Merge branch 'interface-updates-epic' into fix-error-names

src/gene/cli.py

@@ -1,5 +1,4 @@
 """Provides a CLI util to make updates to normalizer database."""
-import logging
 import os
 from pathlib import Path
 from typing import Optional, Tuple
@@ -11,10 +10,6 @@
 from gene.etl.update import update_all_sources, update_normalized, update_source
 from gene.schemas import SourceName
 
-logger = logging.getLogger("gene")
-logger.setLevel(logging.DEBUG)
-
-
 url_description = 'URL endpoint for the application database. Can either be a URL to a local DynamoDB server (e.g. "http://localhost:8001") or a libpq-compliant PostgreSQL connection description (e.g. "postgresql://postgres:password@localhost:5432/gene_normalizer").'
 
 

src/gene/database/dynamodb.py

@@ -31,7 +31,7 @@
     SourceName,
 )
 
-logger = logging.getLogger(__name__)
+_logger = logging.getLogger(__name__)
 
 
 class DynamoDbDatabase(AbstractDatabase):
@@ -165,7 +165,7 @@ def check_schema_initialized(self) -> bool:
         existing_tables = self.list_tables()
         exists = self.gene_table in existing_tables
         if not exists:
-            logger.info(f"{self.gene_table} table is missing or unavailable.")
+            _logger.info(f"{self.gene_table} table is missing or unavailable.")
         return exists
 
     def check_tables_populated(self) -> bool:
@@ -182,7 +182,7 @@ def check_tables_populated(self) -> bool:
             KeyConditionExpression=Key("item_type").eq("source"),
         ).get("Items", [])
         if len(sources) < len(SourceName):
-            logger.info("Gene sources table is missing expected sources.")
+            _logger.info("Gene sources table is missing expected sources.")
             return False
 
         records = self.genes.query(
@@ -191,7 +191,7 @@ def check_tables_populated(self) -> bool:
             Limit=1,
         )
         if len(records.get("Items", [])) < 1:
-            logger.info("Gene records index is empty.")
+            _logger.info("Gene records index is empty.")
             return False
 
         normalized_records = self.genes.query(
@@ -200,7 +200,7 @@ def check_tables_populated(self) -> bool:
             Limit=1,
         )
         if len(normalized_records.get("Items", [])) < 1:
-            logger.info("Normalized gene records index is empty.")
+            _logger.info("Normalized gene records index is empty.")
             return False
 
         return True
@@ -262,10 +262,8 @@ def get_record_by_id(
                 del record["label_and_type"]
                 return record
         except ClientError as e:
-            logger.error(
-                f"boto3 client error on get_records_by_id for "
-                f"search term {concept_id}: "
-                f"{e.response['Error']['Message']}"
+            _logger.error(
+                f"boto3 client error on get_records_by_id for search term {concept_id}: {e.response['Error']['Message']}"
             )
             return None
         except (KeyError, IndexError):  # record doesn't exist
@@ -285,10 +283,8 @@ 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(
-                f"boto3 client error on get_refs_by_type for "
-                f"search term {search_term}: "
-                f"{e.response['Error']['Message']}"
+            _logger.error(
+                f"boto3 client error on get_refs_by_type for search term {search_term}: {e.response['Error']['Message']}"
             )
             return []
 
@@ -389,9 +385,8 @@ def add_record(self, record: Dict, src_name: SourceName) -> None:
         try:
             self.batch.put_item(Item=record)
         except ClientError as e:
-            logger.error(
-                "boto3 client error on add_record for "
-                f"{concept_id}: {e.response['Error']['Message']}"
+            _logger.error(
+                f"boto3 client error on add_record for {concept_id}: {e.response['Error']['Message']}"
             )
         for attr_type, item_type in ITEM_TYPES.items():
             if attr_type in record:
@@ -421,9 +416,8 @@ def add_merged_record(self, record: Dict) -> None:
         try:
             self.batch.put_item(Item=record)
         except ClientError as e:
-            logger.error(
-                "boto3 client error on add_record for "
-                f"{concept_id}: {e.response['Error']['Message']}"
+            _logger.error(
+                f"boto3 client error on add_record for {concept_id}: {e.response['Error']['Message']}"
             )
 
     def _add_ref_record(
@@ -447,10 +441,8 @@ def _add_ref_record(
         try:
             self.batch.put_item(Item=record)
         except ClientError as e:
-            logger.error(
-                f"boto3 client error adding reference {term} for "
-                f"{concept_id} with match type {ref_type}: "
-                f"{e.response['Error']['Message']}"
+            _logger.error(
+                f"boto3 client error adding reference {term} for {concept_id} with match type {ref_type}: {e.response['Error']['Message']}"
             )
 
     def update_merge_ref(self, concept_id: str, merge_ref: Any) -> None:  # noqa: ANN401
@@ -479,9 +471,8 @@ def update_merge_ref(self, concept_id: str, merge_ref: Any) -> None:  # noqa: AN
                     f"No such record exists for keys {label_and_type}, {concept_id}"
                 )
             else:
-                logger.error(
-                    f"boto3 client error in `database.update_record()`: "
-                    f"{e.response['Error']['Message']}"
+                _logger.error(
+                    f"boto3 client error in `database.update_record()`: {e.response['Error']['Message']}"
                 )
 
     def delete_normalized_concepts(self) -> None:

src/gene/database/postgresql.py

@@ -27,7 +27,7 @@
 )
 from gene.schemas import RecordType, RefType, SourceMeta, SourceName
 
-logger = logging.getLogger(__name__)
+_logger = logging.getLogger(__name__)
 
 
 SCRIPTS_DIR = Path(__file__).parent / "postgresql"
@@ -124,7 +124,7 @@ def drop_db(self) -> None:
         with self.conn.cursor() as cur:
             cur.execute(self._drop_db_query)
             self.conn.commit()
-        logger.info("Dropped all existing gene normalizer tables.")
+        _logger.info("Dropped all existing gene normalizer tables.")
 
     def check_schema_initialized(self) -> bool:
         """Check if database schema is properly initialized.
@@ -137,7 +137,7 @@ def check_schema_initialized(self) -> bool:
         except DuplicateTable:
             self.conn.rollback()
         else:
-            logger.info("Gene table existence check failed.")
+            _logger.info("Gene table existence check failed.")
             self.conn.rollback()
             return False
         try:
@@ -146,7 +146,7 @@ def check_schema_initialized(self) -> bool:
         except DuplicateObject:
             self.conn.rollback()
         else:
-            logger.info("Gene foreign key existence check failed.")
+            _logger.info("Gene foreign key existence check failed.")
             self.conn.rollback()
             return False
         try:
@@ -157,7 +157,7 @@ def check_schema_initialized(self) -> bool:
         except DuplicateTable:
             self.conn.rollback()
         else:
-            logger.info("Gene normalized view lookup failed.")
+            _logger.info("Gene normalized view lookup failed.")
             self.conn.rollback()
             return False
         try:
@@ -166,7 +166,7 @@ def check_schema_initialized(self) -> bool:
         except DuplicateTable:
             self.conn.rollback()
         else:
-            logger.info("Gene indexes check failed.")
+            _logger.info("Gene indexes check failed.")
             self.conn.rollback()
             return False
 
@@ -189,21 +189,21 @@ def check_tables_populated(self) -> bool:
             cur.execute(self._check_sources_query)
             results = cur.fetchall()
         if len(results) < len(SourceName):
-            logger.info("Gene sources table is missing expected sources.")
+            _logger.info("Gene sources table is missing expected sources.")
             return False
 
         with self.conn.cursor() as cur:
             cur.execute(self._check_concepts_query)
             result = cur.fetchone()
         if not result or result[0] < 1:
-            logger.info("Gene records table is empty.")
+            _logger.info("Gene records table is empty.")
             return False
 
         with self.conn.cursor() as cur:
             cur.execute(self._check_merged_query)
             result = cur.fetchone()
         if not result or result[0] < 1:
-            logger.info("Normalized gene records table is empty.")
+            _logger.info("Normalized gene records table is empty.")
             return False
 
         return True
@@ -265,7 +265,7 @@ def _drop_indexes(self) -> None:
 
     def _create_tables(self) -> None:
         """Create all tables, indexes, and views."""
-        logger.debug("Creating new gene normalizer tables.")
+        _logger.info("Creating new gene normalizer tables.")
         tables_query = (SCRIPTS_DIR / "create_tables.sql").read_bytes()
 
         with self.conn.cursor() as cur:
@@ -599,7 +599,7 @@ def add_record(self, record: Dict, src_name: SourceName) -> None:
                     cur.execute(self._ins_symbol_query, [record["symbol"], concept_id])
                 self.conn.commit()
             except UniqueViolation:
-                logger.error(f"Record with ID {concept_id} already exists")
+                _logger.error(f"Record with ID {concept_id} already exists")
                 self.conn.rollback()
 
     _add_merged_record_query = b"""

src/gene/etl/base.py

@@ -6,7 +6,6 @@
 from pathlib import Path
 from typing import Dict, List, Optional, Union
 
-import click
 import pydantic
 from biocommons.seqrepo import SeqRepo
 from gffutils.feature import Feature
@@ -15,8 +14,7 @@
 from gene.database import AbstractDatabase
 from gene.schemas import ITEM_TYPES, Gene, GeneSequenceLocation, MatchType, SourceName
 
-logger = logging.getLogger("gene")
-logger.setLevel(logging.DEBUG)
+_logger = logging.getLogger(__name__)
 
 
 class GeneNormalizerEtlError(Exception):
@@ -80,11 +78,11 @@ def perform_etl(self, use_existing: bool = False) -> List[str]:
             uploaded.
         """
         self._extract_data(use_existing)
-        if not self._silent:
-            click.echo("Transforming and loading data to DB...")
+        _logger.info(f"Transforming and loading {self._src_name} data to DB...")
         self._add_meta()
         self._transform_data()
         self._database.complete_write_transaction()
+        _logger.info(f"Data load complete for {self._src_name}.")
         return self._processed_ids
 
     def _extract_data(self, use_existing: bool) -> None:
@@ -95,9 +93,11 @@ def _extract_data(self, use_existing: bool) -> None:
 
         :param bool use_existing: if True, don't try to fetch latest source data
         """
+        _logger.info(f"Gathering {self._src_name} data...")
         self._data_file, self._version = self._data_source.get_latest(
             from_local=use_existing
         )
+        _logger.info(f"Acquired data for {self._src_name}: {self._data_file}")
 
     @abstractmethod
     def _transform_data(self) -> None:
@@ -120,7 +120,7 @@ def _load_gene(self, gene: Dict) -> None:
         try:
             assert Gene(match_type=MatchType.NO_MATCH, **gene)
         except pydantic.ValidationError as e:
-            logger.warning(f"Unable to load {gene} due to validation error: " f"{e}")
+            _logger.warning(f"Unable to load {gene} due to validation error: " f"{e}")
         else:
             concept_id = gene["concept_id"]
             gene["label_and_type"] = f"{concept_id.lower()}##identity"
@@ -221,7 +221,7 @@ def _get_seq_id_aliases(self, seq_id: str) -> List[str]:
         try:
             aliases = self.seqrepo.translate_alias(seq_id, target_namespaces="ga4gh")
         except KeyError as e:
-            logger.warning(f"SeqRepo raised KeyError: {e}")
+            _logger.warning(f"SeqRepo raised KeyError: {e}")
         return aliases
 
     def _get_sequence_location(self, seq_id: str, gene: Feature, params: Dict) -> Dict:
@@ -248,7 +248,7 @@ def _get_sequence_location(self, seq_id: str, gene: Feature, params: Dict) -> Di
                     sequence_id=sequence,
                 ).model_dump()  # type: ignore
             else:
-                logger.warning(
+                _logger.warning(
                     f"{params['concept_id']} has invalid interval:"
                     f"start={gene.start - 1} end={gene.end}"
                 )  # type: ignore

src/gene/etl/ensembl.py

@@ -9,8 +9,7 @@
 from gene.etl.base import Base, GeneNormalizerEtlError
 from gene.schemas import NamespacePrefix, SourceMeta, SourceName, Strand
 
-logger = logging.getLogger("gene")
-logger.setLevel(logging.DEBUG)
+_logger = logging.getLogger(__name__)
 
 
 class Ensembl(Base):
@@ -24,16 +23,18 @@ def _extract_data(self, use_existing: bool) -> None:
 
         :param use_existing: if True, don't try to fetch latest source data
         """
+        _logger.info("Gathering Ensembl data...")
         self._data_file, raw_version = self._data_source.get_latest(
             from_local=use_existing
         )
         match = re.match(r"(GRCh\d+)_(\d+)", raw_version)
         self._assembly = match.groups()[0]
         self._version = match.groups()[1]
+        _logger.info(f"Acquired data for Ensembl: {self._data_file}")
 
     def _transform_data(self) -> None:
         """Transform the Ensembl source."""
-        logger.info("Transforming Ensembl...")
+        _logger.info("Transforming Ensembl data...")
         db = gffutils.create_db(
             str(self._data_file),
             dbfn=":memory:",
@@ -56,7 +57,7 @@ def _transform_data(self) -> None:
                     gene = self._add_gene(f, accession_numbers)
                     if gene:
                         self._load_gene(gene)
-        logger.info("Successfully transformed Ensembl.")
+        _logger.info("Ensembl data transform complete.")
 
     def _add_gene(self, f: Feature, accession_numbers: Dict) -> Dict:
         """Create a transformed gene record.

src/gene/etl/hgnc.py

@@ -15,16 +15,15 @@
     SymbolStatus,
 )
 
-logger = logging.getLogger("gene")
-logger.setLevel(logging.DEBUG)
+_logger = logging.getLogger(__name__)
 
 
 class HGNC(Base):
     """ETL the HGNC source into the normalized database."""
 
     def _transform_data(self) -> None:
         """Transform the HGNC source."""
-        logger.info("Transforming HGNC...")
+        _logger.info("Transforming HGNC data...")
         with open(self._data_file, "r") as f:  # type: ignore
             data = json.load(f)
 
@@ -55,7 +54,7 @@ def _transform_data(self) -> None:
             if "locus_type" in r:
                 gene["gene_type"] = r["locus_type"]
                 self._load_gene(gene)
-        logger.info("Successfully transformed HGNC.")
+        _logger.info("HGNC data transform complete.")
 
     def _get_aliases(self, r: Dict, gene: Dict) -> None:
         """Store aliases in a gene record.
@@ -136,7 +135,7 @@ def _get_xrefs_associated_with(self, r: Dict, gene: Dict) -> None:
                     else:
                         self._get_xref_associated_with(key, src, r, associated_with)
                 else:
-                    logger.warning(f"{key} not in schemas.py")
+                    _logger.warning(f"{key} not in schemas.py")
 
         if xrefs:
             gene["xrefs"] = xrefs