This PR moves the function rethinkdb_date_greater from the end of the vdb/download.py to the beginning, so that it is in scope when the download is called.
This fixes an error when the --interval flag was used for virus downloads in which rethinkdb_date_greater could not be found by add_intervals_command.
@huddlej would you mind taking a look at this just to let me know if this has been moved to the most appropriate location? The (previously broken) command that I have been using to run is:
python3 vdb/download.py --database vdb \
--virus flu \
--fasta_fields strain virus accession collection_date region country division \
location passage_category submitting_lab age gender \
--resolve_method split_passage \
--select locus:na lineage:seasonal_h3n2 \
--interval collection_date:2016-03-30,2018-04-31 \
--path data \
--fstem h3n2_na
This PR moves the function
rethinkdb_date_greater
from the end of thevdb/download.py
to the beginning, so that it is in scope when the download is called.This fixes an error when the
--interval
flag was used for virus downloads in whichrethinkdb_date_greater
could not be found byadd_intervals_command
.@huddlej would you mind taking a look at this just to let me know if this has been moved to the most appropriate location? The (previously broken) command that I have been using to run is: