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Fix Achilles Results Directory Issue in Arachne Node API v1.19.1 #530

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@Volpym Volpym commented Oct 2, 2024

This PR addresses an issue encountered when attempting to generate Achilles results using the Arachne Node API (version 1.19.1) Docker image. Initially, the deployment was successful, and the Arachne Node API was able to connect to an OMOP CDM database and import Achilles results. However, when trying to regenerate Achilles results through the Datanode UI, an error was consistently raised indicating that the directory containing the results could not be found.

2024-10-02 09:25:23.368 DEBUG 49 --- [         task-1] c.o.a.d.s.impl.AchillesServiceImpl       : Achilles result directory: /tmp/achilles_1431357100599896950
2024-10-02 09:25:23.587 DEBUG 49 --- [         task-1] c.o.a.d.s.impl.AchillesServiceImpl       : Pulling image: valepopoulos/achilles-1.7.0:latest
2024-10-02 09:25:25.761 DEBUG 49 --- [         task-1] c.o.a.d.s.impl.AchillesServiceImpl       : Creating container: valepopoulos/achilles-1.7.0:latest
2024-10-02 09:25:25.843 DEBUG 49 --- [         task-1] c.o.a.d.s.impl.AchillesServiceImpl       : Container created: a8367a52b896261e7a83224cc99558b086d5a299af202e34e9d94b344ca18eee
2024-10-02 09:25:25.843 DEBUG 49 --- [         task-1] c.o.a.d.s.impl.AchillesServiceImpl       : Starting container: a8367a52b896261e7a83224cc99558b086d5a299af202e34e9d94b344ca18eee
2024-10-02 09:25:25.982 DEBUG 49 --- [         task-1] c.o.a.d.s.impl.AchillesServiceImpl       : Container running: a8367a52b896261e7a83224cc99558b086d5a299af202e34e9d94b344ca18eee
2024-10-02 09:25:26.043 DEBUG 49 --- [         task-1] c.o.a.d.s.impl.AchillesServiceImpl       : Achilles finished with status code: 0
2024-10-02 09:25:26.043 DEBUG 49 --- [         task-1] c.o.a.d.s.impl.AchillesServiceImpl       : Creating Achilles output results archive
2024-10-02 09:25:26.077 ERROR 49 --- [         task-1] c.o.a.d.s.impl.AchillesServiceImpl       : Achilles failed to execute

java.nio.file.NoSuchFileException: /tmp/achilles_1431357100599896950/chunk_1_test_03090900
        at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86) ~[na:1.8.0_282]
        at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102) ~[na:1.8.0_282]
        at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107) ~[na:1.8.0_282]
        at sun.nio.fs.UnixFileSystemProvider.newDirectoryStream(UnixFileSystemProvider.java:427) ~[na:1.8.0_282]
        at java.nio.file.Files.newDirectoryStream(Files.java:457) ~[na:1.8.0_282]
        at com.odysseusinc.arachne.datanode.service.impl.AchillesServiceImpl.createAchillesOutputResults(AchillesServiceImpl.java:659) ~[classes!/:1.19.1]
        at com.odysseusinc.arachne.datanode.service.impl.AchillesServiceImpl.runAchilles(AchillesServiceImpl.java:566) ~[classes!/:1.19.1]
        at com.odysseusinc.arachne.datanode.service.impl.AchillesServiceImpl.executeAchilles(AchillesServiceImpl.java:234) ~[classes!/:1.19.1]
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_282]
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_282]
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_282]
        at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_282]
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) [spring-aop-5.2.12.RELEASE.jar!/:5.2.12.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) [spring-aop-5.2.12.RELEASE.jar!/:5.2.12.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) [spring-aop-5.2.12.RELEASE.jar!/:5.2.12.RELEASE]
        at org.springframework.aop.interceptor.AsyncExecutionInterceptor.lambda$invoke$0(AsyncExecutionInterceptor.java:115) [spring-aop-5.2.12.RELEASE.jar!/:5.2.12.RELEASE]
        at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_282]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) ~[na:1.8.0_282]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ~[na:1.8.0_282]
        at java.lang.Thread.run(Thread.java:748) ~[na:1.8.0_282]

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