Skip to content

fix(compounds): repair missing compound info during processing#1419

Merged
NishaSharma14 merged 3 commits into
developmentfrom
fix/compound-info-repair
Jun 4, 2026
Merged

fix(compounds): repair missing compound info during processing#1419
NishaSharma14 merged 3 commits into
developmentfrom
fix/compound-info-repair

Conversation

@vcnainala
Copy link
Copy Markdown
Member

Summary

  • Add nmrxiv:repair-missing-compound-info scheduled command with overlap protection.
  • Introduce molecule enrichment and NMRium spectra inspectors used by processing jobs.
  • Hook repair/enrichment into ProcessProject and ProcessSubmission.

Test plan

  • php artisan nmrxiv:repair-missing-compound-info --dry-run (if supported) on staging data.
  • php artisan test tests/Feature/Console/RepairMissingCompoundInfoCommandTest.php tests/Unit/Support/MoleculeEnrichmentInspectorTest.php tests/Unit/Support/NmriumSpectraInfoInspectorTest.php

Add scheduled repair command and enrichment inspectors, and invoke them
from submission and project processing jobs when metadata is incomplete.
@codecov
Copy link
Copy Markdown

codecov Bot commented Jun 3, 2026

Codecov Report

❌ Patch coverage is 70.83333% with 21 lines in your changes missing coverage. Please review.
✅ Project coverage is 75.40%. Comparing base (f12c701) to head (d463d30).

Files with missing lines Patch % Lines
app/Support/Nmr/NmriumSpectraInfoInspector.php 58.33% 15 Missing ⚠️
.../Support/Molecules/MoleculeEnrichmentInspector.php 85.71% 4 Missing ⚠️
app/Jobs/ProcessProject.php 50.00% 2 Missing ⚠️
Additional details and impacted files
@@                Coverage Diff                @@
##             development    #1419      +/-   ##
=================================================
- Coverage          75.43%   75.40%   -0.03%     
- Complexity          3328     3360      +32     
=================================================
  Files                234      236       +2     
  Lines              12473    12545      +72     
=================================================
+ Hits                9409     9460      +51     
- Misses              3064     3085      +21     
Flag Coverage Δ
unittests 75.40% <70.83%> (-0.03%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
  • 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

vcnainala and others added 2 commits June 3, 2026 23:46
Exercise repair command dispatch paths, inspector query methods, and
ProcessProject unique lock TTL to satisfy Codecov patch thresholds.
@NishaSharma14 NishaSharma14 merged commit c8558ef into development Jun 4, 2026
4 of 5 checks passed
@NishaSharma14 NishaSharma14 deleted the fix/compound-info-repair branch June 4, 2026 08:01
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants