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galaxy-iuc / parsec

Access Galaxy at the speed of light with automatically generated BioBlend wrappers
Apache License 2.0
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Remove wait_for_completion in download_datasets from the bioblend call. #24

Closed andreyto closed 5 years ago

andreyto commented 5 years ago

This fixes error from current bioblend dependency, where this argument has been removed. The argument is still accepted by the parsec script for compatibility, but it is ignored. This was tested in this tutorial.

hexylena commented 5 years ago

Thanks for the fix @andreyto, I'll start pinning the bioblend version so we don't have this problem in the future.

hexylena commented 5 years ago

Hi @andreyto, ok, made a new release with pinned bioblend. Parsec is nearly completely automatically generated, so the automatic updating has removed your compatibility flag.

This is a tradeoff I feel comfortable making, as I don't want to extend our auto-generation tool to support this.

It's on pypi now as 1.12.0 :)

andreyto commented 5 years ago

@erasche, yes, this is even better. Thanks a lot! I the absence of R client bindings, parsec is the easiest way for the R users to access Galaxy remotely unless they want to code RESTful calls directly with httr. Great tool.

hexylena commented 5 years ago

@andreyto great, I'm glad to hear it's useful in that case! I'll be sure to add it to the RStudio Galaxy IE while I'm at it.

For the use case in your tutorial, we also have:

Where if your user has GALAXY_URL and API_KEY set, they should just be able to run gx_get(<id>) in their R session and it will return a path. Those two repositories probably have some hardcoded values which need to be fixed for general usage, but maybe it is interesting for you.