biosample-enricher

User Guide

  • Environmental Metadata
    • What It Does
    • Quick Example
    • What Values Can You Get?
      • Currently Supported (✅ Ready to Use)
      • Partially Implemented (⚠️ Use with Caution)
      • Not Yet Implemented (❌ Future Work)
    • Parameters
      • get_environmental_metadata()
    • Return Value Structure
    • Examples
      • Basic Climate Data
      • Mixing Multiple Slot Types
      • Using Specific Providers
      • Weather Data (Requires Datetime)
      • Error Handling
    • Quick Reference
      • All Constants at a Glance
      • Slots by Category
      • Consensus Strategies
      • Slot Status (Reliability)
      • Copy-Paste Slot Lists
      • Checking Available Slots and Providers
    • Limitations and Known Issues
      • Current Limitations
      • Known Issues
      • Future Development
    • See Also
  • Installation
    • Prerequisites
    • Add to Your Project
    • From Source (Development)
  • Quick Start
    • Get NMDC submission values in 3 steps
    • Next Steps
    • Common Use Cases
      • Get climate data
      • Get elevation
      • Mix multiple slot types
      • Handle errors
    • Need Help?
  • CLI Reference
    • Installation
    • Commands Overview
    • biosample-enricher get
    • biosample-enricher info
    • biosample-enricher slots
    • biosample-enricher providers
    • biosample-enricher strategies
    • Available Slots
    • Python API Alternative
    • Troubleshooting
    • Related Documentation
  • Services Overview
    • Main API
    • Underlying Services (Advanced)

API Reference

  • API Index
    • Alphabetical API Index
      • Module Constants
        • _version
        • soil.models
        • environmental_metadata
      • Functions and Methods
        • A
        • B
        • C
        • D
        • E
        • F
        • G
        • H
        • I
        • L
        • M
        • N
        • O
        • P
        • R
        • S
        • T
        • U
        • V
        • W
  • Services
    • Elevation Service
      • ElevationService
        • ElevationService.__init__()
        • ElevationService.from_env()
        • ElevationService.classify_coordinates()
        • ElevationService.classify_biosample_location()
        • ElevationService.select_providers()
        • ElevationService.get_elevation()
        • ElevationService.get_best_elevation()
        • ElevationService.create_output_envelope()
    • Soil Service
      • SoilService
        • SoilService.__init__()
        • SoilService.enrich_location()
        • SoilService.enrich_batch()
        • SoilService.enrich_biosample()
        • SoilService.get_provider_status()
    • Weather Service
      • ClimateNormalsProvider
        • ClimateNormalsProvider.get_climate_normals()
        • ClimateNormalsProvider.__init__()
      • WeatherService
        • WeatherService.__init__()
        • WeatherService.get_weather_for_biosample()
        • WeatherService.get_daily_weather()
        • WeatherService.get_climate_normals()
        • WeatherService.get_provider_info()
    • Marine Service
      • MarineService
        • MarineService.__init__()
        • MarineService.get_marine_data_for_biosample()
        • MarineService.get_comprehensive_marine_data()
    • Land Service
      • LandService
        • LandService.__init__()
        • LandService.enrich_location()
        • LandService.enrich_batch()
        • LandService.enrich_biosample()
        • LandService.get_provider_status()
    • Forward Geocoding Service
      • ForwardGeocodingService
        • ForwardGeocodingService.__init__()
        • ForwardGeocodingService.get_available_providers()
        • ForwardGeocodingService.get_provider()
        • ForwardGeocodingService.get_provider_status()
        • ForwardGeocodingService.geocode()
        • ForwardGeocodingService.geocode_multiple()
        • ForwardGeocodingService.get_coordinates_for_place()
    • Reverse Geocoding Service
      • ReverseGeocodingService
        • ReverseGeocodingService.__init__()
        • ReverseGeocodingService.get_available_providers()
        • ReverseGeocodingService.get_provider()
        • ReverseGeocodingService.reverse_geocode()
        • ReverseGeocodingService.reverse_geocode_multiple()
        • ReverseGeocodingService.compare_providers()
    • OSM Features Service
      • OSMFeaturesService
        • OSMFeaturesService.__init__()
        • OSMFeaturesService.get_combined_features_for_location()
        • OSMFeaturesService.get_features_for_location()
        • OSMFeaturesService.enrich_biosample_location()
        • OSMFeaturesService.get_features_for_biosample()
        • OSMFeaturesService.get_provider_status()
        • OSMFeaturesService.batch_enrich_locations()
  • Models
    • Core Models
      • biosample_enricher.models
        • BiosampleLocation
        • Variable
        • ValueStatus
        • GeoPoint
        • ProviderRef
        • Observation
        • EnrichmentRun
        • OutputEnvelope
        • CoordinateClassification
        • ElevationRequest
        • ElevationResult
        • FetchResult
    • Service-Specific Models
      • Weather Models
        • TemporalQuality
        • WeatherProvider
        • TemporalPrecision
        • WeatherObservation
        • WeatherResult
        • MultiProviderClimateNormals
        • ClimateNormalsResult
      • Marine Models
        • MarineQuality
        • MarineProvider
        • MarinePrecision
        • MarineObservation
        • MarineResult
      • Soil Models
        • SoilObservation
        • SoilResult
        • classify_texture()
      • Land Cover Models
        • LandCoverObservation
        • VegetationObservation
        • LandResult
      • Geocoding Models
        • LocationType
        • GeometryType
        • BoundingBox
        • ForwardGeocodeLocation
        • ForwardGeocodeProvider
        • ForwardGeocodeResult
        • ForwardGeocodeFetchResult
        • AddressComponentType
        • AddressComponent
        • BoundingBox
        • PlaceType
        • ReverseGeocodeLocation
        • ReverseGeocodeProvider
        • ReverseGeocodeResult
        • ReverseGeocodeFetchResult
      • OSM Features Models
        • OSMElementType
        • GeometryType
        • FeatureCategory
        • Coordinates
        • OSMNamedFeature
        • OSMUnnamedCounts
        • OSMQuery
        • OSMFeaturesResult
        • OSMFetchResult
        • GooglePlacesFeature
        • GooglePlacesResult
        • GooglePlacesFetchResult
        • CombinedFeaturesResult
    • Common Patterns
      • Type Safety
      • Coordinate Handling
      • Observation Pattern
    • See Also
  • Providers
    • Provider Documentation
      • Table of Contents
      • Provider Overview
      • Comparison by Domain
        • Elevation
        • Geocoding
        • Land
        • Marine
        • Soil
        • Weather
    • Detailed Provider Profiles
      • Google Elevation API
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • Open Topo Data
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • OSM Elevation (open-elevation.com)
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • USGS 3DEP Elevation
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • Google Geocoding (Forward)
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • Google Reverse Geocoding
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • OSM Nominatim (Forward)
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • OSM Nominatim (Reverse)
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • ESA WorldCover
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • MODIS Vegetation Indices
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • USGS NLCD
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • ESA Ocean Colour CCI
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • GEBCO Bathymetry
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • NOAA OISST
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • ISRIC SoilGrids
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • USDA NRCS Web Soil Survey
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • Meteostat
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • NASA POWER
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
      • Open-Meteo
        • Quick Facts
        • Reliability
        • Cost
        • Strengths & Weaknesses
        • Use Cases
        • NMDC Integration
    • Documentation Generation
      • Documentation Generation Guide
        • Overview
        • Documentation Tools
        • Source of Truth: provider_metadata.yaml
        • Workflow
        • Benefits
        • File Structure
        • Maintenance Notes
        • Example Provider Entry
        • Future Enhancements

Developer Guide

  • Contributing
    • Contributing to Biosample Enricher
      • Table of Contents
      • Code of Conduct
      • Getting Started
        • Prerequisites
        • Finding an Issue
      • Development Setup
        • 1. Fork and Clone
        • 2. Set Up Development Environment
        • 3. Verify Installation
      • Development Workflow
        • Branch Naming
        • Making Changes
        • Pre-commit Hooks
      • Code Standards
        • Python Style
        • Logging Standards
        • CLI Standards
        • Configuration Management
      • Testing Guidelines
        • Test Organization
        • Running Tests
        • Writing Tests
        • Test Quality Requirements
      • Submitting Changes
        • Pull Request Process
        • Git Commit Guidelines
      • Adding New Features
        • Adding a New Provider
        • Project Architecture Patterns
      • Documentation
        • Docstring Format
        • README Updates
      • Release Process (Maintainers)
        • Creating a Release
        • Release Note Categories
        • Semantic Versioning
      • Getting Help
      • Development Resources
      • License
  • Architecture
    • Core Design
    • Key Components
      • get_environmental_metadata()
      • Multi-Provider System
      • HTTP Caching
    • Data Flow
    • Design Principles
    • Future Development
    • Related Documentation
  • Testing
    • Testing Standards for Biosample Enricher
      • ⚠️ Important Architectural Lesson Learned
      • Framework & How to Run
        • Primary Testing Framework
        • Common Test Invocations
      • Test Layout & Philosophy
        • Directory Structure
        • Testing Philosophy
      • Pytest Marks & Fixtures
        • Standard Test Marks
        • Common Fixtures
      • Test Categories & Examples
        • Unit Tests
        • Integration Tests
        • Network Tests
        • Performance Tests
      • Example-Driven Validation
        • Valid Examples
        • Invalid Examples
        • Validation Pattern
      • Tooling & Style
        • Development Environment
        • Pre-commit Hooks
        • CI Integration
      • Mock Strategies
        • External Services
        • Database Operations
      • Test Data Management
        • Small Test Fixtures
        • Parameterized Tests
      • Migration from unittest
      • Running Tests
        • Local Development
        • Continuous Integration
        • Test Configuration
    • Quick Start
    • Test Categories
    • Related Documentation
  • Provider Reliability
    • Biosample Enricher: Provider Reliability Analysis
      • Executive Summary
      • Provider Summary Table
      • Detailed Domain Analysis
        • 1. ELEVATION PROVIDERS
        • 2. SOIL PROVIDERS
        • 3. WEATHER PROVIDERS
        • 4. MARINE PROVIDERS
        • 5. LAND COVER PROVIDERS
        • 6. VEGETATION PROVIDERS
        • 7. GEOCODING PROVIDERS
        • 8. OSM FEATURES PROVIDER
      • Reliability Matrices
        • By API Key Requirement
        • By Coverage
        • By Temporal Data
        • By Implementation Status
      • Critical Reliability Gaps
        • Gap 1: USGS Elevation Service Unreliability
        • Gap 2: Marine Provider Implementations
        • Gap 3: MODIS Vegetation Implementation
        • Gap 4: Limited Soil Depth Support
      • Provider Reliability Recommendations
        • Tier 1: High Reliability (Use as Primary)
        • Tier 2: Moderate Reliability (Use with Fallback)
        • Tier 3: Low Reliability (Development/Testing Only)
      • Timeout Configuration Review
      • API Key Management
        • Required Keys
        • Missing Implementations
      • Rate Limiting Analysis
      • Known Flaky Tests
      • Testing Gaps
        • Not Tested or Untested
        • Recommendations
      • Summary Recommendations
        • Immediate Actions
        • Short Term (1-2 weeks)
        • Medium Term (1-2 months)
      • Appendix: Provider Quick Reference
        • By Domain
    • Provider Roadmap
      • Provider Reliability Roadmap
        • Priority 1: Critical Issues (Must Fix)
        • Priority 2: Important Enhancements (Should Fix)
        • Priority 3: Testing and Documentation
        • Success Metrics
        • Rollout Plan
    • Related Documentation

Project Info

  • Changelog
    • Recent Releases
      • Latest Release
      • All Releases
  • License
biosample-enricher
  • Python Module Index

Python Module Index

b
 
b
- biosample_enricher
    biosample_enricher.elevation.service
    biosample_enricher.forward_geocoding.models
    biosample_enricher.forward_geocoding.service
    biosample_enricher.land.models
    biosample_enricher.land.service
    biosample_enricher.marine.models
    biosample_enricher.marine.service
    biosample_enricher.models
    biosample_enricher.osm_features.models
    biosample_enricher.osm_features.service
    biosample_enricher.reverse_geocoding.service
    biosample_enricher.reverse_geocoding_models
    biosample_enricher.soil.models
    biosample_enricher.soil.service
    biosample_enricher.weather.models
    biosample_enricher.weather.service

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