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Put the subcmd name in the validate_output error message [#1539] #1540

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merged 2 commits into from
Jul 12, 2024
Merged

Put the subcmd name in the validate_output error message [#1539] #1540

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790dcdc
Put the subcmd name in the validate_output error message [#1539]
genehack Jul 11, 2024
58db430
Add some unit tests for validate_records() [#1539]
genehack Jul 12, 2024
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17 changes: 12 additions & 5 deletions augur/curate/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ def register_parser(parent_subparsers):
return parser


def validate_records(records: Iterable[dict], is_input: bool) -> Iterable[dict]:
def validate_records(records: Iterable[dict], subcmd_name: str, is_input: bool) -> Iterable[dict]:
"""
Validate that the provided *records* all have the same fields.
Uses the keys of the first record to check against all other records.
Expand All @@ -131,6 +131,10 @@ def validate_records(records: Iterable[dict], is_input: bool) -> Iterable[dict]:
----------
records: iterable of dict

subcmd_name: str
The name of the subcommand whose output is being validated; used in
error messages displayed to the user.

is_input: bool
Whether the provided records come directly from user provided input
"""
Expand All @@ -140,8 +144,8 @@ def validate_records(records: Iterable[dict], is_input: bool) -> Iterable[dict]:
else:
# Hopefully users should not run into this error as it means we are
# not uniformly adding/removing fields from records
error_message += dedent("""\
Something unexpected happened during the augur curate command.
error_message += dedent(f"""\
Something unexpected happened during the augur curate {subcmd_name} command.
To report this, please open a new issue including the original command:
<https://github.com/nextstrain/augur/issues/new/choose>
""")
Expand Down Expand Up @@ -213,14 +217,17 @@ def run(args):
input files can be provided via the command line options `--metadata` and `--fasta`.
See the command's help message for more details."""))

# Get the name of the subcmd being run
subcmd_name = args.subcommand

# Validate records have the same input fields
validated_input_records = validate_records(records, True)
validated_input_records = validate_records(records, subcmd_name, True)

# Run subcommand to get modified records
modified_records = getattr(args, SUBCOMMAND_ATTRIBUTE).run(args, validated_input_records)

# Validate modified records have the same output fields
validated_output_records = validate_records(modified_records, False)
validated_output_records = validate_records(modified_records, subcmd_name, False)

# Output modified records
# First output FASTA, since the write fasta function yields the records again
Expand Down
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