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Add QuietTestWrapper to suppress excessive test output that exceeds C…
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…I server log output threshold. (#1541)

* Our test output logs were approaching the max size in travis and this reduces test spam to keep them under the threshold.
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@cmnbroad
cmnbroad authored Mar 9, 2021
1 parent 12fa23d commit 39b18c7
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Showing 5 changed files with 73 additions and 61 deletions.
68 changes: 31 additions & 37 deletions src/test/java/htsjdk/samtools/cram/build/ContainerFactoryTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import htsjdk.samtools.SAMRecordQueryNameComparator;
import htsjdk.samtools.cram.ref.ReferenceContext;
import htsjdk.samtools.cram.structure.*;
import htsjdk.samtools.util.QuietTestWrapper;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
Expand All @@ -18,13 +19,6 @@

public class ContainerFactoryTest extends HtsjdkTest {

// wrapper class to suppress expansion/serialization of lists of records during test execution
private static class RecordSupplier implements Supplier<List<SAMRecord>> {
final List<SAMRecord> samRecords;
public RecordSupplier(final List<SAMRecord> samRecords) { this.samRecords = samRecords; }
@Override public List<SAMRecord> get() { return samRecords; }
}

@DataProvider(name="singleContainerSliceDistribution")
private Object[][] getSingleContainerSliceDistribution() {
final int RECORDS_PER_SLICE = 100;
Expand All @@ -33,59 +27,59 @@ private Object[][] getSingleContainerSliceDistribution() {
// expected record count/slice, expected slice refContexts,
{
// 1 full single-ref slice with 1 rec
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(1, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(1, 0)),
RECORDS_PER_SLICE, 1,
new ReferenceContext(0),
1, Arrays.asList(1), Arrays.asList(new ReferenceContext(0))
},
{
// 1 full single-ref slice with 1 rec, but allow > 1 slices/container
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(1, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(1, 0)),
RECORDS_PER_SLICE, 2,
new ReferenceContext(0),
1, Arrays.asList(1), Arrays.asList(new ReferenceContext(0))
},
{
// 1 full single-ref slice with RECORDS_PER_SLICE - 1 records
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE - 1, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE - 1, 0)),
RECORDS_PER_SLICE, 1,
new ReferenceContext(0),
1, Arrays.asList(RECORDS_PER_SLICE - 1), Arrays.asList(new ReferenceContext(0))
},
{
// 1 full single-ref slice with RECORDS_PER_SLICE records
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE, 0)),
RECORDS_PER_SLICE, 1,
new ReferenceContext(0),
1, Arrays.asList(RECORDS_PER_SLICE), Arrays.asList(new ReferenceContext(0))
},
{
// 2 single-ref slices, one with RECORDS_PER_SLICE records, one with 1 record
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE + 1, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE + 1, 0)),
RECORDS_PER_SLICE, 2,
new ReferenceContext(0),
2, Arrays.asList(RECORDS_PER_SLICE, 1),
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0))
},
{
// 2 single-ref slices, one with RECORDS_PER_SLICE records, one with RECORDS_PER_SLICE - 1
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE * 2) - 1, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE * 2) - 1, 0)),
RECORDS_PER_SLICE, 2,
new ReferenceContext(0),
2, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE - 1),
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0))
},
{
// 2 full single-ref slices, each with RECORDS_PER_SLICE records
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0)),
RECORDS_PER_SLICE, 2,
new ReferenceContext(0),
2, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE),
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0))
},
{
// 3 single-ref slices, two with RECORDS_PER_SLICE records, one with 1 record
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE * 2) + 1, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE * 2) + 1, 0)),
RECORDS_PER_SLICE, 3,
new ReferenceContext(0),
3, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE, 1),
Expand All @@ -96,7 +90,7 @@ private Object[][] getSingleContainerSliceDistribution() {
},
{
// 3 full single-ref slices, each with RECORDS_PER_SLICE records
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 3, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 3, 0)),
RECORDS_PER_SLICE, 3,
new ReferenceContext(0),
3, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE, RECORDS_PER_SLICE),
Expand All @@ -106,51 +100,51 @@ private Object[][] getSingleContainerSliceDistribution() {
// now repeat the tests, but using unmapped records
{
// 1 full single-ref (unmapped) slice with 1 rec
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(1)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(1)),
RECORDS_PER_SLICE, 1,
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
1, Arrays.asList(1), Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
},
{
// 1 full single-ref (unmapped) slice with 1 rec, but allow > 1 slices/container
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(1)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(1)),
RECORDS_PER_SLICE, 2,
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
1, Arrays.asList(1), Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
},
{
// 1 full single-ref (unmapped) slice with RECORDS_PER_SLICE - 1 records
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE - 1)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE - 1)),
RECORDS_PER_SLICE, 1,
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
1, Arrays.asList(RECORDS_PER_SLICE - 1), Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
},
{
// 1 full single-ref (unmapped) slice with RECORDS_PER_SLICE records
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE)),
RECORDS_PER_SLICE, 1,
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
1, Arrays.asList(RECORDS_PER_SLICE), Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
},
{
// 2 single-ref (unmapped) slices, one with RECORDS_PER_SLICE records, one with 1 record
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE + 1)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE + 1)),
RECORDS_PER_SLICE, 2,
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
2, Arrays.asList(RECORDS_PER_SLICE, 1),
Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT, ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
},
{
// 2 full single-ref (unmapped) slices, each with RECORDS_PER_SLICE records
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE * 2)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE * 2)),
RECORDS_PER_SLICE, 2,
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
2, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE),
Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT, ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
},
{
// 3 full single-ref (unmapped) slices, each with RECORDS_PER_SLICE records
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE * 3)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE * 3)),
RECORDS_PER_SLICE, 3,
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
3, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE, RECORDS_PER_SLICE),
Expand All @@ -165,7 +159,7 @@ private Object[][] getSingleContainerSliceDistribution() {
// reference context would be more correctly called a "placed" reference context
{
// 1 full single-ref mapped slice with RECORDS_PER_SLICE records
new RecordSupplier(Stream.of(
new QuietTestWrapper<>(Stream.of(
Collections.singletonList(CRAMStructureTestHelper.createSAMRecordUnmappedPlaced(0, 1)),
CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE / 2) - 2, 0),
Collections.singletonList(CRAMStructureTestHelper.createSAMRecordUnmappedPlaced(0, 1)))
Expand All @@ -179,15 +173,15 @@ private Object[][] getSingleContainerSliceDistribution() {
// now queryname sorted
{
// 1 full single-ref slice with RECORDS_PER_SLICE-1 records
new RecordSupplier(CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE - 1,0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE - 1,0)),
RECORDS_PER_SLICE, 1,
new ReferenceContext(0),
1, Arrays.asList(RECORDS_PER_SLICE - 1),
Arrays.asList(new ReferenceContext(0))
},
{
// 2 full single-ref slices, one with with RECORDS_PER_SLICE records and one record
new RecordSupplier(CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE + 1,0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE + 1,0)),
RECORDS_PER_SLICE, 2,
new ReferenceContext(0),
2, Arrays.asList(RECORDS_PER_SLICE, 1),
Expand All @@ -196,7 +190,7 @@ private Object[][] getSingleContainerSliceDistribution() {
{
// use a small number of records from multiple (not coordinate-ordered) reference contexts to
// force creation of a multi-ref container
new RecordSupplier(Stream.of(
new QuietTestWrapper<>(Stream.of(
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(2,1),
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(2,0),
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(2,1))
Expand All @@ -214,7 +208,7 @@ private Object[][] getSingleContainerSliceDistribution() {

@Test(dataProvider = "singleContainerSliceDistribution")
public void testSingleContainerSliceDistribution(
final Supplier<List<SAMRecord>> samRecordSupplier,
final QuietTestWrapper<List<SAMRecord>> samRecordSupplier,
final int readsPerSlice,
final int slicesPerContainer,
final ReferenceContext expectedContainerReferenceContext,
Expand Down Expand Up @@ -257,21 +251,21 @@ private Object[][] getMultipleContainerSliceDistribution() {
// expected slices per container
{
// this generates two containers since it has two containers worth of records mapped to a single ref
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0)),
RECORDS_PER_SLICE, 1,
2, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE),
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0)),
Arrays.asList(1, 1)
},
{
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 3 + 1, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 3 + 1, 0)),
RECORDS_PER_SLICE, 2,
2, Arrays.asList(RECORDS_PER_SLICE * 2, RECORDS_PER_SLICE+ 1),
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0)),
Arrays.asList(2, 2)
},
{
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 4, 0)),
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 4, 0)),
RECORDS_PER_SLICE, 2,
2, Arrays.asList(RECORDS_PER_SLICE * 2, RECORDS_PER_SLICE * 2),
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0)),
Expand All @@ -280,7 +274,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
{
// this generates one container because although it has records mapped to two different reference
// contigs, there aren't enough records to reach the minimum single ref threshold
new RecordSupplier(Stream.of(
new QuietTestWrapper<>(Stream.of(
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE - 1, 0),
CRAMStructureTestHelper.createSAMRecordsMapped(1, 1))
.flatMap(List::stream)
Expand All @@ -293,7 +287,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
{
// this generates one container because it has some mapped (but not enough to reach the
// minimum single ref threshold), and one unmapped
new RecordSupplier(Stream.of(
new QuietTestWrapper<>(Stream.of(
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE - 1, 0),
CRAMStructureTestHelper.createSAMRecordsUnmapped(1))
.flatMap(List::stream)
Expand All @@ -305,7 +299,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
},
{
// this generates two containers since it has some mapped and one unmapped
new RecordSupplier(Stream.of(
new QuietTestWrapper<>(Stream.of(
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0),
CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE))
.flatMap(List::stream)
Expand All @@ -318,7 +312,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
{
// this generates two containers since it has some mapped, but not enough to emit a single
// ref container, and one unmapped, which goes into a second container
new RecordSupplier(Stream.of(
new QuietTestWrapper<>(Stream.of(
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE / 2, 0),
CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE))
.flatMap(List::stream)
Expand All @@ -334,7 +328,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
// even though we allow 2 slices/container, this generates two containers since it has
// some mapped and one unmapped, and we won't emit a second single-ref slice into the
// first container once we've emitted the multi-ref slice!
new RecordSupplier(Stream.of(
new QuietTestWrapper<>(Stream.of(
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE / 2, 0),
CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE))
.flatMap(List::stream)
Expand All @@ -353,7 +347,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
// use records from multiple (not coordinate-ordered) reference contexts to
// force creation of one multi-ref (after name sorting, the first container has a mix of
// ref 0 and ref 1), and one single ref container
new RecordSupplier(Stream.of(
new QuietTestWrapper<>(Stream.of(
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE/2,1),
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE/2,0),
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE,1))
Expand Down
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