The fasta save method has this documentation:
https://github.com/kbaseapps/AssemblyUtil/blob/develop/AssemblyUtil.spec#L141-L145

I'm not quite sure what it's talking about. There is no script call that I can see in the code path, nor does the file necessarily get moved.

Currently if all the contigs are filtered out of a file (or, I suppose if the file is empty initially), the code tries to push it to the Blobstore, intercepts an error message from the Blobstore, and rethrows a more user friendly message.

Instead of pushing a known bad file to the blobstore, just check the file for emptiness and throw an error immediately.

I just disabled all the tests in assemblyutil_get_fastas_tests/py and the test output is now readable. Maybe the test runner is running the files in parallel, interleaving the output?

Reduce chance of race conditions

Things have tried but don't work:

• check return code at the end of unit tests

Adding a method to convert ProteinSequenceSet to Fasta would be really helpful for myself and hopefully other users down the road.

I proposed some changes in merge request #96. I provided some additional information in this request. Please feel free to contact me if I can assist in any way!

Might be able to save some time for larger files. Should be relatively easy to do in one pass based on a cursory inspection of the code

https://github.com/kbaseapps/AssemblyUtil/blob/develop/AssemblyUtil.spec#L100-L135

In docs but not in structure:
type

In structure but not in docs:
external_source
external_source_id

Currently, when unpacking files, zip and tar files will be unpacked and the path of the directory in which the unpack occurred returned. However, the function assumes the returned path is a file and so will fail.

There's currently no way to specify which file in an archive is desired in the API, which indicates that this functionality is as yet unneeded. Throw an error on archive file input instead (which might take changes to DFU...?)

Current use case is specifying a load ID with the batch save method to it's possible to figure out what was uploaded and what wasn't if a load partially fails