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If some requested fields in the --field-map do not exist, then some fields might not be renamed as expected.
This is due to the use of field_map.pop while looping through the list
Preview: <https://nextstrain.org/community/victorlin/nextstrain-test@e88bb6a/ebola/all-outbreaks-pathoplexus>
Downloading the data is trivial with the public API endpoints. Some
de-duplication is required, and the column names were the main hurdle.
There were many unhandled exceptions from augur curate commands which
for the most part I could figure out what was going wrong, however, in
some cases such as apply-geolocation-rules, I couldn't figure out how to
add division info without causing an error.
Discovered in ebola workflow
If some requested fields in the
--field-map
do not exist, then some fields might not be renamed as expected.This is due to the use of
field_map.pop
while looping through the listaugur/augur/curate/rename.py
Lines 60 to 64 in 23b9fff
The indexes doesn't match, resulting in the wrong elements getting dropped:
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