`nexusLIMS.config`#

Centralized environment variable management for NexusLIMS.

This module uses pydantic-settings to define, validate, and access application settings from environment variables and .env files. It provides a single source of truth for configuration, ensuring type safety and simplifying access throughout the application.

The settings object can be imported and used throughout the application. In tests, use refresh_settings() to reload settings after modifying environment variables.

Module Contents#

Classes#

`NemoHarvesterConfig`	Configuration for a single NEMO harvester instance.
`EmailConfig`	Config for email notifications from the nexuslims build-records script.
`Settings`	Manage application settings loaded from environment variables and `.env` files.

Functions#

`refresh_settings`	Refresh the settings singleton from current environment variables.
`clear_settings`	Clear the settings cache without immediately creating a new instance.
`read_labarchives_env`	Read LabArchives settings without triggering full Settings validation.

Data#

`TEST_MODE`
`settings`	The settings “singleton” - accessed like a normal object in the application

API#

nexusLIMS.config.TEST_MODE#

class nexusLIMS.config.NemoHarvesterConfig(/, **data: Any)[source]#

Bases: pydantic.BaseModel

Configuration for a single NEMO harvester instance.

address#: Type: nexusLIMS.config.TestAwareHttpUrl

token#: Type: str

strftime_fmt#: Type: str

strptime_fmt#: Type: str

tz#: Type: str | None

classmethod validate_trailing_slash(v: str | AnyHttpUrl) → str | AnyHttpUrl[source]#: Ensure the API address has a trailing slash.

class nexusLIMS.config.EmailConfig(/, **data: Any)[source]#

Bases: pydantic.BaseModel

Config for email notifications from the nexuslims build-records script.

smtp_host#: Type: str

smtp_port#: Type: int

smtp_username#: Type: str | None

smtp_password#: Type: str | None

use_tls#: Type: bool

sender#: Type: nexusLIMS.config.TestAwareEmailStr

recipients#: Type: list[nexusLIMS.config.TestAwareEmailStr]

Bases: pydantic_settings.BaseSettings

Manage application settings loaded from environment variables and .env files.

This class utilizes pydantic-settings to provide a robust and type-safe way to define, validate, and access all application configurations. It ensures that settings are loaded with proper types and provides descriptions for each.

model_config#: ‘SettingsConfigDict(…)’

NX_FILE_STRATEGY#: Type: typing.Literal[exclusive, inclusive]

NX_IGNORE_PATTERNS#: Type: list[str]

NX_INSTRUMENT_DATA_PATH#: Type: nexusLIMS.config.TestAwareDirectoryPath

NX_DATA_PATH#: Type: nexusLIMS.config.TestAwareDirectoryPath

NX_DB_PATH#: Type: nexusLIMS.config.TestAwareFilePath

NX_CDCS_TOKEN#: Type: str

NX_CDCS_URL#: Type: nexusLIMS.config.TestAwareHttpUrl

NX_LABARCHIVES_ACCESS_KEY_ID#: Type: str | None

NX_LABARCHIVES_ACCESS_PASSWORD#: Type: str | None

NX_LABARCHIVES_USER_ID#: Type: str | None

NX_LABARCHIVES_URL#: Type: nexusLIMS.config.TestAwareHttpUrl | None

NX_LABARCHIVES_NOTEBOOK_ID#: Type: str | None

NX_EXPORT_STRATEGY#: Type: typing.Literal[all, first_success, best_effort]

NX_CERT_BUNDLE_FILE#: Type: nexusLIMS.config.TestAwareFilePath | None

NX_CERT_BUNDLE#: Type: str | None

NX_DISABLE_SSL_VERIFY#: Type: bool

NX_FILE_DELAY_DAYS#: Type: float

NX_CLUSTERING_SENSITIVITY#: Type: float

NX_LOG_PATH#: Type: nexusLIMS.config.TestAwareDirectoryPath | None

NX_RECORDS_PATH#: Type: nexusLIMS.config.TestAwareDirectoryPath | None

NX_LOCAL_PROFILES_PATH#: Type: nexusLIMS.config.TestAwareDirectoryPath | None

NX_ELABFTW_API_KEY#: Type: str | None

NX_ELABFTW_URL#: Type: nexusLIMS.config.TestAwareHttpUrl | None

NX_ELABFTW_EXPERIMENT_CATEGORY#: Type: int | None

NX_ELABFTW_EXPERIMENT_STATUS#: Type: int | None

property nexuslims_instrument_data_path: Path#: Alias for NX_INSTRUMENT_DATA_PATH for easier access.

property lock_file_path: Path#: Path to the record builder lock file.

property log_dir_path: Path#: Base directory for timestamped log files.

property records_dir_path: Path#: Base directory for generated XML records.

nemo_harvesters() → dict[int, NemoHarvesterConfig][source]#

Dynamically discover and parse all NEMO harvester configurations.

Searches environment variables for NX_NEMO_ADDRESS_N patterns and constructs NemoHarvesterConfig objects for each numbered harvester.

Returns:: Dictionary mapping harvester number (1, 2, 3, …) to configuration objects. Empty dict if no harvesters are configured.
Return type:: dict[int, NemoHarvesterConfig]

Examples:

With environment variables:

NX_NEMO_ADDRESS_1=https://nemo1.com/api/
NX_NEMO_TOKEN_1=token123
NX_NEMO_ADDRESS_2=https://nemo2.com/api/
NX_NEMO_TOKEN_2=token456
NX_NEMO_TZ_2=America/New_York

The resulting output will be of the following format:

{
    1: NemoHarvesterConfig(
        address='https://nemo1.com/api/', token='token123', ...
    ),
    2: NemoHarvesterConfig(
        address='https://nemo2.com/api/',
        token='token456',
        tz='America/New_York',
        ...
    )
}

email_config() → EmailConfig | None[source]#

Load email configuration from environment variables if available.

This method is cached per Settings instance for performance.

Returns:: Email configuration object if all required settings are present, None otherwise (email notifications will be disabled).
Return type:: EmailConfig | None

Examples:

With environment variables:

NX_EMAIL_SMTP_HOST=smtp.gmail.com
NX_EMAIL_SENDER=nexuslims@example.com
NX_EMAIL_RECIPIENTS=admin@example.com,team@example.com

Optional variables:

NX_EMAIL_SMTP_PORT=587
NX_EMAIL_SMTP_USERNAME=user@example.com
NX_EMAIL_SMTP_PASSWORD=secret
NX_EMAIL_USE_TLS=true

nexusLIMS.config.refresh_settings() → Settings[source]#

Refresh the settings singleton from current environment variables.

This forces a reload of all settings from the environment. Primarily useful for testing.

Returns:: The newly created settings instance
Return type:: Settings

Examples:

>>> from nexusLIMS.config import settings, refresh_settings
>>> import os
>>>
>>> os.environ["NX_FILE_STRATEGY"] = "inclusive"
>>> refresh_settings()
>>>
>>> assert settings.NX_FILE_STRATEGY == "inclusive"

nexusLIMS.config.clear_settings() → None[source]#

Clear the settings cache without immediately creating a new instance.

The next import or access to settings will create a fresh instance. Useful in test teardown to ensure clean state.

nexusLIMS.config.settings#

‘_SettingsProxy(…)’

The settings “singleton” - accessed like a normal object in the application

nexusLIMS.config.read_labarchives_env(env_path: str | Path = '.env') → dict[str, str | None][source]#

Read LabArchives settings without triggering full Settings validation.

Merges values from the given .env file and the process environment (environment variables take precedence), returning only the five NX_LABARCHIVES_* keys. No other configuration is read or validated.

This is intended for CLI helper commands (e.g. labarchives-get-uid) that need only LabArchives credentials and must not fail due to missing core NexusLIMS settings (NX_INSTRUMENT_DATA_PATH etc.).

Parameters:: env_path (str or Path, optional) – Path to the .env file. Missing files are silently ignored.
Returns:: Mapping of the five NX_LABARCHIVES_* env-var names to their values (or None if not set).
Return type:: dict[str, str | None]

nexusLIMS.config#

Module Contents#

Classes#

Functions#

Data#

API#

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`nexusLIMS.config`#