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    Nicola Soranzo
    @nsoranzo
    There's a "Make Private"
    Oleg Zharkov
    @OlegZharkov
    gearmenu-> make private?
    Nicola Soranzo
    @nsoranzo
    Yep
    Oleg Zharkov
    @OlegZharkov
    well, that doesn't seem to do the trick
    I still see the old interface
    Oleg Zharkov
    @OlegZharkov
    ok, no worries, I found out
    Nicola Soranzo
    @nsoranzo
    Cool
    Oleg Zharkov
    @OlegZharkov
    thanks for the help though
    Brian Kirk
    @BrianKi82112933_twitter
    On my recent galaxy install I can run and install tools fine but nothing from data managers will connect and download or run. Any thoughts as to where I can start looking for reasons as to how that can be. A typical error looks like "urllib.error.URLError:<urlopen error [ERNO -2] Name or service not known>"
    mvdbeek
    @mvdbeek:matrix.org
    [m]
    Hi @BrianKi82112933_twitter, which data manager is this, and is the node that runs the data manager job connected allowed to make outgoing requests ?
    Nate Coraor
    @natefoo:matrix.org
    [m]
    This is new...
    [g2test@galaxy07 ~]$ /cvmfs/test.galaxyproject.org/venv/bin/python /cvmfs/test.galaxyproject.org/galaxy/scripts/manage_db.py -c /srv/galaxy/test/config/galaxy.yml db_version
    Traceback (most recent call last):
      File "/cvmfs/test.galaxyproject.org/galaxy/scripts/manage_db.py", line 28, in <module>
        invoke_migrate_main()
      File "/cvmfs/test.galaxyproject.org/galaxy/scripts/manage_db.py", line 24, in invoke_migrate_main
        main(repository=repo, url=db_url)
      File "/cvmfs/test.galaxyproject.org/venv/lib/python3.6/site-packages/migrate/versioning/shell.py", line 209, in main
        ret = command_func(**kwargs)
      File "/cvmfs/test.galaxyproject.org/venv/lib/python3.6/site-packages/decorator.py", line 214, in fun
        return caller(func, *(extras + args), **kw)
      File "/cvmfs/test.galaxyproject.org/venv/lib/python3.6/site-packages/migrate/versioning/util/__init__.py", line 162, in with_engine
        url = a[0]
    IndexError: tuple index out of range
    Nate Coraor
    @natefoo:matrix.org
    [m]
    sqlalchemy-migrate appears not to have changed in a couple years, could be decorator though.
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Yeah it's yeah it's any version of decorator >=5 and <5.0.5
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Anyone seen this before?
    (.venv)nate@weyerbacher% ~/.virtualenvs/poetry/bin/poetry update --lock
    Updating dependencies
    Resolving dependencies... (2517.8s)
    
      RepositoryError
    
      500 Server Error: Internal Server Error for url: https://wheels.galaxyproject.org/simple/tzlocal/
    
      at ~/.virtualenvs/poetry/lib/python3.7/site-packages/poetry/repositories/legacy_repository.py:393 in _get
          389if response.status_code == 404:
          390return
          391│             response.raise_for_status()
          392except requests.HTTPError as e:
        → 393raise RepositoryError(e)
          394395if response.status_code in (401, 403):
          396self._log(
          397"Authorization error accessing {url}".format(url=response.url),
    I actually get a 404 if I hit that URL in a browser... and tzlocal is not present in wheels.galaxyproject.org's index.html nor do any wheels for it exist in the bucket - but I guess poetry is checking there anyway. Not sure why the 500 unless it's some kind of rate limiting by CloudFront.
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Well it succeeded the second time (after 92 minutes)
    Nicola Soranzo
    @nsoranzo
    Poetry always tries with wheels.galaxyproject.org first, if not found it tries with PyPI. Sometimes it gets a 500 instead of 404 (not sure if it's rate limiting or what), and bails out without retrying.
    which is obviously pretty annoying.
    ifubar (ross lazarus)
    @ifubar:matrix.org
    [m]

    running 21.01

    r = requests.get("http://localhost:8080/api/tools/tacrev/build",params={"key":"13073fde17d06591ce36e596e3c29904"})
    > r.content
    > b'{"err_msg": "History unavailable. Please specify a valid history id", "err_code": 0}'

    Odd. Visiting the same url locally without any parameters gives all the hid I need. The key is valid and the toolid is valid

    Nicola Soranzo
    @nsoranzo
    The history is part of your session when you use a browser, but not when using the API
    ifubar (ross lazarus)
    @ifubar:matrix.org
    [m]
    Thanks @nsoranzo I've tried adding a payload to the params after looking at the api code. Tried bioblend calls but not getting any hda or other ids in the return
    Any way to do this programmatically?
    (easily! - api or bioblend?
    Simon Bray
    @simonbray:matrix.org
    [m]
    Maybe gi.make_get_request(url, params={'history_id': ...}?
    ifubar (ross lazarus)
    @ifubar:matrix.org
    [m]
    Simon Bray: Yes! 👍️ The json has hids and so on - thank you !! Must document this somewhere - very handy.
    >>> r = gi.make_get_request(url="http://localhost:8080/api/tools/tacrev/build",params={"history_id":"f597429621d6eb2b"})
    >>> r.json()
    Simon Bray
    @simonbray:matrix.org
    [m]
    ifubar (ross lazarus): feel free to make a bioblend issue requesting it as an 'official' bioblend method, perhaps that's a good way to document it
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Are there any known issue with the GxIT tests?: galaxyproject/galaxy#11907
    This didn't update pulsar-galaxy-lib so I'm not sure if I caused this or not. It just times out and there's nothing indicating failure in the logs unfortunately.
    Nicola Soranzo
    @nsoranzo
    Yes, I've seen fail these quite regularly.
    BTW, I need to fix the dependency update CI job one of these days.
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Phew, ok, thanks.
    It'd be nice to add a bit of docker status output to those tests.
    Nicola Soranzo
    @nsoranzo
    It seems to me that something outside the Galaxy codebase is making these tests in test/integration/test_interactivetools_api.py fail, it happens to me also on old branches.
    Beatriz Serrano-Solano
    @beatrizserrano
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Zoom chat from the roundtable ^^
    Hopefully that comes through on the gitter side
    Nicola Soranzo
    @nsoranzo
    It does
    @bgruening To answer your question from the chat, that's the SQL query I use to purge rows from the job metrics table to keep their size under control:
    # Delete text job metrics for successful or old jobs (not useful for debugging).
    # Delete numeric job metrics for old unsuccessful jobs (not useful for statistics or debugging).
    DELETE FROM job_metric_text USING job WHERE job_id=job.id AND (job.state='ok' OR CURRENT_TIMESTAMP - job.update_time > '1 year');
    VACUUM FULL job_metric_text;
    DELETE FROM job_metric_numeric USING job WHERE job_id=job.id AND job.state IN ('deleted', 'error') AND CURRENT_TIMESTAMP - job.update_time > '1 year';
    VACUUM FULL job_metric_numeric;
    Björn Grüning
    @bgruening
    should we move this into gxadmin?
    Thanks for sharing!
    Nicola Soranzo
    @nsoranzo
    Thanks for opening galaxyproject/gxadmin#81
    Björn Grüning
    @bgruening
    just wanted to paste the link :)
    Nicola Soranzo
    @nsoranzo
    Beaten you for once :D
    Björn Grüning
    @bgruening
    :-)
    what if the file is compressed?
    Nolan Woods
    @innovate-invent
    @qiagu I think that the compression ratio wouldn't drastically affect that threshold
    Qiang Gu
    @qiagu
    I see