Examples with RunContext com.hartwig.hmftools.common.context.RunContext used on opensource projects

Example 11 with RunContext

use of com.hartwig.hmftools.common.context.RunContext in project hmftools by hartwigmedical.

the class HealthChecksApplication method main.

public static void main(final String... args) throws ParseException, IOException {
    final Options options = createOptions();
    final CommandLine cmd = createCommandLine(options, args);
    String runDirectory = cmd.getOptionValue(RUN_DIRECTORY);
    final String reportFilePath = cmd.getOptionValue(REPORT_FILE_PATH);
    if (runDirectory == null || reportFilePath == null) {
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("Health-Checks", options);
        System.exit(1);
    }
    runDirectory = FolderChecker.build().checkFolder(runDirectory);
    RunContext runContext = ProductionRunContextFactory.fromRunDirectory(runDirectory);
    new HealthChecksApplication(runContext, reportFilePath).run();
}

Example 12 with RunContext

use of com.hartwig.hmftools.common.context.RunContext in project hmftools by hartwigmedical.

the class AmberCheckerTest method testMissing.

@Test(expected = IOException.class)
public void testMissing() throws IOException {
    final RunContext runContext = TestRunContextFactory.forSomaticTest(BASE_DIRECTORY, REF_SAMPLE, "missing");
    checker.run(runContext);
}

Example 13 with RunContext

use of com.hartwig.hmftools.common.context.RunContext in project hmftools by hartwigmedical.

the class PurpleCheckerTest method testMissing.

@Test(expected = IOException.class)
public void testMissing() throws IOException {
    final RunContext runContext = TestRunContextFactory.forSomaticTest(BASE_DIRECTORY, REF_SAMPLE, "missing");
    checker.run(runContext);
}

Example 14 with RunContext

use of com.hartwig.hmftools.common.context.RunContext in project hmftools by hartwigmedical.

the class PurpleCheckerTest method extractDataFromPurpleWorksForSomatic.

@Test
public void extractDataFromPurpleWorksForSomatic() throws IOException {
    final RunContext runContext = TestRunContextFactory.forSomaticTest(BASE_DIRECTORY, REF_SAMPLE, TUMOR_SAMPLE);
    final BaseResult result = checker.run(runContext);
    Assert.assertEquals(CheckType.PURPLE, result.checkType());
    final List<HealthCheck> checks = ((MultiValueResult) result).checks();
    assertCheck(checks, PurpleCheck.AMBER_GENDER.toString(), "MALE");
    assertCheck(checks, PurpleCheck.COBALT_GENDER.toString(), "FEMALE");
    assertCheck(checks, PurpleCheck.PURPLE_SEGMENT_SCORE.toString(), "199");
}

Example 15 with RunContext

use of com.hartwig.hmftools.common.context.RunContext in project hmftools by hartwigmedical.

the class StrelkaCheckerTest method runsCorrectlyForSingleSample.

@Test
public void runsCorrectlyForSingleSample() throws IOException {
    final RunContext runContext = TestRunContextFactory.forSingleSampleTest(RUN_DIRECTORY, REF_SAMPLE);
    final BaseResult result = checker.run(runContext);
    assertTrue(result instanceof NoResult);
}