Configure MetaSalmon

Package options are initialized on loading only when the user has not set a value. Credentials and inheritance settings remain unset. Environment variables are read at call time and are never set by package loading.

Details

The inventories below are generated from the same registry that owns the load defaults. The in-package LLM provider path is deprecated and removed in 0.7.0; its environment variables do not by themselves request a model call. Prefer the external semantic review packet workflow for new review work.

See also

ms_setup_github() for the GitHub credential helper, find_terms() for retrieval, create_sdp() for schema-backed creation.

Options

metasalmon.sdp_schema_source

Default: "auto". SDP schema source: "auto" tries the pinned remote release then the vendored copy; "remote" requires remote loading; "vendored" stays offline.

metasalmon.sdp_schema_base_url

Default: NULL (the pinned SDP release URL at call time). Base URL of a selected SDP schema bundle. When unset, each call resolves the package's current schema-release pin.

metasalmon.sdp_schema_url

Default: NULL. Legacy schema URL override. When nonempty, its schema/sdp.schema.yaml suffix is removed to obtain the bundle base URL; it takes precedence over sdp_schema_base_url.

metasalmon.term_search_timeout

Default: NULL (inherit backend timeout). Positive timeout in seconds. Source-specific environment timeout overrides the global environment timeout, which overrides this option. Unset/invalid falls back to the backend's 30 or 60 seconds.

metasalmon.term_search_parallel

Default: TRUE. Enable parallel term retrieval. METASALMON_TERM_SEARCH_PARALLEL takes precedence.

metasalmon.llm_deprecation_quiet

Default: FALSE. Suppress the in-package LLM deprecation warning. It does not enable a model call. The deprecated provider path is removed in 0.7.0.

metasalmon.validation_message_mode

Default: "default". Internal validation message mode: "default" or "review_ready". create_sdp temporarily sets and restores it; ordinarily leave it unchanged.

metasalmon.validation_semantics_seeded

Default: FALSE. Internal validation message context. create_sdp temporarily sets and restores it; ordinarily leave it unchanged.

metasalmon.knb_adapter

Default: NULL. Internal adapter injection hook for KNB tests. It does not change the closed publication-environment registry.

dataone_token

Default: NULL. Process-local production DataONE JWT. Set only when making an explicitly requested production publication; never persisted or supplied by package loading.

dataone_test_token

Default: NULL. Process-local DataONE test JWT, separate from dataone_token. No credential fallback between test and production.

Environment variables

BIOPORTAL_APIKEY

BioPortal API key. Missing keys produce one warning per loaded package namespace and an empty BioPortal result.

METASALMON_CACHE

Enable the process-local term-result cache with 1, true or yes; unset disables it.

METASALMON_EMBEDDING_RERANK

Enable embedding reranking with 1, true or yes; unset disables it.

METASALMON_EMBEDDING_WEIGHT

Embedding score weight; defaults to 1. Invalid/nonfinite values fall back to 1.

METASALMON_DEBUG

Enable embedding diagnostics with 1 or true; unset disables them.

METASALMON_TERM_SEARCH_TIMEOUT

Global positive retrieval timeout in seconds; overrides the option but yields to the source-specific variable.

METASALMON_TERM_SEARCH_TIMEOUT_<SOURCE>

Positive retrieval timeout for an uppercase source name, such as NVS, ZOOMA or QUDT; highest timeout precedence.

METASALMON_TERM_SEARCH_PARALLEL

Parallel override: 1/true/yes/on enables; 0/false/no/off disables; unset/unrecognized falls back to the option.

METASALMON_TERM_SEARCH_WORKERS

Positive worker-count override; otherwise worker count derives from source count and available cores.

OPENAI_API_KEY

OpenAI credential for the deprecated in-package provider path; only read on explicit LLM assessment.

OPENROUTER_API_KEY

OpenRouter credential for the deprecated in-package provider path; only read on explicit LLM assessment.

CHAPI_API_KEY

Chapi credential for the deprecated in-package provider path; only read on explicit LLM assessment.

METASALMON_LLM_API_KEY

OpenAI-compatible credential and fallback for provider-specific keys. Explicit llm_api_key takes precedence.

METASALMON_LLM_MODEL

Model fallback for the deprecated provider path. Explicit llm_model takes precedence; Chapi checks CHAPI_MODEL first.

CHAPI_MODEL

Chapi model fallback before METASALMON_LLM_MODEL; otherwise the Chapi model default applies.

METASALMON_LLM_BASE_URL

Endpoint fallback for the deprecated provider path. Explicit llm_base_url takes precedence; Chapi checks CHAPI_BASE_URL first.

CHAPI_BASE_URL

Chapi endpoint fallback before METASALMON_LLM_BASE_URL; otherwise the Chapi endpoint default applies.

METASALMON_LLM_REASONING_EFFORT

Reasoning-effort fallback for the deprecated provider path; explicit llm_reasoning_effort takes precedence.

Examples

old <- options(metasalmon.term_search_parallel = FALSE)
getOption("metasalmon.term_search_parallel")
#> [1] FALSE
options(old)