kbaseapps / assemblyutil Goto Github PK

Reduce chance of race conditions

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.

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.

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...?)

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?

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