API Index

Complete alphabetical index of all public functions and methods in biosample-enricher.

Alphabetical API Index

This is a comprehensive alphabetical index of all public functions, methods, and constants in the biosample-enricher package.

Module Constants

Public constants exported by modules (typically used for configuration, validation, or schema definitions).

`_version`

`COMMIT_ID`

Value: Union[str, None]

`COMMIT_ID`

Value: object

`TYPE_CHECKING`

Value: False

`VERSION_TUPLE`

Value: Tuple[Union[int, str], ...]

`VERSION_TUPLE`

Value: object

`soil.models`

`USDA_TEXTURE_CLASSES`

Value: {'Sand': {'sand': (85, 100), 'clay': (0, 10)}, 'Loamy sand': {'sand': (70, 85), 'clay': (0, 15)},...

`environmental_metadata`

`ALL_SUPPORTED_SLOTS`

Value: CLIMATE_SLOTS | WEATHER_SLOTS | ELEVATION_SLOTS | MARINE_SLOTS | SOIL_SLOTS

`CLIMATE_PROVIDERS`

Value: frozenset(['meteostat', 'nasa_power'])

`CLIMATE_SLOTS`

Value: frozenset(['annual_precpt', 'annual_temp'])

`ELEVATION_SLOTS`

Value: frozenset(['elev'])

`MARINE_SLOTS`

Value: frozenset(['depth'])

`SOIL_SLOTS`

Value: frozenset(['ph', 'soil_type'])

`WEATHER_SLOTS`

Value: frozenset(['temp', 'air_temp', 'humidity', 'wind_speed', 'wind_direction', 'solar_irradiance'])

Functions and Methods

A

`analyze`

Type: function
Module: cli_biosample_elevation
Signature: analyze(input_file: Path) -> None
Description: Analyze biosample field mapping without performing elevation lookups.

`analyze`

Type: function
Module: cli_weather
Signature: analyze(input_file: str, source: str, output_dir: str | None, sample_limit: int | None)
Description: Analyze weather enrichment coverage for a collection of biosamples.

B

`BaseElevationProvider.init`

Type: method
Module: elevation.providers.base
Class: BaseElevationProvider
Signature: __init__(self, name: str, endpoint: str, api_version: str) -> None
Description: Initialize the provider.

`BaseElevationProvider.fetch`

Type: method
Module: elevation.providers.base
Class: BaseElevationProvider
Signature: fetch(self, lat: float, lon: float) -> FetchResult
Description: Fetch elevation data for the given coordinates.

`BaseReverseGeocodingProvider.init`

Type: method
Module: reverse_geocoding.providers.base
Class: BaseReverseGeocodingProvider
Signature: __init__(self, name: str, endpoint: str, api_version: str) -> None
Description: Initialize the provider.

`BaseReverseGeocodingProvider.fetch`

Type: method
Module: reverse_geocoding.providers.base
Class: BaseReverseGeocodingProvider
Signature: fetch(self, lat: float, lon: float) -> ReverseGeocodeFetchResult
Description: Fetch reverse geocoding data for the given coordinates.

`batch`

Type: function
Module: cli_soil
Signature: batch(input_file: Path, output: Path, depth: str, lat_col: str, lon_col: str, output_format: str, verbose: bool) -> None
Description: Enrich multiple locations from CSV or JSON file.

`batch`

Type: function
Module: cli_land
Signature: batch(input_file: str, date: datetime | None, time_window: int, output: str, batch_size: int)
Description: Process multiple locations from a file.

`batch`

Type: function
Module: cli_forward_geocoding
Signature: batch(input_file: str, language: str, output: str, batch_size: int)
Description: Process multiple place names from a file.

`batch`

Type: function
Module: cli_osm_features
Signature: batch(input_file: str, radius: int, timeout: int, output: str, batch_size: int)
Description: Process multiple locations from a file.

`batch`

Type: function
Module: cli_marine
Signature: batch(input: str, output: str | None, schema: str, max_samples: int | None)
Description: Batch marine enrichment for multiple biosamples.

`batch_elevation`

Type: function
Module: cli_elevation
Signature: batch_elevation(input_file: Path, output: str, providers: tuple[str, ...], timeout: float, lat_col: str, lon_col: str, id_col: str, no_cache: bool, read_cache: bool, write_cache: bool) -> None
Description: Process elevation lookups from CSV/TSV file.

`BiosampleAdapter.extract_location`

Type: method
Module: adapters
Class: BiosampleAdapter
Signature: extract_location(self, biosample_data: dict[str, Any]) -> BiosampleLocation
Description: Extract standardized location data from a single biosample.

`BiosampleAdapter.extract_locations_batch`

Type: method
Module: adapters
Class: BiosampleAdapter
Signature: extract_locations_batch(self, biosamples: list[dict[str, Any]]) -> list[BiosampleLocation]
Description: Extract location data from multiple biosamples.

`BiosampleElevationBatch.filter_valid_coordinates`

Type: method
Module: biosample_elevation_mapper
Class: BiosampleElevationBatch
Signature: filter_valid_coordinates(biosamples: list[dict[str, Any]]) -> list[dict[str, Any]]
Description: Filter biosamples to only those with valid coordinates.

`BiosampleElevationBatch.get_coordinate_summary`

Type: method
Module: biosample_elevation_mapper
Class: BiosampleElevationBatch
Signature: get_coordinate_summary(biosamples: list[dict[str, Any]]) -> dict[str, Any]
Description: Get summary statistics about coordinates in a biosample collection.

`BiosampleElevationMapper.create_elevation_request`

Type: method
Module: biosample_elevation_mapper
Class: BiosampleElevationMapper
Signature: create_elevation_request(biosample: dict[str, Any], preferred_providers: list[str] | None) -> ElevationRequest | None
Description: Create an ElevationRequest from biosample metadata.

`BiosampleElevationMapper.extract_coordinates`

Type: method
Module: biosample_elevation_mapper
Class: BiosampleElevationMapper
Signature: extract_coordinates(biosample: dict[str, Any]) -> tuple[float, float] | None
Description: Extract latitude and longitude from various biosample field structures.

`BiosampleElevationMapper.get_biosample_id`

Type: method
Module: biosample_elevation_mapper
Class: BiosampleElevationMapper
Signature: get_biosample_id(biosample: dict[str, Any]) -> str
Description: Extract a unique identifier from biosample metadata.

`BiosampleElevationMapper.get_field_mapping_info`

Type: method
Module: biosample_elevation_mapper
Class: BiosampleElevationMapper
Signature: get_field_mapping_info() -> dict[str, Any]
Description: Get comprehensive information about biosample field mappings.

`BiosampleElevationMapper.get_location_context`

Type: method
Module: biosample_elevation_mapper
Class: BiosampleElevationMapper
Signature: get_location_context(biosample: dict[str, Any]) -> dict[str, Any]
Description: Extract additional location context from biosample metadata.

`BiosampleElevationMapper.validate_coordinates`

Type: method
Module: biosample_elevation_mapper
Class: BiosampleElevationMapper
Signature: validate_coordinates(lat: float, lon: float) -> bool
Description: Validate that coordinates are within valid ranges.

`BiosampleLocation.calculate_completeness`

Type: method
Module: models
Class: BiosampleLocation
Signature: calculate_completeness(self) -> 'BiosampleLocation'
Description: Calculate location completeness score based on available fields.

`BiosampleLocation.is_enrichable`

Type: method
Module: models
Class: BiosampleLocation
Signature: is_enrichable(self) -> bool
Description: Check if sample has minimum data for API enrichment.

`BiosampleLocation.to_dict`

Type: method
Module: models
Class: BiosampleLocation
Signature: to_dict(self) -> dict
Description: Convert to dictionary for serialization with enrichable status.

`BiosampleLocation.validate_collection_date`

Type: method
Module: models
Class: BiosampleLocation
Signature: validate_collection_date(cls, v: str | None) -> str | None
Description: Validate collection date format.

`BiosampleMetricsFetcher.init`

Type: method
Module: metrics.fetcher
Class: BiosampleMetricsFetcher
Signature: __init__(self, nmdc_connection_string: str | None, gold_connection_string: str | None, nmdc_database: str, gold_database: str, nmdc_collection: str, gold_collection: str)
Description: Initialize metrics fetcher with database connections.

`BiosampleMetricsFetcher.fetch_all_samples`

Type: method
Module: metrics.fetcher
Class: BiosampleMetricsFetcher
Signature: fetch_all_samples(self, n_per_source: int, enrichable_only: bool) -> dict[str, tuple[list[dict[str, Any]], list[BiosampleLocation]]]
Description: Fetch random samples from both NMDC and GOLD.

`BiosampleMetricsFetcher.fetch_gold_samples`

Type: method
Module: metrics.fetcher
Class: BiosampleMetricsFetcher
Signature: fetch_gold_samples(self, n: int, enrichable_only: bool) -> tuple[list[dict[str, Any]], list[BiosampleLocation]]
Description: Fetch random GOLD samples.

`BiosampleMetricsFetcher.fetch_nmdc_samples`

Type: method
Module: metrics.fetcher
Class: BiosampleMetricsFetcher
Signature: fetch_nmdc_samples(self, n: int, enrichable_only: bool) -> tuple[list[dict[str, Any]], list[BiosampleLocation]]
Description: Fetch random NMDC samples.

C

`calculate_distance_m`

Type: function
Module: elevation.utils
Signature: calculate_distance_m(lat1: float, lon1: float, lat2: float, lon2: float) -> float
Description: Calculate the great circle distance between two points using the Haversine formula.

`canonicalize_coords`

Type: function
Module: http_cache
Signature: canonicalize_coords(params: dict[str, Any]) -> dict[str, Any]
Description: Canonicalize coordinate parameters for consistent caching.

`classify_texture`

Type: function
Module: soil.models
Signature: classify_texture(sand_pct: float, silt_pct: float, clay_pct: float) -> str
Description: Classify soil texture using USDA texture triangle.

`clear`

Type: function
Module: cache_management
Signature: clear(ctx: click.Context, confirm: bool) -> None
Description: Clear all cache entries.

`cli`

Type: function
Module: cache_management
Signature: cli(ctx: click.Context) -> None
Description: HTTP Cache Management CLI.

`cli`

Type: function
Module: elevation_demos
Signature: cli(log_level: str) -> None
Description: Elevation service demonstrations and batch processing.

`cli`

Type: function
Module: cli_biosample_elevation
Signature: cli(log_level: str) -> None
Description: Biosample elevation enrichment CLI with automatic field mapping.

`ClimateNormalsProvider.get_climate_normals`

Type: method
Module: weather.service
Class: ClimateNormalsProvider
Signature: get_climate_normals(self, lat: float, lon: float, start_year: int, end_year: int) -> ClimateNormalsResult

`ClimateNormalsResult.get_annual_precipitation`

Type: method
Module: weather.models
Class: ClimateNormalsResult
Signature: get_annual_precipitation(self) -> float | None
Description: Calculate annual precipitation by summing 12 monthly normals.

`ClimateNormalsResult.get_annual_temperature`

Type: method
Module: weather.models
Class: ClimateNormalsResult
Signature: get_annual_temperature(self) -> float | None
Description: Calculate annual average temperature from 12 monthly normals.

`ClimateNormalsResult.to_submission_schema`

Type: method
Module: weather.models
Class: ClimateNormalsResult
Signature: to_submission_schema(self) -> dict[str, Any]
Description: Extract values in submission-schema compatible format.

`CombinedFeaturesResult.to_enrichment_dict`

Type: method
Module: osm_features.models
Class: CombinedFeaturesResult
Signature: to_enrichment_dict(self) -> dict[str, Any]
Description: Convert combined results to enrichment dictionary.

`compare`

Type: function
Module: cli_forward_geocoding
Signature: compare(query: str, language: str, country: str | None, max_results: int, output: str | None, pretty: bool)
Description: Compare results from all available providers.

`compare_providers`

Type: function
Module: elevation_demos
Signature: compare_providers(lat: float, lon: float, providers: str, output: str) -> None
Description: Compare elevation results from different providers for a single coordinate.

`configure_from_env`

Type: function
Module: logging_config
Signature: configure_from_env() -> logging.Logger
Description: Configure logging from environment variables.

`CoordinateClassifier.init`

Type: method
Module: elevation.classifier
Class: CoordinateClassifier
Signature: __init__(self, enable_online_detection: bool, user_agent: str) -> None
Description: Initialize the coordinate classifier.

`CoordinateClassifier.classify`

Type: method
Module: elevation.classifier
Class: CoordinateClassifier
Signature: classify(self, lat: float, lon: float) -> CoordinateClassification
Description: Classify coordinates to determine appropriate providers.

`CoordinateClassifier.classify_biosample_location`

Type: method
Module: elevation.classifier
Class: CoordinateClassifier
Signature: classify_biosample_location(self, lat: float, lon: float) -> dict
Description: Classify a biosample location for routing and metadata.

`CoverageEvaluator.init`

Type: method
Module: metrics.evaluator
Class: CoverageEvaluator
Signature: __init__(self) -> None
Description: Initialize evaluator with enrichment services.

`CoverageEvaluator.evaluate_batch`

Type: method
Module: metrics.evaluator
Class: CoverageEvaluator
Signature: evaluate_batch(self, samples: list[tuple[dict[str, Any], BiosampleLocation]], source: str) -> list[dict[str, Any]]
Description: Evaluate a batch of samples.

`CoverageEvaluator.evaluate_sample`

Type: method
Module: metrics.evaluator
Class: CoverageEvaluator
Signature: evaluate_sample(self, raw_doc: dict[str, Any], normalized_location: BiosampleLocation, source: str) -> dict[str, Any]
Description: Evaluate a single sample for coverage metrics.

D

`demo`

Type: function
Module: cli_weather
Signature: demo()
Description: Run weather enrichment demonstration.

`demonstrate_field_mapping`

Type: function
Module: biosample_elevation_mapper
Signature: demonstrate_field_mapping() -> None
Description: Demonstrate the field mapping capabilities with example data.

E

`elevation_cli`

Type: function
Module: cli_elevation
Signature: elevation_cli(log_level: str) -> None
Description: Elevation lookup CLI.

`ElevationProvider.choices`

Type: method
Module: providers
Class: ElevationProvider
Signature: choices(cls) -> list[str]
Description: Get list of provider choices for Click.

`ElevationProvider.description`

Type: method
Module: providers
Class: ElevationProvider
Signature: description(cls) -> str
Description: Get formatted description of all available providers.

`ElevationProvider.fetch`

Type: method
Module: elevation.providers.base
Class: ElevationProvider
Signature: fetch(self, lat: float, lon: float) -> FetchResult
Description: Fetch elevation data for the given coordinates.

`ElevationProvider.info`

Type: method
Module: providers
Class: ElevationProvider
Signature: info(cls, provider: 'ElevationProvider | str') -> ProviderInfo
Description: Get detailed information about a provider.

`ElevationService.init`

Type: method
Module: elevation.service
Class: ElevationService
Signature: __init__(self, google_api_key: str | None, enable_google: bool, enable_usgs: bool, enable_osm: bool, enable_open_topo_data: bool, osm_endpoint: str, open_topo_data_endpoint: str) -> None
Description: Initialize the elevation service.

`ElevationService.classify_biosample_location`

Type: method
Module: elevation.service
Class: ElevationService
Signature: classify_biosample_location(self, lat: float, lon: float) -> dict
Description: Classify a biosample location for routing and metadata.

`ElevationService.classify_coordinates`

Type: method
Module: elevation.service
Class: ElevationService
Signature: classify_coordinates(self, lat: float, lon: float) -> CoordinateClassification
Description: Classify coordinates for provider routing.

`ElevationService.create_output_envelope`

Type: method
Module: elevation.service
Class: ElevationService
Signature: create_output_envelope(self, subject_id: str, observations: list[Observation], read_from_cache: bool, write_to_cache: bool) -> OutputEnvelope
Description: Create output envelope with observations.

`ElevationService.from_env`

Type: method
Module: elevation.service
Class: ElevationService
Signature: from_env(cls) -> 'ElevationService'
Description: Create elevation service from environment variables.

`ElevationService.get_best_elevation`

Type: method
Module: elevation.service
Class: ElevationService
Signature: get_best_elevation(self, observations: list[Observation]) -> ElevationResult | None
Description: Select the best elevation from multiple observations.

`ElevationService.get_elevation`

Type: method
Module: elevation.service
Class: ElevationService
Signature: get_elevation(self, request: ElevationRequest) -> list[Observation]
Description: Get elevation observations from multiple providers.

`ElevationService.select_providers`

Type: method
Module: elevation.service
Class: ElevationService
Signature: select_providers(self, classification: CoordinateClassification, preferred: list[str] | None) -> list[ElevationProvider]
Description: Select providers based on coordinate classification.

`enrich`

Type: function
Module: cli_forward_geocoding
Signature: enrich(query: str, language: str, country: str | None)
Description: Get coordinates and enrichment data for biosample place names.

`enrich`

Type: function
Module: cli_osm_features
Signature: enrich(latitude: float, longitude: float, radius: int, timeout: int, providers: str)
Description: Get enrichment data for biosample coordinates.

`enrich`

Type: function
Module: cli_biosample_elevation
Signature: enrich(input_file: Path, output: Path, output_format: str, timeout: float, no_cache: bool, providers: tuple[str, ...], show_mapping: bool) -> None
Description: Enrich biosamples with elevation data using automatic field mapping.

`ESACCIProvider.init`

Type: method
Module: marine.providers.esa_cci
Class: ESACCIProvider
Signature: __init__(self, timeout: int) -> None
Description: Initialize ESA CCI provider.

`ESACCIProvider.get_coverage_period`

Type: method
Module: marine.providers.esa_cci
Class: ESACCIProvider
Signature: get_coverage_period(self) -> dict[str, str]
Description: Get temporal coverage.

`ESACCIProvider.get_marine_data`

Type: method
Module: marine.providers.esa_cci
Class: ESACCIProvider
Signature: get_marine_data(self, latitude: float, longitude: float, target_date: date, _parameters: list[str] | None) -> MarineResult
Description: Get chlorophyll-a data from ESA CCI.

`ESACCIProvider.get_provider_info`

Type: method
Module: marine.providers.esa_cci
Class: ESACCIProvider
Signature: get_provider_info(self) -> dict[str, Any]
Description: Get ESA CCI provider information.

`ESACCIProvider.is_available`

Type: method
Module: marine.providers.esa_cci
Class: ESACCIProvider
Signature: is_available(self, latitude: float, longitude: float, target_date: date) -> bool
Description: Check if ESA CCI data is available for location and date.

`ESACCIProvider.provider_name`

Type: method
Module: marine.providers.esa_cci
Class: ESACCIProvider
Signature: provider_name(self) -> str
Description: Get provider name.

`ESAWorldCoverProvider.init`

Type: method
Module: land.providers.esa_worldcover
Class: ESAWorldCoverProvider
Signature: __init__(self, timeout: int)

`ESAWorldCoverProvider.coverage_description`

Type: method
Module: land.providers.esa_worldcover
Class: ESAWorldCoverProvider
Signature: coverage_description(self) -> str

`ESAWorldCoverProvider.get_land_cover`

Type: method
Module: land.providers.esa_worldcover
Class: ESAWorldCoverProvider
Signature: get_land_cover(self, latitude: float, longitude: float, target_date: date | None) -> list[LandCoverObservation]
Description: Get ESA WorldCover land cover data.

`ESAWorldCoverProvider.is_available`

Type: method
Module: land.providers.esa_worldcover
Class: ESAWorldCoverProvider
Signature: is_available(self) -> bool
Description: Check if ESA WorldCover WMS is available.

`ESAWorldCoverProvider.name`

Type: method
Module: land.providers.esa_worldcover
Class: ESAWorldCoverProvider
Signature: name(self) -> str

`evaluate`

Type: function
Module: cli_metrics
Signature: evaluate(nmdc_samples: int, gold_samples: int, exclude_host: bool, output_dir: Path, nmdc_connection: str | None, gold_connection: str | None, create_plots: bool, verbose: bool, debug_samples: bool, enrichment_lifecycle_dir: Path) -> None
Description: Evaluate enrichment coverage metrics for random samples.

F

`FieldAligner.init`

Type: method
Module: metrics.aligner
Class: FieldAligner
Signature: __init__(self, mappings_file: Path | None)
Description: Initialize field aligner with mappings configuration.

`FieldAligner.align_temporal_data`

Type: method
Module: metrics.aligner
Class: FieldAligner
Signature: align_temporal_data(self, collection_date: str | None, api_date: str | None, tolerance_days: int) -> bool
Description: Check if temporal data is aligned within tolerance.

`FieldAligner.compare_fields`

Type: method
Module: metrics.aligner
Class: FieldAligner
Signature: compare_fields(self, before_doc: dict[str, Any], after_doc: dict[str, Any], source: str) -> dict[str, dict[str, Any]]
Description: Compare field coverage before and after enrichment.

`FieldAligner.extract_all_fields`

Type: method
Module: metrics.aligner
Class: FieldAligner
Signature: extract_all_fields(self, document: dict[str, Any], source: str) -> dict[str, Any]
Description: Extract all mapped fields from a document.

`FieldAligner.extract_field_value`

Type: method
Module: metrics.aligner
Class: FieldAligner
Signature: extract_field_value(self, document: dict[str, Any], path: str, extract_type: str) -> Any
Description: Extract a field value from a document using a path specification.

`FieldAligner.normalize_value`

Type: method
Module: metrics.aligner
Class: FieldAligner
Signature: normalize_value(self, value: Any, field_type: str | None) -> Any
Description: Normalize a field value for comparison.

`FileBiosampleFetcher.init`

Type: method
Module: adapters
Class: FileBiosampleFetcher
Signature: __init__(self, file_path: str | Path, format_type: str)

`FileBiosampleFetcher.detect_format`

Type: method
Module: adapters
Class: FileBiosampleFetcher
Signature: detect_format(self) -> str
Description: Detect file format and biosample type.

`FileBiosampleFetcher.fetch_locations`

Type: method
Module: adapters
Class: FileBiosampleFetcher
Signature: fetch_locations(self, limit: int | None) -> Iterator[BiosampleLocation]
Description: Fetch locations from file (stub implementation).

`forward_geocoding`

Type: function
Module: cli_forward_geocoding
Signature: forward_geocoding()
Description: Forward geocoding commands - convert place names to coordinates.

`ForwardGeocodeResult.get_administrative_summary`

Type: method
Module: forward_geocoding.models
Class: ForwardGeocodeResult
Signature: get_administrative_summary(self) -> dict[str, str]
Description: Get administrative components from best match.

`ForwardGeocodeResult.get_best_match`

Type: method
Module: forward_geocoding.models
Class: ForwardGeocodeResult
Signature: get_best_match(self) -> ForwardGeocodeLocation | None
Description: Get the highest relevance/confidence location result.

`ForwardGeocodeResult.get_coordinates`

Type: method
Module: forward_geocoding.models
Class: ForwardGeocodeResult
Signature: get_coordinates(self) -> tuple[float, float] | None
Description: Get coordinates from best match.

`ForwardGeocodeResult.to_enrichment_dict`

Type: method
Module: forward_geocoding.models
Class: ForwardGeocodeResult
Signature: to_enrichment_dict(self) -> dict[str, Any]
Description: Convert to dictionary suitable for biosample coordinate enrichment.

`ForwardGeocodingProvider.attribution`

Type: method
Module: forward_geocoding.providers.base
Class: ForwardGeocodingProvider
Signature: attribution(self) -> str | None
Description: Required attribution text.

`ForwardGeocodingProvider.is_available`

Type: method
Module: forward_geocoding.providers.base
Class: ForwardGeocodingProvider
Signature: is_available(self) -> bool
Description: Check if provider is available (API key, network, etc.).

`ForwardGeocodingProvider.name`

Type: method
Module: forward_geocoding.providers.base
Class: ForwardGeocodingProvider
Signature: name(self) -> str
Description: Provider name for identification.

`ForwardGeocodingProvider.search`

Type: method
Module: forward_geocoding.providers.base
Class: ForwardGeocodingProvider
Signature: search(self, query: str) -> ForwardGeocodeFetchResult
Description: Perform forward geocoding to convert place names to coordinates.

`ForwardGeocodingProvider.validate_query`

Type: method
Module: forward_geocoding.providers.base
Class: ForwardGeocodingProvider
Signature: validate_query(self, query: str) -> None
Description: Validate place name query input.

`ForwardGeocodingService.init`

Type: method
Module: forward_geocoding.service
Class: ForwardGeocodingService
Signature: __init__(self) -> None
Description: Initialize the forward geocoding service.

`ForwardGeocodingService.geocode`

Type: method
Module: forward_geocoding.service
Class: ForwardGeocodingService
Signature: geocode(self, query: str, provider: str | None) -> ForwardGeocodeResult | None
Description: Perform forward geocoding to convert place name to coordinates.

`ForwardGeocodingService.geocode_multiple`

Type: method
Module: forward_geocoding.service
Class: ForwardGeocodingService
Signature: geocode_multiple(self, query: str, providers: list[str] | None) -> dict[str, ForwardGeocodeResult]
Description: Perform forward geocoding using multiple providers for comparison.

`ForwardGeocodingService.get_available_providers`

Type: method
Module: forward_geocoding.service
Class: ForwardGeocodingService
Signature: get_available_providers(self) -> list[str]
Description: Get list of available provider names.

`ForwardGeocodingService.get_coordinates_for_place`

Type: method
Module: forward_geocoding.service
Class: ForwardGeocodingService
Signature: get_coordinates_for_place(self, place_name: str, prefer_provider: str | None, language: str, country_hint: str | None) -> dict[str, Any]
Description: Get coordinates and enrichment data for a biosample place name.

`ForwardGeocodingService.get_provider`

Type: method
Module: forward_geocoding.service
Class: ForwardGeocodingService
Signature: get_provider(self, name: str) -> ForwardGeocodingProvider | None
Description: Get a specific provider by name.

`ForwardGeocodingService.get_provider_status`

Type: method
Module: forward_geocoding.service
Class: ForwardGeocodingService
Signature: get_provider_status(self) -> dict[str, dict[str, Any]]
Description: Get status information for all providers.

G

`GEBCOProvider.init`

Type: method
Module: marine.providers.gebco
Class: GEBCOProvider
Signature: __init__(self, timeout: int) -> None
Description: Initialize GEBCO provider.

`GEBCOProvider.get_coverage_period`

Type: method
Module: marine.providers.gebco
Class: GEBCOProvider
Signature: get_coverage_period(self) -> dict[str, str]
Description: Get temporal coverage (static dataset).

`GEBCOProvider.get_marine_data`

Type: method
Module: marine.providers.gebco
Class: GEBCOProvider
Signature: get_marine_data(self, latitude: float, longitude: float, target_date: date, _parameters: list[str] | None) -> MarineResult
Description: Get bathymetry data from GEBCO.

`GEBCOProvider.get_provider_info`

Type: method
Module: marine.providers.gebco
Class: GEBCOProvider
Signature: get_provider_info(self) -> dict[str, Any]
Description: Get GEBCO provider information.

`GEBCOProvider.is_available`

Type: method
Module: marine.providers.gebco
Class: GEBCOProvider
Signature: is_available(self, latitude: float, longitude: float, _target_date: date) -> bool
Description: Check if GEBCO data is available for location.

`GEBCOProvider.provider_name`

Type: method
Module: marine.providers.gebco
Class: GEBCOProvider
Signature: provider_name(self) -> str
Description: Get provider name.

`generate_html_dashboard`

Type: function
Module: metrics.dashboard
Signature: generate_html_dashboard(summary_csv: Path, regional_csv: Path | None, output_path: Path | None) -> str
Description: Generate HTML dashboard with embedded data and charts.

`generate_markdown_table`

Type: function
Module: metrics.markdown
Signature: generate_markdown_table(df: pd.DataFrame) -> str
Description: Convert DataFrame to GitHub-flavored markdown table.

`generate_metrics_report`

Type: function
Module: metrics.markdown
Signature: generate_metrics_report(csv_path: Path) -> str
Description: Generate enrichment performance report showing what data types are enriched.

`get_config_dir`

Type: function
Module: paths
Signature: get_config_dir() -> Path
Description: Get the config directory.

`get_data_dir`

Type: function
Module: paths
Signature: get_data_dir() -> Path
Description: Get the data directory.

`get_host_detector`

Type: function
Module: host_detector
Signature: get_host_detector() -> HostDetector
Description: Get or create the singleton host detector instance.

`get_logger`

Type: function
Module: logging_config
Signature: get_logger(name: str) -> logging.Logger
Description: Get a logger instance for a module.

`get_logs_dir`

Type: function
Module: paths
Signature: get_logs_dir() -> Path
Description: Get the logs directory.

`get_package_data_dir`

Type: function
Module: paths
Signature: get_package_data_dir() -> Path
Description: Get the package data directory.

`get_project_root`

Type: function
Module: paths
Signature: get_project_root() -> Path
Description: Get the project root directory.

`get_session`

Type: function
Module: http_cache
Signature: get_session() -> CachedSession
Description: Get cached session with SQLite backend.

`get_environmental_metadata`

Type: function
Module: environmental_metadata
Signature: get_environmental_metadata(lat: float, lon: float, slots: list[str], datetime_obj: datetime | None, providers: list[str] | None) -> dict[str, Any]
Description: Get NMDC submission-schema compliant values for specified slots.

`GOLDBiosampleAdapter.extract_location`

Type: method
Module: adapters
Class: GOLDBiosampleAdapter
Signature: extract_location(self, biosample_data: dict[str, Any], database: Any) -> BiosampleLocation
Description: Extract location data from GOLD biosample document.

`GOLDBiosampleAdapter.extract_locations_batch`

Type: method
Module: adapters
Class: GOLDBiosampleAdapter
Signature: extract_locations_batch(self, biosamples: list[dict[str, Any]]) -> list[BiosampleLocation]
Description: Extract location data from multiple GOLD biosamples.

`GoogleElevationProvider.init`

Type: method
Module: elevation.providers.google
Class: GoogleElevationProvider
Signature: __init__(self, api_key: str | None) -> None
Description: Initialize Google Elevation provider.

`GoogleElevationProvider.fetch`

Type: method
Module: elevation.providers.google
Class: GoogleElevationProvider
Signature: fetch(self, lat: float, lon: float) -> FetchResult
Description: Fetch elevation data from Google Elevation API.

`GoogleForwardGeocodingProvider.init`

Type: method
Module: forward_geocoding.providers.google
Class: GoogleForwardGeocodingProvider
Signature: __init__(self, api_key: str | None)
Description: Initialize Google provider.

`GoogleForwardGeocodingProvider.attribution`

Type: method
Module: forward_geocoding.providers.google
Class: GoogleForwardGeocodingProvider
Signature: attribution(self) -> str

`GoogleForwardGeocodingProvider.is_available`

Type: method
Module: forward_geocoding.providers.google
Class: GoogleForwardGeocodingProvider
Signature: is_available(self) -> bool
Description: Check if Google API is available.

`GoogleForwardGeocodingProvider.name`

Type: method
Module: forward_geocoding.providers.google
Class: GoogleForwardGeocodingProvider
Signature: name(self) -> str

`GoogleForwardGeocodingProvider.search`

Type: method
Module: forward_geocoding.providers.google
Class: GoogleForwardGeocodingProvider
Signature: search(self, query: str) -> ForwardGeocodeFetchResult
Description: Search for places by name using Google Maps Geocoding API.

`GooglePlacesProvider.init`

Type: method
Module: osm_features.google_provider
Class: GooglePlacesProvider
Signature: __init__(self, api_key: str | None)
Description: Initialize Google Places provider.

`GooglePlacesProvider.get_features`

Type: method
Module: osm_features.google_provider
Class: GooglePlacesProvider
Signature: get_features(self, latitude: float, longitude: float, radius_m: int, timeout_s: int) -> GooglePlacesFetchResult
Description: Get geographic features from Google Places API.

`GooglePlacesProvider.is_available`

Type: method
Module: osm_features.google_provider
Class: GooglePlacesProvider
Signature: is_available(self) -> bool
Description: Check if Google Places API is available.

`GooglePlacesResult.get_nearest_feature`

Type: method
Module: osm_features.models
Class: GooglePlacesResult
Signature: get_nearest_feature(self, category: FeatureCategory) -> GooglePlacesFeature | None
Description: Get nearest feature of specified category.

`GooglePlacesResult.to_enrichment_dict`

Type: method
Module: osm_features.models
Class: GooglePlacesResult
Signature: to_enrichment_dict(self) -> dict[str, Any]
Description: Convert to dictionary suitable for biosample enrichment.

`GoogleReverseGeocodingProvider.init`

Type: method
Module: reverse_geocoding.providers.google
Class: GoogleReverseGeocodingProvider
Signature: __init__(self, api_key: str | None) -> None
Description: Initialize Google Geocoding reverse geocoding provider.

`GoogleReverseGeocodingProvider.fetch`

Type: method
Module: reverse_geocoding.providers.google
Class: GoogleReverseGeocodingProvider
Signature: fetch(self, lat: float, lon: float) -> ReverseGeocodeFetchResult
Description: Fetch reverse geocoding data from Google Geocoding API.

H

`HostDetector.init`

Type: method
Module: host_detector
Class: HostDetector
Signature: __init__(self, config_file: Path | None)
Description: Initialize host detector with configuration.

`HostDetector.classify_sample_type`

Type: method
Module: host_detector
Class: HostDetector
Signature: classify_sample_type(self, data: dict[str, Any], source: str) -> str
Description: Classify the sample type based on available metadata.

`HostDetector.is_host_associated`

Type: method
Module: host_detector
Class: HostDetector
Signature: is_host_associated(self, data: dict[str, Any], source: str) -> bool
Description: Detect if a biosample is host-associated.

`HostDetector.is_host_associated_gold`

Type: method
Module: host_detector
Class: HostDetector
Signature: is_host_associated_gold(self, data: dict[str, Any]) -> bool
Description: Detect if GOLD sample is host-associated.

`HostDetector.is_host_associated_nmdc`

Type: method
Module: host_detector
Class: HostDetector
Signature: is_host_associated_nmdc(self, data: dict[str, Any]) -> bool
Description: Detect if NMDC sample is host-associated.

I

`info`

Type: function
Module: cache_management
Signature: info(ctx: click.Context) -> None
Description: Show cache information.

L

`land`

Type: function
Module: cli_land
Signature: land()
Description: Land cover and vegetation enrichment commands.

`LandCoverObservation.validate_location`

Type: method
Module: land.models
Class: LandCoverObservation
Signature: validate_location(cls, v: dict[str, float]) -> dict[str, float]
Description: Validate location coordinates.

`LandCoverProviderBase.coverage_description`

Type: method
Module: land.providers.base
Class: LandCoverProviderBase
Signature: coverage_description(self) -> str
Description: Description of geographic and temporal coverage.

`LandCoverProviderBase.get_land_cover`

Type: method
Module: land.providers.base
Class: LandCoverProviderBase
Signature: get_land_cover(self, latitude: float, longitude: float, target_date: date | None) -> list[LandCoverObservation]
Description: Retrieve land cover data for a specific location and date.

`LandCoverProviderBase.is_available`

Type: method
Module: land.providers.base
Class: LandCoverProviderBase
Signature: is_available(self) -> bool
Description: Check if the provider is currently available.

`LandCoverProviderBase.name`

Type: method
Module: land.providers.base
Class: LandCoverProviderBase
Signature: name(self) -> str
Description: Provider name for identification and logging.

`LandCoverProviderBase.validate_coordinates`

Type: method
Module: land.providers.base
Class: LandCoverProviderBase
Signature: validate_coordinates(self, latitude: float, longitude: float) -> None
Description: Validate coordinate inputs.

`LandResult.to_gold_schema`

Type: method
Module: land.models
Class: LandResult
Signature: to_gold_schema(self) -> dict[str, Any]
Description: Convert to GOLD schema format.

`LandResult.to_nmdc_schema`

Type: method
Module: land.models
Class: LandResult
Signature: to_nmdc_schema(self) -> dict[str, Any]
Description: Convert to NMDC schema format.

`LandResult.validate_requested_location`

Type: method
Module: land.models
Class: LandResult
Signature: validate_requested_location(cls, v: dict[str, float]) -> dict[str, float]
Description: Validate requested location coordinates.

`LandService.init`

Type: method
Module: land.service
Class: LandService
Signature: __init__(self)
Description: Initialize land service with all providers.

`LandService.enrich_batch`

Type: method
Module: land.service
Class: LandService
Signature: enrich_batch(self, locations: list[tuple[float, float]], target_date: date | None, time_window_days: int) -> list[LandResult]
Description: Enrich multiple locations with land cover and vegetation data.

`LandService.enrich_biosample`

Type: method
Module: land.service
Class: LandService
Signature: enrich_biosample(self, sample_data: dict[str, Any]) -> dict[str, Any]
Description: Enrich a single biosample with land cover and vegetation data.

`LandService.enrich_location`

Type: method
Module: land.service
Class: LandService
Signature: enrich_location(self, latitude: float, longitude: float, target_date: date | None, time_window_days: int) -> LandResult
Description: Enrich a single location with land cover and vegetation data.

`LandService.get_provider_status`

Type: method
Module: land.service
Class: LandService
Signature: get_provider_status(self) -> dict[str, dict[str, Any]]
Description: Get status of all land cover and vegetation providers.

`LocationDetector.init`

Type: method
Module: elevation.location_detector
Class: LocationDetector
Signature: __init__(self, user_agent: str)
Description: Initialize the location detector.

`LocationDetector.classify_for_elevation_routing`

Type: method
Module: elevation.location_detector
Class: LocationDetector
Signature: classify_for_elevation_routing(self, lat: float, lon: float) -> dict[str, Any]
Description: Classify coordinates specifically for elevation service routing.

`LocationDetector.detect_location`

Type: method
Module: elevation.location_detector
Class: LocationDetector
Signature: detect_location(self, lat: float, lon: float, prefer_online: bool) -> dict[str, Any]
Description: Detect location characteristics using multiple methods.

`lookup`

Type: function
Module: cli_soil
Signature: lookup(latitude: float, longitude: float, depth: str, output_format: str, verbose: bool) -> None
Description: Look up soil data for a specific location.

`lookup`

Type: function
Module: cli_land
Signature: lookup(lat: float, lon: float, date: datetime | None, time_window: int, output: str | None, pretty: bool)
Description: Look up land cover and vegetation data for a single location.

`lookup`

Type: function
Module: cli_forward_geocoding
Signature: lookup(query: str, provider: str, language: str, country: str | None, max_results: int, output: str | None, pretty: bool)
Description: Look up coordinates for a place name.

`lookup`

Type: function
Module: cli_osm_features
Signature: lookup(latitude: float, longitude: float, radius: int, providers: str, timeout: int, output: str | None, pretty: bool)
Description: Look up geographic features around coordinates.

`lookup`

Type: function
Module: cli_marine
Signature: lookup(lat: float, lon: float, date: str, providers: str, output: str | None, schema: str)
Description: Look up marine data for a specific location and date.

`lookup`

Type: function
Module: cli_weather
Signature: lookup(lat: float, lon: float, date: str, providers: str, output: str | None, schema: str)
Description: Get weather data for specific coordinates and date.

`lookup_elevation`

Type: function
Module: cli_elevation
Signature: lookup_elevation(lat: float, lon: float, providers: tuple[str, ...], output: str | None, subject_id: str, timeout: float, no_cache: bool, read_cache: bool, write_cache: bool) -> None
Description: Look up elevation for a single coordinate.

M

`main`

Type: function
Module: cli
Signature: main() -> None
Description: Biosample Enricher: Infer AI-friendly metadata about biosamples.

`main`

Type: function
Module: schema_inference
Signature: main() -> None

`main`

Type: function
Module: schema_statistics
Signature: main() -> None

`marine_cli`

Type: function
Module: cli_marine
Signature: marine_cli(debug: bool)
Description: Marine enrichment CLI for biosample oceanographic context.

`MarineObservation.validate_value`

Type: method
Module: marine.models
Class: MarineObservation
Signature: validate_value(cls, v)
Description: Validate observation value.

`MarineProviderBase.init`

Type: method
Module: marine.providers.base
Class: MarineProviderBase
Signature: __init__(self, timeout: int) -> None
Description: Initialize provider with timeout setting.

`MarineProviderBase.get_coverage_period`

Type: method
Module: marine.providers.base
Class: MarineProviderBase
Signature: get_coverage_period(self) -> dict[str, str]
Description: Get temporal coverage of the provider.

`MarineProviderBase.get_marine_data`

Type: method
Module: marine.providers.base
Class: MarineProviderBase
Signature: get_marine_data(self, latitude: float, longitude: float, target_date: date, parameters: list[str] | None) -> MarineResult
Description: Get marine data for location and date.

`MarineProviderBase.get_provider_info`

Type: method
Module: marine.providers.base
Class: MarineProviderBase
Signature: get_provider_info(self) -> dict[str, Any]
Description: Get provider metadata and capabilities.

`MarineProviderBase.is_available`

Type: method
Module: marine.providers.base
Class: MarineProviderBase
Signature: is_available(self, latitude: float, longitude: float, target_date: date) -> bool
Description: Check if provider has data for given location and date.

`MarineProviderBase.provider_name`

Type: method
Module: marine.providers.base
Class: MarineProviderBase
Signature: provider_name(self) -> str
Description: Get the provider name.

`MarineResult.get_coverage_metrics`

Type: method
Module: marine.models
Class: MarineResult
Signature: get_coverage_metrics(self) -> dict[str, Any]
Description: Generate coverage metrics for this marine result.

`MarineResult.get_schema_mapping`

Type: method
Module: marine.models
Class: MarineResult
Signature: get_schema_mapping(self, target_schema: str) -> dict[str, Any]
Description: Map marine data to target biosample schema.

`MarineResult.validate_date_format`

Type: method
Module: marine.models
Class: MarineResult
Signature: validate_date_format(cls, v)
Description: Validate date format.

`MarineService.init`

Type: method
Module: marine.service
Class: MarineService
Signature: __init__(self, providers: list[MarineProviderBase] | None)
Description: Initialize marine service with provider chain.

`MarineService.get_comprehensive_marine_data`

Type: method
Module: marine.service
Class: MarineService
Signature: get_comprehensive_marine_data(self, latitude: float, longitude: float, target_date: date) -> MarineResult
Description: Get comprehensive marine data from all available providers.

`MarineService.get_marine_data_for_biosample`

Type: method
Module: marine.service
Class: MarineService
Signature: get_marine_data_for_biosample(self, biosample: dict[str, Any], target_schema: str) -> dict[str, Any]
Description: Get marine data for a biosample and map to target schema.

`MeteostatProvider.init`

Type: method
Module: weather.providers.meteostat
Class: MeteostatProvider
Signature: __init__(self, timeout: int)

`MeteostatProvider.get_climate_normals`

Type: method
Module: weather.providers.meteostat
Class: MeteostatProvider
Signature: get_climate_normals(self, lat: float, lon: float, start_year: int, end_year: int) -> ClimateNormalsResult
Description: Get 30-year climate averages (normals) for a location.

`MeteostatProvider.get_coverage_period`

Type: method
Module: weather.providers.meteostat
Class: MeteostatProvider
Signature: get_coverage_period(self) -> dict[str, str]
Description: Return temporal coverage period.

`MeteostatProvider.get_daily_weather`

Type: method
Module: weather.providers.meteostat
Class: MeteostatProvider
Signature: get_daily_weather(self, lat: float, lon: float, target_date: date, _parameters: list[str] | None) -> WeatherResult
Description: Get daily weather data for specific date and location from MeteoStat.

`MeteostatProvider.get_spatial_resolution`

Type: method
Module: weather.providers.meteostat
Class: MeteostatProvider
Signature: get_spatial_resolution(self) -> str
Description: Return spatial resolution.

`MeteostatProvider.get_supported_parameters`

Type: method
Module: weather.providers.meteostat
Class: MeteostatProvider
Signature: get_supported_parameters(self) -> list[str]
Description: Return list of weather parameters supported by MeteoStat.

`MeteostatProvider.get_temporal_resolution`

Type: method
Module: weather.providers.meteostat
Class: MeteostatProvider
Signature: get_temporal_resolution(self) -> str
Description: Return temporal resolution.

`MeteostatProvider.is_available`

Type: method
Module: weather.providers.meteostat
Class: MeteostatProvider
Signature: is_available(self, _lat: float, _lon: float, target_date: date) -> bool
Description: Check if MeteoStat has data for the given location and date.

`metrics`

Type: function
Module: cli_metrics
Signature: metrics() -> None
Description: Evaluate enrichment coverage metrics.

`MetricsReporter.init`

Type: method
Module: metrics.reporter
Class: MetricsReporter
Signature: __init__(self, output_dir: Path | None)
Description: Initialize reporter with output directory.

`MetricsReporter.generate_detailed_samples`

Type: method
Module: metrics.reporter
Class: MetricsReporter
Signature: generate_detailed_samples(self, evaluations: list[dict[str, Any]], limit: int) -> pd.DataFrame
Description: Generate detailed per-sample results.

`MetricsReporter.generate_regional_table`

Type: method
Module: metrics.reporter
Class: MetricsReporter
Signature: generate_regional_table(self, evaluations: list[dict[str, Any]]) -> pd.DataFrame
Description: Generate coverage table by geographic region.

`MetricsReporter.generate_summary_table`

Type: method
Module: metrics.reporter
Class: MetricsReporter
Signature: generate_summary_table(self, evaluations: list[dict[str, Any]], exclude_host_associated: bool) -> pd.DataFrame
Description: Generate overall coverage summary table.

`MetricsReporter.print_summary`

Type: method
Module: metrics.reporter
Class: MetricsReporter
Signature: print_summary(self, summary_df: pd.DataFrame) -> None
Description: Print summary table to console.

`MetricsReporter.save_all_reports`

Type: method
Module: metrics.reporter
Class: MetricsReporter
Signature: save_all_reports(self, evaluations: list[dict[str, Any]], prefix: str) -> dict[str, Path]
Description: Save all report tables to CSV files.

`MetricsVisualizer.init`

Type: method
Module: metrics.visualizer
Class: MetricsVisualizer
Signature: __init__(self, output_dir: Path | None)
Description: Initialize visualizer with output directory.

`MetricsVisualizer.create_all_visualizations`

Type: method
Module: metrics.visualizer
Class: MetricsVisualizer
Signature: create_all_visualizations(self, evaluations: list[dict[str, Any]], summary_df: pd.DataFrame, regional_df: pd.DataFrame, prefix: str) -> dict[str, Path]
Description: Create all visualization plots.

`MetricsVisualizer.plot_host_association_breakdown`

Type: method
Module: metrics.visualizer
Class: MetricsVisualizer
Signature: plot_host_association_breakdown(self, evaluations: list[dict[str, Any]], save_path: Path | None) -> plt.Figure
Description: Create pie charts showing host-associated vs environmental samples.

`MetricsVisualizer.plot_improvement_bars`

Type: method
Module: metrics.visualizer
Class: MetricsVisualizer
Signature: plot_improvement_bars(self, summary_df: pd.DataFrame, save_path: Path | None) -> plt.Figure
Description: Create bar chart showing improvement percentages.

`MetricsVisualizer.plot_regional_comparison`

Type: method
Module: metrics.visualizer
Class: MetricsVisualizer
Signature: plot_regional_comparison(self, regional_df: pd.DataFrame, save_path: Path | None) -> plt.Figure
Description: Create regional comparison plot.

`MetricsVisualizer.plot_source_datatype_coverage`

Type: method
Module: metrics.visualizer
Class: MetricsVisualizer
Signature: plot_source_datatype_coverage(self, summary_df: pd.DataFrame, save_path: Path | None) -> plt.Figure
Description: Create grouped bar chart for source × data type coverage.

`MODISVegetationProvider.init`

Type: method
Module: land.providers.modis_vegetation
Class: MODISVegetationProvider
Signature: __init__(self, timeout: int)

`MODISVegetationProvider.coverage_description`

Type: method
Module: land.providers.modis_vegetation
Class: MODISVegetationProvider
Signature: coverage_description(self) -> str

`MODISVegetationProvider.get_vegetation_indices`

Type: method
Module: land.providers.modis_vegetation
Class: MODISVegetationProvider
Signature: get_vegetation_indices(self, latitude: float, longitude: float, target_date: date | None, time_window_days: int) -> list[VegetationObservation]
Description: Get MODIS vegetation indices.

`MODISVegetationProvider.is_available`

Type: method
Module: land.providers.modis_vegetation
Class: MODISVegetationProvider
Signature: is_available(self) -> bool
Description: Check if APPEEARS API is available.

`MODISVegetationProvider.name`

Type: method
Module: land.providers.modis_vegetation
Class: MODISVegetationProvider
Signature: name(self) -> str

`MongoGOLDBiosampleFetcher.init`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: __init__(self, connection_string: str | None, database_name: str, collection_name: str)

`MongoGOLDBiosampleFetcher.connect`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: connect(self) -> bool
Description: Establish MongoDB connection.

`MongoGOLDBiosampleFetcher.count_enrichable_samples`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: count_enrichable_samples(self) -> int
Description: Count biosamples with coordinates.

`MongoGOLDBiosampleFetcher.count_total_samples`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: count_total_samples(self) -> int
Description: Count total biosamples in collection.

`MongoGOLDBiosampleFetcher.disconnect`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: disconnect(self) -> None
Description: Close MongoDB connection.

`MongoGOLDBiosampleFetcher.fetch_enrichable_locations`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: fetch_enrichable_locations(self, limit: int | None) -> Iterator[BiosampleLocation]
Description: Fetch only biosamples with coordinates suitable for enrichment.

`MongoGOLDBiosampleFetcher.fetch_locations`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: fetch_locations(self, query: dict[str, Any] | None, limit: int | None) -> Iterator[BiosampleLocation]
Description: Fetch and extract locations from GOLD biosamples.

`MongoGOLDBiosampleFetcher.fetch_locations_by_ids`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: fetch_locations_by_ids(self, ids: list[str], id_field: str) -> Iterator[BiosampleLocation]
Description: Fetch biosamples by specific IDs using native field names.

`MongoGOLDBiosampleFetcher.fetch_random_enrichable_locations`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: fetch_random_enrichable_locations(self, n: int) -> Iterator[BiosampleLocation]
Description: Fetch N random enrichable biosamples from collection.

`MongoGOLDBiosampleFetcher.fetch_random_locations`

Type: method
Module: adapters
Class: MongoGOLDBiosampleFetcher
Signature: fetch_random_locations(self, n: int) -> Iterator[BiosampleLocation]
Description: Fetch N random biosamples from collection.

`MongoNMDCBiosampleFetcher.init`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: __init__(self, connection_string: str | None, database_name: str, collection_name: str)

`MongoNMDCBiosampleFetcher.connect`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: connect(self) -> bool
Description: Establish MongoDB connection.

`MongoNMDCBiosampleFetcher.count_enrichable_samples`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: count_enrichable_samples(self) -> int
Description: Count biosamples with coordinates.

`MongoNMDCBiosampleFetcher.count_total_samples`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: count_total_samples(self) -> int
Description: Count total biosamples in collection.

`MongoNMDCBiosampleFetcher.disconnect`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: disconnect(self) -> None
Description: Close MongoDB connection.

`MongoNMDCBiosampleFetcher.fetch_enrichable_locations`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: fetch_enrichable_locations(self, limit: int | None) -> Iterator[BiosampleLocation]
Description: Fetch only biosamples with coordinates suitable for enrichment.

`MongoNMDCBiosampleFetcher.fetch_locations`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: fetch_locations(self, query: dict[str, Any] | None, limit: int | None) -> Iterator[BiosampleLocation]
Description: Fetch and extract locations from NMDC biosamples.

`MongoNMDCBiosampleFetcher.fetch_locations_by_ids`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: fetch_locations_by_ids(self, ids: list[str], id_field: str) -> Iterator[BiosampleLocation]
Description: Fetch biosamples by specific IDs using native field names.

`MongoNMDCBiosampleFetcher.fetch_random_enrichable_locations`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: fetch_random_enrichable_locations(self, n: int) -> Iterator[BiosampleLocation]
Description: Fetch N random enrichable biosamples from collection.

`MongoNMDCBiosampleFetcher.fetch_random_locations`

Type: method
Module: adapters
Class: MongoNMDCBiosampleFetcher
Signature: fetch_random_locations(self, n: int) -> Iterator[BiosampleLocation]
Description: Fetch N random biosamples from collection.

`MultiProviderClimateNormals.get_consensus_precipitation`

Type: method
Module: weather.models
Class: MultiProviderClimateNormals
Signature: get_consensus_precipitation(self) -> float | None
Description: Calculate consensus annual precipitation across all successful providers.

`MultiProviderClimateNormals.get_consensus_temperature`

Type: method
Module: weather.models
Class: MultiProviderClimateNormals
Signature: get_consensus_temperature(self) -> float | None
Description: Calculate consensus annual temperature across all successful providers.

`MultiProviderClimateNormals.get_provider_result`

Type: method
Module: weather.models
Class: MultiProviderClimateNormals
Signature: get_provider_result(self, provider_name: str) -> 'ClimateNormalsResult | None'
Description: Get result from a specific provider.

`MultiProviderClimateNormals.get_value_ranges`

Type: method
Module: weather.models
Class: MultiProviderClimateNormals
Signature: get_value_ranges(self) -> dict[str, tuple[float, float] | None]
Description: Get min/max range of values across providers.

`MultiProviderClimateNormals.to_submission_schema`

Type: method
Module: weather.models
Class: MultiProviderClimateNormals
Signature: to_submission_schema(self, provider: str | None, strategy: str) -> dict[str, Any]
Description: Extract values in submission-schema compatible format.

N

`NASAPowerProvider.init`

Type: method
Module: weather.providers.nasa_power
Class: NASAPowerProvider
Signature: __init__(self, timeout: int)
Description: Initialize NASA POWER provider.

`NASAPowerProvider.get_climate_normals`

Type: method
Module: weather.providers.nasa_power
Class: NASAPowerProvider
Signature: get_climate_normals(self, lat: float, lon: float, start_year: int, end_year: int) -> ClimateNormalsResult
Description: Get 20-year climate averages from NASA POWER.

`NLCDProvider.init`

Type: method
Module: land.providers.nlcd
Class: NLCDProvider
Signature: __init__(self, timeout: int)

`NLCDProvider.coverage_description`

Type: method
Module: land.providers.nlcd
Class: NLCDProvider
Signature: coverage_description(self) -> str

`NLCDProvider.get_land_cover`

Type: method
Module: land.providers.nlcd
Class: NLCDProvider
Signature: get_land_cover(self, latitude: float, longitude: float, target_date: date | None) -> list[LandCoverObservation]
Description: Get NLCD land cover data.

`NLCDProvider.is_available`

Type: method
Module: land.providers.nlcd
Class: NLCDProvider
Signature: is_available(self) -> bool
Description: Check if NLCD WMS is available.

`NLCDProvider.name`

Type: method
Module: land.providers.nlcd
Class: NLCDProvider
Signature: name(self) -> str

`NMDCBiosampleAdapter.extract_location`

Type: method
Module: adapters
Class: NMDCBiosampleAdapter
Signature: extract_location(self, biosample_data: dict[str, Any]) -> BiosampleLocation
Description: Extract location data from NMDC biosample document.

`NMDCBiosampleAdapter.extract_locations_batch`

Type: method
Module: adapters
Class: NMDCBiosampleAdapter
Signature: extract_locations_batch(self, biosamples: list[dict[str, Any]]) -> list[BiosampleLocation]
Description: Extract location data from multiple NMDC biosamples.

`NOAAOISSTProvider.init`

Type: method
Module: marine.providers.noaa_oisst
Class: NOAAOISSTProvider
Signature: __init__(self, timeout: int) -> None
Description: Initialize NOAA OISST provider.

`NOAAOISSTProvider.get_coverage_period`

Type: method
Module: marine.providers.noaa_oisst
Class: NOAAOISSTProvider
Signature: get_coverage_period(self) -> dict[str, str]
Description: Get temporal coverage.

`NOAAOISSTProvider.get_marine_data`

Type: method
Module: marine.providers.noaa_oisst
Class: NOAAOISSTProvider
Signature: get_marine_data(self, latitude: float, longitude: float, target_date: date, _parameters: list[str] | None) -> MarineResult
Description: Get SST data from NOAA OISST.

`NOAAOISSTProvider.get_provider_info`

Type: method
Module: marine.providers.noaa_oisst
Class: NOAAOISSTProvider
Signature: get_provider_info(self) -> dict[str, Any]
Description: Get NOAA OISST provider information.

`NOAAOISSTProvider.is_available`

Type: method
Module: marine.providers.noaa_oisst
Class: NOAAOISSTProvider
Signature: is_available(self, latitude: float, longitude: float, target_date: date) -> bool
Description: Check if OISST data is available for location and date.

`NOAAOISSTProvider.provider_name`

Type: method
Module: marine.providers.noaa_oisst
Class: NOAAOISSTProvider
Signature: provider_name(self) -> str
Description: Get provider name.

O

`OpenMeteoProvider.init`

Type: method
Module: weather.providers.open_meteo
Class: OpenMeteoProvider
Signature: __init__(self, timeout: int)

`OpenMeteoProvider.get_coverage_period`

Type: method
Module: weather.providers.open_meteo
Class: OpenMeteoProvider
Signature: get_coverage_period(self) -> dict[str, str]
Description: Return temporal coverage period.

`OpenMeteoProvider.get_daily_weather`

Type: method
Module: weather.providers.open_meteo
Class: OpenMeteoProvider
Signature: get_daily_weather(self, lat: float, lon: float, target_date: date, parameters: list[str] | None) -> WeatherResult
Description: Get daily weather data for specific date and location from Open-Meteo.

`OpenMeteoProvider.get_spatial_resolution`

Type: method
Module: weather.providers.open_meteo
Class: OpenMeteoProvider
Signature: get_spatial_resolution(self) -> str
Description: Return spatial resolution.

`OpenMeteoProvider.get_supported_parameters`

Type: method
Module: weather.providers.open_meteo
Class: OpenMeteoProvider
Signature: get_supported_parameters(self) -> list[str]
Description: Return list of weather parameters supported by Open-Meteo.

`OpenMeteoProvider.get_temporal_resolution`

Type: method
Module: weather.providers.open_meteo
Class: OpenMeteoProvider
Signature: get_temporal_resolution(self) -> str
Description: Return temporal resolution.

`OpenMeteoProvider.is_available`

Type: method
Module: weather.providers.open_meteo
Class: OpenMeteoProvider
Signature: is_available(self, _lat: float, _lon: float, target_date: date) -> bool
Description: Check if Open-Meteo has data for the given location and date.

`OpenTopoDataProvider.init`

Type: method
Module: elevation.providers.open_topo_data
Class: OpenTopoDataProvider
Signature: __init__(self, endpoint: str, dataset: str) -> None
Description: Initialize Open Topo Data provider.

`OpenTopoDataProvider.fetch`

Type: method
Module: elevation.providers.open_topo_data
Class: OpenTopoDataProvider
Signature: fetch(self, lat: float, lon: float) -> FetchResult
Description: Fetch elevation data from Open Topo Data API.

`osm_features`

Type: function
Module: cli_osm_features
Signature: osm_features()
Description: OpenStreetMap geographic features commands.

`OSMElevationProvider.init`

Type: method
Module: elevation.providers.osm
Class: OSMElevationProvider
Signature: __init__(self, endpoint: str) -> None
Description: Initialize OSM-like elevation provider.

`OSMElevationProvider.fetch`

Type: method
Module: elevation.providers.osm
Class: OSMElevationProvider
Signature: fetch(self, lat: float, lon: float) -> FetchResult
Description: Fetch elevation data from OpenElevation-style API.

`OSMFeaturesResult.get_distance_summary`

Type: method
Module: osm_features.models
Class: OSMFeaturesResult
Signature: get_distance_summary(self) -> dict[str, Any]
Description: Generate distance summary for key feature categories.

`OSMFeaturesResult.get_feature_counts_by_category`

Type: method
Module: osm_features.models
Class: OSMFeaturesResult
Signature: get_feature_counts_by_category(self) -> dict[str, int]
Description: Get counts of unnamed features by main category.

`OSMFeaturesResult.get_features_by_category`

Type: method
Module: osm_features.models
Class: OSMFeaturesResult
Signature: get_features_by_category(self, category: FeatureCategory) -> list[OSMNamedFeature]
Description: Get all named features of a specific category.

`OSMFeaturesResult.get_nearest_feature`

Type: method
Module: osm_features.models
Class: OSMFeaturesResult
Signature: get_nearest_feature(self, category: FeatureCategory) -> OSMNamedFeature | None
Description: Get the nearest named feature of a specific category.

`OSMFeaturesResult.to_enrichment_dict`

Type: method
Module: osm_features.models
Class: OSMFeaturesResult
Signature: to_enrichment_dict(self) -> dict[str, Any]
Description: Convert to dictionary suitable for biosample enrichment.

`OSMFeaturesService.init`

Type: method
Module: osm_features.service
Class: OSMFeaturesService
Signature: __init__(self, default_radius_m: int, enable_google: bool)
Description: Initialize geographic features service.

`OSMFeaturesService.batch_enrich_locations`

Type: method
Module: osm_features.service
Class: OSMFeaturesService
Signature: batch_enrich_locations(self, locations: list[tuple[float, float]], radius_m: int, timeout_s: int) -> list[dict[str, Any]]
Description: Batch enrich multiple locations with OSM features.

`OSMFeaturesService.enrich_biosample_location`

Type: method
Module: osm_features.service
Class: OSMFeaturesService
Signature: enrich_biosample_location(self, latitude: float, longitude: float, radius_m: int | None, timeout_s: int, use_combined: bool) -> dict[str, Any]
Description: Enrich a biosample location with geographic features from multiple providers.

`OSMFeaturesService.get_combined_features_for_location`

Type: method
Module: osm_features.service
Class: OSMFeaturesService
Signature: get_combined_features_for_location(self, latitude: float, longitude: float, radius_m: int | None, timeout_s: int) -> CombinedFeaturesResult
Description: Get geographic features from both OSM and Google Places providers.

`OSMFeaturesService.get_features_for_biosample`

Type: method
Module: osm_features.service
Class: OSMFeaturesService
Signature: get_features_for_biosample(self, biosample: dict[str, Any], radius_m: int, timeout_s: int) -> dict[str, Any]
Description: Get OSM features for a biosample dictionary.

`OSMFeaturesService.get_features_for_location`

Type: method
Module: osm_features.service
Class: OSMFeaturesService
Signature: get_features_for_location(self, latitude: float, longitude: float, radius_m: int | None, timeout_s: int) -> OSMFeaturesResult | None
Description: Get geographic features around a location from OSM only (for backward compatibility).

`OSMFeaturesService.get_provider_status`

Type: method
Module: osm_features.service
Class: OSMFeaturesService
Signature: get_provider_status(self) -> dict[str, Any]
Description: Get status of all geographic features providers.

`OSMForwardGeocodingProvider.init`

Type: method
Module: forward_geocoding.providers.osm
Class: OSMForwardGeocodingProvider
Signature: __init__(self, base_url: str)
Description: Initialize OSM provider.

`OSMForwardGeocodingProvider.attribution`

Type: method
Module: forward_geocoding.providers.osm
Class: OSMForwardGeocodingProvider
Signature: attribution(self) -> str

`OSMForwardGeocodingProvider.is_available`

Type: method
Module: forward_geocoding.providers.osm
Class: OSMForwardGeocodingProvider
Signature: is_available(self) -> bool
Description: Check if Nominatim API is available.

`OSMForwardGeocodingProvider.name`

Type: method
Module: forward_geocoding.providers.osm
Class: OSMForwardGeocodingProvider
Signature: name(self) -> str

`OSMForwardGeocodingProvider.search`

Type: method
Module: forward_geocoding.providers.osm
Class: OSMForwardGeocodingProvider
Signature: search(self, query: str) -> ForwardGeocodeFetchResult
Description: Search for places by name using OSM Nominatim search API.

`OSMOverpassProvider.init`

Type: method
Module: osm_features.provider
Class: OSMOverpassProvider
Signature: __init__(self, base_url: str)
Description: Initialize OSM Overpass provider.

`OSMOverpassProvider.get_features`

Type: method
Module: osm_features.provider
Class: OSMOverpassProvider
Signature: get_features(self, latitude: float, longitude: float, radius_m: int, timeout_s: int) -> OSMFetchResult
Description: Get geographic features around a location.

`OSMOverpassProvider.is_available`

Type: method
Module: osm_features.provider
Class: OSMOverpassProvider
Signature: is_available(self) -> bool
Description: Check if Overpass API is available.

`OSMReverseGeocodingProvider.init`

Type: method
Module: reverse_geocoding.providers.osm
Class: OSMReverseGeocodingProvider
Signature: __init__(self, endpoint: str, user_agent: str) -> None
Description: Initialize OSM Nominatim reverse geocoding provider.

`OSMReverseGeocodingProvider.fetch`

Type: method
Module: reverse_geocoding.providers.osm
Class: OSMReverseGeocodingProvider
Signature: fetch(self, lat: float, lon: float) -> ReverseGeocodeFetchResult
Description: Fetch reverse geocoding data from OSM Nominatim API.

P

`parse_args`

Type: function
Module: schema_inference
Signature: parse_args() -> argparse.Namespace

`parse_args`

Type: function
Module: schema_statistics
Signature: parse_args() -> argparse.Namespace

`process_biosamples`

Type: function
Module: elevation_demos
Signature: process_biosamples(input_file: Path, output_file: Path, timeout: float, no_cache: bool, providers: tuple[str, ...], output_format: str) -> None
Description: Process elevation lookups for synthetic biosamples JSON file.

`providers`

Type: function
Module: cli_soil
Signature: providers(verbose: bool) -> None
Description: Show status of soil data providers.

`providers`

Type: function
Module: cli_land
Signature: providers()
Description: Show status of all land cover and vegetation providers.

`providers`

Type: function
Module: cli_forward_geocoding
Signature: providers()
Description: Show status of all forward geocoding providers.

`providers`

Type: function
Module: cli_osm_features
Signature: providers()
Description: Show status of OSM features providers.

`providers`

Type: function
Module: cli_marine
Signature: providers()
Description: List available marine data providers and their capabilities.

R

`RateLimiter.init`

Type: method
Module: elevation.location_detector
Class: RateLimiter
Signature: __init__(self) -> None

`RateLimiter.wait_if_needed`

Type: method
Module: elevation.location_detector
Class: RateLimiter
Signature: wait_if_needed(self, service: str, min_interval: float) -> None
Description: Ensure minimum interval between requests for a service.

`request`

Type: function
Module: http_cache
Signature: request(method: str, url: str, read_from_cache: bool, write_to_cache: bool) -> requests.Response
Description: Make cached HTTP request with coordinate canonicalization.

`reset_session`

Type: function
Module: http_cache
Signature: reset_session()
Description: Close and clear the module session (for tests).

`ReverseGeocodeResult.filter_by_type`

Type: method
Module: reverse_geocoding_models
Class: ReverseGeocodeResult
Signature: filter_by_type(self, place_type: PlaceType) -> list[ReverseGeocodeLocation]
Description: Filter locations by place type.

`ReverseGeocodeResult.get_best_match`

Type: method
Module: reverse_geocoding_models
Class: ReverseGeocodeResult
Signature: get_best_match(self) -> ReverseGeocodeLocation | None
Description: Get the best matching location (first in list).

`ReverseGeocodeResult.get_country`

Type: method
Module: reverse_geocoding_models
Class: ReverseGeocodeResult
Signature: get_country(self) -> str | None
Description: Get country from the best match.

`ReverseGeocodeResult.get_formatted_address`

Type: method
Module: reverse_geocoding_models
Class: ReverseGeocodeResult
Signature: get_formatted_address(self) -> str | None
Description: Get formatted address from the best match.

`ReverseGeocodeResult.to_simple_dict`

Type: method
Module: reverse_geocoding_models
Class: ReverseGeocodeResult
Signature: to_simple_dict(self) -> dict[str, Any]
Description: Convert to simple dictionary for easy viewing.

`ReverseGeocodingProvider.choices`

Type: method
Module: providers
Class: ReverseGeocodingProvider
Signature: choices(cls) -> list[str]
Description: Get list of provider choices for Click.

`ReverseGeocodingProvider.description`

Type: method
Module: providers
Class: ReverseGeocodingProvider
Signature: description(cls) -> str
Description: Get formatted description of all available providers.

`ReverseGeocodingProvider.fetch`

Type: method
Module: reverse_geocoding.providers.base
Class: ReverseGeocodingProvider
Signature: fetch(self, lat: float, lon: float) -> ReverseGeocodeFetchResult
Description: Fetch reverse geocoding data for the given coordinates.

`ReverseGeocodingProvider.info`

Type: method
Module: providers
Class: ReverseGeocodingProvider
Signature: info(cls, provider: 'ReverseGeocodingProvider | str') -> ProviderInfo
Description: Get detailed information about a provider.

`ReverseGeocodingService.init`

Type: method
Module: reverse_geocoding.service
Class: ReverseGeocodingService
Signature: __init__(self) -> None
Description: Initialize the reverse geocoding service.

`ReverseGeocodingService.compare_providers`

Type: method
Module: reverse_geocoding.service
Class: ReverseGeocodingService
Signature: compare_providers(self, lat: float, lon: float) -> dict[str, Any]
Description: Compare results from all available providers.

`ReverseGeocodingService.get_available_providers`

Type: method
Module: reverse_geocoding.service
Class: ReverseGeocodingService
Signature: get_available_providers(self) -> list[str]
Description: Get list of available provider names.

`ReverseGeocodingService.get_provider`

Type: method
Module: reverse_geocoding.service
Class: ReverseGeocodingService
Signature: get_provider(self, name: str) -> ReverseGeocodingProvider | None
Description: Get a specific provider by name.

`ReverseGeocodingService.reverse_geocode`

Type: method
Module: reverse_geocoding.service
Class: ReverseGeocodingService
Signature: reverse_geocode(self, lat: float, lon: float, provider: str | None) -> ReverseGeocodeResult | None
Description: Perform reverse geocoding using specified or default provider.

`ReverseGeocodingService.reverse_geocode_multiple`

Type: method
Module: reverse_geocoding.service
Class: ReverseGeocodingService
Signature: reverse_geocode_multiple(self, lat: float, lon: float, providers: list[str] | None) -> dict[str, ReverseGeocodeResult]
Description: Perform reverse geocoding using multiple providers sequentially.

S

`set_session_for_tests`

Type: function
Module: http_cache
Signature: set_session_for_tests(session: CachedSession)
Description: Force http_cache.get_session() to return a provided session (for tests).

`setup_logging`

Type: function
Module: logging_config
Signature: setup_logging(level: str, log_file: str | None, enable_file_logging: bool) -> logging.Logger
Description: Set up centralized logging with console and optional file output.

`show_mapping_info`

Type: function
Module: cli_biosample_elevation
Signature: show_mapping_info() -> None
Description: Display comprehensive field mapping information and examples.

`show_version`

Type: function
Module: cli
Signature: show_version() -> None
Description: Print the biosample-enricher version.

`SmartOpenTopoDataProvider.init`

Type: method
Module: elevation.providers.open_topo_data
Class: SmartOpenTopoDataProvider
Signature: __init__(self, endpoint: str) -> None
Description: Initialize smart provider with automatic dataset selection.

`SmartOpenTopoDataProvider.fetch`

Type: method
Module: elevation.providers.open_topo_data
Class: SmartOpenTopoDataProvider
Signature: fetch(self, lat: float, lon: float) -> FetchResult
Description: Fetch elevation using optimal dataset for location.

`soil`

Type: function
Module: cli_soil
Signature: soil() -> None
Description: Soil enrichment commands for biosample site characterization.

`SoilGridsProvider.init`

Type: method
Module: soil.providers.soilgrids
Class: SoilGridsProvider
Signature: __init__(self, timeout: int)

`SoilGridsProvider.coverage_description`

Type: method
Module: soil.providers.soilgrids
Class: SoilGridsProvider
Signature: coverage_description(self) -> str

`SoilGridsProvider.get_soil_data`

Type: method
Module: soil.providers.soilgrids
Class: SoilGridsProvider
Signature: get_soil_data(self, latitude: float, longitude: float, depth_cm: str | None) -> SoilResult
Description: Get SoilGrids soil data for a location.

`SoilGridsProvider.is_available`

Type: method
Module: soil.providers.soilgrids
Class: SoilGridsProvider
Signature: is_available(self) -> bool
Description: Check if SoilGrids services are available.

`SoilGridsProvider.name`

Type: method
Module: soil.providers.soilgrids
Class: SoilGridsProvider
Signature: name(self) -> str

`SoilObservation.validate_texture_class`

Type: method
Module: soil.models
Class: SoilObservation
Signature: validate_texture_class(cls, v: str | None) -> str | None
Description: Validate USDA texture class names.

`SoilProviderBase.calculate_quality_score`

Type: method
Module: soil.providers.base
Class: SoilProviderBase
Signature: calculate_quality_score(self, distance_m: float | None, confidence: float | None, data_completeness: float) -> float
Description: Calculate overall data quality score.

`SoilProviderBase.coverage_description`

Type: method
Module: soil.providers.base
Class: SoilProviderBase
Signature: coverage_description(self) -> str
Description: Description of geographic and data coverage.

`SoilProviderBase.get_soil_data`

Type: method
Module: soil.providers.base
Class: SoilProviderBase
Signature: get_soil_data(self, latitude: float, longitude: float, depth_cm: str | None) -> SoilResult
Description: Retrieve soil data for a specific location.

`SoilProviderBase.is_available`

Type: method
Module: soil.providers.base
Class: SoilProviderBase
Signature: is_available(self) -> bool
Description: Check if the provider is currently available.

`SoilProviderBase.name`

Type: method
Module: soil.providers.base
Class: SoilProviderBase
Signature: name(self) -> str
Description: Provider name for identification and logging.

`SoilProviderBase.validate_coordinates`

Type: method
Module: soil.providers.base
Class: SoilProviderBase
Signature: validate_coordinates(self, latitude: float, longitude: float) -> None
Description: Validate coordinate inputs.

`SoilResult.to_gold_schema`

Type: method
Module: soil.models
Class: SoilResult
Signature: to_gold_schema(self) -> dict[str, Any]
Description: Convert to GOLD biosample schema format.

`SoilResult.to_nmdc_schema`

Type: method
Module: soil.models
Class: SoilResult
Signature: to_nmdc_schema(self) -> dict[str, Any]
Description: Convert to NMDC biosample schema format.

`SoilService.init`

Type: method
Module: soil.service
Class: SoilService
Signature: __init__(self)
Description: Initialize soil service with providers.

`SoilService.enrich_batch`

Type: method
Module: soil.service
Class: SoilService
Signature: enrich_batch(self, locations: list[tuple[float, float]], depth_cm: str | None) -> list[SoilResult]
Description: Enrich multiple locations with soil data.

`SoilService.enrich_biosample`

Type: method
Module: soil.service
Class: SoilService
Signature: enrich_biosample(self, sample_data: dict) -> dict
Description: Enrich a single biosample with soil data.

`SoilService.enrich_location`

Type: method
Module: soil.service
Class: SoilService
Signature: enrich_location(self, latitude: float, longitude: float, depth_cm: str | None) -> SoilResult
Description: Enrich a single location with soil data.

`SoilService.get_provider_status`

Type: method
Module: soil.service
Class: SoilService
Signature: get_provider_status(self) -> dict[str, dict]
Description: Get status of all soil providers.

T

`test`

Type: function
Module: cli_soil
Signature: test(latitude: float, longitude: float, provider: str, depth: str, verbose: bool) -> None
Description: Test soil data providers at a specific location.

`test`

Type: function
Module: cache_management
Signature: test(ctx: click.Context, url: str, method: str, params: str | None) -> None
Description: Test cache functionality with a request.

`test`

Type: function
Module: cli_land
Signature: test(lat: float, lon: float, date: datetime | None)
Description: Test land enrichment with sample coordinates.

`test`

Type: function
Module: cli_forward_geocoding
Signature: test(query: str)
Description: Test forward geocoding with a sample place name.

`test`

Type: function
Module: cli_osm_features
Signature: test(latitude: float, longitude: float, radius: int)
Description: Test OSM features enrichment with sample coordinates.

`test`

Type: function
Module: cli_marine
Signature: test(lat: float, lon: float, date: str)
Description: Test marine data providers for a specific location and date.

`test_connection`

Type: function
Module: cli_metrics
Signature: test_connection(nmdc_connection: str | None, gold_connection: str | None) -> None
Description: Test database connections.

`typeof`

Type: function
Module: schema_statistics
Signature: typeof(v: Any) -> str

U

`UnifiedBiosampleFetcher.init`

Type: method
Module: adapters
Class: UnifiedBiosampleFetcher
Signature: __init__(self) -> None

`UnifiedBiosampleFetcher.configure_gold_mongo`

Type: method
Module: adapters
Class: UnifiedBiosampleFetcher
Signature: configure_gold_mongo(self, connection_string: str, database: str, collection: str) -> None
Description: Configure GOLD MongoDB connection.

`UnifiedBiosampleFetcher.configure_nmdc_mongo`

Type: method
Module: adapters
Class: UnifiedBiosampleFetcher
Signature: configure_nmdc_mongo(self, connection_string: str, database: str, collection: str) -> None
Description: Configure NMDC MongoDB connection.

`UnifiedBiosampleFetcher.fetch_enrichable_locations`

Type: method
Module: adapters
Class: UnifiedBiosampleFetcher
Signature: fetch_enrichable_locations(self, source: str, limit: int | None) -> Iterator[BiosampleLocation]
Description: Fetch enrichable locations from configured sources.

`UnifiedBiosampleFetcher.fetch_locations_by_ids`

Type: method
Module: adapters
Class: UnifiedBiosampleFetcher
Signature: fetch_locations_by_ids(self, ids: list[str], source: str, id_field: str | None) -> Iterator[BiosampleLocation]
Description: Fetch locations by IDs from configured sources.

`UnifiedBiosampleFetcher.fetch_random_enrichable_locations`

Type: method
Module: adapters
Class: UnifiedBiosampleFetcher
Signature: fetch_random_enrichable_locations(self, n: int, source: str) -> Iterator[BiosampleLocation]
Description: Fetch N random enrichable locations from configured sources.

`UnifiedBiosampleFetcher.fetch_random_locations`

Type: method
Module: adapters
Class: UnifiedBiosampleFetcher
Signature: fetch_random_locations(self, n: int, source: str) -> Iterator[BiosampleLocation]
Description: Fetch N random locations from configured sources.

`UnifiedBiosampleFetcher.get_enrichment_statistics`

Type: method
Module: adapters
Class: UnifiedBiosampleFetcher
Signature: get_enrichment_statistics(self) -> dict[str, Any]
Description: Get statistics about available enrichable samples.

`USDANRCSProvider.init`

Type: method
Module: soil.providers.usda_nrcs
Class: USDANRCSProvider
Signature: __init__(self, timeout: int)

`USDANRCSProvider.coverage_description`

Type: method
Module: soil.providers.usda_nrcs
Class: USDANRCSProvider
Signature: coverage_description(self) -> str

`USDANRCSProvider.get_soil_data`

Type: method
Module: soil.providers.usda_nrcs
Class: USDANRCSProvider
Signature: get_soil_data(self, latitude: float, longitude: float, depth_cm: str | None) -> SoilResult
Description: Get USDA soil taxonomy data for a location.

`USDANRCSProvider.is_available`

Type: method
Module: soil.providers.usda_nrcs
Class: USDANRCSProvider
Signature: is_available(self) -> bool
Description: Check if USDA SDA is available.

`USDANRCSProvider.name`

Type: method
Module: soil.providers.usda_nrcs
Class: USDANRCSProvider
Signature: name(self) -> str

`USGSElevationProvider.init`

Type: method
Module: elevation.providers.usgs
Class: USGSElevationProvider
Signature: __init__(self) -> None
Description: Initialize USGS Elevation provider.

`USGSElevationProvider.fetch`

Type: method
Module: elevation.providers.usgs
Class: USGSElevationProvider
Signature: fetch(self, lat: float, lon: float) -> FetchResult
Description: Fetch elevation data from USGS 3DEP ArcGIS service.

V

`validate_elevation_providers`

Type: function
Module: providers
Signature: validate_elevation_providers(providers_str: str | None) -> list[str] | None
Description: Validate and parse elevation provider string.

`validate_geocoding_providers`

Type: function
Module: providers
Signature: validate_geocoding_providers(providers_str: str | None) -> list[str] | None
Description: Validate and parse reverse geocoding provider string.

`VegetationObservation.validate_location`

Type: method
Module: land.models
Class: VegetationObservation
Signature: validate_location(cls, v: dict[str, float]) -> dict[str, float]
Description: Validate location coordinates.

`VegetationProviderBase.calculate_spatial_distance`

Type: method
Module: land.providers.base
Class: VegetationProviderBase
Signature: calculate_spatial_distance(self, lat1: float, lon1: float, lat2: float, lon2: float) -> float
Description: Calculate distance between two points using Haversine formula.

`VegetationProviderBase.calculate_temporal_offset`

Type: method
Module: land.providers.base
Class: VegetationProviderBase
Signature: calculate_temporal_offset(self, target_date: date, actual_date: date) -> int
Description: Calculate temporal offset between target and actual dates.

`VegetationProviderBase.coverage_description`

Type: method
Module: land.providers.base
Class: VegetationProviderBase
Signature: coverage_description(self) -> str
Description: Description of geographic and temporal coverage.

`VegetationProviderBase.get_vegetation_indices`

Type: method
Module: land.providers.base
Class: VegetationProviderBase
Signature: get_vegetation_indices(self, latitude: float, longitude: float, target_date: date | None, time_window_days: int) -> list[VegetationObservation]
Description: Retrieve vegetation indices for a specific location and date.

`VegetationProviderBase.is_available`

Type: method
Module: land.providers.base
Class: VegetationProviderBase
Signature: is_available(self) -> bool
Description: Check if the provider is currently available.

`VegetationProviderBase.name`

Type: method
Module: land.providers.base
Class: VegetationProviderBase
Signature: name(self) -> str
Description: Provider name for identification and logging.

`VegetationProviderBase.validate_coordinates`

Type: method
Module: land.providers.base
Class: VegetationProviderBase
Signature: validate_coordinates(self, latitude: float, longitude: float) -> None
Description: Validate coordinate inputs.

`visualize`

Type: function
Module: cli_metrics
Signature: visualize(csv_file: Path, output_dir: Path) -> None
Description: Create visualizations from existing metrics CSV file.

W

`walk`

Type: function
Module: schema_statistics
Signature: walk(doc: Any, prefix: str, seen: dict[str, dict], max_examples: int, doc_id: str) -> None
Description: Recursively record stats for each path.

`weather_cli`

Type: function
Module: cli_weather
Signature: weather_cli(debug: bool)
Description: Weather enrichment CLI for biosample environmental context.

`WeatherEnrichmentMetrics.init`

Type: method
Module: weather.metrics
Class: WeatherEnrichmentMetrics
Signature: __init__(self)

`WeatherEnrichmentMetrics.analyze_biosample_collection`

Type: method
Module: weather.metrics
Class: WeatherEnrichmentMetrics
Signature: analyze_biosample_collection(self, biosamples: list[dict[str, Any]], source: str) -> dict[str, Any]
Description: Analyze weather field coverage before and after enrichment for a collection of biosamples.

`WeatherEnrichmentMetrics.export_detailed_results`

Type: method
Module: weather.metrics
Class: WeatherEnrichmentMetrics
Signature: export_detailed_results(self, output_path: str) -> None
Description: Export detailed enrichment results to CSV for further analysis.

`WeatherEnrichmentMetrics.generate_metrics_report`

Type: method
Module: weather.metrics
Class: WeatherEnrichmentMetrics
Signature: generate_metrics_report(self, analyses: list[dict[str, Any]]) -> pd.DataFrame
Description: Generate comprehensive metrics report in tabular format.

`WeatherObservation.validate_value`

Type: method
Module: weather.models
Class: WeatherObservation
Signature: validate_value(cls, v)
Description: Validate that value is either a number or dict with numeric values.

`WeatherProviderBase.init`

Type: method
Module: weather.providers.base
Class: WeatherProviderBase
Signature: __init__(self, timeout: int)

`WeatherProviderBase.get_coverage_period`

Type: method
Module: weather.providers.base
Class: WeatherProviderBase
Signature: get_coverage_period(self) -> dict[str, str]
Description: Return temporal coverage period.

`WeatherProviderBase.get_daily_weather`

Type: method
Module: weather.providers.base
Class: WeatherProviderBase
Signature: get_daily_weather(self, lat: float, lon: float, target_date: date, parameters: list | None) -> WeatherResult
Description: Get weather data for a specific date and location.

`WeatherProviderBase.get_provider_info`

Type: method
Module: weather.providers.base
Class: WeatherProviderBase
Signature: get_provider_info(self) -> dict[str, Any]
Description: Get provider metadata and capabilities.

`WeatherProviderBase.get_spatial_resolution`

Type: method
Module: weather.providers.base
Class: WeatherProviderBase
Signature: get_spatial_resolution(self) -> str
Description: Return spatial resolution (e.g., ‘11km’, ‘station-based’).

`WeatherProviderBase.get_supported_parameters`

Type: method
Module: weather.providers.base
Class: WeatherProviderBase
Signature: get_supported_parameters(self) -> list
Description: Return list of weather parameters this provider supports.

`WeatherProviderBase.get_temporal_resolution`

Type: method
Module: weather.providers.base
Class: WeatherProviderBase
Signature: get_temporal_resolution(self) -> str
Description: Return temporal resolution (e.g., ‘hourly’, ‘daily’).

`WeatherProviderBase.is_available`

Type: method
Module: weather.providers.base
Class: WeatherProviderBase
Signature: is_available(self, lat: float, lon: float, target_date: date) -> bool
Description: Check if provider has data available for given location and date.

`WeatherResult.get_coverage_metrics`

Type: method
Module: weather.models
Class: WeatherResult
Signature: get_coverage_metrics(self) -> dict[str, Any]
Description: Generate before/after coverage metrics for this weather enrichment.

`WeatherResult.get_schema_mapping`

Type: method
Module: weather.models
Class: WeatherResult
Signature: get_schema_mapping(self, target_schema: str) -> dict[str, Any]
Description: Map weather observations to target biosample schema fields.

`WeatherResult.validate_date_format`

Type: method
Module: weather.models
Class: WeatherResult
Signature: validate_date_format(cls, v)
Description: Ensure collection date is in YYYY-MM-DD format.

`WeatherService.init`

Type: method
Module: weather.service
Class: WeatherService
Signature: __init__(self, providers: list[WeatherProviderBase] | None)
Description: Initialize weather service with provider chain.

`WeatherService.get_climate_normals`

Type: method
Module: weather.service
Class: WeatherService
Signature: get_climate_normals(self, lat: float, lon: float, years_back: int, providers: list[str] | None) -> MultiProviderClimateNormals
Description: Get climate averages (normals) for a location from all available providers.

`WeatherService.get_daily_weather`

Type: method
Module: weather.service
Class: WeatherService
Signature: get_daily_weather(self, lat: float, lon: float, target_date: date, parameters: list[str] | None) -> WeatherResult
Description: Get daily weather data by integrating results from all providers.

`WeatherService.get_provider_info`

Type: method
Module: weather.service
Class: WeatherService
Signature: get_provider_info(self) -> list[dict[str, Any]]
Description: Get information about all configured providers.

`WeatherService.get_weather_for_biosample`

Type: method
Module: weather.service
Class: WeatherService
Signature: get_weather_for_biosample(self, biosample: dict[str, Any], target_schema: str) -> dict[str, Any]
Description: Get weather data for a biosample and map to target schema.

This index was automatically generated by scripts/generate_api_index.py

API Index

Alphabetical API Index

Module Constants

_version

COMMIT_ID

COMMIT_ID

TYPE_CHECKING

VERSION_TUPLE

VERSION_TUPLE

soil.models

USDA_TEXTURE_CLASSES

environmental_metadata

ALL_SUPPORTED_SLOTS

CLIMATE_PROVIDERS

CLIMATE_SLOTS

ELEVATION_SLOTS

MARINE_SLOTS

SOIL_SLOTS

WEATHER_SLOTS

Functions and Methods

A

analyze

analyze

B

BaseElevationProvider.__init__

BaseElevationProvider.fetch

BaseReverseGeocodingProvider.__init__

BaseReverseGeocodingProvider.fetch

batch

batch

batch

batch

batch

batch_elevation

BiosampleAdapter.extract_location

BiosampleAdapter.extract_locations_batch

BiosampleElevationBatch.filter_valid_coordinates

BiosampleElevationBatch.get_coordinate_summary

BiosampleElevationMapper.create_elevation_request

BiosampleElevationMapper.extract_coordinates

BiosampleElevationMapper.get_biosample_id

BiosampleElevationMapper.get_field_mapping_info

BiosampleElevationMapper.get_location_context

BiosampleElevationMapper.validate_coordinates

BiosampleLocation.calculate_completeness

BiosampleLocation.is_enrichable

BiosampleLocation.to_dict

BiosampleLocation.validate_collection_date

BiosampleMetricsFetcher.__init__

BiosampleMetricsFetcher.fetch_all_samples

BiosampleMetricsFetcher.fetch_gold_samples

BiosampleMetricsFetcher.fetch_nmdc_samples

C

calculate_distance_m

canonicalize_coords

classify_texture

clear

cli

cli

cli

ClimateNormalsProvider.get_climate_normals

ClimateNormalsResult.get_annual_precipitation

ClimateNormalsResult.get_annual_temperature

ClimateNormalsResult.to_submission_schema

CombinedFeaturesResult.to_enrichment_dict

compare

compare_providers

configure_from_env

CoordinateClassifier.__init__

CoordinateClassifier.classify

CoordinateClassifier.classify_biosample_location

CoverageEvaluator.__init__

CoverageEvaluator.evaluate_batch

CoverageEvaluator.evaluate_sample

D

demo

demonstrate_field_mapping

E

elevation_cli

ElevationProvider.choices

`_version`

`COMMIT_ID`

`COMMIT_ID`

`TYPE_CHECKING`

`VERSION_TUPLE`

`VERSION_TUPLE`

`soil.models`

`USDA_TEXTURE_CLASSES`

`environmental_metadata`

`ALL_SUPPORTED_SLOTS`

`CLIMATE_PROVIDERS`

`CLIMATE_SLOTS`

`ELEVATION_SLOTS`

`MARINE_SLOTS`

`SOIL_SLOTS`

`WEATHER_SLOTS`

`analyze`

`analyze`

`BaseElevationProvider.init`

`BaseElevationProvider.fetch`

`BaseReverseGeocodingProvider.init`

`BaseReverseGeocodingProvider.fetch`

`batch`

`batch`

`batch`

`batch`

`batch`

`batch_elevation`

`BiosampleAdapter.extract_location`

`BiosampleAdapter.extract_locations_batch`

`BiosampleElevationBatch.filter_valid_coordinates`

`BiosampleElevationBatch.get_coordinate_summary`

`BiosampleElevationMapper.create_elevation_request`

`BiosampleElevationMapper.extract_coordinates`

`BiosampleElevationMapper.get_biosample_id`

`BiosampleElevationMapper.get_field_mapping_info`

`BiosampleElevationMapper.get_location_context`

`BiosampleElevationMapper.validate_coordinates`

`BiosampleLocation.calculate_completeness`

`BiosampleLocation.is_enrichable`

`BiosampleLocation.to_dict`

`BiosampleLocation.validate_collection_date`

`BiosampleMetricsFetcher.init`

`BiosampleMetricsFetcher.fetch_all_samples`

`BiosampleMetricsFetcher.fetch_gold_samples`

`BiosampleMetricsFetcher.fetch_nmdc_samples`

`calculate_distance_m`

`canonicalize_coords`

`classify_texture`

`clear`

`cli`

`cli`

`cli`

`ClimateNormalsProvider.get_climate_normals`

`ClimateNormalsResult.get_annual_precipitation`

`ClimateNormalsResult.get_annual_temperature`

`ClimateNormalsResult.to_submission_schema`

`CombinedFeaturesResult.to_enrichment_dict`

`compare`

`compare_providers`

`configure_from_env`

`CoordinateClassifier.init`

`CoordinateClassifier.classify`

`CoordinateClassifier.classify_biosample_location`

`CoverageEvaluator.init`

`CoverageEvaluator.evaluate_batch`

`CoverageEvaluator.evaluate_sample`

`demo`

`demonstrate_field_mapping`

`elevation_cli`

`ElevationProvider.choices`

`ElevationProvider.description`

`ElevationProvider.fetch`

`ElevationProvider.info`

`ElevationService.init`

`ElevationService.classify_biosample_location`

`ElevationService.classify_coordinates`

`ElevationService.create_output_envelope`

`ElevationService.from_env`

`ElevationService.get_best_elevation`