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add more logging
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anna-parker committed Nov 6, 2024
1 parent 4912e88 commit 4882c34
Showing 1 changed file with 3 additions and 0 deletions.
3 changes: 3 additions & 0 deletions ena-submission/src/ena_deposition/create_assembly.py
Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,7 @@ def create_manifest_object(
address.get("country"),
]
address_string = ", ".join([x for x in address_list if x is not None])
logging.info("Created address from group_info")
except Exception as e:
logging.error(f"Was unable to create address, setting address to center_name due to {e}")

Expand All @@ -132,6 +133,7 @@ def create_manifest_object(
)
try:
authors = reformat_authors_from_loculus_to_embl_style(authors)
logging.info("Reformatted authors")
except ValueError as err:
msg = f"Was unable to format authors: {authors} as ENA expects"
logging.error(msg)
Expand Down Expand Up @@ -163,6 +165,7 @@ def create_manifest_object(
organism=organism,
dir=dir,
)
logging.info("Created flatfile")
program = (
metadata["sequencingInstrument"] if metadata.get("sequencingInstrument") else "Unknown"
)
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