Fix Omnipath issue - #86
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Fix OmniPath loading resilience (port NICHESv1 PR RaredonLab#72 / issue RaredonLab#70) Newer OmnipathR (>= ~3.17, incl. 4.1.0) resolves the `organism` argument through ncbi_taxid(), which downloads and coalesces species tables from Ensembl, OMA, and UniProt. When any of those ancillary services is unreachable (e.g. omabrowser.org returning HTTP 502), the call aborts with "Can't combine `..1` and `..3`" even though the OmniPath interaction server itself is fine. load_LRM_database("omnipath") now delegates to a resilient fetcher that: 1. tries the standard OmnipathR path with its console logging muted, 2. falls back to a direct OmniPath REST query using the known NCBI taxon id, bypassing the failing organism-name lookup, and 3. raises an informative network error only if both paths fail. The fallback is base-R only (utils::download.file / read.delim) and adds no new dependencies. Ported from NICHESv1.
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Fix OmniPath loading resilience (port NICHESv1 PR #72 / issue #70)
Newer OmnipathR (>= ~3.17, incl. 4.1.0) resolves the
organismargument through ncbi_taxid(), which downloads and coalesces species tables from Ensembl, OMA, and UniProt. When any of those ancillary services is unreachable (e.g. omabrowser.org returning HTTP 502), the call aborts with "Can't combine..1and..3" even though the OmniPath interaction server itself is fine.load_LRM_database("omnipath") now delegates to a resilient fetcher that:
The fallback is base-R only (utils::download.file / read.delim) and adds no new dependencies. Ported from NICHESv1.