sbg / sevenbridges-cwl Goto Github PK

Currently it appears that if there is no metadata attached to a file on the
SevenBridges platform, calling metadata on a fetch file object returns
None rather than {}. This means code such as key in File.metadata will
cause an error rather than return False. I believe that returning False would
be the expected behaviour.

cc @zymergen-msneddon

Hi @filiptubic !

All these examples are awesome! Two requests for documentation.

1. Create a list of requirements that the docker image should have (like Python, dill and pyYAML)
2. I wonder if we could have an example for a Python tool that globs a file?

Thanks!

"If something isn't on the web, it doesn't exist at all."

Instead of making users install extra dependencies to build the docs locally, would it be nice if we host the package docs online (readthedocs or github pages) and link the url in the repo description section/in the readme, so people can read them directly?

That's what we did for sevenbridges-r.

@kaushik-work @filiptubic

The from_bash function is my most intensively used function in sbg-cwl. It however does not work when the docker image does not have certain tools. For example alpine which is a lightweight distribution I use for testing can not be used.

Importantly, I have existing docker images from existing tools which I can not use because they do not contain the special utilities required by this function.

It would be nice to recast the from_bash mechanism such that it does not depend on any special utilities, for example, by invoking CWL's create file feature.

Thanks!

On windows platforms the get_metadata() function seems to insert \r characters, this makes CWL created on windows unusable.

Thanks!