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  • Apr 08 14:12
    Travis galaxy-iuc/parsec (1.15.0) passed (129)
  • Apr 08 13:21
    Travis galaxy-iuc/parsec (1.15.0) errored (127)
  • Apr 08 13:19
    Travis galaxy-iuc/parsec (master) errored (125)
  • Jun 15 2020 08:42
    pcm32 opened #31
  • Feb 03 2020 08:17
    hexylena closed #30
  • Feb 02 2020 17:13
    pvanheus opened #30
  • Oct 09 2019 19:55
    erasche closed #29
  • Oct 09 2019 19:22
    innovate-invent opened #29
  • Aug 12 2019 09:13
    Travis galaxy-iuc/parsec (1.13.0) passed (122)
  • Aug 12 2019 09:13
    erasche closed #25
  • Aug 12 2019 09:12
    erasche closed #26
  • Aug 12 2019 09:12
    erasche closed #23
  • Aug 05 2019 13:52
    bernt-matthias closed #28
  • Aug 05 2019 13:33
    erasche synchronize #26
  • Aug 05 2019 13:23
    bernt-matthias opened #28
  • Jul 31 2019 07:26
    bernt-matthias closed #27
  • Jul 30 2019 14:00
    erasche synchronize #26
  • Jul 30 2019 12:59
    bernt-matthias opened #27
  • May 15 2019 09:31
    erasche opened #26
  • May 15 2019 09:31
    Travis galaxy-iuc/parsec (unrelease-bioblend) passed (116)
Brad Langhorst
@bwlang
hmm - tried to continue despite the error and i get AttributeError: 'module' object has no attribute 'JSONDecodeError'
do i have the URL right? need https? or trailing slash or somesuch?
Helena Rasche
@erasche
we do a "test" API call to https://fqdn/galaxy/api/configuration
Brad Langhorst
@bwlang
hmm - i don't respond to https this is an internal only server...
Helena Rasche
@erasche
http is fine
if you can curl http://galaxy.neb.com/galaxy/api/configuration from the command line, it should work
perhaps there is some networking issue where parsec is not resolving / not accessing galaxy.neb.com correctly? I assume that's internal + available to everyone on your internal network without a socks proxy or anything in the way?
Brad Langhorst
@bwlang
maybe i need to configure my proxy... that produces 401
Helena Rasche
@erasche
sounds promising!
I have to run to a meeting now, I'll be back in touch aftwards, sorry about this.
Brad Langhorst
@bwlang
no worries... i'll keep poking a bit.
Helena Rasche
@erasche
actually 401 sounds fine, probably needs an API key to access that.
anyway, back later.
Brad Langhorst
@bwlang
might be my proxy config... i think i need to allow unauthenticated access to that end point.
Helena Rasche
@erasche
you shouldn't need to
if you want auth'd access, you want auth'd access. That's just a "Is parsec working?" test, not necessary.
if you've gotten through that, try a parsec histories get_histories
Brad Langhorst
@bwlang
are you texting in your meeting ;) get_histories produces AttributeError: 'module' object has no attribute 'JSONDecodeError'
Helena Rasche
@erasche
ah both. that sounds like it's failing to access properly.
I don't know off the top of my head, can you test something?
Brad Langhorst
@bwlang
i dont' think i can auth with parsec... i've not set the username and password so how could it auth? (my proxy does the auth)
Helena Rasche
@erasche
if you have your API key, just curl http://galaxy.neb.com/api/configuration?key=<your api key>
OH
your proxy does auth, you're using remote user?
Brad Langhorst
@bwlang
yeah - i think i just need to reconfig to allow unauthenticated access to /api
Helena Rasche
@erasche
you need to ensure that the API has unauthenticated access (not actually unauth'd, just the api exception)
Brad Langhorst
@bwlang
just need to re-learn how to do nginx config ;)
thanks... i'll let you know if i have more trouble... might propose a doc change later.
Helena Rasche
@erasche
ok, sounds good. Thanks!
Helena Rasche
@erasche
back now, any success @bwlang ?
Helena Rasche
@erasche
@bwlang additionally if you could share the nginx change you make? I need to make a wiki page for this
including the apache config because I'm not seeing it anywhere
Brad Langhorst
@bwlang
yeah - the links on the galaxy wiki are dead... i did not acheive success with ``` location /api {
       #not working yet... would like to allow access to /api without requiring authentication
       auth_pam off;
       allow all;
       proxy_pass http://galaxy_app;
        proxy_set_header REMOTE_USER $remote_user;
        proxy_set_header   X-Forwarded-Host $host;
        proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
        proxy_buffering on;
        proxy_read_timeout 900;
        proxy_buffers 1000 4k; #yes i'm trying a 4M buffer for galaxy
        proxy_next_upstream error;
    }```
Helena Rasche
@erasche
ok, mine looks like
    <Location "/galaxy/api/">                                                                                                                      
        Satisfy Any
        Allow from all
    </Location>
Brad Langhorst
@bwlang
this is how i have the main proxy working:
      location / {
            auth_pam "NEB Credentials";
            auth_pam_service_name "nginx";
            proxy_pass http://galaxy_app;
            proxy_set_header REMOTE_USER $remote_user;
            proxy_set_header   X-Forwarded-Host $host;
            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
            proxy_buffering on;
            proxy_read_timeout 900;
            proxy_buffers 1000 4k; #yes i'm trying a 4M buffer for galaxy
            proxy_next_upstream error;
        }
Helena Rasche
@erasche
that looks like it should be right, for you. auth_pam off / allow all. Huh, wonder why it isn't working
Brad Langhorst
@bwlang
i'll try the satisfy any now... but then i have to give up, trying to get everything done before I leave for GCC tomorrow night (vacation first) ... I think i saw that you'll be there .
Helena Rasche
@erasche
apache syntax obviously, I'm afraid I really don't know how to help.
yep, sure will. see ya there.
Brad Langhorst
@bwlang
/galaxy/api is only needed if your site is served from a subdir right?
i'm using /api
Helena Rasche
@erasche
yes
correct
Brad Langhorst
@bwlang
bummer that would have been an easy fix... ;) see you later.
Brad Langhorst
@bwlang
hah... the example i posted before with auth_pam off does work ... i was just testing it wrong (used the /galaxy prefix). Now parsec histories get_histories does work for me - thanks!
Helena Rasche
@erasche
ah, awesome! glad to hear it
Alexander Lenail
@zfrenchee
Hello @erasche ! I just found parsec (very cool) and set it up, but immediately got a
Problem loading command toolshed, exception cannot import name 'bioblend_exception'
Problem loading command users, exception cannot import name 'bioblend_exception'
Problem loading command utils, exception cannot import name 'bioblend_exception'
any ideas where this might be coming from?
Alexander Lenail
@zfrenchee
Also, I'd prefer to do most of this work in python. Is it possible to import parsec ? I don't see that in the README
Helena Rasche
@erasche
Hi @zfrenchee, if you want to import parsec, you should probably just import bioblend, parsec doesn't offer much python code on top of a very thin wrapper on bioblend.