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  • Feb 03 08:17
    hexylena closed #30
  • Feb 02 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)
  • May 13 2019 09:17
    erasche assigned #25
  • May 13 2019 09:17
    erasche opened #25
  • Apr 29 2019 14:19
    Travis galaxy-iuc/parsec (1.12.1) errored (114)
  • Apr 10 2019 12:29
    Travis galaxy-iuc/parsec (1.12.0) errored (109)
Helena Rasche
@erasche
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.
When you installed this did you install it from pip or from the source?
Alexander Lenail
@zfrenchee
Hi @erasche . I did pip install. I guess I felt that thin wrapper was valuable, but oh well, I'll just go back to BioBlend
Helena Rasche
@erasche

Ok, thanks for this report. I have a good idea why it is happening, I'll probably put out a new release tomorrow.

as for importing, it's pretty thin. E.g. https://github.com/galaxy-iuc/parsec/blob/master/parsec/commands/histories/get_histories.py#L35 ctx.gi is just the bioblend library reference. 95% of the library is the automatically generated support-code / supporting functions based on bioblend's documentation. We have some custom utility functions and those might be useful to be able to import. If it looks possible to do, I'll document this for the next release.

Alexander Lenail
@zfrenchee
Thanks @erasche !
Brad Langhorst
@bwlang

looks like parsec is working nicely...

parsec histories show_matching_datasets $1 \
 | jq -r 'map (select(.deleted == false) | [.file_name, .name] | join ("\t")) | join ("\n")' \
 | while read file name; do ln -sf "$file" "$name"; done

Works great

Helena Rasche
@erasche
huh! TIL about show_matching_datasets