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pepkit / peppy

Project metadata manager for PEPs in Python
https://pep.databio.org/peppy
BSD 2-Clause "Simplified" License
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Lump warnings of "Not all environment variables were populated in derived attribute source" #364

Open nsheff opened 3 years ago

nsheff commented 3 years ago

https://github.com/pepkit/peppy/blob/7743178da4f16f992b1053fb733fb47f533f0a81/peppy/sample.py#L188-L189

We should collect these messages and display just once per project, rather than once per sample. Otherwise we get output like this:

Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-                          
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-
Not all environment variables were populated in derived attribute source: $REFGENIE_RAW/{genome}-{asset}-