galaxy-iuc/parsec

Galaxy at the speed of light

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>

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

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