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@jsstevenson
jsstevenson committed Jan 4, 2025
1 parent 6f342ed commit 06898c0
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Showing 6 changed files with 30 additions and 26 deletions.
5 changes: 5 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -117,12 +117,14 @@ select = [
"RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
"RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret
"SLF", # https://docs.astral.sh/ruff/rules/#flake8-self-slf
"SLOT", # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
"SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
"ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
"PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
"PGH", # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
"PLC", # https://docs.astral.sh/ruff/rules/#convention-c
"PLE", # https://docs.astral.sh/ruff/rules/#error-e_1
"TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try
"PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf
"FURB", # https://docs.astral.sh/ruff/rules/#refurb-furb
"RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
Expand All @@ -143,6 +145,7 @@ fixable = [
"SIM",
"PLC",
"PLE",
"TRY",
"PERF",
"FURB",
"RUF"
Expand All @@ -161,13 +164,15 @@ fixable = [
# E501 - line-too-long*
# W191 - tab-indentation*
# S321 - suspicious-ftp-lib-usage
# PLC0206 - dict-index-missing-items
# *ignored for compatibility with formatter
ignore = [
"ANN003",
"D203", "D205", "D206", "D213", "D300", "D400", "D415",
"E111", "E114", "E117", "E501",
"W191",
"S321",
"PLC0206"
]

[tool.ruff.lint.per-file-ignores]
Expand Down
6 changes: 3 additions & 3 deletions src/gene/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -206,7 +206,7 @@ def _load_source(
try:
processed_ids += source.perform_etl(use_existing)
except GeneNormalizerEtlError as e:
_logger.error(e)
_logger.exception("ETL error while loading %s", n)
click.echo(f"Encountered error while loading {n}: {e}.")
click.get_current_context().exit()
end_load = timer()
Expand Down Expand Up @@ -322,13 +322,13 @@ def update_normalizer_db(

if len(sources_split) == 0:
err_msg = "Must enter 1 or more source names to update"
raise Exception(err_msg)
raise ValueError(err_msg)

non_sources = set(sources_split) - set(SOURCES)

if len(non_sources) != 0:
err_msg = f"Not valid source(s): {non_sources}"
raise Exception(err_msg)
raise ValueError(err_msg)

parsed_source_names = {SourceName(SOURCES[s]) for s in sources_split}
_update_normalizer(parsed_source_names, db, update_merged, use_existing)
Expand Down
18 changes: 9 additions & 9 deletions src/gene/database/dynamodb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,8 +105,8 @@ def drop_db(self) -> None:
try:
if not self._check_delete_okay():
return
except DatabaseWriteException as e:
raise e
except DatabaseWriteException: # noqa: TRY203
raise

if self.gene_table in self.list_tables():
self.dynamodb.Table(self.gene_table).delete()
Expand Down Expand Up @@ -250,9 +250,9 @@ def get_record_by_id(
response = self.genes.query(KeyConditionExpression=exp)
record = response["Items"][0]
del record["label_and_type"]
return record
return record # noqa: TRY300
except ClientError as e:
_logger.error(
_logger.exception(
"boto3 client error on get_records_by_id for search term %s: %s",
concept_id,
e.response["Error"]["Message"],
Expand All @@ -275,7 +275,7 @@ def get_refs_by_type(self, search_term: str, ref_type: RefType) -> list[str]:
matches = self.genes.query(KeyConditionExpression=filter_exp)
return [m["concept_id"] for m in matches.get("Items", None)]
except ClientError as e:
_logger.error(
_logger.exception(
"boto3 client error on get_refs_by_type for search term %s: %s",
search_term,
e.response["Error"]["Message"],
Expand Down Expand Up @@ -378,7 +378,7 @@ def add_record(self, record: dict, src_name: SourceName) -> None:
try:
self.batch.put_item(Item=record)
except ClientError as e:
_logger.error(
_logger.exception(
"boto3 client error on add_record for %s: %s",
concept_id,
e.response["Error"]["Message"],
Expand Down Expand Up @@ -411,7 +411,7 @@ def add_merged_record(self, record: dict) -> None:
try:
self.batch.put_item(Item=record)
except ClientError as e:
_logger.error(
_logger.exception(
"boto3 client error on add_record for " "%s: %s",
concept_id,
e.response["Error"]["Message"],
Expand All @@ -438,7 +438,7 @@ def _add_ref_record(
try:
self.batch.put_item(Item=record)
except ClientError as e:
_logger.error(
_logger.exception(
"boto3 client error adding reference %s for %s with match type %s: %s",
term,
concept_id,
Expand Down Expand Up @@ -473,7 +473,7 @@ def update_merge_ref(self, concept_id: str, merge_ref: Any) -> None: # noqa: AN
)
raise DatabaseWriteException(err_msg) from e

_logger.error(
_logger.exception(
"boto3 client error in `database.update_record()`: %s",
e.response["Error"]["Message"],
)
Expand Down
6 changes: 3 additions & 3 deletions src/gene/database/postgresql.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,8 +121,8 @@ def drop_db(self) -> None:
try:
if not self._check_delete_okay():
return
except DatabaseWriteException as e:
raise e
except DatabaseWriteException: # noqa: TRY203
raise

with self.conn.cursor() as cur:
cur.execute(self._drop_db_query)
Expand Down Expand Up @@ -601,7 +601,7 @@ def add_record(self, record: dict, src_name: SourceName) -> None: # noqa: ARG00
cur.execute(self._ins_symbol_query, [record["symbol"], concept_id])
self.conn.commit()
except UniqueViolation:
_logger.error("Record with ID %s already exists", concept_id)
_logger.exception("Record with ID %s already exists", concept_id)
self.conn.rollback()

_add_merged_record_query = b"""
Expand Down
8 changes: 4 additions & 4 deletions src/gene/etl/merge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,13 +57,13 @@ def create_merged_concepts(self, record_ids: set[str]) -> None:
self._database.update_merge_ref(concept_id, merge_ref)
except DatabaseWriteException as dw:
if str(dw).startswith("No such record exists"):
_logger.error(
_logger.exception(
"Updating nonexistent record: %s for merge ref to %s",
concept_id,
merge_ref,
)
else:
_logger.error(str(dw))
_logger.exception("Encountered unknown DB write exception")
uploaded_ids |= group
self._database.complete_write_transaction()
_logger.info("Merged concept generation successful.")
Expand Down Expand Up @@ -135,9 +135,9 @@ def record_order(record: dict) -> tuple:
source_rank = SourcePriority[src].value
else:
err_msg = (
f"Prohibited source: {src} in concept_id " f"{record['concept_id']}"
f"Prohibited source: {src} in concept_id {record['concept_id']}"
)
raise Exception(err_msg)
raise ValueError(err_msg)
return source_rank, record["concept_id"]

records.sort(key=record_order)
Expand Down
13 changes: 6 additions & 7 deletions src/gene/query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,9 +168,9 @@ def _fetch_record(
"""
try:
match = self.db.get_record_by_id(concept_id, case_sensitive=False)
except DatabaseReadException as e:
_logger.error(
"Encountered DatabaseReadException looking up %s: %s", concept_id, e
except DatabaseReadException:
_logger.exception(
"Encountered DatabaseReadException looking up %s", concept_id
)
else:
if match:
Expand Down Expand Up @@ -244,10 +244,9 @@ def _get_search_response(self, query: str, sources: set[str]) -> dict:
self._fetch_record(resp, ref, MatchType[item_type.upper()])
matched_concept_ids.append(ref)

except DatabaseReadException as e:
_logger.error(
"Encountered DatabaseReadException %s looking up %s %s: ",
e,
except DatabaseReadException:
_logger.exception(
"Encountered DatabaseReadException looking up %s %s: ",
item_type,
term,
)
Expand Down

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