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oa-configurator

A shared configuration layer for the OMOP-oriented Python stack.

oa-configurator gives OMOP tools a single typed configuration file instead of a tangle of environment variables and package-local .env files.

Key Concepts

  • Connection: A concrete database endpoint (host, dialect, credentials)
  • Database: A named database built on a connection. Comes in two kinds (see Architecture): a plain generic database, or a CDM database with its vocab/results role bundle
  • Provider / Model: The same two-tier pattern as Connection/Database, for LLM and embedding backends
  • Vector Store: Which storage backend an embedding-capable package should use, pointing at a generic database
  • Tool: Per-tool settings, e.g. which database/model/vector store a package uses
  • Logging: One call configures consistent log output for the entire OMOP Python stack

Info

Configuration lives in one TOML file (default ~/.config/omop/config.toml, overridable via OA_CONFIG_PATH) and is loaded once. The Resolver turns logical names into typed, credential-resolved handles ready for use.

Quick Example

from oa_configurator import load_stack_config, Resolver

config = load_stack_config()                        # reads CONFIG_PATH (default ~/.config/omop/config.toml)
resolver = Resolver(config)

database = resolver.resolve_database("cdm")
engine   = database.create_engine()                 # SQLAlchemy Engine, schema_translate_map applied

from oa_configurator import StackConfig, ConnectionConfig, CDMDatabaseConfig, Resolver

config = StackConfig.for_session(
    connections={"local": ConnectionConfig(dialect="postgresql+psycopg", host="localhost",
                                            database_name="omop", password="omop")},
    databases={"cdm": CDMDatabaseConfig(connection="local", schema_name="omop")},
)
engine = Resolver(config).resolve_database("cdm").create_engine()

from oa_configurator import load_stack_config, ConnectionConfig, CDMDatabaseConfig, Resolver

# Load shared team config, redirect one database to a local SQLite connection
engine = (
    Resolver(load_stack_config())
    .with_overrides(
        connections={"local": ConnectionConfig(dialect="sqlite", database_name="/data/local.db")},
        databases={"cdm": CDMDatabaseConfig(connection="local", schema_name="omop")},
    )
    .resolve_database("cdm")
    .create_engine()
)

Next Steps