[IGBF-3422] Investigate Test Failure that is occurring in QuickloadUtilsTest class. - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 10.0.0 Major Release
Labels:
None

Story Points:
2
Epic Link:
Improve IGB for developers
Sprint:
Summer 8 2023 Aug 21

Description

when running IGB without skipping tests, one of the test case is failing in QuickloadUtilsTest
class.
The absolute file path is appeared twice (see below) in the path, and therefore it is not matching with the expected value. Hence, the test case fails

Path

/C:/Users/lorainelab/Desktop/2805/relative%20space/A_thaliana_Apr_2008/Users/lorainelab/Desktop/2805/relative%20space/E_unicornis_Jul_2043/down%20stream/E_unicornis_Jul_2043_down.bed.g

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Issue Links

relates to

IGBF-3379 Edit SCR annotations to use R6 instead of R5 syntax and observe the effects

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Kaushik Gopu added a comment - 28/Aug/23 5:23 PM - edited

After reviewing the code of QuickloadUtilsTest, I found the below issue:

getURI() method takes three parameters filename, genome version, URI, and constructs absolute path by concatenating these parameters.
In the test function, Instead of passing the filename, the entire path is being passed. For this reason, a part of the path is appearing twice in resultant path which leads to failure of the test case.

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Kaushik Gopu added a comment - 28/Aug/23 5:23 PM - edited After reviewing the code of QuickloadUtilsTest, I found the below issue: getURI() method takes three parameters filename, genome version, URI, and constructs absolute path by concatenating these parameters. In the test function, Instead of passing the filename, the entire path is being passed. For this reason, a part of the path is appearing twice in resultant path which leads to failure of the test case.

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Kaushik Gopu added a comment - 29/Aug/23 3:41 PM

fixed the issue, and now IGB should able to run without failing any test cases.
tested in windows, and no test case failures are encountered while compiling.
moving to first level review for testing.
branch to be pulled for testing.

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Kaushik Gopu added a comment - 29/Aug/23 3:41 PM fixed the issue, and now IGB should able to run without failing any test cases. tested in windows, and no test case failures are encountered while compiling. moving to first level review for testing. branch to be pulled for testing.

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Nowlan Freese added a comment - 31/Aug/23 10:41 AM

Tested on Mac using Netbeans debugger. All tests passed correctly.

Ready for pull request to main-JDK8

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Nowlan Freese added a comment - 31/Aug/23 10:41 AM Tested on Mac using Netbeans debugger. All tests passed correctly. Ready for pull request to main-JDK8

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Kaushik Gopu added a comment - 31/Aug/23 12:22 PM

pull request submitted to main-JDK8.

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Kaushik Gopu added a comment - 31/Aug/23 12:22 PM pull request submitted to main-JDK8.

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Ann Loraine added a comment - 01/Sep/23 10:45 AM - edited

To test:

Obtain the code and make sure it can build on a Windows machine.

attn: Karthik Raveendran - please test by running the test cases and checking for errors.

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Ann Loraine added a comment - 01/Sep/23 10:45 AM - edited To test: Obtain the code and make sure it can build on a Windows machine. attn: Karthik Raveendran - please test by running the test cases and checking for errors.

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Karthik Raveendran added a comment - 01/Sep/23 1:52 PM

QuickloadUtilsTest runs without errors.

Note: Another test class in the same module, QuickloadDataProviderTest, is failing 3/5 tests: testassemblyinfo, validateQuickload, validateSupportedGenomeVersions.

java.lang.NullPointerException
	at org.lorainelab.igb.quickload.util.QuickloadUtils.getContextRootKey(QuickloadUtils.java:199)
	at org.lorainelab.igb.quickload.QuickloadDataProvider.getAssemblyInfo(QuickloadDataProvider.java:217)
	at org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest.testAssemblyInfo(QuickloadDataProviderTest.java:64)
	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.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	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.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runner.JUnitCore.run(JUnitCore.java:137)
	at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:69)
	at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38)
	at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11)
	at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35)
	at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:235)
	at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:54)


java.lang.NullPointerException
	at org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest.validateQuickload(QuickloadDataProviderTest.java:82)
	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.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	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.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runner.JUnitCore.run(JUnitCore.java:137)
	at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:69)
	at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38)
	at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11)
	at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35)
	at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:235)
	at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:54)


java.lang.AssertionError
	at org.junit.Assert.fail(Assert.java:87)
	at org.junit.Assert.assertTrue(Assert.java:42)
	at org.junit.Assert.assertTrue(Assert.java:53)
	at org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest.validateSupportedGenomeVersionNames(QuickloadDataProviderTest.java:58)

Closing the issue.

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Karthik Raveendran added a comment - 01/Sep/23 1:52 PM QuickloadUtilsTest runs without errors. Note : Another test class in the same module, QuickloadDataProviderTest, is failing 3/5 tests: testassemblyinfo, validateQuickload, validateSupportedGenomeVersions. java.lang.NullPointerException at org.lorainelab.igb.quickload.util.QuickloadUtils.getContextRootKey(QuickloadUtils.java:199) at org.lorainelab.igb.quickload.QuickloadDataProvider.getAssemblyInfo(QuickloadDataProvider.java:217) at org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest.testAssemblyInfo(QuickloadDataProviderTest.java:64) 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.InvokeMethod.evaluate(InvokeMethod.java:17) at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306) at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100) at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63) 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.runners.ParentRunner$3.evaluate(ParentRunner.java:306) at org.junit.runners.ParentRunner.run(ParentRunner.java:413) at org.junit.runner.JUnitCore.run(JUnitCore.java:137) at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:69) at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38) at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11) at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35) at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:235) at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:54) java.lang.NullPointerException at org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest.validateQuickload(QuickloadDataProviderTest.java:82) 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.InvokeMethod.evaluate(InvokeMethod.java:17) at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306) at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100) at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63) 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.runners.ParentRunner$3.evaluate(ParentRunner.java:306) at org.junit.runners.ParentRunner.run(ParentRunner.java:413) at org.junit.runner.JUnitCore.run(JUnitCore.java:137) at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:69) at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38) at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11) at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35) at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:235) at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:54) java.lang.AssertionError at org.junit.Assert.fail(Assert.java:87) at org.junit.Assert.assertTrue(Assert.java:42) at org.junit.Assert.assertTrue(Assert.java:53) at org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest.validateSupportedGenomeVersionNames(QuickloadDataProviderTest.java:58) Closing the issue.

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Assignee:

Kaushik Gopu

Reporter:

Kaushik Gopu

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Watchers:

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Dates

Created:

28/Aug/23 2:33 PM

Updated:

07/Feb/24 1:51 PM

Resolved:

01/Sep/23 1:53 PM