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Re-enable htsget tests #6668

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Jun 19, 2020
Merged

Re-enable htsget tests #6668

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22 changes: 13 additions & 9 deletions src/test/java/org/broadinstitute/hellbender/tools/HtsgetReaderIntegrationTest.java
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Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
package org.broadinstitute.hellbender.tools;

import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
import org.broadinstitute.hellbender.testutils.SamAssertionUtils;
import org.broadinstitute.hellbender.utils.Utils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
Expand All @@ -13,6 +15,7 @@
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.util.Collections;
import java.util.Map;

import com.google.common.collect.ImmutableMap;
Expand Down Expand Up @@ -58,18 +61,18 @@ Object[][] successfulParameters() {
StandardArgumentDefinitions.INTERVALS_LONG_NAME, "chr1:24000000-25000000"),
"A1-B000168-3_57_F-1-1_R2.mus.Aligned.out.sorted.bam.startend"
},
{ // filter by field
ImmutableMap.of(
HtsgetReader.ID_LONG_NAME, FILE_ID,
HtsgetReader.FIELDS_LONG_NAME, "QNAME"),
"A1-B000168-3_57_F-1-1_R2.mus.Aligned.out.sorted.bam.field"
}
// TODO enable when server update goes in
// { // filter by field
// ImmutableMap.of(
// HtsgetReader.ID_LONG_NAME, FILE_ID,
// HtsgetReader.FIELDS_LONG_NAME, "QNAME"),
// "A1-B000168-3_57_F-1-1_R2.mus.Aligned.out.sorted.bam.field"
// }
};
}

// Test successful combinations of query parameters
// TODO: re-enable and add tags/notags tests once reference server is stable
@Test(dataProvider = "successfulParameters", enabled = false)
@Test(dataProvider = "successfulParameters")
public void testSuccessfulParameters(final Map<String, String> params, final String expectedFileName) throws IOException {
final File expected = new File(getToolTestDataDir(), expectedFileName);
final File output = createTempFile("output", ".bam");
Expand All @@ -80,9 +83,10 @@ public void testSuccessfulParameters(final Map<String, String> params, final Str
params.forEach(args::add);

runCommandLine(args);
IntegrationTestSpec.assertEqualTextFiles(output, expected, null);
SamAssertionUtils.assertEqualBamFiles(output, expected, false, ValidationStringency.LENIENT);
}

//This test is disabled because it takes a long time. It's included in order to run it manually.
@Test(enabled = false)
public void testLargeFileParallelDownload() throws IOException {
final String expectedMd5 = new String(Files.readAllBytes(new File(getToolTestDataDir(), LARGE_FILE_MD5_FILE).toPath()));
Expand Down