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Add mapMetabolites(): metabolite identifier conversion through the MetaboAnalyst API - #284
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…yst API One exported function over MetaboAnalyst's public mapcompounds endpoint, built on the searchExternal HTTP plumbing so tests mock externalPostJson(). Inputs are cleaned and sent in chunks of 200; the reply's "NA" strings and JSON nulls both become NA. The URL is overridable through options(sigrepo.metaboanalyst_url). When tested live on 2026-10-15 only from = "name" returned matches; the documented id input types are passed through as documented but came back unmatched, which the roxygen and NEWS say. Closes #281. Serves #171. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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Closes #281. Serves #171.
What
mapMetabolites(ids, from = "name", timeout = 120)converts metabolite names or identifiers between HMDB, PubChem, ChEBI, KEGG, METLIN and SMILES through MetaboAnalyst's public compound-mapping endpoint (POST https://rest.xialab.ca/api/mapcompounds). One row per distinct input, in input order, with amatchedflag and the canonical compound name. No login, no new dependency.How
R/mapMetabolites.R: the exported function, an input cleaner (trim, drop empty and NA-like values, de-duplicate, refuse values containing the service's;separator), a fetch step throughexternalPostJson()and a parse step that reads both the string"NA"and JSONnullas missing. Long lists go in chunks of 200 because the service takes about 20 to 30 s per request plus a fraction of a second per compound (1000 ids took 117 s in one request; 2500 timed out).externalUrl("metaboanalyst")with thesigrepo.metaboanalyst_urloption, next to the Rummagene, RummaGEO and CORESH entries.tests/testthat/test_mapMetabolites.R: 11 tests, 37 assertions, HTTP mocked, fixture captured from the live service on 2026-10-15.Caveat worth knowing
When tested live on 2026-10-15, only
from = "name"returned matches. The five identifier input types MetaboAnalyst documents (hmdb,pubchem,chebi,kegg,metlin) came back unmatched for known-good ids, whatever the field name or casing. The function passes them through as documented and the roxygen and NEWS say so; checkmatchedbefore relying on an id-based lookup.Tests
Full suite with
devtools::load_all()+testthat::test_dir(): 1204 pass, 0 fail, 84 skip (the database-gated tests, no local stack configured).Out of scope
Enrichment or pathway analysis via MetaboAnalystR, writing mapped ids into
metabolite_xref, and any server, MCP or Shiny exposure.🤖 Generated with Claude Code