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Add QuietTestWrapper to suppress excessive test output that exceeds CI 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.
1 parent 12fa23d commit 39b18c7

5 files changed

Lines changed: 73 additions & 61 deletions

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‎src/test/java/htsjdk/samtools/cram/build/ContainerFactoryTest.java‎

Lines changed: 31 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
55
import htsjdk.samtools.SAMRecordQueryNameComparator;
66
import htsjdk.samtools.cram.ref.ReferenceContext;
77
import htsjdk.samtools.cram.structure.*;
8+
import htsjdk.samtools.util.QuietTestWrapper;
89
import org.testng.Assert;
910
import org.testng.annotations.DataProvider;
1011
import org.testng.annotations.Test;
@@ -18,13 +19,6 @@
1819

1920
public class ContainerFactoryTest extends HtsjdkTest {
2021

21-
// wrapper class to suppress expansion/serialization of lists of records during test execution
22-
private static class RecordSupplier implements Supplier<List<SAMRecord>> {
23-
final List<SAMRecord> samRecords;
24-
public RecordSupplier(final List<SAMRecord> samRecords) { this.samRecords = samRecords; }
25-
@Override public List<SAMRecord> get() { return samRecords; }
26-
}
27-
2822
@DataProvider(name="singleContainerSliceDistribution")
2923
private Object[][] getSingleContainerSliceDistribution() {
3024
final int RECORDS_PER_SLICE = 100;
@@ -33,59 +27,59 @@ private Object[][] getSingleContainerSliceDistribution() {
3327
// expected record count/slice, expected slice refContexts,
3428
{
3529
// 1 full single-ref slice with 1 rec
36-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(1, 0)),
30+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(1, 0)),
3731
RECORDS_PER_SLICE, 1,
3832
new ReferenceContext(0),
3933
1, Arrays.asList(1), Arrays.asList(new ReferenceContext(0))
4034
},
4135
{
4236
// 1 full single-ref slice with 1 rec, but allow > 1 slices/container
43-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(1, 0)),
37+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(1, 0)),
4438
RECORDS_PER_SLICE, 2,
4539
new ReferenceContext(0),
4640
1, Arrays.asList(1), Arrays.asList(new ReferenceContext(0))
4741
},
4842
{
4943
// 1 full single-ref slice with RECORDS_PER_SLICE - 1 records
50-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE - 1, 0)),
44+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE - 1, 0)),
5145
RECORDS_PER_SLICE, 1,
5246
new ReferenceContext(0),
5347
1, Arrays.asList(RECORDS_PER_SLICE - 1), Arrays.asList(new ReferenceContext(0))
5448
},
5549
{
5650
// 1 full single-ref slice with RECORDS_PER_SLICE records
57-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE, 0)),
51+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE, 0)),
5852
RECORDS_PER_SLICE, 1,
5953
new ReferenceContext(0),
6054
1, Arrays.asList(RECORDS_PER_SLICE), Arrays.asList(new ReferenceContext(0))
6155
},
6256
{
6357
// 2 single-ref slices, one with RECORDS_PER_SLICE records, one with 1 record
64-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE + 1, 0)),
58+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE + 1, 0)),
6559
RECORDS_PER_SLICE, 2,
6660
new ReferenceContext(0),
6761
2, Arrays.asList(RECORDS_PER_SLICE, 1),
6862
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0))
6963
},
7064
{
7165
// 2 single-ref slices, one with RECORDS_PER_SLICE records, one with RECORDS_PER_SLICE - 1
72-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE * 2) - 1, 0)),
66+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE * 2) - 1, 0)),
7367
RECORDS_PER_SLICE, 2,
7468
new ReferenceContext(0),
7569
2, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE - 1),
7670
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0))
7771
},
7872
{
7973
// 2 full single-ref slices, each with RECORDS_PER_SLICE records
80-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0)),
74+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0)),
8175
RECORDS_PER_SLICE, 2,
8276
new ReferenceContext(0),
8377
2, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE),
8478
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0))
8579
},
8680
{
8781
// 3 single-ref slices, two with RECORDS_PER_SLICE records, one with 1 record
88-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE * 2) + 1, 0)),
82+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE * 2) + 1, 0)),
8983
RECORDS_PER_SLICE, 3,
9084
new ReferenceContext(0),
9185
3, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE, 1),
@@ -96,7 +90,7 @@ private Object[][] getSingleContainerSliceDistribution() {
9690
},
9791
{
9892
// 3 full single-ref slices, each with RECORDS_PER_SLICE records
99-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 3, 0)),
93+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 3, 0)),
10094
RECORDS_PER_SLICE, 3,
10195
new ReferenceContext(0),
10296
3, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE, RECORDS_PER_SLICE),
@@ -106,51 +100,51 @@ private Object[][] getSingleContainerSliceDistribution() {
106100
// now repeat the tests, but using unmapped records
107101
{
108102
// 1 full single-ref (unmapped) slice with 1 rec
109-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(1)),
103+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(1)),
110104
RECORDS_PER_SLICE, 1,
111105
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
112106
1, Arrays.asList(1), Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
113107
},
114108
{
115109
// 1 full single-ref (unmapped) slice with 1 rec, but allow > 1 slices/container
116-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(1)),
110+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(1)),
117111
RECORDS_PER_SLICE, 2,
118112
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
119113
1, Arrays.asList(1), Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
120114
},
121115
{
122116
// 1 full single-ref (unmapped) slice with RECORDS_PER_SLICE - 1 records
123-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE - 1)),
117+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE - 1)),
124118
RECORDS_PER_SLICE, 1,
125119
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
126120
1, Arrays.asList(RECORDS_PER_SLICE - 1), Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
127121
},
128122
{
129123
// 1 full single-ref (unmapped) slice with RECORDS_PER_SLICE records
130-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE)),
124+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE)),
131125
RECORDS_PER_SLICE, 1,
132126
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
133127
1, Arrays.asList(RECORDS_PER_SLICE), Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
134128
},
135129
{
136130
// 2 single-ref (unmapped) slices, one with RECORDS_PER_SLICE records, one with 1 record
137-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE + 1)),
131+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE + 1)),
138132
RECORDS_PER_SLICE, 2,
139133
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
140134
2, Arrays.asList(RECORDS_PER_SLICE, 1),
141135
Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT, ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
142136
},
143137
{
144138
// 2 full single-ref (unmapped) slices, each with RECORDS_PER_SLICE records
145-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE * 2)),
139+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE * 2)),
146140
RECORDS_PER_SLICE, 2,
147141
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
148142
2, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE),
149143
Arrays.asList(ReferenceContext.UNMAPPED_UNPLACED_CONTEXT, ReferenceContext.UNMAPPED_UNPLACED_CONTEXT)
150144
},
151145
{
152146
// 3 full single-ref (unmapped) slices, each with RECORDS_PER_SLICE records
153-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE * 3)),
147+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE * 3)),
154148
RECORDS_PER_SLICE, 3,
155149
ReferenceContext.UNMAPPED_UNPLACED_CONTEXT,
156150
3, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE, RECORDS_PER_SLICE),
@@ -165,7 +159,7 @@ private Object[][] getSingleContainerSliceDistribution() {
165159
// reference context would be more correctly called a "placed" reference context
166160
{
167161
// 1 full single-ref mapped slice with RECORDS_PER_SLICE records
168-
new RecordSupplier(Stream.of(
162+
new QuietTestWrapper<>(Stream.of(
169163
Collections.singletonList(CRAMStructureTestHelper.createSAMRecordUnmappedPlaced(0, 1)),
170164
CRAMStructureTestHelper.createSAMRecordsMapped((RECORDS_PER_SLICE / 2) - 2, 0),
171165
Collections.singletonList(CRAMStructureTestHelper.createSAMRecordUnmappedPlaced(0, 1)))
@@ -179,15 +173,15 @@ private Object[][] getSingleContainerSliceDistribution() {
179173
// now queryname sorted
180174
{
181175
// 1 full single-ref slice with RECORDS_PER_SLICE-1 records
182-
new RecordSupplier(CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE - 1,0)),
176+
new QuietTestWrapper<>(CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE - 1,0)),
183177
RECORDS_PER_SLICE, 1,
184178
new ReferenceContext(0),
185179
1, Arrays.asList(RECORDS_PER_SLICE - 1),
186180
Arrays.asList(new ReferenceContext(0))
187181
},
188182
{
189183
// 2 full single-ref slices, one with with RECORDS_PER_SLICE records and one record
190-
new RecordSupplier(CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE + 1,0)),
184+
new QuietTestWrapper<>(CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE + 1,0)),
191185
RECORDS_PER_SLICE, 2,
192186
new ReferenceContext(0),
193187
2, Arrays.asList(RECORDS_PER_SLICE, 1),
@@ -196,7 +190,7 @@ private Object[][] getSingleContainerSliceDistribution() {
196190
{
197191
// use a small number of records from multiple (not coordinate-ordered) reference contexts to
198192
// force creation of a multi-ref container
199-
new RecordSupplier(Stream.of(
193+
new QuietTestWrapper<>(Stream.of(
200194
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(2,1),
201195
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(2,0),
202196
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(2,1))
@@ -214,7 +208,7 @@ private Object[][] getSingleContainerSliceDistribution() {
214208

215209
@Test(dataProvider = "singleContainerSliceDistribution")
216210
public void testSingleContainerSliceDistribution(
217-
final Supplier<List<SAMRecord>> samRecordSupplier,
211+
final QuietTestWrapper<List<SAMRecord>> samRecordSupplier,
218212
final int readsPerSlice,
219213
final int slicesPerContainer,
220214
final ReferenceContext expectedContainerReferenceContext,
@@ -257,21 +251,21 @@ private Object[][] getMultipleContainerSliceDistribution() {
257251
// expected slices per container
258252
{
259253
// this generates two containers since it has two containers worth of records mapped to a single ref
260-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0)),
254+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0)),
261255
RECORDS_PER_SLICE, 1,
262256
2, Arrays.asList(RECORDS_PER_SLICE, RECORDS_PER_SLICE),
263257
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0)),
264258
Arrays.asList(1, 1)
265259
},
266260
{
267-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 3 + 1, 0)),
261+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 3 + 1, 0)),
268262
RECORDS_PER_SLICE, 2,
269263
2, Arrays.asList(RECORDS_PER_SLICE * 2, RECORDS_PER_SLICE+ 1),
270264
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0)),
271265
Arrays.asList(2, 2)
272266
},
273267
{
274-
new RecordSupplier(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 4, 0)),
268+
new QuietTestWrapper<>(CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 4, 0)),
275269
RECORDS_PER_SLICE, 2,
276270
2, Arrays.asList(RECORDS_PER_SLICE * 2, RECORDS_PER_SLICE * 2),
277271
Arrays.asList(new ReferenceContext(0), new ReferenceContext(0)),
@@ -280,7 +274,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
280274
{
281275
// this generates one container because although it has records mapped to two different reference
282276
// contigs, there aren't enough records to reach the minimum single ref threshold
283-
new RecordSupplier(Stream.of(
277+
new QuietTestWrapper<>(Stream.of(
284278
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE - 1, 0),
285279
CRAMStructureTestHelper.createSAMRecordsMapped(1, 1))
286280
.flatMap(List::stream)
@@ -293,7 +287,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
293287
{
294288
// this generates one container because it has some mapped (but not enough to reach the
295289
// minimum single ref threshold), and one unmapped
296-
new RecordSupplier(Stream.of(
290+
new QuietTestWrapper<>(Stream.of(
297291
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE - 1, 0),
298292
CRAMStructureTestHelper.createSAMRecordsUnmapped(1))
299293
.flatMap(List::stream)
@@ -305,7 +299,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
305299
},
306300
{
307301
// this generates two containers since it has some mapped and one unmapped
308-
new RecordSupplier(Stream.of(
302+
new QuietTestWrapper<>(Stream.of(
309303
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE * 2, 0),
310304
CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE))
311305
.flatMap(List::stream)
@@ -318,7 +312,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
318312
{
319313
// this generates two containers since it has some mapped, but not enough to emit a single
320314
// ref container, and one unmapped, which goes into a second container
321-
new RecordSupplier(Stream.of(
315+
new QuietTestWrapper<>(Stream.of(
322316
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE / 2, 0),
323317
CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE))
324318
.flatMap(List::stream)
@@ -334,7 +328,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
334328
// even though we allow 2 slices/container, this generates two containers since it has
335329
// some mapped and one unmapped, and we won't emit a second single-ref slice into the
336330
// first container once we've emitted the multi-ref slice!
337-
new RecordSupplier(Stream.of(
331+
new QuietTestWrapper<>(Stream.of(
338332
CRAMStructureTestHelper.createSAMRecordsMapped(RECORDS_PER_SLICE / 2, 0),
339333
CRAMStructureTestHelper.createSAMRecordsUnmapped(RECORDS_PER_SLICE))
340334
.flatMap(List::stream)
@@ -353,7 +347,7 @@ private Object[][] getMultipleContainerSliceDistribution() {
353347
// use records from multiple (not coordinate-ordered) reference contexts to
354348
// force creation of one multi-ref (after name sorting, the first container has a mix of
355349
// ref 0 and ref 1), and one single ref container
356-
new RecordSupplier(Stream.of(
350+
new QuietTestWrapper<>(Stream.of(
357351
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE/2,1),
358352
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE/2,0),
359353
CRAMStructureTestHelper.createQueryNameSortedSAMRecords(RECORDS_PER_SLICE,1))

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