Makefile

# Terraphim Personalized Medicine System
# Makefile for building pre-serialized medical dataset artifacts
#
# One-time setup on developer machine:
#   make artifacts
#   git lfs push origin main   # or: make upload-artifacts
#
# On judge/reviewer machine (after git clone):
#   git lfs pull                # fast: downloads compressed artifacts
#   cargo run -p terraphim-api  # cold-start <5s (loads pre-built artifacts)
#
# S3 fallback (if artifacts exceed 1 GB LFS quota):
#   ARTIFACT_BUCKET=my-bucket make upload-s3
#   ARTIFACT_BUCKET=my-bucket make fetch-s3

ARTIFACT_DIR   := data/artifacts
UMLS_INPUT     := data/automata/words_cui.tsv
SNOMED_VERSION := 20240201

UMLS_ARTIFACT   := $(ARTIFACT_DIR)/umls_automata.bin.zst
SNOMED_ARTIFACT := $(ARTIFACT_DIR)/snomed_hierarchy.bin.zst
CPIC_ARTIFACT   := $(ARTIFACT_DIR)/cpic_database.bin.zst

SNOMED_CONCEPTS       := data/snomed/extracted/sct2_Concept_Full_INT_$(SNOMED_VERSION).txt
SNOMED_DESCRIPTIONS   := data/snomed/extracted/sct2_Description_Full-en_INT_$(SNOMED_VERSION).txt
SNOMED_RELATIONSHIPS  := data/snomed/extracted/sct2_Relationship_Full_INT_$(SNOMED_VERSION).txt

# Release configuration
VERSION      := $(shell git describe --tags --always --dirty 2>/dev/null || echo "0.1.0")
PACKAGE_NAME := terraphim-medgemma-$(VERSION)-linux-x86_64
RELEASE_DIR  := target/release
DIST_DIR     := dist

.PHONY: all artifacts fetch-artifacts upload-s3 fetch-s3 clean-artifacts test snomed-fhir snomed-fhir-check
.PHONY: build-release package checksum clean-release install

all: test

## Build all three pre-serialized artifacts
artifacts: $(UMLS_ARTIFACT) $(SNOMED_ARTIFACT) $(CPIC_ARTIFACT)
	@echo ""
	@echo "=== Artifacts built ==="
	@ls -lh $(ARTIFACT_DIR)/*.bin.zst

## UMLS Aho-Corasick artifact (~14 min build, <100ms load)
$(UMLS_ARTIFACT): $(UMLS_INPUT)
	@mkdir -p $(ARTIFACT_DIR)
	cargo run --release --bin build-umls-artifact -- \
	    --input $(UMLS_INPUT) \
	    --output $(UMLS_ARTIFACT)

## SNOMED CT hierarchy artifact (requires RF2 download first)
$(SNOMED_ARTIFACT): $(SNOMED_CONCEPTS) $(SNOMED_DESCRIPTIONS) $(SNOMED_RELATIONSHIPS)
	@mkdir -p $(ARTIFACT_DIR)
	cargo run --release --bin build-snomed-artifact -- \
	    --concepts       $(SNOMED_CONCEPTS) \
	    --descriptions   $(SNOMED_DESCRIPTIONS) \
	    --relationships  $(SNOMED_RELATIONSHIPS) \
	    --output $(SNOMED_ARTIFACT)

## Download SNOMED RF2 files
## Option A (primary): UMLS API key — fastest, full RF2 release
##   UMLS_API_KEY=xxx make $(SNOMED_CONCEPTS)
## Option B (fallback): Public FHIR server — no key needed, slower (~2h for full set)
##   make snomed-fhir
$(SNOMED_CONCEPTS):
	@if [ -n "$(UMLS_API_KEY)" ]; then \
	    SNOMED_VERSION=$(SNOMED_VERSION) ./scripts/download_snomed.sh; \
	else \
	    echo "No UMLS_API_KEY set. Using public FHIR fallback (no key required)."; \
	    python3 scripts/download_snomed_fhir.py --output data/snomed/extracted; \
	fi

## Download SNOMED via public FHIR API (no UMLS key required)
snomed-fhir:
	python3 scripts/download_snomed_fhir.py --output data/snomed/extracted

## Test FHIR connectivity only
snomed-fhir-check:
	python3 scripts/download_snomed_fhir.py --dry-run

## CPIC pharmacogenomics artifact (downloads from live API)
$(CPIC_ARTIFACT):
	@mkdir -p $(ARTIFACT_DIR)
	cargo run --release --bin build-cpic-artifact -- \
	    --output $(CPIC_ARTIFACT)

## Pull artifacts from Git LFS
fetch-artifacts:
	git lfs pull

## Upload artifacts to S3 (fallback when LFS quota exceeded)
upload-s3:
	@test -n "$(ARTIFACT_BUCKET)" || (echo "Error: ARTIFACT_BUCKET not set" && exit 1)
	aws s3 cp $(ARTIFACT_DIR)/ s3://$(ARTIFACT_BUCKET)/artifacts/ \
	    --recursive --exclude "*" --include "*.bin.zst"

## Download artifacts from S3 (fallback)
fetch-s3:
	@test -n "$(ARTIFACT_BUCKET)" || (echo "Error: ARTIFACT_BUCKET not set" && exit 1)
	@mkdir -p $(ARTIFACT_DIR)
	aws s3 cp s3://$(ARTIFACT_BUCKET)/artifacts/ $(ARTIFACT_DIR)/ \
	    --recursive --exclude "*" --include "*.bin.zst"

## Remove built artifacts (they can be regenerated)
clean-artifacts:
	rm -f $(ARTIFACT_DIR)/*.bin.zst

## Run all tests
test:
	cargo test --lib --workspace
	cd terraphim_pipeline && python -m pytest tests/ -v 2>/dev/null || true

# =============================================================================
# Release and Packaging Targets
# =============================================================================

## Build optimized release binaries for all workspace crates
build-release:
	@echo "Building release binaries..."
	cargo build --release --workspace \
	    --bin terraphim-demo \
	    --bin terraphim-api \
	    --bin build-umls-artifact \
	    --bin build-snomed-artifact \
	    --bin build-cpic-artifact \
	    --bin umls_benchmark \
	    --bin evaluation-runner \
	    --bin primekg-import
	@echo ""
	@echo "=== Release binaries built ==="
	@ls -lh $(RELEASE_DIR)/terraphim-demo $(RELEASE_DIR)/terraphim-api 2>/dev/null || true

## Create distribution tarball with all binaries and data files
package: build-release
	@echo "Creating distribution package..."
	@mkdir -p $(DIST_DIR)/$(PACKAGE_NAME)

	# Copy binaries
	cp $(RELEASE_DIR)/terraphim-demo $(DIST_DIR)/$(PACKAGE_NAME)/
	cp $(RELEASE_DIR)/terraphim-api $(DIST_DIR)/$(PACKAGE_NAME)/
	cp $(RELEASE_DIR)/build-umls-artifact $(DIST_DIR)/$(PACKAGE_NAME)/
	cp $(RELEASE_DIR)/build-snomed-artifact $(DIST_DIR)/$(PACKAGE_NAME)/
	cp $(RELEASE_DIR)/build-cpic-artifact $(DIST_DIR)/$(PACKAGE_NAME)/
	cp $(RELEASE_DIR)/umls_benchmark $(DIST_DIR)/$(PACKAGE_NAME)/
	cp $(RELEASE_DIR)/evaluation-runner $(DIST_DIR)/$(PACKAGE_NAME)/
	cp $(RELEASE_DIR)/primekg-import $(DIST_DIR)/$(PACKAGE_NAME)/

	# Copy data files
	@mkdir -p $(DIST_DIR)/$(PACKAGE_NAME)/data/artifacts
	@if [ -d "$(ARTIFACT_DIR)" ]; then \
	    cp $(ARTIFACT_DIR)/*.bin.zst $(DIST_DIR)/$(PACKAGE_NAME)/data/artifacts/ 2>/dev/null || true; \
	fi

	# Copy documentation
	cp README.md $(DIST_DIR)/$(PACKAGE_NAME)/
	cp LICENSE $(DIST_DIR)/$(PACKAGE_NAME)/ 2>/dev/null || true
	@if [ -d "docs" ]; then \
	    cp -r docs $(DIST_DIR)/$(PACKAGE_NAME)/; \
	fi

	# Copy config files
	@if [ -d "config" ]; then \
	    cp -r config $(DIST_DIR)/$(PACKAGE_NAME)/; \
	fi

	# Create install script
	@./scripts/package.sh $(DIST_DIR)/$(PACKAGE_NAME)

	# Create tarball
	cd $(DIST_DIR) && tar czf $(PACKAGE_NAME).tar.gz $(PACKAGE_NAME)

	@echo ""
	@echo "=== Package created ==="
	@ls -lh $(DIST_DIR)/$(PACKAGE_NAME).tar.gz

## Generate SHA256 checksums for all distribution files
checksum: package
	@echo "Generating checksums..."
	cd $(DIST_DIR) && sha256sum *.tar.gz > checksums.sha256
	@echo ""
	@echo "=== Checksums ==="
	@cat $(DIST_DIR)/checksums.sha256

## Clean release artifacts
clean-release:
	rm -rf $(DIST_DIR)
	cargo clean --release

## Install binaries to system (requires sudo)
install: build-release
	@echo "Installing Terraphim MedGemma..."
	sudo install -m 755 $(RELEASE_DIR)/terraphim-demo /usr/local/bin/
	sudo install -m 755 $(RELEASE_DIR)/terraphim-api /usr/local/bin/
	sudo install -m 755 $(RELEASE_DIR)/build-umls-artifact /usr/local/bin/
	sudo install -m 755 $(RELEASE_DIR)/build-snomed-artifact /usr/local/bin/
	sudo install -m 755 $(RELEASE_DIR)/build-cpic-artifact /usr/local/bin/
	@echo "Installation complete!"

## Uninstall binaries from system (requires sudo)
uninstall:
	@echo "Uninstalling Terraphim MedGemma..."
	sudo rm -f /usr/local/bin/terraphim-demo
	sudo rm -f /usr/local/bin/terraphim-api
	sudo rm -f /usr/local/bin/build-umls-artifact
	sudo rm -f /usr/local/bin/build-snomed-artifact
	sudo rm -f /usr/local/bin/build-cpic-artifact
	@echo "Uninstall complete!"