enhancement!: clean up __init__.py files

docs/scripts/generate_normalize_figure.py

@@ -12,8 +12,8 @@
 
 import gravis as gv
 
-from gene import APP_ROOT
 from gene.database import create_db
+from gene.etl.base import APP_ROOT
 from gene.query import QueryHandler
 from gene.schemas import UnmergedNormalizationService
 

src/gene/__init__.py

@@ -1,65 +1,4 @@
 """The VICC library for normalizing genes."""
-import logging
-from os import environ
-from pathlib import Path
+from .version import __version__
 
-from .version import __version__  # noqa: F401
-
-APP_ROOT = Path(__file__).resolve().parent
-
-logging.basicConfig(
-    filename="gene.log", format="[%(asctime)s] - %(name)s - %(levelname)s : %(message)s"
-)
-logger = logging.getLogger("gene")
-logger.setLevel(logging.DEBUG)
-logger.handlers = []
-
-logging.getLogger("boto3").setLevel(logging.INFO)
-logging.getLogger("botocore").setLevel(logging.INFO)
-logging.getLogger("urllib3").setLevel(logging.INFO)
-logging.getLogger("python_jsonschema_objects").setLevel(logging.INFO)
-logging.getLogger("biocommons.seqrepo.seqaliasdb.seqaliasdb").setLevel(logging.INFO)
-logging.getLogger("biocommons.seqrepo.fastadir.fastadir").setLevel(logging.INFO)
-
-
-SEQREPO_ROOT_DIR = Path(
-    environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")
-)
-
-
-class DownloadException(Exception):  # noqa: N818
-    """Exception for failures relating to source file downloads."""
-
-
-from gene.schemas import (  # noqa: E402
-    NamespacePrefix,
-    RefType,
-    SourceIDAfterNamespace,
-    SourceName,
-)
-
-ITEM_TYPES = {k.lower(): v.value for k, v in RefType.__members__.items()}
-
-# Sources we import directly (HGNC, Ensembl, NCBI)
-SOURCES = {
-    source.value.lower(): source.value for source in SourceName.__members__.values()
-}
-
-# Set of sources we import directly
-XREF_SOURCES = {src.lower() for src in SourceName.__members__}
-
-# use to fetch source name from schema based on concept id namespace
-# e.g. {"hgnc": "HGNC"}
-PREFIX_LOOKUP = {
-    v.value: SourceName[k].value
-    for k, v in NamespacePrefix.__members__.items()
-    if k in SourceName.__members__.keys()
-}
-
-# use to generate namespace prefix from source ID value
-# e.g. {"ensg": "ensembl"}
-NAMESPACE_LOOKUP = {
-    v.value.lower(): NamespacePrefix[k].value
-    for k, v in SourceIDAfterNamespace.__members__.items()
-    if v.value != ""
-}
+__all__ = ["__version__"]

src/gene/cli.py

@@ -7,15 +7,14 @@
 
 import click
 
-from gene import SOURCES
 from gene.database import (
     AbstractDatabase,
     DatabaseReadException,
     DatabaseWriteException,
     create_db,
 )
 from gene.database.database import DatabaseException
-from gene.schemas import SourceName
+from gene.schemas import SOURCES, SourceName
 
 logger = logging.getLogger("gene")
 logger.setLevel(logging.DEBUG)

src/gene/database/dynamodb.py

@@ -11,7 +11,6 @@
 from boto3.dynamodb.conditions import Key
 from botocore.exceptions import ClientError
 
-from gene import ITEM_TYPES, PREFIX_LOOKUP
 from gene.database.database import (
     AWS_ENV_VAR_NAME,
     SKIP_AWS_DB_ENV_NAME,
@@ -23,7 +22,14 @@
     DatabaseWriteException,
     confirm_aws_db_use,
 )
-from gene.schemas import RecordType, RefType, SourceMeta, SourceName
+from gene.schemas import (
+    ITEM_TYPES,
+    PREFIX_LOOKUP,
+    RecordType,
+    RefType,
+    SourceMeta,
+    SourceName,
+)
 
 logger = logging.getLogger(__name__)
 

src/gene/etl/base.py

@@ -6,7 +6,7 @@
 import shutil
 from abc import ABC, abstractmethod
 from ftplib import FTP
-from os import remove
+from os import environ, remove
 from pathlib import Path
 from typing import Callable, Dict, List, Optional
 
@@ -15,14 +15,19 @@
 from dateutil import parser
 from gffutils.feature import Feature
 
-from gene import ITEM_TYPES, SEQREPO_ROOT_DIR
 from gene.database import AbstractDatabase
-from gene.schemas import Gene, GeneSequenceLocation, MatchType, SourceName
+from gene.schemas import ITEM_TYPES, Gene, GeneSequenceLocation, MatchType, SourceName
 
 logger = logging.getLogger("gene")
 logger.setLevel(logging.DEBUG)
 
 
+APP_ROOT = Path(__file__).resolve().parent
+SEQREPO_ROOT_DIR = Path(
+    environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")
+)
+
+
 class Base(ABC):
     """The ETL base class."""
 

src/gene/etl/ensembl.py

@@ -10,9 +10,8 @@
 import requests
 from gffutils.feature import Feature
 
-from gene import APP_ROOT
 from gene.database import AbstractDatabase
-from gene.etl.base import Base
+from gene.etl.base import APP_ROOT, Base
 from gene.etl.exceptions import (
     GeneFileVersionError,
     GeneNormalizerEtlError,

src/gene/etl/hgnc.py

@@ -10,15 +10,15 @@
 
 from dateutil import parser
 
-from gene import APP_ROOT, PREFIX_LOOKUP
 from gene.database import AbstractDatabase
-from gene.etl.base import Base
+from gene.etl.base import APP_ROOT, Base
 from gene.etl.exceptions import (
     GeneFileVersionError,
     GeneNormalizerEtlError,
     GeneSourceFetchError,
 )
 from gene.schemas import (
+    PREFIX_LOOKUP,
     Annotation,
     Chromosome,
     NamespacePrefix,

src/gene/etl/ncbi.py

@@ -9,15 +9,15 @@
 
 import gffutils
 
-from gene import APP_ROOT, PREFIX_LOOKUP
 from gene.database import AbstractDatabase
-from gene.etl.base import Base
+from gene.etl.base import APP_ROOT, Base
 from gene.etl.exceptions import (
     GeneFileVersionError,
     GeneNormalizerEtlError,
     GeneSourceFetchError,
 )
 from gene.schemas import (
+    PREFIX_LOOKUP,
     Annotation,
     Chromosome,
     NamespacePrefix,

src/gene/main.py

@@ -4,10 +4,11 @@
 
 from fastapi import FastAPI, HTTPException, Query
 
-from gene import SOURCES, __version__
+from gene import __version__
 from gene.database import create_db
 from gene.query import QueryHandler
 from gene.schemas import (
+    SOURCES,
     NormalizeService,
     SearchService,
     SourceName,

src/gene/query.py

@@ -1,14 +1,17 @@
 """Provides methods for handling queries."""
+import logging
 import re
 from datetime import datetime
 from typing import Any, Callable, Dict, Iterable, List, Optional, Tuple, TypeVar
 
 from ga4gh.core import core_models, ga4gh_identify
 from ga4gh.vrs import models
 
-from gene import ITEM_TYPES, NAMESPACE_LOOKUP, PREFIX_LOOKUP, logger
 from gene.database import AbstractDatabase, DatabaseReadException
 from gene.schemas import (
+    ITEM_TYPES,
+    NAMESPACE_LOOKUP,
+    PREFIX_LOOKUP,
     BaseGene,
     BaseNormalizationService,
     Gene,
@@ -28,6 +31,7 @@
 )
 from gene.version import __version__
 
+_logger = logging.getLogger(__name__)
 NormService = TypeVar("NormService", bound=BaseNormalizationService)
 
 
@@ -72,7 +76,7 @@ def _emit_warnings(query_str: str) -> List:
                     "non_breaking_space_characters": "Query contains non-breaking space characters"
                 }
             ]
-            logger.warning(
+            _logger.warning(
                 f"Query ({query_str}) contains non-breaking space characters."
             )
         return warnings
@@ -188,14 +192,14 @@ def _fetch_record(
         try:
             match = self.db.get_record_by_id(concept_id, case_sensitive=False)
         except DatabaseReadException as e:
-            logger.error(
+            _logger.error(
                 f"Encountered DatabaseReadException looking up {concept_id}: {e}"
             )
         else:
             if match:
                 self._add_record(response, match, match_type)
             else:
-                logger.error(
+                _logger.error(
                     f"Unable to find expected record for {concept_id} matching as {match_type}"
                 )  # noqa: E501
 
@@ -263,7 +267,7 @@ def _get_search_response(self, query: str, sources: Iterable[SourceName]) -> Dic
                             matched_concept_ids.append(ref)
 
             except DatabaseReadException as e:
-                logger.error(
+                _logger.error(
                     f"Encountered DatabaseReadException looking up {item_type}"
                     f" {term}: {e}"
                 )
@@ -492,7 +496,7 @@ def _handle_failed_merge_ref(record: Dict, response: Dict, query: str) -> Dict:
         :param query: original query value
         :return: response with no match
         """
-        logger.error(
+        _logger.error(
             f"Merge ref lookup failed for ref {record['merge_ref']} "
             f"in record {record['concept_id']} from query {query}"
         )
@@ -557,7 +561,7 @@ def _resolve_merge(
             merge = self.db.get_record_by_id(merge_ref, False, True)
             if merge is None:
                 query = response.query
-                logger.error(
+                _logger.error(
                     f"Merge ref lookup failed for ref {record['merge_ref']} "
                     f"in record {record['concept_id']} from query `{query}`"
                 )

src/gene/schemas.py

@@ -147,6 +147,12 @@ class SourceName(Enum):
     NCBI = "NCBI"
 
 
+# lowercase imported source name to correctly-cased name, e.g. {"ensembl": "Ensembl"}
+SOURCES = {
+    source.value.lower(): source.value for source in SourceName.__members__.values()
+}
+
+
 class SourcePriority(IntEnum):
     """Define priorities for sources when building merged concepts."""
 
@@ -196,6 +202,23 @@ class NamespacePrefix(Enum):
     RFAM = "rfam"
 
 
+# use to fetch source name from schema based on concept id namespace
+# e.g. {"hgnc": "HGNC"}
+PREFIX_LOOKUP = {
+    v.value: SourceName[k].value
+    for k, v in NamespacePrefix.__members__.items()
+    if k in SourceName.__members__.keys()
+}
+
+# use to generate namespace prefix from source ID value
+# e.g. {"ensg": "ensembl"}
+NAMESPACE_LOOKUP = {
+    v.value.lower(): NamespacePrefix[k].value
+    for k, v in SourceIDAfterNamespace.__members__.items()
+    if v.value != ""
+}
+
+
 class DataLicenseAttributes(BaseModel):
     """Define constraints for data license attributes."""
 
@@ -222,6 +245,10 @@ class RefType(str, Enum):
     ASSOCIATED_WITH = "associated_with"
 
 
+# collective name to singular name, e.g. {"previous_symbols": "prev_symbol"}
+ITEM_TYPES = {k.lower(): v.value for k, v in RefType.__members__.items()}
+
+
 class SourceMeta(BaseModel):
     """Metadata for a given source to return in response object."""