Update LoadOmniPath.R - #72
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fix(LoadOmniPath): recover from OmnipathR organism-lookup failures (msraredon#70) RunNICHES(LR.database = "omnipath") aborted with "Can't combine `..1` and `..3`" (coalesce over latin_name_*) whenever an ancillary species-list service (OMA/Ensembl) was unreachable. The failure is upstream: newer OmnipathR (>= ~3.17) resolves `organism` via ncbi_taxid() -> taxon_names_table(), which downloads and strictly coalesces Ensembl/OMA/UniProt organism tables; a failed download yields a logical(NA) column that coalesce() refuses to combine. The OmniPath interaction server itself is unaffected, and NICHES already maps species -> NCBI taxid, so the organism-name translation is unnecessary. LoadOmniPath now fetches through a resilient helper: - try OmnipathR normally (unchanged behavior + caching when services are up); - on failure, fall back to a direct OmniPath REST query (omnipathdb.org/interactions?datasets=ligrecextra&organisms=<taxid>), which bypasses the organism-name lookup; the server performs ortholog translation, so mouse/rat symbols stay correct; - if both paths fail, raise a clear network-oriented error. Also mute OmnipathR's console log noise during the attempt, print a single provenance line (source, version, retrieval date, interaction count), and record it on attr(ground.truth, "omnipath_source"). Verified: human 6658, mouse 4434, rat 4225 interactions. Scope: R/LoadOmniPath.R only; no new dependencies.
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fix(LoadOmniPath): recover from OmnipathR organism-lookup failures (#70)
RunNICHES(LR.database = "omnipath") aborted with
"Can't combine
..1and..3" (coalesce over latin_name_*) whenever an ancillary species-list service (OMA/Ensembl) was unreachable. The failure is upstream: newer OmnipathR (>= ~3.17) resolvesorganismvia ncbi_taxid() -> taxon_names_table(), which downloads and strictly coalesces Ensembl/OMA/UniProt organism tables; a failed download yields a logical(NA) column that coalesce() refuses to combine. The OmniPath interaction server itself is unaffected, and NICHES already maps species -> NCBI taxid, so the organism-name translation is unnecessary.LoadOmniPath now fetches through a resilient helper:
Also mute OmnipathR's console log noise during the attempt, print a single provenance line (source, version, retrieval date, interaction count), and record it on attr(ground.truth, "omnipath_source").
Verified: human 6658, mouse 4434, rat 4225 interactions.
Scope: R/LoadOmniPath.R only; no new dependencies.