database
ensembl.utils.database
¶
Database module.
Query = TypeVar('Query', str, sqlalchemy.sql.expression.ClauseElement, sqlalchemy.sql.expression.TextClause)
module-attribute
¶
StrURL = TypeVar('StrURL', str, sqlalchemy.engine.URL)
module-attribute
¶
DBConnection
¶
Database connection handler, providing also the database's schema and properties.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
url
|
StrURL
|
URL to the database, e.g. |
required |
reflect
|
bool
|
Reflect the database schema or not. |
True
|
Source code in src/ensembl/utils/database/dbconnection.py
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|
db_name: Optional[str]
property
¶
Returns the database name.
dialect: str
property
¶
Returns the SQLAlchemy database dialect name of the database host.
host: Optional[str]
property
¶
Returns the database host.
port: Optional[int]
property
¶
Returns the port of the database host.
tables: dict[str, sqlalchemy.schema.Table]
property
¶
Returns the database tables keyed to their name, or an empty dict if no metadata was loaded.
url: str
property
¶
Returns the database URL.
begin(*args)
¶
Returns a context manager delivering a database connection with a transaction established.
Source code in src/ensembl/utils/database/dbconnection.py
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connect()
¶
Returns a new database connection.
Source code in src/ensembl/utils/database/dbconnection.py
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create_all_tables(metadata)
¶
Create the tables from the metadata and set the metadata.
This assumes the database is empty beforehand. If the tables already exist, they will be ignored.
If there are other tables, you may need to run self.load_metadata()
to update the metadata schema.
Source code in src/ensembl/utils/database/dbconnection.py
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create_table(table)
¶
Create a table in the database and update the metadata. Do nothing if the table already exists.
Source code in src/ensembl/utils/database/dbconnection.py
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dispose()
¶
Disposes of the connection pool.
Source code in src/ensembl/utils/database/dbconnection.py
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get_columns(table)
¶
Returns the column names for the given table.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
table
|
str
|
Table name. |
required |
Source code in src/ensembl/utils/database/dbconnection.py
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get_primary_key_columns(table)
¶
Returns the primary key column names for the given table.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
table
|
str
|
Table name. |
required |
Source code in src/ensembl/utils/database/dbconnection.py
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load_metadata()
¶
Loads the metadata information of the database.
Source code in src/ensembl/utils/database/dbconnection.py
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session_scope()
¶
Provides a transactional scope around a series of operations with rollback in case of failure.
Bear in mind MySQL's storage engine MyISAM does not support rollback transactions, so all the modifications performed to the database will persist.
Source code in src/ensembl/utils/database/dbconnection.py
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test_session_scope()
¶
Provides a transactional scope around a series of operations that will be rolled back at the end.
Bear in mind MySQL's storage engine MyISAM does not support rollback transactions, so all the modifications performed to the database will persist.
Source code in src/ensembl/utils/database/dbconnection.py
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UnitTestDB
¶
Creates and connects to a new test database, applying the schema and importing the data.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
server_url
|
StrURL
|
URL of the server hosting the database. |
required |
metadata
|
MetaData | None
|
Use this metadata to create the schema instead of using an SQL schema file. |
None
|
dump_dir
|
StrPath | None
|
Directory path with the database schema in |
None
|
name
|
str | None
|
Name to give to the new database. If not provided, the last directory name of |
None
|
tmp_path
|
StrPath | None
|
Temp dir where the test db is created if using SQLite (otherwise use current dir). |
None
|
Attributes:
Name | Type | Description |
---|---|---|
dbc |
Database connection handler. |
Raises:
Type | Description |
---|---|
FileNotFoundError
|
If |
Source code in src/ensembl/utils/database/unittestdb.py
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dbc = DBConnection(db_url, connect_args=connect_args, reflect=False)
instance-attribute
¶
drop()
¶
Drops the database.
Source code in src/ensembl/utils/database/unittestdb.py
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|