oa-configurator

oa-configurator is a shared configuration layer for the OMOP-oriented Python stack: one typed config.toml file instead of a tangle of environment variables and package-local .env files.

Core concepts

Connection: a concrete database endpoint (dialect, host, credentials)
Database: a named database built on a connection, one of two kinds: 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-package settings, e.g. which database/model/vector store a package uses

A consuming package subclasses PackageConfigBase, declares its fields with RefTo(...) to name entries in the sections above, and registers via a pyproject.toml entry point. omop-config configure <package> then discovers it and interactively resolves or creates whatever it needs.

Install

pip install oa-configurator

Example

from oa_configurator import load_stack_config, Resolver

config = load_stack_config()          # OA_CONFIG_PATH is read at import; set it before process startup
resolver = Resolver(config)

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

Or without a file, for tests and scripts:

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_db": CDMDatabaseConfig(connection="local", schema_name="omop")},
)
engine = Resolver(config).resolve_database("cdm_db").create_engine()

Security

Passwords and API keys are currently stored in plaintext. Restrict file permissions:

chmod 600 ~/.config/omop/config.toml

secret_source (env-var- and file-backed credential lookup, keeping secrets out of the TOML file entirely) is planned but not yet implemented; see Secrets.

Docs

Full documentation, including the config file reference, CLI usage, and package-integration guide: https://AustralianCancerDataNetwork.github.io/oa-configurator/

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