Build #2

Build: #2 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Check import p a e to structure(examples/ alpha fold/ a f- q5 v s l9- f1-model v4.pdb, examples/ alpha fold/ a f- q5 v s l9- f1-predicted aligned error v4 cmp.json): Test case result

The below summarizes the result of the test "Check import p a e to structure(examples/ alpha fold/ a f- q5 v s l9- f1-model v4.pdb, examples/ alpha fold/ a f- q5 v s l9- f1-predicted aligned error v4 cmp.json)" in build 2 of Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests. View test case history
Description
Check import p a e to structure(examples/ alpha fold/ a f- q5 v s l9- f1-model v4.pdb, examples/ alpha fold/ a f- q5 v s l9- f1-predicted aligned error v4 cmp.json)
Test class
Gradle suite > Gradle test > jalview.ws.dbsources.EBIAlphaFoldTest
Method
checkImportPAEToStructure(examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb, examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json)
Duration
< 1 sec
Status
Failed (New Failure)

Error Log

Classname: java.lang.AssertionError
Message: Exception importing paefile 'examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json'
Stacktrace:
java.lang.AssertionError: Exception importing paefile 'examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json'
	at org.testng.Assert.fail(Assert.java:83)
	at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rp7(EBIAlphaFoldTest.java:91)
	at jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure(EBIAlphaFoldTest.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
	at org.testng.TestRunner.privateRun(TestRunner.java:771)
	at org.testng.TestRunner.run(TestRunner.java:621)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
	at org.testng.SuiteRunner.run(SuiteRunner.java:259)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
	at org.testng.TestNG.run(TestNG.java:1009)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at com.sun.proxy.$Proxy2.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:133)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: java.io.IOException: Stream Closed
	at java.base/java.io.FileInputStream.readBytes(Native Method)
	at java.base/java.io.FileInputStream.read(FileInputStream.java:279)
	at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:252)
	at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:292)
	at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:351)
	at java.base/java.io.FilterInputStream.read(FilterInputStream.java:107)
	at jalview.util.Platform.isGzipStream(Platform.java:602)
	at jalview.util.Platform.checkForGzipStream(Platform.java:644)
	at jalview.util.Platform.parseJSON(Platform.java:534)
	at jalview.ws.dbsources.EBIAlfaFold.parseJSONtoPAEContactMatrix(EBIAlfaFold.java:570)
	at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:605)
	at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:594)
	at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rp7(EBIAlphaFoldTest.java:85)
	... 43 more