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Description
Curate seems to struggle with null JSON values?
$ augur curate transform-strain-name \
--strain-regex '^.+$' \
--backup-fields submissionId accession
...
Traceback (most recent call last):
File "/Users/cr/code/augur/augur/__init__.py", line 71, in run
return args.__command__.run(args)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/cr/code/augur/augur/curate/__init__.py", line 246, in run
dump_ndjson(validated_output_records)
File "/Users/cr/code/augur/augur/io/json.py", line 89, in dump_ndjson
for item in iterable:
^^^^^^^^
File "/Users/cr/code/augur/augur/curate/__init__.py", line 154, in validate_records
for idx, record in enumerate(records):
^^^^^^^^^^^^^^^^^^
File "/Users/cr/code/augur/augur/curate/transform_strain_name.py", line 72, in run
transform_name(
File "/Users/cr/code/augur/augur/curate/transform_strain_name.py", line 21, in transform_name
if strain_name_pattern.match(record.get("strain", "")) is None:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: expected string or bytes-like object, got 'NoneType'
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