Wrap the exact metadata search endpoint
Nobody has claimed this yet.
Assessment
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Newbie friendliness
- 62/100
Research direction
Start from bb_bed_text_search() in the R package, since the new function should mirror its arguments, request handling and result flattening. The payload names the /bed/search/exact endpoint and its parameters (query, genome, assay, limit, offset), so check how the existing wrapper builds its request. Done means a bb_bed_exact_search() that returns the same flattened shape, with annotation fields nested in metadata, and a test showing the K562 / hg38 / ATAC-seq case.
Written by the indexing model from the issue text.
Description
bedhost has /bed/search/exact alongside the text search that bb_bed_text_search() wraps. It takes the same parameters (query, genome, assay, limit, offset) but matches metadata fields exactly instead of ranking the whole corpus by similarity. For query = "K562", genome = "hg38", assay = "ATAC-seq" it returns 1,415 records, all K562 ATAC-seq; the text search for the same terms reports a count of 665k because everything gets a score.
That's the one to use when you mean "all K562 ATAC-seq peaks" rather than "things like that". Proposed:
bb_bed_exact_search(bedbase, query, genome = NULL, assay = NULL, limit = 10, offset = 0)
Same shape and result flattening as bb_bed_text_search(). The annotation fields (cell line, assay, tissue, antibody, treatment) come back nested in metadata the same way.
One of the ways to get ids for #26; part of the workflow in #29.
Drafted with Claude Code.
- Dominant language
- R
- Stars
- 3
- Forks
- 2
- Avg merge
- 3d 18h
- Merged PRs (30d)
- 3
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