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subsample: Print errors from get_referenced_files #1955

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subsample: Print errors from get_referenced_files #1955

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2 changes: 2 additions & 0 deletions CHANGES.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,10 @@

* filter, merge: Fixed formatting of the error message shown when there are duplicate sequence ids. [#1954][] @victorlin
* filter: Adjusted the error message shown when there are missing weights to mention the option of updating values in metadata. [#1956][] @victorlin
* The helper function `augur.subsample.get_referenced_files` now shows errors when used in a lambda expression for a Snakemake input. [#1955][] (@victorlin)

[#1954]: https://github.com/nextstrain/augur/pull/1954
[#1955]: https://github.com/nextstrain/augur/pull/1955
[#1956]: https://github.com/nextstrain/augur/pull/1956

## 33.0.0 (26 January 2026)
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24 changes: 15 additions & 9 deletions augur/subsample.py
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Expand Up @@ -265,15 +265,21 @@ def get_referenced_files(
set
Resolved filepaths
"""
# Load schema, parse and validate config.
schema_validator = load_json_schema("schema-subsample-config.json")
config = _parse_config(config_file, config_section, schema_validator)

# Resolve filepaths.
search_path_objs = _get_search_paths(config_file, search_paths)
config, filepaths = _resolve_filepaths(config, search_path_objs, schema_validator.schema)

return set(filepaths)
# TODO: Remove try/except once Snakemake bug is fixed.
# <https://github.com/snakemake/snakemake/issues/3953>
try:
# Load schema, parse and validate config.
schema_validator = load_json_schema("schema-subsample-config.json")
config = _parse_config(config_file, config_section, schema_validator)

# Resolve filepaths.
search_path_objs = _get_search_paths(config_file, search_paths)
config, filepaths = _resolve_filepaths(config, search_path_objs, schema_validator.schema)

return set(filepaths)
except Exception as e:
print_err(f"ERROR: {e}")
raise e


def _parse_config(filename: str, config_section: Optional[List[str]], schema) -> Dict[str, Any]:
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