Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updating google-cloud-nio dependency to 0.122.5 fails unit tests #145

Open
heuermh opened this issue Jan 28, 2021 · 1 comment · May be fixed by #170
Open

Updating google-cloud-nio dependency to 0.122.5 fails unit tests #145

heuermh opened this issue Jan 28, 2021 · 1 comment · May be fixed by #170
Milestone
0.4.0

Comments

@heuermh
Copy link
Contributor

heuermh commented Jan 28, 2021 

$ mvn clean install
...
[ERROR] Tests run: 44, Failures: 0, Errors: 2, Skipped: 0, Time elapsed: 14.806 s <<< FAILURE! - in org.disq_bio.disq.HtsjdkReadsRddTest
[ERROR] testReadAndWrite(gs://genomics-public-data/NA12878.chr20.sample.bam, null, BAM, 131072, true) [11](org.disq_bio.disq.HtsjdkReadsRddTest)  Time elapsed: 0.322 s  <<< ERROR!
java.lang.ExceptionInInitializerError
	at shaded.cloud_nio.com.google.api.services.storage.Storage.<clinit>(Storage.java:44)
	at shaded.cloud_nio.com.google.api.services.storage.Storage$Builder.build(Storage.java:11194)
	at com.google.cloud.storage.spi.v1.HttpStorageRpc.<init>(HttpStorageRpc.java:121)
	at com.google.cloud.storage.StorageOptions$DefaultStorageRpcFactory.create(StorageOptions.java:55)
	at com.google.cloud.storage.StorageOptions$DefaultStorageRpcFactory.create(StorageOptions.java:49)
	at shaded.cloud_nio.com.google.cloud.ServiceOptions.getRpc(ServiceOptions.java:561)
	at com.google.cloud.storage.StorageOptions.getStorageRpcV1(StorageOptions.java:121)
	at com.google.cloud.storage.StorageImpl.<init>(StorageImpl.java:124)
	at com.google.cloud.storage.StorageOptions$DefaultStorageFactory.create(StorageOptions.java:45)
	at com.google.cloud.storage.StorageOptions$DefaultStorageFactory.create(StorageOptions.java:39)
	at shaded.cloud_nio.com.google.cloud.ServiceOptions.getService(ServiceOptions.java:541)
	at com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider.initStorage(CloudStorageFileSystemProvider.java:214)
	at com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider.getPath(CloudStorageFileSystemProvider.java:273)
	at com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider.getPath(CloudStorageFileSystemProvider.java:87)
	at java.base/java.nio.file.Path.of(Path.java:208)
	at java.base/java.nio.file.Paths.get(Paths.java:97)
	at org.disq_bio.disq.impl.file.NioFileSystemWrapper.asPath(NioFileSystemWrapper.java:126)
	at org.disq_bio.disq.impl.file.NioFileSystemWrapper.asPath(NioFileSystemWrapper.java:148)
	at org.disq_bio.disq.impl.file.NioFileSystemWrapper.isDirectory(NioFileSystemWrapper.java:94)
	at org.disq_bio.disq.HtsjdkReadsRddStorage.read(HtsjdkReadsRddStorage.java:148)
	at org.disq_bio.disq.HtsjdkReadsRddStorage.read(HtsjdkReadsRddStorage.java:127)
	at org.disq_bio.disq.HtsjdkReadsRddTest.testReadAndWrite(HtsjdkReadsRddTest.java:135)
	at jdk.internal.reflect.GeneratedMethodAccessor123.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at junitparams.internal.InvokeParameterisedMethod.evaluate(InvokeParameterisedMethod.java:234)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at junitparams.internal.ParameterisedTestMethodRunner.runMethodInvoker(ParameterisedTestMethodRunner.java:47)
	at junitparams.internal.ParameterisedTestMethodRunner.runTestMethod(ParameterisedTestMethodRunner.java:40)
	at junitparams.internal.ParameterisedTestClassRunner.runParameterisedTest(ParameterisedTestClassRunner.java:146)
	at junitparams.JUnitParamsRunner.runChild(JUnitParamsRunner.java:446)
	at junitparams.JUnitParamsRunner.runChild(JUnitParamsRunner.java:393)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365)
	at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273)
	at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
	at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159)
	at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418)
Caused by: java.lang.IllegalStateException: No match found
	at java.base/java.util.regex.Matcher.group(Matcher.java:645)
	at shaded.cloud_nio.com.google.api.client.googleapis.GoogleUtils.<clinit>(GoogleUtils.java:66)
	... 52 more
@heuermh heuermh added this to the 0.4.0 milestone Jan 28, 2021
@heuermh heuermh mentioned this issue Jan 28, 2021
Merged
@heuermh
Copy link
Contributor Author

heuermh commented Feb 22, 2022 •
edited
Loading

Updating to version 0.123.20 results in

[ERROR] Tests run: 44, Failures: 0, Errors: 2, Skipped: 0, Time elapsed: 34.388 s <<< FAILURE! - in org.disq_bio.disq.HtsjdkReadsRddTest
[ERROR] org.disq_bio.disq.HtsjdkReadsRddTest.testReadAndWrite(gs://genomics-public-data/NA12878.chr20.sample.bam, null, BAM, 131072, true) [11]  Time elapsed: 0.006 s  <<< ERROR!
java.lang.Error: Circular loading of installed providers detected
	at java.nio.file.spi.FileSystemProvider.installedProviders(FileSystemProvider.java:161)
	at java.nio.file.Paths.get(Paths.java:141)
	at org.disq_bio.disq.impl.file.NioFileSystemWrapper.asPath(NioFileSystemWrapper.java:126)
	at org.disq_bio.disq.impl.file.NioFileSystemWrapper.asPath(NioFileSystemWrapper.java:148)
	at org.disq_bio.disq.impl.file.NioFileSystemWrapper.isDirectory(NioFileSystemWrapper.java:94)
	at org.disq_bio.disq.HtsjdkReadsRddStorage.read(HtsjdkReadsRddStorage.java:148)
	at org.disq_bio.disq.HtsjdkReadsRddStorage.read(HtsjdkReadsRddStorage.java:127)
	at org.disq_bio.disq.HtsjdkReadsRddTest.testReadAndWrite(HtsjdkReadsRddTest.java:135)

also

[ERROR] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.947 s <<< FAILURE! - in org.disq_bio.disq.HtsjdkReadsRddHdfsTest
[ERROR] org.disq_bio.disq.HtsjdkReadsRddHdfsTest  Time elapsed: 0.941 s  <<< ERROR!
java.util.ServiceConfigurationError: java.nio.file.spi.FileSystemProvider: Provider com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider could not be instantiated
	at java.util.ServiceLoader.fail(ServiceLoader.java:232)
	at java.util.ServiceLoader.access$100(ServiceLoader.java:185)
	at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:384)
	at java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:404)
	at java.util.ServiceLoader$1.next(ServiceLoader.java:480)
	at java.nio.file.spi.FileSystemProvider.loadInstalledProviders(FileSystemProvider.java:119)
	at java.nio.file.spi.FileSystemProvider.access$000(FileSystemProvider.java:77)
	at java.nio.file.spi.FileSystemProvider$1.run(FileSystemProvider.java:169)
	at java.nio.file.spi.FileSystemProvider$1.run(FileSystemProvider.java:166)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.nio.file.spi.FileSystemProvider.installedProviders(FileSystemProvider.java:166)
	at java.nio.file.Paths.get(Paths.java:141)
	at org.disq_bio.disq.HtsjdkReadsRddHdfsTest.setUpBeforeClass(HtsjdkReadsRddHdfsTest.java:58)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:364)
	at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:272)
	at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:237)
	at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:158)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:428)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:562)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:548)
Caused by: java.lang.NoClassDefFoundError: shaded/cloud_nio/com/google/auth/Credentials
	at com.google.cloud.storage.contrib.nio.StorageOptionsUtil.<clinit>(StorageOptionsUtil.java:40)
	at com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider.<clinit>(CloudStorageFileSystemProvider.java:96)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
	at java.lang.Class.newInstance(Class.java:442)
	at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:380)
	... 30 more
Caused by: java.lang.ClassNotFoundException: shaded.cloud_nio.com.google.auth.Credentials
	at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:355)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
	... 38 more

@heuermh heuermh linked a pull request Feb 23, 2022 that will close this issue
Draft
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
0.4.0
Development

Successfully merging a pull request may close this issue.

Update google-cloud-nio dependency version to 0.123.20 heuermh/disq
1 participant
@heuermh