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 certificatewhich 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.
save_newworks fine, but then using
savegives 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.
apiconfigobject: either it is not properly propagated somehow in the
savecall (that would be an sdk bug, I'm trying to replicate it), or, could it be
apiconfigis not what you expect in some circumstances? Maybe you could add a debug print that prints it out when you get the SSL error.
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.
save: https://gist.github.com/chapmanb/42d2a81321a04350974daed85d76c4d1 The trigger for the error seems to be calling
savewhen you overwrite an existing file. I had included a
removepreviously but it looks like you also need to call
saveafter that and before starting to write to the file. So this works around the problem, but doesn't really solve my underlying issue. When I update this way the collection updates the file, but doesn't get a new version so is not tracking the change. The versioning and ability to see the previous sequence is really what I was hoping for, so could still use the pointers on the right way to do that through the API. Thanks so much for all the help working through this and debugging.
arvados-python-clientand couldn’t reproduce the problem you’re having. I had to do some changes to it, the main one being the fact that
get_connection_config()isn’t available so I just left the
Collectionclass do its thing without passing an api object to it. Maybe the problem is related to that? You can look at the modified script here: https://pastebin.com/6AQk6mxy
We are seeing an issue with the arvados-python-client's arv-mount command in release 2.3:
mkdir -p /tmp/arvados-mount source ~/.arv_key arv-mount --replace --read-only --all /tmp/arvados-mount --exec mkdir -p /home/manager/ontology_files cp /tmp/arvados-mount/by_id/glon1-4zz18-6uskmpf7bz9hhz5/* /home/manager/ontology_files cp /tmp/arvados-mount/by_id/glon1-4zz18-3986qs7m7ydzb0n/some-other-file.bin /home/manager/ontology_files cp: failed to close '/tmp/arvados-mount/by_id/glon1-4zz18-3986qs7m7ydzb0n/some-other-file.bin': Input/output error
We do not observe this failure with 2.2. Any thoughts on why this is happening?