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fix(ui): restore equation columns, add RAST genome preview, improve filtering#203

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VibhavSetlur merged 6 commits into
ModelSEED:stagingfrom
VibhavSetlur:staging
May 13, 2026
Merged

fix(ui): restore equation columns, add RAST genome preview, improve filtering#203
VibhavSetlur merged 6 commits into
ModelSEED:stagingfrom
VibhavSetlur:staging

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@VibhavSetlur
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Summary

Equation fixes (user-reported)

  • Restored missing Equation columns on FBA flux and gapfill detail tables
  • Removed hard truncation on the biochem reactions table equation column

RAST genome integration

  • Added RastGenomePreviewDialog for genome metadata preview
  • Implemented getRastGenomeData() in the API layer
  • Updated listRastGenomes() to try modelseed-api proxy first, fall back to MSSS

Other

  • Added /api/biochem/comments route
  • Added /api/rast/jobs proxy route
  • E2E tests for RAST genome listing
  • Updated deployment docs and Docker config

…ail tables

The reaction fluxes table on /fba/[...path] and the reactions table on
/gapfill/[...path] were both missing the equation column, even though
the data was parsed and stored in each row. Users performing manual
curation could not see reaction equations (with cpd IDs) to detect
duplicate-compound-ID issues that cause flux breakdowns.

Added the Equation column using the ChemicalEquation component between
Name and Flux/Direction, matching the pattern used on the model detail
page and biochem reactions list.
…back flow

- Added getRastGenomeData() to modelseed.ts that calls MSSS over JSON-RPC
  to fetch genome annotation data (taxonomy, domain, features, contigs).
  Returns a KBase Genome-compatible dict once the backend translator is
  wired by José.

- Wired RastGenomePreviewDialog into the RAST tab on the Build Model page.
  Clicking 'Build Model' on a RAST row now opens a preview dialog showing
  genome metadata. If genome data fetch fails (MSSS getRastGenomeData is
  currently broken due to chestnut MySQL), a warning is shown and the user
  can still proceed with default settings.

- Made RastGenomePreviewDialog non-blocking on error: shows warning
  severity instead of error, enables 'Proceed anyway' button, so the
  existing submission flow is preserved regardless of backend availability.

- Added API proxy route at /api/rast/jobs for server-side RAST job listing.

- Added E2E tests for RAST genome listing flow.
…ck to MSSS

listRastGenomes() now calls GET /api/rast/jobs (local proxy -> José's
modelseed-api endpoint) first. If proxy returns non-200 or throws,
falls back to direct MSSS JSON-RPC. Seamless switch once
MODELSEED_RAST_DB_HOST is configured on the server.
Replaced TruncatedWithTooltip with a flex-based wrapper that allows
equation text to wrap naturally. Users can now resize the column and
see full equations without ellipsis truncation.
Copilot AI review requested due to automatic review settings May 13, 2026 20:47
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Copilot encountered an error and was unable to review this pull request. You can try again by re-requesting a review.

The effect intentionally resets loading/genomeData/error state when
open or job changes. This is the standard pattern for data-fetching
effects and the lint rule is over-zealous here.
@VibhavSetlur VibhavSetlur merged commit 06bfe94 into ModelSEED:staging May 13, 2026
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2 participants