data removal results in arki-check errors

[brancomat]

$ # preparo metadata per cancellazione
$ arki-query 'reftime:=2022-05-18 0:00' cosmo/ > qualcosa.md
$ # eseguo cancellazione
$ arki-check --fix --remove qualcosa.md cosmo/
$ # eseguo repack
$ arki-check -f -r cosmo/
cosmo:2022/05-18.grib: index knows of this segment but contains no data for it
cosmo:2022/05-18.grib: segment old enough to be archived
Traceback (most recent call last):
  File "/usr/bin/arki-check", line 11, in <module>
    main()
  File "/usr/bin/arki-check", line 7, in main
    sys.exit(Check.main())
  File "/usr/lib/python3.10/site-packages/arkimet/cmdline/base.py", line 83, in main
    return cmd.run()
  File "/usr/lib/python3.10/site-packages/arkimet/cmdline/check.py", line 125, in run
    arki_check.repack()
RuntimeError: cannot archive /arkitest/cosmo/2022/05-18.grib to /arkitest/cosmo/.archive/last/2022/05-18.grib because the destination already exists

test case: arkitest.tar.gz

(this might be an edge case since I'm using the --remove option with specific metadata to remove all present data)

[spanezz]

It looks like something like this happened:

1. attempted deletion of data not present in the online part of the dataset
2. searching for the data somewhat created bits of a segment (to be understood how)
3. repack tries to archive that, and becomes disappointed because the archive already has a segment for that time period

[spanezz]

Reproduced in test suite. Indeed, deleting nonexisting data creates an empty version of the affected segment

[spanezz]

Reason: deletion happens internally via a dataset writer instead of a checker, despite one needing to run arki-check for it. The writer, which is usually used to append data to a dataset, will always create a segment if it is missing.

A possible way forward is to move the remove method from the writer infrastructure to the checker infrastructure, which is probably something that should have already happened long ago