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broadinstitute / gdctools

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons
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fix edge cases in config file handling #46

Closed noblem closed 7 years ago

noblem commented 7 years ago

Gordon's recent attempt to do

[DEFAULT] CATEGORIES: ...

revealed some lingering inconsistencies in how config content is treated. Even though the problem he saw was easily worked around by instead doing [MIRROR] CATEGORIES: ...

the inconsistencies should be examined so that all config options, for all tols, always operated in this order of decreasing precedence:

CLI tool-specific section file (etc [MIRROR]) [DEFAULT] section

Another thing to resolve is that the docs should clearly specify what config state is amenable to being defined in [DEFAULT] and what is not.

noblem commented 7 years ago

Gordon, I just added you as assignee, but really only so that you could watch the issue rather than fix it.

noblem commented 7 years ago

As of v0.2.3 the coding parts of this have been addressed. Most of the documentation part has been addressed, too, as described in GDCtool.py::config_finalize() method. The description there will need to bubble up to the public/Wiki docs, too

noblem commented 7 years ago

The part of this that speaks to user-level documentation has been moved to #50, making this eligible to be marked Done/Closed.