Add rest api

[mschwoer]

Add simple REST API

[claude]

test comment - please ignore - will be replaced

[claude]

PLACEHOLDER - full review will follow

[claude]

Code Review placeholder - to be replaced

[claude]

Deleting test comments - sorry for the noise

[claude]

LICENSE.txt
README.md
TODO.md
airflow_src
compose.sh
design_docs
docker-compose.yaml
docs
envs
local_test
mcp_server
misc
monitoring
mount.sh
msqc-extractor
nbs
pyproject.toml
rest_api
shared
webapp

[claude]

/home/runner/work/alphakraken/alphakraken/LICENSE.txt

[claude]

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[claude]

                             Apache License
                       Version 2.0, January 2004
                    http://www.apache.org/licenses/

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See the License for the specific language governing permissions and
limitations under the License.

[claude]

Code Review: Add REST API

Nice addition! The overall structure is clean and follows patterns established by mcp_server. Here are the issues I found, roughly ordered by severity.

Bugs

1. Dockerfile: curl not installed, but used in healthcheck

python:3.11-slim-bookworm does not ship with curl. The docker-compose.yaml healthcheck runs curl http://localhost:8090/health, which will always fail.

Fix: add a curl install step to the Dockerfile, or switch to a Python-based healthcheck:

test: ["CMD", "python", "-c", "import urllib.request; urllib.request.urlopen('http://localhost:8090/health')"]

2. Dockerfile: non-root user created after CMD

The COPY instructions (lines 14-15) run as root because USER appuser comes after them on line 24. The conventional order is: RUN useradd, then COPY --chown=appuser, then USER appuser, then EXPOSE/CMD.

3. _to_metrics_list: metrics detection does not match its docstring (service.py:66)

The docstring says "Metrics entries are identified by having a type key", but the code treats any non-empty dict as a metric. A future non-metric dict field on RawFile would be silently consumed and stripped from the output. The guard should also verify that a type key is present.

Code Quality

4. Dead code: double legacy-field harmonization

service.py:71-72 tries to rename raw:gradient_length_m to gradient_length, but interface.py:augment_raw_files_with_metrics (lines 399-401) already does this rename before _to_metrics_list is called. The check in service.py will never trigger.

5. Redundant connect_db() in _query_raw_files (service.py:37)

main.py already calls connect_db() in the lifespan context, so the DB is connected before any request arrives. The extra call in _query_raw_files is a no-op.

6. name_contains filters on id, not original_name (service.py:44)

query.filter(id__icontains=name_contains) filters on the id field, which includes collision-flag prefixes like COLLISION_foo.raw. The parameter name implies searching by filename. Either rename the parameter to id_contains or filter on original_name__icontains.

Security

7. No authentication

The API exposes raw file metadata and metrics with no access control. If access is restricted to VPN members only, document this explicitly in docs/deployment.md. Otherwise, consider adding HTTP Basic Auth at the nginx level.

8. rest-api port exposed directly, bypassing nginx (docker-compose.yaml:387)

Port 8090 is bound on the host directly, making the service reachable without going through nginx. If nginx is the intended sole entry-point (for future auth or rate-limiting), remove the ports entry from the rest-api service and rely on Docker's internal network.

Minor / Nits

9. Commented-out schema fields (schemas.py:19-23)

Delete the commented-out fields (status_details, backup_status, s3_upload_path, instrument_file_status). Track planned additions in a GitHub issue instead.

10. pydantic not pinned in requirements_rest_api.txt

FastAPI and uvicorn are pinned but pydantic is not, which could cause unexpected breakage on a fresh install.

11. No tests

Even a basic unit test for _to_metrics_list and a smoke test for /health would help prevent regressions.

Summary

Category	Count
Bugs	3
Code quality	3
Security	2
Minor/nits	3

Most important fixes before merging: 1 (healthcheck will always fail on slim image), 3 (incorrect metrics detection logic), 2 (Dockerfile layer ordering). The rest are improvements but not blockers.