Add osm overpass (geographical feature) agent

Makefile

@@ -1,11 +1,23 @@
-.PHONY: hello elevation geo hello-world soil weather wiki test-agent test-minimal
+.PHONY: all backup-data clean clean-derived clean-test \
+        elevation geo hello hello-world soil \
+        test test-agent test-feature-aggregation test-minimal test-soil \
+        weather wiki test-agent test-minimal test-soil test-feature-aggregation
 
 RUN_UV_PYTHON=uv run
 RUN_UV_PYTEST=uv run pytest
 
-all: hello elevation geo hello-world soil weather wiki test-agent test-minimal
+# Default target
+all: \
+    local/oak_ridge_features.json local/nmdc-ai-map-enriched.json \
+    local/nmdc-envo-normalized.json local/nmdc-osm-enriched.json \
+    nmdc-osm-envo-test-cases.json \
+    hello hello-world elevation geo soil weather wiki \
+    test-agent test-minimal
+    # Run the agent-test entry point, corresponding to src/agent_test/__init__.py
+
+# Testing targets
+test: test-agent test-minimal test-soil test-feature-aggregation
 
-# Run the agent-test entry point, corresponding to src/agent_test/__init__.py
 hello:
 	$(RUN_UV_PYTHON) agent-test
 
@@ -43,38 +55,100 @@ test-agent:
 test-minimal:
 	$(RUN_UV_PYTEST) tests/test_minimal_agent.py -v
 
-local/nmdc-biosamples.json:
-	wget -O $@ 'https://api.microbiomedata.org/nmdcschema/biosample_set?max_page_size=99999'
+# Directory setup
+local/:
+	mkdir -p $@
 
+# OSM feature extraction for test location (Oak Ridge)
+local/oak_ridge_features.json: src/agent_test/osm_features.py | local/
+	$(RUN_UV_PYTHON) $< --lat 35.97583846 --lon -84.2743123 --radius 1000 --output $@
 
+# NMDC biosample data fetch
+local/nmdc-biosamples.json: | local/
+	wget -O $@ 'https://api.microbiomedata.org/nmdcschema/biosample_set?max_page_size=99999'
 
-local/nmdc-latlon-inferred.json local/nmdc-latlon-summary.json: local/nmdc-biosamples.json
-	$(RUN_UV_PYTHON) src/make_nmdc_biosamples_location_inferences.py \
-		--input $< \
+# Process biosamples to add lat/lon and elevation
+local/nmdc-latlon-inferred.json local/nmdc-latlon-summary.json: src/make_nmdc_biosamples_location_inferences.py local/nmdc-biosamples.json
+	$(RUN_UV_PYTHON) $< \
+		--input $(word 2,$^) \
 		--add-inferred-latlon \
 		--add-inferred-elevation \
-		--random-n 130 \
+		--random-n 1300 \
 		--output local/nmdc-latlon-inferred.json \
 		--summary-output local/nmdc-latlon-summary.json
 
-# Process biosamples with AI interpretation of map images (using both Google Maps & CBORG)
-local/nmdc-ai-map-enriched.json: local/nmdc-latlon-inferred.json
-	$(RUN_UV_PYTHON) src/biosample_map_interpreter.py \
-		--input $< \
+# Process biosamples with map image interpretation
+local/nmdc-ai-map-enriched.json: src/biosample_map_interpreter.py local/nmdc-latlon-inferred.json
+	$(RUN_UV_PYTHON) $< \
+		--input $(word 2,$^) \
 		--output $@ \
 		--max-samples 13 \
 		--map-types satellite,roadmap,terrain \
 		--zoom-levels 13,15,17
 
-# Compare asserted vs inferred environmental values using Claude Sonnet
-local/nmdc-comparison-summary.json local/nmdc-llm-comparison.json: local/nmdc-ai-map-enriched.json
-	$(RUN_UV_PYTHON) src/biosample_llm_comparator.py \
-		--input $< \
+# Extract OSM features for each biosample location (only for locations with confident coordinates)
+local/nmdc-osm-enriched.json: src/biosample_osm_enricher.py local/nmdc-latlon-inferred.json
+	$(RUN_UV_PYTHON) $< \
+		--input $(word 2,$^) \
+		--output $@ \
+		--radius 1000 \
+		--max-distance 10000 \
+		--max-samples 130
+
+# Apply EnvO normalization to OSM features
+local/nmdc-envo-normalized.json: src/biosample_envo_normalizer.py local/nmdc-osm-enriched.json
+	$(RUN_UV_PYTHON) -m src.biosample_envo_normalizer \
+		--input $(word 2,$^) \
+		--output $@ \
+		--max-samples 130 \
+		--max-features 20 \
+		--confidence 0.7 \
+		--biosample-index -1
+
+# Compare asserted vs inferred environmental values
+local/nmdc-comparison-summary.json local/nmdc-llm-comparison.json: src/biosample_llm_comparator.py local/nmdc-ai-map-enriched.json local/nmdc-envo-normalized.json
+	$(RUN_UV_PYTHON) $< \
+		--input $(word 2,$^) \
+		--osm-features $(word 3,$^) \
 		--output local/nmdc-llm-comparison.json \
 		--summary-output local/nmdc-comparison-summary.json \
 		--max-samples 13
 
-# Other map types available:
+test-soil:
+	$(RUN_UV_PYTEST) tests/test_soil_agent.py -v
+
+test-feature-aggregation:
+	$(RUN_UV_PYTEST) tests/test_feature_aggregation.py -v
+
+# Test case management
+nmdc-osm-envo-test-cases.json: local/nmdc-envo-normalized.json
+	$(RUN_UV_PYTHON) -m src.utils.create_test_cases \
+		--select-best-worst $< \
+		--num-samples 5 \
+		--output $@
+
+# Cleanup targets
+clean:
+	rm -rf local/
+
+# Clean only derived files, preserving input data
+clean-derived:
+	# Remove files that can be recreated from scripts and inputs
+	rm -f local/oak_ridge_*.json
+	rm -f local/nmdc-latlon-*.json 
+	rm -f local/nmdc-osm-enriched*.json
+	rm -f local/nmdc-envo-normalized*.json
+	rm -f local/nmdc-ai-map-enriched.json
+	rm -f local/nmdc-llm-comparison.json
+	rm -f local/nmdc-comparison-summary.json
+	rm -f envo_lexical_index.yaml
+
+# Clean test files but keep the main pipeline files
+clean-test:
+	rm -f local/nmdc-*-test*.json
+	rm -f local/oak_ridge_*.json
+
+# Documentation of available map types
 # - hybrid: Combines satellite imagery with road labels
 # - terrain: Already added - shows topographical features
-# - Historical imagery: Available through Earth Engine APIs (separate service)
+# - Historical imagery: Available through Earth Engine APIs (separate service)