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zitoa
marked this pull request as ready for review
November 18, 2025 17:16
The reactome graph panel fetched from reactome.org's live SVG exporter, now Cloudflare-blocked (403) for server-side requests, which crashed the board. Render the locally bundled SBGN files via getPathwayImage (the table is already filtered to pathways that have a local file), and show a note pointing to the table's Reactome link instead of crashing when no diagram is available. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Fetch Reactome's own diagram SVGs (matching reactome.org) from a mirror instead of re-rendering SBGN. The reactome table is now filtered by playbase::reactomeDiagrams() (pathways that resolve to a diagram, incl. sub-pathways), and the plot fetches the native SVG via getPathwayImage. The mirror base URL comes from REACTOME_SVG_URL (env, or the OPTIONS key bridged to the env in global.R); when unset the panel shows the graceful note. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
playdata is the single source for Reactome diagrams (no hosted-mirror fallback), so the OPTIONS->env bridge in global.R is no longer needed. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The reactome table is filtered to pathways that resolve to a diagram (playbase::reactomeDiagrams), so the note branch never fired. getReactomeSVG returns NULL on any failure, so a plain req(img$src, file.exists) keeps the edge case (IO/decompression failure) a graceful blank panel without a crash. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
feat: order samples on heatmap editor
Reactome pathway board: native diagrams, no live reactome.org call
# Conflicts: # components/board.upload/R/upload_module_computepgx.R # components/board.upload/R/upload_module_initial_settings.R # components/board.upload/R/upload_server.R # components/ui/ui-alerts.R
probetype() can hold one value per selected organism now, so
`!(probetype() %in% c("error", "running"))` returned a vector instead
of a scalar, crashing the wizard-lock observeEvent's || chain with
"'length = 3' in coercion to 'logical(1)'" once organism-specific
probetypes were detected.
Contributor
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Shall we merge this? Is it waiting for further feedback? |
Member
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Does it handle correctly is an underscore is already present in the feature name? lipid names, metabolltes, but sometime already gene and protein id may use already undscores? |
Member
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this now needs to point to devel (edgy is no more...) |
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Enable multispecies analysis. Requires bigomics/playbase#361
We have two requirements for any user interested in multi-species:
For multi-species analysis, we append the species to the feature identifier. eg
GENE1_Human
GENE2_Rat