Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
Peter Amstutz
@tetron
but that feature doesn't exist yet
Tom Schoonjans
@tschoonj
and there's no workaround for this currently?
Peter Amstutz
@tetron
the API allows you to provide an explicit token to use when submitting a container
Tom Schoonjans
@tschoonj
aha
that sounds promising
Peter Amstutz
@tetron
I'm checking to see what circumstances the workflow runner passes that parameter
the parameter is "runtime_token" on container_request
Tom Schoonjans
@tschoonj
I assume that this is the runtime_token in the container_requests API?
:)
does arvados-cwl-runner have a similar option?
Peter Amstutz
@tetron
it does not. this is actually isolated from the workflow runner. the workflow runner has the ability to request that a container be submitted to a different cluster than the main one, and runtime_token is how controller provides credentials
so actually something like this might work
run arvados-cwl-runner --local configured to communicate with the login cluster
use arv:ClusterTarget to send all the jobs to cluster B
what would happen is the job is submitted to cluster A, cluster A redirects the request to cluster B along with proper credentials, cluster B receives the job along with credentials recognized by cluster A to access it's data
Tom Schoonjans
@tschoonj
that sounds like something we could test
would this work with 2.2.2 on cluster A?
Peter Amstutz
@tetron
yes
Tom Schoonjans
@tschoonj
many thanks Peter! I will discuss this with our team
Peter Amstutz
@tetron
the workaround is a bit speculative but it is worth a try. the main drawback it that you probably can't run the workflow runner itself as a container, so you'll end up with a bunch of disassociated container records instead of them being grouped under a single leader
but improving this situation is on our roadmap
and probably get a boost in priority
Ward Vandewege
@cure
yeah sounds like we need to prioritize #16888
Peter Amstutz
@tetron
the arvados user group meeting is happening now: https://forum.arvados.org/t/arvados-user-group-video-chat/47/9
Peter Amstutz
@tetron:matrix.org
[m]
@room Aravdos 2.3 has been released! https://forum.arvados.org/t/arvados-2-3-0-released/95
Brad Chapman
@chapmanb
When using the Python API, what is the right function call to update a collection with new files replacing the old ones? I'm happily creating initial containers using save_new, but when trying to create a new version of a collection with new files using a similar approach and calling saveI get the dreaded [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate which I suspect is just telling me I'm not doing it the right way. Are there any cookbook examples of this? I'm having lots of fun learning my way around the API and enjoying using the fabulous new workbench, cool to see all the awesome work you've been doing.
Peter Amstutz
@tetron
are you using playground or arvbox?
@chapmanb
Brad Chapman
@chapmanb
Sorry for the lack of context, this is on playground.
Peter Amstutz
@tetron
so "certificate verify failed" doesn't have anything to do with using the API correctly, it's an SSL issue
but it should just work
where are you running it from?
the playground shell? your laptop? somewhere else?
Brad Chapman
@chapmanb
This is from my laptop. The weird thing is that save_new works fine, but then using save gives that error in the same environment. So I figured I was using the API wrong. If there is a code snippet for how to create a new version of a collection with updated files, I can dig from there.
Ward Vandewege
@cure
@chapmanb hi! hmm, that error is weird. Clearly we need to add such an example to the cookbook, @tetron are you able to help or should I give it a go?
Peter Amstutz
@tetron
sorry, stepped away, back for a bit
@chapmanb it doesn't make sense for save_new() to work and save() to not work if they are communicating with the same API server
so that's really odd
save() is the right API call to commit changes to a collection
Peter Amstutz
@tetron
save_new() creates a new collection and save() saves changes to an existing collection
Brad Chapman
@chapmanb
Thanks y'all, sorry I had to go pickup kids. No rush on this. I added you to the repo and my code is here if I'm doing anything obviously wrong: https://github.com/chapmanb/veggiedb-standardize/blob/d211606c33291bde9ada7942075d380c10cb2179/veggiedb/arvadosio.py#L75 It's the same logic for the actual file addition, just how I initialize and save the collection if it exists versus being new. That's why I figured the error was caused by bad coding, not an actual configuration issue.
Ward Vandewege
@cure
@chapmanb no worries, I've been poking at this a bit. The SSL error is very odd; our best guess is currently that something is going on with the apiconfig object: either it is not properly propagated somehow in the save call (that would be an sdk bug, I'm trying to replicate it), or, could it be apiconfig is not what you expect in some circumstances? Maybe you could add a debug print that prints it out when you get the SSL error.
Ward Vandewege
@cure
@chapmanb the other thing that could be going on here is a pycurl/curl version that is out of date. The "unable to get local issuer certificate" suggests that.
but I don't know why you'd only see it on 'save' and not 'save_new'
Brad Chapman
@chapmanb
Thanks Ward for digging, I'm glad it's not just me that's confused. I've got this all in a pipenv so pretty isolated and repeatable with the python requirement. pycurl is pycurl==7.44.1. apiconfig is consistent between both since the code is the same. I'll try to poke more but it's helpful to hear I'm not doing anything obviously wrong in the code.
Ward Vandewege
@cure
@chapmanb huh I really need to track this down then, I was hoping that apiconfig was screwed up somehow
Brad Chapman
@chapmanb
Thanks Ward, I'm looking at the connection code as well and realizing how different save and save_new are under the covers so will do some debugging. I purposely tried to keep the code on my side as consistent as possible but will also double check that. I appreciate the help.
Ward Vandewege
@cure
I haven't been able to replicate the problem, yet
Peter Amstutz
@tetron:matrix.org
[m]
@chapmanb: yea, can you be more specific about how you run it and under what circumstances you get the error