Fix 4DN index router reading wrong field path in file document — Closes #26

[conradbzura]

Summary

Route the /index/{dcc}/{local_id} sidecar lookup through the DCC-namespaced extra subdocument so 4DN index files can actually be served. Before this change the router read extra.extra_files, but the 4DN scraper writes extras under extra.fourdn.extra_files, so every /index/4dn/<local_id> request returned 404 even when a .bai, .tbi, .beddb, .bw, or .pairs_px2 sidecar was present. Dispatch the lookup by DCC and read the namespaced path. Non-4DN DCCs (ENCODE, HuBMAP) return no extras for now — their sidecar ingestion is not yet in place and will be handled in follow-up issues. Closes #26.

Proposed changes

src/cfdb/api/routers/index.py

Replace the DCC-agnostic extra.get("extra_files") lookup with a DCC-dispatched read. For normalized_dcc == "4dn", read extra.fourdn.extra_files (matching the path written by src/cfdb/services/fourdn.py and materialized by src/cfdb/services/sync.py). For every other DCC, return an empty list so the existing 404 "No index file available" path fires — preserving today's behavior for ENCODE and HuBMAP until their sidecar ingestion lands. Update the handler docstring to describe the DCC-namespaced layout.

tests/test_index.py

Add 13 unit tests for stream_index_file, organized under TestStreamIndexFile. Coverage includes:

• 4DN sidecar lookup for HEAD and GET
• Case-insensitive DCC dispatch
• Regression guard: legacy top-level extra.extra_files is ignored
• Non-4DN DCCs always return no-index
• Empty extras list and malformed entries
• Missing-href entry, unknown DCC rejection, missing file document
• Range handling: valid, malformed, unsatisfiable, missing file size

Tests use the mock_db FakeDB fixture from tests/conftest.py (which monkeypatches cfdb.api.db with an in-memory database), so no MongoDB instance is required. An autouse class fixture stubs locks.wait_for_cutover to a no-op for every test.

Test cases

#	Test Suite	Given	When	Then	Coverage Target
1	TestStreamIndexFile	A 4DN file document with a sidecar entry under extra.fourdn.extra_files	A HEAD request is issued for /index/4dn/<local_id>	Status is 200 with Content-Disposition, Accept-Ranges, and Content-Length headers	4DN sidecar HEAD happy path
2	TestStreamIndexFile	A 4DN file document whose extras live only at the legacy top-level extra.extra_files	A HEAD request is issued	Status is 404 — legacy path is ignored	Regression guard for the pre-fix field path
3	TestStreamIndexFile	A 4DN file document with a sidecar and file_size set	A HEAD request is issued with Range: bytes=0-99	Status is 206 with a correct Content-Range header	Range request handling
4	TestStreamIndexFile	No matching file document in the database	A HEAD request is issued	Status is 404 with detail "File not found"	Missing file document
5	TestStreamIndexFile	An unrecognized DCC name	A HEAD request is issued	Status is 400 with a detail listing valid DCCs	Unknown DCC rejection
6	TestStreamIndexFile	A 4DN sidecar entry missing the href key	A HEAD request is issued	Status is 404 with detail "Index file has no download URL"	Malformed sidecar entry
7	TestStreamIndexFile	A 4DN file document with a sidecar	A HEAD request is issued with DCC "4DN" (mixed case)	Status is 200 — dispatch is case-insensitive	DCC case normalization
8	TestStreamIndexFile	A 4DN file document with a sidecar	A GET request is issued	A StreamingResponse is returned with status 200 and correct headers	GET dispatch path
9	TestStreamIndexFile	A 4DN sidecar entry with no file_size recorded	A HEAD request is issued with a Range header	Status is 500 with detail about unavailable file size	Range without known size
10	TestStreamIndexFile	A 4DN sidecar entry	A HEAD request is issued with a malformed Range header	Status is 400 with detail "Invalid Range header"	Malformed Range header
11	TestStreamIndexFile	A 4DN sidecar entry with file_size=1024	A HEAD request is issued with Range: bytes=2000-3000	Status is 416 with Content-Range: bytes */1024	Unsatisfiable Range
12	TestStreamIndexFile	A HuBMAP file document with arbitrary extras	A HEAD request is issued	Status is 404 — non-4DN DCCs return no index until their branches land	Non-4DN DCC dispatch
13	TestStreamIndexFile	A 4DN file document with an empty extra.fourdn.extra_files list	A HEAD request is issued	Status is 404 with detail "No index file available for this file"	Empty extras list