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feat(deposition): retry assembly creation failures due to FTP login e… #6196

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feat(deposition): retry assembly creation failures due to FTP login e… #6196

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feat(deposition): retry assembly creation failures due to FTP login e…
anna-parker Mar 26, 2026
17b3dc1
improve naming and retry function
anna-parker Mar 26, 2026
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10 changes: 8 additions & 2 deletions ena-submission/src/ena_deposition/create_assembly.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@
get_authors,
get_description,
get_ena_analysis_process,
retry_failed_submissions_for_matching_errors,
set_accession_does_not_exist_error,
trigger_retry_if_exists,
)
from .ena_types import (
DEFAULT_EMBL_PROPERTY_FIELDS,
Expand Down Expand Up @@ -758,12 +758,18 @@ def assembly_table_handle_errors(
)
messages.append(msg)

last_retry_time = trigger_retry_if_exists(
last_retry_time = retry_failed_submissions_for_matching_errors(
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@claude claude bot Mar 26, 2026

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The FTP auth retry will loop indefinitely for persistent credential failures — only the retry_threshold_min cooldown limits frequency, but there's no max attempt count. This pattern already exists for the "does not exist in ENA" case, so it's not a new regression, but it means a persistent misconfiguration will keep retrying forever without alerting. The TODO on line 774 acknowledges this gap.

entries_with_errors,
db_config,
table_name=TableName.ASSEMBLY_TABLE,
retry_threshold_min=config.retry_threshold_min,
last_retry=last_retry_time,
error_substrings=(
Comment on lines 763 to +767
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@claude claude bot Mar 26, 2026

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The first substring ends with "user error.:" — the trailing colon after the full stop looks unusual. Is this literally what ENA returns in the error message? If the colon is part of the actual message (e.g. preceding a stack trace), the match is fine, but it's worth confirming against a real example so the substring doesn't silently stop matching if ENA changes formatting.

"Submit service authentication error. Invalid submission account user "
"name or password. Please try enclosing your password in single quotes. "
"The submission has failed because of a user error.:",
"does not exist in ENA",
),
)
# TODO: Query ENA to check if assembly has in fact been created
# If created update assembly_table
Expand Down
4 changes: 2 additions & 2 deletions ena-submission/src/ena_deposition/create_project.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@
accession_exists,
create_ena_project,
get_alias,
retry_failed_submissions_for_matching_errors,
set_accession_does_not_exist_error,
trigger_retry_if_exists,
)
from .ena_types import (
OrganismType,
Expand Down Expand Up @@ -388,7 +388,7 @@ def project_table_handle_errors(
time=datetime.now(tz=pytz.utc),
slack_retry_threshold_min=config.slack_retry_threshold_min,
)
return trigger_retry_if_exists(
return retry_failed_submissions_for_matching_errors(
entries_with_errors,
db_config,
table_name=TableName.PROJECT_TABLE,
Expand Down
4 changes: 2 additions & 2 deletions ena-submission/src/ena_deposition/create_sample.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@
accession_exists,
create_ena_sample,
get_alias,
retry_failed_submissions_for_matching_errors,
set_accession_does_not_exist_error,
trigger_retry_if_exists,
)
from .ena_types import (
ProjectLink,
Expand Down Expand Up @@ -422,7 +422,7 @@ def sample_table_handle_errors(
time=datetime.now(tz=pytz.utc),
slack_retry_threshold_min=config.slack_retry_threshold_min,
)
last_retry_time = trigger_retry_if_exists(
last_retry_time = retry_failed_submissions_for_matching_errors(
entries_with_errors,
db_config,
table_name=TableName.SAMPLE_TABLE,
Expand Down
7 changes: 4 additions & 3 deletions ena-submission/src/ena_deposition/ena_submission_helper.py
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Expand Up @@ -878,12 +878,12 @@ def set_accession_does_not_exist_error(
logger.warning(f"{accession_type} creation failed and DB update failed.")


def trigger_retry_if_exists(
def retry_failed_submissions_for_matching_errors(
entries_with_errors: Iterable[Mapping[str, Any]],
db_config: SimpleConnectionPool,
table_name: TableName,
retry_threshold_min: int,
error_substring: str = "does not exist in ENA",
error_substrings: Iterable[str] = ("does not exist in ENA",),
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The type Iterable[str] is a subtle footgun here: a plain str is also Iterable[str], so passing "some error" accidentally instead of ("some error",) would silently iterate over individual characters. Consider narrowing to Sequence[str] or tuple[str, ...] to make the interface safer.

last_retry: datetime | None = None,
) -> datetime | None:
if (
Expand All @@ -892,7 +892,8 @@ def trigger_retry_if_exists(
):
return last_retry
for entry in entries_with_errors:
if error_substring not in str(entry.get("errors", "")):
errors = str(entry.get("errors", ""))
if not any(substring in errors for substring in error_substrings):
continue
match table_name:
case TableName.PROJECT_TABLE:
Expand Down
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