feat: replace FDA SQLite pipeline with BioMCP sidecar#12
Draft
SPerekrestova wants to merge 1 commit intomainfrom
Draft
feat: replace FDA SQLite pipeline with BioMCP sidecar#12SPerekrestova wants to merge 1 commit intomainfrom
SPerekrestova wants to merge 1 commit intomainfrom
Conversation
SPerekrestova
force-pushed
the
feature/biomcp-migration
branch
from
c854fb7 to
5f2d15e
Compare
Replaces FDA SQLite pipeline with BioMCP MCP sidecar for drug interaction checking. Adds async MCP client, severity classifier (DeBERTa zero-shot), graceful degradation, and full test suite. Archived: BioMCP v0.8.16 returns unstructured FDA label text instead of structured interaction pairs. Proceeding with DrugBank custom MCP server approach on feature/drugbank-migration instead. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
SPerekrestova
force-pushed
the
feature/biomcp-migration
branch
from
5f2d15e to
ceedabc
Compare
3 tasks
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
mcpSDK), removing ~500 lines of sync/store infrastructureasyncio.gatherfor concurrent per-drug lookups; returnssafe: null+ error message when BioMCP is unavailableKey Changes
app/nlp/severity_classifier.py,app/clients/biomcp_client.pyapp/services/interaction_checker.py(sync → async, FDA → BioMCP)app/api/health.py(/health/datanow reports BioMCP connectivity),app/main.pylifespanapp/data/fda_store.py,scripts/sync_fda_data.py, FDA test files,ijsondependencyDockerfile.biomcp, updateddocker-compose.yml(biomcp service + healthcheck), updated CI pipelineTest Plan
uv run pytest tests/ --ignore=tests/test_rxnorm_client.py)biomcp serve-httpcommand is correct once sidecar is deployed (BioMCP tool schema may need adjustment inbiomcp_client.get_interactions)docker compose build api biomcpto confirm both images build./scripts/smoke-test.sh🤖 Generated with Claude Code