Fix the failure of the test_cleanse.py

[pwalczysko]

What this PR does

The failing test is https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-test-integration/11/testReport/junit/OmeroPy.test.integration.clitest.test_cleanse/TestCleanseFullAdmin/testCleanseNonsenseName/
This PR is removing a line in the test_cleanse.py.

The assertion in that line which checks the existence of a path to a logfile which should have been deleted is not possible on NFS, because:

As the Blitz process is still holding the logfile open, on NFS this file cannot be deleted by NFS although the cleanse script deletes it - it leaves a hidden file behind which the NFS renames to ...nfs.

Testing this PR

Check that the Jenkins build testintegration job is green.

Related reading

See #6461

cc @joshmoore @jburel @sbesson

[joshmoore]

Thanks, @pwalczysko. No immediate objections from my side.

[sbesson]

Do you have any idea on what keeps a reference to the file? In a standard import workflow, I would expect all file handles to be released on completion. Is this another example of latency due to the migration of the infrastructure (i.e. would a delay also allow the test to pass.

[pwalczysko]

Do you have any idea on what keeps a reference to the file?

Blitz, I know that. More precisely dont know, did not go deeper.

(i.e. would a delay also allow the test to pass.

Delay did not work. I did not try polling though, just a plain wait. It was longer than 30 sec afai can remember and the process still did not release the file.

[pwalczysko]

Do you have any idea on what keeps a reference to the file?

new investigation. Definitely a java Blitz process. It is not actively doing something. The leak is not worsening over time. Sometimes the .nfs file gets deleted after a minutes of wait. Sometimes not.

The cmds below shows the file descriptors currently open by process 1114099.

ls -l /proc/1114099/fd | grep .nfs0000008384567c850000160d
l-wx------. 1 omero omero 64 Aug  7 19:22 244 -> /home/omero/workspace/OMERO-test-integration/data/ManagedRepository/c1d4022e-2bcb-47af-a99f-7bb37c1826cf_4813/2026-08/07/.nfs0000008384567c850000160d


...
ps -fp 1114099
UID          PID    PPID  C STIME TTY          TIME CMD
omero    1114099 1114059 20 14:03 ?        01:11:19 java -Xmx9600m --add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED -Djava.awt.headless=tru
(.venv3) bash-5.1$ 


jcmd 1114099 VM.command_line | grep blitz.  # has a very long output below, which shows it is blitz
java_command: ome.services.blitz.Entry --Ice.Config=/home/omero/workspace/OMERO-test-integration/src/dist/var/master/servers/Blitz-0/config/config
java_class_path (initial): lib/server/proj4j.jar:lib/server/calcite-linq4j.jar:lib/server/minio.jar:lib/server/commons-lang3.jar:lib/server/ini4j.jar:lib/server/logback-core.jar:lib/server/spring-expression.jar:lib/server/httpcl.....


ls /proc/1114099/fd | wc -l
272
(.venv3) bash-5.1$ lsof -p 1114099 | grep -c nfs.  # at the time of investigation, Blitz had 19 open files (not supposed to do anything though
19

lsof -p 1114099 | grep nfs | awk '{print $9}' | sort | uniq -c
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs000000838452795f000015d0
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs0000008384527962000015ca
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs000000838452796f000015d9
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs0000008384527975000015c8
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs0000008384527977000015ce
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs0000008384527993000015d1
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs000000838452799b000015cc
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs000000838452799d000015d3
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279a0000015d7
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279a2000015d6
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279c0000015d2
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279c2000015cd
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279c5000015c9
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279c6000015cf
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279c7000015d4
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279c8000015cb
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279ca000015d8
      1 /home/omero/workspace/OMERO-test-integration/data/FullText/.nfs00000083845279cb000015d5
      1 /home/omero/workspace/OMERO-test-integration/data/ManagedRepository/c1d4022e-2bcb-47af-a99f-7bb37c1826cf_4813/2026-08/07/.nfs0000008384567c850000160d

I am afraid I am not getting forward. I am told that we need to enable the enable Java file descriptor tracing. I should restart the java process with -Djava.security.debug=access but we are talking here about Blitz in OMERO server... no idea how to do that. Will leave it there, this is, I can continue after AL if please told how to configure the server with such option.

[pwalczysko]

As discussed with @sbesson , the jury is out on this one. It stably passes with the fix in this PR, but not optimal and possibly underresearched. Will leave open for now.