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    Marius van den Beek
    @mvdbeek
    still shaky in js ;)
    Marius van den Beek
    @mvdbeek
    hmm, actually the gx_get in rstudio doesn't seem to work
    > gx_get(1)
    Traceback (most recent call last):
      File "/usr/local/bin/get", line 18, in <module>
        print( get( args.id, args.identifier_type, args.history_id ) )
      File "/usr/local/lib/python2.7/dist-packages/galaxy_ie_helpers/__init__.py", line 125, in get
        gi = get_galaxy_connection(history_id=history_id, obj=False)
      File "/usr/local/lib/python2.7/dist-packages/galaxy_ie_helpers/__init__.py", line 99, in get_galaxy_connection
        raise Exception(msg)
    Exception: Could not connect to a galaxy instance. Please contact your SysAdmin for help with this error
    same for gx_save
    Dannon
    @dannon
    Hrmm. Any way to get more of a traceback there? Do you see anything at all on the Galaxy side?
    Marius van den Beek
    @mvdbeek
    nothing is reaching galaxy
    I'm running on docker for mac, that might be the issue
    (the IE, galaxy is local)
    did you check if that works with jupyter ?
    yeah: Failed to connect to localhost port 8080: Connection refused from inside the container
    let me see with host.docker.internal
    Marius van den Beek
    @mvdbeek
    success!
    galaxy_infrastructure_url = http://host.docker.internal:8080
    so cool!
    Dannon
    @dannon
    Oh nice. That’s really nifty.
    James Taylor
    @jxtx
    IS THAT REALLY ALL YOU NEED?
    It would be great to update the documentation in the config file since what is there for Mac OS X doesn't work for modern docker on mac and host.docker.internal is easier.
    Dannon
    @dannon
    Yeah, we can roll that into the open PR for IE fixes
    (didn’t actually have a chance to try it yet, but I’ll give it a shot and then can update the docs)
    Marius van den Beek
    @mvdbeek
    might also help @VJalili's to get the kubernetes 2 stage pod PR working. xref https://github.com/galaxyproject/galaxy/pull/7835/files#r282683960
    Martin Cech
    @martenson
    nice detective work y'all
    Marius van den Beek
    @mvdbeek
    @jmchilton I had been looking a bit more into galaxyproject/galaxy#7768 this morning. Would you agree with me that calling get_filename on the object store shouldn't create a dataset if it doesn't exist? I think this would make file creation operations more obvious, and that's what some of the object stores already do
    John Chilton
    @jmchilton
    Absolutely - I literally need it to work that way for remote data stuff I'm working on right now
    I completely forgot about that pull request :|
    Jennifer Hillman-Jackson
    @jennaj
    Does anyone recognize what this problem is? I don't know if came up before... https://help.galaxyproject.org/t/reference-genome-import-from-main-to-local-server/1223/8
    Jennifer Hillman-Jackson
    @jennaj
    ^^ the error from HISAT2 is "error while loading shared libraries: libcrypto.so.1.0.0" -- looks related to openssl/conda from a google
    Jennifer Hillman-Jackson
    @jennaj
    thanks @nsoranzo re ^^ :hamster:
    today is random emoji day. I don't know why.
    Nicola Soranzo
    @nsoranzo
    NP
    Martin Cech
    @martenson
    re galaxyproject/galaxy#7940 I suspect it did a full page refresh in 17.09?
    Marius van den Beek
    @mvdbeek
    I think at some point we stopped listening to updates which broke this
    Martin Cech
    @martenson
    I am not positive we ever did.
    (listen)
    Marius van den Beek
    @mvdbeek
    pretty sure that there is a regression
    it's not major though, just a little annoying
    it's not supposed to be the issue, but I don't understand the backbone listening at all
    Martin Cech
    @martenson
    ping @guerler
    Dannon
    @dannon
    That’s after submission though, not before?
    Marius van den Beek
    @mvdbeek
    right, but who is listening to the collection ?
    I suppose the upload form would also trigger this, so is parent.Galaxy.currHistoryPanel.collection never used again ?
    I should find some time to bisect it, it might be a red herring
    Aysam Guerler
    @guerler
    I can look at it.
    Jennifer Hillman-Jackson
    @jennaj
    Tools always needed a reload for certain types of history content updates. Be nice if those were detected on an already loaded tool panel (maybe with a little double-circle "refresh datasets" icon) if not possible automatically to detect those?
    Or, maybe a "refresh tool" icon at the very top, similar to the history panel refresh?
    Aysam Guerler
    @guerler
    Do you know for what kind of history content updates the tool form did not refresh automatically?
    Jennifer Hillman-Jackson
    @jennaj
    Outputs from tools that are not finished yet
    Aysam Guerler
    @guerler
    I see that the history listener is still there at but it does ot seem to fire properly anymore: https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/mvc/tool/tool-form-base.js#L30
    Jennifer Hillman-Jackson
    @jennaj
    And some uploaded, usually compressed. Seems to be linked to the timing of when the datatype is assigned (and therefore readable by the tool form input select)
    Once the tool form load, and history content changes, that is not being picked up and refreshing the select lists << probably the root issue (if an issue ... would certainly be nicer to not have to reload the tool)