Configuration
Application Configuration
The RecordLinker application is configured via a
pydantic-settings
configuration class. The settings are loaded from environment variables or a .env
file,
allowing for easy customization without modifying the code. When both an environment
variable and a .env
file are present, the environment variable takes precedence.
Configuration Settings
Each setting can be configured as follows:
DB_URI (Required)
-
The URI for the application database.
Example:
postgresql+psycopg2://user:password@localhost/dbname
DB_TABLE_PREFIX (Optional)
-
Prefix applied to all database tables, useful for namespace separation.
Docker Default:
""
Development Default:
""
TEST_DB_URI (Optional)
-
The URI for the application database used when running tests.
Docker Default:
sqlite:///testdb.sqlite3
Development Default:
sqlite:///testdb.sqlite3
CONNECTION_POOL_SIZE (Optional)
-
Number of connections in the MPI database connection pool.
Docker Default:
5
Development Default:
5
CONNECTION_POOL_MAX_OVERFLOW (Optional)
-
Maximum number of overflow connections allowed in the connection pool.
Docker Default:
10
Development Default:
10
LOG_CONFIG (Optional)
-
Path to a logging configuration file, used to configure logging settings on startup. A value of an empty string will cause logging to use default settings.
Docker Default:
"assets/production_log_config.json"
Development Default:
""
INITIAL_ALGORITHMS (Optional)
-
Path to a JSON file with initial algorithms to load if the algorithms table is empty.
Docker Default:
assets/initial_algorithms.json
Development Default:
assets/initial_algorithms.json
Database Options
The DB_URI
and TEST_DB_URI
settings can be configured to connect to a compatible
SQLAlchemy database. By default, the following database
drivers are installed allowing for connections to:
-
sqlite3 (sqlite)
Example:
sqlite:///db.sqlite3
-
psycopg2 (postgresql)
Example:
postgresql+psycopg2://user:password@localhost/dbname
-
pymysql (mysql)
Example:
mysql+pymysql://user:password@localhost/dbname
-
pyodbc (sqlite)
Example:
mssql+pyodbc://user:password@localhost/dbname?driver=ODBC+Driver+17+for+SQL+Server
Docker Configuration
In addition to the above application settings that can be configured via environment variables, the Dockerfile can be built with the build arguments to customize the container.
ENVIRONMENT (Optional)
-
The environment to install python packages for. Options are
dev
orprod
, see thepyproject.toml
file for details on the list of packages installed for each environment.Default:
prod
PORT (Optional)
-
The port the application will listen on.
Default:
8080
USE_MSSQL (Optional)
-
Whether to install the
pyodbc
package for connecting to a Microsoft SQL Server database. This is required if connecting to a Microsoft SQL Server database.Default:
true
USE_OTEL (Optional)
-
Whether to install the
opentelemetry-instrumentation
package for tracing.Default:
false
Note: For information on Algorithm Configuration, see the Reference section.