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NDAR / nda-tools

Python package for interacting with NDA web services. Used to validate, submit, and download data to and from NDA.
MIT License
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Error with vtcmd --warning #2

Closed sean-cho closed 5 years ago

sean-cho commented 5 years ago

Running vtcmd with the -w argument fails to execute properly, see below.

vtcmd genomics_subject02.csv nichd_btb02.csv genomics_sample03.csv -w

Traceback (most recent call last):
  File "/users/swengcho/.conda/envs/cloud/bin/vtcmd", line 10, in <module>
    sys.exit(main())
  File "/users/swengcho/.conda/envs/cloud/lib/python3.7/site-packages/NDATools/clientscripts/vtcmd.py", line 257, in main
    validation_results = validate_files(args.files, w, bp, threads=args.workerThreads, config=config)
  File "/users/swengcho/.conda/envs/cloud/lib/python3.7/site-packages/NDATools/clientscripts/vtcmd.py", line 160, in validate_files
    validation.warnings()
AttributeError: 'Validation' object has no attribute 'warnings'

The issue is traceable here;

https://github.com/NDAR/nda-tools/blob/4a8461e6367bb8672fffc6e41dcbcce8be6efde8/nda-tools-python/NDATools/clientscripts/vtcmd.py#L160

Based on the validation object defined by Validation.py, this should be validation.get_warnings()

ushnaahmad commented 5 years ago

Hi @sean-cho

Thank you for reporting the error. We will be releasing an updated version of nda-tools some time next week and will make sure correct the issue for that release. I'll let you know when it is up.

Thanks again!

sean-cho commented 5 years ago

Hi @ushnaahmad

Thanks for getting back to me. I've made that change on my local copy and it works well.

I appreciate your work developing this tool -- it's great and really helpful! Looking forward to the update.

Thanks!