Error on testcontainers-java

[Ivan-Veselov]

https://github.com/testcontainers/testcontainers-java

ERROR [org.jetbrains.research.groups.ml_methods.refactoring.detection.DefaultBranchesDetectionTool.detect] - Error occurred during refactoring detection for repository: https://github.com/testcontainers/testcontainers-java.git
java.lang.RuntimeException: org.eclipse.jgit.api.errors.CheckoutConflictException: Checkout conflict with files: 
gradle/wrapper/gradle-wrapper.jar
	at org.refactoringminer.api.RefactoringHandler.handleException(RefactoringHandler.java:50)
	at org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl.detect(GitHistoryRefactoringMinerImpl.java:102)
	at org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl.detectAll(GitHistoryRefactoringMinerImpl.java:280)
	at org.jetbrains.research.groups.ml_methods.refactoring.detection.RMiner.detect(RMiner.java:52)
	at org.jetbrains.research.groups.ml_methods.refactoring.detection.DefaultBranchesDetectionTool.detect(DefaultBranchesDetectionTool.java:43)
	at org.jetbrains.research.groups.ml_methods.refactoring.detection.RefactoringDetectionApplication.run(RefactoringDetectionApplication.java:63)
	at org.jetbrains.research.groups.ml_methods.refactoring.detection.RefactoringDetectionApplication.main(RefactoringDetectionApplication.java:23)
Caused by: org.eclipse.jgit.api.errors.CheckoutConflictException: Checkout conflict with files: 
gradle/wrapper/gradle-wrapper.jar
	at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:276)
	at org.refactoringminer.util.GitServiceImpl.checkout(GitServiceImpl.java:120)
	at org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl.detectRefactorings(GitHistoryRefactoringMinerImpl.java:130)
	at org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl.detect(GitHistoryRefactoringMinerImpl.java:97)
	... 5 more
Caused by: org.eclipse.jgit.errors.CheckoutConflictException: Checkout conflict with files: 
gradle/wrapper/gradle-wrapper.jar
	at org.eclipse.jgit.dircache.DirCacheCheckout.doCheckout(DirCacheCheckout.java:467)
	at org.eclipse.jgit.dircache.DirCacheCheckout.checkout(DirCacheCheckout.java:449)
	at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:272)
	... 8 more

[Ivan-Veselov]

Problem 1: RefactoringHandler in RMiner.java should override handleException to log exception occurred during commit processing and skip this commit. Currently in case of a commit failure the whole session is stopped.

[Ivan-Veselov]

Problem 2: cloneIfNotExists uses old repository from a previous run. For us it's better to clone repository from scratch, us we don't plan to process one repository very often.
In my case old repository had a checkout conflict from a previous run and it was impossible to reproduce error without manually deleting this project from /tmp directory.

[Ivan-Veselov]

The actual error happens during checkout on testcontainers/testcontainers-java@fe62ccf

gradle/wrapper/gradle-wrapper.jar becomes modified and does not allow to checkout on another commit.

[Ivan-Veselov]

Probably it's somehow connected with .gitattributes file. May be git tries to replace EOLs in .jar file.