/**
* Test when the samplesheet only contains the vital columns with data.
*
* @throws IOException
*/
@Test
public void testValidMinimalSamplesheet() throws IOException {
List<Sample> actualSamples =
reader.read(getClassLoader().getResource("samplesheets/valid_minimal.csv").getFile());
Assert.assertEquals(actualSamples, expectedValidSamples);
}
/**
* Test when a sample is missing the last field but with a comma ending the previous field.
*
* @throws IOException
*/
@Test(expectedExceptions = IOException.class)
public void testSampleMissingLastFieldEndingWithAComma() throws IOException {
reader.read(
getClassLoader()
.getResource("samplesheets/sample_missing_last_field_comma-ended.csv")
.getFile());
}
/**
* Test when the run value and date are swapped (so columns do not have a correct seeming value
* but is of the same type). Currently, the expected behavior is not checking on this and it
* should pass as long as the type of the value is correct.
*
* @throws IOException
*/
@Test
public void testSampleRunAndSequencingStartDateSwapped() throws IOException {
@SuppressWarnings("unchecked")
List<Sample> expectedSamples = (List<Sample>) expectedValidSamples.clone();
expectedSamples.remove(1);
expectedSamples.add(1, new Sample("sample2", "SN163", 648, 150616, "AHKYLMADXX", 2));
List<Sample> actualSamples =
reader.read(
getClassLoader()
.getResource("samplesheets/sample_run_sequencingStartDate_swapped.csv")
.getFile());
Assert.assertEquals(actualSamples, expectedSamples);
}
/**
* Test when a sample is missing a field.
*
* @throws IOException
*/
@Test(expectedExceptions = IOException.class)
public void testSampleMissingRun() throws IOException {
reader.read(getClassLoader().getResource("samplesheets/sample_missing_run.csv").getFile());
}
/**
* Test when the header of the csv file is missing.
*
* @throws IOException
*/
@Test(expectedExceptions = IOException.class)
public void testHeaderLineIsMissing() throws IOException {
reader.read(getClassLoader().getResource("samplesheets/missing_header_line.csv").getFile());
}
/**
* Test when the header of the csv file is an empty line.
*
* @throws IOException
*/
@Test(expectedExceptions = IOException.class)
public void testHeaderIsAnEmptyLine() throws IOException {
reader.read(getClassLoader().getResource("samplesheets/header_empty_line.csv").getFile());
}