rename

README.md

@@ -57,9 +57,9 @@ $ curl 'https://normalize.cancervariants.org/gene/normalize?q=BRAF' | python -m
 Or utilize the [Python API](https://gene-normalizer.readthedocs.io/en/latest/api/query_api.html) for fast access:
 
 ```python
->>> from gene.database import create_db
+>>> from gene.database import get_db
 >>> from gene.query import QueryHandler
->>> q = QueryHandler(create_db())
+>>> q = QueryHandler(get_db())
 >>> result = q.normalize("KRAS")
 >>> result.normalized_id
 'hgnc:6407'

docs/scripts/generate_normalize_figure.py

@@ -12,7 +12,7 @@
 
 import gravis as gv
 
-from gene.database import create_db
+from gene.database import get_db
 from gene.etl.base import APP_ROOT
 from gene.query import QueryHandler
 from gene.schemas import UnmergedNormalizationService
@@ -80,7 +80,7 @@ def create_gjgf(result: UnmergedNormalizationService) -> Dict:
 
 def gen_norm_figure() -> None:
     """Generate normalized graph figure for docs."""
-    q = QueryHandler(create_db())
+    q = QueryHandler(get_db())
 
     otx2p1 = "OTX2P1"
     otx2p2 = "OTX2P2"

docs/source/index.rst

@@ -30,8 +30,8 @@ The Gene Normalizer can also be installed locally as a Python package for fast a
 .. code-block:: pycon
 
     >>> from gene.query import QueryHandler
-    >>> from gene.database import create_db
-    >>> q = QueryHandler(create_db())
+    >>> from gene.database import get_db
+    >>> q = QueryHandler(get_db())
     >>> result = q.normalize("BRAF")
     >>> result.normalized_id
     'hgnc:1097'

docs/source/usage.rst

@@ -28,17 +28,17 @@ Each search mode can be accessed directly within Python using the :ref:`query AP
 
 .. code-block:: pycon
 
-    >>> from gene.database import create_db
+    >>> from gene.database import get_db
     >>> from gene.query import QueryHandler
-    >>> q = QueryHandler(create_db())
+    >>> q = QueryHandler(get_db())
     >>> normalized_response = q.normalize('HER2')
     >>> normalized_response
     >>> normalized_response.match_type
     <MatchType.ALIAS: 60>
     >>> normalized_response.gene.label
     'ERBB2'
 
-Critically, the ``QueryHandler`` class must receive a database interface instance as its first argument. The most straightforward way to construct a database instance, as demonstrated above, is with the :py:meth:`create_db() <gene.database.database.create_db>` method. This method tries to build a database connection based on a number of conditions, which are resolved in the following order:
+Critically, the ``QueryHandler`` class must receive a database interface instance as its first argument. The most straightforward way to construct a database instance, as demonstrated above, is with the :py:meth:`get_db() <gene.database.database.get_db>` method. This method tries to build a database connection based on a number of conditions, which are resolved in the following order:
 
 1) if environment variable ``GENE_NORM_ENV`` is set to a value, or if the ``aws_instance`` method argument is True, try to create a cloud DynamoDB connection
 2) if the ``db_url`` method argument is given a non-None value, try to create a DB connection to that address (if it looks like a PostgreSQL URL, create a PostgreSQL connection, but otherwise try DynamoDB)

src/gene/cli.py

@@ -5,7 +5,7 @@
 
 import click
 
-from gene.database import create_db
+from gene.database import get_db
 from gene.database.database import DatabaseError
 from gene.etl.update import update_all_sources, update_normalized, update_source
 from gene.schemas import SourceName
@@ -79,7 +79,7 @@ def update(
         click.echo(ctx.get_help())
         ctx.exit(1)
 
-    db = create_db(db_url, aws_instance, silent)
+    db = get_db(db_url, aws_instance, silent)
 
     processed_ids = None
     if all:
@@ -129,7 +129,7 @@ def update_from_remote(data_url: Optional[str], db_url: str, silent: bool) -> No
         click.get_current_context().exit()
     if not data_url:
         data_url = os.environ.get("GENE_NORM_REMOTE_DB_URL")
-    db = create_db(db_url, False, silent)
+    db = get_db(db_url, False, silent)
     try:
         db.load_from_remote(data_url)
     except NotImplementedError:
@@ -165,8 +165,8 @@ def check_db(db_url: str, verbose: bool, silent: bool) -> None:
     This command is equivalent to the combination of the database classes'
     ``check_schema_initialized()`` and ``check_tables_populated()`` methods:
 
-    >>> from gene.database import create_db
-    >>> db = create_db()
+    >>> from gene.database import get_db
+    >>> db = get_db()
     >>> db.check_schema_initialized() and db.check_tables_populated()
     True  # DB passes checks
 
@@ -175,7 +175,7 @@ def check_db(db_url: str, verbose: bool, silent: bool) -> None:
     :param verbose: if true, print result to console
     :param silent: if True, suppress console output
     """  # noqa: D301
-    db = create_db(db_url, False, silent)
+    db = get_db(db_url, False, silent)
     if not db.check_schema_initialized():
         if verbose:
             click.echo("Health check failed: DB schema uninitialized.")
@@ -212,7 +212,7 @@ def dump_database(output_directory: Path, db_url: str, silent: bool) -> None:
     if not output_directory:
         output_directory = Path(".")
 
-    db = create_db(db_url, False, silent)
+    db = get_db(db_url, False, silent)
     try:
         db.export_db(output_directory)
     except NotImplementedError:

src/gene/database/__init__.py

@@ -1,10 +1,18 @@
 """Provide database clients."""
 from .database import (
     AWS_ENV_VAR_NAME,
-    AbstractDatabase,
     DatabaseError,
     DatabaseInitializationError,
     DatabaseReadError,
     DatabaseWriteError,
-    create_db,
+    get_db,
 )
+
+__all__ = [
+    "AWS_ENV_VAR_NAME",
+    "DatabaseError",
+    "DatabaseInitializationError",
+    "DatabaseReadError",
+    "DatabaseWriteError",
+    "get_db",
+]

src/gene/database/database.py

@@ -152,9 +152,9 @@ def get_all_records(self, record_type: RecordType) -> Generator[Dict, None, None
 
         For example,
 
-        >>> from gene.database import create_db
+        >>> from gene.database import get_db
         >>> from gene.schemas import RecordType
-        >>> db = create_db()
+        >>> db = get_db()
         >>> for record in db.get_all_records(RecordType.MERGER):
         >>>     pass  # do something
 
@@ -274,7 +274,7 @@ def confirm_aws_db_use(env_name: AwsEnvName) -> None:
         sys.exit()
 
 
-def create_db(
+def get_db(
     db_url: Optional[str] = None, aws_instance: bool = False, silent: bool = False
 ) -> AbstractDatabase:
     """Database factory method. Checks environment variables and provided parameters
@@ -286,18 +286,18 @@ def create_db(
 
     Some examples:
 
-    >>> from gene.database import create_db
-    >>> default_db = create_db()  # by default, creates DynamoDB connection on port 8000
+    >>> from gene.database import get_db
+    >>> default_db = get_db()  # by default, creates DynamoDB connection on port 8000
     >>>
     >>> postgres_url = "postgresql://postgres@localhost:5432/gene_normalizer"
-    >>> pg_db = create_db(postgres_url)  # creates Postgres connection at port 5432
+    >>> pg_db = get_db(postgres_url)  # creates Postgres connection at port 5432
     >>>
     >>> import os
     >>> os.environ["GENE_NORM_DB_URL"] = "http://localhost:8001"
-    >>> local_db = create_db()  # creates DynamoDB connection on port 8001
+    >>> local_db = get_db()  # creates DynamoDB connection on port 8001
     >>>
     >>> os.environ["GENE_NORM_ENV"] = "Prod"
-    >>> prod_db = create_db()  # creates connection to AWS cloud DynamoDB instance,
+    >>> prod_db = get_db()  # creates connection to AWS cloud DynamoDB instance,
     >>>                        # overruling `GENE_NORM_DB_URL` variable setting
 
     Precedence is handled for connection settings like so:

src/gene/database/dynamodb.py

@@ -321,9 +321,9 @@ def get_all_records(self, record_type: RecordType) -> Generator[Dict, None, None
 
         For example,
 
-        >>> from gene.database import create_db
+        >>> from gene.database import get_db
         >>> from gene.schemas import RecordType
-        >>> db = create_db()
+        >>> db = get_db()
         >>> for record in db.get_all_records(RecordType.MERGER):
         >>>     pass  # do something
 

src/gene/database/postgresql.py

@@ -465,9 +465,9 @@ def get_all_records(self, record_type: RecordType) -> Generator[Dict, None, None
 
         For example,
 
-        >>> from gene.database import create_db
+        >>> from gene.database import get_db
         >>> from gene.schemas import RecordType
-        >>> db = create_db()
+        >>> db = get_db()
         >>> for record in db.get_all_records(RecordType.MERGER):
         >>>     pass  # do something
 

src/gene/etl/update.py

@@ -99,9 +99,9 @@ def update_source(
     For example, to completely refresh HGNC data:
 
     >>> from gene.schemas import SourceName
-    >>> from gene.database import create_db
+    >>> from gene.database import get_db
     >>> from gene.etl.update import update_source
-    >>> db = create_db()
+    >>> db = get_db()
     >>> processed_ids = update_source(SourceName.HGNC, db)
 
     :param source: name of source to update
@@ -203,9 +203,9 @@ def update_all_and_normalize(
 
     For example, to completely refresh all Gene Normalizer data:
 
-    >>> from gene.database import create_db
+    >>> from gene.database import get_db
     >>> from gene.etl.update import update_all_and_normalize
-    >>> db = create_db()
+    >>> db = get_db()
     >>> update_all_and_normalize(db, False)
 
     :param db: database instance

src/gene/main.py

@@ -5,7 +5,7 @@
 from fastapi import FastAPI, HTTPException, Query
 
 from gene import __version__
-from gene.database import create_db
+from gene.database import get_db
 from gene.query import QueryHandler
 from gene.schemas import (
     SOURCES,
@@ -15,7 +15,7 @@
     UnmergedNormalizationService,
 )
 
-db = create_db()
+db = get_db()
 query_handler = QueryHandler(db)
 
 description = """

src/gene/query.py

@@ -42,15 +42,15 @@ class QueryHandler:
 
     def __init__(self, database: AbstractDatabase) -> None:
         """Initialize QueryHandler instance. Requires a created database object to
-        initialize. The most straightforward way to do this is via the ``create_db``
+        initialize. The most straightforward way to do this is via the ``get_db``
         method in the ``gene.database`` module:
 
         >>> from gene.query import QueryHandler
-        >>> from gene.database import create_db
-        >>> q = QueryHandler(create_db())
+        >>> from gene.database import get_db
+        >>> q = QueryHandler(get_db())
 
-        We'll generally call ``create_db`` without any arguments in code examples, for
-        the sake of brevity. See the `usage` page in the docs and the ``create_db`` API
+        We'll generally call ``get_db`` without any arguments in code examples, for
+        the sake of brevity. See the `usage` page in the docs and the ``get_db`` API
         description for more details.
 
         :param database: storage backend to search against
@@ -286,8 +286,8 @@ def search(
         """Return highest match for each source.
 
         >>> from gene.query import QueryHandler
-        >>> from gene.database import create_db
-        >>> q = QueryHandler(create_db())
+        >>> from gene.database import get_db
+        >>> q = QueryHandler(get_db())
         >>> result = q.search("BRAF")
         >>> result.source_matches[0].records[0].concept_id
         'ncbigene:673'
@@ -515,8 +515,8 @@ def normalize(self, query: str) -> NormalizeService:
         Use to retrieve normalized gene concept records:
 
         >>> from gene.query import QueryHandler
-        >>> from gene.database import create_db
-        >>> q = QueryHandler(create_db())
+        >>> from gene.database import get_db
+        >>> q = QueryHandler(get_db())
         >>> result = q.normalize("BRAF")
         >>> result.normalized_id
         'hgnc:1097'
@@ -671,9 +671,9 @@ def normalize_unmerged(self, query: str) -> UnmergedNormalizationService:
         provided query string.
 
         >>> from gene.query import QueryHandler
-        >>> from gene.database import create_db
+        >>> from gene.database import get_db
         >>> from gene.schemas import SourceName
-        >>> q = QueryHandler(create_db())
+        >>> q = QueryHandler(get_db())
         >>> response = q.normalize_unmerged("BRAF")
         >>> response.match_type
         <MatchType.CONCEPT_ID: 100>

tests/conftest.py

@@ -3,13 +3,13 @@
 
 import pytest
 
-from gene.database import AbstractDatabase, create_db
+from gene.database import AbstractDatabase, get_db
 
 
 @pytest.fixture(scope="session")
 def database() -> AbstractDatabase:
     """Create database instance."""
-    return create_db()
+    return get_db()
 
 
 def pytest_addoption(parser):

tests/unit/test_emit_warnings.py

@@ -1,5 +1,5 @@
 """Test the emit_warnings function."""
-from gene.database import create_db
+from gene.database import get_db
 from gene.query import QueryHandler
 
 
@@ -10,7 +10,7 @@ def test_emit_warnings():
             "non_breaking_space_characters": "Query contains non-breaking space characters"
         }
     ]
-    db = create_db()
+    db = get_db()
     query_handler = QueryHandler(db)
 
     # Test emit no warnings