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test: tryWaitRepeat throws InterruptedException
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* use tryWaitRepeat in TestExportImports
* no longer ignore some tests
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@bogovicj
bogovicj committed Oct 9, 2024
1 parent af3c9da commit b5006be
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Showing 3 changed files with 95 additions and 42 deletions.
98 changes: 73 additions & 25 deletions src/test/java/org/janelia/saalfeldlab/n5/TestExportImports.java
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,6 @@ public void testEmptyMeta() throws InterruptedException
}

@Test
@Ignore // TODO intermittent failures on GH actions
public void test4dN5v()
{
final int nChannels = 3;
Expand All @@ -121,7 +120,19 @@ public void test4dN5v()
for( int i = 0; i < nChannels; i++)
{
final String n5PathAndDataset = String.format("%s/%s/c%d/s0", n5RootPath, dataset, i);
final List< ImagePlus > impList = reader.process( n5PathAndDataset, false );

final Optional<List<ImagePlus>> impListOpt = TestRunners.tryWaitRepeat(() -> {
return reader.process(n5PathAndDataset, false);
});

List<ImagePlus> impList;
if (impListOpt.isPresent()) {
impList = impListOpt.get();
} else {
System.err.println(String.format("Skipping test for [ %s : %s ] due to intermittent error ", n5RootPath, dataset));
return;
}

Assert.assertEquals("n5v load channel", 1, impList.size());
Assert.assertTrue("n5v channel equals", equalChannel(imp, i, impList.get(0)));
}
Expand All @@ -136,7 +147,6 @@ public void test4dN5v()
}

@Test
@Ignore // TODO intermittent failures on GH actions
public void testReadWriteParse() throws InterruptedException
{
final HashMap<String,String> typeToExtension = new HashMap<>();
Expand Down Expand Up @@ -281,6 +291,7 @@ public static void singleReadWriteParseTest(

// wait
writer.getExecutorService().awaitTermination(1000, TimeUnit.MILLISECONDS);

readParseTest( imp, outputPath, dataset, blockSizeString, metadataType, compressionType, testMeta, testData, 5);
deleteContainer(outputPath);
}
Expand All @@ -294,7 +305,7 @@ private static void readParseTest(
final String compressionType,
final boolean testMeta,
final boolean testData,
final int nTries) {
final int nTries) throws InterruptedException {

final String readerDataset;
if (metadataType.equals(N5Importer.MetadataN5ViewerKey) || (metadataType.equals(N5Importer.MetadataN5CosemKey) && imp.getNChannels() > 1))
Expand Down Expand Up @@ -372,7 +383,6 @@ public void testRgb() throws InterruptedException
*
*/
@Test
@Ignore // TODO intermittent failures on GH actions
public void testMultiChannel()
{
for( final String suffix : new String[] { ".h5", ".n5", ".zarr" })
Expand All @@ -389,8 +399,7 @@ public void testMultiChannel()
}

@Test
@Ignore // TODO intermittent failures on GH actions
public void testOverwrite() {
public void testOverwrite() throws InterruptedException {

final String n5Root = baseDir + "/overwriteTest.n5";
final String dataset = "dataset";
Expand All @@ -410,33 +419,72 @@ public void testOverwrite() {
writer.setOverwrite(true);
writer.run();

final N5Writer n5 = new N5FSWriter(n5Root);
assertTrue(n5.datasetExists(dataset));
try (final N5Writer n5 = new N5FSWriter(n5Root)) {

assertArrayEquals("size orig", szBig, n5.getDatasetAttributes(dataset).getDimensions());
Optional<DatasetAttributes> dsetAttrsOpt = TestRunners.tryWaitRepeat(() -> {
return n5.getDatasetAttributes(dataset);
});

final N5ScalePyramidExporter writerNoOverride = new N5ScalePyramidExporter();
writerNoOverride.setOptions(impSmall, n5Root, dataset, N5ScalePyramidExporter.AUTO_FORMAT, blockSizeString, false,
N5ScalePyramidExporter.DOWN_SAMPLE, metadataType, compressionString);
writerNoOverride.setOverwrite(false);
writerNoOverride.run();
DatasetAttributes dsetAttrs;
if (dsetAttrsOpt.isPresent()) {
dsetAttrs = dsetAttrsOpt.get();
assertArrayEquals("size orig", szBig, dsetAttrs.getDimensions());
} else {
System.err.println(String.format("Skipping test for [ %s : %s ] due to intermittent error ", n5Root, dataset));
n5.remove();
n5.close();
return;
}
dsetAttrsOpt = Optional.empty();

assertArrayEquals("size after no overwrite", szBig, n5.getDatasetAttributes(dataset).getDimensions());
final N5ScalePyramidExporter writerNoOverride = new N5ScalePyramidExporter();
writerNoOverride.setOptions(impSmall, n5Root, dataset, N5ScalePyramidExporter.AUTO_FORMAT, blockSizeString, false,
N5ScalePyramidExporter.DOWN_SAMPLE, metadataType, compressionString);
writerNoOverride.setOverwrite(false);
writerNoOverride.run();

dsetAttrsOpt = TestRunners.tryWaitRepeat(() -> {
return n5.getDatasetAttributes(dataset);
});

if (dsetAttrsOpt.isPresent()) {
dsetAttrs = dsetAttrsOpt.get();
assertArrayEquals("size after no overwrite", szBig, dsetAttrs.getDimensions());
} else {
System.err.println(String.format("Skipping test for [ %s : %s ] due to intermittent error ", n5Root, dataset));
n5.remove();
n5.close();
return;
}
dsetAttrsOpt = Optional.empty();

final N5ScalePyramidExporter writerOverride = new N5ScalePyramidExporter();
writerOverride.setOptions(impSmall, n5Root, dataset, N5ScalePyramidExporter.AUTO_FORMAT, blockSizeString, false,
N5ScalePyramidExporter.DOWN_SAMPLE, metadataType, compressionString);
writerOverride.setOverwrite(true);
writerOverride.run();
final N5ScalePyramidExporter writerOverride = new N5ScalePyramidExporter();
writerOverride.setOptions(impSmall, n5Root, dataset, N5ScalePyramidExporter.AUTO_FORMAT, blockSizeString, false,
N5ScalePyramidExporter.DOWN_SAMPLE, metadataType, compressionString);
writerOverride.setOverwrite(true);
writerOverride.run();

dsetAttrsOpt = TestRunners.tryWaitRepeat(() -> {
return n5.getDatasetAttributes(dataset);
});

if (dsetAttrsOpt.isPresent()) {
dsetAttrs = dsetAttrsOpt.get();
assertArrayEquals("size after overwrite", szSmall, dsetAttrs.getDimensions());
} else {
System.err.println(String.format("Skipping test for [ %s : %s ] due to intermittent error ", n5Root, dataset));
n5.remove();
n5.close();
return;
}

assertArrayEquals("size after overwrite", szSmall, n5.getDatasetAttributes(dataset).getDimensions());
n5.remove();
n5.close();
}

n5.remove();
n5.close();
}

@Test
@Ignore // TODO intermittent failures on GH actions
public void testFormatOptions() {

final String n5Root = baseDir + "/root_of_some_container";
Expand Down
22 changes: 10 additions & 12 deletions src/test/java/org/janelia/saalfeldlab/n5/TestRunners.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,17 +5,17 @@

public class TestRunners {

public static <T> Optional<T> tryWaitRepeat(Supplier<T> supplier) {
public static <T> Optional<T> tryWaitRepeat(Supplier<T> supplier) throws InterruptedException {

return tryWaitRepeat(supplier, 5, 50, 2);
}

public static <T> Optional<T> tryWaitRepeat(Supplier<T> supplier, int nTries) {
public static <T> Optional<T> tryWaitRepeat(Supplier<T> supplier, int nTries) throws InterruptedException {

return tryWaitRepeat(supplier, nTries, 50, 2);
}

public static <T> Optional<T> tryWaitRepeat(Supplier<T> supplier, int nTries, long waitTimeMillis) {
public static <T> Optional<T> tryWaitRepeat(Supplier<T> supplier, int nTries, long waitTimeMillis) throws InterruptedException {

return tryWaitRepeat(supplier, nTries, waitTimeMillis, 2);
}
Expand All @@ -37,13 +37,14 @@ public static <T> Optional<T> tryWaitRepeat(Supplier<T> supplier, int nTries, lo
* @return an {@link Optional} containing the result from the supplier if a non-null result is returned
* before the maximum number of tries, or an empty {@code Optional} if all attempts fail or
* return null
* @throws InterruptedException thrown if interrupted while waiting
*/
public static <T> Optional<T> tryWaitRepeat(
final Supplier<T> supplier,
final int nTries,
final long initialWaitTimeMillis,
final int waitTimeMultiplier ) {
final Supplier<T> supplier,
final int nTries,
final long initialWaitTimeMillis,
final int waitTimeMultiplier) throws InterruptedException {

int i = 0;
long waitTime = initialWaitTimeMillis;
while (i < nTries) {
Expand All @@ -57,10 +58,7 @@ public static <T> Optional<T> tryWaitRepeat(
return Optional.of(result);
} catch (RuntimeException e) {}

try {
Thread.sleep(waitTime);
} catch (InterruptedException e) {}

Thread.sleep(waitTime);
waitTime *= waitTimeMultiplier;
i++;
}
Expand Down
17 changes: 12 additions & 5 deletions src/test/java/org/janelia/saalfeldlab/n5/metadata/MetadataTests.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ public static void setUp() throws IOException {
}

@Test
public void testCosemMetadataMultiscale() {
public void testCosemMetadataMultiscale() throws InterruptedException {

final N5MetadataParser<?>[] parsers = new N5MetadataParser[]{new N5CosemMetadataParser()};
final N5MetadataParser<?>[] grpparsers = new N5MetadataParser[]{new N5CosemMultiScaleMetadata.CosemMultiScaleParser()};
Expand Down Expand Up @@ -85,7 +85,7 @@ public void testCosemMetadataMultiscale() {
}

@Test
public void testCosemMetadata() {
public void testCosemMetadata() throws InterruptedException {

final double eps = 1e-6;

Expand All @@ -96,7 +96,12 @@ public void testCosemMetadata() {

TestRunners.tryWaitRepeat(() -> {
try {
return discoverer.discoverAndParseRecursive("/");
N5TreeNode node = discoverer.discoverAndParseRecursive("/");
if( node.childrenList().size() < 3 )
return null;
else
return node;

} catch (IOException e) {
return null; // so that the runner tries again
}
Expand Down Expand Up @@ -125,7 +130,7 @@ public void testCosemMetadata() {
}

@Test
public void testN5ViewerMetadata() {
public void testN5ViewerMetadata() throws InterruptedException {

final double eps = 1e-6;

Expand All @@ -147,9 +152,11 @@ public void testN5ViewerMetadata() {
List<N5TreeNode> childrenWithMetadata = n5root.childrenList().stream()
.filter(x -> Objects.nonNull(x.getMetadata()))
.collect(Collectors.toList());

long childrenNoMetadataCount = n5root.childrenList().stream()
.filter(x -> Objects.isNull(x.getMetadata()))
.count();

Assert.assertEquals("discovery node count with single scale metadata", 4, childrenWithMetadata.size());
Assert.assertEquals("discovery node count without single scale metadata", 1, childrenNoMetadataCount);

Expand Down Expand Up @@ -182,7 +189,7 @@ public void testN5ViewerMetadata() {
}

@Test
public void testGenericMetadata() {
public void testGenericMetadata() throws InterruptedException {

final double eps = 1e-6;

Expand Down

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