Class EBIAlphaFoldTest

Class	Tests	Fail	Error	Time (secs)	% Tests Success
EBIAlphaFoldTest	1616	22	00	12.396	0.87587.5%

Tests	Started	Status	Time (secs)	Message
EBIAlphaFoldTest.testImportPAEAndStructureForMultiChainSeqsEBIAlphaFoldTest.testImportPAEAndStructureForMultiChainSeqs	17830842592593 Jul 14:10:59	3FAIL	0.5330.533	Couln't create a mapping for this matrix. Couln't create a mapping for this matrix. java.lang.Error: Couln't create a mapping for this matrix. at jalview.ws.datamodel.alphafold.MappableContactMatrix.liftOver(MappableContactMatrix.java:189) at jalview.ws.datamodel.alphafold.MappableContactMatrix.liftOver(MappableContactMatrix.java:38) at mc_view.PDBChain.transferResidueAnnotation(PDBChain.java:715) at jalview.structure.StructureSelectionManager.getNWMappings(StructureSelectionManager.java:1014) at jalview.structure.StructureSelectionManager.computeMapping(StructureSelectionManager.java:749) at jalview.ws.dbsources.EBIAlphaFoldTest.testImportPAEAndStructureForMultiChainSeqs(EBIAlphaFoldTest.java:194) 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)
EBIAlphaFoldTest.checkImportPAEToStructureEBIAlphaFoldTest.checkImportPAEToStructure	17830842567853 Jul 14:10:56	3FAIL	0.5620.562	Exception importing paefile 'examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json' Exception importing paefile 'examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json' 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.checkImportPAEToStructure(EBIAlphaFoldTest.java:96) 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:625) at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:660) at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:649) at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rrg(EBIAlphaFoldTest.java:90) ... 43 more
EBIAlphaFoldTest.checkImportPAEToStructureEBIAlphaFoldTest.checkImportPAEToStructure	17830842553143 Jul 14:10:55	1PASS	0.9260.926
EBIAlphaFoldTest.checkImportPAEForStructureEBIAlphaFoldTest.checkImportPAEForStructure	17830842541953 Jul 14:10:54	1PASS	1.1061.106
EBIAlphaFoldTest.checkPAEimportEBIAlphaFoldTest.checkPAEimport	17830842586643 Jul 14:10:58	1PASS	0.5340.534
EBIAlphaFoldTest.checkImportPAEForStructureEBIAlphaFoldTest.checkImportPAEForStructure	17830842525083 Jul 14:10:52	1PASS	1.6861.686
EBIAlphaFoldTest.checkPAEimportEBIAlphaFoldTest.checkPAEimport	17830842591993 Jul 14:10:59	1PASS	0.0590.059
EBIAlphaFoldTest.checkPAEimportEBIAlphaFoldTest.checkPAEimport	17830842574233 Jul 14:10:57	1PASS	0.0140.014
EBIAlphaFoldTest.checkPAEimportEBIAlphaFoldTest.checkPAEimport	17830842574383 Jul 14:10:57	1PASS	0.6940.694
EBIAlphaFoldTest.checkImportPAEToStructureEBIAlphaFoldTest.checkImportPAEToStructure	17830842573483 Jul 14:10:57	1PASS	0.0740.074
EBIAlphaFoldTest.checkImportPAEForStructureEBIAlphaFoldTest.checkImportPAEForStructure	17830842505503 Jul 14:10:50	1PASS	1.9581.958
EBIAlphaFoldTest.checkImportPAEToStructureEBIAlphaFoldTest.checkImportPAEToStructure	17830842562413 Jul 14:10:56	1PASS	0.5440.544
EBIAlphaFoldTest.checkImportPAEForStructureEBIAlphaFoldTest.checkImportPAEForStructure	17830842473803 Jul 14:10:47	1PASS	0.530.53
EBIAlphaFoldTest.checkImportPAEForStructureEBIAlphaFoldTest.checkImportPAEForStructure	17830842479113 Jul 14:10:47	1PASS	2.6382.638
EBIAlphaFoldTest.checkPAEimportEBIAlphaFoldTest.checkPAEimport	17830842581353 Jul 14:10:58	1PASS	0.5280.528
EBIAlphaFoldTest.checkImportPAEToStructureEBIAlphaFoldTest.checkImportPAEToStructure	17830842553033 Jul 14:10:55	1PASS	0.010.01

Coverage Report

Class EBIAlphaFoldTest