_xyData(file = l, verbose =  TRUE), "list")

  ##check plot warning (and import of spectrum)
  expect_warning(plot(read_xyData(file = system.file("extdata/TLSpectrum.xsyg", package = "rxylib"), verbose =  FALSE)))

  ##check empty data
  expect_output(print(read_xyData(file = "https://raw.githubusercontent.com/R-Lum/rxylib/master/tests/testdata/TLSpectrum_Empty.xsyg", verbose =  FALSE)))

})

test_that("Methods test", {
  testthat::skip_on_cran()
  local_edition(3)

  ##check S3 methods
  test_dataset <- read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/03yag02.mca")
  expect_output(print(test_dataset))
  expect_silent(plot(test_dataset))
  expect_silent(plot(test_dataset, block = 1))
  expect_null(plot(test_dataset, block = 2))

  test_dataset <- read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/background_8.CNF")

  expect_output(print(test_dataset))
  rm(test_dataset)

})

test_that("Check all formats", {
  testthat::skip_on_cran()
  local_edition(3)

  ##load example data step by step from GitHub
    ##Canberra MCA
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/03yag02.mca"),
                type = "list")
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/04nacl02.mca"),
                type = "list")

    ##Canberra CNF
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/SMP00011.CNF"), type = "list")
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/background_8.CNF"), type = "list")

    ##Check ChiPlot
    expect_type(read_xyData(file = system.file("extdata/ExampleChiPlot.chi", package = "rxylib")), type = "list")

    ##Powder Diffraction CIF
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/1517474.cif"), type = "list")

    ##PI WinSpec SPE
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/1d-1.spe"), type = "list")
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/1d-2.spe"), type = "list")
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/1d-3.spe"), type = "list")

    ##Siemens/Bruker RAW
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/BT86.raw"), type = "list")
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/Cu3Au-1.raw"), type = "list")
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/Cu3Au-2.raw"), type = "list")
    expect_type(read_xyData(file = "https://github.com/wojdyr/xylib/raw/master/samples/format1.raw"), type = "list")

    ##Bruker ESP300-E SPC
    expect_type(read_xyData(file = "https://github.com/tzerk/ESR/raw/master/inst/extdata/mollusc.SPC"), type = "list")

    ##Bruker Diffrac-AT UXD
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/BT86_.UXD"), type = "list")

    ##Non-obious format
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/D1A5.dat"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/PSI_DMC.dat"), type = "list")
    #expect_type(read_xyData(file = "http://www.mx.iucr.org/iucr-top/comm/cpd/QARR/rd/cpd-1a.rd"), type = "list")

    ##Spectra / VGX 900
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/Spectra.1"), type = "list")

    ##PANalytical XRDML
      ## version with "intensities" node
      expect_type(
        read_xyData(
          file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/empyrean.xrdml"),
        type = "list")

      ## version with "counts" node
      ## TODO (check xylib page)
      expect_type(
      read_xyData(
        file = "https://raw.githubusercontent.com/wojdyr/xylib/075db1e4261daffe0e86e655b3a5af39869faec5/samples/examples.xrdml"),
      type = "list")

    ##VAMAS ISO-14976
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/mjr9_116a.vms"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/mjr9_59c.vms"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/mjr9_64c.vms"), type = "list")

    ##SPECS SpecsLab2 xy
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/mm-specs.xy"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/specsxy_example.xy"), type = "list")

    ##TXT
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/pesa.txt"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/with_commas.txt"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/with_sigma.txt"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/xy_text.txt"), type = "list")

    ##CSV or TSV
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/small.tsv"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/test1.csv"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/test2.csv"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/test3.csv"), type = "list")
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/test4.csv"), type = "list")

    ##Freiberg Instruments (FI) Lexsyg
    expect_type(read_xyData(file = "https://raw.githubusercontent.com/wojdyr/xylib/master/samples/rfqm_uv.xsyg"), type = "list")

    ##XFIT XDD
    ##commented 2017-11-03 ... server down?
    #expect_type(read_xyData(file = "http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/krumm/Software/windows/stereo/Y2O3.XDD"), type = "list")

    ##Philips UDF
    ##commented 2017-11-03 ... server down?
    expect_type(read_xyData(file = "http://www.cristal.org/DU-SDPD/semaine-2/na5+nac.udf"), type = "list")

    ##DBWS data
    expect_type(read_xyData("http://mysite.du.edu/~balzar/lebailbr.dbw"), type = "list")

    ##Rigaku (dat)
    expect_type(read_xyData("https://raw.githubusercontent.com/R-Lum/rxylib/master/tests/testdata/ExampleRigaku.dat"), type = "list")

    ##Sietronics Sieray CPI detected
#     expect_type(read_xyData("https://www.chemistry.ohio-state.edu/~woodward/ceo2br.cpi
# "), type = "list")

})

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rxylib documentation built on Nov. 3, 2023, 5:09 p.m.

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